VARNA32x32.png0000644000000000000000000000360312405576624011650 0ustar rootrootPNG  IHDR szzsBIT|d pHYsxxtEXtSoftwarewww.inkscape.org<IDATX}LsPP)#"Bb MZ:!).6kX--h;'PlPYb]q|-H!9zخy뾟뽟WƁρ@GΤXz5vd2@)7$,T]lra)--?Ȋ8Qv.nʆ Hpp0tvvFUUV5p۶m"""bq't :cIIIaddF#;v֭[ܾ}֭[GEEyyy֝B\\l߾}68::""##1LL&=zD``/?0 vb&_ iii133CDDf p6㥹4<<,EEE MD Iqq=qR𻑑9y$4mAAAl6;F}}=@ޥ`^,++#.. Xhmm%88L4u6+WR M<088Ț5k0b&.4SN:ttig9rfR3p&Z/v3NMMIAAdI7nTWWEee%yyyLPZ 990: v-^$/_7ߪn,OIOO'))͛7cZ#t N^\@ee%!!!deeֆ6{}P)))?W| 9j|1ܹR]]===ܽ{łLLLt_,< >|ݍ(( n@xx8֢iQQQ2@|"2:7DvijZdRXX('G]ʏZ4.p lͅW^CEE>>>{!""u|8bWtOOdg9#200 ߗv)((I4ͽگD"b~;BS&X8xs0XV9O"u#+q5Rp{8 <P\hl61GnܼySZ[[EuNY *>782tJAN-,P)M?:}1Sc32۸ gѵ(.Jc{ 4 @徃-D~-͟\0k׀xٯ8ҁp KC cj߶wrֽpT)[PW>  M pūεW{M+Kr۽q- E̼}5Hq_Rkq̗> Uefz9:Y BEC 6Ği"T*hwRv<÷/ :J܂;xH9GSh[.x/"8:; rD?W@8^@)yrPHj^; @vq Ψ9NuVhw?%P"zPuAh*=?Œm'\DOB8<sD,* |A(_Dp]η|]my304 7@#`C=BKbn5–f?IENDB`BugsAndProblems0000644000000000000000000000057411620715270012535 0ustar rootroot - Ajouter message d'erreur lors du chargement - Grer affichage partiel/hybridisation Problemes connus : probleme de focus => gene raccourcis clavier. //cadre mal placé pour le mode Line donc deplacement spécial probleme lors de l'affichage d'un ARN sans base dans le AboutVarna, lors d'un click droit sur la figure, il est possible de redemander un aboutVarna.TODO.txt0000644000000000000000000000222612000510504011047 0ustar rootrootFonctionnalites ajouter : RNAML : Inclure dans .jar num base dans angle => produit vectoriel deplacement dans l'algo NAView identique a celui de l'aglo Radial =>besoin de creer des centre de rotation en mode NAView faire un export de tte les info de varna en xml qui sauvegarde ttes les info (seq, struct, couleurs et coords) faire un import du fichier xml pour charge les modif apporte a l'arn Limiter la hauteur des arcs au strict necessaire en mode Line pour le dessin Ex: Dans (.(((...)))..(((...))).), la boucle exterieure n'a pas besoin d'tre hauteur 22, seulement hauteur 4, pour ne pas rentrer en conflit avec les arcs dessins en dessous. A la limite, on pourrait la dessiner hauteur 5 pour marquer la difference entre les helices dans cette reprsentation. Courbes de bzier en reprsentation circulaire. * Rendre val min et max accessibles * Si possible, coder des mcanismes de bulges pour les nucleotides non apparis * Recharger palette partir du code HTML * Appliquer palette unique tous les fichiers chargs * Charger annotations chem prob partir de fichier * Charger donnes shape csv (problme) (2 colonne) fr/0000755000000000000000000000000012275611430010164 5ustar rootrootfr/orsay/0000755000000000000000000000000012275611430011321 5ustar rootrootfr/orsay/lri/0000755000000000000000000000000012275611430012107 5ustar rootrootfr/orsay/lri/varna/0000755000000000000000000000000012275611452013222 5ustar rootrootfr/orsay/lri/varna/components/0000755000000000000000000000000012275611432015405 5ustar rootrootfr/orsay/lri/varna/components/AnnotationTableModel.java0000644000000000000000000000501311620715272022312 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.components; import java.util.ArrayList; import javax.swing.table.AbstractTableModel; public class AnnotationTableModel extends AbstractTableModel { /** * */ private static final long serialVersionUID = 1L; private String[] columnNames = { "Annotation" }; private ArrayList> data = new ArrayList>(); public AnnotationTableModel(ArrayList annot) { ArrayList ligne; for (int i = 0; i < annot.size(); i++) { ligne = new ArrayList(); ligne.add(annot.get(i)); data.add(ligne); } } public int getColumnCount() { return columnNames.length; } public int getRowCount() { return data.size(); } public String getColumnName(int col) { return columnNames[col]; } public Object getValueAt(int row, int col) { return data.get(row).get(col); } /* * JTable uses this method to determine the default renderer/ editor for * each cell. If we didn't implement this method, then the last column would * contain text ("true"/"false"), rather than a check box. */ @SuppressWarnings("unchecked") public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } public boolean isCellEditable(int row, int col) { // Note that the data/cell address is constant, // no matter where the cell appears onscreen. if (col < 1) { return false; } else { return true; } } public void setValueAt(Object value, int row, int col) { data.get(row).set(col, value); fireTableCellUpdated(row, col); } }fr/orsay/lri/varna/components/BaseTableModel.java0000644000000000000000000000644611722506506021066 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.components; import java.awt.Color; import java.util.ArrayList; import javax.swing.table.AbstractTableModel; import fr.orsay.lri.varna.models.BaseList; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModelBaseStyle; public class BaseTableModel extends AbstractTableModel { /** * */ private static final long serialVersionUID = 1L; private String[] columnNames = { "Numbers", "Base", "Outline Color", "Inner Color", "Name Color", "Number Color" }; private ArrayList> data = new ArrayList>(); private ArrayList _bases; private boolean _singleBases = true; public BaseTableModel(ArrayList bases) { _bases = bases; ArrayList ligne; for (int i = 0; i < bases.size(); i++) { ligne = new ArrayList(); BaseList bl = bases.get(i); if (bl.size()!=1) { _singleBases = false; } ligne.add(bl.getNumbers()); ligne.add(bl.getContents()); ligne.add(bl.getAverageOutlineColor()); ligne.add(bl.getAverageInnerColor()); ligne.add(bl.getAverageNameColor()); ligne.add(bl.getAverageNumberColor()); this.data.add(ligne); } } public int getColumnCount() { return columnNames.length; } public int getRowCount() { return data.size(); } public String getColumnName(int col) { return columnNames[col]; } public Object getValueAt(int row, int col) { return data.get(row).get(col); } /* * JTable uses this method to determine the default renderer/ editor for * each cell. If we didn't implement this method, then the last column would * contain text ("true"/"false"), rather than a check box. */ @SuppressWarnings("unchecked") public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } public boolean isCellEditable(int row, int col) { // Note that the data/cell address is constant, // no matter where the cell appears onscreen. if (col < 1) { return false; } else { return true; } } public void setValueAt(Object value, int row, int col) { data.get(row).set(col, value); if (col == 1 && _singleBases) { ModeleBase mb = _bases.get(row).getBases().get(0); mb.setContent(value.toString()); } fireTableCellUpdated(row, col); } }fr/orsay/lri/varna/components/GradientEditorPanel.java0000644000000000000000000002302411620715272022135 0ustar rootrootpackage fr.orsay.lri.varna.components; import java.awt.Color; import java.awt.Cursor; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.RenderingHints; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import javax.swing.JColorChooser; import javax.swing.JPanel; import fr.orsay.lri.varna.models.rna.ModeleColorMap; public class GradientEditorPanel extends JPanel implements MouseListener, MouseMotionListener{ ModeleColorMap _mcm; public GradientEditorPanel (ModeleColorMap mcm) { _mcm = mcm; this.addMouseListener( this); this.addMouseMotionListener(this); } public void setColorMap(ModeleColorMap mcm) { _mcm = mcm; } public ModeleColorMap getColorMap() { return _mcm; } private final static int TRIGGERS_SEMI_WIDTH = 2; private final static int PALETTE_HEIGHT = 11; private final static int REMOVE_HEIGHT = 11; private final static int TOLERANCE = 5; private final static int GAP = 4; private final Color EDGES = Color.gray.brighter(); private final Color BUTTONS = Color.LIGHT_GRAY.brighter(); public int getStartChoose() { return getHeight()-PALETTE_HEIGHT-REMOVE_HEIGHT-GAP-1; } public int getEndChoose() { return getStartChoose()+PALETTE_HEIGHT; } public int getStartRemove() { return getEndChoose()+GAP; } public int getEndRemove() { return getStartRemove()+REMOVE_HEIGHT; } private int getStripeHeight() { return getHeight()-PALETTE_HEIGHT-REMOVE_HEIGHT-2*GAP-1; } private Color alterColor(Color c, int inc) { int nr = Math.min(Math.max(c.getRed()+inc, 0),255); int ng = Math.min(Math.max(c.getGreen()+inc, 0),255); int nb = Math.min(Math.max(c.getBlue()+inc, 0),255); return new Color(nr,ng,nb); } public void paintComponent(Graphics g) { super.paintComponent(g); Graphics2D g2d = (Graphics2D) g; g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); int height = getStripeHeight(); double v1 = _mcm.getMinValue(); double v2 = _mcm.getMaxValue(); for (int i=0;i<=getWidth();i++) { double ratio = (((double)i)/((double)getWidth())); double val = v1+(v2-v1)*ratio; g2d.setColor(_mcm.getColorForValue(val)); g2d.drawLine(i, 0, i, height); } for(int i=0;i<_mcm.getNumColors();i++) { double val = _mcm.getValueAt(i); Color c = _mcm.getColorAt(i); double norm = (val-_mcm.getMinValue())/(_mcm.getMaxValue()-_mcm.getMinValue()); int x = (int)(norm*(getWidth()-1)); // Target g2d.setColor(c); g2d.fillRect(x-TRIGGERS_SEMI_WIDTH+1, 0, 2*TRIGGERS_SEMI_WIDTH-1, getHeight()-1); g2d.setColor(EDGES); g2d.drawLine(x-TRIGGERS_SEMI_WIDTH, 0, x-TRIGGERS_SEMI_WIDTH, getHeight()); g2d.drawLine(x+TRIGGERS_SEMI_WIDTH, 0, x+TRIGGERS_SEMI_WIDTH, getHeight()); if (i==0) { // Choose Color g2d.setColor(EDGES); g2d.drawRect(x,height+GAP,PALETTE_HEIGHT,2*PALETTE_HEIGHT+GAP); g2d.setColor(c); g2d.fillRect(x+1,height+GAP+1,PALETTE_HEIGHT-1,2*PALETTE_HEIGHT+GAP-1); } else if (i==_mcm.getNumColors()-1) { // Choose Color g2d.setColor(EDGES); g2d.drawRect(x-PALETTE_HEIGHT,height+GAP,PALETTE_HEIGHT,2*PALETTE_HEIGHT+GAP); g2d.setColor(c); g2d.fillRect(x-PALETTE_HEIGHT+1,height+GAP+1,PALETTE_HEIGHT-1,2*PALETTE_HEIGHT+GAP-1); } else { // Choose Color g2d.setColor(EDGES); g2d.drawRect(x-PALETTE_HEIGHT/2,height+GAP,PALETTE_HEIGHT,PALETTE_HEIGHT); g2d.setColor(alterColor(c,-15)); g2d.fillRect(x-PALETTE_HEIGHT/2+1,height+GAP+1,PALETTE_HEIGHT-1,PALETTE_HEIGHT-1); g2d.setColor(c); g2d.fillOval(x-PALETTE_HEIGHT/2+1,height+GAP+1,PALETTE_HEIGHT-1,PALETTE_HEIGHT-1); g2d.setColor(alterColor(c,10)); g2d.fillOval(x-PALETTE_HEIGHT/2+1+2,height+GAP+1+2,PALETTE_HEIGHT-1-4,PALETTE_HEIGHT-1-4); // Remove Color g2d.setColor(EDGES); g2d.drawRect(x-PALETTE_HEIGHT/2,height+2*GAP+PALETTE_HEIGHT,REMOVE_HEIGHT,REMOVE_HEIGHT); g2d.setColor(BUTTONS); g2d.fillRect(x-PALETTE_HEIGHT/2+1,height+2*GAP+1+PALETTE_HEIGHT,REMOVE_HEIGHT-1,REMOVE_HEIGHT-1); int xcross1 = x-PALETTE_HEIGHT/2+2; int ycross1 = height+2*GAP+PALETTE_HEIGHT +2; int xcross2 = xcross1+REMOVE_HEIGHT-4; int ycross2 = ycross1+REMOVE_HEIGHT-4; g2d.setColor(Color.red); g2d.drawLine(xcross1, ycross1, xcross2 , ycross2); g2d.drawLine(xcross1, ycross2, xcross2 , ycross1); } } } private boolean isChooseColor(int x, int y) { if (_selectedIndex != -1) { if ((_selectedIndex ==0)||(_selectedIndex == _mcm.getNumColors()-1)) return (y<=getEndRemove() && y>=getStartChoose() && Math.abs(getXPos(_selectedIndex)-x)<=PALETTE_HEIGHT); if (y<=getEndChoose() && y>=getStartChoose()) { return Math.abs(getXPos(_selectedIndex)-x)<=PALETTE_HEIGHT/2; } } return false; } private boolean isRemove(int x, int y) { if (_selectedIndex != -1) { if ((_selectedIndex ==0)||(_selectedIndex == _mcm.getNumColors()-1)) return false; if (y<=getEndRemove() && y>=getStartRemove()) { return Math.abs(getXPos(_selectedIndex)-x)<=PALETTE_HEIGHT/2; } } return false; } private int getXPos(int i) { double val = _mcm.getValueAt(i); double norm = (val-_mcm.getMinValue())/(_mcm.getMaxValue()-_mcm.getMinValue()); return (int)(norm*(getWidth()-1)); } private int locateSelectedIndex(int x, int y) { double dist = Double.MAX_VALUE; int index = -1; for(int i=0;i<_mcm.getNumColors();i++) { int xp = getXPos(i); double tmpDist = Math.abs(x-xp); if (tmpDistTOLERANCE) { double val = _mcm.getMinValue()+ arg0.getX()*(_mcm.getMaxValue()-_mcm.getMinValue())/(getWidth()-1); Color nc = JColorChooser.showDialog(this, "Choose new color" ,_mcm.getColorAt(_selectedIndex)); if (nc != null) { _mcm.addColor(val, nc); repaint(); firePropertyChange("PaletteChanged","a","b"); } } } } public void mouseEntered(MouseEvent arg0) { // TODO Auto-generated method stub } public void mouseExited(MouseEvent arg0) { // TODO Auto-generated method stub } public void mousePressed(MouseEvent arg0) { requestFocus(); _selectedIndex = locateSelectedIndex(arg0.getX(),arg0.getY()); if (_selectedIndex!=-1) { if (isChooseColor(arg0.getX(),arg0.getY())) { Color nc = JColorChooser.showDialog(this, "Choose new color" ,_mcm.getColorAt(_selectedIndex)); if (nc != null) { double nv = _mcm.getValueAt(_selectedIndex); replaceEntry(_selectedIndex, nc, nv); _selectedIndex = -1; } } } } public void mouseReleased(MouseEvent arg0) { _selectedIndex = -1; } private void replaceEntry(int index, Color nc, double nv) { ModeleColorMap cm = new ModeleColorMap(); for(int i=0;i<_mcm.getNumColors();i++) { if (i!=index) { double val = _mcm.getValueAt(i); Color c = _mcm.getColorAt(i); cm.addColor(val, c); } else { cm.addColor(nv, nc); } } _mcm = cm; repaint(); firePropertyChange("PaletteChanged","a","b"); } private void removeEntry(int index) { ModeleColorMap cm = new ModeleColorMap(); for(int i=0;i<_mcm.getNumColors();i++) { if (i!=index) { double val = _mcm.getValueAt(i); Color c = _mcm.getColorAt(i); cm.addColor(val, c); } } _mcm = cm; repaint(); firePropertyChange("PaletteChanged","a","b"); } public void mouseDragged(MouseEvent arg0) { if ((_selectedIndex!=-1)&&(_selectedIndex!=0)&&(_selectedIndex!=_mcm.getNumColors()-1)) { Color c = _mcm.getColorAt(_selectedIndex); double val = _mcm.getMinValue()+ arg0.getX()*(_mcm.getMaxValue()-_mcm.getMinValue())/(getWidth()-1); replaceEntry(_selectedIndex, c, val); } } public void mouseMoved(MouseEvent arg0) { Cursor c = Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR); _selectedIndex = locateSelectedIndex(arg0.getX(),arg0.getY()); if (_selectedIndex!=-1) { if (isChooseColor(arg0.getX(),arg0.getY())) { c = Cursor.getPredefinedCursor(Cursor.HAND_CURSOR); } else if ((_selectedIndex != 0)&&(_selectedIndex != _mcm.getNumColors()-1)) { if (isRemove(arg0.getX(),arg0.getY())) { c = Cursor.getPredefinedCursor(Cursor.HAND_CURSOR); } else if (Math.abs(getXPos(_selectedIndex)-arg0.getX())<=TOLERANCE) { c = Cursor.getPredefinedCursor(Cursor.E_RESIZE_CURSOR); } else if (arg0.getY() r.y+r.height/2) { dropTargetIndex += 1; } } //System.out.println(dropTargetIndex); repaint(); } public void drop (DropTargetDropEvent dtde) { //System.out.println ("drop()!"); if (dtde.getSource() != dropTarget) { //System.out.println ("rejecting for bad source (" + // dtde.getSource().getClass().getName() + ")"); dtde.rejectDrop(); return; } Point dropPoint = dtde.getLocation(); int index = locationToIndex (dropPoint); if (index != -1) { Rectangle r = getCellBounds(index,index); if (dropPoint.y > r.y+r.height/2) { index += 1; } } //System.out.println ("drop index is " + index); boolean dropped = false; try { if ((index == -1) || (index == draggedIndex)|| (index == draggedIndex+1)) { //System.out.println ("dropped onto self"); dtde.rejectDrop(); return; } dtde.acceptDrop (DnDConstants.ACTION_MOVE); //System.out.println ("accepted"); Object dragged = dtde.getTransferable().getTransferData(localObjectFlavor); // move items - note that indicies for insert will // change if [removed] source was before target //System.out.println ("drop " + draggedIndex + " to " + index); boolean sourceBeforeTarget = (draggedIndex < index); //System.out.println ("source is" + // (sourceBeforeTarget ? "" : " not") + // " before target"); //System.out.println ("insert at " + // (sourceBeforeTarget ? index-1 : index)); DefaultListModel mod = (DefaultListModel) getModel(); mod.remove (draggedIndex); mod.add ((sourceBeforeTarget ? index-1 : index), dragged); dropped = true; } catch (Exception e) { e.printStackTrace(); } dtde.dropComplete (dropped); } private class ReorderableListCellRenderer extends DefaultListCellRenderer { boolean isTargetCell; boolean isLastItem; public ReorderableListCellRenderer() { super(); } public Component getListCellRendererComponent (JList list, Object value, int index, boolean isSelected, boolean hasFocus) { isTargetCell = (index == dropTargetIndex); isLastItem = (index == list.getModel().getSize()-1) && (dropTargetIndex == list.getModel().getSize()); boolean showSelected = isSelected; return super.getListCellRendererComponent (list, value, index, showSelected, hasFocus); } public void paintComponent (Graphics g) { super.paintComponent(g); if (isTargetCell) { g.setColor(Color.black); g.drawLine (0, 0, getSize().width, 0); } if (isLastItem) { g.setColor(Color.black); g.drawLine (0, getSize().height-1, getSize().width, getSize().height-1); } } } private class RJLTransferable implements Transferable { Object object; public RJLTransferable (Object o) { object = o; } public Object getTransferData(DataFlavor df) throws UnsupportedFlavorException, IOException { if (isDataFlavorSupported (df)) return object; else throw new UnsupportedFlavorException(df); } public boolean isDataFlavorSupported (DataFlavor df) { return (df.equals (localObjectFlavor)); } public DataFlavor[] getTransferDataFlavors () { return supportedFlavors; } } } fr/orsay/lri/varna/components/ZoomWindow.java0000644000000000000000000001117012032325004020350 0ustar rootrootpackage fr.orsay.lri.varna.components; import java.awt.BasicStroke; import java.awt.Color; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Point; import java.awt.Polygon; import java.awt.Rectangle; import java.awt.RenderingHints; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.GeneralPath; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.awt.geom.Point2D.Double; import java.awt.image.BufferedImage; import java.awt.image.ImageObserver; import javax.swing.JPanel; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.export.SwingGraphics; import fr.orsay.lri.varna.models.export.VueVARNAGraphics; public class ZoomWindow extends JPanel implements ImageObserver, Runnable, MouseMotionListener, MouseListener { VARNAPanel _vp = null; BufferedImage _bi = null; Rectangle2D.Double rnaRect = null; public ZoomWindow(VARNAPanel vp) { _vp = vp; addMouseMotionListener(this); addMouseListener(this); } public synchronized void setPanel(VARNAPanel vp) { _vp = vp; } public synchronized void drawPanel() { if (getWidth()>0 && getHeight()>0) { _bi= new BufferedImage(getWidth(),getHeight(),BufferedImage.TYPE_4BYTE_ABGR); Graphics2D g2 = _bi.createGraphics(); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); VueVARNAGraphics g2D = new SwingGraphics(g2); rnaRect =_vp.renderRNA(g2D,new Rectangle2D.Double(0,0,getWidth(),getHeight()),false,true); Point2D.Double p1 = _vp.panelToLogicPoint(new Point2D.Double(0.,0.)); Point2D.Double p2 = _vp.panelToLogicPoint(new Point2D.Double(_vp.getWidth(),_vp.getHeight())); double w = p2.x-p1.x; double h = p2.y-p1.y; Rectangle2D.Double rnaBox = _vp.getRNA().getBBox(); double ratiox = w/rnaBox.width; double ratioy = h/rnaBox.height; Rectangle2D.Double rvisible = new Rectangle2D.Double(rnaRect.x+rnaRect.width*(double)(p1.x-rnaBox.x)/(double)rnaBox.width, rnaRect.y+rnaRect.height*(double)(p1.y-rnaBox.y)/(double)rnaBox.height, ratiox*rnaRect.width, ratioy*rnaRect.height); //g2D.drawRect(rleft.x,rleft.y,rleft.width,rleft.height); Color shade = new Color(.9f,.9f,.9f,.4f); g2.setStroke(new BasicStroke(1.0f)); g2.setColor(shade); /*Polygon north = new Polygon(new int[]{0,getWidth(),(int)rvisible.x, (int)(rvisible.x+rvisible.width+1),},new int[]{},1);*/ g2.fillRect(0,0,getWidth(),(int)rvisible.y); g2.fillRect(0,(int)rvisible.y,(int)rvisible.x,(int)rvisible.height+1); g2.fillRect((int)(rvisible.x+rvisible.width),(int)rvisible.y,(int)(getHeight()-(rvisible.x+rvisible.width)),(int)(rvisible.height+1)); g2.fillRect(0,(int)(rvisible.y+rvisible.height),getWidth(),(int)(getHeight()-(rvisible.y+rvisible.height))); g2.setColor(new Color(.7f,.7f,.7f,.3f)); g2.draw(rvisible); g2.drawLine(0, 0, (int)rvisible.x, (int)rvisible.y); g2D.drawLine(getWidth(), 0, rvisible.x+rvisible.width, rvisible.y); g2D.drawLine(getWidth(), getHeight(), rvisible.x+rvisible.width, rvisible.y+rvisible.height); g2D.drawLine(0, getHeight(), rvisible.x, rvisible.y+rvisible.height); g2.dispose(); } } public void paintComponent(Graphics g) { setBackground(_vp.getBackground()); super.paintComponent(g); drawPanel(); if (_bi!=null) { g.drawImage(_bi,0,0,this); } } public void run() { while(true) { repaint(); try { Thread.sleep(500); } catch (InterruptedException e) { e.printStackTrace(); } } } public void mouseDragged(MouseEvent e) { // TODO Auto-generated method stub } public void mouseMoved(MouseEvent e) { // TODO Auto-generated method stub } public void mouseClicked(MouseEvent e) { /*if (rnaRect!=null) { int x= e.getX(); int y= e.getY(); double ratioX = ((double)(x-rnaRect.getMinX())/((double)rnaRect.width)); double ratioY = ((double)(y-rnaRect.getMinY())/((double)rnaRect.height)); _vp.centerViewOn(ratioX,ratioY ); }*/ } public void mousePressed(MouseEvent e) { // TODO Auto-generated method stub } public void mouseReleased(MouseEvent e) { // TODO Auto-generated method stub } public void mouseEntered(MouseEvent e) { // TODO Auto-generated method stub } public void mouseExited(MouseEvent e) { // TODO Auto-generated method stub } } fr/orsay/lri/varna/components/ColorRenderer.java0000644000000000000000000000254611620715272021024 0ustar rootroot package fr.orsay.lri.varna.components; import java.awt.Color; import java.awt.Component; import javax.swing.BorderFactory; import javax.swing.JLabel; import javax.swing.JTable; import javax.swing.border.Border; import javax.swing.table.TableCellRenderer; public class ColorRenderer extends JLabel implements TableCellRenderer { /** * */ private static final long serialVersionUID = 1L; Border unselectedBorder = null; Border selectedBorder = null; boolean isBordered = true; public ColorRenderer(boolean isBordered) { this.isBordered = isBordered; setOpaque(true); // MUST do this for background to show up. } public Component getTableCellRendererComponent(JTable table, Object color, boolean isSelected, boolean hasFocus, int row, int column) { Color newColor = (Color) color; setBackground(newColor); if (isBordered) { if (isSelected) { if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, table.getSelectionBackground()); } setBorder(selectedBorder); } else { if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, table.getBackground()); } setBorder(unselectedBorder); } } setToolTipText("RGB value: " + newColor.getRed() + ", " + newColor.getGreen() + ", " + newColor.getBlue()); return this; } } fr/orsay/lri/varna/components/VARNAConsole.java0000644000000000000000000000557111620715272020452 0ustar rootrootpackage fr.orsay.lri.varna.components; import java.awt.BorderLayout; import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.io.IOException; import javax.swing.JButton; import javax.swing.JEditorPane; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTextArea; import javax.swing.JTextField; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurScriptParser; import fr.orsay.lri.varna.models.VARNAConfig; public class VARNAConsole extends JFrame implements ActionListener, FocusListener, KeyListener { private VARNAPanel _vp; private JButton _quitButton; private JPanel _contentPanel; private JPanel _quitPanel; private JTextField _input; private JEditorPane _output; private JScrollPane _scrolls; public VARNAConsole(VARNAPanel vp) { _vp = vp; init(); } private void init() { _quitButton = new JButton("Exit"); _quitPanel = new JPanel(); _contentPanel = new JPanel(); _input = new JTextField("Your command here..."); _output = new JEditorPane(); _scrolls = new JScrollPane(_output); _input.addFocusListener(this); _input.addKeyListener(this); _output.setText(VARNAConfig.getFullName()+" console\n"); _output.setPreferredSize(new Dimension(500,300)); _output.setEditable(false); _quitPanel.add(_quitButton); _quitButton.addActionListener(this); _contentPanel.setLayout(new BorderLayout()); _contentPanel.add(_scrolls,BorderLayout.CENTER); _contentPanel.add(_input,BorderLayout.SOUTH); getContentPane().setLayout(new BorderLayout()); getContentPane().add(_contentPanel,BorderLayout.CENTER); getContentPane().add(_quitPanel,BorderLayout.SOUTH); pack(); } public void actionPerformed(ActionEvent arg0) { setVisible(false); } private boolean _firstFocus = true; public void focusGained(FocusEvent arg0) { if (_firstFocus) { _input.setSelectionStart(0); _input.setSelectionEnd(_input.getText().length()); _firstFocus = false; } } public void focusLost(FocusEvent arg0) { // TODO Auto-generated method stub } public void keyPressed(KeyEvent arg0) { // TODO Auto-generated method stub } public void keyReleased(KeyEvent arg0) { // TODO Auto-generated method stub } public void keyTyped(KeyEvent arg0) { // TODO Auto-generated method stub char c = arg0.getKeyChar(); if (c=='\n') { try { ControleurScriptParser.executeScript(_vp,_input.getText()); } catch (Exception e) { _output.setText(_output.getText()+e.getMessage()+'\n'); e.printStackTrace(); } } } } fr/orsay/lri/varna/models/0000755000000000000000000000000012275611442014504 5ustar rootrootfr/orsay/lri/varna/models/VARNAConfigLoader.java0000644000000000000000000014004512415265012020471 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models; /* * VARNA is a Java library for quick automated drawings RNA secondary structure * Copyright (C) 2007 Yann Ponty * * This program is free software: you can redistribute it and/or modify it under * the terms of the GNU General Public License as published by the Free Software * Foundation, either version 3 of the License, or (at your option) any later * version. * * This program is distributed in the hope that it will be useful, but WITHOUT * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more * details. * * You should have received a copy of the GNU General Public License along with * this program. If not, see . */ import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.Point; import java.awt.geom.Point2D; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.net.URL; import java.net.URLConnection; import java.util.ArrayList; import java.util.Collection; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.interfaces.InterfaceParameterLoader; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.ModelBaseStyle; import fr.orsay.lri.varna.models.rna.RNA; /** * An RNA 2d Panel demo applet * * @author Yann Ponty * */ public class VARNAConfigLoader { private static final int MAXSTYLE = 50; // Applet Options public static String algoOpt = "algorithm"; public static String annotationsOpt = "annotations"; public static String applyBasesStyleOpt = "applyBasesStyle"; public static String auxBPsOpt = "auxBPs"; public static String autoHelicesOpt = "autoHelices"; public static String autoInteriorLoopsOpt = "autoInteriorLoops"; public static String autoTerminalLoopsOpt = "autoTerminalLoops"; public static String backboneColorOpt = "backbone"; public static String backgroundColorOpt = "background"; public static String baseInnerColorOpt = "baseInner"; public static String baseNameColorOpt = "baseName"; public static String baseNumbersColorOpt = "baseNum"; public static String baseOutlineColorOpt = "baseOutline"; public static String basesStyleOpt = "basesStyle"; public static String borderOpt = "border"; public static String bondColorOpt = "bp"; public static String bpIncrementOpt = "bpIncrement"; public static String bpStyleOpt = "bpStyle"; public static String colorMapOpt = "colorMap"; public static String colorMapCaptionOpt = "colorMapCaption"; public static String colorMapDefOpt = "colorMapStyle"; public static String colorMapMinOpt = "colorMapMin"; public static String colorMapMaxOpt = "colorMapMax"; public static String comparisonModeOpt = "comparisonMode"; public static String chemProbOpt = "chemProb"; public static String customBasesOpt = "customBases"; public static String customBPsOpt = "customBPs"; public static String drawNCOpt = "drawNC"; public static String drawBasesOpt = "drawBases"; public static String drawTertiaryOpt = "drawTertiary"; public static String drawColorMapOpt = "drawColorMap"; public static String drawBackboneOpt = "drawBackbone"; public static String errorOpt = "error"; public static String fillBasesOpt = "fillBases"; public static String firstSequenceForComparisonOpt = "firstSequence"; public static String firstStructureForComparisonOpt = "firstStructure"; public static String flatExteriorLoopOpt = "flat"; public static String flipOpt = "flip"; public static String gapsBaseColorOpt = "gapsColor"; public static String highlightRegionOpt = "highlightRegion"; public static String nonStandardColorOpt = "nsBasesColor"; public static String numColumnsOpt = "rows"; public static String numRowsOpt = "columns"; public static String orientationOpt = "orientation"; public static String modifiableOpt = "modifiable"; public static String periodNumOpt = "periodNum"; public static String rotationOpt = "rotation"; public static String secondSequenceForComparisonOpt = "secondSequence"; public static String secondStructureForComparisonOpt = "secondStructure"; public static String sequenceOpt = "sequenceDBN"; public static String spaceBetweenBasesOpt = "spaceBetweenBases"; public static String structureOpt = "structureDBN"; public static String titleOpt = "title"; public static String titleColorOpt = "titleColor"; public static String titleSizeOpt = "titleSize"; public static String URLOpt = "url"; public static String warningOpt = "warning"; public static String zoomOpt = "zoom"; public static String zoomAmountOpt = "zoomAmount"; // Applet assignable parameters private String _algo; public String _annotations; public String _chemProbs; private double _rotation; private String _sseq; private String _sstruct; private int _numRows; private int _numColumns; private String _title; private int _titleSize; private Color _titleColor; private String _auxBPs; private String _highlightRegion; private boolean _autoHelices; private boolean _autoInteriorLoops; private boolean _autoTerminalLoops; private boolean _drawBackbone; private Color _backboneColor; private Color _bondColor; private VARNAConfig.BP_STYLE _bpStyle; private Color _baseOutlineColor; private Color _baseInnerColor; private Color _baseNumColor; private Color _baseNameColor; private Color _gapsColor; private Color _nonStandardColor; private boolean _flatExteriorLoop; private String _flip; private String _customBases; private String _customBPs; private String _colorMapStyle; private String _colorMapCaption; private String _colorMapValues; private double _colorMapMin = Double.MIN_VALUE; private double _colorMapMax = Double.MAX_VALUE; private double _spaceBetweenBases = Double.MIN_VALUE; private boolean _drawNC; private boolean _drawBases; private boolean _drawTertiary; private boolean _drawColorMap; private boolean _fillBases; private int _periodResNum; private Dimension _border; private Color _backgroundColor; private String _orientation; private boolean _warning, _error; private boolean _modifiable; private double _zoom, _zoomAmount; private ArrayList _basesStyleList; private boolean _comparisonMode; private String _firstSequence; private String _secondSequence; private String _firstStructure; private String _secondStructure; private VARNAPanel _mainSurface; private boolean _useNonStandardColor; private boolean _useGapsColor; private double _bpIncrement; private boolean _useInnerBaseColor; private boolean _useBaseNameColor; private boolean _useBaseNumbersColor; private boolean _useBaseOutlineColor; private String _URL; protected ArrayList _VARNAPanelList = new ArrayList(); InterfaceParameterLoader _optionProducer; public VARNAConfigLoader(InterfaceParameterLoader il) { _optionProducer = il; } public ArrayList createVARNAPanels() throws ExceptionParameterError, ExceptionModeleStyleBaseSyntaxError, ExceptionNonEqualLength, IOException, ExceptionFileFormatOrSyntax, ExceptionLoadingFailed { _VARNAPanelList.clear(); retrieveParametersValues(); return _VARNAPanelList; } public int getNbRows() { return this._numRows; } public int getNbColumns() { return this._numColumns; } private void initValues() { // Applet assignable parameters _algo = "radiate"; _auxBPs = ""; _autoHelices = false; _autoInteriorLoops = false; _autoTerminalLoops = false; _annotations = ""; _backgroundColor = VARNAConfig.DEFAULT_BACKGROUND_COLOR; _customBases = ""; _customBPs = ""; _chemProbs = ""; _colorMapStyle = ""; _colorMapValues = ""; _colorMapCaption = ""; _drawColorMap = false; _drawBases = true; _fillBases = true; _drawNC = true; _drawTertiary = true; _border = new Dimension(0, 0); _sseq = "";// = // "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA"; _sstruct = "";// = // "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."; _periodResNum = VARNAConfig.DEFAULT_PERIOD; _rotation = 0.0; _title = ""; _titleSize = VARNAConfig.DEFAULT_TITLE_FONT.getSize(); _backboneColor = VARNAConfig.DEFAULT_BACKBONE_COLOR; _drawBackbone = true; _bondColor = VARNAConfig.DEFAULT_BOND_COLOR; _bpStyle = VARNAConfig.DEFAULT_BP_STYLE; _highlightRegion = ""; _baseOutlineColor = VARNAConfig.BASE_OUTLINE_COLOR_DEFAULT; _baseInnerColor = VARNAConfig.BASE_INNER_COLOR_DEFAULT; _baseNumColor = VARNAConfig.BASE_NUMBER_COLOR_DEFAULT; _baseNameColor = VARNAConfig.BASE_NAME_COLOR_DEFAULT; _titleColor = VARNAConfig.DEFAULT_TITLE_COLOR; _warning = false; _error = true; _modifiable = true; _zoom = VARNAConfig.DEFAULT_ZOOM; _zoomAmount = VARNAConfig.DEFAULT_AMOUNT; _comparisonMode = false; _firstSequence = ""; _firstStructure = ""; _secondSequence = ""; _secondStructure = ""; _gapsColor = VARNAConfig.DEFAULT_DASH_BASE_COLOR; _useGapsColor = false; _nonStandardColor = VARNAConfig.DEFAULT_SPECIAL_BASE_COLOR; _useNonStandardColor = false; _useInnerBaseColor = false; _useBaseNameColor = false; _useBaseNumbersColor = false; _useBaseOutlineColor = false; _bpIncrement = VARNAConfig.DEFAULT_BP_INCREMENT; _URL = ""; _flatExteriorLoop = true; _flip = ""; _orientation = ""; _spaceBetweenBases = VARNAConfig.DEFAULT_SPACE_BETWEEN_BASES; } public static Color getSafeColor(String col, Color def) { Color result; try { result = Color.decode(col); } catch (NumberFormatException e) { try { result = Color.getColor(col, def); } catch (Exception e2) { // Not a valid color return def; } } return result; } public static final String LEONTIS_WESTHOF_BP_STYLE = "lw"; public static final String LEONTIS_WESTHOF_BP_STYLE_ALT = "lwalt"; public static final String SIMPLE_BP_STYLE = "simple"; public static final String RNAVIZ_BP_STYLE = "rnaviz"; public static final String NONE_BP_STYLE = "none"; private VARNAConfig.BP_STYLE getSafeBPStyle(String opt, VARNAConfig.BP_STYLE def) { VARNAConfig.BP_STYLE b = VARNAConfig.BP_STYLE.getStyle(opt); if (b!= null) { return b; } else { return def; } } public static String[][] getParameterInfo() { String[][] info = { // Parameter Name Kind of Value Description { algoOpt, "String", "Drawing algorithm, choosen from [" + VARNAConfigLoader.ALGORITHM_NAVIEW + "," + VARNAConfigLoader.ALGORITHM_LINE + "," + VARNAConfigLoader.ALGORITHM_RADIATE + "," + VARNAConfigLoader.ALGORITHM_CIRCULAR + "]" }, { annotationsOpt, "string", "A set of textual annotations" }, { applyBasesStyleOpt, "String", "Base style application" }, { auxBPsOpt, "String", "Adds a list of (possibly non-canonical) base-pairs to those already defined by the main secondary structure (Ex: \"(1,10);(2,11);(3,12)\"). Custom BP styles can be specified (Ex: \"(2,11):thickness=4;(3,12):color=#FF0000\")." }, { autoHelicesOpt, "", "" }, { autoInteriorLoopsOpt, "", "" }, { autoTerminalLoopsOpt, "", "" }, { backboneColorOpt, "Color", "Backbone color (Ex: #334455)" }, { backgroundColorOpt, "Color", "Background color (Ex: #334455)" }, { baseInnerColorOpt, "Color", "Default value for inner base color (Ex: #334455)" }, { baseNameColorOpt, "Color", "Residues font color (Ex: #334455)" }, { baseNumbersColorOpt, "Color", "Base numbers font color (Ex: #334455)" }, { baseOutlineColorOpt, "Color", "Base outline color (Ex: #334455)" }, { basesStyleOpt, "String", "Base style declaration" }, { borderOpt, "String", "Border width and height in pixels (Ex: \"20x40\")" }, { bondColorOpt, "Color", "Base pair color (Ex: #334455)" }, { bpIncrementOpt, "float", "Distance between nested base-pairs (i.e. arcs) in linear representation" }, { bpStyleOpt, "String", "Look and feel for base pairs drawings, choosen from [" + VARNAConfigLoader.LEONTIS_WESTHOF_BP_STYLE+ "," + VARNAConfigLoader.LEONTIS_WESTHOF_BP_STYLE_ALT+ "," + VARNAConfigLoader.NONE_BP_STYLE + "," + VARNAConfigLoader.SIMPLE_BP_STYLE + "," + VARNAConfigLoader.RNAVIZ_BP_STYLE + "]" }, { chemProbOpt, "", "" }, { colorMapOpt, "String", "Associates a list of numerical values (eg '0.2,0.4,0.6,0.8') with the RNA bases with respect to their natural order, and modifies the color used to fill these bases according to current color map style." }, { colorMapCaptionOpt, "String", "Sets current color map caption." }, { colorMapDefOpt, "String", "Selects a specific color map style. It can be either one of the predefined styles (eg 'red', 'green', 'blue', 'bw', 'heat', 'energy') or a new one (eg '0:#FFFF00;1:#ffFFFF;6:#FF0000')." }, { colorMapMinOpt, "", "" }, { colorMapMaxOpt, "", "" }, { comparisonModeOpt, "boolean", "Activates comparison mode" }, { customBasesOpt, "", "" }, { customBPsOpt, "", "" }, { drawBackboneOpt, "boolean", "True if the backbone must be drawn, false otherwise" }, { drawColorMapOpt, "", "" }, { drawNCOpt, "boolean", "Toggles on/off display of non-canonical base-pairs" }, { drawBasesOpt, "boolean", "Shows/hide the outline of bases" }, { drawTertiaryOpt, "boolean", "Toggles on/off display of tertiary interaction, ie pseudoknots" }, { errorOpt, "boolean", "Show errors" }, { fillBasesOpt, "boolean", "Fills or leaves empty the inner portions of bases" }, { firstSequenceForComparisonOpt, "String", "In comparison mode, sequence of first RNA" }, { firstStructureForComparisonOpt, "String", "In comparison mode, structure of first RNA" }, { flatExteriorLoopOpt, "boolean", "Toggles on/off (true/false) drawing exterior bases on a straight line" }, { flipOpt, "String", "Draws a set of exterior helices, identified by the argument string, in clockwise order (default drawing is counter-clockwise). The argument is a semicolon-separated list of helices, each identified by a base or a base-pair (eg. \"2;20-34\")." }, { gapsBaseColorOpt, "Color", "Define and use custom color for gaps bases in comparison mode" }, { highlightRegionOpt, "string", "Highlight a set of contiguous regions" }, { modifiableOpt, "boolean", "Allows/prohibits modifications" }, { nonStandardColorOpt, "Color", "Define and use custom color for non-standard bases in comparison mode" }, { numColumnsOpt, "int", "Sets number of columns" }, { numRowsOpt, "int", "Sets number of rows" }, { orientationOpt, "float", "Sets the general orientation of an RNA, i.e. the deviation of the longest axis (defined by the most distant couple of bases) from the horizontal axis." }, { periodNumOpt, "int", "Periodicity of base-numbering" }, { secondSequenceForComparisonOpt, "String", "In comparison mode, sequence of second RNA" }, { secondStructureForComparisonOpt, "String", "In comparison mode, structure of second RNA" }, { sequenceOpt, "String", "Raw RNA sequence" }, { structureOpt, "String", "RNA structure given in dot bracket notation (DBN)" }, { rotationOpt, "float", "Rotates RNA after initial drawing (Ex: '20' for a 20 degree counter-clockwise rotation)" }, { titleOpt, "String", "RNA drawing title" }, { titleColorOpt, "Color", "Title color (Ex: #334455)" }, { titleSizeOpt, "int", "Title font size" }, { spaceBetweenBasesOpt, "float", "Sets the space between consecutive bases" }, { warningOpt, "boolean", "Show warnings" }, { zoomOpt, "int", "Zoom coefficient" }, { zoomAmountOpt, "int", "Zoom increment on user interaction" } }; return info; } private void retrieveParametersValues() throws ExceptionParameterError { _numRows = 1; _numColumns = 1; _basesStyleList = new ArrayList(); try { _numRows = Integer.parseInt(_optionProducer.getParameterValue( numRowsOpt, "" + _numRows)); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "'" + _optionProducer.getParameterValue(numRowsOpt, "" + _numRows) + "' is not a integer value for the number of rows !"); } try { _numColumns = Integer.parseInt(_optionProducer.getParameterValue( numColumnsOpt, "" + _numColumns)); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "'" + _optionProducer.getParameterValue(numColumnsOpt, "" + _numColumns) + "' is not a integer value for the number of columns !"); } String tmp = null; for (int i = 0; i < MAXSTYLE; i++) { String opt = basesStyleOpt + i; tmp = _optionProducer.getParameterValue(opt, null); // System.out.println(opt+"->"+tmp); if (tmp != null) { ModelBaseStyle msb = new ModelBaseStyle(); try { msb.assignParameters(tmp); } catch (ExceptionModeleStyleBaseSyntaxError e) { VARNAPanel.emitWarningStatic(e, null); } _basesStyleList.add(msb); } else { _basesStyleList.add(null); } } // _containerApplet.getLayout(). int x; String n; initValues(); for (int i = 0; i < _numColumns; i++) { for (int j = 0; j < _numRows; j++) { try { // initValues(); x = 1 + j + i * _numRows; n = "" + x; if ((_numColumns == 1) && (_numRows == 1)) { n = ""; } _useGapsColor = false; _useNonStandardColor = false; tmp = _optionProducer.getParameterValue(baseNameColorOpt + n, ""); if (!tmp.equals("")) { _useBaseNameColor = true; _baseNameColor = getSafeColor(tmp, _baseNameColor); } tmp = _optionProducer.getParameterValue(baseNumbersColorOpt + n, ""); if (!tmp.equals("")) { _useBaseNumbersColor = true; _baseNumColor = getSafeColor(tmp, _baseNumColor); } tmp = _optionProducer.getParameterValue(baseOutlineColorOpt + n, ""); if (!tmp.equals("")) { _useBaseOutlineColor = true; _baseOutlineColor = getSafeColor(tmp, _baseOutlineColor); } tmp = _optionProducer.getParameterValue(baseInnerColorOpt + n, ""); if (!tmp.equals("")) { _useInnerBaseColor = true; _baseInnerColor = getSafeColor(tmp, _baseInnerColor); } tmp = _optionProducer.getParameterValue(nonStandardColorOpt + n, ""); if (!tmp.equals("")) { _nonStandardColor = getSafeColor(tmp, _nonStandardColor); _useNonStandardColor = true; } tmp = _optionProducer.getParameterValue(gapsBaseColorOpt + n, _gapsColor.toString()); if (!tmp.equals("")) { _gapsColor = getSafeColor(tmp, _gapsColor); _useGapsColor = true; } try { _rotation = Double.parseDouble(_optionProducer .getParameterValue(rotationOpt + n, Double.toString(_rotation))); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "'" + _optionProducer.getParameterValue(rotationOpt + n, "" + _rotation) + "' is not a valid float value for rotation!"); } try { _colorMapMin = Double.parseDouble(_optionProducer .getParameterValue(colorMapMinOpt + n, Double.toString(this._colorMapMin))); } catch (NumberFormatException e) { throw new ExceptionParameterError( e.getMessage(), "'" + _optionProducer.getParameterValue( colorMapMinOpt + n, "" + _colorMapMin) + "' is not a valid double value for min color map values range!"); } try { _colorMapMax = Double.parseDouble(_optionProducer .getParameterValue(colorMapMaxOpt + n, Double.toString(this._colorMapMax))); } catch (NumberFormatException e) { throw new ExceptionParameterError( e.getMessage(), "'" + _optionProducer.getParameterValue( colorMapMaxOpt + n, "" + _colorMapMax) + "' is not a valid double value for max color map values range!"); } try { _bpIncrement = Double.parseDouble(_optionProducer .getParameterValue(bpIncrementOpt + n, Double.toString(_bpIncrement))); } catch (NumberFormatException e) { } try { _periodResNum = Integer.parseInt(_optionProducer .getParameterValue(periodNumOpt + n, "" + _periodResNum)); } catch (NumberFormatException e) { throw new ExceptionParameterError( e.getMessage(), "'" + _optionProducer.getParameterValue( periodNumOpt + n, "" + _periodResNum) + "' is not a valid integer value for the period of residue numbers!"); } try { _titleSize = Integer.parseInt(_optionProducer .getParameterValue(titleSizeOpt + n, "" + _titleSize)); } catch (NumberFormatException e) { throw new ExceptionParameterError( e.getMessage(), "'" + _optionProducer.getParameterValue( titleSizeOpt + n, "" + _titleSize) + "' is not a valid integer value for the number of rows !"); } try { _zoom = Double.parseDouble(_optionProducer .getParameterValue(zoomOpt + n, "" + _zoom)); } catch (NumberFormatException e) { throw new ExceptionParameterError( e.getMessage(), "'" + _optionProducer.getParameterValue( zoomOpt + n, "" + _zoom) + "' is not a valid integer value for the zoom !"); } try { _zoomAmount = Double.parseDouble(_optionProducer .getParameterValue(zoomAmountOpt + n, "" + _zoomAmount)); } catch (NumberFormatException e) { throw new ExceptionParameterError( e.getMessage(), "'" + _optionProducer.getParameterValue( zoomAmountOpt + n, "" + _zoomAmount) + "' is not a valid integer value for the zoom amount!"); } try { _spaceBetweenBases = Double.parseDouble(_optionProducer .getParameterValue(spaceBetweenBasesOpt + n, "" + _spaceBetweenBases)); } catch (NumberFormatException e) { throw new ExceptionParameterError( e.getMessage(), "'" + _optionProducer.getParameterValue( spaceBetweenBasesOpt + n, "" + _spaceBetweenBases) + "' is not a valid integer value for the base spacing!"); } _drawBases = Boolean.parseBoolean(_optionProducer .getParameterValue(drawBasesOpt + n, "" + _drawBases)); _fillBases = Boolean.parseBoolean(_optionProducer .getParameterValue(fillBasesOpt + n, "" + _fillBases)); _autoHelices = Boolean.parseBoolean(_optionProducer .getParameterValue(autoHelicesOpt + n, "" + _autoHelices)); _drawColorMap = Boolean.parseBoolean(_optionProducer .getParameterValue(drawColorMapOpt + n, "" + _drawColorMap)); _drawBackbone = Boolean.parseBoolean(_optionProducer .getParameterValue(drawBackboneOpt + n, "" + _drawBackbone)); _colorMapValues = _optionProducer.getParameterValue( colorMapOpt + n, _colorMapValues); _autoTerminalLoops = Boolean.parseBoolean(_optionProducer .getParameterValue(autoTerminalLoopsOpt + n, "" + _autoTerminalLoops)); _autoInteriorLoops = Boolean.parseBoolean(_optionProducer .getParameterValue(autoInteriorLoopsOpt + n, "" + _autoInteriorLoops)); _drawNC = Boolean.parseBoolean(_optionProducer .getParameterValue(drawNCOpt + n, "" + _drawNC)); _flatExteriorLoop = Boolean.parseBoolean(_optionProducer .getParameterValue(flatExteriorLoopOpt + n, "" + _flatExteriorLoop)); _drawTertiary = Boolean.parseBoolean(_optionProducer .getParameterValue(drawTertiaryOpt + n, "" + _drawTertiary)); _warning = Boolean.parseBoolean(_optionProducer .getParameterValue(warningOpt + n, "false")); _error = Boolean.parseBoolean(_optionProducer .getParameterValue(errorOpt + n, "true")); _border = parseDimension(_optionProducer.getParameterValue( borderOpt + n, "0X0")); _comparisonMode = Boolean.parseBoolean(_optionProducer .getParameterValue(comparisonModeOpt + n, "false")); _firstSequence = _optionProducer.getParameterValue( firstSequenceForComparisonOpt + n, _firstSequence); _firstStructure = _optionProducer .getParameterValue(firstStructureForComparisonOpt + n, _firstStructure); _secondSequence = _optionProducer .getParameterValue(secondSequenceForComparisonOpt + n, _secondSequence); _secondStructure = _optionProducer.getParameterValue( secondStructureForComparisonOpt + n, _secondStructure); _annotations = _optionProducer.getParameterValue( annotationsOpt + n, _annotations); _URL = _optionProducer.getParameterValue(URLOpt + n, _URL); _algo = _optionProducer.getParameterValue(algoOpt + n, _algo); _customBases = _optionProducer.getParameterValue( customBasesOpt + n, _customBases); _auxBPs = _optionProducer.getParameterValue(auxBPsOpt + n, _auxBPs); _highlightRegion = _optionProducer.getParameterValue( highlightRegionOpt + n, _highlightRegion); _chemProbs = _optionProducer.getParameterValue(chemProbOpt + n, _chemProbs); _customBPs = _optionProducer.getParameterValue(customBPsOpt + n, _customBPs); _colorMapStyle = _optionProducer.getParameterValue( colorMapDefOpt + n, _colorMapStyle); _colorMapCaption = _optionProducer.getParameterValue( colorMapCaptionOpt + n, _colorMapCaption); _backboneColor = getSafeColor( _optionProducer.getParameterValue(backboneColorOpt + n, _backboneColor.toString()), _backboneColor); _backgroundColor = getSafeColor( _optionProducer.getParameterValue( backgroundColorOpt + n, _backgroundColor.toString()), _backgroundColor); _bondColor = getSafeColor( _optionProducer.getParameterValue(bondColorOpt + n, _bondColor.toString()), _bondColor); _bpStyle = getSafeBPStyle( _optionProducer.getParameterValue(bpStyleOpt + n, ""), _bpStyle); _flip = _optionProducer.getParameterValue( flipOpt + n, _flip); _orientation = _optionProducer.getParameterValue( orientationOpt + n, _orientation); _titleColor = getSafeColor( _optionProducer.getParameterValue( titleColorOpt + n, _titleColor.toString()), _titleColor); if (!_URL.equals("")) { _sstruct = ""; _sseq = ""; _title = ""; } _title = _optionProducer.getParameterValue(titleOpt + n, _title); if (_comparisonMode && _firstSequence != null && _firstStructure != null && _secondSequence != null && _secondStructure != null) { } else { _sseq = _optionProducer.getParameterValue(sequenceOpt + n, _sseq); _sstruct = _optionProducer.getParameterValue( structureOpt + n, _sstruct); if (!_sseq.equals("") && !_sstruct.equals("")) { _URL = ""; } _comparisonMode = false; } // applique les valeurs des parametres recuperees applyValues(n); } catch (ExceptionParameterError e) { VARNAPanel.errorDialogStatic(e, _mainSurface); } catch (ExceptionNonEqualLength e) { VARNAPanel.errorDialogStatic(e, _mainSurface); } catch (IOException e) { VARNAPanel.errorDialogStatic(e, _mainSurface); } catch (ExceptionFileFormatOrSyntax e) { VARNAPanel.errorDialogStatic(e, _mainSurface); } catch (ExceptionLoadingFailed e) { VARNAPanel.errorDialogStatic(e, _mainSurface); } }// fin de boucle sur les lignes }// fin de boucle sur les colonnes } private RNA _defaultRNA = new RNA(); public void setRNA(RNA r) { _defaultRNA = r; } public static final String ALGORITHM_CIRCULAR = "circular"; public static final String ALGORITHM_NAVIEW = "naview"; public static final String ALGORITHM_LINE = "line"; public static final String ALGORITHM_RADIATE = "radiate"; public static final String ALGORITHM_VARNA_VIEW = "varnaview"; public static final String ALGORITHM_MOTIF_VIEW = "motifview"; private void applyValues(String n) throws ExceptionParameterError, ExceptionNonEqualLength, IOException, ExceptionFileFormatOrSyntax, ExceptionLoadingFailed { boolean applyOptions = true; int algoCode; if (_algo.equals(ALGORITHM_CIRCULAR)) algoCode = RNA.DRAW_MODE_CIRCULAR; else if (_algo.equals(ALGORITHM_NAVIEW)) algoCode = RNA.DRAW_MODE_NAVIEW; else if (_algo.equals(ALGORITHM_LINE)) algoCode = RNA.DRAW_MODE_LINEAR; else if (_algo.equals(ALGORITHM_RADIATE)) algoCode = RNA.DRAW_MODE_RADIATE; else if (_algo.equals(ALGORITHM_VARNA_VIEW)) algoCode = RNA.DRAW_MODE_VARNA_VIEW; else if (_algo.equals(ALGORITHM_MOTIF_VIEW)) algoCode = RNA.DRAW_MODE_MOTIFVIEW; else algoCode = RNA.DRAW_MODE_RADIATE; if (_comparisonMode) { _mainSurface = new VARNAPanel(_firstSequence, _firstStructure, _secondSequence, _secondStructure, algoCode, ""); } else { _mainSurface = new VARNAPanel(); } _VARNAPanelList.add(_mainSurface); _mainSurface.setSpaceBetweenBases(_spaceBetweenBases); _mainSurface.setTitle(_title); if (!_URL.equals("")) { URL url = null; try { _mainSurface.setSpaceBetweenBases(_spaceBetweenBases); url = new URL(_URL); URLConnection connexion = url.openConnection(); connexion.setUseCaches(false); InputStream r = connexion.getInputStream(); InputStreamReader inr = new InputStreamReader(r); if (_URL.toLowerCase().endsWith( VARNAPanel.VARNA_SESSION_EXTENSION)) { FullBackup f; f = VARNAPanel.importSession(r, _URL); _mainSurface.setConfig(f.config); _mainSurface.showRNA(f.rna); applyOptions = false; } else { Collection rnas = RNAFactory.loadSecStr( new BufferedReader(inr), RNAFactory.guessFileTypeFromExtension(_URL)); if (rnas.isEmpty()) { throw new ExceptionFileFormatOrSyntax( "No RNA in file '" + _URL + "'."); } RNA rna = rnas.iterator().next(); rna.drawRNA(algoCode, _mainSurface.getConfig()); _mainSurface.drawRNA(rna, algoCode); } if (!_title.isEmpty()) { _mainSurface.setTitle(_title); } } catch (ExceptionFileFormatOrSyntax e) { if (url != null) e.setPath(url.getPath()); } catch (ExceptionDrawingAlgorithm e) { _mainSurface.emitWarning(e.getMessage()); } } else { if (!_comparisonMode) { if (!_sstruct.equals("")) { _mainSurface.drawRNA(_sseq, _sstruct, algoCode); } else { try { System.err.println("Printing default RNA "+_defaultRNA); _defaultRNA.drawRNA(algoCode, _mainSurface.getConfig()); } catch (ExceptionDrawingAlgorithm e) { e.printStackTrace(); } _mainSurface.drawRNA(_defaultRNA); } } } if (applyOptions) { if (_useInnerBaseColor) { _mainSurface.setBaseInnerColor(_baseInnerColor); } if (_useBaseOutlineColor) { _mainSurface.setBaseOutlineColor(_baseOutlineColor); } if (_useBaseNameColor) { _mainSurface.setBaseNameColor(_baseNameColor); } if (_useBaseNumbersColor) { _mainSurface.setBaseNumbersColor(_baseNumColor); } _mainSurface.setBackground(_backgroundColor); _mainSurface.setNumPeriod(_periodResNum); _mainSurface.setBackboneColor(_backboneColor); _mainSurface.setDefaultBPColor(_bondColor); _mainSurface.setBPHeightIncrement(_bpIncrement); _mainSurface.setBPStyle(_bpStyle); _mainSurface.setDrawBackbone(_drawBackbone); _mainSurface.setTitleFontColor(_titleColor); _mainSurface.setTitleFontSize(_titleSize); _mainSurface.getPopupMenu().get_itemShowWarnings() .setState(_warning); _mainSurface.setErrorsOn(_error); _mainSurface.setFlatExteriorLoop(_flatExteriorLoop); _mainSurface.setZoom(_zoom); _mainSurface.setZoomIncrement(_zoomAmount); _mainSurface.setBorderSize(_border); if (_useGapsColor) { _mainSurface.setGapsBasesColor(this._gapsColor); _mainSurface.setColorGapsBases(true); } if (_useNonStandardColor) { _mainSurface.setNonStandardBasesColor(_nonStandardColor); _mainSurface.setColorNonStandardBases(true); } _mainSurface.setShowNonPlanarBP(_drawTertiary); _mainSurface.setShowNonCanonicalBP(_drawNC); applyBasesStyle(n); if (!_customBases.equals("")) applyBasesCustomStyles(_mainSurface); if (!_highlightRegion.equals("")) applyHighlightRegion(_mainSurface); if (!_auxBPs.equals("")) applyAuxBPs(_mainSurface); if (!_chemProbs.equals("")) applyChemProbs(_mainSurface); if (!_customBPs.equals("")) applyBPsCustomStyles(_mainSurface); _mainSurface.setDrawOutlineBases(_drawBases); _mainSurface.setFillBases(_fillBases); _mainSurface.drawRNA(); if (!_annotations.equals("")) applyAnnotations(_mainSurface); if (_autoHelices) _mainSurface.getVARNAUI().UIAutoAnnotateHelices(); if (_autoTerminalLoops) _mainSurface.getVARNAUI().UIAutoAnnotateTerminalLoops(); if (_autoInteriorLoops) _mainSurface.getVARNAUI().UIAutoAnnotateInteriorLoops(); if (!_orientation.equals("")) { try { double d = 360 * _mainSurface.getOrientation() / (2. * Math.PI); _rotation = Double.parseDouble(_orientation) - d; } catch (NumberFormatException e) { // TODO : Add some code here... } } _mainSurface.globalRotation(_rotation); _mainSurface.setModifiable(_modifiable); _mainSurface.setColorMapCaption(_colorMapCaption); applyColorMapStyle(_mainSurface); applyFlips(_mainSurface); applyColorMapValues(_mainSurface); // if (!_drawColorMap) // _mainSurface.drawColorMap(_drawColorMap); } // ajoute le VARNAPanel au conteneur } private void applyBasesStyle(String n) throws ExceptionParameterError { String tmp = null; for (int numStyle = 0; numStyle < _basesStyleList.size(); numStyle++) { if (_basesStyleList.get(numStyle) != null) { tmp = _optionProducer.getParameterValue(applyBasesStyleOpt + (numStyle) + "on" + n, null); ArrayList indicesList = new ArrayList(); if (tmp != null) { String[] basesList = tmp.split(","); for (int k = 0; k < basesList.length; k++) { String cand = basesList[k].trim(); try { String[] args = cand.split("-"); if (args.length == 1) { int baseNum = Integer.parseInt(cand); int index = _mainSurface.getRNA() .getIndexFromBaseNumber(baseNum); if (index != -1) { indicesList.add(index); } } else if (args.length == 2) { int baseNumFrom = Integer.parseInt(args[0] .trim()); int indexFrom = _mainSurface.getRNA() .getIndexFromBaseNumber(baseNumFrom); int baseNumTo = Integer .parseInt(args[1].trim()); int indexTo = _mainSurface.getRNA() .getIndexFromBaseNumber(baseNumTo); if ((indexFrom != -1) && (indexTo != -1)) { for (int l = indexFrom; l <= indexTo; l++) indicesList.add(l); } } } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "Bad Base Index: " + basesList[k]); } } for (int k = 0; k < indicesList.size(); k++) { int index = indicesList.get(k); if ((index >= 0) && (index < _mainSurface.getRNA() .get_listeBases().size())) { _mainSurface .getRNA() .get_listeBases() .get(index) .setStyleBase(_basesStyleList.get(numStyle)); } } } } }// fin de boucle sur les styles } private void applyColorMapStyle(VARNAPanel vp) { if (_colorMapStyle.length() != 0) { vp.setColorMap(ModeleColorMap.parseColorMap(_colorMapStyle)); } } private void applyColorMapValues(VARNAPanel vp) { if (!_colorMapValues.equals("")) { String[] values = _colorMapValues.split("[;,]"); ArrayList vals = new ArrayList(); for (int i = 0; i < values.length; i++) { try { vals.add(Double.parseDouble(values[i])); } catch (Exception e) { } } Double[] result = new Double[vals.size()]; vals.toArray(result); vp.setColorMapValues(result); ModeleColorMap cm = vp.getColorMap(); if (_colorMapMin != Double.MIN_VALUE) { // System.out.println("[A]"+_colorMapMin); cm.setMinValue(_colorMapMin); } if (_colorMapMax != Double.MAX_VALUE) { cm.setMaxValue(_colorMapMax); } _drawColorMap = true; } } private void applyBasesCustomStyles(VARNAPanel vp) { String[] baseStyles = _customBases.split(";"); for (int i = 0; i < baseStyles.length; i++) { String thisStyle = baseStyles[i]; String[] data = thisStyle.split(":"); try { if (data.length == 2) { int baseNum = Integer.parseInt(data[0]); int index = _mainSurface.getRNA().getIndexFromBaseNumber( baseNum); if (index != -1) { String style = data[1]; ModelBaseStyle msb = vp.getRNA().get_listeBases() .get(index).getStyleBase().clone(); msb.assignParameters(style); vp.getRNA().get_listeBases().get(index) .setStyleBase(msb); } } } catch (Exception e) { System.err.println("ApplyBasesCustomStyle: " + e.toString()); } } } private void applyHighlightRegion(VARNAPanel vp) { String[] regions = _highlightRegion.split(";"); for (int i = 0; i < regions.length; i++) { String region = regions[i]; // System.out.println(region); try { HighlightRegionAnnotation nt = HighlightRegionAnnotation .parseHighlightRegionAnnotation(region, vp); if (nt != null) { // System.out.println(nt); vp.addHighlightRegion(nt); } } catch (Exception e) { System.err.println("applyHighlightRegion: " + e.toString()); } } } private Dimension parseDimension(String s) { Dimension d = new Dimension(0, 0); try { s = s.toLowerCase(); int i = s.indexOf('x'); String w = s.substring(0, i); String h = s.substring(i + 1); d.width = Integer.parseInt(w); d.height = Integer.parseInt(h); } catch (NumberFormatException e) { } return d; } private void applyBPsCustomStyles(VARNAPanel vp) { String[] baseStyles = _customBPs.split(";"); for (int i = 0; i < baseStyles.length; i++) { String thisStyle = baseStyles[i]; String[] data = thisStyle.split(":"); try { if (data.length == 2) { String indices = data[0]; String style = data[1]; String[] data2 = indices.split(","); if (data2.length == 2) { String s1 = data2[0]; String s2 = data2[1]; if (s1.startsWith("(") && s2.endsWith(")")) { int a = Integer.parseInt(s1.substring(1)); int b = Integer.parseInt(s2.substring(0, s2.length() - 1)); ModeleBP msbp = vp.getRNA().getBPStyle(a, b); if (msbp != null) { msbp.assignParameters(style); } } } } } catch (Exception e) { System.err.println("ApplyBPsCustomStyle: " + e.toString()); } } } private void applyChemProbs(VARNAPanel vp) { String[] chemProbs = _chemProbs.split(";"); for (int i = 0; i < chemProbs.length; i++) { String thisAnn = chemProbs[i]; String[] data = thisAnn.split(":"); try { if (data.length == 2) { String indices = data[0]; String style = data[1]; String[] data2 = indices.split("-"); if (data2.length == 2) { int a = Integer.parseInt(data2[0]); int b = Integer.parseInt(data2[1]); int c = vp.getRNA().getIndexFromBaseNumber(a); int d = vp.getRNA().getIndexFromBaseNumber(b); ArrayList mbl = vp.getRNA() .get_listeBases(); ChemProbAnnotation cpa = new ChemProbAnnotation( mbl.get(c), mbl.get(d), style); vp.getRNA().addChemProbAnnotation(cpa); } } } catch (Exception e) { System.err.println("ChempProbs: " + e.toString()); } } } private void applyAuxBPs(VARNAPanel vp) { String[] baseStyles = _auxBPs.split(";"); for (int i = 0; i < baseStyles.length; i++) { String thisStyle = baseStyles[i]; String[] data = thisStyle.split(":"); try { if (data.length >= 1) { String indices = data[0]; String[] data2 = indices.split(","); if (data2.length == 2) { String s1 = data2[0]; String s2 = data2[1]; if (s1.startsWith("(") && s2.endsWith(")")) { int a = Integer.parseInt(s1.substring(1)); int b = Integer.parseInt(s2.substring(0, s2.length() - 1)); int c = vp.getRNA().getIndexFromBaseNumber(a); int d = vp.getRNA().getIndexFromBaseNumber(b); ModeleBP msbp = new ModeleBP(vp.getRNA() .get_listeBases().get(c), vp.getRNA() .get_listeBases().get(d)); if (data.length >= 2) { String style = data[1]; msbp.assignParameters(style); } vp.getRNA() .addBPToStructureUsingNumbers(a, b, msbp); } } } } catch (ExceptionModeleStyleBaseSyntaxError e1) { System.err.println("AuxApplyBPs: " + e1.toString()); } catch (ExceptionParameterError e) { // TODO Auto-generated catch block e.printStackTrace(); } } } private void applyFlips(VARNAPanel vp) { String[] flips = _flip.split(";"); for (String s: flips) { if (!s.isEmpty()) { try{ String[] data = s.split("-"); int number = -1; if (data.length==1) { number = Integer.parseInt(data[0]); } else if (data.length==2) { number = Integer.parseInt(data[1]); } if (number!=-1) { int i = vp.getRNA().getIndexFromBaseNumber(number); Point h = vp.getRNA().getExteriorHelix(i); vp.getRNA().flipHelix(h); } } catch (Exception e) { System.err.println("Flip Helices: " + e.toString()); } } } } /** * Format: * string:[type=[H|B|L|P]|x=double|y=double|anchor=int|size=int|color * =Color]; * * @param vp */ private void applyAnnotations(VARNAPanel vp) { String[] annotations = _annotations.split(";"); for (int i = 0; i < annotations.length; i++) { String thisAnn = annotations[i]; String[] data = thisAnn.split(":"); String text = ""; int anchor = -1; int x = -1; int y = -1; TextAnnotation.AnchorType type = TextAnnotation.AnchorType.LOOP; Font font = TextAnnotation.DEFAULTFONT; Color color = TextAnnotation.DEFAULTCOLOR; TextAnnotation ann = null; try { if (data.length == 2) { text = data[0]; String[] data2 = data[1].split(","); for (int j = 0; j < data2.length; j++) { String opt = data2[j]; String[] data3 = opt.split("="); if (data3.length == 2) { String name = data3[0].toLowerCase(); String value = data3[1]; if (name.equals("type")) { if (value.toUpperCase().equals("H")) { type = TextAnnotation.AnchorType.HELIX; } else if (value.toUpperCase().equals("L")) { type = TextAnnotation.AnchorType.LOOP; } else if (value.toUpperCase().equals("P")) { type = TextAnnotation.AnchorType.POSITION; } else if (value.toUpperCase().equals("B")) { type = TextAnnotation.AnchorType.BASE; } } else if (name.equals("x")) { x = Integer.parseInt(value); } else if (name.equals("y")) { y = Integer.parseInt(value); } else if (name.equals("anchor")) { anchor = Integer.parseInt(value); } else if (name.equals("size")) { font = font.deriveFont((float) Integer .parseInt(value)); } else if (name.equals("color")) { color = getSafeColor(value, color); } } } switch (type) { case POSITION: if ((x != -1) && (y != -1)) { Point2D.Double p = vp .panelToLogicPoint(new Point2D.Double(x, y)); ann = new TextAnnotation(text, p.x, p.y); } break; case BASE: if (anchor != -1) { int index = vp.getRNA().getIndexFromBaseNumber( anchor); ModeleBase mb = vp.getRNA().get_listeBases() .get(index); ann = new TextAnnotation(text, mb); } break; case HELIX: if (anchor != -1) { ArrayList mbl = new ArrayList(); int index = vp.getRNA().getIndexFromBaseNumber( anchor); ArrayList il = vp.getRNA() .findHelix(index); for (int k : il) { mbl.add(vp.getRNA().get_listeBases().get(k)); } ann = new TextAnnotation(text, mbl, type); } break; case LOOP: if (anchor != -1) { ArrayList mbl = new ArrayList(); int index = vp.getRNA().getIndexFromBaseNumber( anchor); ArrayList il = vp.getRNA().findLoop(index); for (int k : il) { mbl.add(vp.getRNA().get_listeBases().get(k)); } ann = new TextAnnotation(text, mbl, type); } break; } if (ann != null) { ann.setColor(color); ann.setFont(font); vp.addAnnotation(ann); } } } catch (Exception e) { System.err.println("Apply Annotations: " + e.toString()); } } } } fr/orsay/lri/varna/models/VARNAConfig.java0000644000000000000000000004465312541142112017345 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models; import java.awt.Color; import java.awt.Font; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.ObjectInputStream; import java.io.ObjectOutputStream; import java.io.Serializable; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.Attributes; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.ModeleBPStyle; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.utils.XMLUtils; public class VARNAConfig implements Serializable, Cloneable { /** * */ private static final long serialVersionUID = 2853916694420964233L; /** * */ public static final int MAJOR_VERSION = 3; public static final int MINOR_VERSION = 9; public static String getFullName() { return "VARNA "+MAJOR_VERSION+"."+MINOR_VERSION; } /** * Enum types and internal classes */ public enum BP_STYLE implements Serializable { NONE, SIMPLE, RNAVIZ, LW, LW_ALT; public String toString() { switch(this) { case LW: return "Leontis/Westhof (Centered)"; case SIMPLE: return "Line"; case RNAVIZ: return "Circles"; case NONE: return "None"; case LW_ALT: return "Leontis/Westhof (End)"; } return "Unspecified"; } public String getOpt() { switch(this) { case NONE: return "none"; case SIMPLE: return "simple"; case LW: return "lw"; case RNAVIZ: return "rnaviz"; case LW_ALT: return "lwalt"; } return "x"; } public static BP_STYLE getStyle(String opt) { for(BP_STYLE b: BP_STYLE.values()) { if (opt.toLowerCase().equals(b.getOpt().toLowerCase())) return b; } return null; } }; /** * Default values for config options */ public static final double MAX_ZOOM = 60; public static final double MIN_ZOOM = 0.5; public static final double DEFAULT_ZOOM = 1; public static final double MAX_AMOUNT = 2; public static final double MIN_AMOUNT = 1.01; public static final double DEFAULT_AMOUNT = 1.2; public static final double DEFAULT_BP_THICKNESS = 1.0; public static final double DEFAULT_DIST_NUMBERS = 3.0; public static final int DEFAULT_PERIOD = 10; public static final Color DEFAULT_TITLE_COLOR = Color.black; public static final Color DEFAULT_BACKBONE_COLOR = Color.DARK_GRAY.brighter(); public static final Color DEFAULT_BOND_COLOR = Color.blue; public static final Color DEFAULT_SPECIAL_BASE_COLOR = Color.green.brighter(); public static final Color DEFAULT_DASH_BASE_COLOR = Color.yellow.brighter(); public static final double DEFAULT_BASE_OUTLINE_THICKNESS = 1.5; public static final Color BASE_OUTLINE_COLOR_DEFAULT = Color.DARK_GRAY.brighter(); public static final Color BASE_INNER_COLOR_DEFAULT = new Color(242, 242,242); public static final Color BASE_NUMBER_COLOR_DEFAULT = Color.DARK_GRAY; public static final Color BASE_NAME_COLOR_DEFAULT = Color.black; public static final Color DEFAULT_HOVER_COLOR = new Color(230, 230,230); public static final Color DEFAULT_BACKGROUND_COLOR = Color.WHITE; public static final Font DEFAULT_TITLE_FONT = new Font("SansSerif", Font.BOLD,18); public static final Font DEFAULT_BASE_FONT = new Font("SansSerif", Font.PLAIN, 18); public static final Font DEFAULT_NUMBERS_FONT = new Font("SansSerif", Font.BOLD, 18); public static final Font DEFAULT_MESSAGE_FONT = Font.decode("dialog-PLAIN-25"); public static final Color DEFAULT_MESSAGE_COLOR = new Color(230, 230,230); public static final BP_STYLE DEFAULT_BP_STYLE = BP_STYLE.LW; public static final ModeleColorMap DEFAULT_COLOR_MAP = ModeleColorMap.defaultColorMap(); public static final Color DEFAULT_COLOR_MAP_OUTLINE = Color.gray; public static final double DEFAULT_BP_INCREMENT = 0.65; public static double DEFAULT_COLOR_MAP_WIDTH = 120; public static double DEFAULT_COLOR_MAP_HEIGHT = 30; public static double DEFAULT_COLOR_MAP_X_OFFSET = 40; public static double DEFAULT_COLOR_MAP_Y_OFFSET = 0; public static int DEFAULT_COLOR_MAP_STRIPE_WIDTH = 2; public static int DEFAULT_COLOR_MAP_FONT_SIZE = 20; public static Color DEFAULT_COLOR_MAP_FONT_COLOR = Color.gray.darker(); public static double DEFAULT_SPACE_BETWEEN_BASES = 1.0; /** * Various options. */ public static String XML_VAR_DRAW_OUTLINE = "drawoutline"; public static String XML_VAR_FILL_BASE = "fillbase"; public static String XML_VAR_AUTO_FIT = "autofit"; public static String XML_VAR_AUTO_CENTER = "autocenter"; public static String XML_VAR_MODIFIABLE = "modifiable"; public static String XML_VAR_ERRORS = "errors"; public static String XML_VAR_SPECIAL_BASES = "specialbases"; public static String XML_VAR_DASH_BASES = "dashbases"; public static String XML_VAR_USE_BASE_BPS = "usebasebps"; public static String XML_VAR_DRAW_NC = "drawnc"; public static String XML_VAR_DRAW_NON_PLANAR = "drawnonplanar"; public static String XML_VAR_SHOW_WARNINGS = "warnings"; public static String XML_VAR_COMPARISON_MODE = "comparison"; public static String XML_VAR_FLAT = "flat"; public static String XML_VAR_DRAW_BACKGROUND = "drawbackground"; public static String XML_VAR_COLOR_MAP = "drawcm"; public static String XML_VAR_DRAW_BACKBONE = "drawbackbone"; public static String XML_VAR_CM_HEIGHT = "cmh"; public static String XML_VAR_CM_WIDTH = "cmw"; public static String XML_VAR_CM_X_OFFSET = "cmx"; public static String XML_VAR_CM_Y_OFFSET = "cmy"; public static String XML_VAR_DEFAULT_ZOOM = "defaultzoom"; public static String XML_VAR_ZOOM_AMOUNT = "zoominc"; public static String XML_VAR_BP_THICKNESS = "bpthick"; public static String XML_VAR_BASE_THICKNESS = "basethick"; public static String XML_VAR_DIST_NUMBERS = "distnumbers"; public static String XML_VAR_NUM_PERIOD = "numperiod"; public static String XML_VAR_MAIN_BP_STYLE = "bpstyle"; public static String XML_VAR_CM = "cm"; public static String XML_VAR_BACKBONE_COLOR = "backbonecol"; public static String XML_VAR_HOVER_COLOR = "hovercol"; public static String XML_VAR_BACKGROUND_COLOR = "backgroundcol"; public static String XML_VAR_BOND_COLOR = "bondcol"; public static String XML_VAR_TITLE_COLOR = "titlecol"; public static String XML_VAR_SPECIAL_BASES_COLOR = "specialco"; public static String XML_VAR_DASH_BASES_COLOR = "dashcol"; public static String XML_VAR_SPACE_BETWEEN_BASES = "spacebetweenbases"; public static String XML_VAR_TITLE_FONT = "titlefont"; public static String XML_VAR_NUMBERS_FONT = "numbersfont"; public static String XML_VAR_FONT_BASES = "basefont"; public static String XML_VAR_CM_CAPTION = "cmcaption"; public static String XML_VAR_TITLE = "title"; public boolean _drawOutlineBases = true; public boolean _fillBases = true; public boolean _autoFit = true; public boolean _autoCenter = true; public boolean _modifiable = true; public boolean _errorsOn = false; public boolean _colorSpecialBases = false; public boolean _colorDashBases = false; public boolean _useBaseColorsForBPs = false; public boolean _drawnNonCanonicalBP = true; public boolean _drawnNonPlanarBP = true; public boolean _showWarnings = false; public boolean _comparisonMode = false; public boolean _flatExteriorLoop = true; public boolean _drawBackground = false; public boolean _drawColorMap = false; public boolean _drawBackbone = true; public double _colorMapHeight = DEFAULT_COLOR_MAP_HEIGHT; public double _colorMapWidth = DEFAULT_COLOR_MAP_WIDTH; public double _colorMapXOffset = DEFAULT_COLOR_MAP_X_OFFSET; public double _colorMapYOffset = DEFAULT_COLOR_MAP_Y_OFFSET; public double _zoom = DEFAULT_ZOOM; public double _zoomAmount = DEFAULT_AMOUNT; public double _bpThickness = 1.0; public double _baseThickness = DEFAULT_BASE_OUTLINE_THICKNESS; public double _distNumbers = DEFAULT_DIST_NUMBERS; public double _spaceBetweenBases = DEFAULT_SPACE_BETWEEN_BASES; public int _numPeriod = DEFAULT_PERIOD; public BP_STYLE _mainBPStyle = DEFAULT_BP_STYLE; public ModeleColorMap _cm = DEFAULT_COLOR_MAP; public Color _backboneColor = DEFAULT_BACKBONE_COLOR; public Color _hoverColor = DEFAULT_HOVER_COLOR; public Color _backgroundColor = DEFAULT_BACKGROUND_COLOR; public Color _bondColor = DEFAULT_BOND_COLOR; public Color _titleColor = DEFAULT_TITLE_COLOR; public Color _specialBasesColor = DEFAULT_SPECIAL_BASE_COLOR; public Color _dashBasesColor = DEFAULT_DASH_BASE_COLOR; public Font _titleFont = DEFAULT_TITLE_FONT; public Font _numbersFont = DEFAULT_NUMBERS_FONT; public Font _fontBasesGeneral = DEFAULT_BASE_FONT; public String _colorMapCaption = ""; //public String _title = ""; public static String XML_ELEMENT_NAME = "config"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_DRAW_OUTLINE,"CDATA", ""+_drawOutlineBases); atts.addAttribute("","",XML_VAR_FILL_BASE,"CDATA", ""+_fillBases); atts.addAttribute("","",XML_VAR_AUTO_FIT,"CDATA", ""+_autoFit); atts.addAttribute("","",XML_VAR_AUTO_CENTER,"CDATA", ""+_autoCenter); atts.addAttribute("","",XML_VAR_MODIFIABLE,"CDATA", ""+_modifiable); atts.addAttribute("","",XML_VAR_ERRORS,"CDATA", ""+_errorsOn); atts.addAttribute("","",XML_VAR_SPECIAL_BASES,"CDATA", ""+_colorSpecialBases); atts.addAttribute("","",XML_VAR_DASH_BASES,"CDATA", ""+_colorDashBases); atts.addAttribute("","",XML_VAR_USE_BASE_BPS,"CDATA", ""+_useBaseColorsForBPs); atts.addAttribute("","",XML_VAR_DRAW_NC,"CDATA", ""+_drawnNonCanonicalBP); atts.addAttribute("","",XML_VAR_DRAW_NON_PLANAR,"CDATA",""+_drawnNonPlanarBP); atts.addAttribute("","",XML_VAR_SHOW_WARNINGS,"CDATA", ""+_showWarnings); atts.addAttribute("","",XML_VAR_COMPARISON_MODE,"CDATA",""+_comparisonMode); atts.addAttribute("","",XML_VAR_FLAT,"CDATA", ""+_flatExteriorLoop); atts.addAttribute("","",XML_VAR_DRAW_BACKGROUND,"CDATA",""+_drawBackground); atts.addAttribute("","",XML_VAR_COLOR_MAP,"CDATA", ""+_drawColorMap); atts.addAttribute("","",XML_VAR_DRAW_BACKBONE,"CDATA", ""+_drawBackbone); atts.addAttribute("","",XML_VAR_CM_HEIGHT,"CDATA", ""+_colorMapHeight); atts.addAttribute("","",XML_VAR_CM_WIDTH,"CDATA", ""+_colorMapWidth); atts.addAttribute("","",XML_VAR_CM_X_OFFSET,"CDATA", ""+_colorMapXOffset); atts.addAttribute("","",XML_VAR_CM_Y_OFFSET,"CDATA", ""+_colorMapYOffset); atts.addAttribute("","",XML_VAR_DEFAULT_ZOOM,"CDATA", ""+_zoom); atts.addAttribute("","",XML_VAR_ZOOM_AMOUNT,"CDATA", ""+_zoomAmount); atts.addAttribute("","",XML_VAR_BP_THICKNESS,"CDATA", ""+_bpThickness); atts.addAttribute("","",XML_VAR_BASE_THICKNESS,"CDATA", ""+_baseThickness); atts.addAttribute("","",XML_VAR_DIST_NUMBERS,"CDATA", ""+_distNumbers); atts.addAttribute("","",XML_VAR_SPACE_BETWEEN_BASES,"CDATA", ""+_spaceBetweenBases); atts.addAttribute("","",XML_VAR_NUM_PERIOD,"CDATA", ""+_numPeriod); atts.addAttribute("","",XML_VAR_MAIN_BP_STYLE,"CDATA", ""+_mainBPStyle.getOpt()); atts.addAttribute("","",XML_VAR_BACKBONE_COLOR,"CDATA", XMLUtils.toHTMLNotation(_backboneColor)); atts.addAttribute("","",XML_VAR_HOVER_COLOR,"CDATA", XMLUtils.toHTMLNotation(_hoverColor)); atts.addAttribute("","",XML_VAR_BACKGROUND_COLOR,"CDATA", XMLUtils.toHTMLNotation(_backgroundColor)); atts.addAttribute("","",XML_VAR_BOND_COLOR,"CDATA", XMLUtils.toHTMLNotation(_bondColor)); atts.addAttribute("","",XML_VAR_TITLE_COLOR,"CDATA", XMLUtils.toHTMLNotation(_titleColor)); atts.addAttribute("","",XML_VAR_SPECIAL_BASES_COLOR,"CDATA",XMLUtils.toHTMLNotation(_specialBasesColor)); atts.addAttribute("","",XML_VAR_DASH_BASES_COLOR,"CDATA", XMLUtils.toHTMLNotation(_dashBasesColor)); atts.addAttribute("","",XML_VAR_CM,"CDATA", _cm.getParamEncoding()); hd.startElement("","",XML_ELEMENT_NAME,atts); XMLUtils.toXML(hd, _titleFont,XML_VAR_TITLE_FONT); XMLUtils.toXML(hd, _numbersFont,XML_VAR_NUMBERS_FONT); XMLUtils.toXML(hd, _fontBasesGeneral,XML_VAR_FONT_BASES); XMLUtils.exportCDATAElem(hd,XML_VAR_CM_CAPTION, _colorMapCaption); hd.endElement("","",XML_ELEMENT_NAME); } public void loadFromXMLAttributes(Attributes attributes) { _drawOutlineBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_OUTLINE)); _fillBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_FILL_BASE)); _autoFit = Boolean.parseBoolean(attributes.getValue(XML_VAR_AUTO_FIT)); _autoCenter = Boolean.parseBoolean(attributes.getValue(XML_VAR_AUTO_CENTER)); _modifiable = Boolean.parseBoolean(attributes.getValue(XML_VAR_MODIFIABLE)); _errorsOn = Boolean.parseBoolean(attributes.getValue(XML_VAR_ERRORS)); _colorSpecialBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_SPECIAL_BASES)); _colorDashBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_DASH_BASES)); _useBaseColorsForBPs = Boolean.parseBoolean(attributes.getValue(XML_VAR_USE_BASE_BPS)); _drawnNonCanonicalBP = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_NC)); _drawnNonPlanarBP = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_NON_PLANAR)); _showWarnings = Boolean.parseBoolean(attributes.getValue(XML_VAR_SHOW_WARNINGS)); _comparisonMode = Boolean.parseBoolean(attributes.getValue(XML_VAR_COMPARISON_MODE)); _flatExteriorLoop = Boolean.parseBoolean(attributes.getValue(XML_VAR_FLAT)); _drawBackground = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_BACKGROUND)); _drawColorMap = Boolean.parseBoolean(attributes.getValue(XML_VAR_COLOR_MAP)); _drawBackbone = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_BACKBONE)); _colorMapHeight = Double.parseDouble(attributes.getValue(XML_VAR_CM_HEIGHT)); _colorMapWidth = Double.parseDouble(attributes.getValue(XML_VAR_CM_WIDTH)); _colorMapXOffset = Double.parseDouble(attributes.getValue(XML_VAR_CM_X_OFFSET)); _colorMapYOffset = Double.parseDouble(attributes.getValue(XML_VAR_CM_Y_OFFSET)); _zoom = Double.parseDouble(attributes.getValue(XML_VAR_DEFAULT_ZOOM)); _zoomAmount = Double.parseDouble(attributes.getValue(XML_VAR_ZOOM_AMOUNT)); _bpThickness = Double.parseDouble(attributes.getValue(XML_VAR_BP_THICKNESS)); _baseThickness = Double.parseDouble(attributes.getValue(XML_VAR_BASE_THICKNESS)); _distNumbers = Double.parseDouble(attributes.getValue(XML_VAR_DIST_NUMBERS)); _spaceBetweenBases = XMLUtils.getDouble(attributes, XML_VAR_SPACE_BETWEEN_BASES, DEFAULT_SPACE_BETWEEN_BASES); _numPeriod = Integer.parseInt(attributes.getValue(XML_VAR_NUM_PERIOD)); _mainBPStyle = BP_STYLE.getStyle(attributes.getValue(XML_VAR_MAIN_BP_STYLE)); _backboneColor = Color.decode(attributes.getValue(XML_VAR_BACKBONE_COLOR)); _hoverColor = Color.decode(attributes.getValue(XML_VAR_HOVER_COLOR)); _backgroundColor = Color.decode(attributes.getValue(XML_VAR_BACKGROUND_COLOR)); _bondColor = Color.decode(attributes.getValue(XML_VAR_BOND_COLOR)); _titleColor = Color.decode(attributes.getValue(XML_VAR_TITLE_COLOR)); _specialBasesColor = Color.decode(attributes.getValue(XML_VAR_SPECIAL_BASES_COLOR)); _dashBasesColor = Color.decode(attributes.getValue(XML_VAR_DASH_BASES_COLOR)); _cm = ModeleColorMap.parseColorMap(attributes.getValue(XML_VAR_CM)); } public VARNAConfig clone () { try { ByteArrayOutputStream out = new ByteArrayOutputStream (); ObjectOutputStream oout = new ObjectOutputStream (out); oout.writeObject (this); ObjectInputStream in = new ObjectInputStream ( new ByteArrayInputStream (out.toByteArray ())); return (VARNAConfig)in.readObject (); } catch (Exception e) { throw new RuntimeException ("cannot clone class [" + this.getClass ().getName () + "] via serialization: " + e.toString ()); } } } fr/orsay/lri/varna/models/treealign/0000755000000000000000000000000012275611440016454 5ustar rootrootfr/orsay/lri/varna/models/treealign/RNANodeValue2WrongTypeException.java0000644000000000000000000000035511620715272025366 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * @author Raphael Champeimont * */ public class RNANodeValue2WrongTypeException extends NullPointerException { private static final long serialVersionUID = -2709057098523675088L; } fr/orsay/lri/varna/models/treealign/TreeGraphviz.java0000644000000000000000000000663311620715272021742 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.FileWriter; import java.io.IOException; import java.io.InputStreamReader; import java.io.OutputStreamWriter; /** * This class translates a Tree to a graphviz file. * @author Raphael Champeimont * * @param the type of values in the tree */ public class TreeGraphviz { /** * Generates a PostScript file using graphviz. * The dot command must be available. */ public static void treeToGraphvizPostscript(Tree tree, String filename, String title) throws IOException { // generate graphviz source String graphvizSource = treeToGraphviz(tree, title); // open output file BufferedWriter fbw; fbw = new BufferedWriter(new FileWriter(filename)); // execute graphviz Process proc = Runtime.getRuntime().exec("dot -Tps"); BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(proc.getOutputStream())); BufferedReader br = new BufferedReader(new InputStreamReader(proc.getInputStream())); BufferedReader bre = new BufferedReader(new InputStreamReader(proc.getErrorStream())); bw.write(graphvizSource); bw.close(); { String line = null; while ((line = br.readLine()) != null) { fbw.write(line + "\n"); } } { String line = null; while ((line = bre.readLine()) != null) { System.err.println(line); } } // wait for graphviz to end try { proc.waitFor(); } catch (InterruptedException e) { e.printStackTrace(); } // close file fbw.close(); } /** * Like treeToGraphvizPostscript(Tree,String,String) but with the title * equal to the filename. */ public static void treeToGraphvizPostscript(Tree tree, String filename) throws IOException { treeToGraphvizPostscript(tree, filename, filename); } /** * Creates a graphviz source file from a Tree. * @param title the title of the graph */ public static void treeToGraphvizFile(Tree tree, String filename, String title) throws IOException { BufferedWriter bw; bw = new BufferedWriter(new FileWriter(filename)); bw.write(treeToGraphviz(tree, filename)); bw.close(); } /** * Like treeToGraphvizFile(Tree,String,String) but with the title * equal to the filename. */ public static void treeToGraphvizFile(Tree tree, String filename) throws IOException { treeToGraphvizFile(tree, filename, filename); } /** * Creates a graphviz source from a Tree. * @param title the title of the graph */ public static String treeToGraphviz(Tree tree, String title) { return "digraph \"" + title + "\" {\n" + subtreeToGraphviz(tree) + "}\n"; } private static String subtreeToGraphviz(Tree tree) { String s = ""; String myId = tree.toGraphvizNodeId(); s += "\"" + myId + "\" [label=\"" + ((tree.getValue() != null) ? tree.getValue().toGraphvizNodeName() : "null") + "\"]\n"; for (Tree child: tree.getChildren()) { s += "\"" + myId + "\" -> \"" + child.toGraphvizNodeId() + "\"\n"; s += subtreeToGraphviz(child); } return s; } } fr/orsay/lri/varna/models/treealign/RNANodeValue2.java0000644000000000000000000000562512120444566021636 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; import java.util.ArrayList; import java.util.List; /** * In this model, nodes are either: * 1. a couple of paired bases, and in that case they may have children, * in this case singleNode is true * 2. a single base that comes from a broken base pair * (broken during planarization), without children, * in this case singleNode is true * 3. a list of consecutive non-paired bases, without children. * in this case singleNode is false * Note that case 2 happens only if original sequences contained * pseudoknots, otherwise this case can be ignored. * * @author Raphael Champeimont * */ public class RNANodeValue2 implements GraphvizDrawableNodeValue { /** * Says whether we have a single node or a list of nodes. */ private boolean singleNode = true; /** * Defined if singleNode is true. */ private RNANodeValue node; /** * Defined if singleNode is false; */ private List nodes; public RNANodeValue2(boolean singleNode) { this.singleNode = singleNode; if (singleNode) { node = new RNANodeValue(); } else { nodes = new ArrayList(); } } /** * In case of a single node, return it. * Will throw RNANodeValue2WrongTypeException if singleNode = false. */ public RNANodeValue getNode() { if (singleNode) { return node; } else { throw (new RNANodeValue2WrongTypeException()); } } public void setNode(RNANodeValue node) { if (singleNode) { this.node = node; } else { throw (new RNANodeValue2WrongTypeException()); } } /** * In case of multiple nodes, return them. * Will throw RNANodeValue2WrongTypeException if singleNode = true. */ public List getNodes() { if (!singleNode) { return nodes; } else { throw (new RNANodeValue2WrongTypeException()); } } /** * In case of multiple nodes, return the sequence of nucleotides. */ public char[] computeSequence() { if (!singleNode) { final int n = nodes.size(); char[] sequence = new char[n]; for (int i=0; i nodes) { if (!singleNode) { this.nodes = nodes; } else { throw (new RNANodeValue2WrongTypeException()); } } public boolean isSingleNode() { return singleNode; } public String toString() { if (singleNode) { return node.toString(); } else { String s = ""; for (RNANodeValue node: nodes) { if (s != "") { s += " "; } s += node.toString(); } return s; } } public String toGraphvizNodeName() { if (singleNode) { return node.toGraphvizNodeName(); } else { String s = ""; for (RNANodeValue node: nodes) { if (s != "") { s += " "; } s += node.toGraphvizNodeName(); } return s; } } } fr/orsay/lri/varna/models/treealign/AlignedNode.java0000644000000000000000000000277511620715272021504 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * The type of node values in an alignment. * Contains a reference to both original nodes. * This class implements GraphvizDrawableNodeValue but it will only work * if the original nodes implement it. * @author Raphael Champeimont * @param The type of values in the original first tree. * @param The type of values in the original second tree. */ public class AlignedNode implements GraphvizDrawableNodeValue { private Tree leftNode; private Tree rightNode; public Tree getLeftNode() { return leftNode; } public void setLeftNode(Tree leftNode) { this.leftNode = leftNode; } public Tree getRightNode() { return rightNode; } public void setRightNode(Tree rightNode) { this.rightNode = rightNode; } private String maybeNodeToGraphvizNodeName(Tree tree) { return (tree != null && tree.getValue() != null) ? tree.getValue().toGraphvizNodeName() : "_"; } /** * This method will work only if the left and right node * already implement GraphvizDrawableNodeValue. */ @SuppressWarnings("unchecked") public String toGraphvizNodeName() { return "(" + maybeNodeToGraphvizNodeName((Tree) leftNode) + "," + maybeNodeToGraphvizNodeName((Tree) rightNode) + ")"; } } fr/orsay/lri/varna/models/treealign/ExampleDistance3.java0000644000000000000000000001211311620715272022447 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; import java.util.ArrayList; /** * * * @author Raphael Champeimont */ public class ExampleDistance3 implements TreeAlignLabelDistanceSymmetric { public double f(RNANodeValue2 v1, RNANodeValue2 v2) { if (v1 == null) { if (v2 == null) { return 0; } else if (!v2.isSingleNode()) { // v2 is a list of bases // We insert all bases, with a cost of 1 for each base. return v2.getNodes().size(); } else { // v2 is a single node return 2; } } else if (!v1.isSingleNode()) { // v1 is a list of bases if (v2 == null) { return v1.getNodes().size(); } else if (!v2.isSingleNode()) { // v2 is a list of bases // We compute the sequence distance return alignSequenceNodes(v1, v2).getDistance(); } else { // v2 is a single node return 2 + v1.getNodes().size(); } } else { // v1 is a single node // all the same as when v1 == null if (v2 == null) { return 2; } else if (!v2.isSingleNode()) { // v2 is a list of bases return 2 + v2.getNodes().size(); } else { // v2 is a single node String l1 = v1.getNode().getLeftNucleotide(); String r1 = v1.getNode().getRightNucleotide(); String l2 = v2.getNode().getLeftNucleotide(); String r2 = v2.getNode().getRightNucleotide(); // We have cost(subst((x,y) to (x',y'))) = 1 // when x != x' and y != y'. // It means it is less than substituting 2 non-paired bases return (!l1.equals(l2) ? 0.5 : 0) + (!r1.equals(r2) ? 0.5 : 0); } } } public class SequenceAlignResult { private double distance; private int[][] alignment; public double getDistance() { return distance; } public void setDistance(double distance) { this.distance = distance; } /** The result array is a matrix of height 2 * and width at most length(sequence A) + length(sequence B). * with result[0] is the alignment for A * and result[1] the alignment for B. * The alignment consists int the indexes of the original * bases positions, with -1 when there is no match. */ public int[][] getAlignment() { return alignment; } public void setAlignment(int[][] alignment) { this.alignment = alignment; } } /** * Align two sequences contained in nodes. * Both nodes have to be non-single nodes, otherwise an * RNANodeValue2WrongTypeException exception will be thrown. */ public SequenceAlignResult alignSequenceNodes(RNANodeValue2 v1, RNANodeValue2 v2) { char[] A = v1.computeSequence(); char[] B = v2.computeSequence(); return alignSequences(A, B); } /** * Align sequences using the Needleman-Wunsch algorithm. * Time: O(A.length * B.length) * Space: O(A.length * B.length) * Space used by the returned object: O(A.length + B.length) */ public SequenceAlignResult alignSequences(char[] A, char[] B) { SequenceAlignResult result = new SequenceAlignResult(); final int la = A.length; final int lb = B.length; double[][] F = new double[la+1][lb+1]; int[][] decisions = new int[la+1][lb+1]; final double d = 1; // insertion/deletion cost final double substCost = 1; // substitution cost for (int i=0; i<=la; i++) F[i][0] = d*i; for (int j=0; j<=lb; j++) F[0][j] = d*j; for (int i=1; i<=la; i++) for (int j=1; j<=lb; j++) { double min; int decision; double match = F[i-1][j-1] + (A[i-1] == B[j-1] ? 0 : substCost); double delete = F[i-1][j] + d; if (match < delete) { decision = 1; min = match; } else { decision = 2; min = delete; } double insert = F[i][j-1] + d; if (insert < min) { decision = 3; min = insert; } F[i][j] = min; decisions[i][j] = decision; } result.setDistance(F[la][lb]); int[][] alignment = computeAlignment(F, decisions, A, B); result.setAlignment(alignment); return result; } private int[][] computeAlignment(double[][] F, int[][] decisions, char[] A, char[] B) { // At worst the alignment will be of length (A.length + B.length) ArrayList AlignmentA = new ArrayList(A.length + B.length); ArrayList AlignmentB = new ArrayList(A.length + B.length); int i = A.length; int j = B.length; while (i > 0 && j > 0) { int decision = decisions[i][j]; switch (decision) { case 1: AlignmentA.add(i-1); AlignmentB.add(j-1); i = i - 1; j = j - 1; break; case 2: AlignmentA.add(i-1); AlignmentB.add(-1); i = i - 1; break; case 3: AlignmentA.add(-1); AlignmentB.add(j-1); j = j - 1; break; default: throw (new Error("Bug in ExampleDistance3: decision = " + decision)); } } while (i > 0) { AlignmentA.add(i-1); AlignmentB.add(-1); i = i - 1; } while (j > 0) { AlignmentA.add(-1); AlignmentB.add(j-1); j = j - 1; } // Convert the ArrayLists to the right format: // We need to reverse the list and change the numbering of int l = AlignmentA.size(); int[][] result = new int[2][l]; for (i=0; i { public double f(RNANodeValue2 v1, RNANodeValue2 v2) { if (v1 == null) { if (v2 == null) { return 0; } else if (!v2.isSingleNode()) { // v2 is a list of bases return v2.getNodes().size(); } else { // v2 is a single node return 2; } } else if (!v1.isSingleNode()) { // v1 is a list of bases if (v2 == null) { return v1.getNodes().size(); } else if (!v2.isSingleNode()) { // v2 is a list of bases return Math.abs(v2.getNodes().size() - v1.getNodes().size()); } else { // v2 is a single node return 2 + v1.getNodes().size(); } } else { // v1 is a single node // all the same as when v1 == null if (v2 == null) { return 2; } else if (!v2.isSingleNode()) { // v2 is a list of bases return 2 + v2.getNodes().size(); } else { // v2 is a single node return 0; } } } } fr/orsay/lri/varna/models/treealign/TreeAlignException.java0000644000000000000000000000042611620715272023053 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * @author Raphael Champeimont * */ public class TreeAlignException extends Exception { private static final long serialVersionUID = 7782935062930780231L; public TreeAlignException(String message) { super(message); } } fr/orsay/lri/varna/models/treealign/RNATree.java0000644000000000000000000001210611722472550020562 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; import java.util.ArrayList; import java.util.List; import fr.orsay.lri.varna.exceptions.MappingException; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.RNA; /** * This class contains all functions that are specific to trees * (class Tree) of RNA. * * @author Raphael Champeimont * */ public class RNATree { /** * Convert an RNA object into a RNA tree. * The root node will have a null value because it is a fake * node added to have a tree (otherwise we would have a forest). */ public static Tree RNATreeFromRNA(RNA rna) { ConvertToTree converter = new ConvertToTree(rna); return converter.toTreeAux(0); } private static class ConvertToTree { private RNA rna; private int i = 0; /** Starts at the current position i in the sequence and converts the sequence * to a tree. * @return the created tree */ public Tree toTreeAux(int depth) { Tree tree = new Tree(); List> children = tree.getChildren(); // No value because it is a fake root tree.setValue(null); int length = rna.getSize(); while (i < length) { ModeleBase base = rna.getBaseAt(i); int indexOfAssociatedBase = base.getElementStructure(); if (indexOfAssociatedBase >= 0) { if (indexOfAssociatedBase > i) { // left parenthesis, we must analyze the children RNANodeValue childValue = new RNANodeValue(); childValue.setLeftBasePosition(i); childValue.setRightBasePosition(indexOfAssociatedBase); childValue.setOrigin(RNANodeValue.Origin.BASE_PAIR_FROM_HELIX); if (base instanceof ModeleBaseNucleotide) { childValue.setLeftNucleotide(((ModeleBaseNucleotide) base).getBase()); childValue.setRightNucleotide(((ModeleBaseNucleotide) rna.getBaseAt(indexOfAssociatedBase)).getBase()); } i++; Tree child = toTreeAux(depth+1); child.setValue(childValue); children.add(child); } else { // right parenthesis, we have finished analyzing the children i++; break; } } else { // we have a non-paired base Tree child = new Tree(); RNANodeValue childValue = new RNANodeValue(); childValue.setLeftBasePosition(i); if (base instanceof ModeleBaseNucleotide) { childValue.setLeftNucleotide(((ModeleBaseNucleotide) base).getBase()); } // Even in this case (getElementStructure() < 0) // this base may still come from an helix which may have // been broken to remove a pseudoknot. childValue.setOrigin(RNANodeValue.Origin.BASE_FROM_UNPAIRED_REGION); ArrayList auxBasePairs = rna.getAuxBPs(i); for (ModeleBP auxBasePair: auxBasePairs) { if (auxBasePair.isCanonical()) { int partner5 = ((ModeleBaseNucleotide) auxBasePair.getPartner5()).getIndex(); int partner3 = ((ModeleBaseNucleotide) auxBasePair.getPartner3()).getIndex(); if (i == partner5) { childValue.setOrigin(RNANodeValue.Origin.BASE_FROM_HELIX_STRAND5); } else if (i == partner3) { childValue.setOrigin(RNANodeValue.Origin.BASE_FROM_HELIX_STRAND3); } else { System.err.println("Warning: Base index is " + i + " but neither endpoint matches it (edge endpoints are " + partner5 + " and " + partner3 + ")."); } } } child.setValue(childValue); children.add(child); i++; } } return tree; } public ConvertToTree(RNA rna) { this.rna = rna; } } /** * Convert an RNA tree alignment into a Mapping. */ public static Mapping mappingFromAlignment(Tree> alignment) throws MappingException { ConvertToMapping converter = new ConvertToMapping(); return converter.convert(alignment); } private static class ConvertToMapping { private Mapping m; public Mapping convert(Tree> tree) throws MappingException { m = new Mapping(); convertSubTree(tree); return m; } private void convertSubTree(Tree> tree) throws MappingException { AlignedNode alignedNode = tree.getValue(); Tree leftNode = alignedNode.getLeftNode(); Tree rightNode = alignedNode.getRightNode(); if (leftNode != null && rightNode != null) { RNANodeValue v1 = leftNode.getValue(); RNANodeValue v2 = rightNode.getValue(); int l1 = v1.getLeftBasePosition(); int r1 = v1.getRightBasePosition(); int l2 = v2.getLeftBasePosition(); int r2 = v2.getRightBasePosition(); if (l1 >= 0 && l2 >= 0) { m.addCouple(l1, l2); } if (r1 >= 0 && r2 >= 0) { m.addCouple(r1, r2); } } for (Tree> child: tree.getChildren()) { convertSubTree(child); } } } } fr/orsay/lri/varna/models/treealign/RNATree2Exception.java0000644000000000000000000000042611620715272022523 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * @author Raphael Champeimont * */ public class RNATree2Exception extends Exception { private static final long serialVersionUID = 2034802149835891010L; public RNATree2Exception(String message) { super(message); } } fr/orsay/lri/varna/models/treealign/Tree.java0000644000000000000000000001010311620715272020212 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; import java.util.*; /** * An object of this class is a rooted tree, where children are ordered. * The tree is iterable, and the default iterator is DFS * (depth-first search), with the fathers given before the children. * * @param The type of values on nodes. * @author Raphael Champeimont */ public class Tree implements Iterable> { private List> children; private T value; private Tree tree = this; public T getValue() { return value; } public void setValue(T value) { this.value = value; } /** * Returns the list of children. * The return list has a O(1) access time to any of its elements * (ie. it is like an array and unlike a linked list) */ public List> getChildren() { return children; } /** * This method replaces the list of children of a tree with the list given * as argument. Be careful, because it means the list will be kept as a * reference (it will not be copied) so if you later modify the list * you passed as an argument here, it will modify the list of children. * Note that the List object you give must have a 0(1) access time to * elements (because someone calling getChildren() can expect that property). * This method may be useful if you have already built a list of children * and you don't want to use this.getChildren.addAll() to avoid a O(n) copy. * In that case you would simply call the constructor that takes no argument * to create an empty tree and then call replaceChildrenListBy(children) * where children is the list of children you have built. * @param children the new list of children */ public void replaceChildrenListBy(List> children) { this.children = children; } /** * Creates a tree, with the given set of children. * The given set is any collection that implements Iterable. * The set is iterated on and its elements are copied (as references). */ public Tree(Iterable> children) { this(); for (Tree child: children) { this.children.add(child); } } /** * Creates a tree, with an empty list of children. */ public Tree() { children = new ArrayList>(); } /** * Returns the number of children of the root node. */ public int rootDegree() { return children.size(); } /** * Count the nodes in the tree. * Time: O(n) * @return the number of nodes in the tree */ public int countNodes() { int count = 1; for (Tree child: children) { count += child.countNodes(); } return count; } /** * Compute the tree degree, ie. the max over nodes of the node degree. * Time: O(n) * @return the maximum node degree */ public int computeDegree() { int max = children.size(); for (Tree child: children) { int maxCandidate = child.computeDegree(); if (maxCandidate > max) { max = maxCandidate; } } return max; } /** * Returns a string unique to this node. */ public String toGraphvizNodeId() { return super.toString(); } public Iterator> iterator() { return (new DFSPrefixIterator()); } /** * An iterator that returns the nodes in prefix (fathers before * children) DFS (go deep first) order. */ public class DFSPrefixIterator implements Iterator> { private LinkedList> remainingNodes = new LinkedList>(); public boolean hasNext() { return !remainingNodes.isEmpty(); } public Tree next() { if (remainingNodes.isEmpty()) { throw (new NoSuchElementException()); } Tree currentNode = remainingNodes.getLast(); remainingNodes.removeLast(); List> children = currentNode.getChildren(); int n = children.size(); // The children access is in O(1) so this loop is O(n) for (int i=n-1; i>=0; i--) { // We add the children is their reverse order so they // are given in the original order by the iterator remainingNodes.add(children.get(i)); } return currentNode; } public DFSPrefixIterator() { remainingNodes.add(tree); } public void remove() { throw (new UnsupportedOperationException()); } } } fr/orsay/lri/varna/models/treealign/GraphvizDrawableNodeValue.java0000644000000000000000000000057511620715272024366 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * A tree can be displayed using graphviz (using class TreeGraphviz) * if the node values in the tree implement this interface. * * @author Raphael Champeimont */ public interface GraphvizDrawableNodeValue { /** * Returns a string that will be displayed on the node by graphviz. */ public String toGraphvizNodeName(); } fr/orsay/lri/varna/models/treealign/TreeAlignLabelDistanceSymmetric.java0000644000000000000000000000055111620715272025503 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * Same as TreeAlignLabelDistanceAsymmetric, but elements on both * trees are of the same type, and the function is symmetric, ie. * f(x,y) = f(y,x) . * * @param */ public interface TreeAlignLabelDistanceSymmetric extends TreeAlignLabelDistanceAsymmetric { } fr/orsay/lri/varna/models/treealign/TreeAlignResult.java0000644000000000000000000000130711620715272022372 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * The result of aligning a tree T1 with a tree T2. * On the resulting tree, each node has a value * of type AlignedNode. * @author Raphael Champeimont */ public class TreeAlignResult { private Tree> alignment; private double distance; public Tree> getAlignment() { return alignment; } public void setAlignment(Tree> alignment) { this.alignment = alignment; } public double getDistance() { return distance; } public void setDistance(double distance) { this.distance = distance; } } fr/orsay/lri/varna/models/treealign/RNANodeValue.java0000644000000000000000000000515112120444566021546 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; /** * We use the following convention: If the node is marked by a couple (n,m) * these integers are stored in leftBasePosition and rightBasePosition * (ie. we have a pair of bases), if only * one value is present, it is stored in leftBasePosition and rightBasePosition * contains -1 (ie. we have a non-paired base). * The right and left nucleotides follow the same rule, but are optional, * and '_' is used as undefined instead of -1. * Note that it is part of the contract of this class that default * values are -1 and _. * * @author Raphael Champeimont */ public class RNANodeValue implements GraphvizDrawableNodeValue { private int leftBasePosition = -1; private int rightBasePosition = -1; private String leftNucleotide = "_"; private String rightNucleotide = "_"; public enum Origin { BASE_PAIR_FROM_HELIX, BASE_FROM_HELIX_STRAND5, BASE_FROM_HELIX_STRAND3, BASE_FROM_UNPAIRED_REGION; } /** * Used to store the origin of this base / base pair. */ private Origin origin = null; public Origin getOrigin() { return origin; } public void setOrigin(Origin comesFromAnHelix) { this.origin = comesFromAnHelix; } public String getLeftNucleotide() { return leftNucleotide; } public void setLeftNucleotide(String leftNucleotide) { this.leftNucleotide = leftNucleotide; } public String getRightNucleotide() { return rightNucleotide; } public void setRightNucleotide(String rightNucleotide) { this.rightNucleotide = rightNucleotide; } public int getLeftBasePosition() { return leftBasePosition; } public void setLeftBasePosition(int leftBasePosition) { this.leftBasePosition = leftBasePosition; } public int getRightBasePosition() { return rightBasePosition; } public void setRightBasePosition(int rightBasePosition) { this.rightBasePosition = rightBasePosition; } public String toGraphvizNodeName() { if (rightNucleotide.equals("_")) { if (leftNucleotide.equals("_")) { if (rightBasePosition == -1) { if (leftBasePosition == -1) { return super.toString(); } else { return Integer.toString(leftBasePosition); } } else { return "(" + leftBasePosition + "," + rightBasePosition + ")"; } } else { return leftNucleotide; } } else { return "(" + leftNucleotide + "," + rightNucleotide + ")"; } } public String toString() { if (rightBasePosition == -1) { if (leftBasePosition == -1) { return super.toString(); } else { return Integer.toString(leftBasePosition); } } else { return "(" + leftBasePosition + "," + rightBasePosition + ")"; } } } fr/orsay/lri/varna/models/treealign/RNATree2.java0000644000000000000000000001444412134015500020635 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; import java.util.ArrayList; import java.util.LinkedList; import java.util.List; import fr.orsay.lri.varna.exceptions.MappingException; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.RNA; /** * This class contains all functions that are specific to trees * (class Tree) of RNA, with RNANodeValue2. * * @author Raphael Champeimont * */ public class RNATree2 { /** * Convert an RNA object into a RNA tree with RNANodeValue2. * @throws RNATree2Exception */ public static Tree RNATree2FromRNA(RNA rna) throws RNATree2Exception { Tree fullTree = RNATree.RNATreeFromRNA(rna); return RNATree2FromRNATree(fullTree); } /** * Convert from RNANodeValue model to RNANodeValue2 model, * ie. compact consecutive non-paired bases. */ public static Tree RNATree2FromRNATree(Tree originalTree) throws RNATree2Exception { Tree newTree = new Tree(); // Root in original tree is fake, so make a fake root newTree.setValue(null); newTree.replaceChildrenListBy(RNAForest2FromRNAForest(originalTree.getChildren())); return newTree; } private static void RNAForest2FromRNAForestCommitNonPaired(List> forest, List consecutiveNonPairedBases) { // add the group of non-paired bases if there is one if (consecutiveNonPairedBases.size() > 0) { RNANodeValue2 groupOfConsecutiveBases = new RNANodeValue2(false); groupOfConsecutiveBases.getNodes().addAll(consecutiveNonPairedBases); Tree groupOfConsecutiveBasesNode = new Tree(); groupOfConsecutiveBasesNode.setValue(groupOfConsecutiveBases); forest.add(groupOfConsecutiveBasesNode); consecutiveNonPairedBases.clear(); } } private static List> RNAForest2FromRNAForest(List> originalForest) throws RNATree2Exception { List> forest = new ArrayList>(); List consecutiveNonPairedBases = new LinkedList(); for (Tree originalTree: originalForest) { if (originalTree.getValue().getRightBasePosition() == -1) { // non-paired base if (originalTree.getChildren().size() > 0) { throw (new RNATree2Exception("Non-paired base cannot have children.")); } switch (originalTree.getValue().getOrigin()) { case BASE_FROM_HELIX_STRAND5: case BASE_FROM_HELIX_STRAND3: // This base is part of a broken base pair // if we have gathered some non-paired bases, add a node with // the group of them RNAForest2FromRNAForestCommitNonPaired(forest, consecutiveNonPairedBases); // now add the node RNANodeValue2 pairedBase = new RNANodeValue2(true); pairedBase.setNode(originalTree.getValue()); Tree pairedBaseNode = new Tree(); pairedBaseNode.setValue(pairedBase); forest.add(pairedBaseNode); break; case BASE_FROM_UNPAIRED_REGION: consecutiveNonPairedBases.add(originalTree.getValue()); break; case BASE_PAIR_FROM_HELIX: throw (new RNATree2Exception("Origin is BASE_PAIR_FROM_HELIX but this is not a pair.")); } } else { // paired bases // if we have gathered some non-paired bases, add a node with // the group of them RNAForest2FromRNAForestCommitNonPaired(forest, consecutiveNonPairedBases); // now add the node RNANodeValue2 pairedBase = new RNANodeValue2(true); pairedBase.setNode(originalTree.getValue()); Tree pairedBaseNode = new Tree(); pairedBaseNode.setValue(pairedBase); pairedBaseNode.replaceChildrenListBy(RNAForest2FromRNAForest(originalTree.getChildren())); forest.add(pairedBaseNode); } } // if there we have some non-paired bases, add them grouped RNAForest2FromRNAForestCommitNonPaired(forest, consecutiveNonPairedBases); return forest; } /** * Convert an RNA tree (with RNANodeValue2) alignment into a Mapping. */ public static Mapping mappingFromAlignment(Tree> alignment) throws MappingException { ConvertToMapping converter = new ConvertToMapping(); return converter.convert(alignment); } private static class ConvertToMapping { private Mapping m; ExampleDistance3 sequenceAligner = new ExampleDistance3(); public Mapping convert(Tree> tree) throws MappingException { m = new Mapping(); convertSubTree(tree); return m; } private void convertSubTree(Tree> tree) throws MappingException { AlignedNode alignedNode = tree.getValue(); Tree leftNode = alignedNode.getLeftNode(); Tree rightNode = alignedNode.getRightNode(); if (leftNode != null && rightNode != null) { RNANodeValue2 v1 = leftNode.getValue(); RNANodeValue2 v2 = rightNode.getValue(); if (v1.isSingleNode() && v2.isSingleNode()) { // we have aligned (x,y) with (x',y') // so we map x with x' and y with y' RNANodeValue vsn1 = v1.getNode(); RNANodeValue vsn2 = v2.getNode(); int l1 = vsn1.getLeftBasePosition(); int r1 = vsn1.getRightBasePosition(); int l2 = vsn2.getLeftBasePosition(); int r2 = vsn2.getRightBasePosition(); if (l1 >= 0 && l2 >= 0) { m.addCouple(l1, l2); } if (r1 >= 0 && r2 >= 0) { m.addCouple(r1, r2); } } else if (!v1.isSingleNode() && !v2.isSingleNode()) { // We have aligned x1 x2 ... xn with y1 y2 ... ym. // So we will now (re-)compute this sequence alignment. int[][] sequenceAlignment = sequenceAligner.alignSequenceNodes(v1, v2).getAlignment(); int l = sequenceAlignment[0].length; for (int i=0; i> child: tree.getChildren()) { convertSubTree(child); } } } } fr/orsay/lri/varna/models/treealign/TreeAlignLabelDistanceAsymmetric.java0000644000000000000000000000117311620715272025645 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; public interface TreeAlignLabelDistanceAsymmetric { /** * Returns the substitution cost between v1 and v2. * We use the convention that a null reference is a blank, * ie. f(x, null) is the cost of deleting x * and f(null, x) is the cost of inserting x. * We won't use f(null, null). * We suppose f is such that: * f(x,x) = 0 * 0 <= f(x,y) < +infinity * You may also want to have the triangle inequality, * although the alignment algorithm does not require it: * f(x,z) <= f(x,y) + f(y,z) */ public double f(ValueType1 x, ValueType2 y); } fr/orsay/lri/varna/models/treealign/TreeAlign.java0000644000000000000000000006074711620715272021210 0ustar rootrootpackage fr.orsay.lri.varna.models.treealign; import java.util.*; /** * Tree alignment algorithm. * This class implements the tree alignment algorithm * for ordered trees explained in article: * T. Jiang, L. Wang, K. Zhang, * Alignment of trees - an alternative to tree edit, * Theoret. Comput. Sci. 143 (1995). * Other references: * - Claire Herrbach, Alain Denise and Serge Dulucq. * Average complexity of the Jiang-Wang-Zhang pairwise tree alignment * algorithm and of a RNA secondary structure alignment algorithm. * Theoretical Computer Science 411 (2010) 2423-2432. * * Our implementation supposes that the trees will never have more * than 32000 nodes and that the total distance will never require more * significant digits that a float (single precision) has. * * @author Raphael Champeimont * @param The type of values on nodes in the first tree. * @param The type of values on nodes in the second tree. */ public class TreeAlign { private class TreeData { /** * The tree. */ public Tree tree; /** * The tree size (number of nodes). */ public int size = -1; /** * The number of children of a node is called the node degree. * This variable is the maximum node degree in the tree. */ public int degree = -1; /** * The number of children of a node is called the node degree. * degree[i] is the degree of node i, with i being an index in nodes. */ public int[] degrees; /** * The trees as an array of its nodes (subtrees rooted at each node * in fact), in postorder. */ public Tree[] nodes; /** * children[i] is the array of children (as indexes in nodes) * of i (an index in nodes) */ public int[][] children; /** * Values of nodes. */ public ValueType[] values; } /** * The distance function between labels. */ private TreeAlignLabelDistanceAsymmetric labelDist; /** * Create a TreeAlignSymmetric object, which can align trees. * The distance function will be called only once on every pair * of nodes. The result is then kept in a matrix, so you need not manage * yourself a cache of f(value1, value2). * Note that it is permitted to have null values on nodes, * so comparing a node with a non-null value with a node with a null * value will give the same cost as to insert the first node. * This can be useful if you tree has "fake" nodes. * @param labelDist The label distance. */ public TreeAlign(TreeAlignLabelDistanceAsymmetric labelDist) { this.labelDist = labelDist; } private class ConvertTreeToArray { private int nextNodeIndex = 0; private TreeData treeData; public ConvertTreeToArray(TreeData treeData) { this.treeData = treeData; } private void convertTreeToArrayAux( Tree subtree, int[] siblingIndexes, int siblingNumber) throws TreeAlignException { // We want it in postorder, so first we put the children List> children = subtree.getChildren(); int numberOfChildren = children.size(); int[] childrenIndexes = new int[numberOfChildren]; int myIndex = -1; { int i = 0; for (Tree child: children) { convertTreeToArrayAux(child, childrenIndexes, i); i++; } } // Compute the maximum degree if (numberOfChildren > treeData.degree) { treeData.degree = numberOfChildren; } // Now we add the node (root of the given subtree). myIndex = nextNodeIndex; nextNodeIndex++; treeData.nodes[myIndex] = subtree; // Record how many children I have treeData.degrees[myIndex] = numberOfChildren; // Store my value in an array ValueType v = subtree.getValue(); treeData.values[myIndex] = v; // Tell the caller my index siblingIndexes[siblingNumber] = myIndex; // Record my children indexes treeData.children[myIndex] = childrenIndexes; } /** * Reads: treeData.tree * Computes: treeData.nodes, treeData.degree, treeData.degrees * treeData.fathers, treeData.children, treeData.size, * treeData.values * Converts a tree to an array of nodes, in postorder. * We also compute the maximum node degree in the tree. * @throws TreeAlignException */ @SuppressWarnings("unchecked") public void convert() throws TreeAlignException { treeData.degree = 0; treeData.size = treeData.tree.countNodes(); // we didn't write new Tree[treeData.size] because // java does not support generics with arrays treeData.nodes = new Tree[treeData.size]; treeData.children = new int[treeData.size][]; treeData.degrees = new int[treeData.size]; treeData.values = (ValueType[]) new Object[treeData.size]; int rootIndex[] = new int[1]; convertTreeToArrayAux(treeData.tree, rootIndex, 0); } } /** * For arrays that take at least O(|T1|*|T2|) we take care * not to use too big data types. */ private class Aligner { /** * The first tree. */ private TreeData treeData1; /** * The second tree. */ private TreeData treeData2; /** * DF1[i][j_t] is DFL for (i,j,s,t) with s=0. * See description of DFL in Aligner.computeAlignmentP1(). * DF1 and DF2 are the "big" arrays, ie. those that may the space * complexity what it is. */ private float[][][][] DF1; /** * DF2[j][i_s] is DFL for (i,j,s,t) with t=0. * See description of DFL in Aligner.computeAlignmentP1(). */ private float[][][][] DF2; /** * This arrays have the same shape as respectively DF1. * They are used to remember which term in the minimum won, so that * we can compute the alignment. * Decision1 is a case number (< 10) * and Decision2 is a child index, hence the types. */ private byte[][][][] DF1Decisions1; private short[][][][] DF1Decisions2; /** * This arrays have the same shape as respectively DF2. * They are used to remember which term in the minimum won, so that * we can compute the alignment. */ private byte[][][][] DF2Decisions1; private short[][][][] DF2Decisions2; /** * Distances between subtrees. * DT[i][j] is the distance between the subtree rooted at i in the first tree * and the subtree rooted at j in the second tree. */ private float[][] DT; /** * This array has the same shape as DT, but is used to remember which * case gave the minimum, so that we can later compute the alignment. */ private byte[][] DTDecisions1; private short[][] DTDecisions2; /** * Distances between labels. * DL[i][j] is the distance labelDist.f(value(T1[i]), value(T2[i])). * By convention, we say that value(T1[|T1|]) = null * and value(T2[|T2|]) = null */ private float[][] DL; /** * DET1[i] is the distance between the empty tree and T1[i] * (the subtree rooted at node i in the first tree). */ private float[] DET1; /** * Same as DET1, but for second tree. */ private float[] DET2; /** * DEF1[i] is the distance between the empty forest and F1[i] * (the forest of children of node i in the first tree). */ private float[] DEF1; /** * Same as DEF1, but for second tree. */ private float[] DEF2; /** * @param i node in T1 * @param s number of first child of i to consider * @param m_i degree of i * @param j node in T2 * @param t number of first child of j to consider * @param n_j degree of j * @param DFx which array to fill (DF1 or DF2) */ private void computeAlignmentP1(int i, int s, int m_i, int j, int t, int n_j, int DFx) { /** * DFL[pr][qr] is D(F1[i_s, i_p], F2[j_t, j_q]) * where p=s+pr-1 and q=t+qr-1 (ie. pr=p-s+1 and qr=q-t+1) * By convention, F1[i_s, i_{s-1}] and F2[j_t, j_{t-1}] are the * empty forests. * Said differently, DFL[pr][qr] is the distance between the forest * of the pr first children of i, starting with child s * (first child is s = 0), and the forest of the qr first children * of j, starting with child t (first child is t = 0). * This array is allocated for a fixed value of (i,j,s,t). */ float[][] DFL; /** * Same shape as DFL, but to remember which term gave the min, * so that we can later compute the alignment. */ byte[][] DFLDecisions1; short[][] DFLDecisions2; DFL = new float[m_i-s+2][n_j-t+2]; DFL[0][0] = 0; // D(empty forest, empty forest) = 0 DFLDecisions1 = new byte[m_i-s+2][n_j-t+2]; DFLDecisions2 = new short[m_i-s+2][n_j-t+2]; // Compute indexes of i_s and j_t because we will need them int i_s = m_i != 0 ? treeData1.children[i][s] : -1; int j_t = n_j != 0 ? treeData2.children[j][t] : -1; for (int p=s; p(treeData1)).convert(); (new ConvertTreeToArray(treeData2)).convert(); // Allocate necessary arrays DT = new float[treeData1.size][treeData2.size]; DTDecisions1 = new byte[treeData1.size][treeData2.size]; DTDecisions2 = new short[treeData1.size][treeData2.size]; DL = new float[treeData1.size+1][treeData2.size+1]; DET1 = new float[treeData1.size]; DET2 = new float[treeData2.size]; DEF1 = new float[treeData1.size]; DEF2 = new float[treeData2.size]; DF1 = new float[treeData1.size][treeData2.size][][]; DF1Decisions1 = new byte[treeData1.size][treeData2.size][][]; DF1Decisions2 = new short[treeData1.size][treeData2.size][][]; DF2 = new float[treeData2.size][treeData1.size][][]; DF2Decisions1 = new byte[treeData2.size][treeData1.size][][]; DF2Decisions2 = new short[treeData2.size][treeData1.size][][]; DL[treeData1.size][treeData2.size] = (float) labelDist.f(null, null); for (int i=0; i T1, Tree T2) { treeData1 = new TreeData(); treeData1.tree = T1; treeData2 = new TreeData(); treeData2.tree = T2; } /** Align F1[i_s,i_p] with F2[j_t,j_q]. * If p = s-1, by convention it means F1[i_s,i_p] = empty forest. * Idem for q=t-1. */ private List>> computeForestAlignment(int i, int s, int p, int j, int t, int q) { if (p == s-1) { // left forest is the empty forest List>> result = new ArrayList>>(); for (int k=t; k<=q; k++) { result.add(treeInserted(treeData2.children[j][k])); } return result; } else { if (q == t-1) { // right forest is the empty forest List>> result = new ArrayList>>(); for (int k=s; k<=p; k++) { result.add(treeDeleted(treeData1.children[i][k])); } return result; } else { // both forests are non-empty int decision1, k; if (s == 0) { decision1 = DF1Decisions1 [i] [treeData2.children[j][t]] [p-s+1] [q-t+1]; k = DF1Decisions2 [i] [treeData2.children[j][t]] [p-s+1] [q-t+1]; } else if (t == 0) { decision1 = DF2Decisions1 [j] [treeData1.children[i][s]] [p-s+1] [q-t+1]; k = DF2Decisions2 [j] [treeData1.children[i][s]] [p-s+1] [q-t+1]; } else { throw (new Error("TreeAlignSymmetric bug: both s and t are non-zero")); } switch (decision1) { case 1: { List>> result; result = computeForestAlignment(i, s, p-1, j, t, q); result.add(treeDeleted(treeData1.children[i][p])); return result; } case 2: { List>> result; result = computeForestAlignment(i, s, p, j, t, q-1); result.add(treeInserted(treeData2.children[j][q])); return result; } case 3: { List>> result; result = computeForestAlignment(i, s, p-1, j, t, q-1); result.add(computeTreeAlignment(treeData1.children[i][p], treeData2.children[j][q])); return result; } case 4: { List>> result; result = computeForestAlignment(i, s, k-1, j, t, q-1); int j_q = treeData2.children[j][q]; Tree> insertedNode = new Tree>(); AlignedNode insertedNodeValue = new AlignedNode(); insertedNodeValue.setLeftNode(null); insertedNodeValue.setRightNode((Tree) treeData2.nodes[j_q]); insertedNode.setValue(insertedNodeValue); insertedNode.replaceChildrenListBy(computeForestAlignment(i, k, p, j_q, 0, treeData2.degrees[j_q]-1)); result.add(insertedNode); return result; } case 5: { List>> result; result = computeForestAlignment(i, s, p-1, j, t, k-1); int i_p = treeData1.children[i][p]; Tree> deletedNode = new Tree>(); AlignedNode deletedNodeValue = new AlignedNode(); deletedNodeValue.setLeftNode((Tree) treeData1.nodes[i_p]); deletedNodeValue.setRightNode(null); deletedNode.setValue(deletedNodeValue); deletedNode.replaceChildrenListBy(computeForestAlignment(i_p, 0, treeData1.degrees[i_p]-1, j, k, q)); result.add(deletedNode); return result; } default: throw (new Error("TreeAlign: decision1 = " + decision1)); } } } } /** * Align T1[i] with the empty tree. * @return the alignment */ private Tree> treeDeleted(int i) { Tree> root = new Tree>(); AlignedNode alignedNode = new AlignedNode(); alignedNode.setLeftNode(treeData1.nodes[i]); alignedNode.setRightNode(null); root.setValue(alignedNode); for (int r = 0; r> treeInserted(int j) { Tree> root = new Tree>(); AlignedNode alignedNode = new AlignedNode(); alignedNode.setLeftNode(null); alignedNode.setRightNode(treeData2.nodes[j]); root.setValue(alignedNode); for (int r = 0; r> computeTreeAlignment(int i, int j) { switch (DTDecisions1[i][j]) { case 1: { Tree> root = new Tree>(); // Compute the value of the node AlignedNode alignedNode = new AlignedNode(); alignedNode.setLeftNode(null); alignedNode.setRightNode(treeData2.nodes[j]); root.setValue(alignedNode); // Compute the children for (int r = 0; r> root = new Tree>(); // Compute the value of the node AlignedNode alignedNode = new AlignedNode(); alignedNode.setLeftNode(treeData1.nodes[i]); alignedNode.setRightNode(null); root.setValue(alignedNode); // Compute the children for (int r = 0; r> root = new Tree>(); // Compute the value of the node AlignedNode alignedNode = new AlignedNode(); alignedNode.setLeftNode(treeData1.nodes[i]); alignedNode.setRightNode(treeData2.nodes[j]); root.setValue(alignedNode); // Compute the children List>> children = computeForestAlignment(i, 0, treeData1.degrees[i]-1, j, 0, treeData2.degrees[j]-1); root.replaceChildrenListBy(children); return root; } default: throw (new Error("TreeAlign: DTDecisions1[i][j] = " + DTDecisions1[i][j])); } } public Tree> computeAlignment() { return computeTreeAlignment(treeData1.size-1, treeData2.size-1); } } /** * Align T1 with T2, computing both the distance and the alignment. * Time: O(|T1|*|T2|*(deg(T1)+deg(T2))^2) * Space: O(|T1|*|T2|*(deg(T1)+deg(T2))) * Average (over possible trees) time: O(|T1|*|T2|) * @param T1 The first tree. * @param T2 The second tree. * @return The distance and the alignment. * @throws TreeAlignException */ public TreeAlignResult align(Tree T1, Tree T2) throws TreeAlignException { TreeAlignResult result = new TreeAlignResult(); Aligner aligner = new Aligner(T1, T2); result.setDistance(aligner.align()); result.setAlignment(aligner.computeAlignment()); return result; } /** * Takes a alignment, and compute the distance between the two * original trees. If you have called align(), the result object already * contains the distance D and the alignment A. If you call * distanceFromAlignment on the alignment A it will compute the distance D. */ public float distanceFromAlignment(Tree> alignment) { Tree originalT1Node; Tree originalT2Node; originalT1Node = alignment.getValue().getLeftNode(); originalT2Node = alignment.getValue().getRightNode(); float d = (float) labelDist.f( originalT1Node != null ? originalT1Node.getValue() : null, originalT2Node != null ? originalT2Node.getValue() : null); for (Tree> child: alignment.getChildren()) { d += distanceFromAlignment(child); } return d; } } fr/orsay/lri/varna/models/FullBackup.java0000644000000000000000000000130212415525512017371 0ustar rootrootpackage fr.orsay.lri.varna.models; import java.io.Serializable; import fr.orsay.lri.varna.models.rna.RNA; public class FullBackup implements Serializable{ /** * */ private static final long serialVersionUID = -5468893731117925140L; public VARNAConfig config; public RNA rna; public String name; public FullBackup(VARNAConfig c, RNA r, String n){ config = c; rna = r; name = n; } public FullBackup(RNA r, String n){ config = null; rna = r; name = n; } public String toString() { return name; } public boolean hasConfig() { return config!=null; } } fr/orsay/lri/varna/models/export/0000755000000000000000000000000012275611434016026 5ustar rootrootfr/orsay/lri/varna/models/export/FillCircleCommand.java0000644000000000000000000000331011620715270022171 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.Color; import java.awt.geom.Point2D; public class FillCircleCommand extends GraphicElement { private Point2D.Double _base; private double _radius; private double _thickness; private Color _color; public FillCircleCommand(Point2D.Double base, double radius, double thickness, Color color) { _base = base; _radius = radius; _thickness = thickness; _color = color; } public Point2D.Double get_base() { return _base; } public double get_radius() { return _radius; } public double get_thickness() { return _thickness; } public Color get_color() { return _color; } } fr/orsay/lri/varna/models/export/SwingGraphics.java0000644000000000000000000000731112050227532021434 0ustar rootrootpackage fr.orsay.lri.varna.models.export; import java.awt.BasicStroke; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics2D; import java.awt.Shape; import java.awt.Stroke; import java.awt.geom.Arc2D.Double; import java.awt.geom.Ellipse2D; import java.awt.geom.GeneralPath; import java.awt.geom.Rectangle2D; public class SwingGraphics implements VueVARNAGraphics { private BasicStroke _dashedStroke; private BasicStroke _plainStroke; Graphics2D _g2d; private boolean _debug = false; public SwingGraphics(Graphics2D g2d) { _g2d = g2d; float[] dash = { 5.0f, 5.0f }; _dashedStroke = new BasicStroke(1.0f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 3.0f, dash, 0); _plainStroke = new BasicStroke(1.0f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 3.0f); } public Dimension getStringDimension(String s) { FontMetrics fm = _g2d.getFontMetrics(); Rectangle2D r = fm.getStringBounds(s, _g2d); return (new Dimension((int) r.getWidth(), (int) fm.getAscent() - fm.getDescent())); } public void drawStringCentered(String res, double x, double y) { Dimension d = getStringDimension(res); x -= (double) d.width / 2.0; y += (double) d.height / 2.0; if (_debug) { Stroke bck = _g2d.getStroke(); _g2d.setStroke(_plainStroke); _g2d.draw(new Rectangle2D.Double(x, y - d.height, d.width, d.height)); _g2d.setStroke(bck); } _g2d.drawString(res, (float) (x), (float) (y)); } public void draw(GeneralPath s) { _g2d.draw(s); } public void drawArc(double x, double y, double rx, double ry, double angleStart, double angleEnd) { _g2d.drawArc((int) (x-rx/2.), (int) (y-ry/2.), (int) rx, (int) ry, (int) angleStart, (int) angleEnd); } public void drawLine(double x1, double y1, double x2, double y2) { _g2d.drawLine((int)x1, (int)y1, (int)x2, (int)y2); } public void drawCircle(double x, double y, double r) { _g2d.draw(new Ellipse2D.Double(x, y, r, r)); } public void drawRect(double x, double y, double w, double h) { _g2d.drawRect((int)x, (int)y, (int)w, (int)h); } public void drawRoundRect(double x, double y, double w, double h, double rx, double ry) { _g2d.drawRoundRect((int)x, (int)y, (int)w, (int)h, (int)rx, (int)ry); } public void drawString(String s, double x, double y) { _g2d.drawString(s, (float)x, (float)y); } public void fill(GeneralPath s) { _g2d.fill(s); } public void fillCircle(double x, double y, double r) { _g2d.fill(new Ellipse2D.Double(x, y, r, r)); } public void fillRect(double x, double y, double w, double h) { _g2d.fill(new Rectangle2D.Double(x, y, w, h)); } public void fillRoundRect(double x, double y, double w, double h, double rx, double ry) { _g2d.fillRoundRect((int)x, (int)y, (int)w, (int)h, (int)rx, (int)ry); } public Color getColor() { return _g2d.getColor(); } public void setColor(Color c) { _g2d.setColor(c); } public void setSelectionStroke() { _g2d.setStroke(_dashedStroke); } public void setFont(Font f) { _g2d.setFont(f); } public void setPlainStroke() { _g2d.setStroke(_plainStroke); } private BasicStroke deriveStroke(BasicStroke s, double t) { return new BasicStroke((float)t, s.getEndCap(), s.getLineJoin(), s.getMiterLimit(), s.getDashArray(), s.getDashPhase()) ; } public void setStrokeThickness(double t) { boolean dashed = (_g2d.getStroke()==_dashedStroke); _plainStroke = deriveStroke(_plainStroke, t); //_dashedStroke = deriveStroke(_dashedStroke, t); if(dashed) { _g2d.setStroke(_dashedStroke); } else { _g2d.setStroke(_plainStroke); } } } fr/orsay/lri/varna/models/export/VueVARNAGraphics.java0000644000000000000000000000240711726103326021700 0ustar rootrootpackage fr.orsay.lri.varna.models.export; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.Shape; import java.awt.Stroke; import java.awt.geom.GeneralPath; public interface VueVARNAGraphics { public Dimension getStringDimension(String s); public void drawStringCentered(String res, double x, double y); public void setColor(Color c); public Color getColor(); public void drawLine(double x1, double y1, double x2, double y2); public void drawRect(double x, double y, double w, double h); public void fillRect(double x, double y, double w, double h); public void drawCircle(double x, double y, double r); public void fillCircle(double x, double y, double r); public void drawRoundRect(double x, double y, double w, double h, double rx, double ry); public void fillRoundRect(double x, double y, double w, double h, double rx, double ry); public void drawArc(double x, double y, double rx, double ry, double angleStart, double angleEnd); //public void drawString(String s, double x, double y); public void draw(GeneralPath s); public void fill(GeneralPath s); public void setFont(Font f); public void setSelectionStroke(); public void setPlainStroke(); public void setStrokeThickness(double t); } fr/orsay/lri/varna/models/export/PSExport.java0000644000000000000000000002122311620715270020411 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.Color; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.awt.geom.Point2D.Double; /** * @author ponty * */ public class PSExport extends SecStrDrawingProducer { public PSExport() { super(); super.setScale(0.4); } private String PSMacros() { String setFontSize = // Params [fontsize|...] "/setbasefont \n" + "{ /Helvetica-Bold findfont\n" + // => // [font|scale|...] " exch scalefont\n" + // => [scaled_font|...] " setfont \n" + // => [...] " } def\n\n"; String writeTextCentered = // Params [txt|size|...] "/txtcenter \n" + "{ dup \n" + // => [txt|txt|size|...] " stringwidth pop\n" + // => [wtxt|txt|size|...] " 2 div neg \n" + // => [-wtxt/2|txt|size|...] " 3 -1 roll \n" + // => [size|-wtxt/2|txt...] " 2 div neg\n" + // => [-size/2|-wtxt/2|txt|...] " rmoveto\n" + // => [txt|...] " show\n" + // => [...] " } def\n\n"; String drawEllipse = "/ellipse {\n" + " /endangle exch def\n" + " /startangle exch def\n" + " /yrad exch def\n" + " /xrad exch def\n" + " /y exch def\n" + " /x exch def\n" + " /savematrix matrix currentmatrix def\n" + " x y translate\n" + " xrad yrad scale\n" + " 0 0 1 startangle endangle arc\n" + " savematrix setmatrix\n" + " } def\n\n"; return setFontSize + writeTextCentered + drawEllipse; } private String EPSHeader(double minX, double maxX, double minY, double maxY) { String bbox = PSBBox(minX, minY, maxX, maxY); String init = "%!PS-Adobe-3.0\n" + "%%Pages: 1\n" + bbox + "%%EndComments\n" + "%%Page: 1 1\n"; String macros = PSMacros(); return init + macros; } private String EPSFooter() { return "showpage\n" + "%%EndPage: 1\n" + "%%EOF"; } private String PSNewPath() { return ("newpath\n"); } private String PSMoveTo(double x, double y) { return ("" + x + " " + y + " moveto\n"); } private String PSLineTo(double dx, double dy) { return ("" + dx + " " + dy + " lineto\n"); } private String PSRLineTo(double dx, double dy) { return ("" + dx + " " + dy + " rlineto\n"); } private String PSSetLineWidth(double thickness) { thickness /= 2; return ("" + thickness + " setlinewidth\n"); } private String PSStroke() { return ("stroke\n"); } private String PSArc(double x, double y, double radiusX, double radiusY, double angleFrom, double angleTo) { double centerX = x + radiusX / 2.0; double centerY = y; // return (centerX + " " + centerY + " "+ radiusX/2.0+" " + angleFrom + // " " + angleTo + " arc\n"); return (centerX + " " + centerY + " " + radiusX / 2.0 + " " + radiusY / 2.0 + " " + angleFrom + " " + angleTo + " ellipse\n"); } private String PSArc(double x, double y, double radius, double angleFrom, double angleTo) { return ("" + x + " " + y + " " + radius + " " + angleFrom + " " + angleTo + " arc\n"); } private String PSBBox(double minX, double maxX, double minY, double maxY) { String norm = ("%%BoundingBox: " + (long) Math.floor(minX) + " " + (long) Math.floor(minY) + " " + (long) Math.ceil(maxX) + " " + (long) Math.ceil(maxY) + "\n"); String high = ("%%HighResBoundingBox: " + (long) Math.floor(minX) + " " + (long) Math.floor(minY) + " " + (long) Math.ceil(maxX) + " " + (long) Math.ceil(maxY) + "\n"); return norm + high; } private String PSText(String txt) { return ("(" + txt + ") "); } @SuppressWarnings("unused") private String PSShow() { return ("show\n"); } private String PSClosePath() { return ("closepath\n"); } private String PSFill() { return ("fill\n"); } private String PSSetColor(Color col) { return ("" + (((double) col.getRed()) / 255.0) + " " + (((double) col.getGreen()) / 255.0) + " " + (((double) col.getBlue()) / 255.0) + " setrgbcolor\n"); } private String fontName(int font) { switch (font) { case (FONT_TIMES_ROMAN): return "/Times-Roman"; case (FONT_TIMES_BOLD): return "/Times-Bold"; case (FONT_TIMES_ITALIC): return "/Times-Italic"; case (FONT_TIMES_BOLD_ITALIC): return "/Times-BoldItalic"; case (FONT_HELVETICA): return "/Helvetica"; case (FONT_HELVETICA_BOLD): return "/Helvetica-Bold"; case (FONT_HELVETICA_OBLIQUE): return "/Helvetica-Oblique"; case (FONT_HELVETICA_BOLD_OBLIQUE): return "/Helvetica-BoldOblique"; case (FONT_COURIER): return "/Courier"; case (FONT_COURIER_BOLD): return "/Courier-Bold"; case (FONT_COURIER_OBLIQUE): return "/Courier-Oblique"; case (FONT_COURIER_BOLD_OBLIQUE): return "/Courier-BoldOblique"; } return "/Helvetica"; } private String PSSetFont(int font, double size) { return (fontName(font) + " findfont " + size + " scalefont setfont\n"); } public String setFontS(int font, double size) { _fontsize = (long) (0.4 * size); return PSSetFont(font, _fontsize); } public String setColorS(Color col) { super.setColorS(col); String result = PSSetColor(col); return result; } public String drawLineS(Point2D.Double p0, Point2D.Double p1, double thickness) { String tmp = ""; tmp += PSMoveTo(p0.x, p0.y); tmp += PSLineTo(p1.x, p1.y); tmp += PSSetLineWidth(thickness); tmp += PSStroke(); return tmp; } public String drawTextS(Point2D.Double p, String txt) { String tmp = ""; tmp += PSMoveTo(p.x, p.y); tmp += ("" + (_fontsize / 2.0 + 1) + " \n"); tmp += PSText(txt); tmp += (" txtcenter\n"); return tmp; } public String drawRectangleS(Point2D.Double orig, Point2D.Double dims, double thickness) { String tmp = PSNewPath(); tmp += PSMoveTo(orig.x, orig.y); tmp += PSRLineTo(0, dims.y); tmp += PSRLineTo(dims.x, 0); tmp += PSRLineTo(0, -dims.y); tmp += PSClosePath(); tmp += PSSetLineWidth(thickness); tmp += PSStroke(); return tmp; } public String drawCircleS(Point2D.Double p, double radius, double thickness) { String tmp = PSNewPath(); tmp += PSArc(p.x, p.y, radius, 0, 360); tmp += PSSetLineWidth(thickness); tmp += PSStroke(); return tmp; } public String fillCircleS(Point2D.Double p, double radius, double thickness, Color color) { String tmp = PSNewPath(); tmp += PSArc(p.x, p.y, radius, 0, 360); tmp += PSSetLineWidth(thickness); tmp += PSSetColor(color); tmp += PSFill(); return tmp; } public String footerS() { return EPSFooter(); } public String headerS(Rectangle2D.Double bb) { return EPSHeader(bb.x, bb.y, bb.x + bb.width, bb.y + bb.height); } @Override public String drawArcS(Point2D.Double origine, double width, double height, double startAngle, double endAngle) { return PSArc(origine.x, origine.y, width, height, startAngle, endAngle) + PSStroke(); } @Override public String drawPolygonS(Double[] points, double thickness) { String tmp = PSNewPath(); tmp += PSSetLineWidth(thickness); for (int i = 0; i < points.length; i++) { if (i == 0) { tmp += PSMoveTo(points[i].x, points[i].y); } else { tmp += PSLineTo(points[i].x, points[i].y); } } tmp += PSClosePath(); tmp += PSStroke(); return tmp; } @Override public String fillPolygonS(Double[] points, Color color) { Color bck = _curColor; String tmp = PSNewPath(); for (int i = 0; i < points.length; i++) { if (i == 0) { tmp += PSMoveTo(points[i].x, points[i].y); } else { tmp += PSLineTo(points[i].x, points[i].y); } } tmp += PSClosePath(); tmp += PSSetColor(color); tmp += PSFill(); tmp += PSSetColor(bck); return tmp; } }fr/orsay/lri/varna/models/export/CircleCommand.java0000644000000000000000000000306711620715270021373 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.geom.Point2D; public class CircleCommand extends GraphicElement { private Point2D.Double _base; private double _radius; private double _thickness; public CircleCommand(Point2D.Double base, double radius, double thickness) { _base = base; _radius = radius; _thickness = thickness; } public Point2D.Double get_base() { return _base; } public double get_radius() { return _radius; } public double get_thickness() { return _thickness; } } fr/orsay/lri/varna/models/export/PolygonCommand.java0000644000000000000000000000272511620715270021621 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.geom.Point2D; public class PolygonCommand extends GraphicElement { private Point2D.Double[] _points; private double _thickness; public PolygonCommand(Point2D.Double[] points, double thickness) { _points = points; _thickness = thickness; } public Point2D.Double[] get_points() { return _points; } public double get_thickness() { return _thickness; } } fr/orsay/lri/varna/models/export/LineCommand.java0000644000000000000000000000310111620715270021046 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.geom.Point2D; public class LineCommand extends GraphicElement { private Point2D.Double _orig; private Point2D.Double _dest; private double _thickness; public LineCommand(Point2D.Double orig, Point2D.Double dest, double thickness) { _orig = orig; _dest = dest; _thickness = thickness; } public Point2D.Double get_orig() { return _orig; } public Point2D.Double get_dest() { return _dest; } public double get_thickness() { return _thickness; } } fr/orsay/lri/varna/models/export/SVGExport.java0000644000000000000000000001300112000510504020503 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.Color; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.awt.geom.Point2D.Double; public class SVGExport extends SecStrDrawingProducer { private double _fontsize = 10.0; private Rectangle2D.Double _bb = new Rectangle2D.Double(0, 0, 10, 10); double _thickness = 2.0; public SVGExport() { super(); super.setScale(0.5); } private String getRGBString(Color col) { int rpc = (int) ((((double) col.getRed()) / 255.0) * 100); int gpc = (int) ((((double) col.getGreen()) / 255.0) * 100); int bpc = (int) ((((double) col.getBlue()) / 255.0) * 100); return "rgb(" + rpc + "%, " + gpc + "%, " + bpc + "%)"; } public String drawCircleS(Point2D.Double base, double radius, double thickness) { _thickness = thickness; return "\n"; } public String drawLineS(Point2D.Double orig, Point2D.Double dest, double thickness) { _thickness = thickness; return "\n"; } public String drawRectangleS(Point2D.Double orig, Point2D.Double dims, double thickness) { _thickness = thickness; return ""; } public String drawTextS(Point2D.Double base, String txt) { //System.out.println(txt); return "" + txt + "\n"; } public String fillCircleS(Point2D.Double base, double radius, double thickness, Color col) { _thickness = thickness; return "\n"; } public String footerS() { return "\n"; } public String headerS(Rectangle2D.Double bb) { _bb = bb; return "\n" + "\n" + "\n" + "\n"; } public String setFontS(int font, double size) { _fontsize = 0.5 * size; return ""; } public String drawArcS(Point2D.Double o, double width, double height, double startAngle, double endAngle) { // TODO: This hack assumes a (0,180) type of angle. Needs to be // corrected for further usage. double rx = width / 2.0; double ry = height / 2.0; double xs = o.x; double ys = (_bb.height - o.y); double xe = o.x + width; double ye = (_bb.height - o.y); String d = "\n"; return d; } public String drawPolygonS(Double[] points, double thickness) { String result = "\n"; return result; } @Override public String fillPolygonS(Double[] points, Color col) { String result = "\n"; return result; } } �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/export/ArcCommand.java����������������������������������������������������0000644�0000000�0000000�00000003442�11620715270�020674� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.geom.Point2D; public class ArcCommand extends GraphicElement { private Point2D.Double origine; private double width, height; private double startAngle, endAngle; public ArcCommand(Point2D.Double origine, double width, double height, double startAngle, double endAngle) { this.origine = origine; this.width = width; this.height = height; this.startAngle = startAngle; this.endAngle = endAngle; } public Point2D.Double getOrigine() { return origine; } public double getWidth() { return width; } public double getHeight() { return height; } public double getStartAngle() { return startAngle; } public double getEndAngle() { return endAngle; } } ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/export/XFIGExport.java����������������������������������������������������0000644�0000000�0000000�00000015332�11620715270�020630� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.Color; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.awt.geom.Point2D.Double; import java.util.Hashtable; public class XFIGExport extends SecStrDrawingProducer { private int _font = SecStrDrawingProducer.FONT_TIMES_ROMAN; @SuppressWarnings("unused") private StringBuffer buf = new StringBuffer(); private Hashtable _definedCols = new Hashtable(); // From XFig 3.2 file format, indexed RGB colors are in the range [32,543] private int _nextColCode = 32; private final static int UPPER_BOUND_COLOR_CODE = 543; public XFIGExport() { super(); super.setScale(20.0); } private String ensureColorDefinition(Color col) { if (!_definedCols.containsKey(col)) { if (_nextColCode < UPPER_BOUND_COLOR_CODE) { int curColorCode = _nextColCode; _definedCols.put(col, curColorCode); _nextColCode++; String RGBR = Integer.toHexString(col.getRed()); if (RGBR.length() < 2) { RGBR = "0" + RGBR; } String RGBG = Integer.toHexString(col.getGreen()); if (RGBG.length() < 2) { RGBG = "0" + RGBG; } String RGBB = Integer.toHexString(col.getBlue()); if (RGBB.length() < 2) { RGBB = "0" + RGBB; } String RGBHex = "#" + RGBR + RGBG + RGBB; RGBHex = RGBHex.toUpperCase(); return "0 " + curColorCode + " " + RGBHex + "\n"; } } return ""; } private int getColorCode(Color col) { if (_definedCols.containsKey(col)) { return _definedCols.get(col); } return 0; } private int getCurColorCode() { if (_definedCols.containsKey(_curColor)) { return _definedCols.get(_curColor); } return 0; } private String XFIGHeader() { return "#FIG 3.2\n" + "Landscape\n" + "Center\n" + "Inches\n" + "Letter \n" + "100.00\n" + "Single\n" + "-2\n" + "1200 2\n"; } public String drawCircleS(Point2D.Double p, double radius, double thickness) { return ("1 3 0 " + (long) thickness + " " + getCurColorCode() + " 7 50 -1 -1 0.000 1 0.0000 " + (long) p.x + " " + (long) -p.y + " " + (long) radius + " " + (long) radius + " 1 1 1 1\n"); } public String drawLineS(Point2D.Double p0, Point2D.Double p1, double thickness) { return ("2 1 0 " + (long) thickness + " " + getCurColorCode() + " 7 60 -1 -1 0.000 0 0 -1 0 0 2\n" + " " + (long) p0.x + " " + (long) -p0.y + " " + (long) p1.x + " " + (long) -p1.y + "\n"); } public String drawRectangleS(Point2D.Double p, Point2D.Double dims, double thickness) { return ("2 2 0 " + (long) thickness + " " + getCurColorCode() + " 7 50 -1 -1 0.000 0 0 -1 0 0 5\n" + "\t " + (long) (p.x) + " " + (long) (-p.y) + " " + (long) (p.x + dims.x) + " " + (long) (-p.y) + " " + (long) (p.x + dims.x) + " " + (long) -(p.y + dims.y) + " " + (long) (p.x) + " " + (long) -(p.y + dims.y) + " " + (long) (p.x) + " " + (long) -(p.y) + "\n"); } public String drawTextS(Point2D.Double p, String txt) { return ("4 1 " + getCurColorCode() + " 40 -1 " + _font + " " + (long) _fontsize + " 0.0000 6 " + (long) 4 * _fontsize + " " + (long) (2 * _fontsize) + " " + (long) (p.x) + " " + (long) -(p.y - 6 * _fontsize) + " " + txt + "\\001\n"); } public String fillCircleS(Point2D.Double p, double radius, double thickness, Color col) { String coldef = ensureColorDefinition(col); return (coldef + "1 3 0 " + (long) thickness + " 0 " + getColorCode(col) + " 50 0 20 0.000 1 0.0000 " + (long) p.x + " " + (long) -p.y + " " + (long) radius + " " + (long) radius + " 1 1 1 1\n"); } public String setFontS(int font, double size) { _font = font; _fontsize = 1.2 * size; return ""; } public String setColorS(Color col) { super.setColorS(col); return (ensureColorDefinition(col)); } public String footerS() { return ""; } public String headerS(Rectangle2D.Double bb) { return XFIGHeader(); } @Override public String drawArcS(Point2D.Double origine, double width, double height, double startAngle, double endAngle) { double p1x = origine.x; double p1y = -origine.y; double p2x = origine.x + width / 2.0; double p2y = -origine.y - height / 2.0; double p3x = origine.x + width; double p3y = p1y; double cx = (p1x + p3x) / 2.0; double cy = p3y + height / 2.0; return ("5 1 0 1 " + getCurColorCode() + " 7 50 0 -1 4.000 0 0 0 0 " + cx + " " + cy + " " + (int) p1x + " " + (int) p1y + " " + (int) p2x + " " + (int) p2y + " " + (int) p3x + " " + (int) p3y + "\n"); } @Override public String drawPolygonS(Double[] points, double thickness) { if (points.length > 0) { String result = "2 3 0 1 " + getCurColorCode() + " 7 40 0 -1 4.000 0 0 0 0 0 " + (points.length + 1) + "\n"; for (int i = 0; i < points.length; i++) { result += (int) Math.round(points[i].x) + " " + (int) Math.round(-points[i].y) + " "; } result += (int) Math.round(points[0].x) + " " + (int) Math.round(-points[0].y) + " "; result += "\n"; return result; } else { return ""; } } @Override public String fillPolygonS(Double[] points, Color col) { if (points.length > 0) { String coldef = ensureColorDefinition(col); String result = "2 3 0 1 0 " + getColorCode(col) + " 35 0 0 4.000 0 0 0 0 0 " + (points.length + 1) + "\n"; for (int i = 0; i < points.length; i++) { result += (int) Math.round(points[i].x) + " " + (int) Math.round(-points[i].y) + " "; } result += (int) Math.round(points[0].x) + " " + (int) Math.round(-points[0].y) + " "; result += "\n"; return coldef + result; } else { return ""; } } }������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/export/SecStrDrawingProducer.java�����������������������������������������0000644�0000000�0000000�00000030200�12000510504�023065� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.export; import java.awt.Color; import java.awt.geom.AffineTransform; import java.awt.geom.GeneralPath; import java.awt.geom.PathIterator; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.util.Vector; public abstract class SecStrDrawingProducer { public static final int FONT_TIMES_ROMAN = 0; public static final int FONT_TIMES_BOLD = 1; public static final int FONT_TIMES_ITALIC = 2; public static final int FONT_TIMES_BOLD_ITALIC = 3; public static final int FONT_HELVETICA = 16; public static final int FONT_HELVETICA_OBLIQUE = 17; public static final int FONT_HELVETICA_BOLD = 18; public static final int FONT_HELVETICA_BOLD_OBLIQUE = 19; public static final int FONT_COURIER = 12; public static final int FONT_COURIER_BOLD = 13; public static final int FONT_COURIER_OBLIQUE = 14; public static final int FONT_COURIER_BOLD_OBLIQUE = 15; private Vector _commands = new Vector(); private double _scale = 1.0; private double _xmin = Double.MAX_VALUE; private double _ymin = Double.MAX_VALUE; private double _xmax = -Double.MAX_VALUE; private double _ymax = -Double.MAX_VALUE; protected Color _curColor = Color.black; protected Color _backgroundColor = null; protected double _fontsize = 10.0; protected int _font = FONT_HELVETICA_BOLD; public Color getCurrentColor() { return _curColor; } public double getCurFontSize() { return _fontsize; } public int getCurrentFont() { return _font; } public abstract String drawLineS(Point2D.Double orig, Point2D.Double dest, double thickness); public abstract String drawArcS(Point2D.Double origine, double width, double height, double startAngle, double endAngle); public abstract String drawTextS(Point2D.Double base, String txt); public abstract String drawRectangleS(Point2D.Double orig, Point2D.Double dims, double thickness); public abstract String drawCircleS(Point2D.Double base, double radius, double thickness); public abstract String fillCircleS(Point2D.Double base, double radius, double thickness, Color color); public abstract String drawPolygonS(Point2D.Double[] points, double thickness); public abstract String fillPolygonS(Point2D.Double[] points, Color color); public abstract String setFontS(int font, double size); public String setColorS(Color col) { _curColor = col; return ""; } public abstract String headerS(Rectangle2D.Double bb); public abstract String footerS(); @SuppressWarnings("unused") private void resetBoundingBox() { _xmin = Double.MAX_VALUE; _ymin = Double.MAX_VALUE; _xmax = -Double.MAX_VALUE; _ymax = -Double.MAX_VALUE; } private void updateBoundingBox(double x, double y) { _xmin = Math.min(_xmin, x - 10); _ymin = Math.min(_ymin, y - 10); _xmax = Math.max(_xmax, x + 10); _ymax = Math.max(_ymax, y + 10); } public void drawLine(double x0, double y0, double x1, double y1, double thickness) { updateBoundingBox(x0, y0); updateBoundingBox(x1, y1); _commands.add(new LineCommand(new Point2D.Double(x0, y0), new Point2D.Double(x1, y1), thickness)); } public void drawArc(Point2D.Double origine, double width, double height, double startAngle, double endAngle) { updateBoundingBox(origine.x + width, origine.y + height/2); _commands.add(new ArcCommand(origine, width, height, startAngle, endAngle)); } public void drawText(double x, double y, String txt) { updateBoundingBox(x, y); _commands.add(new TextCommand(new Point2D.Double(x, y), new String(txt))); } public void drawRectangle(double x, double y, double w, double h, double thickness) { updateBoundingBox(x, y); updateBoundingBox(x + w, y + h); _commands.add(new RectangleCommand(new Point2D.Double(x, y), new Point2D.Double(w, h), thickness)); } public void fillRectangle(double x, double y, double w, double h, Color color) { double [] xtab = new double[4]; double [] ytab = new double[4]; xtab[0] = x; xtab[1] = x+w; xtab[2] = x+w; xtab[3] = x; ytab[0] = y; ytab[1] = y; ytab[2] = y+h; ytab[3] = y+h; fillPolygon(xtab, ytab, color); } public void drawCircle(double x, double y, double radius, double thickness) { updateBoundingBox(x - radius, y - radius); updateBoundingBox(x + radius, y + radius); _commands.add(new CircleCommand(new Point2D.Double(x, y), radius, thickness)); } public void setColor(Color col) { _curColor = col; _commands.add(new ColorCommand(col)); } public void setBackgroundColor(Color col){ _backgroundColor = col; } public void removeBackgroundColor(){ _backgroundColor = null; } public void fillCircle(double x, double y, double radius, double thickness, Color color) { updateBoundingBox(x - radius, y - radius); updateBoundingBox(x + radius, y + radius); _commands.add(new FillCircleCommand(new Point2D.Double(x, y), radius, thickness, color)); } public void drawPolygon(double[] xtab, double[] ytab, double thickness) { if (xtab.length == ytab.length) { Point2D.Double points[] = new Point2D.Double[xtab.length]; for (int i = 0; i < xtab.length; i++) { points[i] = new Point2D.Double(xtab[i], ytab[i]); updateBoundingBox(xtab[i], ytab[i]); } _commands.add(new PolygonCommand(points, thickness)); } } public void drawPolygon(GeneralPath p, double thickness) { PathIterator pi = p.getPathIterator(null); Vector v = new Vector(); double[] coords = new double[6]; while (!pi.isDone()) { int code = pi.currentSegment(coords); if (code == PathIterator.SEG_MOVETO) { v.add(new Point2D.Double(coords[0],coords[1])); } if (code == PathIterator.SEG_LINETO) { v.add(new Point2D.Double(coords[0],coords[1])); } pi.next(); } double[] xtab = new double[v.size()]; double[] ytab = new double[v.size()]; for(int i=0;i v = new Vector(); double[] coords = new double[6]; while (!pi.isDone()) { int code = pi.currentSegment(coords); if (code == PathIterator.SEG_MOVETO) { v.add(new Point2D.Double(coords[0],coords[1])); } if (code == PathIterator.SEG_LINETO) { v.add(new Point2D.Double(coords[0],coords[1])); } pi.next(); } double[] xtab = new double[v.size()]; double[] ytab = new double[v.size()]; for(int i=0;i seqnames = new ArrayList(); ArrayList sequences = new ArrayList(); BatchBenchmark.readFASTA(new File(rootdir, "alignment.fasta"), seqnames, sequences); BufferedWriter outbufASS = new BufferedWriter(new FileWriter(new File(rootdir, "all_secondary_structures.fasta"))); String consensusSecStr = sequences.get(0); int[] consensusSecStrInt = RNAFactory.parseSecStr(consensusSecStr); List templates = new ArrayList(); for (int i=1; i" + seqname + "\n"); outbuf.write(nt + "\n"); outbuf.write(ss + "\n"); outbuf.close(); outbufASS.write(">" + seqname + "\n"); outbufASS.write(ss + "\n"); templates.add(templateFile); } outbufASS.close(); } public static void main(String[] args) throws Exception { new BatchBenchmarkPrepare().benchmarkAllDir(new File(new File("templates"), "RNaseP_bact_a")); } } ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNATemplateMapping.java�����������������������������������������0000644�0000000�0000000�00000011043�11620715272�022773� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import java.util.ArrayList; import java.util.HashMap; import java.util.Map; import java.util.Set; import fr.orsay.lri.varna.applications.templateEditor.Couple; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix; /** * A RNATemplateMapping is a mapping between bases in an RNA sequence * and elements in a RNA template. * A base is mapped to only one template element * but a template element can be mapped to several bases. * This class is designed to be similar to the Mapping class. * * @author Raphael Champeimont */ public class RNATemplateMapping { private Map map = new HashMap(); private Map> invmap = new HashMap>(); /** * Alignment distance. */ private double distance; public double getDistance() { return distance; } public void setDistance(double distance) { this.distance = distance; } /** * Tell this mapping object that this base index and this element are * mapped with each other. This will throw RNATemplateMappingException * and do nothing if the base index is already in the mapping. */ public void addCouple(int baseIndex, RNATemplateElement templateElement) throws RNATemplateMappingException { if (map.containsKey(baseIndex)) { throw (new RNATemplateMappingException("Base index already in mapping: " + baseIndex)); } if (baseIndex < 0) { throw (new RNATemplateMappingException("Invalid base index: " + baseIndex)); } map.put(baseIndex, templateElement); if (!invmap.containsKey(templateElement)) { invmap.put(templateElement, new ArrayList()); } invmap.get(templateElement).add(baseIndex); } public String showCompact(RNA r) { HashMap > ranges = new HashMap >(); for(int i:map.keySet()) { RNATemplateElement t = map.get(i); String k = t.getName(); if (t instanceof RNATemplate.RNATemplateHelix) { k += " (" + ((RNATemplateHelix) t).getCaption() + ")"; ModeleBase mb = r.getBaseAt(i); if (mb.getElementStructure()>i) k = k+":5'"; else k = k+":3'"; } if (!ranges.containsKey(k)) { ranges.put(k, new Couple(Integer.MAX_VALUE,Integer.MIN_VALUE)); } Couple c = ranges.get(k); c.first = Math.min(c.first, i); c.second = Math.max(c.second, i); } String result = ""; for(String k:ranges.keySet()) { Couple c = ranges.get(k); RNATemplateElement t = map.get(c.first); String type = ((t instanceof RNATemplate.RNATemplateHelix)?"strand":"loop"); if (t instanceof RNATemplate.RNATemplateHelix) { if (k.endsWith("5'")) { Couple c3 = ranges.get(k.replace("5'", "3'")); result += "dummyID\t1\t"+k.replace(":5'", "")+"\t"+type+"\t"+c.first+"-"+c.second+":"+c3.first+"-"+c3.second+"\n"; } } else if (t instanceof RNATemplate.RNATemplateUnpairedSequence) { result += "dummyID\t1\t"+k+"\t"+type+"\t"+c.first+"-"+c.second+"\n"; } } result += "alignment distance = " + distance; return result; } /** * If the given base index is in the mapping, return the * corresponding template element, otherwise return null. */ public RNATemplateElement getPartner(int baseIndex) { if (map.containsKey(baseIndex)) { return map.get(baseIndex); } else { return null; } } /** * If the given template element is in the mapping, return an ArrayList * containing the corresponding base indexes, otherwise return null. * Note that you should not modify the returned ArrayList because * no copy is made, so if you modify it this mapping object will * contain inconsistent data. */ public ArrayList getAncestor(RNATemplateElement templateElement) { if (invmap.containsKey(templateElement)) { return invmap.get(templateElement); } else { return null; } } /** * Return a set containing all the base indexes in the mapping. * You should not modify the returned set. */ public Set getSourceElemsAsSet() { return map.keySet(); } /** * Return a set containing all the template elements in the mapping. * You should not modify the return set. */ public Set getTargetElemsAsSet() { return invmap.keySet(); } } ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNANodeValueTemplateSequence.java�������������������������������0000644�0000000�0000000�00000001207�11620715272�024754� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence; /** * See RNANodeValueTemplate. * * @author Raphael Champeimont */ public class RNANodeValueTemplateSequence extends RNANodeValueTemplate { /** * The sequence this node came from. */ private RNATemplateUnpairedSequence sequence; public String toGraphvizNodeName() { return "S(len=" + sequence.getLength() + ")"; } public RNATemplateUnpairedSequence getSequence() { return sequence; } public void setSequence(RNATemplateUnpairedSequence sequence) { this.sequence = sequence; } } �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/Benchmark.java��������������������������������������������������0000644�0000000�0000000�00000007531�12120444566�021245� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import java.awt.geom.Line2D; import java.util.Arrays; import fr.orsay.lri.varna.models.geom.LinesIntersect; import fr.orsay.lri.varna.models.rna.RNA; /** * @author Raphael Champeimont * */ public class Benchmark { private RNA rna; // number of backbone crossings public int backboneCrossings; // average distance between unpaired consecutive bases public double averageUnpairedDistance; // median distance between consecutive bases public double medianConsecutiveBaseDistance; // Number of consecutive bases that are too near from each other public int tooNearConsecutiveBases; // Number of consecutive bases that are too far from each other public int tooFarConsecutiveBases; // Parameters public double targetConsecutiveBaseDistance = RNA.LOOP_DISTANCE; // If consecutive bases are nearer that tooNearFactor * target distance, we call them too near. public double tooNearFactor = 0.5; // If consecutive bases are further that tooFarFactor * target distance, we call them too far. public double tooFarFactor = 2; public Benchmark(RNA rna) { this.rna = rna; computeAll(); } private void computeAll() { // Compute number of backbone crossings { int n = rna.getSize(); Line2D.Double[] lines = new Line2D.Double[n-1]; for (int i=0; i tooFarFactor*targetConsecutiveBaseDistance) { tooFarConsecutiveBases++; } } } } @SuppressWarnings("unused") private int percent(int a, int b) { return (int) Math.round((double) a / (double) b * 100.0); } public void printAll() { System.out.println("Benchmark:"); System.out.println("\tBackbone crossings = " + backboneCrossings); System.out.println("\tAverage unpaired distance = " + averageUnpairedDistance); System.out.println("\tMedian of consecutive base distance = " + medianConsecutiveBaseDistance); System.out.println("\tNumber of too near consecutive bases = " + tooNearConsecutiveBases); // + " ie. " + percent(tooNearConsecutiveBases, rna.getSize()-1) + " %"); System.out.println("\tNumber of too far consecutive bases = " + tooFarConsecutiveBases); // + " ie. " + percent(tooFarConsecutiveBases, rna.getSize()-1) + " %"); } } �����������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNANodeValueTemplateBrokenBasePair.java�������������������������0000644�0000000�0000000�00000001567�11620715272�026044� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix; /** * See RNANodeValueTemplate. * * @author Raphael Champeimont */ public class RNANodeValueTemplateBrokenBasePair extends RNANodeValueTemplate { /** * The original template element this node came from. */ private RNATemplateHelix helix; /** * The position (in the 5' to 3' order) * of this base in the original helix. */ private int positionInHelix; public String toGraphvizNodeName() { return "BH[" + positionInHelix + "]"; } public RNATemplateHelix getHelix() { return helix; } public void setHelix(RNATemplateHelix helix) { this.helix = helix; } public int getPositionInHelix() { return positionInHelix; } public void setPositionInHelix(int positionInHelix) { this.positionInHelix = positionInHelix; } } �����������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNATemplate.java������������������������������������������������0000644�0000000�0000000�00000157656�11620715272�021504� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import java.awt.Point; import java.awt.geom.Point2D; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.NoSuchElementException; import java.util.Set; import java.util.Stack; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.OutputKeys; import javax.xml.transform.Result; import javax.xml.transform.Source; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerConfigurationException; import javax.xml.transform.TransformerException; import javax.xml.transform.TransformerFactory; import javax.xml.transform.TransformerFactoryConfigurationError; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import org.xml.sax.SAXException; import fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate; import fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration; import fr.orsay.lri.varna.exceptions.ExceptionXmlLoading; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint; import fr.orsay.lri.varna.models.treealign.Tree; /** * A model for RNA templates. * A template is a way to display an RNA secondary structure. * * @author Raphael Champeimont */ public class RNATemplate { /** * The list of template elements. */ private Collection elements = new ArrayList(); /** * Tells whether the template contains elements. */ public boolean isEmpty() { return elements.isEmpty(); } /** * The first endpoint (in sequence order) of the template. * If there are multiple connected components, the first elements of one * connected component will be returned. * If the template contains no elements, null is returned. * If there is a cycle, an arbitrary endpoint will be returned * (as it then does not make sense to define the first endpoint). * Time: O(n) */ public RNATemplateElement getFirst() { return getFirstEndPoint().getElement(); } /** * The first endpoint edge endpoint (in sequence order) of the template. * If there are multiple connected components, the first elements of one * connected component will be returned. * If the template contains no elements, null is returned. * If there is a cycle, an arbitrary endpoint will be returned * (as it then does not make sense to define the first endpoint). * Time: O(n) */ public EdgeEndPoint getFirstEndPoint() { if (elements.isEmpty()) { return null; } else { Set knownEndPoints = new HashSet(); EdgeEndPoint currentEndPoint = getAnyEndPoint(); while (true) { if (knownEndPoints.contains(currentEndPoint)) { // There is a cycle in the template, so we stop there // to avoid looping infinitely. return currentEndPoint; } knownEndPoints.add(currentEndPoint); EdgeEndPoint previousEndPoint = currentEndPoint.getPreviousEndPoint(); if (previousEndPoint == null) { return currentEndPoint; } else { currentEndPoint = previousEndPoint; } } } } /** * Return an arbitrary element of the template, * null if empty. * Time: O(1) */ public RNATemplateElement getAny() { if (elements.isEmpty()) { return null; } else { return elements.iterator().next(); } } /** * Return an arbitrary endpoint of the template, * null if empty. * Time: O(1) */ public EdgeEndPoint getAnyEndPoint() { if (isEmpty()) { return null; } else { return getAny().getIn1EndPoint(); } } /** * Variable containing "this", used by the internal class * to access this object. */ private final RNATemplate template = this; /** * To get an iterator of this class, use rnaIterator(). * See rnaIterator() for documentation. */ private class RNAIterator implements Iterator { private Iterator iter = vertexIterator(); public boolean hasNext() { return iter.hasNext(); } public RNATemplateElement next() { if (! hasNext()) { throw (new NoSuchElementException()); } EdgeEndPoint currentEndPoint = iter.next(); switch (currentEndPoint.getPosition()) { // We skip "IN" endpoints, so that we don't return elements twice case IN1: case IN2: // We get the corresponding "OUT" endpoint currentEndPoint = iter.next(); break; } return currentEndPoint.getElement(); } public void remove() { throw (new UnsupportedOperationException()); } } /** * Iterates over the elements of the template, in the sequence order. * Helixes will be given twice. * Only one connected component will be iterated on. * Note that if there is a cycle, the iterator may return a infinite * number of elements. */ public Iterator rnaIterator() { return new RNAIterator(); } /** * Iterates over all elements (each endpoint is given only once) * in an arbitrary order. */ public Iterator classicIterator() { return elements.iterator(); } private class VertexIterator implements Iterator { private EdgeEndPoint endpoint = getFirstEndPoint(); public boolean hasNext() { return (endpoint != null); } public EdgeEndPoint next() { if (endpoint == null) { throw (new NoSuchElementException()); } EdgeEndPoint currentEndPoint = endpoint; endpoint = currentEndPoint.getNextEndPoint(); return currentEndPoint; } public void remove() { throw (new UnsupportedOperationException()); } } /** * Iterates over the elements edge endpoints of the template, * in the sequence order. * Only one connected component will be iterated on. * Note that if there is a cycle, the iterator may return a infinite * number of elements. */ public Iterator vertexIterator() { return new VertexIterator(); } private class MakeEdgeList { List list = new LinkedList(); private void addEdgeIfNecessary(EdgeEndPoint endPoint) { if (endPoint.isConnected()) { list.add(endPoint); } } public List make() { for (RNATemplateElement element: elements) { if (element instanceof RNATemplateHelix) { RNATemplateHelix helix = (RNATemplateHelix) element; addEdgeIfNecessary(helix.getIn1()); addEdgeIfNecessary(helix.getIn2()); } else if (element instanceof RNATemplateUnpairedSequence) { RNATemplateUnpairedSequence sequence = (RNATemplateUnpairedSequence) element; addEdgeIfNecessary(sequence.getIn()); } } return list; } } /** * Return over all edges in an arbitrary order. * For each edge, the first (5' side) endpoint will be given. */ public List makeEdgeList() { MakeEdgeList listMaker = new MakeEdgeList(); return listMaker.make(); } private class RemovePseudoKnots { /** * The elements of the template as an array, in the order of the * RNA sequence. Note that helixes will appear twice, * and non-paired sequences don't appear. */ private ArrayList helixesSeq; /** * For any i, * j = helixesStruct[i] is the index in helixesSeq * where the same helix also appears. * It means we have for all i: * helixesSeq[helixesStruct[i]] == helixesSeq[i] */ private ArrayList helixesStruct; /** * The same as helixesStruct, but without the pseudoknots, * ie. helixesStructWithoutPseudoKnots[i] may be -1 * even though helixesStruct[i] != -1 . */ private int[] helixesStructWithoutPseudoKnots; private void initArrays() throws ExceptionInvalidRNATemplate { helixesSeq = new ArrayList(); helixesStruct = new ArrayList(); Map knownHelixes = new Hashtable(); Iterator iter = rnaIterator(); while (iter.hasNext()) { RNATemplateElement element = iter.next(); if (element instanceof RNATemplateHelix) { helixesSeq.add((RNATemplateHelix) element); int index = helixesSeq.size() - 1; if (knownHelixes.containsKey(element)) { // This is the second time we meet this helix. int otherOccurenceIndex = knownHelixes.get(element); helixesStruct.add(otherOccurenceIndex); if (helixesStruct.get(otherOccurenceIndex) != -1) { throw (new ExceptionInvalidRNATemplate("We met an helix 3 times. Is there a cycle?")); } // Now we know the partner of the other part of // the helix. helixesStruct.set(otherOccurenceIndex, index); } else { // This is the first time we meet this helix. // Remember its index knownHelixes.put((RNATemplateHelix) element, index); // For the moment we don't know where the other part // of the helix is, but this will be found later. helixesStruct.add(-1); } } } } /** * Tells whether there is a pseudoknot. * Adapted from RNAMLParser.isSelfCrossing() */ private boolean isSelfCrossing() { Stack intervals = new Stack(); intervals.add(new Point(0, helixesStruct.size() - 1)); while (!intervals.empty()) { Point p = intervals.pop(); if (p.x <= p.y) { if (helixesStruct.get(p.x) == -1) { intervals.push(new Point(p.x + 1, p.y)); } else { int i = p.x; int j = p.y; int k = helixesStruct.get(i); if ((k <= i) || (k > j)) { return true; } else { intervals.push(new Point(i + 1, k - 1)); intervals.push(new Point(k + 1, j)); } } } } return false; } /** * We compute helixesStructWithoutPseudoKnots * from helixesStruct by replacing values by -1 * for the helixes we cut (the bases are become non-paired). * We try to cut as few base pairs as possible. */ private void removePseudoKnotsAux() { if (!isSelfCrossing()) { helixesStructWithoutPseudoKnots = new int[helixesStruct.size()]; for (int i=0; i tab[i][j]) { tab[i][j] = (short) tmp; backtrack[i][j] = (short) k; } } } } // debug //RNATemplateTests.printShortMatrix(tab); Stack intervals = new Stack(); intervals.add(new Point(0, length - 1)); while (!intervals.empty()) { Point p = intervals.pop(); if (p.x <= p.y) { if (backtrack[p.x][p.y] == -1) { result[p.x] = -1; intervals.push(new Point(p.x + 1, p.y)); } else { int i = p.x; int j = p.y; int k = backtrack[i][j]; result[i] = k; result[k] = i; intervals.push(new Point(i + 1, k - 1)); intervals.push(new Point(k + 1, j)); } } } helixesStructWithoutPseudoKnots = result; } } private Set makeSet() { Set removedHelixes = new HashSet(); for (int i=0; i removePseudoKnots() throws ExceptionInvalidRNATemplate { initArrays(); removePseudoKnotsAux(); // debug //printIntArrayList(helixesStruct); //printIntArray(helixesStructWithoutPseudoKnots); return makeSet(); } } private class ConvertToTree { private Set removedHelixes; public ConvertToTree(Set removedHelixes) { this.removedHelixes = removedHelixes; } private Iterator iter = template.rnaIterator(); private Set knownHelixes = new HashSet(); public Tree convert() throws ExceptionInvalidRNATemplate { Tree root = new Tree(); // No value, this is a fake node because we need a root. root.setValue(null); makeChildren(root); return root; } private void makeChildren(Tree father) throws ExceptionInvalidRNATemplate { List> children = father.getChildren(); while (true) { try { RNATemplateElement element = iter.next(); if (element instanceof RNATemplateHelix) { RNATemplateHelix helix = (RNATemplateHelix) element; if (removedHelixes.contains(helix)) { // Helix was removed boolean firstPartOfHelix; if (knownHelixes.contains(helix)) { firstPartOfHelix = false; } else { knownHelixes.add(helix); firstPartOfHelix = true; } int helixLength = helix.getLength(); // Maybe we could allow helixes of length 0? // If we want to then this code can be changed in the future. if (helixLength < 1) { throw (new ExceptionInvalidRNATemplate("Helix length < 1")); } int firstPosition = firstPartOfHelix ? 0 : helixLength; int afterLastPosition = firstPartOfHelix ? helixLength : 2*helixLength; for (int i=firstPosition; i child = new Tree(); child.setValue(value); father.getChildren().add(child); } } else { // We have an non-removed helix if (knownHelixes.contains(helix)) { if ((! (father.getValue() instanceof RNANodeValueTemplateBasePair)) || ((RNANodeValueTemplateBasePair) father.getValue()).getHelix() != helix) { // We have already met this helix, so unless it is our father, // we have a pseudoknot (didn't we remove them???). throw (new ExceptionInvalidRNATemplate("Unexpected helix. Looks like there still are pseudoknots even after we removed them so something is wrong about the template.")); } else { // As we have found the father, we have finished our work // with the children. return; } } else { knownHelixes.add(helix); int helixLength = helix.getLength(); // Maybe we could allow helixes of length 0? // If we want to then this code can be changed in the future. if (helixLength < 1) { throw (new ExceptionInvalidRNATemplate("Helix length < 1")); } Tree lastChild = father; for (int i=0; i child = new Tree(); child.setValue(value); lastChild.getChildren().add(child); lastChild = child; } // Now we put what follows as children of lastChild makeChildren(lastChild); } } } else if (element instanceof RNATemplateUnpairedSequence) { RNATemplateUnpairedSequence sequence = (RNATemplateUnpairedSequence) element; int seqLength = sequence.getLength(); // Maybe we could allow sequences of length 0? // If we want to then this code can be changed in the future. if (seqLength < 1) { throw (new ExceptionInvalidRNATemplate("Non-paired sequence length < 1")); } RNANodeValueTemplateSequence value = new RNANodeValueTemplateSequence(); value.setSequence(sequence); Tree child = new Tree(); child.setValue(value); children.add(child); } else { throw (new ExceptionInvalidRNATemplate("We have an endpoint which is neither an helix nor a sequence. What is that?")); } } catch (NoSuchElementException e) { // We are at the end of elements so if everything is ok // the father must be the root. if (father.getValue() == null) { return; // Work finished. } else { throw (new ExceptionInvalidRNATemplate("Unexpected end of template endpoint list.")); } } } } } /** * Tells whether the connected component to which endPoint belongs to * is cyclic. */ public boolean connectedComponentIsCyclic(EdgeEndPoint endPoint) { Set knownEndPoints = new HashSet(); EdgeEndPoint currentEndPoint = endPoint; while (true) { if (knownEndPoints.contains(currentEndPoint)) { return true; } knownEndPoints.add(currentEndPoint); EdgeEndPoint previousEndPoint = currentEndPoint.getPreviousEndPoint(); if (previousEndPoint == null) { return false; } else { currentEndPoint = previousEndPoint; } } } /** * Tells whether the template elements are all connected, ie. if the * graph (edge endpoints being vertices) is connected. */ public boolean isConnected() { if (isEmpty()) { return true; } // Count all vertices int n = 0; for (RNATemplateElement element: elements) { if (element instanceof RNATemplateHelix) { n += 4; } else if (element instanceof RNATemplateUnpairedSequence) { n += 2; } } // Now try reaching all vertices Set knownEndPoints = new HashSet(); EdgeEndPoint currentEndPoint = getFirstEndPoint(); while (true) { if (knownEndPoints.contains(currentEndPoint)) { // We are back to our original endpoint, so stop break; } knownEndPoints.add(currentEndPoint); EdgeEndPoint nextEndPoint = currentEndPoint.getNextEndPoint(); if (nextEndPoint == null) { break; } else { currentEndPoint = nextEndPoint; } } // The graph is connected iff the number of reached vertices // is equal to the total number of vertices. return (knownEndPoints.size() == n); } /** * Checks whether this template is a valid RNA template, ie. * it is non-empty, it does not contain a cycle and all elements are in one * connected component. */ public void checkIsValidTemplate() throws ExceptionInvalidRNATemplate { if (isEmpty()) { throw (new ExceptionInvalidRNATemplate("The template is empty.")); } if (! isConnected()) { throw (new ExceptionInvalidRNATemplate("The template is a non-connected graph.")); } // Now we know the graph is connected. if (connectedComponentIsCyclic(getAnyEndPoint())) { throw (new ExceptionInvalidRNATemplate("The template is cyclic.")); } } /** * Make a tree of the template. For this, we will remove pseudoknots, * taking care to remove as few base pair links as possible. * Requires the template to be valid and will check the validity * (will call checkIsValidTemplate()). * Calling this method will automatically call computeIn1Is(). */ public Tree toTree() throws ExceptionInvalidRNATemplate { // Compute the helix in1Is fields. // We also rely on computeIn1Is() for checking the template validity. computeIn1Is(); // Remove pseudoknots RemovePseudoKnots pseudoKnotKiller = new RemovePseudoKnots(); Set removedHelixes = pseudoKnotKiller.removePseudoKnots(); // Convert to tree ConvertToTree converter = new ConvertToTree(removedHelixes); return converter.convert(); } /** * Generate an RNA sequence that exactly matches the template. * Requires the template to be valid and will check the validity * (will call checkIsValidTemplate()). */ public RNA toRNA() throws ExceptionInvalidRNATemplate { // First, we check this is a valid template checkIsValidTemplate(); ArrayList str = new ArrayList(); Map> helixes = new HashMap>(); Iterator iter = rnaIterator(); while (iter.hasNext()) { RNATemplateElement element = iter.next(); if (element instanceof RNATemplateHelix) { RNATemplateHelix helix = (RNATemplateHelix) element; int n = helix.getLength(); if (helixes.containsKey(helix)) { int firstBase = str.size(); ArrayList helixMembers = helixes.get(helix); for (int i = 0; i < n; i++) { int indexOfAssociatedBase = helixMembers.get(n-1-i); str.set(indexOfAssociatedBase, firstBase + i); str.add(indexOfAssociatedBase); } } else { int firstBase = str.size(); ArrayList helixMembers = new ArrayList(); for (int i = 0; i < n; i++) { // We don't known yet where the associated base is str.add(-1); helixMembers.add(firstBase + i); } helixes.put(helix, helixMembers); } } else if (element instanceof RNATemplateUnpairedSequence) { RNATemplateUnpairedSequence sequence = (RNATemplateUnpairedSequence) element; int n = sequence.getLength(); for (int i=0; i elementNames = new HashMap(); private Element connectionsXmlElement; private Document document; private void addConnectionIfNecessary(EdgeEndPoint endPoint) { if (endPoint != null && endPoint.isConnected()) { RNATemplateElement e1 = endPoint.getElement(); EdgeEndPointPosition p1 = endPoint.getPosition(); RNATemplateElement e2 = endPoint.getOtherElement(); EdgeEndPointPosition p2 = endPoint.getOtherEndPoint().getPosition(); Element xmlElement = document.createElement("edge"); { Element fromXmlElement = document.createElement("from"); fromXmlElement.setAttribute("endpoint", elementNames.get(e1)); fromXmlElement.setAttribute("position", p1.toString()); xmlElement.appendChild(fromXmlElement); } { Element toXmlElement = document.createElement("to"); toXmlElement.setAttribute("endpoint", elementNames.get(e2)); toXmlElement.setAttribute("position", p2.toString()); xmlElement.appendChild(toXmlElement); } connectionsXmlElement.appendChild(xmlElement); } } public Document toXMLDocument() throws ExceptionXMLGeneration, ExceptionInvalidRNATemplate { try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = factory.newDocumentBuilder(); document = builder.newDocument(); Element root = document.createElement("RNATemplate"); document.appendChild(root); Element elementsXmlElement = document.createElement("elements"); root.appendChild(elementsXmlElement); connectionsXmlElement = document.createElement("edges"); root.appendChild(connectionsXmlElement); // First pass, we create a mapping between java references and names (strings) { int nextHelix = 1; int nextNonPairedSequence = 1; for (RNATemplateElement templateElement: elements) { if (templateElement instanceof RNATemplateHelix) { RNATemplateHelix helix = (RNATemplateHelix) templateElement; if (! elementNames.containsKey(helix)) { elementNames.put(helix, "H ID " + nextHelix); nextHelix++; } } else if (templateElement instanceof RNATemplateUnpairedSequence) { RNATemplateUnpairedSequence sequence = (RNATemplateUnpairedSequence) templateElement; if (! elementNames.containsKey(sequence)) { elementNames.put(sequence, "S ID " + nextNonPairedSequence); nextNonPairedSequence++; } } else { throw (new ExceptionInvalidRNATemplate("We have an endpoint which is neither an helix nor a sequence. What is that?")); } } } // Now we generate the XML document for (RNATemplateElement templateElement: elements) { String elementXmlName = elementNames.get(templateElement); Element xmlElement; if (templateElement instanceof RNATemplateHelix) { RNATemplateHelix helix = (RNATemplateHelix) templateElement; xmlElement = document.createElement("helix"); xmlElement.setAttribute("id", elementXmlName); xmlElement.setAttribute("length", Integer.toString(helix.getLength())); xmlElement.setAttribute("flipped", Boolean.toString(helix.isFlipped())); if (helix.hasCaption()) { xmlElement.setAttribute("caption", helix.getCaption()); } { Element startPositionXmlElement = document.createElement("startPosition"); startPositionXmlElement.setAttribute("x", Double.toString(helix.getStartPosition().x)); startPositionXmlElement.setAttribute("y", Double.toString(helix.getStartPosition().y)); xmlElement.appendChild(startPositionXmlElement); } { Element endPositionXmlElement = document.createElement("endPosition"); endPositionXmlElement.setAttribute("x", Double.toString(helix.getEndPosition().x)); endPositionXmlElement.setAttribute("y", Double.toString(helix.getEndPosition().y)); xmlElement.appendChild(endPositionXmlElement); } addConnectionIfNecessary(helix.getOut1()); addConnectionIfNecessary(helix.getOut2()); } else if (templateElement instanceof RNATemplateUnpairedSequence) { RNATemplateUnpairedSequence sequence = (RNATemplateUnpairedSequence) templateElement; xmlElement = document.createElement("sequence"); xmlElement.setAttribute("id", elementXmlName); xmlElement.setAttribute("length", Integer.toString(sequence.getLength())); { Element vertex5XmlElement = document.createElement("vertex5"); vertex5XmlElement.setAttribute("x", Double.toString(sequence.getVertex5().x)); vertex5XmlElement.setAttribute("y", Double.toString(sequence.getVertex5().y)); xmlElement.appendChild(vertex5XmlElement); } { Element vertex3XmlElement = document.createElement("vertex3"); vertex3XmlElement.setAttribute("x", Double.toString(sequence.getVertex3().x)); vertex3XmlElement.setAttribute("y", Double.toString(sequence.getVertex3().y)); xmlElement.appendChild(vertex3XmlElement); } { Element inTangentVectorXmlElement = document.createElement("inTangentVector"); inTangentVectorXmlElement.setAttribute("angle", Double.toString(sequence.getInTangentVectorAngle())); inTangentVectorXmlElement.setAttribute("length", Double.toString(sequence.getInTangentVectorLength())); xmlElement.appendChild(inTangentVectorXmlElement); } { Element outTangentVectorXmlElement = document.createElement("outTangentVector"); outTangentVectorXmlElement.setAttribute("angle", Double.toString(sequence.getOutTangentVectorAngle())); outTangentVectorXmlElement.setAttribute("length", Double.toString(sequence.getOutTangentVectorLength())); xmlElement.appendChild(outTangentVectorXmlElement); } addConnectionIfNecessary(sequence.getOut()); } else { throw (new ExceptionInvalidRNATemplate("We have an endpoint which is neither an helix nor a sequence. What is that?")); } elementsXmlElement.appendChild(xmlElement); } return document; } catch (ParserConfigurationException e) { throw (new ExceptionXMLGeneration("ParserConfigurationException: " + e.getMessage())); } } } public void toXMLFile(File file) throws ExceptionXMLGeneration, ExceptionInvalidRNATemplate { try { Document xmlDocument = toXMLDocument(); Source source = new DOMSource(xmlDocument); Result result = new StreamResult(file); Transformer transformer; transformer = TransformerFactory.newInstance().newTransformer(); transformer.setOutputProperty(OutputKeys.INDENT, "yes"); transformer.transform(source, result); } catch (TransformerConfigurationException e) { throw (new ExceptionXMLGeneration("TransformerConfigurationException: " + e.getMessage())); } catch (TransformerFactoryConfigurationError e) { throw (new ExceptionXMLGeneration("TransformerFactoryConfigurationError: " + e.getMessage())); } catch (TransformerException e) { throw (new ExceptionXMLGeneration("TransformerException: " + e.getMessage())); } } public Document toXMLDocument() throws ExceptionXMLGeneration, ExceptionInvalidRNATemplate { ConvertToXml converter = new ConvertToXml(); return converter.toXMLDocument(); } private class LoadFromXml { private Document xmlDocument; private Map elementNames = new HashMap(); public LoadFromXml(Document xmlDocument) { this.xmlDocument = xmlDocument; } private Point2D.Double pointFromXml(Element xmlPoint) { Point2D.Double point = new Point2D.Double(); point.x = Double.parseDouble(xmlPoint.getAttribute("x")); point.y = Double.parseDouble(xmlPoint.getAttribute("y")); return point; } private double vectorLengthFromXml(Element xmlVector) { return Double.parseDouble(xmlVector.getAttribute("length")); } private double vectorAngleFromXml(Element xmlVector) { return Double.parseDouble(xmlVector.getAttribute("angle")); } /** * Takes an element of the form: * * and returns the corresponding EdgeEndPoint object. */ private EdgeEndPoint endPointFromXml(Element xmlEdgeEndPoint) throws ExceptionXmlLoading { String elementId = xmlEdgeEndPoint.getAttribute("endpoint"); if (elementId == null || elementId == "") throw (new ExceptionXmlLoading ("Missing endpoint attribute on " + xmlEdgeEndPoint)); String positionOnElement = xmlEdgeEndPoint.getAttribute("position"); if (positionOnElement == null || positionOnElement == "") throw (new ExceptionXmlLoading ("Missing position attribute on " + xmlEdgeEndPoint)); if (elementNames.containsKey(elementId)) { RNATemplateElement templateElement = elementNames.get(elementId); EdgeEndPointPosition relativePosition = EdgeEndPointPosition.valueOf(positionOnElement); if (relativePosition == null) throw (new ExceptionXmlLoading ("Could not compute relativePosition")); return templateElement.getEndPointFromPosition(relativePosition); } else { throw (new ExceptionXmlLoading("Edge is connected on unkown element: " + elementId)); } } private String connectErrMsg(EdgeEndPoint v1, EdgeEndPoint v2, String reason) { return "Error while connecting\n" + v1.toString() + " to\n" + v2.toString() + " because:\n" + reason; } private void connect(EdgeEndPoint v1, EdgeEndPoint v2) throws ExceptionXmlLoading { if (v1 == null || v2 == null) { throw (new ExceptionXmlLoading("Invalid edge: missing endpoint\n v1 = " + v1 + "\n v2 = " + v2)); } if (v2.isConnected()) { throw (new ExceptionXmlLoading(connectErrMsg(v1, v2, "Second vertex is already connected to " + v2.getOtherElement().toString()))); } if (v1.isConnected()) { throw (new ExceptionXmlLoading(connectErrMsg(v1, v2, "First vertex is already connected to " + v1.getOtherElement().toString()))); } try { v1.connectTo(v2); } catch (ExceptionEdgeEndpointAlreadyConnected e) { throw (new ExceptionXmlLoading("A vertex is on two edges at the same time: " + e.getMessage())); } catch (ExceptionInvalidRNATemplate e) { throw (new ExceptionXmlLoading("ExceptionInvalidRNATemplate: " + e.getMessage())); } } public void load() throws ExceptionXmlLoading { // First part: we load all elements from the XML tree Element xmlElements = (Element) xmlDocument.getElementsByTagName("elements").item(0); { NodeList xmlElementsChildren = xmlElements.getChildNodes(); for (int i=0; i iter = vertexIterator(); Set knownHelices = new HashSet(); while (iter.hasNext()) { EdgeEndPoint endPoint = iter.next(); RNATemplateElement templateElement = endPoint.getElement(); if (templateElement instanceof RNATemplateHelix) { RNATemplateHelix helix = (RNATemplateHelix) templateElement; if (! knownHelices.contains(helix)) { // first time we meet this helix switch (endPoint.getPosition()) { case IN1: case OUT1: helix.setIn1Is(In1Is.IN1_IS_5PRIME); break; case IN2: case OUT2: helix.setIn1Is(In1Is.IN1_IS_3PRIME); break; } knownHelices.add(helix); } } } } /** * Remove the element from the template. * The element is automatically disconnected from any other element. * Returns true if and only if the element was present in the template, * otherwise nothing was done. */ public boolean removeElement(RNATemplateElement element) throws ExceptionInvalidRNATemplate { if (elements.contains(element)) { element.disconnectFromAny(); elements.remove(element); return true; } else { return false; } } /** * Position of an endpoint on an endpoint. * Not all values make sense for any endpoint. * For an helix, all four make sense, but for a non-paired * sequence, only IN1 and OUT1 make sense. */ public enum EdgeEndPointPosition { IN1, IN2, OUT1, OUT2; } private static int NEXT_ID = 1; /** * An endpoint of an RNA template, * it can be an helix or a sequence of non-paired bases. * * You cannot create an object of this class directly, * use RNATemplateHelix or RNATemplateUnpairedSequence instead. * * @author Raphael Champeimont */ public abstract class RNATemplateElement { public int _id = NEXT_ID++; public String getName() {return "RNATemplate"+_id; } /** * This variable is just there so that "this" can be accessed by a name * from the internal class EdgeEndPoint. */ private final RNATemplateElement element = this; /** * When the endpoint is created, it is added to the list of elements * in this template. To remove it, call RNATemplate.removeElement(). */ public RNATemplateElement() { elements.add(this); } /** * Disconnect this endpoint from any other elements it may be connected to. */ public abstract void disconnectFromAny(); /** * Get the the IN endpoint in the case of a sequence * and the IN1 endpoint in the case of an helix. */ public abstract EdgeEndPoint getIn1EndPoint(); /** * Returns the template to which this endpoint belongs. */ public RNATemplate getParentTemplate() { return template; } /** * Provided endpoint is an endpoint of this endpoint, get the next * endpoint, either on this same endpoint, or or the connected endpoint. * Note that you should use the getNextEndPoint() method of the endpoint * itself directly. */ protected abstract EdgeEndPoint getNextEndPoint(EdgeEndPoint endpoint); /** * Provided endpoint is an endpoint of this endpoint, get the previous * endpoint, either on this same endpoint, or or the connected endpoint. * Note that you should use the getPreviousEndPoint() method of the endpoint * itself directly. */ protected abstract EdgeEndPoint getPreviousEndPoint(EdgeEndPoint endpoint); /** * An edge endpoint is where an edge can connect. */ public class EdgeEndPoint { private EdgeEndPoint() { } /** * Get the next endpoint. If this endpoint is an "in" endpoint, * returns the corresponding "out" endpoint. If this endpoint * is an "out" endpoint, return the connected endpoint if there is * one, otherwise return null. */ public EdgeEndPoint getNextEndPoint() { return element.getNextEndPoint(this); } /** * Same as getNextEndPoint(), but with the previous endpoint. */ public EdgeEndPoint getPreviousEndPoint() { return element.getPreviousEndPoint(this); } /** * Get the position on the endpoint where this endpoint is. */ public EdgeEndPointPosition getPosition() { return element.getPositionFromEndPoint(this); } private EdgeEndPoint otherEndPoint; /** * Returns the endpoint on which this edge endpoint is. */ public RNATemplateElement getElement() { return element; } /** * Returns the other endpoint of the edge. * Will be null if there is no edge connecter to this endpoint. */ public EdgeEndPoint getOtherEndPoint() { return otherEndPoint; } /** * Returns the endpoint at the other endpoint of the edge. * Will be null if there is no edge connecter to this endpoint. */ public RNATemplateElement getOtherElement() { return (otherEndPoint != null) ? otherEndPoint.getElement() : null; } /** * Disconnect this endpoint from the other, ie. delete the edge * between them. Note that this will modify both endpoints, and that * x.disconnect() is equivalent to x.getOtherEndPoint().disconnect(). * If this endpoint is not connected, does nothing. */ public void disconnect() { if (otherEndPoint != null) { otherEndPoint.otherEndPoint = null; otherEndPoint = null; } } /** * Tells whether this endpoint is connected with an edge to * an other endpoint. */ public boolean isConnected() { return (otherEndPoint != null); } /** * Create an edge between two edge endpoints. * This is a symmetric operation and it will modify both endpoints. * It means x.connectTo(y) is equivalent to y.connectTo(x). * The edge endpoint must be free (ie. not yet connected). * Also, elements connected together must belong to the same template. */ public void connectTo(EdgeEndPoint otherEndPoint) throws ExceptionEdgeEndpointAlreadyConnected, ExceptionInvalidRNATemplate { if (this.otherEndPoint != null || otherEndPoint.otherEndPoint != null) { throw (new ExceptionEdgeEndpointAlreadyConnected()); } if (template != otherEndPoint.getElement().getParentTemplate()) { throw (new ExceptionInvalidRNATemplate("Elements from different templates cannot be connected with each other.")); } this.otherEndPoint = otherEndPoint; otherEndPoint.otherEndPoint = this; } public String toString() { return "Edge endpoint on element " + element.toString() + " at position " + getPosition().toString(); } } /** * Get the EdgeEndPoint object corresponding to the the given * position on this endpoint. */ public abstract EdgeEndPoint getEndPointFromPosition(EdgeEndPointPosition position); /** * The inverse of getEndPointFromPosition. */ public abstract EdgeEndPointPosition getPositionFromEndPoint(EdgeEndPoint endPoint); /** * Connect the endpoint at position positionHere of this endpoint * to the otherEndPoint. */ public void connectTo( EdgeEndPointPosition positionHere, EdgeEndPoint otherEndPoint) throws ExceptionEdgeEndpointAlreadyConnected, ExceptionInvalidRNATemplate { EdgeEndPoint endPointHere = getEndPointFromPosition(positionHere); endPointHere.connectTo(otherEndPoint); } /** * Connect the endpoint at position positionHere of this endpoint * to the endpoint of otherElement at position positionOnOtherElement. * @throws ExceptionInvalidRNATemplate * @throws ExceptionEdgeEndpointAlreadyConnected, ExceptionEdgeEndpointAlreadyConnected */ public void connectTo( EdgeEndPointPosition positionHere, RNATemplateElement otherElement, EdgeEndPointPosition positionOnOtherElement) throws ExceptionEdgeEndpointAlreadyConnected, ExceptionEdgeEndpointAlreadyConnected, ExceptionInvalidRNATemplate { EdgeEndPoint otherEndPoint = otherElement.getEndPointFromPosition(positionOnOtherElement); connectTo(positionHere, otherEndPoint); } } /** * An helix in an RNA template. * * @author Raphael Champeimont */ public class RNATemplateHelix extends RNATemplateElement { /** * Number of base pairs in the helix. */ private int length; /** * Position of the helix start point, * ie. the middle in the line [x,y] where (x,y) * x is the base at the IN1 edge endpoint and * y is the base at the OUT2 edge endpoint. */ private Point2D.Double startPosition; /** * Position of the helix end point, * ie. the middle in the line [x,y] where (x,y) * x is the base at the OUT1 edge endpoint and * y is the base at the IN2 edge endpoint. */ private Point2D.Double endPosition; /** * Tells whether the helix is flipped. */ private boolean flipped = false; public boolean isFlipped() { return flipped; } public void setFlipped(boolean flipped) { this.flipped = flipped; } /** * For an helix, tells us whether IN1/OUT1 is the 5' strand * (the first strand we meet if we follow the RNA sequence) * or the 3' strand (the second we meet if we follow the RNA sequence). * This information cannot be known locally, we need the complete * template to compute it, see RNATemplate.computeIn1Is(). */ private In1Is in1Is = null; public In1Is getIn1Is() { return in1Is; } public void setIn1Is(In1Is in1Is) { this.in1Is = in1Is; } /** * A string displayed on the helix. */ private String caption = null; public String getCaption() { return caption; } public void setCaption(String caption) { this.caption = caption; } public boolean hasCaption() { return caption != null; } /** * If we go through all bases of the RNA from first to last, * we will pass twice through this helix. On time, we arrive * from in1, and leave by out2, and the other time we arrive from * in2 and leave by out2. * Whether we go through in1/out1 or in2/out2 the first time * is written in the in1Is field. */ private final EdgeEndPoint in1, out1, in2, out2; private String _name; public RNATemplateHelix(String name) { in1 = new EdgeEndPoint(); out1 = new EdgeEndPoint(); in2 = new EdgeEndPoint(); out2 = new EdgeEndPoint(); _name = name; } public String toString() { return "Helix @" + Integer.toHexString(hashCode()) + " len=" + length + " caption=" + caption; } public String getName() {return ""+_name; } public int getLength() { return length; } public void setLength(int length) { this.length = length; } public Point2D.Double getStartPosition() { return startPosition; } public void setStartPosition(Point2D.Double startPosition) { this.startPosition = startPosition; } public Point2D.Double getEndPosition() { return endPosition; } public void setEndPosition(Point2D.Double endPosition) { this.endPosition = endPosition; } public EdgeEndPoint getIn1() { return in1; } public EdgeEndPoint getOut1() { return out1; } public EdgeEndPoint getIn2() { return in2; } public EdgeEndPoint getOut2() { return out2; } public void disconnectFromAny() { getIn1().disconnect(); getIn2().disconnect(); getOut1().disconnect(); getOut2().disconnect(); } protected EdgeEndPoint getNextEndPoint(EdgeEndPoint endpoint) { if (endpoint == in1) { return out1; } else if (endpoint == in2) { return out2; } else { return endpoint.getOtherEndPoint(); } } protected EdgeEndPoint getPreviousEndPoint(EdgeEndPoint endpoint) { if (endpoint == out1) { return in1; } else if (endpoint == out2) { return in2; } else { return endpoint.getOtherEndPoint(); } } public EdgeEndPoint getIn1EndPoint() { return in1; } public EdgeEndPoint getEndPointFromPosition( EdgeEndPointPosition position) { switch (position) { case IN1: return getIn1(); case IN2: return getIn2(); case OUT1: return getOut1(); case OUT2: return getOut2(); default: return null; } } public EdgeEndPointPosition getPositionFromEndPoint( EdgeEndPoint endPoint) { if (endPoint == in1) { return EdgeEndPointPosition.IN1; } else if (endPoint == in2) { return EdgeEndPointPosition.IN2; } else if (endPoint == out1) { return EdgeEndPointPosition.OUT1; } else if (endPoint == out2) { return EdgeEndPointPosition.OUT2; } else { return null; } } } /** * A sequence of non-paired bases in an RNA template. * * @author Raphael Champeimont */ public class RNATemplateUnpairedSequence extends RNATemplateElement { /** * Number of (non-paired) bases. */ private int length; private static final double defaultTangentVectorAngle = Math.PI / 2; private static final double defaultTangentVectorLength = 100; /** * The sequence is drawn along a cubic Bezier curve. * The curve can be defined by 2 vectors, one for the start of the line * and the other for the end. They are the tangents to the line at * the beginning and the end of the line. * Each vector can be defined by its length and its absolute angle. * The angles are given in radians. */ private double inTangentVectorAngle = defaultTangentVectorAngle, inTangentVectorLength = defaultTangentVectorLength, outTangentVectorAngle = defaultTangentVectorAngle, outTangentVectorLength = defaultTangentVectorLength; /** * Position of the begginning (at the "in" endpoint) of the line. * It is only useful when the sequence is not yet connected to an helix. * (Otherwise we can deduce it from this helix position). */ private Point2D.Double vertex5; /** * Position of the end (at the "out" endpoint) of the line. * It is only useful when the sequence is not yet connected to an helix. * (Otherwise we can deduce it from this helix position). */ private Point2D.Double vertex3; public Point2D.Double getVertex5() { return vertex5; } public void setVertex5(Point2D.Double vertex5) { this.vertex5 = vertex5; } public Point2D.Double getVertex3() { return vertex3; } public void setVertex3(Point2D.Double vertex3) { this.vertex3 = vertex3; } /** * The helixes connected on both sides. * They must be helixes because only helixes have absolute positions, * and the positions of the starting and ending points of the sequence * are those stored in the helixes. */ private final EdgeEndPoint in, out; private String _name; public RNATemplateUnpairedSequence(String name) { in = new EdgeEndPoint(); out = new EdgeEndPoint(); _name = name; } public String toString() { return "Sequence @" + Integer.toHexString(hashCode()) + " len=" + length; } public String getName() {return ""+_name; } public int getLength() { return length; } public void setLength(int length) { this.length = length; } public double getInTangentVectorAngle() { return inTangentVectorAngle; } public void setInTangentVectorAngle(double inTangentVectorAngle) { this.inTangentVectorAngle = inTangentVectorAngle; } public double getInTangentVectorLength() { return inTangentVectorLength; } public void setInTangentVectorLength(double inTangentVectorLength) { this.inTangentVectorLength = inTangentVectorLength; } public double getOutTangentVectorAngle() { return outTangentVectorAngle; } public void setOutTangentVectorAngle(double outTangentVectorAngle) { this.outTangentVectorAngle = outTangentVectorAngle; } public double getOutTangentVectorLength() { return outTangentVectorLength; } public void setOutTangentVectorLength(double outTangentVectorLength) { this.outTangentVectorLength = outTangentVectorLength; } public EdgeEndPoint getIn() { return in; } public EdgeEndPoint getOut() { return out; } public void disconnectFromAny() { getIn().disconnect(); getOut().disconnect(); } protected EdgeEndPoint getNextEndPoint(EdgeEndPoint endpoint) { if (endpoint == in) { return out; } else { return endpoint.getOtherEndPoint(); } } protected EdgeEndPoint getPreviousEndPoint(EdgeEndPoint endpoint) { if (endpoint == out) { return in; } else { return endpoint.getOtherEndPoint(); } } public EdgeEndPoint getIn1EndPoint() { return in; } public EdgeEndPoint getEndPointFromPosition( EdgeEndPointPosition position) { switch (position) { case IN1: return getIn(); case OUT1: return getOut(); default: return null; } } public EdgeEndPointPosition getPositionFromEndPoint( EdgeEndPoint endPoint) { if (endPoint == in) { return EdgeEndPointPosition.IN1; } else if (endPoint == out) { return EdgeEndPointPosition.OUT1; } else { return null; } } } } ����������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNATemplateDrawingAlgorithmException.java�����������������������0000644�0000000�0000000�00000000743�11620715272�026526� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm; /** * Exception thrown in case of failure of the template-based * RNA drawing algorithm. * * @author Raphael Champeimont */ public class RNATemplateDrawingAlgorithmException extends ExceptionDrawingAlgorithm { private static final long serialVersionUID = 1701307036024533400L; public RNATemplateDrawingAlgorithmException(String message) { super(message); } } �����������������������������fr/orsay/lri/varna/models/templates/RNATemplateMappingException.java��������������������������������0000644�0000000�0000000�00000000731�11620715272�024654� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; /** * This exception is thrown when we discover that a template is invalid * (it contains impossible connections between elements). * * @author Raphael Champeimont */ public class RNATemplateMappingException extends Exception { private static final long serialVersionUID = -201638492590138354L; public RNATemplateMappingException(String message) { super(message); } public RNATemplateMappingException() { } } ���������������������������������������fr/orsay/lri/varna/models/templates/RNANodeValue2TemplateDistance.java������������������������������0000644�0000000�0000000�00000006123�11620715272�025022� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import fr.orsay.lri.varna.models.treealign.RNANodeValue; import fr.orsay.lri.varna.models.treealign.RNANodeValue2; import fr.orsay.lri.varna.models.treealign.TreeAlignLabelDistanceAsymmetric; /** * Distance between an RNANodeValue2 and an RNANodeValueTemplate. * * @author Raphael Champeimont * */ public class RNANodeValue2TemplateDistance implements TreeAlignLabelDistanceAsymmetric { public double delete(RNANodeValue2 v) { if (v == null) { // deleting nothing costs nothing return 0; } else { if (v.isSingleNode()) { if (v.getNode().getRightBasePosition() < 0) { // delete one base (that comes from a broken base pair) return 1; } else { // delete a base pair return 2; } } else { // delete a sequence return v.getNodes().size(); } } } public double insert(RNANodeValueTemplate v) { if (v == null) { // inserting nothing costs nothing return 0; } else { if (v instanceof RNANodeValueTemplateSequence) { return ((RNANodeValueTemplateSequence) v).getSequence().getLength(); } else if (v instanceof RNANodeValueTemplateBrokenBasePair) { // insert one base return 1; } else { // this is a base pair // delete the base pair return 2; } } } public double f(RNANodeValue2 v1, RNANodeValueTemplate v2) { if (v1 == null) { return insert(v2); } else if (v2 == null) { return delete(v1); } else if (!v1.isSingleNode()) { // v1 is a sequence if (v2 instanceof RNANodeValueTemplateSequence) { // the cost is the difference between the sequence lengths return Math.abs(v1.getNodes().size() - ((RNANodeValueTemplateSequence) v2).getSequence().getLength()); } else { // a sequence cannot be changed in something else return Double.POSITIVE_INFINITY; } } else if (v1.getNode().getRightBasePosition() >= 0) { // v1 is a base pair if (v2 instanceof RNANodeValueTemplateBasePair) { // ok, a base pair can be mapped to a base pair return 0; } else { // a base pair cannot be changed in something else return Double.POSITIVE_INFINITY; } } else { // v1 is a broken base pair if (v2 instanceof RNANodeValueTemplateBrokenBasePair) { RNANodeValueTemplateBrokenBasePair brokenBasePair = ((RNANodeValueTemplateBrokenBasePair) v2); boolean strand5onTemplateSide = brokenBasePair.getPositionInHelix() < brokenBasePair.getHelix().getLength(); boolean strand3onTemplateSide = ! strand5onTemplateSide; boolean strand5onRNASide = (v1.getNode().getOrigin() == RNANodeValue.Origin.BASE_FROM_HELIX_STRAND5); boolean strand3onRNASide = (v1.getNode().getOrigin() == RNANodeValue.Origin.BASE_FROM_HELIX_STRAND3); if ((strand5onTemplateSide && strand5onRNASide) || (strand3onTemplateSide && strand3onRNASide)) { // Ok they can be mapped together return 0.0; } else { // A base on a 5' strand of an helix // cannot be mapped to base on a 3' strand of an helix return Double.POSITIVE_INFINITY; } } else { return Double.POSITIVE_INFINITY; } } } } ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/DrawRNATemplateCurveMethod.java���������������������������������0000644�0000000�0000000�00000001346�12243524622�024447� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/** * File written by Raphael Champeimont * UMR 7238 Genomique des Microorganismes */ package fr.orsay.lri.varna.models.templates; /** * @author Raphael Champeimont * How should we draw unpaired regions? */ public enum DrawRNATemplateCurveMethod { // use what is in the template EXACTLY_AS_IN_TEMPLATE("Bezier"), // use ellipses, ignoring Bezier parameters from template (useful mostly for debugging ellipses) ALWAYS_REPLACE_BY_ELLIPSES("Ellipses"), // replace by ellipse where it is a good idea SMART("Auto-Select"); String _msg; private DrawRNATemplateCurveMethod(String msg){ _msg=msg; } public String toString() { return _msg; } public static DrawRNATemplateCurveMethod getDefault() { return SMART; } } ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNANodeValueTemplate.java���������������������������������������0000644�0000000�0000000�00000001117�11620715272�023263� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import fr.orsay.lri.varna.models.treealign.GraphvizDrawableNodeValue; /** * An node from an RNA template is either a sequence of non-paired bases, * a base pair originally belonging to an helix, * or a single base originally belonging to an helix but which was broken * in order to remove pseudoknots. * * @author Raphael Champeimont */ public abstract class RNANodeValueTemplate implements GraphvizDrawableNodeValue { public String toString() { return toGraphvizNodeName(); } public abstract String toGraphvizNodeName(); } �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNANodeValueTemplateBasePair.java�������������������������������0000644�0000000�0000000�00000001566�11620715272�024702� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix; /** * See RNANodeValueTemplate. * * @author Raphael Champeimont */ public class RNANodeValueTemplateBasePair extends RNANodeValueTemplate { /** * The original template element this node came from. */ private RNATemplateHelix helix; /** * The position (in the 5' to 3' order) * of this base pair in the original helix. */ private int positionInHelix; public String toGraphvizNodeName() { return "H[" + positionInHelix + "]"; } public RNATemplateHelix getHelix() { return helix; } public void setHelix(RNATemplateHelix helix) { this.helix = helix; } public int getPositionInHelix() { return positionInHelix; } public void setPositionInHelix(int positionInHelix) { this.positionInHelix = positionInHelix; } } ������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/DrawRNATemplateMethod.java��������������������������������������0000644�0000000�0000000�00000002005�12243525124�023431� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/** * File written by Raphael Champeimont * UMR 7238 Genomique des Microorganismes */ package fr.orsay.lri.varna.models.templates; /** * What to do in case some helices are of a different length * in the template and the actual helix. * Possibles values are: * 0 - No adjustment is done. * A longer than expected helix might bump into an other helix. * 1 - Scaling factors (actual length / template length) are calculated, * the maximum scaling factor L is extracted, then all helix positions * are multiplied by L. * 2 - Same as 1, but L is computed as the minimum value such that there * are no backbone intersections. */ public enum DrawRNATemplateMethod { NOADJUST("No Adjust"), MAXSCALINGFACTOR("Max Scaling"), NOINTERSECT("Non-crossing"), HELIXTRANSLATE("Helix Translation"); String _msg; public static DrawRNATemplateMethod getDefault() { return HELIXTRANSLATE; } public String toString() { return _msg; } private DrawRNATemplateMethod(String msg) { _msg = msg; } }���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/BatchBenchmark.java���������������������������������������������0000644�0000000�0000000�00000017366�12120444566�022216� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/** * File written by Raphael Champeimont * UMR 7238 Genomique des Microorganismes */ package fr.orsay.lri.varna.models.templates; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.File; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.List; import fr.orsay.lri.varna.exceptions.ExceptionExportFailed; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.exceptions.ExceptionXmlLoading; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.RNA; public class BatchBenchmark { private VARNAConfig conf = new VARNAConfig(); public static RNA loadRNA(File file) throws ExceptionFileFormatOrSyntax, ExceptionUnmatchedClosingParentheses, FileNotFoundException, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed { Collection rnas = RNAFactory.loadSecStr(file.getPath()); if (rnas.isEmpty()) { throw new ExceptionFileFormatOrSyntax( "No RNA could be parsed from that source."); } return rnas.iterator().next(); } public void benchmarkRNA(File templatePath, File rnaPath, BufferedWriter outbuf) throws ExceptionXmlLoading, RNATemplateDrawingAlgorithmException, ExceptionFileFormatOrSyntax, ExceptionUnmatchedClosingParentheses, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionNAViewAlgorithm, IOException { // load template RNATemplate template = RNATemplate.fromXMLFile(templatePath); // load RNA RNA rna = loadRNA(rnaPath); for (int algo=0; algo<=100; algo++) { String algoname = ""; // draw RNA switch (algo) { //case 0: // rna.drawRNALine(conf); // algoname = "Linear"; // break; //case 1: // rna.drawRNACircle(conf); // algoname = "Circular"; // break; case 2: rna.drawRNARadiate(conf); algoname = "Radiate"; break; case 3: rna.drawRNANAView(conf); algoname = "NAView"; break; case 10: algoname = "Template/noadj"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOADJUST, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE); break; case 11: algoname = "Template/noadj/ellipses"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOADJUST, DrawRNATemplateCurveMethod.ALWAYS_REPLACE_BY_ELLIPSES); break; case 12: algoname = "Template/noadj/smart"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOADJUST, DrawRNATemplateCurveMethod.SMART); break; /* case 5: algoname = "Template/maxfactor"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.MAXSCALINGFACTOR, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE); break; */ case 6: algoname = "Template/mininter"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOINTERSECT, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE); break; case 30: algoname = "Template/translate"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.HELIXTRANSLATE, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE); break; case 31: algoname = "Template/translate/ellipses"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.HELIXTRANSLATE, DrawRNATemplateCurveMethod.ALWAYS_REPLACE_BY_ELLIPSES); break; case 32: algoname = "Template/translate/smart"; rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.HELIXTRANSLATE, DrawRNATemplateCurveMethod.SMART); break; default: continue; } // benchmark Benchmark benchmark = new Benchmark(rna); // print results outbuf.write( removeExt(rnaPath.getName()) + "\t" + algoname + "\t" + benchmark.backboneCrossings // averageUnpairedDistance % -> best is 100 + "\t" + (benchmark.averageUnpairedDistance / benchmark.targetConsecutiveBaseDistance *100) + "\t" + benchmark.tooNearConsecutiveBases + "\t" + benchmark.tooFarConsecutiveBases + "\n"); } } public void runBenchmark(List templates, List rnas, File outfile) throws Exception { if (templates.size() != rnas.size()) { throw new Error("templates and rnas list size differ"); } BufferedWriter outbuf = new BufferedWriter(new FileWriter(outfile)); outbuf.write("RNA\tAlgorithm\tBackbone crossings\tAverage unpaired distance %\tToo near\tToo far\n"); for (int i=0; i templates = new ArrayList(); List rnas = new ArrayList(); for (String seq: seqlist) { templates.add(new File(root, "RNase P E Coli.xml")); rnas.add(new File(root, seq)); } runBenchmark(templates, rnas, outfile); } public static void readFASTA(File file, List seqnames, List sequences) throws IOException { BufferedReader buf = new BufferedReader(new FileReader(file)); String line = buf.readLine(); while (line != null) { if (line.length() != 0) { if (line.charAt(0) == '>') { String id = line.substring(1); // remove the > seqnames.add(id); sequences.add(""); } else { sequences.set(sequences.size()-1, sequences.get(sequences.size()-1) + line); } } line = buf.readLine(); } buf.close(); } /** * We assume given directory contains a alignemnt.fasta file, * of which the first sequence is the consensus structure, * and the other sequences are aligned nucleotides. * The principle is to convert it to a set of secondary structure, * using the following rule: * - keep the same nucleotides as in original sequence * - keep base pairs where both bases of the pair are non-gaps in our sequence */ public void benchmarkAllDir(File rootdir) throws Exception { File seqdir = new File(rootdir, "sequences"); File templateFile = new File(rootdir, "template.xml"); File sequenceFiles[] = seqdir.listFiles(); Arrays.sort(sequenceFiles); List templates = new ArrayList(); List rnas = new ArrayList(); for (File seq: sequenceFiles) { if (!seq.getPath().endsWith(".dbn")) continue; rnas.add(seq); templates.add(templateFile); } File outfile = new File(rootdir, "benchmark.txt"); runBenchmark(templates, rnas, outfile); } public static void main(String[] args) throws Exception { File templatesDir = new File("templates"); if (args.length < 1) { System.out.println("Command-line argument required: RNA"); System.out.println("Example: RNaseP_bact_a"); System.exit(1); } //new BatchBenchmark().runExamples(); for (String arg: args) { new BatchBenchmark().benchmarkAllDir(new File(templatesDir, arg)); } } /** * Return the given file path without the (last) extension. */ public static String removeExt(String path) { return path.substring(0, path.lastIndexOf('.')); } public static File removeExt(File path) { return new File(removeExt(path.getPath())); } } ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/templates/RNATemplateAlign.java�������������������������������������������0000644�0000000�0000000�00000037643�12120444566�022451� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.templates; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.LinkedList; import java.util.List; import java.util.Map; import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence; import fr.orsay.lri.varna.models.treealign.AlignedNode; import fr.orsay.lri.varna.models.treealign.RNANodeValue; import fr.orsay.lri.varna.models.treealign.RNANodeValue2; import fr.orsay.lri.varna.models.treealign.RNATree2; import fr.orsay.lri.varna.models.treealign.RNATree2Exception; import fr.orsay.lri.varna.models.treealign.Tree; import fr.orsay.lri.varna.models.treealign.TreeAlign; import fr.orsay.lri.varna.models.treealign.TreeAlignException; import fr.orsay.lri.varna.models.treealign.TreeAlignResult; /** * This class is about the alignment between a tree of RNANodeValue2 * and a tree of RNANodeValueTemplate. * * @author Raphael Champeimont */ public class RNATemplateAlign { // We check this node can be part of a non-broken helix. private static boolean canBePartOfAnHelix(RNANodeValue2 leftNodeValue) { return (leftNodeValue != null) && leftNodeValue.isSingleNode() && leftNodeValue.getNode().getRightBasePosition() > 0; } private static boolean canBePartOfASequence(RNANodeValue2 leftNodeValue) { return (leftNodeValue != null) && !leftNodeValue.isSingleNode(); } private static boolean canBePartOfABrokenHelix(RNANodeValue2 leftNodeValue) { return (leftNodeValue != null) && leftNodeValue.isSingleNode() && leftNodeValue.getNode().getRightBasePosition() < 0; } /** * This method takes an alignment between a tree of RNANodeValue2 * of RNANodeValue and a tree of RNANodeValue2 of RNANodeValueTemplate, * and the original RNA object that was used to create the first tree * in the alignment. * It returns the corresponding RNATemplateMapping. */ public static RNATemplateMapping makeTemplateMapping(TreeAlignResult alignResult, RNA rna) throws RNATemplateMappingException { RNATemplateMapping mapping = new RNATemplateMapping(); Tree> alignment = alignResult.getAlignment(); mapping.setDistance(alignResult.getDistance()); // Map sequences and helices together, without managing pseudoknots { // We will go through the tree using a DFS // The reason why this algorithm is not trivial is that we may have // a longer helix on the RNA side than on the template side, in which // case some nodes on the RNA side are going to be alone while we // would want them to be part of the helix. RNATemplateHelix currentHelix = null; LinkedList>> remainingNodes = new LinkedList>>(); List nodesInSameHelix = new LinkedList(); remainingNodes.add(alignment); while (!remainingNodes.isEmpty()) { Tree> node = remainingNodes.getLast(); remainingNodes.removeLast(); Tree leftNode = node.getValue().getLeftNode(); Tree rightNode = node.getValue().getRightNode(); // Do we have something on RNA side? if (leftNode != null && leftNode.getValue() != null) { RNANodeValue2 leftNodeValue = leftNode.getValue(); // Do we have something on template side? if (rightNode != null && rightNode.getValue() != null) { RNANodeValueTemplate rightNodeValue = rightNode.getValue(); if (rightNodeValue instanceof RNANodeValueTemplateBasePair && canBePartOfAnHelix(leftNodeValue)) { RNATemplateHelix helix = ((RNANodeValueTemplateBasePair) rightNodeValue).getHelix(); currentHelix = helix; int i = leftNodeValue.getNode().getLeftBasePosition(); int j = leftNodeValue.getNode().getRightBasePosition(); mapping.addCouple(i, helix); mapping.addCouple(j, helix); // Maybe we have marked nodes as part of the same helix // when we didn't know yet which helix it was. if (nodesInSameHelix.size() > 0) { for (RNANodeValue2 v: nodesInSameHelix) { int k = v.getNode().getLeftBasePosition(); int l = v.getNode().getRightBasePosition(); // We want to check nodesInSameHelix is a parent helix and not a sibling. boolean validExtension = (k < i) && (j < l); if (validExtension) { mapping.addCouple(v.getNode().getLeftBasePosition(), helix); mapping.addCouple(v.getNode().getRightBasePosition(), helix); } } } nodesInSameHelix.clear(); } else if (rightNodeValue instanceof RNANodeValueTemplateSequence && canBePartOfASequence(leftNodeValue)) { currentHelix = null; nodesInSameHelix.clear(); RNATemplateUnpairedSequence sequence = ((RNANodeValueTemplateSequence) rightNodeValue).getSequence(); for (RNANodeValue nodeValue: leftNode.getValue().getNodes()) { mapping.addCouple(nodeValue.getLeftBasePosition(), sequence); } } else { // Pseudoknot in template currentHelix = null; nodesInSameHelix.clear(); } } else { // We have nothing on template side if (canBePartOfAnHelix(leftNodeValue)) { if (currentHelix != null) { // We may be in this case when the RNA // contains a longer helix than in the template int i = leftNodeValue.getNode().getLeftBasePosition(); int j = leftNodeValue.getNode().getRightBasePosition(); int k = Integer.MAX_VALUE; int l = Integer.MIN_VALUE; for (int b: mapping.getAncestor(currentHelix)) { k = Math.min(k, b); l = Math.max(l, b); } // We want to check currentHelix is a parent helix and not a sibling. boolean validExtension = (k < i) && (j < l); if (validExtension) { mapping.addCouple(i, currentHelix); mapping.addCouple(j, currentHelix); } } else { // Maybe this left node is part of an helix // which is smaller in the template nodesInSameHelix.add(leftNodeValue); } } } } // If this node has children, add them in the stack List>> children = node.getChildren(); int n = children.size(); if (n > 0) { int helixChildren = 0; // For each subtree, we want the sequences (in RNA side) to be treated first // and then the helix nodes, because finding an aligned sequence tells // us we cannot grow a current helix ArrayList>> addToStack1 = new ArrayList>>(); ArrayList>> addToStack2 = new ArrayList>>(); for (int i=0; i> child = children.get(i); Tree RNAchild = child.getValue().getLeftNode(); if (RNAchild != null && RNAchild.getValue() != null && (canBePartOfAnHelix(RNAchild.getValue()) || canBePartOfABrokenHelix(RNAchild.getValue()) )) { helixChildren++; addToStack2.add(child); } else { addToStack1.add(child); } } // We add the children in their reverse order so they // are given in the original order by the iterator for (int i=addToStack2.size()-1; i>=0; i--) { remainingNodes.add(addToStack2.get(i)); } for (int i=addToStack1.size()-1; i>=0; i--) { remainingNodes.add(addToStack1.get(i)); } if (helixChildren >= 2) { // We cannot "grow" the current helix, because we have a multiloop // in the RNA. currentHelix = null; //nodesInSameHelix.clear(); } } } } // Now recover pseudoknots (broken helices) { // First create a temporary mapping with broken helices LinkedList>> remainingNodes = new LinkedList>>(); remainingNodes.add(alignment); RNATemplateMapping tempPKMapping = new RNATemplateMapping(); while (!remainingNodes.isEmpty()) { Tree> node = remainingNodes.getLast(); remainingNodes.removeLast(); List>> children = node.getChildren(); int n = children.size(); if (n > 0) { for (int i=n-1; i>=0; i--) { // We add the children in their reverse order so they // are given in the original order by the iterator remainingNodes.add(children.get(i)); } List nodesInSameHelix = new LinkedList(); RNATemplateHelix currentHelix = null; for (Tree> child: node.getChildren()) { Tree leftNode = child.getValue().getLeftNode(); Tree rightNode = child.getValue().getRightNode(); if (leftNode != null && leftNode.getValue() != null) { RNANodeValue2 leftNodeValue = leftNode.getValue(); // We have a real left (RNA side) node if (rightNode != null && rightNode.getValue() != null) { // We have a real right (template side) node RNANodeValueTemplate rightNodeValue = rightNode.getValue(); if (rightNodeValue instanceof RNANodeValueTemplateBrokenBasePair && canBePartOfABrokenHelix(leftNodeValue)) { RNATemplateHelix helix = ((RNANodeValueTemplateBrokenBasePair) rightNodeValue).getHelix(); currentHelix = helix; tempPKMapping.addCouple(leftNodeValue.getNode().getLeftBasePosition(), helix); // Maybe we have marked nodes as part of the same helix // when we didn't know yet which helix it was. for (RNANodeValue2 v: nodesInSameHelix) { tempPKMapping.addCouple(v.getNode().getLeftBasePosition(), helix); } nodesInSameHelix.clear(); } else { currentHelix = null; nodesInSameHelix.clear(); } } else { // We have no right (template side) node if (canBePartOfABrokenHelix(leftNodeValue)) { if (currentHelix != null) { // We may be in this case if the RNA sequence // contains a longer helix than in the template tempPKMapping.addCouple(leftNodeValue.getNode().getLeftBasePosition(), currentHelix); } else { // Maybe this left node is part of an helix // which is smaller in the template nodesInSameHelix.add(leftNodeValue); } } else { currentHelix = null; nodesInSameHelix.clear(); } } } else { currentHelix = null; nodesInSameHelix.clear(); } } } } // As parts of broken helices were aligned independently, // we need to check for consistency, ie. keep only bases for // which the associated base is also aligned with the same helix. for (RNATemplateElement element: tempPKMapping.getTargetElemsAsSet()) { RNATemplateHelix helix = (RNATemplateHelix) element; HashSet basesInHelix = new HashSet(tempPKMapping.getAncestor(helix)); for (int baseIndex: basesInHelix) { System.out.println("PK: " + helix + " aligned with " + baseIndex); boolean baseOK = false; // Search for an associated base aligned with the same helix ArrayList auxBasePairs = rna.getAuxBPs(baseIndex); for (ModeleBP auxBasePair: auxBasePairs) { int partner5 = ((ModeleBaseNucleotide) auxBasePair.getPartner5()).getIndex(); int partner3 = ((ModeleBaseNucleotide) auxBasePair.getPartner3()).getIndex(); if (baseIndex == partner5) { if (basesInHelix.contains(partner3)) { baseOK = true; break; } } else if (baseIndex == partner3) { if (basesInHelix.contains(partner5)) { baseOK = true; break; } } } if (baseOK) { // Add it to the real mapping mapping.addCouple(baseIndex, helix); } } } } return mapping; } public static void printMapping(RNATemplateMapping mapping, RNATemplate template, String sequence) { Iterator iter = template.rnaIterator(); while (iter.hasNext()) { RNATemplateElement element = iter.next(); System.out.println(element.toString()); ArrayList A = mapping.getAncestor(element); if (A != null) { RNATemplateAlign.printIntArrayList(A); for (int n=A.size(), i=0; i alignRNAWithTemplate(RNA rna, RNATemplate template) throws RNATemplateDrawingAlgorithmException { try { Tree rnaAsTree = RNATree2.RNATree2FromRNA(rna); Tree templateAsTree = template.toTree(); TreeAlign treeAlign = new TreeAlign(new RNANodeValue2TemplateDistance()); TreeAlignResult result = treeAlign.align(rnaAsTree, templateAsTree); return result; } catch (RNATree2Exception e) { throw (new RNATemplateDrawingAlgorithmException("RNATree2Exception: " + e.getMessage())); } catch (ExceptionInvalidRNATemplate e) { throw (new RNATemplateDrawingAlgorithmException("ExceptionInvalidRNATemplate: " + e.getMessage())); } catch (TreeAlignException e) { throw (new RNATemplateDrawingAlgorithmException("TreeAlignException: " + e.getMessage())); } } /** * Map an RNA with an RNATemplate using tree alignment. */ public static RNATemplateMapping mapRNAWithTemplate(RNA rna, RNATemplate template) throws RNATemplateDrawingAlgorithmException { try { TreeAlignResult alignResult = RNATemplateAlign.alignRNAWithTemplate(rna, template); RNATemplateMapping mapping = RNATemplateAlign.makeTemplateMapping(alignResult, rna); return mapping; } catch (RNATemplateMappingException e) { e.printStackTrace(); throw (new RNATemplateDrawingAlgorithmException("RNATemplateMappingException: " + e.getMessage())); } } /** * Print an integer array. */ public static void printIntArray(int[] A) { for (int i=0; i A) { for (int i=0; i l) { if (l != null) { int n = l.size(); int[] result = new int[n]; for (int i=0; i 0) { return Math.acos(x / l); } else if (y < 0) { return - Math.acos(x / l); } else { return x > 0 ? 0 : Math.PI; } } } ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/geom/CubicBezierCurve.java������������������������������������������������0000644�0000000�0000000�00000012131�12120444566�021467� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.geom; import java.awt.geom.Point2D; /** * This class implements a cubic Bezier curve * with a constant speed parametrization. * The Bezier curve is approximated by a sequence of n straight lines, * where the n+1 points between the lines are * { B(k/n), k=0,1,...,n } where B is the standard * parametrization given here: * http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves * You can then use the constant speed parametrization over this sequence * of straight lines. * * @author Raphael Champeimont */ public class CubicBezierCurve { /** * The four points defining the curve. */ private Point2D.Double P0, P1, P2, P3; private int n; /** * The number of lines approximating the Bezier curve. */ public int getN() { return n; } /** * Get the (exact) length of the approximation curve. */ public double getApproxCurveLength() { return lengths[n-1]; } /** * The n+1 points between the n lines. */ private Point2D.Double[] points; /** * Array of length n. * lengths[i] is the sum of lengths of lines up to and including the * line starting at point points[i]. */ private double[] lengths; /** * Array of length n. * The vectors along each line, with a norm of 1. */ private Point2D.Double[] unitVectors; /** * The standard exact cubic Bezier curve parametrization. * Argument t must be in [0,1]. */ public Point2D.Double standardParam(double t) { double x = Math.pow(1-t,3) * P0.x + 3 * Math.pow(1-t,2) * t * P1.x + 3 * (1-t) * t * t * P2.x + t * t * t * P3.x; double y = Math.pow(1-t,3) * P0.y + 3 * Math.pow(1-t,2) * t * P1.y + 3 * (1-t) * t * t * P2.y + t * t * t * P3.y; return new Point2D.Double(x, y); } /** * Uniform approximated parameterization. * A value in t must be in [0, getApproxCurveLength()]. * We have built a function f such that f(t) is the position of * the point on the approximation curve (n straight lines). * The interesting property is that the length of the curve * { f(t), t in [0,l] } is exactly l. * The java function is simply the application of f over each element * of a sorted array, ie. uniformParam(t)[k] = f(t[k]). * Computation time is O(n+m) where n is the number of lines in which * the curve is divided and m is the length of the array given as an * argument. The use of a sorted array instead of m calls to the * function enables us to have a complexity of O(n+m) instead of O(n*m) * because we don't need to search in all the n possible lines for * each value in t (as we know their are in increasing order). */ public Point2D.Double[] uniformParam(double[] t) { int m = t.length; Point2D.Double[] result = new Point2D.Double[m]; int line = 0; for (int i=0; i= n) { // In theory should not happen, but float computation != math. line = n-1; } if (t[i] < 0) { throw (new IllegalArgumentException("t[" + i + "] < 0")); } // So now we know on which line we are double lengthOnLine = t[i] - (line != 0 ? lengths[line-1] : 0); double x = points[line].x + unitVectors[line].x * lengthOnLine; double y = points[line].y + unitVectors[line].y * lengthOnLine; result[i] = new Point2D.Double(x, y); } return result; } /** * A Bezier curve can be defined by four points, * see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves * Here we give this four points and a integer to say in how many * line segments we want to cut the Bezier curve (if n is bigger * the computation takes longer but the precision is better). * The number of lines must be at least 1. */ public CubicBezierCurve( Point2D.Double P0, Point2D.Double P1, Point2D.Double P2, Point2D.Double P3, int n) { this.P0 = P0; this.P1 = P1; this.P2 = P2; this.P3 = P3; this.n = n; if (n < 1) { throw (new IllegalArgumentException("n must be at least 1")); } computeData(); } private void computeData() { points = new Point2D.Double[n+1]; for (int k=0; k<=n; k++) { points[k] = standardParam(((double) k) / n); } lengths = new double[n]; unitVectors = new Point2D.Double[n]; double sum = 0; for (int i=0; i returning 0"); return 0; } // We want a precision of 0.01 on arc length if (Math.abs(f_x_n_plus_1 - f_x_n) < 0.01) { if (debug) System.out.println("#steps = " + steps); return x_n_plus_1; } x_n = x_n_plus_1; f_x_n = f_x_n_plus_1; steps++; } } } private static double f(double a, double b) { // This is Ramanujan's approximation of an ellipse circumference // Nice because it is fast to compute (no need to compute an integral) // and the derivative is also simple (and fast to compute). return Math.PI*(3*(a+b) - Math.sqrt(10*a*b + 3*(a*a + b*b))); } private static double fprime(double a, double b) { return Math.PI*(3 - (5*b + 3*a)/Math.sqrt(10*a*b + 3*(a*a + b*b))); } /* private static void test(double a, double b, double l) { double a2 = computeEllipseAxis(b, l); System.out.println("true a=" + a + " l=" + l + " estimated a=" + a2 + " l(from true a)=" + f(a,b)); } private static void test(double b, double l) { double a2 = computeEllipseAxis(b, l); System.out.println("true l=" + l + " estimated a=" + a2); } public static void main(String[] args) { double b = 4; test(100, b, 401.3143); test(7, b, 35.20316); test(4, b, 25.13274); test(1, b, 17.15684); test(0.5, b, 16.37248); test(0.25, b, 16.11448); test(0.1, b, 16.02288); test(0.01, b, 16.00034); test(0, b, 16); test(10000, b, 40000.03); } */ /* public static void main(String[] args) { test(222.89291150684895, 2240); } */ } �����������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/geom/ComputeArcCenter.java������������������������������������������������0000644�0000000�0000000�00000003365�12120444566�021510� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/** * File written by Raphael Champeimont * UMR 7238 Genomique des Microorganismes */ package fr.orsay.lri.varna.models.geom; public class ComputeArcCenter { /** * Given an arc length (l) and segment length (delta) of the arc, * find where to put the center, returned as a position of the perpendicular * bisector of the segment. The positive side is the one where the arc is drawn. * It works using Newton's method. */ public static double computeArcCenter(double delta, double l) { double x_n = 0; double x_n_plus_1, f_x_n, f_x_n_plus_1; f_x_n = f(x_n,delta); while (true) { x_n_plus_1 = x_n - (f_x_n - l)/fprime(x_n,delta); f_x_n_plus_1 = f(x_n_plus_1,delta); // We want a precision of 0.1 on arc length if (x_n_plus_1 == Double.NEGATIVE_INFINITY || Math.abs(f_x_n_plus_1 - f_x_n) < 0.1) { //System.out.println("computeArcCenter: steps = " + steps + " result = " + x_n_plus_1); return x_n_plus_1; } x_n = x_n_plus_1; f_x_n = f_x_n_plus_1; } } private static double f(double c, double delta) { if (c < 0) { return 2*Math.atan(delta/(-2*c)) * Math.sqrt(delta*delta/4 + c*c); } else if (c != 0) { // c > 0 return (2*Math.PI - 2*Math.atan(delta/(2*c))) * Math.sqrt(delta*delta/4 + c*c); } else { // c == 0 return Math.PI * Math.sqrt(delta*delta/4 + c*c); } } /** * d/dc f(c,delta) */ private static double fprime(double c, double delta) { if (c < 0) { return delta/(c*c + delta/4)*Math.sqrt(delta*delta/4 + c*c) + 2*Math.atan(delta/(-2*c))*c/Math.sqrt(delta*delta/4 + c*c); } else if (c != 0) { // c > 0 return delta/(c*c + delta/4)*Math.sqrt(delta*delta/4 + c*c) + (2*Math.PI - 2*Math.atan(delta/(-2*c)))*c/Math.sqrt(delta*delta/4 + c*c); } else { // c == 0 return 2; } } }���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/geom/LinesIntersect.java��������������������������������������������������0000644�0000000�0000000�00000006016�12120444566�021234� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/** * File written by Raphael Champeimont * UMR 7238 Genomique des Microorganismes */ package fr.orsay.lri.varna.models.geom; import java.awt.geom.Line2D; import java.awt.geom.Point2D; /** * Like Line2D.Double.linesIntersect() of the standard library, but without the bug! * See this: http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6457965 * This result is incorrect with, for example: * System.out.println(Line2D.Double.linesIntersect(179.2690296114372, 1527.2309703885628, 150.9847583639753, 1498.946699141101, 94.4162158690515, 1442.378156646177, 66.1319446215896, 1414.0938853987152)); * (real example observed on an RNA with no intersection at all) * This lines obviously don't intersect (both X and Y ranges are clearly disjoint!) * but linesIntersect() returns true. * Here we provide a bug-free function. */ public class LinesIntersect { /** * Returns whether segment from (x1,y1) to (x2,y2) * intersect with segment from (x3,y3) to (x4,y4). */ public static boolean linesIntersect( double x1, double y1, double x2, double y2, double x3, double y3, double x4, double y4) { double denom = (y4 - y3) * (x2 - x1) - (x4 - x3) * (y2 - y1); if (denom == 0.0) { // Lines are parallel. return false; } double ua = ((x4 - x3) * (y1 - y3) - (y4 - y3) * (x1 - x3)) / denom; double ub = ((x2 - x1) * (y1 - y3) - (y2 - y1) * (x1 - x3)) / denom; return (ua >= 0.0 && ua <= 1.0 && ub >= 0.0 && ub <= 1.0); } /** * Returns whether segment from p1 to p2 intersects segment from p3 to p4. */ public static boolean linesIntersect( Point2D.Double p1, Point2D.Double p2, Point2D.Double p3, Point2D.Double p4) { return linesIntersect(p1.x, p1.y, p2.x, p2.y, p3.x, p3.y, p4.x, p4.y); } /** * Returns whether the two segment intersect. */ public static boolean linesIntersect(Line2D.Double line1, Line2D.Double line2) { return linesIntersect( line1.x1, line1.y1, line1.x2, line1.y2, line2.x1, line2.y1, line2.x2, line2.y2); } private static void test( double x1, double y1, double x2, double y2, double x3, double y3, double x4, double y4, boolean expectedResult) { boolean a = linesIntersect(x1, y1, x2, y2, x3, y3, x4, y4); boolean b = Line2D.Double.linesIntersect(x1, y1, x2, y2, x3, y3, x4, y4); System.out.println("ours says " + a + " which is " + (a == expectedResult ? "correct" : "INCORRECT") + " / Line2D.Double says " + b + " which is " + (b == expectedResult ? "correct" : "INCORRECT")); } public static void main(String[] args) { test(179.2690296114372, 1527.2309703885628, 150.9847583639753, 1498.946699141101, 94.4162158690515, 1442.378156646177, 66.1319446215896, 1414.0938853987152, false); test(0, 0, 0, 0, 1, 1, 1, 1, false); test(0, 0, 0.5, 0.5, 1, 1, 2, 2, false); test(0, 0, 2, 2, 0, 2, 2, 0, true); test(0, 0, 2, 2, 4, 0, 3, 2, false); } } ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/geom/HalfEllipse.java�����������������������������������������������������0000644�0000000�0000000�00000011441�12120444566�020467� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.geom; import java.awt.geom.AffineTransform; import java.awt.geom.Point2D; /** * Ellipse, with axis = X and Y. * This class is useful for constant speed parameterization * (just like CubicBezierCurve). * The ellipse drawn is in fact an half-ellipse, from 0 to PI. * * @author Raphael Champeimont */ public class HalfEllipse { /** * The four points defining the curve. */ private double a, b; private int n; /** * The number of lines approximating the curve. */ public int getN() { return n; } /** * Get the (exact) length of the approximation curve. */ public double getApproxCurveLength() { return lengths[n-1]; } /** * The n+1 points between the n lines. */ private Point2D.Double[] points; /** * Array of length n. * lengths[i] is the sum of lengths of lines up to and including the * line starting at point points[i]. */ private double[] lengths; /** * Array of length n. * The vectors along each line, with a norm of 1. */ private Point2D.Double[] unitVectors; /** * The standard ellipse parameterization. * Argument t must be in [0,1]. */ public Point2D.Double standardParam(double t) { double x = a*Math.cos(t*Math.PI); double y = b*Math.sin(t*Math.PI); return new Point2D.Double(x, y); } /** * Uniform approximated parameterization. * A value in t must be in [0, getApproxCurveLength()]. * We have built a function f such that f(t) is the position of * the point on the approximation curve (n straight lines). * The interesting property is that the length of the curve * { f(t), t in [0,l] } is exactly l. * The java function is simply the application of f over each element * of a sorted array, ie. uniformParam(t)[k] = f(t[k]). * Computation time is O(n+m) where n is the number of lines in which * the curve is divided and m is the length of the array given as an * argument. The use of a sorted array instead of m calls to the * function enables us to have a complexity of O(n+m) instead of O(n*m) * because we don't need to search in all the n possible lines for * each value in t (as we know their are in increasing order). */ public Point2D.Double[] uniformParam(double[] t) { int m = t.length; Point2D.Double[] result = new Point2D.Double[m]; int line = 0; for (int i=0; i= n) { // In theory should not happen, but float computation != math. line = n-1; } if (t[i] < 0) { throw (new IllegalArgumentException("t[" + i + "] < 0")); } // So now we know on which line we are double lengthOnLine = t[i] - (line != 0 ? lengths[line-1] : 0); double x = points[line].x + unitVectors[line].x * lengthOnLine; double y = points[line].y + unitVectors[line].y * lengthOnLine; result[i] = new Point2D.Double(x, y); } return result; } /** * An ellipse that has axis equal to X and Y axis needs only * two numbers (half-axis lengths) to be defined. * They are resp. a for X axis and b for Y axis. * n = how many line segments we want to cut the curve * (if n is bigger the computation takes longer but the precision is better). * The number of lines must be at least 1. */ public HalfEllipse(double a, double b, int n) { this.a = a; this.b = b; this.n = n; if (n < 1) { throw (new IllegalArgumentException("n must be at least 1")); } computeData(); } /** * Returns that affine transform that moves the ellipse * given by this class such that its 0/pi axis matches P0-P1. */ public static AffineTransform matchAxisA(Point2D.Double P0, Point2D.Double P1) { double theta = MiscGeom.angleFromVector(P0.x-P1.x, P0.y-P1.y); Point2D.Double mid = new Point2D.Double((P0.x+P1.x)/2, (P0.y+P1.y)/2); AffineTransform transform = new AffineTransform(); transform.translate(mid.x, mid.y); transform.rotate(theta); return transform; } private void computeData() { points = new Point2D.Double[n+1]; for (int k=0; k<=n; k++) { points[k] = standardParam(((double) k) / n); } lengths = new double[n]; unitVectors = new Point2D.Double[n]; double sum = 0; for (int i=0; i _bases = new HashSet(); private String _caption; public BaseList( BaseList b) { _caption = b._caption; _bases = new HashSet(b._bases); } public BaseList( String caption) { _caption = caption; } public BaseList( String caption, ModeleBase mb) { this(caption); addBase(mb); } public boolean contains(ModeleBase mb) { return _bases.contains(mb); } public String getCaption() { return _caption; } public void addBase(ModeleBase b) { _bases.add(b); } public void removeBase(ModeleBase b) { _bases.remove(b); } public void addBases(Collection mbs) { _bases.addAll(mbs); } public ArrayList getBases() { return new ArrayList(_bases); } public void clear() { _bases.clear(); } public static Color getAverageColor(ArrayList cols) { int r=0,g=0,b=0; for (Color c : cols) { r += c.getRed(); g += c.getGreen(); b += c.getBlue(); } if (cols.size()>0) { r /= cols.size(); g /= cols.size(); b /= cols.size(); } return new Color(r,g,b); } public Color getAverageOutlineColor() { ArrayList cols = new ArrayList(); for (ModeleBase mb : _bases) { cols.add(mb.getStyleBase().get_base_outline_color()); } return getAverageColor(cols); } public Color getAverageNameColor() { ArrayList cols = new ArrayList(); for (ModeleBase mb : _bases) { cols.add(mb.getStyleBase().get_base_name_color()); } return getAverageColor(cols); } public Color getAverageNumberColor() { ArrayList cols = new ArrayList(); for (ModeleBase mb : _bases) { cols.add(mb.getStyleBase().get_base_number_color()); } return getAverageColor(cols); } public Color getAverageInnerColor() { ArrayList cols = new ArrayList(); for (ModeleBase mb : _bases) { cols.add(mb.getStyleBase().get_base_inner_color()); } return getAverageColor(cols); } public String getNumbers() { String result = ""; boolean first = true; for (ModeleBase mb:_bases) { if (!first) { result += ","; } else { first = false; } result += "" + mb.getBaseNumber(); } result += ""; return result; } public String getContents() { String result = ""; boolean first = true; for (ModeleBase mb:_bases) { if (!first) { result += ","; } else { first = false; } result += "" + mb.getContent(); } result += ""; return result; } public ArrayList getIndices() { ArrayList indices = new ArrayList(); for (ModeleBase mb : _bases) { indices.add(mb.getIndex()); } return indices; } /** * Returns, in a new BaseList, the intersection of the current BaseList and of the argument. * @param mb The base list to be used for the intersection * @return The intersection of the current base list and the argument. */ public BaseList retainAll(BaseList mb) { HashSet cp = new HashSet(); cp.addAll(_bases); cp.retainAll(mb._bases); BaseList result = new BaseList("TmpIntersection"); result.addBases(cp); return result; } /** * Returns, in a new BaseList, the list consisting of the current BaseList minus the list passed as argument. * @param mb The base list to be subtracted from the current one * @return The current base list minus the list passed as argument. */ public BaseList removeAll(BaseList mb) { HashSet cp = new HashSet(); cp.addAll(_bases); cp.removeAll(mb._bases); BaseList result = new BaseList("TmpMinus"); result.addBases(cp); return result; } public int size() { return _bases.size(); } } ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/annotations/��������������������������������������������������������������0000755�0000000�0000000�00000000000�12275611442�017041� 5����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/annotations/TextAnnotation.java�������������������������������������������0000644�0000000�0000000�00000025376�12243423356�022700� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.annotations; import java.awt.Color; import java.awt.Font; import java.awt.geom.Point2D; import java.io.Serializable; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.ArrayList; import java.util.Collections; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModelBaseStyle; import fr.orsay.lri.varna.models.rna.VARNAPoint; import fr.orsay.lri.varna.utils.XMLUtils; /** * The annotated text model * * @author Darty@lri.fr * */ public class TextAnnotation implements Serializable { /** * */ private static final long serialVersionUID = 465236085501860747L; public enum AnchorType{ POSITION, BASE, HELIX, LOOP }; /** * default text color */ public static final Color DEFAULTCOLOR = Color.black; /** * default text font */ public static final Font DEFAULTFONT = new Font("Arial", Font.PLAIN, 12); private String _text; private AnchorType _typeAnchor; private Color _color; private double _angle; private Object _anchor; private Font _font; public static String XML_ELEMENT_NAME = "textAnnotation"; public static String XML_VAR_TYPE_NAME = "type"; public static String XML_VAR_COLOR_NAME = "color"; public static String XML_VAR_ANGLE_NAME = "angle"; public static String XML_VAR_TEXT_NAME = "text"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_TYPE_NAME,"CDATA",""+_typeAnchor); atts.addAttribute("","",XML_VAR_COLOR_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_color)); atts.addAttribute("","",XML_VAR_ANGLE_NAME,"CDATA",""+_angle); hd.startElement("","",XML_ELEMENT_NAME,atts); atts.clear(); hd.startElement("","",XML_VAR_TEXT_NAME,atts); XMLUtils.exportCDATAString(hd, _text); hd.endElement("","",XML_VAR_TEXT_NAME); switch (_typeAnchor) { case POSITION: ((VARNAPoint)_anchor).toXML(hd,"pos"); break; case BASE: XMLUtils.toXML(hd, (ModeleBase)_anchor); break; case HELIX: XMLUtils.toXML(hd, (ArrayList)_anchor); break; case LOOP: XMLUtils.toXML(hd, (ArrayList)_anchor); break; } XMLUtils.toXML(hd, _font); hd.endElement("","",XML_ELEMENT_NAME); } /** * creates an annoted text on a VARNAPanel with the specified text * * @param texte Textual content of the annotation */ public TextAnnotation(String texte) { _text = texte; _color = DEFAULTCOLOR; _font = DEFAULTFONT; _angle = 0; } /** * /** creates an annoted text on a VARNAPanel with the specified text and * is static position * * @param texte * @param x * @param y */ public TextAnnotation(String texte, double x, double y) { this(texte); _anchor = new VARNAPoint(x, y); _typeAnchor = AnchorType.POSITION; } /** * creates an annoted text on a VARNAPanel with the specified text fixed to * a base * * @param texte * @param mb */ public TextAnnotation(String texte, ModeleBase mb) { this(texte); _anchor = mb; _typeAnchor = AnchorType.BASE; } /** * creates an annoted text on a VARNAPanel with the specified text fixed to * a helix (if type is HELIX) or to a loop (if type is LOOP) * * @param texte * @param listeBase * @param type * @throws Exception */ public TextAnnotation(String texte, ArrayList listeBase, AnchorType type) throws Exception { this(texte); _anchor = listeBase; if (type == AnchorType.HELIX) _typeAnchor = AnchorType.HELIX; else if (type == AnchorType.LOOP) _typeAnchor = AnchorType.LOOP; else throw new Exception("Bad argument"); } /** * creates an annoted text from another one * * @param textAnnotation */ public TextAnnotation(TextAnnotation textAnnotation) { _anchor = textAnnotation.getAncrage(); _font = textAnnotation.getFont(); _text = textAnnotation.getTexte(); _typeAnchor = textAnnotation.getType(); } /** * * @return the text */ public String getTexte() { return _text; } public void setText(String _texte) { this._text = _texte; } /** * * @return the font */ public Font getFont() { return _font; } public void setFont(Font _font) { this._font = _font; } public Object getAncrage() { return _anchor; } public void setAncrage(ModeleBase mb) { _anchor = mb; _typeAnchor = AnchorType.BASE; } public void setAncrage(double x, double y) { _anchor = new VARNAPoint(x, y); _typeAnchor = AnchorType.POSITION; } public void setAncrage(ArrayList list, AnchorType type) throws Exception { _anchor = list; if (type == AnchorType.HELIX) _typeAnchor = AnchorType.HELIX; else if (type == AnchorType.LOOP) _typeAnchor = AnchorType.LOOP; else throw new Exception("Bad argument"); } public AnchorType getType() { return _typeAnchor; } public void setType(AnchorType t) { _typeAnchor = t; } public Color getColor() { return _color; } public void setColor(Color color) { this._color = color; } public String getHelixDescription() { ArrayList listeBase = ((ArrayList)_anchor); int minA = Integer.MAX_VALUE,maxA = Integer.MIN_VALUE; int minB = Integer.MAX_VALUE,maxB = Integer.MIN_VALUE; for(ModeleBase mb : listeBase) { int i = mb.getBaseNumber(); if (mb.getElementStructure()>i) { minA = Math.min(minA, i); maxA = Math.max(maxA, i); } else { minB = Math.min(minB, i); maxB = Math.max(maxB, i); } } return "["+minA+","+maxA+"] ["+minB+","+maxB+"]"; } public String getLoopDescription() { ArrayList listeBase = ((ArrayList)_anchor); int min = Integer.MAX_VALUE,max = Integer.MIN_VALUE; for(ModeleBase mb : listeBase) { int i = mb.getBaseNumber(); min = Math.min(min, i); max = Math.max(max, i); } return "["+min+","+max+"]"; } public String toString() { String tmp = "["+_text+"] "; switch (_typeAnchor) { case POSITION: NumberFormat formatter = new DecimalFormat(".00"); return tmp+" at ("+formatter.format(getCenterPosition().x)+","+formatter.format(getCenterPosition().y)+")"; case BASE: return tmp+" on base "+((ModeleBase) _anchor).getBaseNumber(); case HELIX: return tmp+" on helix "+getHelixDescription(); case LOOP: return tmp+" on loop "+getLoopDescription(); default: return tmp; } } /** * * @return the text position center */ public Point2D.Double getCenterPosition() { switch (_typeAnchor) { case POSITION: return ((VARNAPoint) _anchor).toPoint2D(); case BASE: return ((ModeleBase) _anchor).getCoords(); case HELIX: return calculLoopHelix(); case LOOP: return calculLoop(); default: return new Point2D.Double(0., 0.); } } private Point2D.Double calculLoop() { ArrayList liste = extractedArrayListModeleBaseFromAncrage(); double totalX = 0., totalY = 0.; for (ModeleBase base : liste) { totalX += base.getCoords().x; totalY += base.getCoords().y; } return new Point2D.Double(totalX / liste.size(), totalY / liste.size()); } private Point2D.Double calculLoopHelix() { ArrayList liste = extractedArrayListModeleBaseFromAncrage(); Collections.sort(liste); double totalX = 0., totalY = 0.; double num=0.0; for (int i=0;i0 && (i extractedArrayListModeleBaseFromAncrage() { return (ArrayList) _anchor; } /** * clone a TextAnnotation */ public TextAnnotation clone() { TextAnnotation textAnnot = null; try { switch (_typeAnchor) { case BASE: textAnnot = new TextAnnotation(_text, (ModeleBase) _anchor); break; case POSITION: textAnnot = new TextAnnotation(_text, ((VARNAPoint) _anchor).x, ((VARNAPoint) _anchor).y); break; case LOOP: textAnnot = new TextAnnotation(_text, extractedArrayListModeleBaseFromAncrage(), AnchorType.LOOP); break; case HELIX: textAnnot = new TextAnnotation(_text, extractedArrayListModeleBaseFromAncrage(), AnchorType.HELIX); break; default: break; } } catch (Exception e) { e.printStackTrace(); } textAnnot.setFont(_font); textAnnot.setColor(_color); return textAnnot; } /** * copy a textAnnotation * * @param textAnnotation */ public void copy(TextAnnotation textAnnotation) { _anchor = textAnnotation.getAncrage(); _font = textAnnotation.getFont(); _text = textAnnotation.getTexte(); _typeAnchor = textAnnotation.getType(); _color = textAnnotation.getColor(); _angle = textAnnotation.getAngleInDegres(); } /** * * @return the angle in degrees */ public double getAngleInDegres() { // if (_typeAncrage == TextAnnotation.HELIX) // _angle = calculAngleDegres(); return _angle; } /** * * @return the angle in radians */ public double getAngleInRadians() { return (getAngleInDegres() * Math.PI) / 180.; } public void setAngleInDegres(double _angle) { this._angle = _angle; } public void setAngleInRadians(double _angle) { this._angle = _angle * 180 / Math.PI; } } ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/annotations/ChemProbAnnotation.java���������������������������������������0000644�0000000�0000000�00000015507�12243365130�023441� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.annotations; import java.awt.Color; import java.awt.geom.Point2D; import java.io.Serializable; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.utils.XMLUtils; public class ChemProbAnnotation implements Serializable { /** * */ private static final long serialVersionUID = 5833315460145031242L; public enum ChemProbAnnotationType { TRIANGLE, ARROW, PIN, DOT; }; public static double DEFAULT_INTENSITY = 1.0; public static ChemProbAnnotationType DEFAULT_TYPE = ChemProbAnnotationType.ARROW; public static Color DEFAULT_COLOR = Color.blue.darker(); private ModeleBase _mbfst; private ModeleBase _mbsnd; private Color _color; private double _intensity; private ChemProbAnnotationType _type; private boolean _outward; public static String XML_ELEMENT_NAME = "ChemProbAnnotation"; public static String XML_VAR_INDEX5_NAME = "Index5"; public static String XML_VAR_INDEX3_NAME = "Index3"; public static String XML_VAR_COLOR_NAME = "Color"; public static String XML_VAR_INTENSITY_NAME = "Intensity"; public static String XML_VAR_TYPE_NAME = "Type"; public static String XML_VAR_OUTWARD_NAME = "Outward"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_INDEX5_NAME,"CDATA",""+_mbfst.getIndex()); atts.addAttribute("","",XML_VAR_INDEX3_NAME,"CDATA",""+_mbsnd.getIndex()); atts.addAttribute("","",XML_VAR_COLOR_NAME,"CDATA",XMLUtils.toHTMLNotation(_color)); atts.addAttribute("","",XML_VAR_INTENSITY_NAME,"CDATA",""+_intensity); atts.addAttribute("","",XML_VAR_TYPE_NAME,"CDATA",""+_type); atts.addAttribute("","",XML_VAR_OUTWARD_NAME,"CDATA",""+_outward); hd.startElement("","",XML_ELEMENT_NAME,atts); hd.endElement("","",XML_ELEMENT_NAME); } public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, String styleDesc) { this(mbfst,mbsnd); applyStyle(styleDesc); } public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd) { this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,ChemProbAnnotation.DEFAULT_INTENSITY); } public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, double intensity) { this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,intensity); } public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type) { this(mbfst,mbsnd,type,ChemProbAnnotation.DEFAULT_INTENSITY); } public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity) { this(mbfst,mbsnd, type, intensity, DEFAULT_COLOR, true); } public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity, Color color, boolean out) { if (mbfst.getIndex()>mbsnd.getIndex()) { ModeleBase tmp = mbsnd; mbsnd = mbfst; mbfst = tmp; } _mbfst = mbfst; _mbsnd = mbsnd; _type = type; _intensity = intensity; _color = color; _outward = out; } public boolean isOut() { return _outward; } public void setOut(boolean b) { _outward = b; } public Color getColor() { return _color; } public double getIntensity() { return _intensity; } public ChemProbAnnotationType getType() { return _type; } public void setColor(Color c){ _color = c; } public void setIntensity(double d){ _intensity = d; } public Point2D.Double getAnchorPosition() { Point2D.Double result = new Point2D.Double( (_mbfst.getCoords().x+_mbsnd.getCoords().x)/2.0, (_mbfst.getCoords().y+_mbsnd.getCoords().y)/2.0); return result; } public Point2D.Double getDirVector() { Point2D.Double norm = getNormalVector(); Point2D.Double result = new Point2D.Double(-norm.y,norm.x); Point2D.Double anchor = getAnchorPosition(); Point2D.Double center = new Point2D.Double( (_mbfst.getCenter().x+_mbsnd.getCenter().x)/2.0, (_mbfst.getCenter().y+_mbsnd.getCenter().y)/2.0); Point2D.Double vradius = new Point2D.Double( (center.x-anchor.x)/2.0, (center.y-anchor.y)/2.0); if (_outward) { if (result.x*vradius.x+result.y*vradius.y>0) { return new Point2D.Double(-result.x,-result.y); } } else { if (result.x*vradius.x+result.y*vradius.y<0) { return new Point2D.Double(-result.x,-result.y); } } return result; } public Point2D.Double getNormalVector() { Point2D.Double tmp; if (_mbfst==_mbsnd) { tmp = new Point2D.Double( (-(_mbsnd.getCenter().y-_mbsnd.getCoords().y)), ((_mbsnd.getCenter().x-_mbsnd.getCoords().x))); } else { tmp = new Point2D.Double( (_mbsnd.getCoords().x-_mbfst.getCoords().x)/2.0, (_mbsnd.getCoords().y-_mbfst.getCoords().y)/2.0); } double norm = tmp.distance(0, 0); Point2D.Double result = new Point2D.Double(tmp.x/norm,tmp.y/norm); return result; } public static ChemProbAnnotationType annotTypeFromString(String value) { if (value.toLowerCase().equals("arrow")) {return ChemProbAnnotationType.ARROW;} else if (value.toLowerCase().equals("triangle")) {return ChemProbAnnotationType.TRIANGLE;} else if (value.toLowerCase().equals("pin")) {return ChemProbAnnotationType.PIN;} else if (value.toLowerCase().equals("dot")) {return ChemProbAnnotationType.DOT;} else {return ChemProbAnnotationType.ARROW;} } public void applyStyle(String styleDesc) { String[] chemProbs = styleDesc.split(","); for (int i = 0; i < chemProbs.length; i++) { String thisStyle = chemProbs[i]; String[] data = thisStyle.split("="); if (data.length==2) { String name = data[0]; String value = data[1]; if (name.toLowerCase().equals("color")) { Color c = Color.decode(value); if (c==null) { c = _color; } setColor(c); } else if (name.toLowerCase().equals("intensity")) { _intensity = Double.parseDouble(value); } else if (name.toLowerCase().equals("dir")) { _outward = value.toLowerCase().equals("out"); } else if (name.toLowerCase().equals("glyph")) { _type= annotTypeFromString(value); } } } } public void setType(ChemProbAnnotationType s) { _type = s; } public ChemProbAnnotation clone() { ChemProbAnnotation result = new ChemProbAnnotation(this._mbfst,this._mbsnd); result._intensity = _intensity; result._type = _type; result._color= _color; result._outward = _outward; return result; } public String toString() { return "Chem. prob. "+this._type+" Base#"+this._mbfst.getBaseNumber()+"-"+this._mbsnd.getBaseNumber(); } } �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/annotations/HighlightRegionAnnotation.java��������������������������������0000644�0000000�0000000�00000025541�12442101046�025007� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������package fr.orsay.lri.varna.models.annotations; import java.awt.Color; import java.awt.Shape; import java.awt.geom.GeneralPath; import java.awt.geom.Point2D; import java.io.Serializable; import java.util.ArrayList; import java.util.Collection; import java.util.LinkedList; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurClicMovement; import fr.orsay.lri.varna.models.VARNAConfigLoader; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.models.rna.VARNAPoint; import fr.orsay.lri.varna.utils.XMLUtils; import fr.orsay.lri.varna.views.VueHighlightRegionEdit; import fr.orsay.lri.varna.views.VueUI; public class HighlightRegionAnnotation implements Serializable { private static final long serialVersionUID = 7087014168028684775L; public static final Color DEFAULT_OUTLINE_COLOR = Color.decode("#6ed86e"); public static final Color DEFAULT_FILL_COLOR = Color.decode("#bcffdd"); public static final double DEFAULT_RADIUS = 16.0; private Color _outlineColor = DEFAULT_OUTLINE_COLOR; private Color _fillColor = DEFAULT_FILL_COLOR; private double _radius = DEFAULT_RADIUS; private ArrayList _bases; public static String XML_ELEMENT_NAME = "region"; public static String XML_VAR_OUTLINE_NAME = "outline"; public static String XML_VAR_FILL_NAME = "fill"; public static String XML_VAR_RADIUS_NAME = "radius"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_OUTLINE_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_outlineColor)); atts.addAttribute("","",XML_VAR_FILL_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_fillColor)); atts.addAttribute("","",XML_VAR_RADIUS_NAME,"CDATA",""+_radius); hd.startElement("","",XML_ELEMENT_NAME,atts); XMLUtils.toXML(hd, _bases); hd.endElement("","",XML_ELEMENT_NAME); } public HighlightRegionAnnotation(RNA r, int startIndex, int stopIndex) { this(r.getBasesBetween(startIndex, stopIndex)); } public HighlightRegionAnnotation() { this(new ArrayList()); } public HighlightRegionAnnotation(ArrayList b) { this(b,DEFAULT_FILL_COLOR,DEFAULT_OUTLINE_COLOR,DEFAULT_RADIUS); } public HighlightRegionAnnotation(ArrayList b,Color fill, Color outline, double radius) { _bases = b; _fillColor = fill; _outlineColor = outline; _radius = radius; } public HighlightRegionAnnotation clone() { return new HighlightRegionAnnotation(_bases,_fillColor,_outlineColor,_radius); } public int getMinIndex() { int min = Integer.MAX_VALUE; for (ModeleBase mb : _bases) { min = Math.min(min, mb.getIndex()); } return min; } public int getMaxIndex() { int max = Integer.MIN_VALUE; for (ModeleBase mb : _bases) { max = Math.max(max, mb.getIndex()); } return max; } public void setOutlineColor(Color c) { _outlineColor = c; } public ArrayList getBases() { return _bases; } public void setBases(ArrayList b) { _bases = b; } public void setFillColor(Color c) { _fillColor = c; } public Color getFillColor() { return _fillColor; } public Color getOutlineColor() { return _outlineColor; } public double getRadius() { return _radius; } public void setRadius(double v) { _radius = v; } public static final int NUM_STEPS_ROUNDED_CORNERS = 16; private Point2D.Double symImage(Point2D.Double p, Point2D.Double center) { return new Point2D.Double(2.*center.x-p.x, 2.*center.y-p.y); } private LinkedList buildRoundedCorner(Point2D.Double p1, Point2D.Double p2, Point2D.Double anotherPoint) { LinkedList result = new LinkedList(); Point2D.Double m = new Point2D.Double((p1.x+p2.x)/2.0,(p1.y+p2.y)/2.0); double rad = p1.distance(p2)/2.; double angle = Math.atan2(p1.y-m.y, p1.x-m.x); double incr = Math.PI/((double)NUM_STEPS_ROUNDED_CORNERS+1); Point2D.Double pdir = new Point2D.Double(m.x+rad*Math.cos(angle+Math.PI/2.),m.y+rad*Math.sin(angle+Math.PI/2.)); if (pdir.distance(anotherPoint) pointList = new LinkedList(); for (int i = 0;i0) { Point2D.Double prev1 = pointList.getLast(); Point2D.Double prev2 = pointList.getFirst(); if ((interForward.distance(prev1)+interBackward.distance(prev2))<(interForward.distance(prev2)+interBackward.distance(prev1))) { pointList.addLast(interForward); pointList.addFirst(interBackward); } else { pointList.addFirst(interForward); pointList.addLast(interBackward); } } else { pointList.addLast(interForward); pointList.addFirst(interBackward); } } } if (getBases().size()==1) { int midl = pointList.size()/2; Point2D.Double mid = pointList.get(midl); Point2D.Double apoint = new Point2D.Double(mid.x+1.,mid.y); LinkedList pointListStart = buildRoundedCorner(pointList.get(midl-1), pointList.get(midl), apoint); pointList.addAll(midl, pointListStart); mid = pointList.get(midl); apoint = new Point2D.Double(mid.x+1.,mid.y); LinkedList pointListEnd = buildRoundedCorner(pointList.get(pointList.size()-1),pointList.get(0), apoint); pointList.addAll(0,pointListEnd); } else if (getBases().size()>1) { int midl = pointList.size()/2; Point2D.Double apoint = symImage(pointList.get(midl),pointList.get(midl-1)); LinkedList pointListStart = buildRoundedCorner(pointList.get(midl-1), pointList.get(midl), apoint); pointList.addAll(midl, pointListStart); apoint = symImage(realCoords[getBases().get(getBases().size()-1).getIndex()], realCoords[getBases().get(getBases().size()-2).getIndex()]); LinkedList pointListEnd = buildRoundedCorner(pointList.get(pointList.size()-1),pointList.get(0), apoint); pointList.addAll(0,pointListEnd); } if (pointList.size()>0) { Point2D.Double point = pointList.get(0); p.moveTo((float)point.x, (float)point.y); for (int i=1;i bases = vp.getRNA().getBasesBetween(i, j); if (parts.length>1) { try { String[] options = parts[1].split(","); for (int k = 0; k < options.length; k++) { //System.out.println(options[k]); try { String[] data = options[k].split("="); String lhs = data[0].toLowerCase(); String rhs = data[1]; if (lhs.equals("fill")) { fill = VARNAConfigLoader.getSafeColor(rhs, fill); } else if (lhs.equals("outline")) { outline = VARNAConfigLoader.getSafeColor(rhs, outline); } else if (lhs.equals("radius")) { radius = Double.parseDouble(rhs); } } catch(Exception e) { } } } catch(Exception e) { e.printStackTrace(); } } return new HighlightRegionAnnotation(bases,fill,outline,radius); } catch(Exception e) { e.printStackTrace(); } return null; } public String toString() { //String result = "HighlightRegionAnnotation["; //result += "fill:"+_fillColor.toString(); //result += ",outline:"+_outlineColor.toString(); //result += ",radius:"+_radius; //return result+"]"; String result = "Highlighted region "+getMinIndex()+"-"+getMaxIndex(); return result; } } ���������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/rna/����������������������������������������������������������������������0000755�0000000�0000000�00000000000�12275611440�015262� 5����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������fr/orsay/lri/varna/models/rna/ModeleBasesComparison.java��������������������������������������������0000644�0000000�0000000�00000023260�12272075140�022344� 0����������������������������������������������������������������������������������������������������ustar �root����������������������������root�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.rna; import java.awt.Color; import java.awt.geom.Point2D; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.utils.XMLUtils; /** * The RNA base comparison model. In each bases we'll place two * characters representing nitrogenous bases of both RNA that have to be * compared. So, in each base in the comparison model, we'll have a couple of * bases, with the same coordinates on the final drawing. * * @author Masson * */ public class ModeleBasesComparison extends ModeleBase { /* * LOCAL FIELDS */ /** * */ private static final long serialVersionUID = -2733063250714562463L; /** * The base of the first RNA associated with the base of the second RNA. */ private Character _base1; /** * The base of the second RNA associated with the base of the first RNA. */ private Character _base2; /** * This ModeleBasesComparison owning statement. It's value will be 0 if this * base is common for both RNA that had been compared, 1 if this base is * related to the first RNA, 2 if related to the second. Default is -1. */ private int _appartenance = -1; /** * This base's offset in the sequence */ private int _index; public static String XML_ELEMENT_NAME = "NTPair"; public static String XML_VAR_FIRST_CONTENT_NAME = "base1"; public static String XML_VAR_SECOND_CONTENT_NAME = "base2"; public static String XML_VAR_MEMBERSHIP_NAME = "type"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_INDEX_NAME,"CDATA",""+_index); atts.addAttribute("","",XML_VAR_NUMBER_NAME,"CDATA",""+_realIndex); atts.addAttribute("","",XML_VAR_CUSTOM_DRAWN_NAME,"CDATA",""+_colorie); atts.addAttribute("","",XML_VAR_LABEL_NAME,"CDATA",""+_label); atts.addAttribute("","",XML_VAR_MEMBERSHIP_NAME,"CDATA",""+_appartenance); atts.addAttribute("","","VALUE","CDATA",""+_value); hd.startElement("","",XML_ELEMENT_NAME,atts); atts.clear(); hd.startElement("","",XML_VAR_FIRST_CONTENT_NAME,atts); XMLUtils.exportCDATAString(hd, ""+_base1); hd.endElement("","",XML_VAR_FIRST_CONTENT_NAME); atts.clear(); hd.startElement("","",XML_VAR_SECOND_CONTENT_NAME,atts); XMLUtils.exportCDATAString(hd, ""+_base2); hd.endElement("","",XML_VAR_SECOND_CONTENT_NAME); _coords.toXML(hd,XML_VAR_POSITION_NAME); _center.toXML(hd,XML_VAR_CENTER_NAME); if (_colorie) { _styleBase.toXML(hd); } hd.endElement("","",XML_ELEMENT_NAME); } /* * -> END LOCAL FIELDS <-- */ public static Color FIRST_RNA_COLOR = Color.decode("#FFDD99"); public static Color SECOND_RNA_COLOR = Color.decode("#99DDFF"); public static Color BOTH_RNA_COLOR = Color.decode("#99DD99"); public static Color DEFAULT_RNA_COLOR = Color.white; /* * CONSTRUCTORS */ /** * Creates a new comparison base with the default display style and no * nitrogenous bases. */ public ModeleBasesComparison(int index) { this(' ', ' ', index); } /** * Creates a new comparison base at the specified coordinates, with the * default display style and no nitrogenous bases. * * @param coords * - The coordinates in which the comparison base has to be * placed. */ public ModeleBasesComparison(Point2D coords, int index) { this(' ', ' ', new Point2D.Double(coords.getX(), coords.getY()), index); } /** * Creates a new comparison base with the specified nitrogenous bases. * * @param base1 * - The first RNA' nitrogenous base * @param base2 * - The second RNA' nitrogenous base */ public ModeleBasesComparison(char base1, char base2, int index) { this(base1, base2, -1, index); } /** * Creates a new comparison base with the specified nitrogenous bases, at * the specified coordinates. * * @param base1 * - The first RNA' nitrogenous base * @param base2 * - The second RNA' nitrogenous base * @param coords * - The coordinates in which the comparison base has to be * placed. */ public ModeleBasesComparison(char base1, char base2, Point2D coords, int index) { this(new Point2D.Double(coords.getX(), coords.getY()), base1, base2, true, new ModelBaseStyle(), -1, index); } /** * Creates a new comparison base with the specified nitrogenous bases. * * @param base1 * - The first RNA' nitrogenous base * @param base2 * - The second RNA' nitrogenous base */ public ModeleBasesComparison(char base1, char base2, int elementStructure, int index) { this(new Point2D.Double(), base1, base2, true, new ModelBaseStyle(), elementStructure, index); } /** * Creates a new comparison base with the specified nitrogenous bases. * * @param coords * - This base's XY coordinates * @param base1 * - The first RNA' nitrogenous base * @param base2 * - The second RNA' nitrogenous base * @param colorie * - Whether or not this base will be drawn * @param mb * - The drawing style for this base * @param elementStructure * - The index of a bp partner in the secondary structure * @param index * - Index of this base in its initial sequence */ public ModeleBasesComparison(Point2D coords, char base1, char base2, boolean colorie, ModelBaseStyle mb, int elementStructure, int index) { _colorie = colorie; _base1 = base1; _base2 = base2; _styleBase = mb; _coords = new VARNAPoint(coords.getX(), coords.getY()); _index = index; } /* * -> END CONSTRUCTORS <-- */ /* * GETTERS & SETTERS */ /** * Return the display style associated to this comparison base. * * @return The display style associated to this comparison base. */ public ModelBaseStyle getStyleBase() { if (_colorie) return _styleBase; return new ModelBaseStyle(); } /** * Allows to know if this comparison base is colored. * * @return TRUE if this comparison base is colored, else FALSE. */ public Boolean getColored() { return _colorie; } /** * Sets the coloration authorization of this comparison base. * * @param colored * - TRUE if this comparison base has to be colored, else FALSE. */ public void set_colored(Boolean colored) { this._colorie = colored; } /** * Return the base of the first RNA in this comparison base. * * @return The base of the first RNA in this comparison base. */ public Character getBase1() { return _base1; } /** * Sets the base of the first RNA in this comparison base. * * @param _base1 * - The base of the first RNA in this comparison base. */ public void setBase1(Character _base1) { this._base1 = _base1; } /** * Return the base of the second RNA in this comparison base. * * @return The base of the second RNA in this comparison base. */ public Character getBase2() { return _base2; } /** * Sets the base of the second RNA in this comparison base. * * @param _base2 * - The base of the second RNA in this comparison base. */ public void setBase2(Character _base2) { this._base2 = _base2; } /* * --> END GETTERS & SETTERS <-- */ /** * Gets the string representation of the two bases in this * ModeleBasesComparison. * * @return the string representation of the two bases in this * ModeleBasesComparison. */ public String getBases() { return String.valueOf(_base1) + String.valueOf(_base2); } public String getContent() { return getBases(); } /** * Gets this base's related RNA. * * @return 0 if this base is common for both RNA
* 1 if this base is related to the first RNA
* 2 if this base is related to the second RNA */ public int get_appartenance() { return _appartenance; } /** * Sets this base's related RNA. * * @param _appartenance * : 0 if this base is common for both RNA
* 1 if this base is related to the first RNA
* 2 if this base is related to the second RNA. */ public void set_appartenance(int _appartenance) { if (_appartenance == 0) { this.getStyleBase().setBaseInnerColor(BOTH_RNA_COLOR); } else if (_appartenance == 1) { this.getStyleBase().setBaseInnerColor(FIRST_RNA_COLOR); } else if (_appartenance == 2) { this.getStyleBase().setBaseInnerColor(SECOND_RNA_COLOR); } else { this.getStyleBase().setBaseInnerColor(DEFAULT_RNA_COLOR); } this._appartenance = _appartenance; } public int getIndex() { return _index; } @Override public void setContent(String s) { this.setBase1(s.charAt(0)); this.setBase2(s.charAt(1)); } } fr/orsay/lri/varna/models/rna/ModelBaseStyle.java0000644000000000000000000002055411722524460021010 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.rna; import java.awt.Color; import java.awt.Font; import java.io.Serializable; import java.util.ArrayList; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.utils.XMLUtils; /** * The display Style of a rna base with the base name font, the ouline, * innerline, number and name color * * @author darty * */ public class ModelBaseStyle implements Cloneable, Serializable { /** * */ private static final long serialVersionUID = -4331494086323517208L; private Color _base_outline_color, _base_inner_color, _base_number_color, _base_name_color; private boolean _selected; public static String XML_ELEMENT_NAME = "basestyle"; public static String XML_VAR_OUTLINE_NAME = "outline"; public static String XML_VAR_INNER_NAME = "inner"; public static String XML_VAR_NUMBER_NAME = "num"; public static String XML_VAR_NAME_NAME = "name"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_OUTLINE_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_base_outline_color)); atts.addAttribute("","",XML_VAR_INNER_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_base_inner_color)); atts.addAttribute("","",XML_VAR_NUMBER_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_base_number_color)); atts.addAttribute("","",XML_VAR_NAME_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_base_name_color)); hd.startElement("","",XML_ELEMENT_NAME,atts); hd.endElement("","",XML_ELEMENT_NAME); } public ModelBaseStyle clone() { ModelBaseStyle result = new ModelBaseStyle(); result._base_inner_color = this._base_inner_color; result._base_name_color = this._base_name_color; result._base_number_color = this._base_number_color; result._base_outline_color = this._base_outline_color; result._selected = this._selected; return result; } /** * Creates a new base style with default colors and font * * @see VARNAConfig#BASE_OUTLINE_COLOR_DEFAULT * @see VARNAConfig#BASE_INNER_COLOR_DEFAULT * @see VARNAConfig#BASE_NUMBER_COLOR_DEFAULT * @see VARNAConfig#BASE_NAME_COLOR_DEFAULT * */ public ModelBaseStyle() { _base_outline_color = VARNAConfig.BASE_OUTLINE_COLOR_DEFAULT; _base_inner_color = VARNAConfig.BASE_INNER_COLOR_DEFAULT; _base_number_color = VARNAConfig.BASE_NUMBER_COLOR_DEFAULT; _base_name_color = VARNAConfig.BASE_NAME_COLOR_DEFAULT; _selected = false; } /** * Creates a new base style with custom colors and custom font * * @param outline * The out line color of the base * @param inner * The inner line color of the base * @param number * The number color of the base * @param name * The name color of the base * @param font * The name font of the base */ public ModelBaseStyle(Color outline, Color inner, Color number, Color name, Font font) { _base_outline_color = outline; _base_inner_color = inner; _base_number_color = number; _base_name_color = name; } public ModelBaseStyle(String parameterValue) throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError { this(); assignParameters(parameterValue); } public ModelBaseStyle(ModelBaseStyle msb) { _base_outline_color = msb.get_base_outline_color(); _base_inner_color = msb.get_base_inner_color(); _base_number_color = msb.get_base_number_color(); _base_name_color = msb.get_base_name_color(); } public Color get_base_outline_color() { return _base_outline_color; } public void setBaseOutlineColor(Color _base_outline_color) { this._base_outline_color = _base_outline_color; } public Color get_base_inner_color() { return _base_inner_color; } public void setBaseInnerColor(Color _base_inner_color) { this._base_inner_color = _base_inner_color; } public Color get_base_number_color() { return _base_number_color; } public void setBaseNumberColor(Color _base_numbers_color) { this._base_number_color = _base_numbers_color; } public Color get_base_name_color() { return _base_name_color; } public void setBaseNameColor(Color _base_name_color) { this._base_name_color = _base_name_color; } public static final String PARAM_INNER_COLOR = "fill"; public static final String PARAM_OUTLINE_COLOR = "outline"; public static final String PARAM_TEXT_COLOR = "label"; public static final String PARAM_NUMBER_COLOR = "number"; public static Color getSafeColor(String col) { Color result; try { result = Color.decode(col); } catch (NumberFormatException e) { result = Color.getColor(col, Color.green); } return result; } public void assignParameters(String parametersValue) throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError { if (parametersValue.equals("")) return; String[] parametersL = parametersValue.split(","); ArrayList namesArray = new ArrayList(); ArrayList valuesArray = new ArrayList(); String[] param; for (int i = 0; i < parametersL.length; i++) { param = parametersL[i].split("="); if (param.length != 2) throw new ExceptionModeleStyleBaseSyntaxError( "Bad parameter: '" + param[0] + "' ..."); namesArray.add(param[0].replace(" ", "")); valuesArray.add(param[1].replace(" ", "")); } for (int i = 0; i < namesArray.size(); i++) { if (namesArray.get(i).toLowerCase().equals(PARAM_INNER_COLOR)) { try { setBaseInnerColor(getSafeColor(valuesArray.get(i))); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "Bad inner color Syntax:" + valuesArray.get(i)); } } else if (namesArray.get(i).toLowerCase().equals(PARAM_TEXT_COLOR)) { try { setBaseNameColor(getSafeColor(valuesArray.get(i))); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "Bad name color Syntax:" + valuesArray.get(i)); } } else if (namesArray.get(i).toLowerCase().equals( PARAM_NUMBER_COLOR)) { try { setBaseNumberColor(getSafeColor(valuesArray.get(i))); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "Bad numbers color Syntax:" + valuesArray.get(i)); } } else if (namesArray.get(i).toLowerCase().equals( PARAM_OUTLINE_COLOR)) { try { setBaseOutlineColor(getSafeColor(valuesArray.get(i))); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "Bad outline color Syntax:" + valuesArray.get(i)); } } else throw new ExceptionModeleStyleBaseSyntaxError( "Unknown parameter:" + namesArray.get(i)); } } /** * Find the font style integer from a string. Return null if * the font style is unknown. * * @param s * The string to decode * @return The font style integer as Font.PLAIN. */ public static Integer StyleToInteger(String s) { Integer style; if (s.toLowerCase().equals("italic")) style = Font.ITALIC; else if (s.toLowerCase().equals("bold")) style = Font.BOLD; else if (s.toLowerCase().equals("plain")) style = Font.PLAIN; else style = null; return style; } } fr/orsay/lri/varna/models/rna/StructureTemp.java0000644000000000000000000000141611620715270020754 0ustar rootrootpackage fr.orsay.lri.varna.models.rna; import java.io.Serializable; import java.util.ArrayList; import java.util.Iterator; public class StructureTemp implements Serializable{ /** * */ private static final long serialVersionUID = -436852923461989105L; private ArrayList _struct = new ArrayList(); public StructureTemp(){ } public void addStrand(ModeleStrand ms){ this._struct.add(ms); } public int sizeStruct() { return this._struct.size(); } public ModeleStrand getStrand(int a) { return this._struct.get(a); } public ArrayList getListStrands() { return _struct; } public void clearListStrands() { this._struct.clear(); } public boolean isEmpty() { return this._struct.isEmpty(); } } fr/orsay/lri/varna/models/rna/DrawRNATemplate.java0000644000000000000000000013702512377430020021063 0ustar rootroot/** * File written by Raphael Champeimont * UMR 7238 Genomique des Microorganismes */ package fr.orsay.lri.varna.models.rna; import java.awt.geom.AffineTransform; import java.awt.geom.Line2D; import java.awt.geom.Point2D; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.Map; import java.util.Set; import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.geom.ComputeArcCenter; import fr.orsay.lri.varna.models.geom.ComputeEllipseAxis; import fr.orsay.lri.varna.models.geom.CubicBezierCurve; import fr.orsay.lri.varna.models.geom.HalfEllipse; import fr.orsay.lri.varna.models.geom.LinesIntersect; import fr.orsay.lri.varna.models.geom.MiscGeom; import fr.orsay.lri.varna.models.templates.DrawRNATemplateCurveMethod; import fr.orsay.lri.varna.models.templates.DrawRNATemplateMethod; import fr.orsay.lri.varna.models.templates.RNANodeValueTemplate; import fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair; import fr.orsay.lri.varna.models.templates.RNATemplate; import fr.orsay.lri.varna.models.templates.RNATemplateAlign; import fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException; import fr.orsay.lri.varna.models.templates.RNATemplateMapping; import fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition; import fr.orsay.lri.varna.models.templates.RNATemplate.In1Is; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint; import fr.orsay.lri.varna.models.treealign.Tree; public class DrawRNATemplate { private RNA rna; private RNATemplateMapping mapping; private ArrayList _listeBases; public DrawRNATemplate(RNA rna) { this.rna = rna; this._listeBases = rna.getListeBases(); } public RNATemplateMapping getMapping() { return mapping; } /** * Draw this RNA like the given template. * The helixLengthAdjustmentMethod argument tells what to do in case * some helices are of a different length in the template and the * actual helix. See class DrawRNATemplateMethod above for possible values. */ public void drawRNATemplate( RNATemplate template, VARNAConfig conf, DrawRNATemplateMethod helixLengthAdjustmentMethod, DrawRNATemplateCurveMethod curveMethod) throws RNATemplateDrawingAlgorithmException { // debug // try { // RNA perfectMatchingRNA = template.toRNA(); // System.out.println("An RNA that would perfectly match this template would be:"); // System.out.println(perfectMatchingRNA.getStructDBN()); // } catch (ExceptionInvalidRNATemplate e) { // e.printStackTrace(); // } mapping = RNATemplateAlign.mapRNAWithTemplate(rna, template); //System.out.println(mapping.showCompact(this)); // debug // RNATemplateAlign.printMapping(mapping, template, getSeq()); // try { // TreeGraphviz.treeToGraphvizPostscript(alignment, "alignment_graphviz.ps"); // } catch (IOException e) { // e.printStackTrace(); // } Iterator iter; double globalIncreaseFactor = 1; Map translateVectors = null; if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.MAXSCALINGFACTOR) { // Compute increase factors for helices. Map lengthIncreaseFactor = new HashMap(); double maxLengthIncreaseFactor = Double.NEGATIVE_INFINITY; //RNATemplateHelix maxIncreaseHelix = null; iter = template.rnaIterator(); while (iter.hasNext()) { RNATemplateElement element = iter.next(); if (element instanceof RNATemplateHelix && mapping.getAncestor(element) != null && !lengthIncreaseFactor.containsKey(element)) { RNATemplateHelix helix = (RNATemplateHelix) element; int[] basesInHelixArray = RNATemplateAlign.intArrayFromList(mapping.getAncestor(helix)); Arrays.sort(basesInHelixArray); double l = computeLengthIncreaseFactor(basesInHelixArray, helix); lengthIncreaseFactor.put(helix, l); if (l > maxLengthIncreaseFactor) { maxLengthIncreaseFactor = l; //maxIncreaseHelix = helix; } } } // debug //System.out.println("Max helix length increase factor = " + maxLengthIncreaseFactor + " reached with helix " + maxIncreaseHelix);; globalIncreaseFactor = Math.max(1, maxLengthIncreaseFactor); } else if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.HELIXTRANSLATE) { try { // Now we need to propagate this helices translations Tree templateAsTree = template.toTree(); translateVectors = computeHelixTranslations(templateAsTree, mapping); } catch (ExceptionInvalidRNATemplate e) { throw (new RNATemplateDrawingAlgorithmException("ExceptionInvalidRNATemplate: " + e.getMessage())); } } // Allocate the coords and centers arrays // We create Point2D.Double objects in it but the algorithms // we use may choose to create new Point2D.Double objects or to // modify those created here. Point2D.Double[] coords = new Point2D.Double[_listeBases.size()]; Point2D.Double[] centers = new Point2D.Double[_listeBases.size()]; double[] angles = new double[_listeBases.size()]; for (int i = 0; i < _listeBases.size(); i++) { coords[i] = new Point2D.Double(0, 0); centers[i] = new Point2D.Double(0, 0); } boolean computeCoords = true; while (computeCoords) { computeCoords = false; // Compute coords and centers Set alreadyDrawnHelixes = new HashSet(); RNATemplateHelix lastMappedHelix = null; EdgeEndPoint howWeGotOutOfLastHelix = null; int howWeGotOutOfLastHelixBaseIndex = 0; iter = template.rnaIterator(); RNATemplateElement element = null; while (iter.hasNext()) { element = iter.next(); if (element instanceof RNATemplateHelix && mapping.getAncestor(element) != null) { // We have a mapping between an helix in the RNA sequence // and an helix in the template. RNATemplateHelix helix = (RNATemplateHelix) element; boolean firstTimeWeMeetThisHelix; int[] basesInHelixArray = RNATemplateAlign.intArrayFromList(mapping.getAncestor(helix)); Arrays.sort(basesInHelixArray); // Draw this helix if it has not already been done if (!alreadyDrawnHelixes.contains(helix)) { firstTimeWeMeetThisHelix = true; drawHelixLikeTemplateHelix(basesInHelixArray, helix, coords, centers,angles, globalIncreaseFactor, translateVectors); alreadyDrawnHelixes.add(helix); } else { firstTimeWeMeetThisHelix = false; } EdgeEndPoint howWeGetInCurrentHelix; if (firstTimeWeMeetThisHelix) { if (helix.getIn1Is() == In1Is.IN1_IS_5PRIME) { howWeGetInCurrentHelix = helix.getIn1(); } else { howWeGetInCurrentHelix = helix.getIn2(); } } else { if (helix.getIn1Is() == In1Is.IN1_IS_5PRIME) { howWeGetInCurrentHelix = helix.getIn2(); } else { howWeGetInCurrentHelix = helix.getIn1(); } } Point2D.Double P0 = new Point2D.Double(); Point2D.Double P3 = new Point2D.Double(); if (lastMappedHelix != null) { // Now draw the RNA sequence (possibly containing helixes) // between the last template drawn helix and this one. if (lastMappedHelix == helix) { // Last helix is the same as the current one so // nothing matched (or at best a single // non-paired sequence) so we will just // use the Radiate algorithm Point2D.Double helixVector = new Point2D.Double(); computeHelixEndPointDirections(howWeGotOutOfLastHelix, helixVector, new Point2D.Double()); double angle = MiscGeom.angleFromVector(helixVector); int b1 = basesInHelixArray[basesInHelixArray.length/2 - 1]; P0.setLocation(coords[b1]); int b2 = basesInHelixArray[basesInHelixArray.length/2]; P3.setLocation(coords[b2]); Point2D.Double loopCenter = new Point2D.Double((P0.x + P3.x)/2, (P0.y + P3.y)/2); rna.drawLoop(b1, b2, loopCenter.x, loopCenter.y, angle, coords, centers, angles); // If the helix is flipped, we need to compute the symmetric // of the whole loop. if (helix.isFlipped()) { symmetric(loopCenter, helixVector, coords, b1, b2); symmetric(loopCenter, helixVector, centers, b1, b2); } } else { // No helices matched between the last helix and // the current one, so we draw what is between // using the radiate algorithm but on the Bezier curve. int b1 = howWeGotOutOfLastHelixBaseIndex; int b2 = firstTimeWeMeetThisHelix ? basesInHelixArray[0] : basesInHelixArray[basesInHelixArray.length/2]; P0.setLocation(coords[b1]); P3.setLocation(coords[b2]); Point2D.Double P1, P2; if (howWeGotOutOfLastHelix.getOtherElement() instanceof RNATemplateUnpairedSequence && howWeGetInCurrentHelix.getOtherElement() instanceof RNATemplateUnpairedSequence) { // We will draw the bases on a Bezier curve P1 = new Point2D.Double(); computeBezierTangentVectorTarget(howWeGotOutOfLastHelix, P0, P1); P2 = new Point2D.Double(); computeBezierTangentVectorTarget(howWeGetInCurrentHelix, P3, P2); } else { // We will draw the bases on a straight line between P0 and P3 P1 = null; P2 = null; } drawAlongCurve(b1, b2, P0, P1, P2, P3, coords, centers, angles, curveMethod, lastMappedHelix.isFlipped()); } } else if (basesInHelixArray[0] > 0) { // Here we draw what is before the first mapped helix. RNATemplateUnpairedSequence templateSequence; // Try to find our template sequence as the mapped element of base 0 RNATemplateElement templateSequenceCandidate = mapping.getPartner(0); if (templateSequenceCandidate != null && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) { templateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate; } else { // Try other idea: first template element if it is a sequence templateSequenceCandidate = template.getFirst(); if (templateSequenceCandidate != null && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) { templateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate; } else { // We don't know where to start templateSequence = null; } } int b1 = 0; int b2 = firstTimeWeMeetThisHelix ? basesInHelixArray[0] : basesInHelixArray[basesInHelixArray.length/2]; P3.setLocation(coords[b2]); if (templateSequence != null) { coords[0].setLocation(templateSequence.getVertex5()); coords[0].x *= globalIncreaseFactor; coords[0].y *= globalIncreaseFactor; } else { // Put b1 at an ideal distance from b2, using the "flat exterior loop" method double idealLength = computeStraightLineIdealLength(b1, b2); Point2D.Double j = new Point2D.Double(); if (howWeGetInCurrentHelix != null) { computeHelixEndPointDirections(howWeGetInCurrentHelix, new Point2D.Double(), j); } else { j.setLocation(1, 0); } coords[b1].setLocation(coords[b2].x + j.x*idealLength, coords[b2].y + j.y*idealLength); } P0.setLocation(coords[0]); Point2D.Double P1, P2; if (howWeGetInCurrentHelix.getOtherElement() instanceof RNATemplateUnpairedSequence && templateSequence != null) { // We will draw the bases on a Bezier curve P1 = new Point2D.Double(); computeBezierTangentVectorTarget(templateSequence.getIn(), P0, P1); P2 = new Point2D.Double(); computeBezierTangentVectorTarget(howWeGetInCurrentHelix, P3, P2); } else { // We will draw the bases on a straight line between P0 and P3 P1 = null; P2 = null; } drawAlongCurve(b1, b2, P0, P1, P2, P3, coords, centers, angles, curveMethod, false); } lastMappedHelix = helix; howWeGotOutOfLastHelix = howWeGetInCurrentHelix.getNextEndPoint(); if (firstTimeWeMeetThisHelix) { howWeGotOutOfLastHelixBaseIndex = basesInHelixArray[basesInHelixArray.length/2-1]; } else { howWeGotOutOfLastHelixBaseIndex = basesInHelixArray[basesInHelixArray.length-1]; } } } // end template iteration // Now we need to draw what is after the last mapped helix. if (howWeGotOutOfLastHelixBaseIndex < coords.length-1 && element != null && coords.length > 1) { RNATemplateUnpairedSequence beginTemplateSequence = null; if (lastMappedHelix == null) { // No helix at all matched between the template and RNA! // So the sequence we want to draw is the full RNA. // Try to find our template sequence as the mapped element of base 0 RNATemplateElement templateSequenceCandidate = mapping.getPartner(0); if (templateSequenceCandidate != null && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) { beginTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate; } else { // Try other idea: first template element if it is a sequence templateSequenceCandidate = template.getFirst(); if (templateSequenceCandidate != null && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) { beginTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate; } else { // We don't know where to start beginTemplateSequence = null; } } if (beginTemplateSequence != null) { coords[0].setLocation(beginTemplateSequence.getVertex5()); coords[0].x *= globalIncreaseFactor; coords[0].y *= globalIncreaseFactor; } } RNATemplateUnpairedSequence endTemplateSequence; // Try to find our template sequence as the mapped element of last base RNATemplateElement templateSequenceCandidate = mapping.getPartner(coords.length-1); if (templateSequenceCandidate != null && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) { endTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate; } else { // Try other idea: last template element if it is a sequence templateSequenceCandidate = element; if (templateSequenceCandidate != null && templateSequenceCandidate instanceof RNATemplateUnpairedSequence) { endTemplateSequence = (RNATemplateUnpairedSequence) templateSequenceCandidate; } else { // We don't know where to end endTemplateSequence = null; } } int b1 = howWeGotOutOfLastHelixBaseIndex; int b2 = coords.length - 1; if (endTemplateSequence != null) { coords[b2].setLocation(endTemplateSequence.getVertex3()); coords[b2].x *= globalIncreaseFactor; coords[b2].y *= globalIncreaseFactor; } else { // Put b2 at an ideal distance from b1, using the "flat exterior loop" method double idealLength = computeStraightLineIdealLength(b1, b2); Point2D.Double j = new Point2D.Double(); if (howWeGotOutOfLastHelix != null) { computeHelixEndPointDirections(howWeGotOutOfLastHelix, new Point2D.Double(), j); } else { j.setLocation(1, 0); } coords[b2].setLocation(coords[b1].x + j.x*idealLength, coords[b1].y + j.y*idealLength); } Point2D.Double P0 = new Point2D.Double(); Point2D.Double P3 = new Point2D.Double(); P0.setLocation(coords[b1]); P3.setLocation(coords[b2]); Point2D.Double P1, P2; if (howWeGotOutOfLastHelix != null && howWeGotOutOfLastHelix.getOtherElement() instanceof RNATemplateUnpairedSequence && endTemplateSequence != null) { // We will draw the bases on a Bezier curve P1 = new Point2D.Double(); computeBezierTangentVectorTarget(howWeGotOutOfLastHelix, P0, P1); P2 = new Point2D.Double(); computeBezierTangentVectorTarget(endTemplateSequence.getOut(), P3, P2); } else if (lastMappedHelix == null && beginTemplateSequence != null && endTemplateSequence != null) { // We will draw the bases on a Bezier curve P1 = new Point2D.Double(); computeBezierTangentVectorTarget(beginTemplateSequence.getIn(), P0, P1); P2 = new Point2D.Double(); computeBezierTangentVectorTarget(endTemplateSequence.getOut(), P3, P2); } else { // We will draw the bases on a straight line between P0 and P3 P1 = null; P2 = null; } drawAlongCurve(b1, b2, P0, P1, P2, P3, coords, centers, angles, curveMethod, lastMappedHelix != null ? lastMappedHelix.isFlipped() : false); } if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.NOINTERSECT && coords.length > 3) { // Are we happy with this value of globalIncreaseFactor? Line2D.Double[] lines = new Line2D.Double[coords.length-1]; for (int i=0; i 0) { // Don't increase more than a maximum value if (globalIncreaseFactor < 3) { globalIncreaseFactor += 0.1; //System.out.println("globalIncreaseFactor increased to " + globalIncreaseFactor); // Compute the drawing again computeCoords = true; } } } } // debug if (helixLengthAdjustmentMethod == DrawRNATemplateMethod.MAXSCALINGFACTOR || helixLengthAdjustmentMethod == DrawRNATemplateMethod.NOINTERSECT) { //System.out.println("globalIncreaseFactor = " + globalIncreaseFactor); } // Now we actually move the bases, according to arrays coords and centers // and taking in account the space between bases parameter. for (int i = 0; i < _listeBases.size(); i++) { _listeBases.get(i).setCoords( new Point2D.Double(coords[i].x * conf._spaceBetweenBases, coords[i].y * conf._spaceBetweenBases)); _listeBases.get(i).setCenter( new Point2D.Double(centers[i].x * conf._spaceBetweenBases, centers[i].y * conf._spaceBetweenBases)); } } /** * IN: Argument helixEndPoint is an IN argument (will be read), * and must contain an helix edge endpoint. * * The other arguments are OUT arguments * (must be existing objects, content will be overwritten). * * OUT: The i argument will contain a vector colinear to the vector * from the helix startPosition to endPosition or the opposite * depending on there the endpoint is (the endpoint will be on the * destination side of the vector). ||i|| = 1 * * OUT: The j vector will contain an vector that is colinear * to the last/first base pair connection on the side of this endpoint. * The vector will be oriented to the side of the given endpoint. * ||j|| = 1 */ private void computeHelixEndPointDirections( EdgeEndPoint helixEndPoint, // IN Point2D.Double i, // OUT Point2D.Double j // OUT ) { RNATemplateHelix helix = (RNATemplateHelix) helixEndPoint.getElement(); Point2D.Double startpos = helix.getStartPosition(); Point2D.Double endpos = helix.getEndPosition(); Point2D.Double helixVector = new Point2D.Double(); switch (helixEndPoint.getPosition()) { case IN1: case OUT2: helixVector.x = startpos.x - endpos.x; helixVector.y = startpos.y - endpos.y; break; case IN2: case OUT1: helixVector.x = endpos.x - startpos.x; helixVector.y = endpos.y - startpos.y; break; } double helixVectorLength = Math.hypot(helixVector.x, helixVector.y); // i is the vector which is colinear to helixVector and such that ||i|| = 1 i.x = helixVector.x / helixVectorLength; i.y = helixVector.y / helixVectorLength; // Find j such that it is orthogonal to i, ||j|| = 1 // and j goes to the side where the sequence will be connected switch (helixEndPoint.getPosition()) { case IN1: case IN2: // rotation of +pi/2 j.x = - i.y; j.y = i.x; break; case OUT1: case OUT2: // rotation of -pi/2 j.x = i.y; j.y = - i.x; break; } if (helix.isFlipped()) { j.x = - j.x; j.y = - j.y; } } /** * A cubic Bezier curve can be defined by 4 points, * see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves * For each of the curve end points, there is the last/first point of the * curve and a point which gives the direction and length of the tangent * vector on that side. This two points are respectively curveEndPoint * and curveVectorOtherPoint. * IN: Argument helixVector is the vector formed by the helix, * in the right direction for our sequence. * IN: Argument curveEndPoint is the position of the endpoint on the helix. * OUT: Argument curveVectorOtherPoint must be allocated * and the values will be modified. */ private void computeBezierTangentVectorTarget( EdgeEndPoint endPoint, Point2D.Double curveEndPoint, Point2D.Double curveVectorOtherPoint) throws RNATemplateDrawingAlgorithmException { boolean sequenceEndPointIsIn; RNATemplateUnpairedSequence sequence; if (endPoint.getElement() instanceof RNATemplateHelix) { sequence = (RNATemplateUnpairedSequence) endPoint.getOtherElement(); EdgeEndPointPosition endPointPositionOnHelix = endPoint.getPosition(); switch (endPointPositionOnHelix) { case IN1: case IN2: sequenceEndPointIsIn = false; break; default: sequenceEndPointIsIn = true; } EdgeEndPoint endPointOnHelix = sequenceEndPointIsIn ? sequence.getIn().getOtherEndPoint() : sequence.getOut().getOtherEndPoint(); if (endPointOnHelix == null) { throw (new RNATemplateDrawingAlgorithmException("Sequence is not connected to an helix.")); } } else { // The endpoint is on an unpaired sequence. sequence = (RNATemplateUnpairedSequence) endPoint.getElement(); if (endPoint == sequence.getIn()) { // endpoint is 5' sequenceEndPointIsIn = true; } else { sequenceEndPointIsIn = false; } } double l = sequenceEndPointIsIn ? sequence.getInTangentVectorLength() : sequence.getOutTangentVectorLength(); // Compute the absolute angle our line makes to the helix double theta = sequenceEndPointIsIn ? sequence.getInTangentVectorAngle() : sequence.getOutTangentVectorAngle(); // Compute v, the tangent vector of the Bezier curve Point2D.Double v = new Point2D.Double(); v.x = l * Math.cos(theta); v.y = l * Math.sin(theta); curveVectorOtherPoint.x = curveEndPoint.x + v.x; curveVectorOtherPoint.y = curveEndPoint.y + v.y; } /** * Compute (actual helix length / helix length in template). */ private double computeLengthIncreaseFactor( int[] basesInHelixArray, // IN RNATemplateHelix helix // IN ) { double templateLength = computeHelixTemplateLength(helix); double realLength = computeHelixRealLength(basesInHelixArray); return realLength / templateLength; } /** * Compute (actual helix vector - helix vector in template). */ private Point2D.Double computeLengthIncreaseDelta( int[] basesInHelixArray, // IN RNATemplateHelix helix // IN ) { double templateLength = computeHelixTemplateLength(helix); double realLength = computeHelixRealLength(basesInHelixArray); Point2D.Double i = new Point2D.Double(); computeTemplateHelixVectors(helix, null, i, null); return new Point2D.Double(i.x*(realLength-templateLength), i.y*(realLength-templateLength)); } /** * Compute helix interesting vectors from template helix. * @param helix The template helix you want to compute the vectors from. * @param o This point coordinates will be set the origin of the helix (or not if null), * ie. the point in the middle of the base pair with the two most extreme bases. * @param i Will be set to the normalized helix vector. (nothing done if null) * @param j Will be set to the normalized helix base pair vector (5' -> 3'). (nothing done if null) */ private void computeTemplateHelixVectors( RNATemplateHelix helix, // IN Point2D.Double o, // OUT Point2D.Double i, // OUT Point2D.Double j // OUT ) { Point2D.Double startpos, endpos; if (helix.getIn1Is() == In1Is.IN1_IS_5PRIME) { startpos = helix.getStartPosition(); endpos = helix.getEndPosition(); } else { endpos = helix.getStartPosition(); startpos = helix.getEndPosition(); } if (o != null) { o.x = startpos.x; o.y = startpos.y; } if (i != null || j != null) { // (i_x,i_y) is the vector between two consecutive bases of the same side of an helix if (i == null) i = new Point2D.Double(); i.x = (endpos.x - startpos.x); i.y = (endpos.y - startpos.y); double i_original_norm = Math.hypot(i.x, i.y); // change its norm to 1 i.x = i.x / i_original_norm; i.y = i.y / i_original_norm; if (j != null) { j.x = - i.y; j.y = i.x; if (helix.isFlipped()) { j.x = - j.x; j.y = - j.y; } double j_original_norm = Math.hypot(j.x, j.y); // change (j_x,j_y) so that its norm is 1 j.x = j.x / j_original_norm; j.y = j.y / j_original_norm; } } } /** * Estimate bulge arc length. */ private double estimateBulgeArcLength(int firstBase, int lastBase) { if (firstBase + 1 == lastBase) return RNA.LOOP_DISTANCE; // there is actually no bulge double len = 0.0; int k = firstBase; while (k < lastBase) { int l = _listeBases.get(k).getElementStructure(); if (k < l && l < lastBase) { len += RNA.BASE_PAIR_DISTANCE; k = l; } else { len += RNA.LOOP_DISTANCE; k++; } } return len; } /** * Estimate bulge width, the given first and last bases must be those in the helix. */ private double estimateBulgeWidth(int firstBase, int lastBase) { double len = estimateBulgeArcLength(firstBase, lastBase); return 2 * (len / Math.PI); } /** * Get helix length in template. */ private double computeHelixTemplateLength(RNATemplateHelix helix) { return Math.hypot(helix.getStartPosition().x - helix.getEndPosition().x, helix.getStartPosition().y - helix.getEndPosition().y); } /** * Compute helix actual length (as drawHelixLikeTemplateHelix() would draw it). */ private double computeHelixRealLength(int[] basesInHelixArray) { return drawHelixLikeTemplateHelix(basesInHelixArray, null, null, null, null, 0, null); } /** * Result type of countUnpairedLine(), see below. */ private static class UnpairedLineCounts { public int nBP, nLD, total; } /** * If we are drawing an unpaired region that may contains helices, * and we are drawing it on a line (curve or straight, doesn't matter), * how many intervals should have a base-pair length (start of an helix) * and how many should have a consecutive unpaired bases length? * Returns an array with three elements: * - answer to first question * - answer to second question * - sum of both, ie. total number of intervals * (this is NOT lastBase-firstBase because bases deep in helices do not count) */ private UnpairedLineCounts countUnpairedLine(int firstBase, int lastBase) { UnpairedLineCounts counts = new UnpairedLineCounts(); int nBP = 0; int nLD = 0; { int b = firstBase; while (b < lastBase) { int l = _listeBases.get(b).getElementStructure(); if (b < l && l < lastBase) { nBP++; b = l; } else { nLD++; b++; } } } counts.nBP = nBP; counts.nLD = nLD; counts.total = nBP + nLD; return counts; } /** * Draw the given helix (given as a *SORTED* array of indexes) * like defined in the given template helix. * OUT: The bases positions are not changed in fact, * instead the coords and centers arrays are modified. * IN: The helix origin position is multiplied by scaleHelixOrigin * and translateVectors.get(helix) is added. * RETURN VALUE: * The length of the drawn helix. * */ private double drawHelixLikeTemplateHelix( int[] basesInHelixArray, // IN RNATemplateHelix helix, // IN (optional, ie. may be null) Point2D.Double[] coords, // OUT (optional, ie. may be null) Point2D.Double[] centers, // OUT (optional, ie. may be null) double[] angles, // OUT double scaleHelixOrigin, // IN Map translateVectors // IN (optional, ie. may be null) ) { int n = basesInHelixArray.length / 2; if (n == 0) return 0; // Default values when not template helix is provided: Point2D.Double o = new Point2D.Double(0, 0); Point2D.Double i = new Point2D.Double(1, 0); Point2D.Double j = new Point2D.Double(0, 1); boolean flipped = false; if (helix != null) { computeTemplateHelixVectors(helix, o, i, j); flipped = helix.isFlipped(); } Point2D.Double li = new Point2D.Double(i.x*RNA.LOOP_DISTANCE, i.y*RNA.LOOP_DISTANCE); // We want o to be the point where the first base (5' end) is o.x = (o.x - j.x * RNA.BASE_PAIR_DISTANCE / 2) * scaleHelixOrigin; o.y = (o.y - j.y * RNA.BASE_PAIR_DISTANCE / 2) * scaleHelixOrigin; if (translateVectors != null && translateVectors.containsKey(helix)) { Point2D.Double v = translateVectors.get(helix); o.x = o.x + v.x; o.y = o.y + v.y; } // We need this array so that we can store positions even if coords == null Point2D.Double[] helixBasesPositions = new Point2D.Double[basesInHelixArray.length]; for (int k=0; k= 1 && (basesInHelixArray[k] != basesInHelixArray[k-1] + 1 || basesInHelixArray[kp+1] != basesInHelixArray[kp] + 1); if (k >= 1) { if (basesInHelixArray[k] < basesInHelixArray[k-1] || basesInHelixArray[kp+1] < basesInHelixArray[kp]) { throw new Error("Internal bug: basesInHelixArray must be sorted"); } if (bulge) { // Estimate a good distance (delta) between the previous base pair and this one double delta1 = estimateBulgeWidth(basesInHelixArray[k-1], basesInHelixArray[k]); double delta2 = estimateBulgeWidth(basesInHelixArray[kp], basesInHelixArray[kp+1]); // The biggest bulge defines the width double delta = Math.max(delta1, delta2); if (coords != null) { // Now, where do we put the bases that are part of the bulge? for (int side=0; side<2; side++) { Point2D.Double pstart = new Point2D.Double(); Point2D.Double pend = new Point2D.Double(); Point2D.Double bisectVect = new Point2D.Double(); Point2D.Double is = new Point2D.Double(); int firstBase, lastBase; double alphasign = flipped ? -1 : 1; if (side == 0) { firstBase = basesInHelixArray[k-1]; lastBase = basesInHelixArray[k]; pstart.setLocation(o.x + accDelta.x, o.y + accDelta.y); pend.setLocation(o.x + accDelta.x + i.x*delta, o.y + accDelta.y + i.y*delta); bisectVect.setLocation(-j.x, -j.y); is.setLocation(i); } else { firstBase = basesInHelixArray[kp]; lastBase = basesInHelixArray[kp+1]; pstart.setLocation(o.x + accDelta.x + i.x*delta + j.x*RNA.BASE_PAIR_DISTANCE, o.y + accDelta.y + i.y*delta + j.y*RNA.BASE_PAIR_DISTANCE); pend.setLocation(o.x + accDelta.x + j.x*RNA.BASE_PAIR_DISTANCE, o.y + accDelta.y + j.y*RNA.BASE_PAIR_DISTANCE); bisectVect.setLocation(j); is.setLocation(-i.x, -i.y); } double arclen = estimateBulgeArcLength(firstBase, lastBase); double centerOnBisect = ComputeArcCenter.computeArcCenter(delta, arclen); // Should we draw the base on an arc or simply use a line? if (centerOnBisect > -1000) { Point2D.Double center = new Point2D.Double(pstart.x + is.x*delta/2 + bisectVect.x*centerOnBisect, pstart.y + is.y*delta/2 + bisectVect.y*centerOnBisect); int b = firstBase; double len = 0; double r = Math.hypot(pstart.x - center.x, pstart.y - center.y); double alpha0 = MiscGeom.angleFromVector(pstart.x - center.x, pstart.y - center.y); while (b < lastBase) { int l = _listeBases.get(b).getElementStructure(); if (b < l && l < lastBase) { len += RNA.BASE_PAIR_DISTANCE; b = l; } else { len += RNA.LOOP_DISTANCE; b++; } if (b < lastBase) { coords[b].x = center.x + r*Math.cos(alpha0 + alphasign*len/r); coords[b].y = center.y + r*Math.sin(alpha0 + alphasign*len/r); } } } else { // Draw on a line // Distance between paired bases cannot be changed // (imposed by helix width) but distance between other // bases can be adjusted. UnpairedLineCounts counts = countUnpairedLine(firstBase, lastBase); double LD = Math.max((delta - counts.nBP*RNA.BASE_PAIR_DISTANCE) / (double) counts.nLD, 0); //System.out.println("nBP=" + nBP + " nLD=" + nLD); double len = 0; { int b = firstBase; while (b < lastBase) { int l = _listeBases.get(b).getElementStructure(); if (b < l && l < lastBase) { len += RNA.BASE_PAIR_DISTANCE; b = l; } else { len += LD; b++; } if (b < lastBase) { coords[b].x = pstart.x + is.x*len; coords[b].y = pstart.y + is.y*len; } } } //System.out.println("len=" + len + " delta=" + delta + " d(pstart,pend)=" + Math.hypot(pend.x-pstart.x, pend.y-pstart.y)); } // Does the bulge contain an helix? // If so, use drawLoop() to draw it. { int b = firstBase; while (b < lastBase) { int l = _listeBases.get(b).getElementStructure(); if (b < l && l < lastBase) { // Helix present in bulge Point2D.Double b1pos = coords[b]; Point2D.Double b2pos = coords[l]; double beta = MiscGeom.angleFromVector(b2pos.x - b1pos.x, b2pos.y - b1pos.y) - Math.PI / 2 + (flipped ? Math.PI : 0); Point2D.Double loopCenter = new Point2D.Double((b1pos.x + b2pos.x)/2, (b1pos.y + b2pos.y)/2); rna.drawLoop(b, l, loopCenter.x, loopCenter.y, beta, coords, centers, angles); // If the helix is flipped, we need to compute the symmetric // of the whole loop. if (helix.isFlipped()) { Point2D.Double v = new Point2D.Double(Math.cos(beta), Math.sin(beta)); symmetric(loopCenter, v, coords, b, l); symmetric(loopCenter, v, centers, b, l); } // Continue b = l; } else { b++; } } } } } accDelta.x += i.x*delta; accDelta.y += i.y*delta; p1.x = o.x + accDelta.x; p1.y = o.y + accDelta.y; p2.x = p1.x + j.x*RNA.BASE_PAIR_DISTANCE; p2.y = p1.y + j.y*RNA.BASE_PAIR_DISTANCE; } else { accDelta.x += li.x; accDelta.y += li.y; p1.x = o.x + accDelta.x; p1.y = o.y + accDelta.y; p2.x = p1.x + j.x*RNA.BASE_PAIR_DISTANCE; p2.y = p1.y + j.y*RNA.BASE_PAIR_DISTANCE; } } else { // First base pair p1.x = o.x; p1.y = o.y; p2.x = p1.x + j.x*RNA.BASE_PAIR_DISTANCE; p2.y = p1.y + j.y*RNA.BASE_PAIR_DISTANCE; } } Point2D.Double p1 = helixBasesPositions[0]; Point2D.Double p2 = helixBasesPositions[n-1]; if (coords != null) { for (int k=0; k alongBezierCurve = new ArrayList(); for (int depth=0, i=firstBase; i<=lastBase; i++) { int k = _listeBases.get(i).getElementStructure(); if (k < 0 || k > lastBase || k < firstBase) { if (depth == 0) { alongBezierCurve.add(i); } } else { if (i < k) { if (depth == 0) { alongBezierCurve.add(i); alongBezierCurve.add(k); } depth++; } else { depth--; } } } // number of bases along the Bezier curve int n = alongBezierCurve.size(); int[] alongBezierCurveArray = RNATemplateAlign.intArrayFromList(alongBezierCurve); if (n > 0) { if (curveMethod == DrawRNATemplateCurveMethod.ALWAYS_REPLACE_BY_ELLIPSES) { drawOnEllipse(firstBase, lastBase, P0, P3, coords, centers, reverse); } else if (curveMethod == DrawRNATemplateCurveMethod.SMART) { boolean passed; if (P1 != null && P2 != null) { passed = drawOnBezierCurve(firstBase, lastBase, P0, P1, P2, P3, coords, centers, true); } else { passed = drawOnStraightLine(firstBase, lastBase, P0, P3, coords, centers, true); } if (!passed) { drawOnEllipse(firstBase, lastBase, P0, P3, coords, centers, reverse); } } else { if (P1 != null && P2 != null) { drawOnBezierCurve(firstBase, lastBase, P0, P1, P2, P3, coords, centers, false); } else { drawOnStraightLine(firstBase, lastBase, P0, P3, coords, centers, false); } } } // Now use the radiate algorithm to draw the helixes for (int k=0; k tree, // IN Map translateVectors, // OUT (must be initialized) RNATemplateMapping mapping, // IN Point2D.Double parentDeltaVector // IN ) { RNANodeValueTemplate nvt = tree.getValue(); Point2D.Double newDeltaVector = parentDeltaVector; if (nvt instanceof RNANodeValueTemplateBasePair) { RNATemplateHelix helix = ((RNANodeValueTemplateBasePair) nvt).getHelix(); if (! translateVectors.containsKey(helix)) { translateVectors.put(helix, parentDeltaVector); int[] basesInHelixArray; if (mapping.getAncestor(helix) != null) { basesInHelixArray = RNATemplateAlign.intArrayFromList(mapping.getAncestor(helix)); Arrays.sort(basesInHelixArray); } else { basesInHelixArray = new int[0]; } Point2D.Double helixDeltaVector = computeLengthIncreaseDelta(basesInHelixArray, helix); newDeltaVector = new Point2D.Double(parentDeltaVector.x+helixDeltaVector.x, parentDeltaVector.y+helixDeltaVector.y); } } for (Tree subtree: tree.getChildren()) { computeHelixTranslations(subtree, translateVectors, mapping, newDeltaVector); } } private Map computeHelixTranslations( Tree tree, // IN RNATemplateMapping mapping // IN ) { Map translateVectors = new HashMap(); computeHelixTranslations(tree, translateVectors, mapping, new Point2D.Double(0,0)); return translateVectors; } } fr/orsay/lri/varna/models/rna/ModeleBP.java0000644000000000000000000002360011722525122017552 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.rna; import java.awt.Color; import java.io.Serializable; import java.util.ArrayList; import java.util.Random; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.models.VARNAConfig; public class ModeleBP implements Serializable, Comparable { /** * */ private static final long serialVersionUID = -1344722280822711931L; public enum Edge { WC, SUGAR, HOOGSTEEN; } public enum Stericity { CIS, TRANS; } private ModeleBase _partner5; private Edge _edge5; private ModeleBase _partner3; private Edge _edge3; private Stericity _stericity; private ModeleBPStyle _style; public static String XML_ELEMENT_NAME = "bp"; public static String XML_VAR_PARTNER5_NAME = "part5"; public static String XML_VAR_EDGE5_NAME = "edge5"; public static String XML_VAR_PARTNER3_NAME = "part3"; public static String XML_VAR_EDGE3_NAME = "edge3"; public static String XML_VAR_STERICITY_NAME = "orient"; public static String XML_VAR_SEC_STR_NAME = "secstr"; public void toXML(TransformerHandler hd, boolean inSecondaryStructure) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_PARTNER5_NAME,"CDATA",""+_partner5.getIndex()); atts.addAttribute("","",XML_VAR_PARTNER3_NAME,"CDATA",""+_partner3.getIndex()); atts.addAttribute("","",XML_VAR_EDGE5_NAME,"CDATA",""+_edge5); atts.addAttribute("","",XML_VAR_EDGE3_NAME,"CDATA",""+_edge3); atts.addAttribute("","",XML_VAR_STERICITY_NAME,"CDATA",""+_stericity); atts.addAttribute("","",XML_VAR_SEC_STR_NAME,"CDATA",""+inSecondaryStructure); hd.startElement("","",XML_ELEMENT_NAME,atts); _style.toXML(hd); hd.endElement("","",XML_ELEMENT_NAME); } public void toXML(TransformerHandler hd) throws SAXException { toXML(hd, false); } public ModeleBP(ModeleBase part5, ModeleBase part3) { this(part5, part3, Edge.WC, Edge.WC, Stericity.CIS); } //private static Random rnd = new Random(System.currentTimeMillis()); public ModeleBP(ModeleBase part5, ModeleBase part3, Edge edge5, Edge edge3, Stericity ster) { _partner5 = part5; _partner3 = part3; _edge5 = edge5; _edge3 = edge3; _stericity = ster; _style = new ModeleBPStyle(); } public ModeleBP(String text) throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError { _style = new ModeleBPStyle(); assignParameters(text); } public void setStericity(Stericity s) { _stericity = s; } public void setEdge5(Edge e) { _edge5 = e; } public void setEdge3(Edge e) { _edge3 = e; } public void setStyle(ModeleBPStyle e) { _style = e; } public ModeleBPStyle getStyle() { return _style; } public boolean isCanonicalGC() { String si = _partner5.getContent(); String sj = _partner3.getContent(); if ((si.length() >= 1) && (sj.length() >= 1)) { char ci = si.toUpperCase().charAt(0); char cj = sj.toUpperCase().charAt(0); if (((ci == 'G') && (cj == 'C')) || ((ci == 'C') && (cj == 'G'))) { return isCanonical() && (getStericity() == Stericity.CIS); } } return false; } public boolean isCanonicalAU() { String si = _partner5.getContent(); String sj = _partner3.getContent(); if ((si.length() >= 1) && (sj.length() >= 1)) { char ci = si.toUpperCase().charAt(0); char cj = sj.toUpperCase().charAt(0); if (((ci == 'A') && (cj == 'U')) || ((ci == 'U') && (cj == 'A'))) { return isCanonical(); } } return false; } public boolean isWobbleUG() { String si = _partner5.getContent(); String sj = _partner3.getContent(); if ((si.length() >= 1) && (sj.length() >= 1)) { char ci = si.toUpperCase().charAt(0); char cj = sj.toUpperCase().charAt(0); if (((ci == 'G') && (cj == 'U')) || ((ci == 'U') && (cj == 'G'))) { return (isCanonical()); } } return false; } public boolean isCanonical() { return (_edge5 == Edge.WC) && (_edge3 == Edge.WC) && (_stericity == Stericity.CIS); } public Stericity getStericity() { return _stericity; } public boolean isCIS() { return (_stericity == Stericity.CIS); } public boolean isTRANS() { return (_stericity == Stericity.TRANS); } public Edge getEdgePartner5() { return _edge5; } public Edge getEdgePartner3() { return _edge3; } public ModeleBase getPartner(ModeleBase mb) { if (mb == _partner3) return _partner5; else return _partner3; } public ModeleBase getPartner5() { return _partner5; } public ModeleBase getPartner3() { return _partner3; } public int getIndex5() { return _partner5.getIndex(); } public int getIndex3() { return _partner3.getIndex(); } public void setPartner5(ModeleBase mb) { _partner5 = mb; } public void setPartner3(ModeleBase mb) { _partner3 = mb; } public static final String PARAM_COLOR = "color"; public static final String PARAM_THICKNESS = "thickness"; public static final String PARAM_EDGE5 = "edge5"; public static final String PARAM_EDGE3 = "edge3"; public static final String PARAM_STERICITY = "stericity"; public static final String VALUE_WATSON_CRICK = "wc"; public static final String VALUE_HOOGSTEEN = "h"; public static final String VALUE_SUGAR = "s"; public static final String VALUE_CIS = "cis"; public static final String VALUE_TRANS = "trans"; public void assignParameters(String parametersValue) throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError { if (parametersValue.equals("")) return; String[] parametersL = parametersValue.split(","); ArrayList namesArray = new ArrayList(); ArrayList valuesArray = new ArrayList(); String[] param; for (int i = 0; i < parametersL.length; i++) { param = parametersL[i].split("="); if (param.length != 2) throw new ExceptionModeleStyleBaseSyntaxError( "Bad parameter: '" + param[0] + "' ..."); namesArray.add(param[0].replace(" ", "")); valuesArray.add(param[1].replace(" ", "")); } for (int i = 0; i < namesArray.size(); i++) { if (namesArray.get(i).toLowerCase().equals(PARAM_COLOR)) { try { _style.setCustomColor(ModelBaseStyle .getSafeColor(valuesArray.get(i))); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "Bad inner color Syntax:" + valuesArray.get(i)); } } else if (namesArray.get(i).toLowerCase().equals(PARAM_THICKNESS)) { try { _style.setThickness(Double.parseDouble(valuesArray.get(i))); } catch (NumberFormatException e) { throw new ExceptionParameterError(e.getMessage(), "Bad value for bp thickness:" + valuesArray.get(i)); } } else if (namesArray.get(i).toLowerCase().equals(PARAM_EDGE5)) { String s = valuesArray.get(i); if (s.toLowerCase().equals(VALUE_WATSON_CRICK)) { setEdge5(Edge.WC); } else if (s.toLowerCase().equals(VALUE_HOOGSTEEN)) { setEdge5(Edge.HOOGSTEEN); } else if (s.toLowerCase().equals(VALUE_SUGAR)) { setEdge5(Edge.SUGAR); } else throw new ExceptionParameterError("Bad value for edge:" + valuesArray.get(i)); } else if (namesArray.get(i).toLowerCase().equals(PARAM_EDGE3)) { String s = valuesArray.get(i); if (s.toLowerCase().equals(VALUE_WATSON_CRICK)) { setEdge3(Edge.WC); } else if (s.toLowerCase().equals(VALUE_HOOGSTEEN)) { setEdge3(Edge.HOOGSTEEN); } else if (s.toLowerCase().equals(VALUE_SUGAR)) { setEdge3(Edge.SUGAR); } else throw new ExceptionParameterError("Bad value for edge:" + valuesArray.get(i)); } else if (namesArray.get(i).toLowerCase().equals(PARAM_STERICITY)) { String s = valuesArray.get(i); if (s.toLowerCase().equals(VALUE_CIS)) { setStericity(Stericity.CIS); } else if (s.toLowerCase().equals(VALUE_TRANS)) { setStericity(Stericity.TRANS); } else throw new ExceptionParameterError( "Bad value for stericity:" + valuesArray.get(i)); } else throw new ExceptionModeleStyleBaseSyntaxError( "Unknown parameter:" + namesArray.get(i)); } } public String toString() { String result = ""; result += "(" + _partner5.getIndex() + "," + _partner3.getIndex() + ")"; //result += " [" + _partner5.getElementStructure() + "," // + _partner3.getElementStructure() + "]\n"; //result += " 5':" + _partner5 + "\n"; //result += " 3':" + _partner3; return result; } public int compareTo(ModeleBP mb) { if (getIndex5()!=mb.getIndex5()) { return getIndex5()-mb.getIndex5(); } return getIndex3()-mb.getIndex3(); } } fr/orsay/lri/varna/models/rna/VARNASecDraw.java0000644000000000000000000005667311674411620020266 0ustar rootrootpackage fr.orsay.lri.varna.models.rna; import java.awt.Rectangle; import java.awt.Shape; import java.awt.geom.AffineTransform; import java.awt.geom.Area; import java.awt.geom.GeneralPath; import java.awt.geom.PathIterator; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.lang.reflect.Array; import java.util.ArrayList; import java.util.Arrays; import java.util.LinkedList; import java.util.Random; import java.util.Stack; import java.util.Vector; import fr.orsay.lri.varna.VARNAPanel; public class VARNASecDraw { public static VARNAPanel _vp = null; public abstract class Portion { public abstract ArrayList getBaseList(); public abstract int getNumBases(); public abstract GeneralPath getOutline(RNA r); }; public class UnpairedPortion extends Portion { int _pos; int _len; public UnpairedPortion(int pos, int len) { _len = len; _pos = pos; } @Override public ArrayList getBaseList() { // TODO Auto-generated method stub return null; } public String toString() { return "U["+_pos+","+(_pos+_len-1)+"]"; } public int getNumBases() { return _len; } public GeneralPath getOutline(RNA r) { GeneralPath gp = new GeneralPath(); ArrayList l = r.get_listeBases(); Point2D.Double p0 = l.get(_pos).getCoords(); gp.moveTo((float)p0.x, (float)p0.y); for (int i=1;i<_len;i++) { Point2D.Double p = l.get(_pos+i).getCoords(); gp.lineTo((float)p.x, (float)p.y); } return gp; } }; public class PairedPortion extends Portion { int _pos1; int _pos2; int _len; RNATree _r; public PairedPortion(int pos1,int pos2, int len, RNATree r) { _pos1 = pos1; _pos2 = pos2; _len = len; _r =r; } @Override public ArrayList getBaseList() { // TODO Auto-generated method stub return null; } public String toString() { return "H["+_pos1+","+(_pos1+_len-1)+"]["+(_pos2-_len+1)+","+(_pos2)+"]\n"+_r.toString(); } @Override public int getNumBases() { return 2*_len; } public GeneralPath getLocalOutline(RNA r) { GeneralPath gp = new GeneralPath(); if (_len>0) { ArrayList l = r.get_listeBases(); Point2D.Double p1 = l.get(_pos1).getCoords(); Point2D.Double p2 = l.get(_pos1+_len-1).getCoords(); Point2D.Double p3 = l.get(_pos2-_len+1).getCoords(); Point2D.Double p4 = l.get(_pos2).getCoords(); gp.moveTo((float)p1.x, (float)p1.y); gp.lineTo((float)p2.x, (float)p2.y); gp.lineTo((float)p3.x, (float)p3.y); gp.lineTo((float)p4.x, (float)p4.y); } return gp; } public GeneralPath getOutline(RNA r) { return getOutline(r,false); } public GeneralPath getOutline(RNA r, boolean local) { ArrayList l = r.get_listeBases(); Point2D.Double p1 = l.get(_pos1).getCoords(); Point2D.Double p2 = l.get(_pos1+_len-1).getCoords(); Point2D.Double p3 = l.get(_pos2-_len+1).getCoords(); Point2D.Double p4 = l.get(_pos2).getCoords(); GeneralPath gp = new GeneralPath(); gp.moveTo((float)p1.x, (float)p1.y); gp.lineTo((float)p2.x, (float)p2.y); if (!local) gp.append(_r.getOutline(r), true); gp.lineTo((float)p3.x, (float)p3.y); gp.lineTo((float)p4.x, (float)p4.y); return gp; } }; public int _depth = 0; public class RNATree { ArrayList _portions = new ArrayList(); int _numPairedPortions=0; public RNATree() { } public void addPortion(Portion p) { _portions.add(p); if (p instanceof PairedPortion) { _numPairedPortions++; } } public int getNumPortions() { return _portions.size(); } public Portion getPortion(int i) { return _portions.get(i); } public String toString() { String result = ""; _depth++; for (int i=0;i<_portions.size();i++ ) { result += String.format("%1$#" + _depth + "s", ' '); result += _portions.get(i).toString(); if (i<_portions.size()-1) result += "\n"; } _depth--; return result; } public GeneralPath getOutline(RNA r) { GeneralPath result = new GeneralPath(); for (int i=0;i<_portions.size();i++) { result.append(_portions.get(i).getOutline(r),true); } return result; } }; private void buildTree(int i, int j, RNATree parent, RNA r) { //LinkedList s = new LinkedList(); //s.add(new BuildTreeArgs(xi, xj, xparent,xr)); //while(s.size()!=0) //{ //BuildTreeArgs a = s.removeLast(); if (i >= j) { parent.addPortion(new UnpairedPortion(i,j-i+1)); } // BasePaired if (r.get_listeBases().get(i).getElementStructure() == j) { int i1 = i; int j1 = j; boolean over = false; while( (i+1=0)&& (i+1<=j-1) && !over) { if (r.get_listeBases().get(i).getElementStructure() != j) { over = true; } else { i++;j--; } } int i2 = i; int j2 = j; RNATree t = new RNATree(); if (i0) { parent.addPortion(new UnpairedPortion(start,len)); } buildTree(k, l, parent, r); k = l + 1; start = k; len = 0; } else { len++; k++; } } if (len>0) { parent.addPortion(new UnpairedPortion(start,len)); } } } /* public void drawTree(double x0, double y0, RNATree t, double dir, RNA r, double straightness) { boolean collision = true; double x=x0; double y=y0; double multRadius = 1.0; double initCirc = r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE; for (int i=0;i shapes = new ArrayList(); for (int i=0;i0) { collision = false; for (int i=0;(i=0) && !stop) { if (p[i]==prev-1) { prev = p[i]; i--; } else { stop = true; } } if (i<0) throw new Exception("No more placement available"); p[i]++; i++; while(i shapes = new ArrayList(); int curH = 0; for (int i=0;i0) { collision = false; for (int i=0;(i _children = new ArrayList(); ArrayList _indices = new ArrayList(); PairedPortion _p; RNA _r; HelixEmbedding _parent; public HelixEmbedding(Point2D.Double support, PairedPortion p, RNA r, HelixEmbedding parent) { _support = support; _clip = p.getLocalOutline(r); _p = p; _r = r; _parent = parent; } public void addHelixEmbedding(HelixEmbedding h, int index) { _children.add(h); _indices.add(index); } public GeneralPath getShape() { return _clip; } public int chooseNextMove() { int i = _parent._children.indexOf(this); int min; int max; if (_parent._children.size() mbl = _r.get_listeBases(); if (_p._len>0) { PathIterator pi = _clip.getPathIterator(AffineTransform.getRotateInstance(0.0)); ArrayList p = new ArrayList(); while(!pi.isDone()) { double[] args = new double[6]; int type= pi.currentSegment(args); if ((type == PathIterator.SEG_MOVETO) || (type == PathIterator.SEG_LINETO)) { Point2D.Double np = new Point2D.Double(args[0],args[1]); p.add(np); System.out.println(Arrays.toString(args)); } pi.next(); } if (p.size()<4) { return; } Point2D.Double startLeft = p.get(0); Point2D.Double endLeft = p.get(1); Point2D.Double endRight = p.get(2); Point2D.Double startRight = p.get(3); double d = startLeft.distance(endLeft); double vx = endLeft.x-startLeft.x; double vy = endLeft.y-startLeft.y; double interval = 0.0; if (_p._len>1) { vx/=d; vy/=d; interval = d/((double)_p._len-1); System.out.println("DELTA: "+interval+" "+_r.LOOP_DISTANCE); } for (int n=0;n<_p._len;n++) { int i = _p._pos1 + n; int j = _p._pos2 - n; ModeleBase mbLeft = mbl.get(i); mbLeft.setCoords(new Point2D.Double(startLeft.x+n*vx*interval, startLeft.y+n*vy*interval)); ModeleBase mbRight = mbl.get(j); mbRight.setCoords(new Point2D.Double(startRight.x+n*vx*interval, startRight.y+n*vy*interval)); } } for (int i=0;i<_children.size();i++) { _children.get(i).reflectCoordinates(); } if (_children.size()>0) { Point2D.Double center = _children.get(0)._support; for (int i=0;i<_p._r.getNumPortions();i++) { Portion p = _p._r.getPortion(i); if (p instanceof UnpairedPortion) { UnpairedPortion up = (UnpairedPortion) p; for (int j=0;j mbl, RNA r) { if ((_children.size()==0)&&(_p._r.getNumPortions()==1)) { Portion p = _p._r.getPortion(0); if (p instanceof UnpairedPortion) { UnpairedPortion up = (UnpairedPortion) p; double rad = determineRadius(1,up.getNumBases(),_r); int a = _p._pos1+_p._len-1; int b = _p._pos2-(_p._len-1); ModeleBase mbLeft = mbl.get(a); ModeleBase mbRight = mbl.get(b); Point2D.Double pl = mbLeft.getCoords(); Point2D.Double pr = mbRight.getCoords(); Point2D.Double pm = new Point2D.Double((pl.x+pr.x)/2.0,(pl.y+pr.y)/2.0); double vx = (pl.x-pr.x)/pl.distance(pr); double vy = (pl.y-pr.y)/pl.distance(pr); double vnx = -vy, vny = vx; Point2D.Double pc = new Point2D.Double(pm.x+rad*vnx,pm.y+rad*vny); double circ = r.LOOP_DISTANCE*(1.0+up.getNumBases())+r.BASE_PAIR_DISTANCE; double incrLoop = Math.PI*2.0*r.LOOP_DISTANCE/circ; double angle = Math.PI*2.0*r.BASE_PAIR_DISTANCE/(2.0*circ); for (int j=0;j all) throws Exception { double x=x0; double y=y0; int numHelices = 0; int numUBases = 0; double totCirc = r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE; for (int i=0;i all = new ArrayList(); HelixEmbedding root = null; try { root = new HelixEmbedding(new Point2D.Double(0.0,0.0),new PairedPortion(0,0,0,t),r,null); predrawTree(0,0,t,0.0,r,root,all); int steps=1000; double prevbadness = Double.MAX_VALUE; while((steps>0)&&(prevbadness>0)) { // Generating new structure HelixEmbedding chosen = all.get(_rnd.nextInt(all.size())); int delta = chosen.chooseNextMove(); // Draw current if (_vp!=null) { GeneralPath p = new GeneralPath(); for (int i=0;i0) { chosen.cancelMove(delta); } else { prevbadness = badness; } System.out.println(badness); steps--; } if (root!=null) { root.reflectCoordinates(); } } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return t; }; }fr/orsay/lri/varna/models/rna/ModeleColorMap.java0000644000000000000000000002027712464217670021006 0ustar rootrootpackage fr.orsay.lri.varna.models.rna; import java.awt.Color; import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.StreamTokenizer; import java.util.ArrayList; import java.util.Arrays; import java.util.Formatter; import java.util.Vector; public class ModeleColorMap implements Cloneable, Serializable{ /** * */ private static final long serialVersionUID = 4055062096061553106L; private Vector _map; private Vector _values; public static final Color DEFAULT_COLOR = Color.GREEN; public enum NamedColorMapTypes { RED ("red",ModeleColorMap.redColorMap()), BLUE ("blue",ModeleColorMap.blueColorMap()), GREEN ("green",ModeleColorMap.greenColorMap()), HEAT ("heat",ModeleColorMap.heatColorMap()), ENERGY ("energy",ModeleColorMap.energyColorMap()), ROCKNROLL ("rocknroll",ModeleColorMap.rockNRollColorMap()), VIENNA ("vienna",ModeleColorMap.viennaColorMap()), BW ("bw",ModeleColorMap.bwColorMap()); String _id; ModeleColorMap _cm; private NamedColorMapTypes(String id, ModeleColorMap cm) { _id = id; _cm = cm; } public String getId() { return _id; } public ModeleColorMap getColorMap() { return _cm; } public String toString() { return _id; } } public ModeleColorMap() { this(new Vector(),new Vector()); } public ModeleColorMap(Vector map, Vector values) { _map = map; _values = values; } public void addColor(double val, Color col) { int offset = Arrays.binarySearch(_values.toArray(), val) ; if (offset<0) { int inspoint = (-offset)-1; _map.insertElementAt(col, inspoint); _values.insertElementAt(val,inspoint); } } public double getMinValue() { if (_values.size()>0) return _values.get(0); return 0.0; } public double getMaxValue() { if (_values.size()>0) return _values.get(_values.size()-1); return 0.0; } public Color getMinColor() { if (_map.size()>0) return _map.get(0); return DEFAULT_COLOR; } public Color getMaxColor() { if (_map.size()>0) return _map.get(_map.size()-1); return DEFAULT_COLOR; } public int getNumColors() { return (_map.size()); } public Color getColorAt(int i) { return (_map.get(i)); } public Double getValueAt(int i) { return (_values.get(i)); } public Color getColorForValue(double val) { Color result; if (val<=getMinValue()) { result = getMinColor(); } else if (val>=getMaxValue()) { result = getMaxColor(); } else { int offset = Arrays.binarySearch(_values.toArray(), val) ; if (offset>=0) { result = _map.get(offset); } else { int inspoint = (-offset)-1; Color c1 = _map.get(inspoint); double v1 = _values.get(inspoint); if (inspoint>0) { Color c2 = _map.get(inspoint-1); double v2 = _values.get(inspoint-1); double blendCoeff = (v2-val)/(v2-v1); result = new Color((int)(blendCoeff*c1.getRed()+(1.0-blendCoeff)*c2.getRed()), (int)(blendCoeff*c1.getGreen()+(1.0-blendCoeff)*c2.getGreen()), (int)(blendCoeff*c1.getBlue()+(1.0-blendCoeff)*c2.getBlue())); } else { result = c1; } } } return result; } public static ModeleColorMap energyColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(1.0,new Color(128,50,50).brighter()); cm.addColor(0.9,new Color(255,50,50).brighter()); cm.addColor(0.65,new Color(255,255,50).brighter()); cm.addColor(0.55,new Color(20,255,50).brighter()); cm.addColor(0.2,new Color(50,50,255).brighter()); cm.addColor(0.0,new Color(50,50,128).brighter()); return cm; } public static ModeleColorMap viennaColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(0.0,new Color(0,80,220)); cm.addColor(0.1,new Color(0,139,220)); cm.addColor(0.2,new Color(0,220,218)); cm.addColor(0.3,new Color(0,220,123)); cm.addColor(0.4,new Color(0,220,49)); cm.addColor(0.5,new Color(34,220,0)); cm.addColor(0.6,new Color(109,220,0)); cm.addColor(0.7,new Color(199,220,0)); cm.addColor(0.8,new Color(220,165,0)); cm.addColor(0.9,new Color(220,86,0)); cm.addColor(1.0,new Color(220,0,0)); return cm; } public static ModeleColorMap bwColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(0.0,Color.white); cm.addColor(1.0,Color.gray.darker()); return cm; } public static ModeleColorMap greenColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(0.0,Color.gray.brighter().brighter()); cm.addColor(1.0,Color.green.darker()); return cm; } public static ModeleColorMap blueColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(0.0,Color.gray.brighter().brighter()); cm.addColor(1.0,Color.blue); return cm; } public static ModeleColorMap redColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(0.0,Color.gray.brighter().brighter()); cm.addColor(1.0,Color.red); return cm; } public static ModeleColorMap heatColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(0.0,Color.yellow); cm.addColor(1.0,Color.red); return cm; } public static ModeleColorMap rockNRollColorMap() { ModeleColorMap cm = new ModeleColorMap(); cm.addColor(0.0,Color.red.brighter()); cm.addColor(1.0,Color.black); cm.addColor(2.0,Color.green.brighter()); return cm; } public static ModeleColorMap defaultColorMap() { return energyColorMap(); } public static ModeleColorMap parseColorMap(String s) { String[] data = s.split("[;,]"); if (data.length==1) { String name = data[0].toLowerCase(); for (NamedColorMapTypes p : NamedColorMapTypes.values()) { if (name.equals(p.getId().toLowerCase())) { return p.getColorMap(); } } return ModeleColorMap.defaultColorMap(); } else { ModeleColorMap cm = new ModeleColorMap(); for(int i=0;i1) return cm; } return ModeleColorMap.defaultColorMap(); } public void setMinValue(double newMin) { rescale(newMin,getMaxValue()); } public void setMaxValue(double newMax) { rescale(getMinValue(),newMax); } public void rescale(double newMin, double newMax) { double minBck = getMinValue(); double maxBck = getMaxValue(); double spanBck = maxBck-minBck; if (newMax!=newMin) { newMax = Math.max(newMax,newMin+1.0); for (int i=0;i<_values.size();i++) { double valBck = _values.get(i); _values.set(i, newMin+(newMax-newMin)*(valBck-minBck)/(spanBck)); } } } public ModeleColorMap clone() { ModeleColorMap cm = new ModeleColorMap(); cm._map = (Vector) _map.clone(); cm._values = (Vector)_values.clone(); return cm; } public boolean equals(ModeleColorMap cm) { if ( getNumColors()!=cm.getNumColors()) return false; for (int i=0;i { private ModeleBP _BP; /** * The base style. */ protected ModelBaseStyle _styleBase = new ModelBaseStyle(); /** * TRUE if this InterfaceBase has to be colored, else FALSE. */ protected Boolean _colorie = new Boolean(true); /** * The coordinate representation of this InterfaceBase on the final graphic. */ protected VARNAPoint _coords = new VARNAPoint(); /** * The nearest loop center of this InterfaceBase. */ protected VARNAPoint _center = new VARNAPoint(); /** * The label of this base. */ protected String _label = ""; protected double _value; protected int _realIndex = -1; public abstract void toXML(TransformerHandler hd) throws SAXException; /** * The internal index for this Base */ public abstract int getIndex(); public abstract String getContent(); public abstract void setContent(String s); /** * Gets this InterfaceBase style. * * @return this InterfaceBase style. */ public ModelBaseStyle getStyleBase() { return _styleBase; } public double getValue() { return _value; } public void setValue(double d) { _value = d; } /** * Sets this InterfaceBase style. * * @param base * - This InterfaceBase new style. */ public void setStyleBase(ModelBaseStyle base) { _styleBase = new ModelBaseStyle(base); } /** * Gets this InterfaceBase color statement. * * @return TRUE if this InterfaceBase has to be colored, else FALSE. */ public final Boolean getColorie() { return _colorie; } /** * Sets this InterfaceBase color statement. * * @param _colorie * - TRUE if you want this InterfaceBase to be colored, else * FALSE */ public final void setColorie(Boolean _colorie) { this._colorie = _colorie; } /** * Gets this InterfaceBase associated structure element. * * @return this InterfaceBase associated structure element. */ public int getElementStructure() { if (_BP==null) return -1; else { if (_BP.getPartner5()==this) return _BP.getPartner3().getIndex(); else return _BP.getPartner5().getIndex(); } } /** * Sets this InterfaceBase assiocated structure element. * * @param structure * - This new assiocated structure element. public void setElementStructure(int structure) { setElementStructure(structure, new ModeleBP()); } */ /** * Sets this InterfaceBase associated structure element. * * @param structure * - This new associated structure element. * @param type * - The type of this base pair. */ public void setElementStructure(int structure, ModeleBP type) { // _elementStructure = structure; _BP = type; } public void removeElementStructure() { // _elementStructure = -1; _BP = null; } /** * Gets the base pair type for this element. * * @return the base pair type for this element. */ public ModeleBP getStyleBP() { return _BP; } /** * Sets the base pair type for this element. * * @param type * - The new base pair type for this element. */ public void setStyleBP(ModeleBP type) { _BP = type; } public int getBaseNumber() { return _realIndex; } public void setBaseNumber(int bn) { _realIndex = bn; } public Point2D.Double getCoords() { return new Point2D.Double(_coords.x,_coords.y); } public void setCoords(Point2D.Double coords) { this._coords.x = coords.x; this._coords.y = coords.y; } public Point2D.Double getCenter() { return new Point2D.Double(_center.x,_center.y); } public void setCenter(Point2D.Double center) { this._center.x = center.x; this._center.y = center.y; } public String getLabel() { if (_label==null || _label.equals("")) { return ""+this.getBaseNumber(); } else { return _label; } } public void setLabel(String s) { _label= s; } public void setLabel(Point2D.Double center) { this._center.x = center.x; this._center.y = center.y; } public int compareTo(ModeleBase other) { int nombre1 = ((ModeleBase) other).getIndex(); int nombre2 = this.getIndex(); if (nombre1 > nombre2) return -1; else if(nombre1 == nombre2) return 0; else return 1; } public static String XML_VAR_TYPE_NAME = "type"; public static String XML_VAR_INDEX_NAME = "index"; public static String XML_VAR_LABEL_NAME = "label"; public static String XML_VAR_VALUE_NAME = "val"; public static String XML_VAR_POSITION_NAME = "pos"; public static String XML_VAR_CENTER_NAME = "center"; public static String XML_VAR_NUMBER_NAME = "num"; public static String XML_VAR_CUSTOM_DRAWN_NAME = "custom"; } fr/orsay/lri/varna/models/rna/ModeleBPStyle.java0000644000000000000000000000734611722525156020613 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.rna; import java.awt.Color; import java.io.Serializable; import java.util.ArrayList; import java.util.Random; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.utils.XMLUtils; public class ModeleBPStyle implements Serializable { /** * */ private static final long serialVersionUID = 3006493290669550139L; /** * */ private boolean _isCustomColored = false; private Color _color = VARNAConfig.DEFAULT_BOND_COLOR; private double _thickness = -1.0; private double _bent = 0.0; public static String XML_ELEMENT_NAME = "BPstyle"; public static String XML_VAR_CUSTOM_STYLED_NAME = "custom"; public static String XML_VAR_COLOR_NAME = "color"; public static String XML_VAR_THICKNESS_NAME = "thickness"; public static String XML_VAR_BENT_NAME = "bent"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("","",XML_VAR_CUSTOM_STYLED_NAME,"CDATA",""+_isCustomColored); atts.addAttribute("","",XML_VAR_COLOR_NAME,"CDATA",XMLUtils.toHTMLNotation(_color)); atts.addAttribute("","",XML_VAR_THICKNESS_NAME,"CDATA",""+_thickness); atts.addAttribute("","",XML_VAR_BENT_NAME,"CDATA",""+_bent); hd.startElement("","",XML_ELEMENT_NAME,atts); hd.endElement("","",XML_ELEMENT_NAME); } public double getBent() { return _bent; } public boolean isBent() { return (_bent!=0.0); } public void setBent(double b) { _bent = b; } public ModeleBPStyle() { } public void setCustomColor(Color c) { _isCustomColored = true; _color = c; } public void useDefaultColor() { _isCustomColored = false; } public boolean isCustomColored() { return _isCustomColored; } public Color getCustomColor() { return _color; } /** * Returns the current custom color if such a color is defined to be used * (through setCustomColor), or returns the default color. * * @param def * - The default color is no custom color is defined * @return The color to be used to draw this base-pair */ public Color getColor(Color def) { if (isCustomColored()) { return _color; } else { return def; } } public double getThickness(double def) { if (_thickness > 0) return _thickness; else return def; } public void setThickness(double thickness) { _thickness = thickness; } } fr/orsay/lri/varna/models/rna/VARNAPoint.java0000644000000000000000000000321411722525256020013 0ustar rootrootpackage fr.orsay.lri.varna.models.rna; import java.awt.geom.Point2D; import java.awt.geom.Point2D.Double; import java.io.Serializable; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; public class VARNAPoint implements Serializable { private static final long serialVersionUID = 8815373295131046029L; public double x = 0.0; public double y = 0.0; public void toXML(TransformerHandler hd) throws SAXException { toXML(hd,""); } public static String XML_ELEMENT_NAME = "p"; public static String XML_VAR_ROLE_NAME = "r"; public static String XML_VAR_X_NAME = "x"; public static String XML_VAR_Y_NAME = "y"; public void toXML(TransformerHandler hd, String role) throws SAXException { AttributesImpl atts = new AttributesImpl(); if (!role.equals("")) { atts.addAttribute("","",XML_VAR_ROLE_NAME,"CDATA",""+role); } atts.addAttribute("","",XML_VAR_X_NAME,"CDATA",""+x); atts.addAttribute("","",XML_VAR_Y_NAME,"CDATA",""+y); hd.startElement("","",XML_ELEMENT_NAME,atts); hd.endElement("","",XML_ELEMENT_NAME); } public VARNAPoint() { this(0.0,0.0); } public VARNAPoint(double px, double py) { x = px; y = py; } public VARNAPoint(Point2D.Double p) { this(p.x,p.y); } public double getX() { return x; } public double getY() { return y; } public Point2D.Double toPoint2D() { return new Point2D.Double(x,y); } public String toString() { return "("+x+","+y+")" ; } } fr/orsay/lri/varna/models/rna/ModeleBackboneElement.java0000644000000000000000000000441112265610152022267 0ustar rootrootpackage fr.orsay.lri.varna.models.rna; import java.awt.Color; import java.io.Serializable; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.utils.XMLUtils; public class ModeleBackboneElement implements Serializable{ /** * */ private static final long serialVersionUID = -614968737102943216L; public ModeleBackboneElement(int index, BackboneType t) { _index=index; if (t==BackboneType.CUSTOM_COLOR) { throw new IllegalArgumentException("Error: Missing Color while constructing Backbone"); } _type=t; } public ModeleBackboneElement(int index, Color c) { _index=index; _type=BackboneType.CUSTOM_COLOR; _color = c; } public enum BackboneType{ SOLID_TYPE ("solid"), DISCONTINUOUS_TYPE ("discontinuous"), MISSING_PART_TYPE ("missing"), CUSTOM_COLOR ("custom"); private String label; BackboneType(String s) { label = s; } public String getLabel() { return label; } public static BackboneType getType(String lbl) { BackboneType[] vals = BackboneType.values(); for(int i=0;iRNAViz */ public static final int DRAW_MODE_RADIATE = 2; /** * Selects the NAView algorithm. */ public static final int DRAW_MODE_NAVIEW = 3; /** * Selects the linear algorithm. */ public static final int DRAW_MODE_LINEAR = 4; public static final int DRAW_MODE_VARNA_VIEW = 5; /** * Selects the RNAView algorithm. */ public static final int DRAW_MODE_MOTIFVIEW = 6; public static final int DRAW_MODE_TEMPLATE = 7; public static final int DEFAULT_DRAW_MODE = DRAW_MODE_RADIATE; public int BASE_RADIUS = 10; public static final double LOOP_DISTANCE = 40.0; // distance between base // pairs in an helix public static final double BASE_PAIR_DISTANCE = 65.0; // distance between // the two bases of // a pair public static final double MULTILOOP_DISTANCE = 35.0; public static final double VIRTUAL_LOOP_RADIUS = 40.0; public double CHEM_PROB_DIST = 14; public double CHEM_PROB_BASE_LENGTH = 30; public double CHEM_PROB_ARROW_HEIGHT = 10; public double CHEM_PROB_ARROW_WIDTH = 5; public double CHEM_PROB_TRIANGLE_WIDTH = 2.5; public double CHEM_PROB_PIN_SEMIDIAG = 6; public double CHEM_PROB_DOT_RADIUS = 6.; public static double CHEM_PROB_ARROW_THICKNESS = 2.0; public static ArrayList NormalBases = new ArrayList(); { NormalBases.add("a"); NormalBases.add("c"); NormalBases.add("g"); NormalBases.add("u"); NormalBases.add("t"); } public GeneralPath _debugShape = null; /** * The draw algorithm mode */ private int _drawMode = DRAW_MODE_RADIATE; private boolean _drawn = false; private String _name = ""; private String _id = ""; public double _bpHeightIncrement = VARNAConfig.DEFAULT_BP_INCREMENT; /** * the base list */ private ArrayList _listeBases; /** * the strand list */ StructureTemp _listStrands = new StructureTemp(); /** * Additional bonds and info can be specified here. */ private ArrayList _structureAux = new ArrayList(); private ArrayList _listeAnnotations = new ArrayList(); private ArrayList _listeRegionHighlights = new ArrayList(); private ArrayList _chemProbAnnotations = new ArrayList(); private ModeleBackbone _backbone = new ModeleBackbone(); public static String XML_ELEMENT_NAME = "RNA"; public static String XML_VAR_BASE_SPACING_NAME = "spacing"; public static String XML_VAR_DRAWN_NAME = "drawn"; public static String XML_VAR_NAME_NAME = "name"; public static String XML_VAR_DRAWN_MODE_NAME = "mode"; public static String XML_VAR_ID_NAME = "id"; public static String XML_VAR_BP_HEIGHT_NAME = "delta"; public static String XML_VAR_BASES_NAME = "bases"; public static String XML_VAR_BASEPAIRS_NAME = "BPs"; public static String XML_VAR_ANNOTATIONS_NAME = "annotations"; public static String XML_VAR_BACKBONE_NAME = "backbone"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); atts.addAttribute("", "", XML_VAR_DRAWN_NAME, "CDATA", "" + _drawn); atts.addAttribute("", "", XML_VAR_DRAWN_MODE_NAME, "CDATA", "" + _drawMode); atts.addAttribute("", "", XML_VAR_ID_NAME, "CDATA", "" + _id); atts.addAttribute("", "", XML_VAR_BP_HEIGHT_NAME, "CDATA", "" + _bpHeightIncrement); hd.startElement("", "", XML_ELEMENT_NAME, atts); atts.clear(); hd.startElement("", "", XML_VAR_NAME_NAME, atts); XMLUtils.exportCDATAString(hd, "" + _name); hd.endElement("", "", XML_VAR_NAME_NAME); atts.clear(); hd.startElement("", "", XML_VAR_BASES_NAME, atts); for (ModeleBase mb : _listeBases) { mb.toXML(hd); } hd.endElement("", "", XML_VAR_BASES_NAME); atts.clear(); hd.startElement("", "", XML_VAR_BASEPAIRS_NAME, atts); for (ModeleBP mbp : getSecStrBPs()) { mbp.toXML(hd, true); } for (ModeleBP mbp : _structureAux) { mbp.toXML(hd, false); } hd.endElement("", "", XML_VAR_BASEPAIRS_NAME); atts.clear(); getBackbone().toXML(hd); atts.clear(); hd.startElement("", "", XML_VAR_ANNOTATIONS_NAME, atts); for (TextAnnotation ta : _listeAnnotations) { ta.toXML(hd); } for (HighlightRegionAnnotation hra : _listeRegionHighlights) { hra.toXML(hd); } for (ChemProbAnnotation cpa : _chemProbAnnotations) { cpa.toXML(hd); } hd.endElement("", "", XML_VAR_ANNOTATIONS_NAME); hd.endElement("", "", XML_ELEMENT_NAME); } public ModeleBackbone getBackbone() { return _backbone; } public void setBackbone(ModeleBackbone b) { _backbone = b; } transient private ArrayList _listeVARNAListener = new ArrayList(); public RNA() { this(""); } public RNA(String name) { _name = name; _listeBases = new ArrayList(); _drawn = false; init(); } public String toString() { if (_name.equals("")) { return getStructDBN(); } else { return _name; } } public RNA(RNA r) { _drawMode = r._drawMode; _listeBases.addAll(r._listeBases); _listeVARNAListener = (ArrayList) r._listeVARNAListener; _drawn = r._drawn; init(); } public void init() { } public void saveRNADBN(String path, String title) throws ExceptionWritingForbidden { try { FileWriter out = new FileWriter(path); if (!title.equals("")) { out.write("> " + title + "\n"); } out.write(getListeBasesToString()); out.write('\n'); String str = ""; for (int i = 0; i < _listeBases.size(); i++) { if (_listeBases.get(i).getElementStructure() == -1) { str += '.'; } else { if (_listeBases.get(i).getElementStructure() > i) { str += '('; } else { str += ')'; } } } out.write(str); out.write('\n'); out.close(); } catch (IOException e) { throw new ExceptionWritingForbidden(e.getMessage()); } } public Color getBaseInnerColor(int i, VARNAConfig conf) { Color result = _listeBases.get(i).getStyleBase().get_base_inner_color(); String res = _listeBases.get(i).getContent(); if (conf._drawColorMap) { result = conf._cm.getColorForValue(_listeBases.get(i).getValue()); } else if ((conf._colorDashBases && (res.contains("-")))) { result = conf._dashBasesColor; } else if ((conf._colorSpecialBases && !NormalBases.contains(res .toLowerCase()))) { result = conf._specialBasesColor; } return result; } public Color getBaseOuterColor(int i, VARNAConfig conf) { Color result = _listeBases.get(i).getStyleBase() .get_base_outline_color(); return result; } private static double correctComponent(double c) { c = c / 255.0; if (c <= 0.03928) c = c/12.92; else c = Math.pow(((c+0.055)/1.055) , 2.4); return c; } public static double getLuminance(Color c) { return 0.2126 * correctComponent(c.getRed()) + 0.7152 * correctComponent(c.getGreen()) + 0.0722 * correctComponent(c.getBlue()); } public static boolean whiteLabelPreferrable(Color c) { if (getLuminance(c) > 0.179) return false; return true; } public Color getBaseNameColor(int i, VARNAConfig conf) { Color result = _listeBases.get(i).getStyleBase().get_base_name_color(); if ( RNA.whiteLabelPreferrable(getBaseInnerColor(i, conf))) { result=Color.white; } return result; } public Color getBasePairColor(ModeleBP bp, VARNAConfig conf) { Color bondColor = conf._bondColor; if (conf._useBaseColorsForBPs) { bondColor = _listeBases.get(bp.getPartner5().getIndex()) .getStyleBase().get_base_inner_color(); } if (bp != null) { bondColor = bp.getStyle().getColor(bondColor); } return bondColor; } public double getBasePairThickness(ModeleBP bp, VARNAConfig conf) { double thickness = bp.getStyle().getThickness(conf._bpThickness); return thickness; } private void drawSymbol(SecStrDrawingProducer out, double posx, double posy, double normx, double normy, double radius, boolean isCIS, ModeleBP.Edge e, double thickness) { Color bck = out.getCurrentColor(); switch (e) { case WC: if (isCIS) { out.fillCircle(posx, posy, (radius / 2.0), thickness, bck); } else { out.fillCircle(posx, posy, (radius / 2.0), thickness, Color.white); out.setColor(bck); out.drawCircle(posx, posy, (radius / 2.0), thickness); } break; case HOOGSTEEN: { double xtab[] = new double[4]; double ytab[] = new double[4]; xtab[0] = posx - radius * normx / 2.0 - radius * normy / 2.0; ytab[0] = posy - radius * normy / 2.0 + radius * normx / 2.0; xtab[1] = posx + radius * normx / 2.0 - radius * normy / 2.0; ytab[1] = posy + radius * normy / 2.0 + radius * normx / 2.0; xtab[2] = posx + radius * normx / 2.0 + radius * normy / 2.0; ytab[2] = posy + radius * normy / 2.0 - radius * normx / 2.0; xtab[3] = posx - radius * normx / 2.0 + radius * normy / 2.0; ytab[3] = posy - radius * normy / 2.0 - radius * normx / 2.0; if (isCIS) { out.fillPolygon(xtab, ytab, bck); } else { out.fillPolygon(xtab, ytab, Color.white); out.setColor(bck); out.drawPolygon(xtab, ytab, thickness); } } break; case SUGAR: { double ix = radius * normx / 2.0; double iy = radius * normy / 2.0; double jx = radius * normy / 2.0; double jy = -radius * normx / 2.0; double xtab[] = new double[3]; double ytab[] = new double[3]; xtab[0] = posx - ix + jx; ytab[0] = posy - iy + jy; xtab[1] = posx + ix + jx; ytab[1] = posy + iy + jy; xtab[2] = posx - jx; ytab[2] = posy - jy; if (isCIS) { out.fillPolygon(xtab, ytab, bck); } else { out.fillPolygon(xtab, ytab, Color.white); out.setColor(bck); out.drawPolygon(xtab, ytab, thickness); } } break; } out.setColor(bck); } private void drawBasePairArc(SecStrDrawingProducer out, int i, int j, Point2D.Double orig, Point2D.Double dest, ModeleBP style, VARNAConfig conf) { double coef; double distance; if (j - i == 1) coef = _bpHeightIncrement * 2; else coef = _bpHeightIncrement * 1; distance = (int) Math.round(dest.x - orig.x); if (conf._mainBPStyle != BP_STYLE.LW) { out.drawArc(orig, distance, distance * coef, 0, 180); } else { double thickness = getBasePairThickness(style, conf); double radiusCircle = ((BASE_PAIR_DISTANCE - BASE_RADIUS) / 5.0); if (style.isCanonical()) { if (style.isCanonicalGC()) { if ((orig.x != dest.x) || (orig.y != dest.y)) { out.drawArc(new Point2D.Double(orig.x + BASE_RADIUS / 4., orig.y), distance - BASE_RADIUS / 2., distance * coef - BASE_RADIUS / 2, 0, 180); out.drawArc(new Point2D.Double(orig.x - BASE_RADIUS / 4., orig.y), distance + BASE_RADIUS / 2., distance * coef + BASE_RADIUS / 2, 0, 180); } } else if (!style.isWobbleUG()) { double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; out.drawArc(orig, distance, distance * coef, 0, 180); drawSymbol(out, cx, cy + distance * coef / 2., 1., 0, radiusCircle, style.isCIS(), style.getEdgePartner5(), thickness); } else { out.drawArc(orig, distance, distance * coef, 0, 180); } } else { ModeleBP.Edge p1 = style.getEdgePartner5(); ModeleBP.Edge p2 = style.getEdgePartner3(); double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; out.drawArc(orig, distance, distance * coef, 0, 180); if (p1 == p2) { drawSymbol(out, cx, cy + distance * coef / 2., 1., 0, radiusCircle, style.isCIS(), style.getEdgePartner5(), thickness); } else { drawSymbol(out, cx - BASE_RADIUS, cy + distance * coef / 2., 1., 0, radiusCircle, style.isCIS(), p1, thickness); drawSymbol(out, cx + BASE_RADIUS, cy + distance * coef / 2., 1., 0, radiusCircle, style.isCIS(), p2, thickness); } } } } private void drawBasePair(SecStrDrawingProducer out, Point2D.Double orig, Point2D.Double dest, ModeleBP style, VARNAConfig conf) { double dx = dest.x - orig.x; double dy = dest.y - orig.y; double dist = Math.sqrt((dest.x - orig.x) * (dest.x - orig.x) + (dest.y - orig.y) * (dest.y - orig.y)); dx /= dist; dy /= dist; double nx = -dy; double ny = dx; orig = new Point2D.Double(orig.x + BASE_RADIUS * dx, orig.y + BASE_RADIUS * dy); dest = new Point2D.Double(dest.x - BASE_RADIUS * dx, dest.y - BASE_RADIUS * dy); if (conf._mainBPStyle == VARNAConfig.BP_STYLE.LW) { double thickness = getBasePairThickness(style, conf); double radiusCircle = ((BASE_PAIR_DISTANCE - BASE_RADIUS) / 5.0); if (style.isCanonical()) { if (style.isCanonicalGC()) { if ((orig.x != dest.x) || (orig.y != dest.y)) { nx *= BASE_RADIUS / 4.0; ny *= BASE_RADIUS / 4.0; out.drawLine((orig.x + nx), (orig.y + ny), (dest.x + nx), (dest.y + ny), conf._bpThickness); out.drawLine((orig.x - nx), (orig.y - ny), (dest.x - nx), (dest.y - ny), conf._bpThickness); } } else if (style.isCanonicalAU()) { out.drawLine(orig.x, orig.y, dest.x, dest.y, conf._bpThickness); } else if (style.isWobbleUG()) { double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; out.drawLine(orig.x, orig.y, dest.x, dest.y, conf._bpThickness); drawSymbol(out, cx, cy, nx, ny, radiusCircle, false, ModeleBP.Edge.WC, thickness); } else { double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; out.drawLine(orig.x, orig.y, dest.x, dest.y, conf._bpThickness); drawSymbol(out, cx, cy, nx, ny, radiusCircle, style.isCIS(), style.getEdgePartner5(), thickness); } } else { ModeleBP.Edge p1 = style.getEdgePartner5(); ModeleBP.Edge p2 = style.getEdgePartner3(); double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; out.drawLine(orig.x, orig.y, dest.x, dest.y, conf._bpThickness); if (p1 == p2) { drawSymbol(out, cx, cy, nx, ny, radiusCircle, style.isCIS(), p1, thickness); } else { double vdx = (dest.x - orig.x); double vdy = (dest.y - orig.y); vdx /= 6.0; vdy /= 6.0; drawSymbol(out, cx + vdx, cy + vdy, nx, ny, radiusCircle, style.isCIS(), p2, thickness); drawSymbol(out, cx - vdx, cy - vdy, nx, ny, radiusCircle, style.isCIS(), p1, thickness); } } } else if (conf._mainBPStyle == VARNAConfig.BP_STYLE.RNAVIZ) { double xcenter = (orig.x + dest.x) / 2.0; double ycenter = (orig.y + dest.y) / 2.0; out.fillCircle(xcenter, ycenter, 3.0 * conf._bpThickness, conf._bpThickness, out.getCurrentColor()); } else if (conf._mainBPStyle == VARNAConfig.BP_STYLE.SIMPLE) { out.drawLine(orig.x, orig.y, dest.x, dest.y, conf._bpThickness); } } private void drawColorMap(VARNAConfig _conf, SecStrDrawingProducer out) { double v1 = _conf._cm.getMinValue(); double v2 = _conf._cm.getMaxValue(); int x, y; double xSpaceAvail = 0; double ySpaceAvail = 0; double thickness = 1.0; /* * ySpaceAvail = * Math.min((getHeight()-rnabbox.height*scaleFactor-getTitleHeight * ())/2.0,scaleFactor*(_conf._colorMapHeight+VARNAConfig. * DEFAULT_COLOR_MAP_FONT_SIZE)); if ((int)ySpaceAvail==0) { xSpaceAvail * = * Math.min((getWidth()-rnabbox.width*scaleFactor)/2,scaleFactor*(_conf * ._colorMapWidth)+VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH); } */ Rectangle2D.Double currentBBox = out.getBoundingBox(); double xBase = (currentBBox.getMaxX() - _conf._colorMapWidth - _conf._colorMapXOffset); // double yBase = (minY - _conf._colorMapHeight + // _conf._colorMapYOffset); double yBase = (currentBBox.getMinY() - _conf._colorMapHeight - VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE); for (int i = 0; i < _conf._colorMapWidth; i++) { double ratio = (((double) i) / ((double) _conf._colorMapWidth - 1)); double val = v1 + (v2 - v1) * ratio; Color c = _conf._cm.getColorForValue(val); x = (int) (xBase + i); y = (int) yBase; out.fillRectangle(x, y, VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH, _conf._colorMapHeight, c); } out.setColor(VARNAConfig.DEFAULT_COLOR_MAP_OUTLINE); out.drawRectangle(xBase, yBase, (double) _conf._colorMapWidth + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH - 1, _conf._colorMapHeight, thickness); out.setColor(VARNAConfig.DEFAULT_COLOR_MAP_FONT_COLOR); out.setFont(out.getCurrentFont(), VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.5); out.drawText(xBase, yBase + _conf._colorMapHeight + VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7, "" + _conf._cm.getMinValue()); out.drawText(xBase + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH + _conf._colorMapWidth, yBase + _conf._colorMapHeight + VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7, "" + _conf._cm.getMaxValue()); out.drawText( xBase + (VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH + _conf._colorMapWidth) / 2.0, yBase - (VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7), _conf._colorMapCaption); } private void renderRegionHighlights(SecStrDrawingProducer out, Point2D.Double[] realCoords, Point2D.Double[] realCenters) { for (HighlightRegionAnnotation r : _listeRegionHighlights) { GeneralPath s = r.getShape(realCoords, realCenters, 1.0); out.setColor(r.getFillColor()); out.fillPolygon(s, r.getFillColor()); out.setColor(r.getOutlineColor()); out.drawPolygon(s, 1l); } } private void saveRNA(String path, VARNAConfig conf, double scale, SecStrDrawingProducer out) throws ExceptionWritingForbidden { out.setScale(scale); // Computing bounding boxes double EPSMargin = 40; double minX = Double.MAX_VALUE; double maxX = Double.MIN_VALUE; double minY = Double.MAX_VALUE; double maxY = Double.MIN_VALUE; double x0, y0, x1, y1, xc, yc, xp, yp, dx, dy, norm; for (int i = 0; i < _listeBases.size(); i++) { minX = Math.min(minX, (_listeBases.get(i).getCoords().getX() - BASE_RADIUS - EPSMargin)); minY = Math.min(minY, -(_listeBases.get(i).getCoords().getY() - BASE_RADIUS - EPSMargin)); maxX = Math.max(maxX, (_listeBases.get(i).getCoords().getX() + BASE_RADIUS + EPSMargin)); maxY = Math.max(maxY, -(_listeBases.get(i).getCoords().getY() + BASE_RADIUS + EPSMargin)); } // Rescaling everything Point2D.Double[] coords = new Point2D.Double[_listeBases.size()]; Point2D.Double[] centers = new Point2D.Double[_listeBases.size()]; for (int i = 0; i < _listeBases.size(); i++) { xp = (_listeBases.get(i).getCoords().getX() - minX); yp = -(_listeBases.get(i).getCoords().getY() - minY); coords[i] = new Point2D.Double(xp, yp); Point2D.Double centerBck = getCenter(i); if (get_drawMode() == RNA.DRAW_MODE_NAVIEW || get_drawMode() == RNA.DRAW_MODE_RADIATE) { if ((_listeBases.get(i).getElementStructure() != -1) && i < _listeBases.size() - 1 && i > 1) { ModeleBase b1 = get_listeBases().get(i - 1); ModeleBase b2 = get_listeBases().get(i + 1); int j1 = b1.getElementStructure(); int j2 = b2.getElementStructure(); if ((j1 == -1) ^ (j2 == -1)) { // alors la position du nombre associé doit etre // décalé Point2D.Double a1 = b1.getCoords(); Point2D.Double a2 = b2.getCoords(); Point2D.Double c1 = b1.getCenter(); Point2D.Double c2 = b2.getCenter(); centerBck.x = _listeBases.get(i).getCoords().x + (c1.x - a1.x) / c1.distance(a1) + (c2.x - a2.x) / c2.distance(a2); centerBck.y = _listeBases.get(i).getCoords().y + (c1.y - a1.y) / c1.distance(a1) + (c2.y - a2.y) / c2.distance(a2); } } } xc = (centerBck.getX() - minX); yc = -(centerBck.getY() - minY); centers[i] = new Point2D.Double(xc, yc); } // Drawing background if (conf._drawBackground) out.setBackgroundColor(conf._backgroundColor); // Drawing region highlights renderRegionHighlights(out, coords, centers); // Drawing backbone for (int i = 1; i < _listeBases.size(); i++) { Point2D.Double p1 = coords[i - 1]; Point2D.Double p2 = coords[i]; x0 = p1.x; y0 = p1.y; x1 = p2.x; y1 = p2.y; Point2D.Double vn = new Point2D.Double(); double dist = p1.distance(p2); int a = _listeBases.get(i - 1).getElementStructure(); int b = _listeBases.get(i).getElementStructure(); BackboneType bt = _backbone.getTypeBefore(i); boolean consecutivePair = (a == i) && (b == i - 1); if (dist > 0) { if (bt != BackboneType.DISCONTINUOUS_TYPE) { Color c = _backbone.getColorBefore(i, conf._backboneColor); if (bt == BackboneType.MISSING_PART_TYPE) { c.brighter(); } out.setColor(c); vn.x = (x1 - x0) / dist; vn.y = (y1 - y0) / dist; if (consecutivePair &&(getDrawMode() != RNA.DRAW_MODE_LINEAR) && (getDrawMode() != RNA.DRAW_MODE_CIRCULAR)) { int dir = 0; if (i + 1 < coords.length) { dir = (testDirectionality(i - 1, i, i + 1) ? -1 : 1); } else if (i - 2 >= 0) { dir = (testDirectionality(i - 2, i - 1, i) ? -1 : 1); } Point2D.Double centerSeg = new Point2D.Double( (p1.x + p2.x) / 2.0, (p1.y + p2.y) / 2.0); double centerDist = RNA.VIRTUAL_LOOP_RADIUS * scale; Point2D.Double centerLoop = new Point2D.Double( centerSeg.x + centerDist * dir * vn.y, centerSeg.y - centerDist * dir * vn.x); out.drawLine(centerLoop.x - 5, centerLoop.y, centerLoop.x + 5, centerLoop.y, 2.0); out.drawLine(centerLoop.x, centerLoop.y - 5, centerLoop.x, centerLoop.y + 5, 2.0); double radius = centerLoop.distance(p1); double a1 = 360. * (Math.atan2(dir * (p1.x - centerLoop.x), dir * (p1.y - centerLoop.y))) / (2. * Math.PI); double a2 = 360. * (Math.atan2(dir * (centerLoop.x - p2.x), dir * (centerLoop.y - p2.y))) / (2. * Math.PI); if (a1 < 0) { a1 += 360.; } if (a2 < 0) { a2 += 360.; } double angle = a2 - a1; if (dir * (a2 - a1) < 0.) angle += dir * 360.; out.drawArc(centerLoop, 2. * radius, 2. * radius, a1, angle); } else { out.drawLine((x0 + BASE_RADIUS * vn.x), (y0 + BASE_RADIUS * vn.y), (x1 - BASE_RADIUS * vn.x), (y1 - BASE_RADIUS * vn.y), 1.0); } } } } // Drawing bonds for (int i = 0; i < _listeBases.size(); i++) { if (_listeBases.get(i).getElementStructure() > i) { ModeleBP style = _listeBases.get(i).getStyleBP(); if (style.isCanonical() || conf._drawnNonCanonicalBP) { Color bpcol = getBasePairColor(style, conf); out.setColor(bpcol); int j = _listeBases.get(i).getElementStructure(); x0 = coords[i].x; y0 = coords[i].y; x1 = coords[j].x; y1 = coords[j].y; dx = x1 - x0; dy = y1 - y0; norm = Math.sqrt(dx * dx + dy * dy); dx /= norm; dy /= norm; if (_drawMode == DRAW_MODE_CIRCULAR || _drawMode == DRAW_MODE_RADIATE || _drawMode == DRAW_MODE_NAVIEW) { drawBasePair(out, new Point2D.Double(x0, y0), new Point2D.Double(x1, y1), style, conf); } else if (_drawMode == DRAW_MODE_LINEAR) { drawBasePairArc(out, i, j, new Point2D.Double(x0, y0), new Point2D.Double(x1, y1), style, conf); } } } } // Drawing additional bonds if (conf._drawnNonPlanarBP) { for (int i = 0; i < _structureAux.size(); i++) { ModeleBP bp = _structureAux.get(i); out.setColor(getBasePairColor(bp, conf)); int a = bp.getPartner5().getIndex(); int b = bp.getPartner3().getIndex(); if (bp.isCanonical() || conf._drawnNonCanonicalBP) { x0 = coords[a].x; y0 = coords[a].y; x1 = coords[b].x; y1 = coords[b].y; dx = x1 - x0; dy = y1 - y0; norm = Math.sqrt(dx * dx + dy * dy); dx /= norm; dy /= norm; if ((_drawMode == DRAW_MODE_CIRCULAR) || (_drawMode == DRAW_MODE_RADIATE) || _drawMode == DRAW_MODE_NAVIEW) { drawBasePair(out, new Point2D.Double(x0, y0), new Point2D.Double(x1, y1), bp, conf); } else if (_drawMode == DRAW_MODE_LINEAR) { drawBasePairArc(out, a, b, new Point2D.Double(x0, y0), new Point2D.Double(x1, y1), bp, conf); } } } } // Drawing Bases double baseFontSize = (1.5 * BASE_RADIUS); out.setFont(PSExport.FONT_HELVETICA_BOLD, baseFontSize); for (int i = 0; i < _listeBases.size(); i++) { x0 = coords[i].x; y0 = coords[i].y; if (_listeBases.get(i) instanceof ModeleBasesComparison) { ModeleBasesComparison mb = (ModeleBasesComparison) _listeBases .get(i); if (conf._fillBases) { out.fillRectangle(x0 - 1.5 * BASE_RADIUS, y0 - BASE_RADIUS, 3 * BASE_RADIUS, 2 * BASE_RADIUS, getBaseInnerColor(i, conf)); } if (conf._drawOutlineBases) { out.setColor(getBaseOuterColor(i, conf)); out.drawRectangle(x0 - 1.5 * BASE_RADIUS, y0 - BASE_RADIUS, 3 * BASE_RADIUS, 2 * BASE_RADIUS, 1l); out.drawLine(x0, y0 - BASE_RADIUS, x0, y0 + BASE_RADIUS, 1l); } out.setColor(getBaseNameColor(i, conf)); out.drawText(x0 - .75 * BASE_RADIUS, y0, "" + mb.getBase1()); out.drawText(x0 + .75 * BASE_RADIUS, y0, "" + mb.getBase2()); } else if (_listeBases.get(i) instanceof ModeleBaseNucleotide) { if (conf._fillBases) { out.fillCircle(x0, y0, BASE_RADIUS, 1l, getBaseInnerColor(i, conf)); } if (conf._drawOutlineBases) { out.setColor(getBaseOuterColor(i, conf)); out.drawCircle(x0, y0, BASE_RADIUS, 1l); } out.setColor(getBaseNameColor(i, conf)); out.drawText(x0, y0, _listeBases.get(i).getContent()); } } // Drawing base numbers double numFontSize = (double) (1.5 * BASE_RADIUS); out.setFont(PSExport.FONT_HELVETICA_BOLD, numFontSize); for (int i = 0; i < _listeBases.size(); i++) { int basenum = _listeBases.get(i).getBaseNumber(); if (basenum == -1) { basenum = i + 1; } ModeleBase mb = _listeBases.get(i); if (this.isNumberDrawn(mb, conf._numPeriod)) { out.setColor(mb.getStyleBase() .get_base_number_color()); x0 = coords[i].x; y0 = coords[i].y; x1 = centers[i].x; y1 = centers[i].y; dx = x1 - x0; dy = y1 - y0; norm = Math.sqrt(dx * dx + dy * dy); dx /= norm; dy /= norm; out.drawLine((x0 - 1.5 * BASE_RADIUS * dx), (y0 - 1.5 * BASE_RADIUS * dy), (x0 - 2.5 * BASE_RADIUS * dx), (y0 - 2.5 * BASE_RADIUS * dy), 1); out.drawText( (x0 - (conf._distNumbers + 1.0) * BASE_RADIUS * dx), (y0 - (conf._distNumbers + 1.0) * BASE_RADIUS * dy), mb.getLabel()); } } renderAnnotations(out, minX, minY, conf); // Draw color map if (conf._drawColorMap) { drawColorMap(conf, out); } // Drawing Title Rectangle2D.Double currentBBox = out.getBoundingBox(); double titleFontSize = (2.0 * conf._titleFont.getSize()); out.setColor(conf._titleColor); out.setFont(PSExport.FONT_HELVETICA, titleFontSize); double yTitle = currentBBox.y - titleFontSize / 2.0; if (!getName().equals("")) { out.drawText((maxX - minX) / 2.0, yTitle, getName()); } OutputStreamWriter fout; try { fout = new OutputStreamWriter(new FileOutputStream(path), "UTF-8"); fout.write(out.export()); fout.close(); } catch (IOException e) { throw new ExceptionWritingForbidden(e.getMessage()); } } Point2D.Double buildCaptionPosition(ModeleBase mb, double heightEstimate, VARNAConfig conf) { double radius = 2.0; if (isNumberDrawn(mb, conf._numPeriod)) { radius += (conf._distNumbers + 1.0); } Point2D.Double center = mb.getCenter(); Point2D.Double p = mb.getCoords(); double realDistance = BASE_RADIUS * radius + heightEstimate; return new Point2D.Double(center.getX() + (p.getX() - center.getX()) * ((p.distance(center) + realDistance) / p.distance(center)), center.getY() + (p.getY() - center.getY()) * ((p.distance(center) + realDistance) / p .distance(center))); } public double getBPHeightIncrement() { return this._bpHeightIncrement; } public void setBPHeightIncrement(double d) { _bpHeightIncrement = d; } private void drawChemProbAnnotation(SecStrDrawingProducer out, ChemProbAnnotation cpa, Point2D.Double anchor, double minX, double minY) { out.setColor(cpa.getColor()); Point2D.Double v = cpa.getDirVector(); Point2D.Double vn = cpa.getNormalVector(); Point2D.Double base = new Point2D.Double((anchor.x + CHEM_PROB_DIST * v.x), (anchor.y + CHEM_PROB_DIST * v.y)); Point2D.Double edge = new Point2D.Double( (base.x + CHEM_PROB_BASE_LENGTH * cpa.getIntensity() * v.x), (base.y + CHEM_PROB_BASE_LENGTH * cpa.getIntensity() * v.y)); double thickness = CHEM_PROB_ARROW_THICKNESS * cpa.getIntensity(); switch (cpa.getType()) { case ARROW: { Point2D.Double arrowTip1 = new Point2D.Double( (base.x + cpa.getIntensity() * (CHEM_PROB_ARROW_WIDTH * vn.x + CHEM_PROB_ARROW_HEIGHT * v.x)), (base.y + cpa.getIntensity() * (CHEM_PROB_ARROW_WIDTH * vn.y + CHEM_PROB_ARROW_HEIGHT * v.y))); Point2D.Double arrowTip2 = new Point2D.Double( (base.x + cpa.getIntensity() * (-CHEM_PROB_ARROW_WIDTH * vn.x + CHEM_PROB_ARROW_HEIGHT * v.x)), (base.y + cpa.getIntensity() * (-CHEM_PROB_ARROW_WIDTH * vn.y + CHEM_PROB_ARROW_HEIGHT * v.y))); out.drawLine(base.x - minX, minY - base.y, edge.x - minX, minY - edge.y, thickness); out.drawLine(base.x - minX, minY - base.y, arrowTip1.x - minX, minY - arrowTip1.y, thickness); out.drawLine(base.x - minX, minY - base.y, arrowTip2.x - minX, minY - arrowTip2.y, thickness); } break; case PIN: { Point2D.Double side1 = new Point2D.Double( (edge.x - cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * v.x)), (edge.y - cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * v.y))); Point2D.Double side2 = new Point2D.Double( (edge.x - cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * vn.x)), (edge.y - cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * vn.y))); Point2D.Double side3 = new Point2D.Double( (edge.x + cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * v.x)), (edge.y + cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * v.y))); Point2D.Double side4 = new Point2D.Double( (edge.x + cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * vn.x)), (edge.y + cpa.getIntensity() * (CHEM_PROB_PIN_SEMIDIAG * vn.y))); GeneralPath p2 = new GeneralPath(); p2.moveTo((float) (side1.x - minX), (float) (minY - side1.y)); p2.lineTo((float) (side2.x - minX), (float) (minY - side2.y)); p2.lineTo((float) (side3.x - minX), (float) (minY - side3.y)); p2.lineTo((float) (side4.x - minX), (float) (minY - side4.y)); p2.closePath(); out.fillPolygon(p2, cpa.getColor()); out.drawLine(base.x - minX, minY - base.y, edge.x - minX, minY - edge.y, thickness); } break; case TRIANGLE: { Point2D.Double arrowTip1 = new Point2D.Double( (edge.x + cpa.getIntensity() * (CHEM_PROB_TRIANGLE_WIDTH * vn.x)), (edge.y + cpa.getIntensity() * (CHEM_PROB_TRIANGLE_WIDTH * vn.y))); Point2D.Double arrowTip2 = new Point2D.Double( (edge.x + cpa.getIntensity() * (-CHEM_PROB_TRIANGLE_WIDTH * vn.x)), (edge.y + cpa.getIntensity() * (-CHEM_PROB_TRIANGLE_WIDTH * vn.y))); GeneralPath p2 = new GeneralPath(); p2.moveTo((float) (base.x - minX), (float) (minY - base.y)); p2.lineTo((float) (arrowTip1.x - minX), (float) (minY - arrowTip1.y)); p2.lineTo((float) (arrowTip2.x - minX), (float) (minY - arrowTip2.y)); p2.closePath(); out.fillPolygon(p2, cpa.getColor()); } break; case DOT: { Double radius = CHEM_PROB_DOT_RADIUS * cpa.getIntensity(); Point2D.Double center = new Point2D.Double((base.x + radius * v.x) - minX, minY - (base.y + radius * v.y)); out.fillCircle(center.x, center.y, radius, thickness, cpa.getColor()); } break; } } private void renderAnnotations(SecStrDrawingProducer out, double minX, double minY, VARNAConfig conf) { for (TextAnnotation textAnnotation : getAnnotations()) { out.setColor(textAnnotation.getColor()); out.setFont(PSExport.FONT_HELVETICA_BOLD, 2.0 * textAnnotation .getFont().getSize()); Point2D.Double position = textAnnotation.getCenterPosition(); if (textAnnotation.getType() == TextAnnotation.AnchorType.BASE) { ModeleBase mb = (ModeleBase) textAnnotation.getAncrage(); double fontHeight = Math.ceil(textAnnotation.getFont() .getSize()); position = buildCaptionPosition(mb, fontHeight, conf); } out.drawText(position.x - minX, -(position.y - minY), textAnnotation.getTexte()); } for (ChemProbAnnotation cpa : getChemProbAnnotations()) { Point2D.Double anchor = cpa.getAnchorPosition(); drawChemProbAnnotation(out, cpa, anchor, minX, minY); } } public boolean isNumberDrawn(ModeleBase mb, int numPeriod) { if (numPeriod <= 0) return false; return ((mb.getIndex() == 0) || ((mb.getBaseNumber()) % numPeriod == 0) || (mb .getIndex() == get_listeBases().size() - 1)); } public void saveRNAEPS(String path, VARNAConfig conf) throws ExceptionWritingForbidden { PSExport out = new PSExport(); saveRNA(path, conf, 0.4, out); } public void saveRNAXFIG(String path, VARNAConfig conf) throws ExceptionWritingForbidden { XFIGExport out = new XFIGExport(); saveRNA(path, conf, 20, out); } public void saveRNASVG(String path, VARNAConfig conf) throws ExceptionWritingForbidden { SVGExport out = new SVGExport(); saveRNA(path, conf, 0.5, out); } public Rectangle2D.Double getBBox() { Rectangle2D.Double result = new Rectangle2D.Double(10, 10, 10, 10); double minx, maxx, miny, maxy; minx = Double.MAX_VALUE; miny = Double.MAX_VALUE; maxx = -Double.MAX_VALUE; maxy = -Double.MAX_VALUE; for (int i = 0; i < _listeBases.size(); i++) { minx = Math.min( _listeBases.get(i).getCoords().getX() - BASE_RADIUS, minx); miny = Math.min( _listeBases.get(i).getCoords().getY() - BASE_RADIUS, miny); maxx = Math.max( _listeBases.get(i).getCoords().getX() + BASE_RADIUS, maxx); maxy = Math.max( _listeBases.get(i).getCoords().getY() + BASE_RADIUS, maxy); } result.x = minx; result.y = miny; result.width = Math.max(maxx - minx, 1); result.height = Math.max(maxy - miny, 1); if (_drawMode == RNA.DRAW_MODE_LINEAR) { double realHeight = _bpHeightIncrement * result.width / 2.0; result.height += realHeight; result.y -= realHeight; } return result; } public void setCoord(int index, Point2D.Double p) { setCoord(index, p.x, p.y); } public void setCoord(int index, double x, double y) { if (index < _listeBases.size()) { _listeBases.get(index).setCoords(new Point2D.Double(x, y)); } } public Point2D.Double getCoords(int i) { if (i < _listeBases.size() && i >= 0) { return _listeBases.get(i).getCoords(); } return new Point2D.Double(); } public String getBaseContent(int i) { if ((i >= 0) && (i < _listeBases.size())) { return _listeBases.get(i).getContent(); } return ""; } public int getBaseNumber(int i) { if ((i >= 0) && (i < _listeBases.size())) { return _listeBases.get(i).getBaseNumber(); } return -1; } public Point2D.Double getCenter(int i) { if (i < _listeBases.size()) { return _listeBases.get(i).getCenter(); } return new Point2D.Double(); } public void setCenter(int i, double x, double y) { setCenter(i, new Point2D.Double(x, y)); } public void setCenter(int i, Point2D.Double p) { if (i < _listeBases.size()) { _listeBases.get(i).setCenter(p); } } public void drawRNACircle(VARNAConfig conf) { _drawn = true; _drawMode = DRAW_MODE_CIRCULAR; int radius = (int) ((3 * (_listeBases.size() + 1) * BASE_RADIUS) / (2 * Math.PI)); double angle; for (int i = 0; i < _listeBases.size(); i++) { angle = -((((double) -(i + 1)) * 2.0 * Math.PI) / ((double) (_listeBases.size() + 1)) - Math.PI / 2.0); _listeBases .get(i) .setCoords( new Point2D.Double( (radius * Math.cos(angle) * conf._spaceBetweenBases), (radius * Math.sin(angle) * conf._spaceBetweenBases))); _listeBases.get(i).setCenter(new Point2D.Double(0, 0)); } } public void drawRNAVARNAView(VARNAConfig conf) { _drawn = true; _drawMode = DRAW_MODE_VARNA_VIEW; VARNASecDraw vs = new VARNASecDraw(); vs.drawRNA(1, this); } public void drawRNALine(VARNAConfig conf) { _drawn = true; _drawMode = DRAW_MODE_LINEAR; for (int i = 0; i < get_listeBases().size(); i++) { get_listeBases().get(i).setCoords( new Point2D.Double(i * conf._spaceBetweenBases * 20, 0)); get_listeBases().get(i).setCenter( new Point2D.Double(i * conf._spaceBetweenBases * 20, -10)); } } public RNATemplateMapping drawRNATemplate(RNATemplate template, VARNAConfig conf) throws RNATemplateDrawingAlgorithmException { return drawRNATemplate(template, conf, DrawRNATemplateMethod.getDefault(), DrawRNATemplateCurveMethod.getDefault()); } public RNATemplateMapping drawRNATemplate(RNATemplate template, VARNAConfig conf, DrawRNATemplateMethod helixLengthAdjustmentMethod) throws RNATemplateDrawingAlgorithmException { return drawRNATemplate(template, conf, helixLengthAdjustmentMethod, DrawRNATemplateCurveMethod.getDefault()); } public RNATemplateMapping drawRNATemplate(RNATemplate template, VARNAConfig conf, DrawRNATemplateMethod helixLengthAdjustmentMethod, DrawRNATemplateCurveMethod curveMethod) throws RNATemplateDrawingAlgorithmException { _drawn = true; _drawMode = DRAW_MODE_TEMPLATE; DrawRNATemplate drawRNATemplate = new DrawRNATemplate(this); drawRNATemplate.drawRNATemplate(template, conf, helixLengthAdjustmentMethod, curveMethod); return drawRNATemplate.getMapping(); } private static double objFun(int n1, int n2, double r, double bpdist, double multidist) { return (((double) n1) * 2.0 * Math.asin(((double) bpdist) / (2.0 * r)) + ((double) n2) * 2.0 * Math.asin(((double) multidist) / (2.0 * r)) - (2.0 * Math.PI)); } public double determineRadius(int nbHel, int nbUnpaired, double startRadius) { return determineRadius(nbHel, nbUnpaired, startRadius, BASE_PAIR_DISTANCE, MULTILOOP_DISTANCE); } public static double determineRadius(int nbHel, int nbUnpaired, double startRadius, double bpdist, double multidist) { double xmin = bpdist / 2.0; double xmax = 3.0 * multidist + 1; double x = (xmin + xmax) / 2.0; double y = 10000.0; double ymin = -1000.0; double ymax = 1000.0; int numIt = 0; double precision = 0.00001; while ((Math.abs(y) > precision) && (numIt < 10000)) { x = (xmin + xmax) / 2.0; y = objFun(nbHel, nbUnpaired, x, bpdist, multidist); ymin = objFun(nbHel, nbUnpaired, xmax, bpdist, multidist); ymax = objFun(nbHel, nbUnpaired, xmin, bpdist, multidist); if (ymin > 0.0) { xmax = xmax + (xmax - xmin); } else if ((y <= 0.0) && (ymax > 0.0)) { xmax = x; } else if ((y >= 0.0) && (ymin < 0.0)) { xmin = x; } else if (ymax < 0.0) { xmin = Math.max(xmin - (x - xmin), Math.max(bpdist / 2.0, multidist / 2.0)); xmax = x; } numIt++; } return x; } public void drawRNA(VARNAConfig conf) throws ExceptionNAViewAlgorithm { drawRNA(RNA.DEFAULT_DRAW_MODE, conf); } public void drawRNA(int mode, VARNAConfig conf) throws ExceptionNAViewAlgorithm { _drawMode = mode; switch (get_drawMode()) { case RNA.DRAW_MODE_RADIATE: drawRNARadiate(conf); break; case RNA.DRAW_MODE_LINEAR: drawRNALine(conf); break; case RNA.DRAW_MODE_CIRCULAR: drawRNACircle(conf); break; case RNA.DRAW_MODE_NAVIEW: drawRNANAView(conf); break; case RNA.DRAW_MODE_VARNA_VIEW: drawRNAVARNAView(conf); break; default: break; } } public int getDrawMode() { return _drawMode; } public static double HYSTERESIS_EPSILON = .15; public static final double[] HYSTERESIS_ATTRACTORS = {0.,Math.PI/4.,Math.PI/2.,3.*Math.PI/4.,Math.PI,5.*(Math.PI)/4.,3.*(Math.PI)/2,7.*(Math.PI)/4.}; public static double normalizeAngle(double angle) { return normalizeAngle(angle,0.); } public static double normalizeAngle(double angle, double fromVal) { double toVal = fromVal +2.*Math.PI; double result = angle; while(result= toVal) { result -= 2.*Math.PI; } return result; } public static double correctHysteresis(double angle) { double result = normalizeAngle(angle); for (int i=0;i bases) { double mydist = Math.abs(radius*(angle / (bases.size() + 1))); double addedRadius= 0.; Point2D.Double PA = new Point2D.Double(center.x + radius * Math.cos(base + pHel), center.y + radius * Math.sin(base + pHel)); Point2D.Double PB = new Point2D.Double(center.x + radius * Math.cos(base + pHel+angle), center.y + radius * Math.sin(base + pHel+angle)); double dist = PA.distance(PB); Point2D.Double VN = new Point2D.Double((PB.y-PA.y)/dist,(-PB.x+PA.x)/dist); if (mydist<2*BASE_RADIUS) { addedRadius=Math.min(1.0,(2*BASE_RADIUS-mydist)/4)*computeRadius(mydist, 2.29*(bases.size() + 1)*BASE_RADIUS-mydist); } ArrayList pos = computeNewAngles(bases.size(),center,VN, angle,base + pHel,radius,addedRadius); for (int i = 0; i < bases.size(); i++) { int k = bases.get(i); setCoord(k, pos.get(i)); } } private double computeRadius(double b, double pobj) { double a=b, aL=a, aU=Double.POSITIVE_INFINITY; double h = (a-b)*(a-b)/((a+b)*(a+b)); double p = Math.PI*(a+b)*(1+h/4.+h*h/64.+h*h*h/256.+25.*h*h*h*h/16384.)/2.0; double aold = a+1.; while ((Math.abs(p-pobj)>10e-4)&&(aold!=a)){ aold = a; if (p prevBases,Vector nextBases) { if (isDirect) { double anglePrev = normalizeAngle(pLimL - pHelR); double angleNext = normalizeAngle(pHelL - pLimR); distributeUnpaired(radius,anglePrev, pHelR, base, center,prevBases); distributeUnpaired(radius,-angleNext, pHelL, base, center,nextBases); } else { double anglePrev = normalizeAngle(pHelL - pLimR); double angleNext = normalizeAngle(pLimL - pHelR); distributeUnpaired(radius,-anglePrev, pHelL, base, center,prevBases); distributeUnpaired(radius,angleNext, pHelR, base, center,nextBases); } } private static Point2D.Double getPoint(double angleLine, double angleBulge, Point2D.Double center, Point2D.Double VN,double radius, double addedRadius, double dirBulge) { return new Point2D.Double( center.x + radius * Math.cos(angleLine)+ dirBulge*addedRadius*Math.sin(angleBulge)*VN.x, center.y + radius * Math.sin(angleLine)+ dirBulge*addedRadius*Math.sin(angleBulge)*VN.y); } private ArrayList computeNewAngles(int numPoints, Point2D.Double center, Point2D.Double VN, double angle, double angleBase, double radius, double addedRadius) { ArrayList result = new ArrayList(); if (numPoints>0) { ArrayList factors = new ArrayList(); Point2D.Double prevP = new Point2D.Double( center.x + radius * Math.cos(angleBase), center.y + radius * Math.sin(angleBase)); double fact = 0.; double angleBulge = 0.; double dirBulge = (angle<0)?-1.:1.; double dtarget =2.*BASE_RADIUS; for (int i = 0; i < numPoints; i++) { double lbound = fact; double ubound = 1.0; double angleLine = angleBase + angle*fact; angleBulge = Math.PI*fact; Point2D.Double currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge); int numIter = 0; while ((Math.abs(currP.distance(prevP)-dtarget)>0.01)&& (numIter<100)) { if (currP.distance(prevP)> dtarget) { ubound = fact; fact = (fact+lbound)/2.0; } else { lbound = fact; fact = (fact+ubound)/2.0; } angleLine = angleBase + angle*fact; angleBulge = Math.PI*fact; currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge); numIter++; } factors.add(fact); prevP = currP; } double rescale = 1.0/(factors.get(factors.size()-1)+factors.get(0)); for(int j=0;j0) { prevP = getPoint(angleBase, 0, center,VN,radius, addedRadius, dirBulge); double totDist = 0.0; for(int j=0;j(); prevP = new Point2D.Double( center.x + radius * Math.cos(angleBase), center.y + radius * Math.sin(angleBase)); for (int i = 0; i < numPoints; i++) { double lbound = fact; double ubound = 1.5; double angleLine = angleBase + angle*fact; angleBulge = Math.PI*fact; Point2D.Double currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge); int numIter = 0; while ((Math.abs(currP.distance(prevP)-dtarget)>0.01)&& (numIter<100)) { if (currP.distance(prevP)> dtarget) { ubound = fact; fact = (fact+lbound)/2.0; } else { lbound = fact; fact = (fact+ubound)/2.0; } angleLine = angleBase + angle*fact; angleBulge = Math.PI*fact; currP = getPoint(angleLine, angleBulge, center,VN,radius, addedRadius, dirBulge); numIter++; } factors.add(fact); prevP = currP; } rescale = 1.0/(factors.get(factors.size()-1)+factors.get(0)); for(int j=0;j j) { return; } // BasePaired if (_listeBases.get(i).getElementStructure() == j) { double normalAngle = Math.PI / 2.0; centers[i] = new Point2D.Double(x, y); centers[j] = new Point2D.Double(x, y); coords[i].x = (x + BASE_PAIR_DISTANCE * Math.cos(dirAngle - normalAngle) / 2.0); coords[i].y = (y + BASE_PAIR_DISTANCE * Math.sin(dirAngle - normalAngle) / 2.0); coords[j].x = (x + BASE_PAIR_DISTANCE * Math.cos(dirAngle + normalAngle) / 2.0); coords[j].y = (y + BASE_PAIR_DISTANCE * Math.sin(dirAngle + normalAngle) / 2.0); drawLoop(i + 1, j - 1, x + LOOP_DISTANCE * Math.cos(dirAngle), y + LOOP_DISTANCE * Math.sin(dirAngle), dirAngle, coords, centers, angles); } else { int k = i; Vector basesMultiLoop = new Vector(); Vector helices = new Vector(); int l; while (k <= j) { l = _listeBases.get(k).getElementStructure(); if (l > k) { basesMultiLoop.add(new Integer(k)); basesMultiLoop.add(new Integer(l)); helices.add(new Integer(k)); k = l + 1; } else { basesMultiLoop.add(new Integer(k)); k++; } } int mlSize = basesMultiLoop.size() + 2; int numHelices = helices.size() + 1; double totalLength = MULTILOOP_DISTANCE * (mlSize - numHelices) + BASE_PAIR_DISTANCE * numHelices; double multiLoopRadius; double angleIncrementML; double angleIncrementBP; if (mlSize > 3) { multiLoopRadius = determineRadius(numHelices, mlSize - numHelices, (totalLength) / (2.0 * Math.PI), BASE_PAIR_DISTANCE, MULTILOOP_DISTANCE); angleIncrementML = -2.0 * Math.asin(((float) MULTILOOP_DISTANCE) / (2.0 * multiLoopRadius)); angleIncrementBP = -2.0 * Math.asin(((float) BASE_PAIR_DISTANCE) / (2.0 * multiLoopRadius)); } else { multiLoopRadius = 35.0; angleIncrementBP = -2.0 * Math.asin(((float) BASE_PAIR_DISTANCE) / (2.0 * multiLoopRadius)); angleIncrementML = (-2.0 * Math.PI - angleIncrementBP) / 2.0; } // System.out.println("MLr:"+multiLoopRadius+" iBP:"+angleIncrementBP+" iML:"+angleIncrementML); double centerDist = Math.sqrt(Math.max(Math.pow(multiLoopRadius, 2) - Math.pow(BASE_PAIR_DISTANCE / 2.0, 2), 0.0)) - LOOP_DISTANCE; Point2D.Double mlCenter = new Point2D.Double( (x + (centerDist * Math.cos(dirAngle))), (y + (centerDist * Math.sin(dirAngle)))); // Base directing angle for (multi|hairpin) loop, from the center's // perspective double baseAngle = dirAngle // U-turn + Math.PI // Account for already drawn supporting base-pair + 0.5 * angleIncrementBP // Base cannot be paired twice, so next base is at // "unpaired base distance" + 1.0 * angleIncrementML; ArrayList currUnpaired = new ArrayList(); Couple currInterval = new Couple(0.,baseAngle-1.0 * angleIncrementML); ArrayList,Couple>> intervals = new ArrayList,Couple>>(); for (k = basesMultiLoop.size() - 1; k >= 0; k--) { l = basesMultiLoop.get(k).intValue(); //System.out.println(l+" "); centers[l] = mlCenter; boolean isPaired = (_listeBases.get(l).getElementStructure() != -1); boolean isPaired3 = isPaired && (_listeBases.get(l).getElementStructure() < l); boolean isPaired5 = isPaired && !isPaired3; if (isPaired3) { baseAngle = correctHysteresis(baseAngle+angleIncrementBP/2.)-angleIncrementBP/2.; currInterval.first = baseAngle; intervals.add(new Couple,Couple>(currUnpaired,currInterval)); currInterval = new Couple(-1.,-1.); currUnpaired = new ArrayList(); } else if (isPaired5) { currInterval.second = baseAngle; } else { currUnpaired.add(l); } angles[l] = baseAngle; if (isPaired3) { baseAngle += angleIncrementBP; } else { baseAngle += angleIncrementML; } } currInterval.first = dirAngle - Math.PI - 0.5 * angleIncrementBP; intervals.add(new Couple,Couple>(currUnpaired,currInterval)); //System.out.println("Inc. ML:"+angleIncrementML+" BP:"+angleIncrementBP); for(Couple,Couple> inter: intervals) { //double mid = inter.second.second; double mina = inter.second.first; double maxa = normalizeAngle(inter.second.second,mina); //System.out.println(""+mina+" " +maxa); for (int n=0;n= 0; k--) { l = basesMultiLoop.get(k).intValue(); coords[l].x = mlCenter.x + multiLoopRadius * Math.cos(angles[l]); coords[l].y = mlCenter.y + multiLoopRadius * Math.sin(angles[l]); } // System.out.println("n1:"+n1+" n2:"+n2); double newAngle; int m, n; for (k = 0; k < helices.size(); k++) { m = helices.get(k).intValue(); n = _listeBases.get(m).getElementStructure(); newAngle = (angles[m] + angles[n]) / 2.0; drawLoop(m + 1, n - 1, (LOOP_DISTANCE * Math.cos(newAngle)) + (coords[m].x + coords[n].x) / 2.0, (LOOP_DISTANCE * Math.sin(newAngle)) + (coords[m].y + coords[n].y) / 2.0, newAngle, coords, centers, angles); } } } private Vector getPreviousUnpaired(Point h) { Vector prevBases = new Vector(); boolean over = false; int i = h.y + 1; while (!over) { if (i >=get_listeBases().size()) { over = true; } else { if (get_listeBases().get(i) .getElementStructure() == -1) { prevBases.add(new Integer(i)); } else { over = true; } } i++; } return prevBases; } private Vector getNextUnpaired(Point h) { boolean over = false; int i = h.x - 1; Vector nextBases = new Vector(); while (!over) { if (i < 0) { over = true; } else { if (get_listeBases().get(i) .getElementStructure() == -1) { nextBases.add(new Integer(i)); } else { over = true; } } i--; } return nextBases; } public void rotateEverything(double delta, double base, double pLimL, double pLimR, Point h, Point ml, Hashtable backupPos) { boolean isDirect = testDirectionality(ml.x, ml.y, h.x); Point2D.Double center = get_listeBases().get(h.x).getCenter(); for(int k=h.x;k<=h.y;k++) { backupPos.put(k, getBaseAt(k).getCoords()); } rotateHelix(center, h.x, h.y, delta); // Re-assigns unpaired atoms Point2D.Double helixStart = getCoords(h.x); Point2D.Double helixStop = getCoords(h.y); double pHelR,pHelL; if (isDirect) { pHelR = computeAngle(center, helixStop) - base; pHelL = computeAngle(center, helixStart) - base; } else { pHelL = computeAngle(center, helixStop) - base; pHelR = computeAngle(center, helixStart) - base; } Vector prevBases = getPreviousUnpaired(h); Vector nextBases = getNextUnpaired(h); double radius = center.distance(helixStart); for (int j = 0; j < prevBases.size(); j++) { int k = prevBases.get(j); backupPos.put(k, getCoords(k)); } for (int j = 0; j < nextBases.size(); j++) { int k = nextBases.get(j); backupPos.put(k, getCoords(k)); } fixUnpairedPositions(isDirect, pHelR, pLimL, pLimR, pHelL, radius, base,center,prevBases,nextBases); } public void drawRNARadiate() { drawRNARadiate(-1.0, VARNAConfig.DEFAULT_SPACE_BETWEEN_BASES, true); } public void drawRNARadiate(VARNAConfig conf) { drawRNARadiate(-1.0, conf._spaceBetweenBases, conf._flatExteriorLoop); } public static final double FLAT_RECURSIVE_INCREMENT = 20.; public void drawRNARadiate(double dirAngle, double _spaceBetweenBases, boolean flatExteriorLoop) { _drawn = true; _drawMode = DRAW_MODE_RADIATE; Point2D.Double[] coords = new Point2D.Double[_listeBases.size()]; Point2D.Double[] centers = new Point2D.Double[_listeBases.size()]; double[] angles = new double[_listeBases.size()]; for (int i = 0; i < _listeBases.size(); i++) { coords[i] = new Point2D.Double(0, 0); centers[i] = new Point2D.Double(0, 0); } if (flatExteriorLoop) { dirAngle += 1.0 - Math.PI / 2.0; int i = 0; double x = 0.0; double y = 0.0; double vx = -Math.sin(dirAngle); double vy = Math.cos(dirAngle); while (i < _listeBases.size()) { coords[i].x = x; coords[i].y = y; centers[i].x = x + BASE_PAIR_DISTANCE * vy; centers[i].y = y - BASE_PAIR_DISTANCE * vx; int j = _listeBases.get(i).getElementStructure(); if (j > i) { double increment = 0.; if (i+1<_listeBases.size()) { if (_listeBases.get(i+1).getElementStructure()==-1) { //increment = -FLAT_RECURSIVE_INCREMENT; } } drawLoop(i, j, x + (BASE_PAIR_DISTANCE * vx / 2.0), y + (BASE_PAIR_DISTANCE * vy / 2.0)+increment, dirAngle, coords, centers, angles); centers[i].x = coords[i].x + BASE_PAIR_DISTANCE * vy; centers[i].y = y - BASE_PAIR_DISTANCE * vx; i = j; x += BASE_PAIR_DISTANCE * vx; y += BASE_PAIR_DISTANCE * vy; centers[i].x = coords[i].x + BASE_PAIR_DISTANCE * vy; centers[i].y = y - BASE_PAIR_DISTANCE * vx; } x += MULTILOOP_DISTANCE * vx; y += MULTILOOP_DISTANCE * vy; i += 1; } } else { drawLoop(0, _listeBases.size() - 1, 0, 0, dirAngle, coords, centers, angles); } for (int i = 0; i < _listeBases.size(); i++) { _listeBases.get(i).setCoords( new Point2D.Double(coords[i].x * _spaceBetweenBases, coords[i].y * _spaceBetweenBases)); _listeBases.get(i).setCenter( new Point2D.Double(centers[i].x * _spaceBetweenBases, centers[i].y * _spaceBetweenBases)); } // TODO // change les centres des bases de la premiere helice vers la boucle la // plus proche } public void drawRNANAView(VARNAConfig conf) throws ExceptionNAViewAlgorithm { _drawMode = DRAW_MODE_NAVIEW; _drawn = true; ArrayList X = new ArrayList(_listeBases.size()); ArrayList Y = new ArrayList(_listeBases.size()); ArrayList pair_table = new ArrayList(_listeBases.size()); for (int i = 0; i < _listeBases.size(); i++) { pair_table.add(Short.valueOf(String.valueOf(_listeBases.get(i) .getElementStructure()))); } NAView naView = new NAView(); naView.naview_xy_coordinates(pair_table, X, Y); // Updating individual base positions for (int i = 0; i < _listeBases.size(); i++) { _listeBases.get(i).setCoords( new Point2D.Double( X.get(i) * 2.5 * conf._spaceBetweenBases, Y.get(i) * 2.5 * conf._spaceBetweenBases)); } // Updating centers for (int i = 0; i < _listeBases.size(); i++) { int indicePartner = _listeBases.get(i).getElementStructure(); if (indicePartner != -1) { Point2D.Double base = _listeBases.get(i).getCoords(); Point2D.Double partner = _listeBases.get(indicePartner) .getCoords(); _listeBases.get(i).setCenter( new Point2D.Double((base.x + partner.x) / 2.0, (base.y + partner.y) / 2.0)); } else { Vector loop = getLoopBases(i); double tmpx = 0.0; double tmpy = 0.0; for (int j = 0; j < loop.size(); j++) { int partner = loop.elementAt(j); Point2D.Double loopmember = _listeBases.get(partner) .getCoords(); tmpx += loopmember.x; tmpy += loopmember.y; } _listeBases.get(i).setCenter( new Point2D.Double(tmpx / loop.size(), tmpy / loop.size())); } } } /* * public void drawMOTIFView() { _drawn = true; _drawMode = * DRAW_MODE_MOTIFVIEW; int spaceBetweenStrand =0; Motif motif = new * Motif(this,get_listeBases()); motif.listStrand(); for (int i = 0; i < * motif.getListStrand().sizeStruct(); i++ ){ for (int j = 0; j < * motif.getListStrand().getStrand(i).sizeStrand(); j++ ){ int indice = * motif.getListStrand().getStrand(i).getMB(j).getIndex(); * get_listeBases().get(indice).setCoords( new Point2D.Double(0,0)); * get_listeBases().get(indice).setCenter( new Point2D.Double(0, 0)); * * } } //Recherche du brin central int centralStrand = * motif.getCentralStrand(); * * //Cas o? l'on a un motif en ?toile if(centralStrand!=-1){ //On positionne * le brin central motif.positionneSpecificStrand(centralStrand, * spaceBetweenStrand); * * //On place les autres brins par rapport a ce brin central * motif.orderStrands(centralStrand); } * * else { centralStrand = 0; motif.positionneStrand(); motif.ajusteStrand(); * } motif.reajustement(); motif.deviationBasePair(); * motif.setCenterMotif(); } */ public ArrayList getAllPartners(int indice) { ArrayList result = new ArrayList(); ModeleBase me = this.getBaseAt(indice); int i = me.getElementStructure(); if (i != -1) { result.add(getBaseAt(i)); } ArrayList msbps = getAuxBPs(indice); for (ModeleBP m : msbps) { result.add(m.getPartner(me)); } return result; } public int get_drawMode() { return _drawMode; } public void setDrawMode(int drawMode) { _drawMode = drawMode; } public Set getSeparatorPositions(String s) { HashSet result = new HashSet(); int index = s.indexOf(DBNStrandSep); while (index >= 0) { result.add(index); index = s.indexOf(DBNStrandSep, index + 1); } return result; } public static String DBNStrandSep = "&"; public void setRNA(String seq, String str) throws ExceptionFileFormatOrSyntax, ExceptionUnmatchedClosingParentheses { ArrayList al = RNA.explodeSequence(seq); Set sepPos = getSeparatorPositions(str); ArrayList alRes = new ArrayList(); Set resSepPos = new HashSet(); String strRes = ""; for (int i = 0; i < al.size(); i++) { if (sepPos.contains(i) && al.get(i).equals(DBNStrandSep)) { resSepPos.add(alRes.size() - 1); } else { alRes.add(al.get(i)); if (i s = RNA.explodeSequence(seq); int[] str = new int[s.size()]; for (int i = 0; i < str.length; i++) { str[i] = -1; } try { setRNA(s, str); } catch (ExceptionFileFormatOrSyntax e) { // TODO Auto-generated catch block e.printStackTrace(); } } public void setRNA(String seq, int[] str) throws ExceptionFileFormatOrSyntax, ExceptionUnmatchedClosingParentheses { setRNA(RNA.explodeSequence(seq), str); } public void setRNA(String[] seq, int[] str) throws ExceptionFileFormatOrSyntax { setRNA(seq, str, 1); } public void setRNA(List seq, int[] str) throws ExceptionFileFormatOrSyntax { setRNA(seq.toArray(new String[seq.size()]), str, 1); } public void setRNA(List seq, int[] str, int baseIndex) throws ExceptionFileFormatOrSyntax { setRNA(seq.toArray(new String[seq.size()]), str, baseIndex); } public void setRNA(String[] seq, int[] str, int baseIndex) throws ExceptionFileFormatOrSyntax { clearAnnotations(); _listeBases = new ArrayList(); if (seq.length != str.length) { warningEmition("Sequence length " + seq.length + " differs from that of secondary structure " + str.length + ". \nAdapting sequence length ..."); if (seq.length < str.length) { String[] nseq = new String[str.length]; for (int i = 0; i < seq.length; i++) { nseq[i] = seq[i]; } for (int i = seq.length; i < nseq.length; i++) { nseq[i] = ""; } seq = nseq; } else { String[] seqTmp = new String[str.length]; for (int i = 0; i < str.length; i++) { seqTmp[i] = seq[i]; } seq = seqTmp; } } for (int i = 0; i < str.length; i++) { _listeBases.add(new ModeleBaseNucleotide(seq[i], i, baseIndex + i)); } applyStruct(str); } /** * Sets the RNA to be drawn. Uses when comparison mode is on. Will draw the * super-structure passed in parameters and apply specials styles to the * bases owning by each RNA alignment and both. * * @param seq * - The sequence of the super-structure This sequence shall be * designed like this: * firstRNA1stBaseSecondRNA1stBaseFirstRNA2ndBaseSecondRNA2ndBase [...] *
* Example: AAC-GUAGA--UGG * @param struct * - The super-structure * @param basesOwn * - The RNA owning bases array (each index will be:0 when common * base, 1 when first RNA alignment base, 2 when second RNA * alignment base) * @throws ExceptionUnmatchedClosingParentheses * @throws ExceptionFileFormatOrSyntax */ public void setRNA(String seq, String struct, ArrayList basesOwn) throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax { clearAnnotations(); _listeBases = new ArrayList(); // On "parse" la structure (repérage des points, tiret et couples // parentheses ouvrante/fermante) int[] array_struct = parseStruct(struct); int size = struct.length(); int j = 0; for (int i = 0; i < size; i++) { ModeleBase mb; if (seq.charAt(j) != seq.charAt(j + 1)) { ModeleBasesComparison mbc = new ModeleBasesComparison( seq.charAt(j), seq.charAt(j + 1), i); mbc.set_appartenance(basesOwn.get(i)); mbc.setBaseNumber(i + 1); mb = mbc; } else { mb = new ModeleBaseNucleotide("" + seq.charAt(j), i, i + 1); } _listeBases.add(mb); j += 2; } for (int i = 0; i < size; i++) { if (array_struct[i] != -1) { this.addBPNow(i, array_struct[i]); } j += 2; } } public void setRNA(List seq, String dbnStr) throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax { clearAnnotations(); int[] finStr = RNAFactory.parseSecStr(dbnStr); setRNA(seq, finStr); } public static ArrayList explodeSequence(String seq) { ArrayList analyzedSeq = new ArrayList(); int i = 0; while (i < seq.length()) { if (seq.charAt(i) == '{') { boolean found = false; String buf = ""; i++; while (!found & (i < seq.length())) { if (seq.charAt(i) != '}') { buf += seq.charAt(i); i++; } else { found = true; } } analyzedSeq.add(buf); } else { analyzedSeq.add("" + seq.charAt(i)); } i++; } return analyzedSeq; } public int[] parseStruct(String str) throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax { int[] result = new int[str.length()]; int unexpectedChar = -1; Stack p = new Stack(); for (int i = 0; i < str.length(); i++) { char c = str.charAt(i); if (c == '(') { p.push(new Integer(i)); } else if (c == '.' || c == '-' || c == ':') { result[i] = -1; } else if (c == ')') { if (p.size() == 0) { throw new ExceptionUnmatchedClosingParentheses(i + 1); } int j = p.pop().intValue(); result[i] = j; result[j] = i; } else { if (unexpectedChar == -1) unexpectedChar = i; break; } } if (unexpectedChar != -1) { // warningEmition("Unexpected Character at index:" + // unexpectedChar); } if (p.size() != 0) { throw new ExceptionUnmatchedClosingParentheses( p.pop().intValue() + 1); } return result; } public Point getHelixInterval(int index) { if ((index < 0) || (index >= _listeBases.size())) { return new Point(index, index); } int j = _listeBases.get(index).getElementStructure(); if (j != -1) { int minH = index; int maxH = index; if (j > index) { maxH = j; } else { minH = j; } boolean over = false; while (!over) { if ((minH < 0) || (maxH >= _listeBases.size())) { over = true; } else { if (_listeBases.get(minH).getElementStructure() == maxH) { minH--; maxH++; } else { over = true; } } } minH++; maxH--; return new Point(minH, maxH); } return new Point(0, 0); } public Point getExteriorHelix(int index) { Point h = getHelixInterval(index); int a = -1; int b = -1; while (!((h.x==0)&&(h.y==0))) { a = h.x; b = h.y; h = getHelixInterval(a-1); } return new Point(a, b); } public ArrayList getHelix(int index) { ArrayList result = new ArrayList(); if ((index < 0) || (index >= _listeBases.size())) { return result; } Point p = getHelixInterval(index); for (int i = p.x; i <= p.y; i++) { result.add(i); result.add(this._listeBases.get(i).getElementStructure()); } return result; } public Point getMultiLoop(int index) { if ((index < 0) || (index >= _listeBases.size())) { return new Point(index, index); } Point h = getHelixInterval(index); int minH = h.x - 1; int maxH = h.y + 1; boolean over = false; while (!over) { if (minH < 0) { over = true; minH = 0; } else { if (_listeBases.get(minH).getElementStructure() == -1) { minH--; } else if (_listeBases.get(minH).getElementStructure() < minH) { minH = _listeBases.get(minH).getElementStructure() - 1; } else { over = true; } } } over = false; while (!over) { if (maxH > _listeBases.size() - 1) { over = true; maxH = _listeBases.size() - 1; } else { if (_listeBases.get(maxH).getElementStructure() == -1) { maxH++; } else if (_listeBases.get(maxH).getElementStructure() > maxH) { maxH = _listeBases.get(maxH).getElementStructure() + 1; } else { over = true; } } } return new Point(minH, maxH); } public Vector getLoopBases(int startIndex) { Vector result = new Vector(); if ((startIndex < 0) || (startIndex >= _listeBases.size())) { return result; } int index = startIndex; result.add(startIndex); if (_listeBases.get(index).getElementStructure() <= index) { index = (index + 1) % _listeBases.size(); } else { index = _listeBases.get(index).getElementStructure(); result.add(index); index = (index + 1) % _listeBases.size(); } while (index != startIndex) { result.add(index); if (_listeBases.get(index).getElementStructure() == -1) { index = (index + 1) % _listeBases.size(); } else { index = _listeBases.get(index).getElementStructure(); result.add(index); index = (index + 1) % _listeBases.size(); } } return result; } /** * Returns the RNA secondary structure displayed by this panel as a * well-parenthesized word, accordingly to the DBN format * * @return This panel's secondary structure */ public String getStructDBN() { String result = ""; for (int i = 0; i < _listeBases.size(); i++) { int j = _listeBases.get(i).getElementStructure(); if (j == -1) { result += "."; } else if (i > j) { result += ")"; } else { result += "("; } } return addStrandSeparators(result); } private ArrayList getNonCrossingSubset( ArrayList> rankedBPs) { ArrayList currentBPs = new ArrayList(); Stack pile = new Stack(); for (int i = 0; i < rankedBPs.size(); i++) { ArrayList lbp = rankedBPs.get(i); if (!lbp.isEmpty()) { ModeleBP bp = lbp.get(0); boolean ok = true; if (!pile.empty()) { int x = pile.peek(); if ((bp.getIndex3() >= x)) { ok = false; } } if (ok) { lbp.remove(0); currentBPs.add(bp); pile.add(bp.getIndex3()); } } if (!pile.empty() && (i == pile.peek())) { pile.pop(); } } return currentBPs; } public ArrayList paginateStructure() { ArrayList result = new ArrayList(); // Mumbo jumbo to sort the basepair list ArrayList bps = this.getAllBPs(); ModeleBP[] mt = new ModeleBP[bps.size()]; bps.toArray(mt); Arrays.sort(mt, new Comparator() { public int compare(ModeleBP arg0, ModeleBP arg1) { if (arg0.getIndex5() != arg1.getIndex5()) return arg0.getIndex5() - arg1.getIndex5(); else return arg0.getIndex3() - arg1.getIndex3(); } }); ArrayList> rankedBps = new ArrayList>(); for (int i = 0; i < getSize(); i++) { rankedBps.add(new ArrayList()); } for (int i = 0; i < mt.length; i++) { rankedBps.get(mt[i].getIndex5()).add(mt[i]); } while (!bps.isEmpty()) { //System.out.println("Page: " + result.size()); ArrayList currentBPs = getNonCrossingSubset(rankedBps); int[] ss = new int[this.getSize()]; for (int i = 0; i < ss.length; i++) { ss[i] = -1; } for (int i = 0; i < currentBPs.size(); i++) { ModeleBP mbp = currentBPs.get(i); ss[mbp.getIndex3()] = mbp.getIndex5(); ss[mbp.getIndex5()] = mbp.getIndex3(); } bps.removeAll(currentBPs); result.add(ss); } return result; } private void showBasic(int[] res) { for (int i = 0; i < res.length; i++) { System.out.print(res[i] + ","); } System.out.println(); } public int[] getStrandShifts() { int[] result = new int[getSize()]; int acc = 0; for (int i=0;i pages = paginateStructure(); char[] res = new char[getSize()]; for (int i = 0; i < res.length; i++) { res[i] = '.'; } char[] open = { '(', '[', '{', '<', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N' }; char[] close = { ')', ']', '}', '>', 'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n' }; for (int p = 0; p < Math.min(pages.size(), open.length); p++) { int[] page = pages.get(p); //showBasic(page); for (int i = 0; i < res.length; i++) { if (page[i] != -1 && page[i] > i && res[i] == '.' && res[page[i]] == '.') { res[i] = open[p]; res[page[i]] = close[p]; } } } result = ""; for (int i = 0; i < res.length; i++) { result += res[i]; } } return addStrandSeparators(result); } public String getStructDBN(int[] str) { String result = ""; for (int i = 0; i < str.length; i++) { if (str[i] == -1) { result += "."; } else if (str[i] > i) { result += "("; } else { result += ")"; } } return addStrandSeparators(result); } /** * Returns the raw nucleotides sequence for the displayed RNA * * @return The RNA sequence */ public String getSeq() { String result = ""; for (int i = 0; i < _listeBases.size(); i++) { result += ((ModeleBase) _listeBases.get(i)).getContent(); } return addStrandSeparators(result); } public String getStructBPSEQ() { String result = ""; int[] str = getNonOverlappingStruct(); for (int i = 0; i < _listeBases.size(); i++) { result += (i + 1) + " " + ((ModeleBaseNucleotide) _listeBases.get(i)).getContent() + " " + (str[i] + 1) + "\n"; } return result; } public int[] getNonCrossingStruct() { int[] result = new int[_listeBases.size()]; // Adding "planar" base-pairs for (int i = 0; i < _listeBases.size(); i++) { result[i] = _listeBases.get(i).getElementStructure(); } return result; } public int[] getNonOverlappingStruct() { int[] result = getNonCrossingStruct(); // Adding additional base pairs when possible (No more than one // base-pair per base) for (int i = 0; i < _structureAux.size(); i++) { ModeleBP msbp = _structureAux.get(i); ModeleBase mb5 = msbp.getPartner5(); ModeleBase mb3 = msbp.getPartner3(); int j5 = mb5.getIndex(); int j3 = mb3.getIndex(); if ((result[j3] == -1) && (result[j5] == -1)) { result[j3] = j5; result[j5] = j3; } } return result; } public String getStructCT() { String result = ""; for (int i = 0; i < _listeBases.size(); i++) { result += (i + 1) + " " + ((ModeleBase) _listeBases.get(i)).getContent() + " " + i + " " + (i + 2) + " " + (_listeBases.get(i).getElementStructure() + 1) + " " + (i + 1) + "\n"; } return result; } public void saveAsBPSEQ(String path, String title) throws ExceptionExportFailed, ExceptionPermissionDenied { try { FileWriter f = new FileWriter(path); f.write("# " + title + "\n"); f.write(this.getStructBPSEQ() + "\n"); f.close(); } catch (IOException e) { throw new ExceptionExportFailed(e.getMessage(), path); } } public void saveAsCT(String path, String title) throws ExceptionExportFailed, ExceptionPermissionDenied { try { FileWriter f = new FileWriter(path); f.write("" + _listeBases.size() + " " + title + "\n"); f.write(this.getStructCT() + "\n"); f.close(); } catch (IOException e) { throw new ExceptionExportFailed(e.getMessage(), path); } } public void saveAsDBN(String path, String title) throws ExceptionExportFailed, ExceptionPermissionDenied { try { FileWriter f = new FileWriter(path); f.write("> " + title + "\n"); f.write(getListeBasesToString() + "\n"); f.write(getStructDBN() + "\n"); f.close(); } catch (IOException e) { throw new ExceptionExportFailed(e.getMessage(), path); } } public String getListeBasesToString() { String s = new String(); for (int i = 0; i < _listeBases.size(); i++) { s += ((ModeleBaseNucleotide) _listeBases.get(i)).getContent(); } return addStrandSeparators(s); } public void applyBPs(ArrayList allbps) { ArrayList planar = new ArrayList(); ArrayList others = new ArrayList(); // System.err.println("Sequence: "+this.getSeq()); RNAMLParser.planarize(allbps, planar, others, getSize()); // System.err.println("All:"+allbps); // System.err.println("=> Planar: "+planar); // System.err.println("=> Others: "+others); for (ModeleBP mb : planar) { addBPnow(mb.getPartner5().getIndex(), mb.getPartner3().getIndex(), mb); } for (ModeleBP mb : others) { addBPAux(mb.getPartner5().getIndex(), mb.getPartner3().getIndex(), mb); } } public void set_listeBases(ArrayList _liste) { this._listeBases = _liste; } public void addVARNAListener(InterfaceVARNAListener rl) { _listeVARNAListener.add(rl); } public void warningEmition(String warningMessage) { for (int i = 0; i < _listeVARNAListener.size(); i++) { _listeVARNAListener.get(i).onWarningEmitted(warningMessage); } } public void applyStyleOnBases(ArrayList basesList, ModelBaseStyle style) { for (int i = 1; i < basesList.size(); i++) { _listeBases.get(basesList.get(i)).setStyleBase(style); } } private int[] correctReciprocity(int[] str) { int[] result = new int[str.length]; for (int i = 0; i < str.length; i++) { if (str[i] != -1) { if (i == str[str[i]]) { result[i] = str[i]; } else { str[str[i]] = i; } } else { result[i] = -1; } } return result; } private void applyStruct(int[] str) throws ExceptionFileFormatOrSyntax { str = correctReciprocity(str); int[] planarSubset = RNAMLParser.planarize(str); _structureAux.clear(); for (int i = 0; i < planarSubset.length; i++) { if (str[i] > i) { if (planarSubset[i] > i) { addBPNow(i, planarSubset[i]); } else if ((planarSubset[i] != str[i])) { addBPAux(i, str[i]); } } } } public ArrayList get_listeBases() { return _listeBases; } public int getSize() { return _listeBases.size(); } public ArrayList findAll() { ArrayList listAll = new ArrayList(); for (int i = 0; i < get_listeBases().size(); i++) { listAll.add(i); } return listAll; } public ArrayList findBulge(int index) { ArrayList listUp = new ArrayList(); if (get_listeBases().get(index).getElementStructure() == -1) { int i = index; boolean over = false; while ((i < get_listeBases().size()) && !over) { int j = get_listeBases().get(i).getElementStructure(); if (j == -1) { listUp.add(i); i++; } else { over = true; } } i = index - 1; over = false; while ((i >= 0) && !over) { int j = get_listeBases().get(i).getElementStructure(); if (j == -1) { listUp.add(i); i--; } else { over = true; } } } return listUp; } public ArrayList findStem(int index) { ArrayList listUp = new ArrayList(); int i = index; do { listUp.add(i); int j = get_listeBases().get(i).getElementStructure(); if (j == -1) { i = (i + 1) % getSize(); } else { if ((j < i) && (index <= i) && (j <= index)) { i = j; } else { i = (i + 1) % getSize(); } } } while (i != index); return listUp; } public int getHelixCountOnLoop(int indice) { int cptHelice = 0; if (indice < 0 || indice >= get_listeBases().size()) return cptHelice; int i = indice; int j = get_listeBases().get(i).getElementStructure(); // Only way to distinguish "supporting base-pair" from others boolean justJumped = false; if ((j != -1) && (j < i)) { i = j + 1; indice = i; } do { j = get_listeBases().get(i).getElementStructure(); if ((j != -1) && (!justJumped)) { i = j; justJumped = true; cptHelice++; } else { i = (i + 1) % get_listeBases().size(); justJumped = false; } } while (i != indice); return cptHelice; } public ArrayList findLoop(int indice) { return findLoopForward(indice); } public ArrayList findLoopForward(int indice) { ArrayList base = new ArrayList(); if (indice < 0 || indice >= get_listeBases().size()) return base; int i = indice; int j = get_listeBases().get(i).getElementStructure(); // Only way to distinguish "supporting base-pair" from others boolean justJumped = false; if (j != -1) { i = Math.min(i, j) + 1; indice = i; } do { base.add(i); j = get_listeBases().get(i).getElementStructure(); if ((j != -1) && (!justJumped)) { i = j; justJumped = true; } else { i = (i + 1) % get_listeBases().size(); justJumped = false; } } while (i != indice); return base; } public ArrayList findPair(int indice) { ArrayList base = new ArrayList(); int j = get_listeBases().get(indice).getElementStructure(); if (j != -1) { base.add(Math.min(indice, j)); base.add(Math.max(indice, j)); } return base; } public ArrayList findLoopBackward(int indice) { ArrayList base = new ArrayList(); if (indice < 0 || indice >= get_listeBases().size()) return base; int i = indice; int j = get_listeBases().get(i).getElementStructure(); // Only way to distinguish "supporting base-pair" from others boolean justJumped = false; if (j != -1) { i = Math.min(i, j) - 1; indice = i; } if (i < 0) { return base; } do { base.add(i); j = get_listeBases().get(i).getElementStructure(); if ((j != -1) && (!justJumped)) { i = j; justJumped = true; } else { i = (i + get_listeBases().size() - 1) % get_listeBases().size(); justJumped = false; } } while (i != indice); return base; } public ArrayList findHelix(int indice) { ArrayList list = new ArrayList(); if (get_listeBases().get(indice).getElementStructure() != -1) { list.add(indice); list.add(get_listeBases().get(indice).getElementStructure()); int i = 1, prec = get_listeBases().get(indice) .getElementStructure(); while (indice + i < get_listeBases().size() && get_listeBases().get(indice + i).getElementStructure() != -1 && get_listeBases().get(indice + i).getElementStructure() == prec - 1) { list.add(indice + i); list.add(get_listeBases().get(indice + i).getElementStructure()); prec = get_listeBases().get(indice + i).getElementStructure(); i++; } i = -1; prec = get_listeBases().get(indice).getElementStructure(); while (indice + i >= 0 && get_listeBases().get(indice + i).getElementStructure() != -1 && get_listeBases().get(indice + i).getElementStructure() == prec + 1) { list.add(indice + i); list.add(get_listeBases().get(indice + i).getElementStructure()); prec = get_listeBases().get(indice + i).getElementStructure(); i--; } } return list; } public ArrayList find3Prime(int indice) { ArrayList list = new ArrayList(); boolean over = false; while ((indice >= 0) && !over) { over = (get_listeBases().get(indice).getElementStructure() != -1); indice--; } indice++; if (over) { indice++; } for (int i = indice; i < get_listeBases().size(); i++) { list.add(i); if (get_listeBases().get(i).getElementStructure() != -1) { return new ArrayList(); } } return list; } public ArrayList find5Prime(int indice) { ArrayList list = new ArrayList(); for (int i = 0; i <= indice; i++) { list.add(i); if (get_listeBases().get(i).getElementStructure() != -1) { return new ArrayList(); } } return list; } public static Double angle(Point2D.Double p1, Point2D.Double p2, Point2D.Double p3) { Double alpha = Math.atan2(p1.y - p2.y, p1.x - p2.x); Double beta = Math.atan2(p3.y - p2.y, p3.x - p2.x); Double angle = (beta - alpha); // Correction de l'angle pour le resituer entre 0 et 2PI while (angle < 0.0 || angle > 2 * Math.PI) { if (angle < 0.0) angle += 2 * Math.PI; else if (angle > 2 * Math.PI) angle -= 2 * Math.PI; } return angle; } public ArrayList findNonPairedBaseGroup(Integer get_nearestBase) { // detection 3', 5', bulge ArrayList list = new ArrayList(); int indice = get_nearestBase; boolean nonpairedUp = true, nonpairedDown = true; while (indice < get_listeBases().size() && nonpairedUp) { if (get_listeBases().get(indice).getElementStructure() == -1) { list.add(indice); indice++; } else { nonpairedUp = false; } } indice = get_nearestBase - 1; while (indice >= 0 && nonpairedDown) { if (get_listeBases().get(indice).getElementStructure() == -1) { list.add(indice); indice--; } else { nonpairedDown = false; } } return list; } /* * public boolean getDrawn() { return _drawn; } */ public ArrayList getStructureAux() { return _structureAux; } /** * Translates a base number into its corresponding index. Although both * should be unique, base numbers are not necessarily contiguous, and * indices should be preferred for any reasonably complex algorithmic * treatment. * * @param num * The base number * @return The first index whose associated Base model has base number * num, -1 of no such base model exists. */ public int getIndexFromBaseNumber(int num) { for (int i = 0; i < this._listeBases.size(); i++) { if (_listeBases.get(i).getBaseNumber() == num) { return i; } } return -1; } /** * Adds a base pair to this RNA's structure. Tries to add it to the * secondary structure first, eventually adding it to the 'tertiary' * interactions if it clashes with the current secondary structure. * * @param baseNumber5 * - Base number of the origin of this base pair * @param baseNumber3 * - Base number of the destination of this base pair */ public void addBPToStructureUsingNumbers(int baseNumber5, int baseNumber3) { int i = getIndexFromBaseNumber(baseNumber5); int j = getIndexFromBaseNumber(baseNumber3); addBP(i, j); } /** * Adds a base pair to this RNA's structure. Tries to add it to the * secondary structure first, possibly adding it to the 'tertiary' * interactions if it clashes with the current secondary structure. * * @param number5 * - Base number of the origin of this base pair * @param number3 * - Base number of the destination of this base pair */ public void addBPToStructureUsingNumbers(int number5, int number3, ModeleBP msbp) { addBP(getIndexFromBaseNumber(number5), getIndexFromBaseNumber(number3), msbp); } public void addBP(int index5, int index3) { int i = index5; int j = index3; ModeleBase part5 = _listeBases.get(i); ModeleBase part3 = _listeBases.get(j); ModeleBP msbp = new ModeleBP(part5, part3); addBP(i, j, msbp); } public void addBP(int index5, int index3, ModeleBP msbp) { int i = index5; int j = index3; if (j < i) { int k = j; j = i; i = k; } if (i != -1) { for (int k = i; k <= j; k++) { ModeleBase tmp = _listeBases.get(k); int l = tmp.getElementStructure(); if (l != -1) { if ((l <= i) || (l >= j)) { addBPAux(i, j, msbp); return; } } } addBPnow(i, j, msbp); } } public void removeBP(ModeleBP ms) { if (_structureAux.contains(ms)) { _structureAux.remove(ms); } else { ModeleBase m5 = ms.getPartner5(); ModeleBase m3 = ms.getPartner3(); int i = m5.getIndex(); int j = m3.getIndex(); if ((m5.getElementStructure() == m3.getIndex()) && (m3.getElementStructure() == m5.getIndex())) { m5.removeElementStructure(); m3.removeElementStructure(); } } } /** * Register base-pair, no question asked. More precisely, this function will * not try to determine if the base-pairs crosses any other. * * @param i * @param j * @param msbp */ private void addBPNow(int i, int j) { if (j < i) { int k = j; j = i; i = k; } ModeleBase part5 = _listeBases.get(i); ModeleBase part3 = _listeBases.get(j); ModeleBP msbp = new ModeleBP(part5, part3); addBPnow(i, j, msbp); } /** * Register base-pair, no question asked. More precisely, this function will * not try to determine if the base-pairs crosses any other. * * @param i * @param j * @param msbp */ private void addBPnow(int i, int j, ModeleBP msbp) { if (j < i) { int k = j; j = i; i = k; } ModeleBase part5 = _listeBases.get(i); ModeleBase part3 = _listeBases.get(j); msbp.setPartner5(part5); msbp.setPartner3(part3); part5.setElementStructure(j, msbp); part3.setElementStructure(i, msbp); } public void addBPAux(int i, int j) { ModeleBase part5 = _listeBases.get(i); ModeleBase part3 = _listeBases.get(j); ModeleBP msbp = new ModeleBP(part5, part3); addBPAux(i, j, msbp); } public void addBPAux(int i, int j, ModeleBP msbp) { if (j < i) { int k = j; j = i; i = k; } ModeleBase part5 = _listeBases.get(i); ModeleBase part3 = _listeBases.get(j); msbp.setPartner5(part5); msbp.setPartner3(part3); _structureAux.add(msbp); } public ArrayList getBPsAt(int i) { ArrayList result = new ArrayList(); if (_listeBases.get(i).getElementStructure() != -1) { result.add(_listeBases.get(i).getStyleBP()); } for (int k = 0; k < _structureAux.size(); k++) { ModeleBP bp = _structureAux.get(k); if ((bp.getPartner5().getIndex() == i) || (bp.getPartner3().getIndex() == i)) { result.add(bp); } } return result; } public ModeleBP getBPStyle(int i, int j) { ModeleBP result = null; if (i > j) { int k = j; j = i; i = k; } if (_listeBases.get(i).getElementStructure() == j) { result = _listeBases.get(i).getStyleBP(); } for (int k = 0; k < _structureAux.size(); k++) { ModeleBP bp = _structureAux.get(k); if ((bp.getPartner5().getIndex() == i) && (bp.getPartner3().getIndex() == j)) { result = bp; } } return result; } public ArrayList getSecStrBPs() { ArrayList result = new ArrayList(); for (int i = 0; i < this.getSize(); i++) { ModeleBase mb = _listeBases.get(i); int k = mb.getElementStructure(); if ((k != -1) && (k > i)) { result.add(mb.getStyleBP()); } } return result; } public ArrayList getAuxBPs() { ArrayList result = new ArrayList(); for (ModeleBP bp : _structureAux) { result.add(bp); } return result; } public ArrayList getAllBPs() { ArrayList result = new ArrayList(); result.addAll(getSecStrBPs()); result.addAll(getAuxBPs()); return result; } public ArrayList getAuxBPs(int i) { ArrayList result = new ArrayList(); for (ModeleBP bp : _structureAux) { if ((bp.getPartner5().getIndex() == i) || (bp.getPartner3().getIndex() == i)) { result.add(bp); } } return result; } public void setBaseInnerColor(Color c) { for (int i = 0; i < _listeBases.size(); i++) { ModeleBase mb = _listeBases.get(i); mb.getStyleBase().setBaseInnerColor(c); } } public void setBaseNumbersColor(Color c) { for (int i = 0; i < _listeBases.size(); i++) { ModeleBase mb = _listeBases.get(i); mb.getStyleBase().setBaseNumberColor(c); } } public void setBaseNameColor(Color c) { for (int i = 0; i < _listeBases.size(); i++) { ModeleBase mb = _listeBases.get(i); mb.getStyleBase().setBaseNameColor(c); } } public void setBaseOutlineColor(Color c) { for (int i = 0; i < _listeBases.size(); i++) { ModeleBase mb = _listeBases.get(i); mb.getStyleBase().setBaseOutlineColor(c); } } public String getName() { return _name; } public void setName(String n) { _name = n; } public ArrayList getAnnotations() { return _listeAnnotations; } public boolean removeAnnotation(TextAnnotation t) { return _listeAnnotations.remove(t); } public void addAnnotation(TextAnnotation t) { _listeAnnotations.add(t); } public void removeAnnotation(String filter) { ArrayList condamne = new ArrayList(); for (TextAnnotation t : _listeAnnotations) { if (t.getTexte().contains(filter)) { condamne.add(t); } } for (TextAnnotation t : condamne) { _listeAnnotations.remove(t); } } public void clearAnnotations() { _listeAnnotations.clear(); } private boolean _strandEndsAnnotated = false; public void autoAnnotateStrandEnds() { if (!_strandEndsAnnotated) { int tailleListBases = _listeBases.size(); boolean endAnnotate = false; addAnnotation(new TextAnnotation("5'", _listeBases.get(0))); for (int i = 0; i < _listeBases.size() - 1; i++) { int realposA = _listeBases.get(i).getBaseNumber(); int realposB = _listeBases.get(i + 1).getBaseNumber(); if (realposB - realposA != 1) { addAnnotation(new TextAnnotation("3'", _listeBases.get(i))); addAnnotation(new TextAnnotation("5'", _listeBases.get(i + 1))); if (i + 1 == _listeBases.size() - 1) { endAnnotate = true; } } } if (!endAnnotate) { addAnnotation(new TextAnnotation("3'", _listeBases.get(tailleListBases - 1))); } _strandEndsAnnotated = true; } else { removeAnnotation("3'"); removeAnnotation("5'"); _strandEndsAnnotated = false; } } public void autoAnnotateHelices() { Stack p = new Stack(); p.push(0); int nbH = 1; while (!p.empty()) { int i = p.pop(); if (i < _listeBases.size()) { ModeleBase mb = _listeBases.get(i); int j = mb.getElementStructure(); if (j == -1) { p.push(i + 1); } else { if (j > i) { ModeleBase mbp = _listeBases.get(j); p.push(j + 1); ArrayList h = new ArrayList(); int k = 1; while (mb.getElementStructure() == mbp.getIndex()) { h.add(mb); h.add(mbp); mb = _listeBases.get(i + k); mbp = _listeBases.get(j - k); k++; } try { addAnnotation(new TextAnnotation("H" + nbH++, h, TextAnnotation.AnchorType.HELIX)); } catch (Exception e) { e.printStackTrace(); } p.push(i + k); } } } } } public void autoAnnotateTerminalLoops() { Stack p = new Stack(); p.push(0); int nbT = 1; while (!p.empty()) { int i = p.pop(); if (i < _listeBases.size()) { ModeleBase mb = _listeBases.get(i); int j = mb.getElementStructure(); if (j == -1) { int k = 1; ArrayList t = new ArrayList(); while ((i + k < getSize()) && (mb.getElementStructure() == -1)) { t.add(mb); mb = _listeBases.get(i + k); k++; } if (mb.getElementStructure() != -1) { if (mb.getElementStructure() == i - 1) { try { t.add(_listeBases.get(i - 1)); t.add(_listeBases.get(i + k - 1)); addAnnotation(new TextAnnotation("T" + nbT++, t, TextAnnotation.AnchorType.LOOP)); } catch (Exception e) { e.printStackTrace(); } } p.push(i + k - 1); } } else { if (j > i) { p.push(j + 1); p.push(i + 1); } } } } } public void autoAnnotateInteriorLoops() { Stack p = new Stack(); p.push(0); int nbT = 1; while (!p.empty()) { int i = p.pop(); if (i < _listeBases.size()) { ModeleBase mb = _listeBases.get(i); int j = mb.getElementStructure(); if (j == -1) { int k = i + 1; ArrayList t = new ArrayList(); boolean terminal = true; while ((k < getSize()) && ((mb.getElementStructure() >= i) || (mb .getElementStructure() == -1))) { t.add(mb); mb = _listeBases.get(k); if ((mb.getElementStructure() == -1) || (mb.getElementStructure() < k)) k++; else { p.push(k); terminal = false; k = mb.getElementStructure(); } } if (mb.getElementStructure() != -1) { if ((mb.getElementStructure() == i - 1) && !terminal) { try { t.add(_listeBases.get(i - 1)); t.add(_listeBases.get(k - 1)); addAnnotation(new TextAnnotation("I" + nbT++, t, TextAnnotation.AnchorType.LOOP)); } catch (Exception e) { e.printStackTrace(); } p.push(k - 1); } } } else { if (j > i) { p.push(i + 1); } } } } } @SuppressWarnings("unchecked") public TextAnnotation getAnnotation(TextAnnotation.AnchorType type, ModeleBase base) { TextAnnotation result = null; for (TextAnnotation t : _listeAnnotations) { if (t.getType() == type) { switch (type) { case BASE: if (base == (ModeleBase) t.getAncrage()) return t; break; case HELIX: case LOOP: { ArrayList mbl = (ArrayList) t .getAncrage(); if (mbl.contains(base)) return t; } break; } } } return result; } public void addChemProbAnnotation(ChemProbAnnotation cpa) { //System.err.println(cpa.isOut()); _chemProbAnnotations.add(cpa); } public ArrayList getChemProbAnnotations() { return _chemProbAnnotations; } public void setColorMapValues(Double[] values, ModeleColorMap cm) { setColorMapValues(values, cm, false); } public void adaptColorMapToValues(ModeleColorMap cm) { double min = Double.MAX_VALUE; double max = Double.MIN_VALUE; for (int i = 0; i < Math.min(_listeBases.size(), _listeBases.size()); i++) { ModeleBase mb = _listeBases.get(i); max = Math.max(max, mb.getValue()); min = Math.min(min, mb.getValue()); } cm.rescale(min, max); } private ArrayList loadDotPlot(StreamTokenizer st) { ArrayList result = new ArrayList(); try { boolean inSeq = false; String sequence = ""; ArrayList accumulator = new ArrayList(); int type = st.nextToken(); Hashtable,Double> BP = new Hashtable,Double>(); while (type != StreamTokenizer.TT_EOF) { switch (type) { case (StreamTokenizer.TT_NUMBER): accumulator.add(st.nval); break; case (StreamTokenizer.TT_EOL): break; case (StreamTokenizer.TT_WORD): if (st.sval.equals("/sequence")) { inSeq = true; } else if (st.sval.equals("ubox")) { int i = accumulator.get(accumulator.size()-3).intValue()-1; int j = accumulator.get(accumulator.size()-2).intValue()-1; double val = accumulator.get(accumulator.size()-1); //System.err.println((char) type); BP.put(new Couple(Math.min(i, j), Math.max(i, j)),val*val); accumulator.clear(); } else if (inSeq) { sequence += st.sval; } break; case ')': inSeq = false; break; } type = st.nextToken(); } for (int i = 0; i < getSize(); i++) { int j = getBaseAt(i).getElementStructure(); if (j != -1) { Couple coor = new Couple( Math.min(i, j), Math.max(i, j)); if (BP.containsKey(coor)) { result.add(BP.get(coor)); } else { result.add(0.); } } else { double acc = 1.0; for (int k = 0; k < getSize(); k++) { Couple coor = new Couple( Math.min(i, k), Math.max(i, k)); if (BP.containsKey(coor)) { acc -= BP.get(coor); } } result.add(acc); } } } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } return result; } public void readValues(Reader r, ModeleColorMap cm) { try { StreamTokenizer st = new StreamTokenizer(r); st.eolIsSignificant(true); st.wordChars('/', '/'); st.parseNumbers(); ArrayList vals = new ArrayList(); ArrayList curVals = new ArrayList(); int type = st.nextToken(); boolean isDotPlot = false; if (type=='%') { vals = loadDotPlot(st); isDotPlot = true; } else { while (type != StreamTokenizer.TT_EOF) { switch (type) { case (StreamTokenizer.TT_NUMBER): curVals.add(st.nval); break; case (StreamTokenizer.TT_EOL): if (curVals.size() > 0) { vals.add(curVals.get(curVals.size()-1)); curVals = new ArrayList(); } break; } type = st.nextToken(); } if (curVals.size() > 0) vals.add(curVals.get(curVals.size()-1)); } Double[] v = new Double[vals.size()]; for (int i = 0; i < Math.min(vals.size(), getSize()); i++) { v[i] = vals.get(i); } setColorMapValues(v, cm, true); if (isDotPlot) { cm.setMinValue(0.0); cm.setMaxValue(1.0); } } catch (IOException e) { e.printStackTrace(); } } public void setColorMapValues(Double[] values, ModeleColorMap cm, boolean rescaleColorMap) { if (values.length > 0) { for (int i = 0; i < Math.min(values.length, _listeBases.size()); i++) { ModeleBase mb = _listeBases.get(i); mb.setValue(values[i]); } if (rescaleColorMap) { adaptColorMapToValues(cm); } } } public Double[] getColorMapValues() { Double[] values = new Double[_listeBases.size()]; for (int i = 0; i < _listeBases.size(); i++) { values[i] = _listeBases.get(i).getValue(); } return values; } public void rescaleColorMap(ModeleColorMap cm) { Double max = Double.MIN_VALUE; Double min = Double.MAX_VALUE; for (int i = 0; i < _listeBases.size(); i++) { Double value = _listeBases.get(i).getValue(); max = Math.max(max, value); min = Math.min(min, value); } cm.rescale(min, max); } public void addBase(ModeleBase mb) { _listeBases.add(mb); } public void setSequence(String s) { setSequence(RNA.explodeSequence(s)); } public void setSequence(List s) { int i = 0; int j = 0; while ((i < s.size()) && (j < _listeBases.size())) { ModeleBase mb = _listeBases.get(j); if (mb instanceof ModeleBaseNucleotide) { ((ModeleBaseNucleotide) mb).setBase(s.get(i)); i++; j++; } else if (mb instanceof ModeleBasesComparison) { ((ModeleBasesComparison) mb) .setBase1(((s.get(i).length() > 0) ? s.get(i).charAt(0) : ' ')); ((ModeleBasesComparison) mb) .setBase2(((s.get(i + 1).length() > 0) ? s.get(i + 1) .charAt(0) : ' ')); i += 2; j++; } else j++; } for (i = _listeBases.size(); i < s.size(); i++) { _listeBases.add(new ModeleBaseNucleotide(s.get(i), i)); } } public void eraseSequence() { int j = 0; while ((j < _listeBases.size())) { ModeleBase mb = _listeBases.get(j); if (mb instanceof ModeleBaseNucleotide) { ((ModeleBaseNucleotide) mb).setBase(""); j++; } else if (mb instanceof ModeleBasesComparison) { ((ModeleBasesComparison) mb).setBase1(' '); ((ModeleBasesComparison) mb).setBase2(' '); j++; } else j++; } } public RNA clone() { try { ByteArrayOutputStream out = new ByteArrayOutputStream(); ObjectOutputStream oout = new ObjectOutputStream(out); oout.writeObject(this); ObjectInputStream in = new ObjectInputStream( new ByteArrayInputStream(out.toByteArray())); return (RNA) in.readObject(); } catch (Exception e) { throw new RuntimeException("cannot clone class [" + this.getClass().getName() + "] via serialization: " + e.toString()); } } /** * Returns the base at index index. Indices are contiguous in * the sequence over an interval [0,this.getSize()-1], where * n is the length of the sequence. * * @param index * The index, 0 ≤ index < this.getSize(), of the * base model * @return The base model of index index */ public ModeleBase getBaseAt(int index) { return this._listeBases.get(index); } /** * Returns the set of bases of indices in indices. Indices are * contiguous in the sequence, and belong to an interval * [0,n-1], where n is the length of the sequence. * * @param indices * A Collection of indices i, * 0 ≤ index < this.getSize(), where some base * models are found. * @return A list of base model of indices in indices */ public ArrayList getBasesAt( Collection indices) { ArrayList mbs = new ArrayList(); for (int i : indices) { mbs.add(getBaseAt(i)); } return mbs; } public ArrayList getBasesBetween(int from, int to) { ArrayList mbs = new ArrayList(); int bck = Math.min(from, to); to = Math.max(from, to); from = bck; for (int i = from; i <= to; i++) { mbs.add(getBaseAt(i)); } return mbs; } public void addHighlightRegion(HighlightRegionAnnotation n) { _listeRegionHighlights.add(n); } public void removeHighlightRegion(HighlightRegionAnnotation n) { _listeRegionHighlights.remove(n); } public void removeChemProbAnnotation(ChemProbAnnotation a) { _chemProbAnnotations.remove(a); } public void clearChemProbAnnotations() { _chemProbAnnotations.clear(); } public void addHighlightRegion(int from, int to, Color fill, Color outline, double radius) { _listeRegionHighlights.add(new HighlightRegionAnnotation( getBasesBetween(from, to), fill, outline, radius)); } public void addHighlightRegion(int from, int to) { _listeRegionHighlights.add(new HighlightRegionAnnotation( getBasesBetween(from, to))); } public ArrayList getHighlightRegion() { return _listeRegionHighlights; } /** * Rotates the RNA coordinates by a certain angle * * @param angleDegres * Rotation angle, in degrees */ public void globalRotation(Double angleDegres) { if (_listeBases.size() > 0) { // angle en radian Double angle = angleDegres * Math.PI / 180; // initialisation du minimum et dumaximum Double maxX = _listeBases.get(0).getCoords().x; Double maxY = _listeBases.get(0).getCoords().y; Double minX = _listeBases.get(0).getCoords().x; Double minY = _listeBases.get(0).getCoords().y; // mise a jour du minimum et du maximum for (int i = 0; i < _listeBases.size(); i++) { if (_listeBases.get(i).getCoords().getX() < minX) minX = _listeBases.get(i).getCoords().getX(); if (_listeBases.get(i).getCoords().getY() < minY) minY = _listeBases.get(i).getCoords().getY(); if (_listeBases.get(i).getCoords().getX() > maxX) maxX = _listeBases.get(i).getCoords().getX(); if (_listeBases.get(i).getCoords().getX() > maxY) maxY = _listeBases.get(i).getCoords().getY(); } // creation du point central Point2D.Double centre = new Point2D.Double((maxX - minX) / 2, (maxY - minY) / 2); Double x, y; for (int i = 0; i < _listeBases.size(); i++) { // application de la rotation au centre de chaque base // x' = cos(theta)*(x-xc) - sin(theta)*(y-yc) + xc x = Math.cos(angle) * (_listeBases.get(i).getCenter().getX() - centre.x) - Math.sin(angle) * (_listeBases.get(i).getCenter().getY() - centre.y) + centre.x; // y' = sin(theta)*(x-xc) + cos(theta)*(y-yc) + yc y = Math.sin(angle) * (_listeBases.get(i).getCenter().getX() - centre.x) + Math.cos(angle) * (_listeBases.get(i).getCenter().getY() - centre.y) + centre.y; _listeBases.get(i).setCenter(new Point2D.Double(x, y)); // application de la rotation au coordonnees de chaque // base // x' = cos(theta)*(x-xc) - sin(theta)*(y-yc) + xc x = Math.cos(angle) * (_listeBases.get(i).getCoords().getX() - centre.x) - Math.sin(angle) * (_listeBases.get(i).getCoords().getY() - centre.y) + centre.x; // y' = sin(theta)*(x-xc) + cos(theta)*(y-yc) + yc y = Math.sin(angle) * (_listeBases.get(i).getCoords().getX() - centre.x) + Math.cos(angle) * (_listeBases.get(i).getCoords().getY() - centre.y) + centre.y; _listeBases.get(i).setCoords(new Point2D.Double(x, y)); } } } private static double MIN_DISTANCE = 10.; /** * Flip an helix around its supporting base */ public void flipHelix(Point h) { if (h.x!=-1 && h.y!=-1 && h.x!=h.y) { int hBeg=h.x; int hEnd=h.y; Point2D.Double A = getCoords(hBeg); Point2D.Double B = getCoords(hEnd); Point2D.Double AB = new Point2D.Double(B.x - A.x, B.y - A.y); double normAB = Math.sqrt(AB.x * AB.x + AB.y * AB.y); // Creating a coordinate system centered on A and having // unit x-vector Ox. Point2D.Double O = A; Point2D.Double Ox = new Point2D.Double(AB.x / normAB, AB.y / normAB); Hashtable old = new Hashtable(); for (int i = hBeg + 1; i < hEnd; i++) { Point2D.Double P = getCoords(i); Point2D.Double nP = project(O, Ox, P); old.put(i, nP); setCoord(i, nP); Point2D.Double Center = getCenter(i); setCenter(i, project(O, Ox, Center)); } } } public static Point2D.Double project(Point2D.Double O, Point2D.Double Ox, Point2D.Double C) { Point2D.Double OC = new Point2D.Double(C.x - O.x, C.y - O.y); // Projection of OC on OI => OX double normOX = (Ox.x * OC.x + Ox.y * OC.y); Point2D.Double OX = new Point2D.Double((normOX * Ox.x), (normOX * Ox.y)); // Portion of OC orthogonal to Ox => XC Point2D.Double XC = new Point2D.Double(OC.x - OX.x, OC.y - OX.y); // Reflexive image of C with respect to Ox => CP Point2D.Double OCP = new Point2D.Double(OX.x - XC.x, OX.y - XC.y); Point2D.Double CP = new Point2D.Double(O.x + OCP.x, O.y + OCP.y); return CP; } public boolean testDirectionality(int i, int j, int k) { // Which direction are we heading toward? Point2D.Double pi = getCoords(i); Point2D.Double pj = getCoords(j); Point2D.Double pk = getCoords(k); return testDirectionality(pi, pj, pk); } public static boolean testDirectionality(Point2D.Double pi, Point2D.Double pj, Point2D.Double pk) { // Which direction are we heading toward? double test = (pj.x - pi.x) * (pk.y - pj.y) - (pj.y - pi.y) * (pk.x - pj.x); return test < 0.0; } public double getOrientation() { double maxDist = Double.MIN_VALUE; double angle = 0; for (int i = 0; i < _listeBases.size(); i++) { ModeleBase b1 = _listeBases.get(i); for (int j = i + 1; j < _listeBases.size(); j++) { ModeleBase b2 = _listeBases.get(j); Point2D.Double p1 = b1._coords.toPoint2D(); Point2D.Double p2 = b2._coords.toPoint2D(); double dist = p1.distance(p2); if (dist > maxDist) { maxDist = dist; angle = computeAngle(p1, p2); } } } return angle; } public boolean hasVirtualLoops() { boolean consecutiveBPs = false; for (int i = 0; i < _listeBases.size(); i++) { int j = _listeBases.get(i).getElementStructure(); if (j == i + 1) { consecutiveBPs = true; } } return ((_drawMode != DRAW_MODE_LINEAR) && (_drawMode != DRAW_MODE_CIRCULAR) && (consecutiveBPs)); } public String getHTMLDescription() { String result = ""; result += ""; result += ""; result += ""; return result + "
Name:" + this._name + "
Length:" + this.getSize() + " nts
Base-pairs:" + this.getAllBPs().size() + "
"; } public String getID() { return _id; } public void setID(String id) { _id = id; } public static ArrayList getGapPositions(String gapString) { ArrayList result = new ArrayList(); for (int i = 0; i < gapString.length(); i++) { char c = gapString.charAt(i); if (c == '.' || c == ':') { result.add(i); } } return result; } public RNA restrictTo(String gapString) { return restrictTo(getGapPositions(gapString)); } public RNA restrictTo(ArrayList positions) { RNA result = new RNA(); String oldSeq = this.getSeq(); String newSeq = ""; HashSet removedPos = new HashSet(positions); int[] matching = new int[oldSeq.length()]; int j = 0; for (int i = 0; i < oldSeq.length(); i++) { matching[i] = j; if (!removedPos.contains(i)) { newSeq += oldSeq.charAt(i); j++; } } result.setRNA(newSeq); for (ModeleBP m : getAllBPs()) { if (removedPos.contains(m.getIndex5()) || removedPos.contains(m.getIndex3())) { int i5 = matching[m.getIndex5()]; int i3 = matching[m.getIndex3()]; ModeleBP msbp = new ModeleBP(result.getBaseAt(i5), result.getBaseAt(i3), m.getEdgePartner5(), m.getEdgePartner3(), m.getStericity()); result.addBP(i5, i3, msbp); } } return result; } public void rescale(double d) { for (ModeleBase mb : _listeBases) { mb._coords.x *= d; mb._coords.y *= d; mb._center.x *= d; mb._center.y *= d; } } /** * Necessary for DrawRNATemplate (which is why the method is * package-visible). */ ArrayList getListeBases() { return _listeBases; } } fr/orsay/lri/varna/models/rna/ModeleBackbone.java0000644000000000000000000000335512265603114020763 0ustar rootrootpackage fr.orsay.lri.varna.models.rna; import java.awt.Color; import java.io.Serializable; import java.util.ArrayList; import java.util.Hashtable; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.models.rna.ModeleBackboneElement.BackboneType; import fr.orsay.lri.varna.utils.XMLUtils; public class ModeleBackbone implements Serializable{ /** * */ private Hashtable elems = new Hashtable(); private static final long serialVersionUID = -614968737102943216L; public static String XML_ELEMENT_NAME = "backbone"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); hd.startElement("","",XML_ELEMENT_NAME,atts); for (ModeleBackboneElement bck:elems.values()) { bck.toXML(hd); } hd.endElement("","",XML_ELEMENT_NAME); atts.clear(); } public void addElement(ModeleBackboneElement mbe) { elems.put(mbe.getIndex(),mbe); } public BackboneType getTypeBefore(int indexBase) { return getTypeAfter(indexBase-1); } public BackboneType getTypeAfter(int indexBase) { if (elems.containsKey(indexBase)) return elems.get(indexBase).getType(); else return BackboneType.SOLID_TYPE; } public Color getColorBefore(int indexBase, Color defCol) { return getColorAfter(indexBase-1,defCol); } public Color getColorAfter(int indexBase, Color defCol) { if (elems.containsKey(indexBase)) { Color c = elems.get(indexBase).getColor(); if (c != null) return c; } return defCol; } } fr/orsay/lri/varna/models/rna/ModeleStrand.java0000644000000000000000000000266211620715270020513 0ustar rootrootpackage fr.orsay.lri.varna.models.rna; import java.util.ArrayList; public class ModeleStrand { private ArrayList _strand = new ArrayList(); private boolean hasBeenPlaced = false; private boolean strandLeft = false; private boolean strandRight = false; private int levelPosition; public ModeleStrand(){ } public void addBase(ModeleBase mb){ this._strand.add(mb); } public void addBase(int index, ModeleBase mb){ this._strand.add(index, mb); } public int sizeStrand() { return this._strand.size(); } public ModeleBase getMB(int a) { return this._strand.get(a); } public ArrayList getArrayListMB() { return this._strand; } public int getLevelPosition(){ return this.levelPosition; } public void setLevelPosition(int a){ this.levelPosition=a; } public boolean getStrandRight(){ return this.strandRight; } public void setStrandRight(boolean bool){ this.strandRight=bool; } public boolean getStrandLeft(){ return this.strandLeft; } public void setStrandLeft(boolean bool){ this.strandLeft=bool; } public boolean hasBeenPlaced(){ return this.hasBeenPlaced; } public void setHasBeenPlaced(boolean bool){ this.hasBeenPlaced =bool; } public boolean existInStrand(int a){ int size =sizeStrand(); boolean exist=false; for (int i=0; i _mapping = new Hashtable(); Hashtable _invMapping = new Hashtable(); public Mapping() { } public void addCouple(int i, int j) throws MappingException { if (_mapping.containsKey(i) || _invMapping.containsKey(j)) { throw new MappingException( MappingException.MULTIPLE_PARTNERS_DEFINITION_ATTEMPT); } _mapping.put(new Integer(i), new Integer(j)); _invMapping.put(new Integer(j), new Integer(i)); } public int getPartner(int i) { if (!_mapping.containsKey(i)) return UNKNOWN; else return _mapping.get(i); } public int getAncestor(int j) { if (!_invMapping.containsKey(j)) return UNKNOWN; else return _invMapping.get(j); } public int[] getSourceElems() { int[] elems = new int[_mapping.size()]; Enumeration en = _mapping.keys(); int i = 0; while (en.hasMoreElements()) { int a = en.nextElement(); elems[i] = a; i++; } return elems; } public int[] getTargetElems() { int[] elems = new int[_invMapping.size()]; Enumeration en = _invMapping.keys(); int i = 0; while (en.hasMoreElements()) { int a = en.nextElement(); elems[i] = a; i++; } return elems; } public static Mapping readMappingFromAlignment(String m, String n) throws MappingException { Mapping map = new Mapping(); if (m.length() != n.length()) { throw new MappingException(MappingException.BAD_ALIGNMENT_INPUT); } int i = 0; int j = 0; for (int k = 0; k < m.length(); k++) { char a = m.charAt(k); char b = n.charAt(k); if ((a != '-') && (a != ':') && (b != '-') && (b != ':')) { map.addCouple(i, j); } if ((a != '-') && (a != ':')) { j++; } if ((b != '-') && (b != ':')) { i++; } } return map; } public static Mapping DefaultMapping(int n, int m) { Mapping map = new Mapping(); try { for (int i = 0; i < Math.min(n, m); i++) { map.addCouple(i, i); } } catch (MappingException e) { e.printStackTrace(); } return map; } public static Mapping DefaultOutermostMapping(int n, int m) { Mapping map = new Mapping(); try { int k = Math.min(n, m); int i = 0; int j = 0; boolean pile = true; while (i <= (k - 1) - j) { if (pile) { map.addCouple(i, i); i++; } else { map.addCouple(n - 1 - j, m - 1 - j); j++; } pile = !pile; } } catch (MappingException e) { e.printStackTrace(); } // System.println(map); return map; } public String toString() { Enumeration en = _mapping.keys(); String tmp = ""; int l1 = 0; int l2 = 0; int maxIndex = 0; while (en.hasMoreElements()) { Integer i = en.nextElement(); Integer j = _mapping.get(i); l1 = Math.max(l1,i); l2 = Math.max(l2,j); tmp += "("+i+","+j+")"; } maxIndex = Math.max(maxIndex,Math.max(l1,l2)); String tmp1 = ""; String tmp2 = ""; en = _mapping.keys(); int i = l1; int j = l2; while (en.hasMoreElements()) { Integer a = en.nextElement(); Integer b = _mapping.get(a); while(a _subscripts = new HashMap(); private static HashMap _superscripts = new HashMap(); private static HashMap _commands = new HashMap(); { _subscripts.put('0', '\u2080'); _subscripts.put('1', '\u2081'); _subscripts.put('2', '\u2082'); _subscripts.put('3', '\u2083'); _subscripts.put('4', '\u2084'); _subscripts.put('5', '\u2085'); _subscripts.put('6', '\u2086'); _subscripts.put('7', '\u2087'); _subscripts.put('8', '\u2088'); _subscripts.put('9', '\u2089'); _subscripts.put('+', '\u208A'); _subscripts.put('-', '\u208B'); _subscripts.put('a', '\u2090'); _subscripts.put('e', '\u2091'); _subscripts.put('o', '\u2092'); _subscripts.put('i', '\u1D62'); _subscripts.put('r', '\u1D63'); _subscripts.put('u', '\u1D64'); _subscripts.put('v', '\u1D65'); _subscripts.put('x', '\u2093'); _superscripts.put('0', '\u2070'); _superscripts.put('1', '\u00B9'); _superscripts.put('2', '\u00B2'); _superscripts.put('3', '\u00B3'); _superscripts.put('4', '\u2074'); _superscripts.put('5', '\u2075'); _superscripts.put('6', '\u2076'); _superscripts.put('7', '\u2077'); _superscripts.put('8', '\u2078'); _superscripts.put('9', '\u2079'); _superscripts.put('+', '\u207A'); _superscripts.put('-', '\u207B'); _superscripts.put('i', '\u2071'); _superscripts.put('n', '\u207F'); _commands.put("alpha", '\u03B1'); _commands.put("beta", '\u03B2'); _commands.put("gamma", '\u03B3'); _commands.put("delta", '\u03B4'); _commands.put("epsilon",'\u03B5'); _commands.put("zeta", '\u03B6'); _commands.put("eta", '\u03B7'); _commands.put("theta", '\u03B8'); _commands.put("iota", '\u03B9'); _commands.put("kappa", '\u03BA'); _commands.put("lambda", '\u03BB'); _commands.put("mu", '\u03BC'); _commands.put("nu", '\u03BD'); _commands.put("xi", '\u03BE'); _commands.put("omicron",'\u03BF'); _commands.put("pi", '\u03C1'); _commands.put("rho", '\u03C2'); _commands.put("sigma", '\u03C3'); _commands.put("tau", '\u03C4'); _commands.put("upsilon",'\u03C5'); _commands.put("phi", '\u03C6'); _commands.put("chi", '\u03C7'); _commands.put("psi", '\u03C8'); _commands.put("omega", '\u03C9'); _commands.put("Psi", '\u03A8'); _commands.put("Phi", '\u03A6'); _commands.put("Sigma", '\u03A3'); _commands.put("Pi", '\u03A0'); _commands.put("Theta", '\u0398'); _commands.put("Omega", '\u03A9'); _commands.put("Gamma", '\u0393'); _commands.put("Delta", '\u0394'); _commands.put("Lambda", '\u039B'); } private static String decode(String s) { if (s.length()<=1) { return s; } STATE_SPECIAL_CHARS_STATES state = STATE_SPECIAL_CHARS_STATES.NORMAL; String result = ""; String buffer = ""; for(int i=0;i _indices; private double _dx; private double _dy; private VARNAPanel _vp; public BasesShiftEdit(ArrayList indices, double dx, double dy, VARNAPanel p) { _indices = indices; _dx = dx; _dy = dy; _vp = p; } public void undo() throws CannotUndoException { for (int index: _indices) { ModeleBase mb = _vp.getRNA().getBaseAt(index); _vp.getRNA().setCoord(index,new Point2D.Double(mb.getCoords().x-_dx,mb.getCoords().y-_dy)); _vp.getRNA().setCenter(index,new Point2D.Double(mb.getCenter().x-_dx,mb.getCenter().y-_dy)); } _vp.repaint(); } public void redo() throws CannotRedoException { for (int index: _indices) { ModeleBase mb = _vp.getRNA().getBaseAt(index); _vp.getRNA().setCoord(index,new Point2D.Double(mb.getCoords().x+_dx,mb.getCoords().y+_dy)); _vp.getRNA().setCenter(index,new Point2D.Double(mb.getCenter().x-_dx,mb.getCenter().y-_dy)); } _vp.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Base #"+_indices+" shifted"; } public boolean addEdit(UndoableEdit anEdit) { if (anEdit instanceof BasesShiftEdit) { BasesShiftEdit e = (BasesShiftEdit) anEdit; if (e._indices.equals(_indices)) { Point2D.Double tot = new Point2D.Double(_dx+e._dx,_dy+e._dy); if (tot.distance(0.0, 0.0)Math.PI) { totAngle -= 2.0*Math.PI; } if (Math.abs(totAngle).7 || cumFact<1.3) { _factor *= e._factor; return true; } } return false; } }; public static class RotateRNAEdit extends AbstractUndoableEdit { private double _angle; private VARNAPanel _vp; public RotateRNAEdit( double angle, VARNAPanel vp) { _angle = angle; _vp = vp; } public void undo() throws CannotUndoException { _vp.getRNA().globalRotation(-_angle); _vp.repaint(); } public void redo() throws CannotRedoException { _vp.getRNA().globalRotation(_angle); _vp.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Rotate RNA angle:"+_angle+"";} public boolean addEdit(UndoableEdit anEdit) { if (anEdit instanceof RotateRNAEdit) { RotateRNAEdit e = (RotateRNAEdit) anEdit; if (Math.abs(_angle+e._angle)<30) { _angle += e._angle; return true; } } return false; } }; public static class RedrawEdit extends AbstractUndoableEdit { private int _prevMode; private int _newMode; private boolean _prevFlat; private boolean _newFlat; private ArrayList _backupCoords = new ArrayList(); private ArrayList _backupCenters = new ArrayList(); private VARNAPanel _vp; public RedrawEdit(VARNAPanel vp,boolean newFlat) { this(vp.getRNA().getDrawMode(),vp,newFlat); } public RedrawEdit(int newMode, VARNAPanel vp) { this(newMode,vp,vp.getFlatExteriorLoop()); } public RedrawEdit(int newMode, VARNAPanel vp, boolean newFlat) { _vp = vp; _newMode = newMode; _newFlat = newFlat; _prevFlat = _vp.getFlatExteriorLoop(); for (ModeleBase mb: _vp.getRNA().get_listeBases()) { _backupCoords.add(new Point2D.Double(mb.getCoords().x,mb.getCoords().y)); _backupCenters.add(new Point2D.Double(mb.getCenter().x,mb.getCenter().y)); } _prevMode = _vp.getDrawMode(); } public void undo() throws CannotUndoException { RNA r = _vp.getRNA(); _vp.setFlatExteriorLoop(_prevFlat); r.setDrawMode(_prevMode); for (int index =0;index<_vp.getRNA().get_listeBases().size();index++) { Point2D.Double oldCoord = _backupCoords.get(index); Point2D.Double oldCenter = _backupCenters.get(index); r.setCoord(index, oldCoord); r.setCenter(index, oldCenter); } _vp.repaint(); } public void redo() throws CannotRedoException { try { _vp.setFlatExteriorLoop(_newFlat); _vp.getRNA().drawRNA(_newMode,_vp.getConfig()); } catch (ExceptionNAViewAlgorithm e) { e.printStackTrace(); } _vp.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Redraw whole RNA";} public boolean addEdit(UndoableEdit anEdit) { return false; } }; } fr/orsay/lri/varna/models/naView/0000755000000000000000000000000012275611440015733 5ustar rootrootfr/orsay/lri/varna/models/naView/Connection.java0000644000000000000000000000510111620715272020673 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.naView; public class Connection { private Loop loop = new Loop(); private Region region = new Region(); // Start and end form the 1st base pair of the region. private int start, end; private double xrad, yrad, angle; // True if segment between this connection and the // next must be extruded out of the circle private boolean extruded; // True if the extruded segment must be drawn long. private boolean broken; private boolean _isNull=false; public boolean isNull() { return _isNull; } public void setNull(boolean isNull) { _isNull = isNull; } public Loop getLoop() { return loop; } public void setLoop(Loop loop) { this.loop = loop; } public Region getRegion() { return region; } public void setRegion(Region region) { this.region = region; } public int getStart() { return start; } public void setStart(int start) { this.start = start; } public int getEnd() { return end; } public void setEnd(int end) { this.end = end; } public double getXrad() { return xrad; } public void setXrad(double xrad) { this.xrad = xrad; } public double getYrad() { return yrad; } public void setYrad(double yrad) { this.yrad = yrad; } public double getAngle() { return angle; } public void setAngle(double angle) { this.angle = angle; } public boolean isExtruded() { return extruded; } public void setExtruded(boolean extruded) { this.extruded = extruded; } public boolean isBroken() { return broken; } public void setBroken(boolean broken) { this.broken = broken; } } fr/orsay/lri/varna/models/naView/Base.java0000644000000000000000000000335011620715272017452 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.naView; public class Base { private int mate; private double x, y; private boolean extracted; private Region region = new Region(); public int getMate() { return mate; } public void setMate(int mate) { this.mate = mate; } public double getX() { return x; } public void setX(double x) { //System.out.println(" Base.setX()"); this.x = x; } public double getY() { return y; } public void setY(double y) { this.y = y; } public boolean isExtracted() { return extracted; } public void setExtracted(boolean extracted) { this.extracted = extracted; } public Region getRegion() { return region; } public void setRegion(Region region) { this.region = region; } } fr/orsay/lri/varna/models/naView/Loop.java0000644000000000000000000000562511620715272017520 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.naView; import java.util.ArrayList; import java.util.Hashtable; public class Loop { private int nconnection; private ArrayList connections = new ArrayList(); private Hashtable _connections = new Hashtable(); private int number; private int depth; private boolean mark; private double x, y, radius; public int getNconnection() { return nconnection; } public void setNconnection(int nconnection) { this.nconnection = nconnection; } public void setConnection(int i, Connection c) { Integer n = new Integer(i); if (c != null) _connections.put(n, c); else { if (!_connections.containsKey(n)) { _connections.put(n, new Connection()); } _connections.get(i).setNull(true); } } public Connection getConnection(int i) { Integer n = new Integer(i); if (!_connections.containsKey(n)) { _connections.put(n, new Connection()); } Connection c = _connections.get(n); if (c.isNull()) return null; else return c; } public void addConnection(int i, Connection c) { _connections.put(_connections.size(),c); } public int getNumber() { return number; } public void setNumber(int number) { this.number = number; } public int getDepth() { return depth; } public void setDepth(int depth) { this.depth = depth; } public boolean isMark() { return mark; } public void setMark(boolean mark) { this.mark = mark; } public double getX() { return x; } public void setX(double x) { this.x = x; } public double getY() { return y; } public void setY(double y) { this.y = y; } public double getRadius() { return radius; } public void setRadius(double radius) { this.radius = radius; } public String toString() { String result = "Loop:"; result += " nconnection "+nconnection; result += " depth "+depth; return result; } } fr/orsay/lri/varna/models/naView/NAView.java0000644000000000000000000011123011620715272017726 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.naView; import java.util.ArrayList; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNAObservable; public class NAView { private final double ANUM = 9999.0; private final int MAXITER = 500; private ArrayList bases; private int nbase, nregion, loop_count; private Loop root = new Loop(); private ArrayList loops; private ArrayList regions; private Radloop rlphead = new Radloop(); private double lencut=0.8; private final double RADIUS_REDUCTION_FACTOR = 1.4; // show algorithm step by step private boolean debug = false; private double angleinc; private double _h; private ArrayList _listeVARNAListener = new ArrayList(); private boolean noIterationFailureYet = true; double HELIX_FACTOR = 0.6; double BACKBONE_DISTANCE = 27; public int naview_xy_coordinates(ArrayList pair_table2, ArrayList x, ArrayList y) throws ExceptionNAViewAlgorithm { if (debug) System.out.println("naview_xy_coordinates"); if (pair_table2.size() == 0) return 0; int i; ArrayList pair_table = new ArrayList(pair_table2 .size() + 1); pair_table.add(pair_table2.size()); for (int j = 0; j < pair_table2.size(); j++) { pair_table.add(pair_table2.get(j) + 1); } if (debug) { infoStructure(pair_table); } // length nbase = pair_table.get(0); bases = new ArrayList(nbase + 1); for (int index = 0; index < bases.size(); index++) { bases.add(new Base()); } regions = new ArrayList(); for (int index = 0; index < nbase + 1; index++) { regions.add(new Region()); } read_in_bases(pair_table); if (debug) infoBasesMate(); rlphead = null; find_regions(); if (debug) infoRegions(); loop_count = 0; loops = new ArrayList(nbase + 1); for (int index = 0; index < nbase + 1; index++) { loops.add(new Loop()); } construct_loop(0); if (debug) infoBasesExtracted(); find_central_loop(); if (debug) infoRoot(); if (debug) dump_loops(); traverse_loop(root, null); for (i = 0; i < nbase; i++) { x.add(100 + BACKBONE_DISTANCE * bases.get(i + 1).getX()); y.add(100 + BACKBONE_DISTANCE * bases.get(i + 1).getY()); } return nbase; } private void infoStructure(ArrayList pair_table) { System.out.println("structure:"); for (int j = 0; j < pair_table.size(); j++) { System.out.print("#" + j + ":" + pair_table.get(j) + "\t"); if (j % 10 == 0) System.out.println(); } System.out.println(); } private void infoBasesMate() { System.out.println("Bases mate:"); for (int index = 0; index < bases.size(); index++) { System.out.print("#" + index + ":" + bases.get(index).getMate() + "\t"); if (index % 10 == 0) System.out.println(); } System.out.println(); } private void infoRegions() { System.out.println("regions:"); for (int index = 0; index < regions.size(); index++) { System.out.print("(" + regions.get(index).getStart1() + "," + regions.get(index).getStart2() + ";" + regions.get(index).getEnd1() + "," + regions.get(index).getEnd2() + ")\t\t"); if (index % 5 == 0) System.out.println(); } System.out.println(); } private void infoBasesExtracted() { System.out.println("Bases extracted:"); for (int index = 0; index < bases.size(); index++) { System.out.print("i=" + index + ":" + bases.get(index).isExtracted() + "\t"); if (index % 5 == 0) System.out.println(); } System.out.println(); } private void infoRoot() { System.out.println("root" + root.getNconnection() + ";" + root.getNumber()); System.out.println("\troot : "); System.out.println("\tdepth=" + root.getDepth()); System.out.println("\tmark=" + root.isMark()); System.out.println("\tnumber=" + root.getNumber()); System.out.println("\tradius=" + root.getRadius()); System.out.println("\tx=" + root.getX()); System.out.println("\ty=" + root.getY()); System.out.println("\tnconnection=" + root.getNconnection()); } private void read_in_bases(ArrayList pair_table) { if (debug) System.out.println("read_in_bases"); int i, npairs; // Set up an origin. bases.add(new Base()); bases.get(0).setMate(0); bases.get(0).setExtracted(false); bases.get(0).setX(ANUM); bases.get(0).setY(ANUM); for (npairs = 0, i = 1; i <= nbase; i++) { bases.add(new Base()); bases.get(i).setExtracted(false); bases.get(i).setX(ANUM); bases.get(i).setY(ANUM); bases.get(i).setMate(pair_table.get(i)); if ((int) pair_table.get(i) > i) npairs++; } // must have at least 1 pair to avoid segfault if (npairs == 0) { bases.get(1).setMate(nbase); bases.get(nbase).setMate(1); } } /** * Identifies the regions in the structure. */ private void find_regions() { if (debug) System.out.println("find_regions"); int i, mate, nb1; nb1 = nbase + 1; ArrayList mark = new ArrayList(nb1); for (i = 0; i < nb1; i++) mark.add(false); nregion = 0; for (i = 0; i <= nbase; i++) { if ((mate = bases.get(i).getMate()) != 0 && !mark.get(i)) { regions.get(nregion).setStart1(i); regions.get(nregion).setEnd2(mate); mark.set(i, true); mark.set(mate, true); bases.get(i).setRegion(regions.get(nregion)); bases.get(mate).setRegion(regions.get(nregion)); for (i++, mate--; i < mate && bases.get(i).getMate() == mate; i++, mate--) { mark.set(mate, true); mark.set(i, true); bases.get(i).setRegion(regions.get(nregion)); bases.get(mate).setRegion(regions.get(nregion)); } regions.get(nregion).setEnd1(--i); regions.get(nregion).setStart2(mate + 1); if (debug) { if (nregion == 0) System.out.printf("\nRegions are:\n"); System.out.printf( "Region %d is %d-%d and %d-%d with gap of %d.\n", nregion + 1, regions.get(nregion).getStart1(), regions.get(nregion).getEnd1(), regions .get(nregion).getStart2(), regions.get( nregion).getEnd2(), regions.get(nregion) .getStart2() - regions.get(nregion).getEnd1() + 1); } nregion++; } } } /** * Starting at residue ibase, recursively constructs the loop containing * said base and all deeper bases. * * @throws ExceptionNAViewAlgorithm */ private Loop construct_loop(int ibase) throws ExceptionNAViewAlgorithm { if (debug) System.out.println("construct_loop"); int i, mate; Loop retloop = new Loop(), lp = new Loop(); Connection cp = new Connection(); Region rp = new Region(); Radloop rlp = new Radloop(); retloop = loops.get(loop_count++); retloop.setNconnection(0); //System.out.println(""+ibase+" "+nbase); //ArrayList a = new ArrayList(nbase + 1); //retloop.setConnections(a); // for (int index = 0; index < nbase + 1; index++) // retloop.getConnections().add(new Connection()); //for (int index = 0; index < nbase + 1; index++) // retloop.addConnection(index,new Connection()); retloop.setDepth(0); retloop.setNumber(loop_count); retloop.setRadius(0.0); for (rlp = rlphead; rlp != null; rlp = rlp.getNext()) if (rlp.getLoopnumber() == loop_count) retloop.setRadius(rlp.getRadius()); i = ibase; do { if ((mate = bases.get(i).getMate()) != 0) { rp = bases.get(i).getRegion(); if (!bases.get(rp.getStart1()).isExtracted()) { if (i == rp.getStart1()) { bases.get(rp.getStart1()).setExtracted(true); bases.get(rp.getEnd1()).setExtracted(true); bases.get(rp.getStart2()).setExtracted(true); bases.get(rp.getEnd2()).setExtracted(true); lp = construct_loop(rp.getEnd1() < nbase ? rp.getEnd1() + 1 : 0); } else if (i == rp.getStart2()) { bases.get(rp.getStart2()).setExtracted(true); bases.get(rp.getEnd2()).setExtracted(true); bases.get(rp.getStart1()).setExtracted(true); bases.get(rp.getEnd1()).setExtracted(true); lp = construct_loop(rp.getEnd2() < nbase ? rp.getEnd2() + 1 : 0); } else { throw new ExceptionNAViewAlgorithm( "naview:Error detected in construct_loop. i = " + i + " not found in region table.\n"); } retloop.setNconnection(retloop.getNconnection() + 1); cp = new Connection(); retloop.setConnection(retloop.getNconnection() - 1, cp); retloop.setConnection(retloop.getNconnection(), null); cp.setLoop(lp); cp.setRegion(rp); if (i == rp.getStart1()) { cp.setStart(rp.getStart1()); cp.setEnd(rp.getEnd2()); } else { cp.setStart(rp.getStart2()); cp.setEnd(rp.getEnd1()); } cp.setExtruded(false); cp.setBroken(false); lp.setNconnection(lp.getNconnection() + 1); cp = new Connection(); lp.setConnection(lp.getNconnection() - 1, cp); lp.setConnection(lp.getNconnection(), null); cp.setLoop(retloop); cp.setRegion(rp); if (i == rp.getStart1()) { cp.setStart(rp.getStart2()); cp.setEnd(rp.getEnd1()); } else { cp.setStart(rp.getStart1()); cp.setEnd(rp.getEnd2()); } cp.setExtruded(false); cp.setBroken(false); } i = mate; } if (++i > nbase) i = 0; } while (i != ibase); return retloop; } /** * Displays all the loops. */ private void dump_loops() { System.out.println("dump_loops"); int il, ilp, irp; Loop lp; Connection cp; System.out.printf("\nRoot loop is #%d\n", loops.indexOf(root) + 1); for (il = 0; il < loop_count; il++) { lp = loops.get(il); System.out.printf("Loop %d has %d connections:\n", il + 1, lp .getNconnection()); for (int i = 0; (cp = lp.getConnection(i)) != null; i++) { ilp = (loops.indexOf(cp.getLoop())) + 1; irp = (regions.indexOf(cp.getRegion())) + 1; System.out.printf(" Loop %d Region %d (%d-%d)\n", ilp, irp, cp .getStart(), cp.getEnd()); } } } /** * Find node of greatest branching that is deepest. */ private void find_central_loop() { if (debug) System.out.println("find_central_loop"); Loop lp = new Loop(); int maxconn, maxdepth, i; determine_depths(); maxconn = 0; maxdepth = -1; for (i = 0; i < loop_count; i++) { lp = loops.get(i); if (lp.getNconnection() > maxconn) { maxdepth = lp.getDepth(); maxconn = lp.getNconnection(); root = lp; } else if (lp.getDepth() > maxdepth && lp.getNconnection() == maxconn) { maxdepth = lp.getDepth(); root = lp; } } } /** * Determine the depth of all loops. */ private void determine_depths() { if (debug) System.out.println("determine_depths"); Loop lp = new Loop(); int i, j; for (i = 0; i < loop_count; i++) { lp = loops.get(i); for (j = 0; j < loop_count; j++) loops.get(j).setMark(false); lp.setDepth(depth(lp)); } } /** * Determines the depth of loop, lp. Depth is defined as the minimum * distance to a leaf loop where a leaf loop is one that has only one or no * connections. */ private int depth(Loop lp) { if (debug) System.out.println("depth"); int count, ret, d; if (lp.getNconnection() <= 1) return 0; if (lp.isMark()) return -1; lp.setMark(true); count = 0; ret = 0; for (int i = 0; lp.getConnection(i) != null; i++) { d = depth(lp.getConnection(i).getLoop()); if (d >= 0) { if (++count == 1) ret = d; else if (ret > d) ret = d; } } lp.setMark(false); return ret + 1; } /** * This is the workhorse of the display program. The algorithm is recursive * based on processing individual loops. Each base pairing region is * displayed using the direction given by the circle diagram, and the * connections between the regions is drawn by equally spaced points. The * radius of the loop is set to minimize the square error for lengths * between sequential bases in the loops. The "correct" length for base * links is 1. If the least squares fitting of the radius results in loops * being less than 1/2 unit apart, then that segment is extruded. * * The variable, anchor_connection, gives the connection to the loop * processed in an previous level of recursion. * * @throws ExceptionNAViewAlgorithm */ private void traverse_loop(Loop lp, Connection anchor_connection) throws ExceptionNAViewAlgorithm { if (debug) System.out.println(" traverse_loop"); double xs, ys, xe, ye, xn, yn, angleinc, r; double radius, xc, yc, xo, yo, astart, aend, a; Connection cp, cpnext, acp, cpprev; int i, j, n, ic; double da, maxang; int count, icstart, icend, icmiddle, icroot; boolean done, done_all_connections, rooted; int sign; double midx, midy, nrx, nry, mx, my, vx, vy, dotmv, nmidx, nmidy; int icstart1, icup, icdown, icnext, direction; double dan, dx, dy, rr; double cpx, cpy, cpnextx, cpnexty, cnx, cny, rcn, rc, lnx, lny, rl, ac, acn, sx, sy, dcp; int imaxloop = 0; angleinc = 2 * Math.PI / (nbase + 1); acp = null; icroot = -1; int indice = 0; for (ic = 0; (cp = lp.getConnection(indice)) != null; indice++, ic++) { // xs = cos(angleinc*cp.setStart(); ys = sin(angleinc*cp.setStart(); // xe = // cos(angleinc*cp.setEnd()); ye = sin(angleinc*cp.setEnd()); xs = -Math.sin(angleinc * cp.getStart()); ys = Math.cos(angleinc * cp.getStart()); xe = -Math.sin(angleinc * cp.getEnd()); ye = Math.cos(angleinc * cp.getEnd()); xn = ye - ys; yn = xs - xe; r = Math.sqrt(xn * xn + yn * yn); cp.setXrad(xn / r); cp.setYrad(yn / r); cp.setAngle(Math.atan2(yn, xn)); if (cp.getAngle() < 0.0) cp.setAngle(cp.getAngle() + 2 * Math.PI); if (anchor_connection != null && anchor_connection.getRegion() == cp.getRegion()) { acp = cp; icroot = ic; } } // remplacement d'une etiquette de goto set_radius: while (true) { determine_radius(lp, lencut); radius = lp.getRadius()/RADIUS_REDUCTION_FACTOR; if (anchor_connection == null) xc = yc = 0.0; else { xo = (bases.get(acp.getStart()).getX() + bases .get(acp.getEnd()).getX()) / 2.0; yo = (bases.get(acp.getStart()).getY() + bases .get(acp.getEnd()).getY()) / 2.0; xc = xo - radius * acp.getXrad(); yc = yo - radius * acp.getYrad(); } // The construction of the connectors will proceed in blocks of // connected connectors, where a connected connector pairs means two // connectors that are forced out of the drawn circle because they // are too close together in angle. // First, find the start of a block of connected connectors if (icroot == -1) icstart = 0; else icstart = icroot; cp = lp.getConnection(icstart); count = 0; if (debug) { System.out.printf("Now processing loop %d\n", lp.getNumber()); System.out.println(" "+lp); } done = false; do { j = icstart - 1; if (j < 0) j = lp.getNconnection() - 1; cpprev = lp.getConnection(j); if (!connected_connection(cpprev, cp)) { done = true; } else { icstart = j; cp = cpprev; } if (++count > lp.getNconnection()) { // Here everything is connected. Break on maximum angular // separation between connections. maxang = -1.0; for (ic = 0; ic < lp.getNconnection(); ic++) { j = ic + 1; if (j >= lp.getNconnection()) j = 0; cp = lp.getConnection(ic); cpnext = lp.getConnection(j); ac = cpnext.getAngle() - cp.getAngle(); if (ac < 0.0) ac += 2 * Math.PI; if (ac > maxang) { maxang = ac; imaxloop = ic; } } icend = imaxloop; icstart = imaxloop + 1; if (icstart >= lp.getNconnection()) icstart = 0; cp = lp.getConnection(icend); cp.setBroken(true); done = true; } } while (!done); done_all_connections = false; icstart1 = icstart; if (debug) System.out.printf(" Icstart1 = %d\n", icstart1); while (!done_all_connections) { count = 0; done = false; icend = icstart; rooted = false; while (!done) { cp = lp.getConnection(icend); if (icend == icroot) rooted = true; j = icend + 1; if (j >= lp.getNconnection()) { j = 0; } cpnext = lp.getConnection(j); if (connected_connection(cp, cpnext)) { if (++count >= lp.getNconnection()) break; icend = j; } else { done = true; } } icmiddle = find_ic_middle(icstart, icend, anchor_connection, acp, lp); ic = icup = icdown = icmiddle; if (debug) System.out.printf(" IC start = %d middle = %d end = %d\n", icstart, icmiddle, icend); done = false; direction = 0; while (!done) { if (direction < 0) { ic = icup; } else if (direction == 0) { ic = icmiddle; } else { ic = icdown; } if (ic >= 0) { cp = lp.getConnection(ic); if (anchor_connection == null || acp != cp) { if (direction == 0) { astart = cp.getAngle() - Math.asin(1.0 / 2.0 / radius); aend = cp.getAngle() + Math.asin(1.0 / 2.0 / radius); bases.get(cp.getStart()).setX( xc + radius * Math.cos(astart)); bases.get(cp.getStart()).setY( yc + radius * Math.sin(astart)); bases.get(cp.getEnd()).setX( xc + radius * Math.cos(aend)); bases.get(cp.getEnd()).setY( yc + radius * Math.sin(aend)); } else if (direction < 0) { j = ic + 1; if (j >= lp.getNconnection()) j = 0; cp = lp.getConnection(ic); cpnext = lp.getConnection(j); cpx = cp.getXrad(); cpy = cp.getYrad(); ac = (cp.getAngle() + cpnext.getAngle()) / 2.0; if (cp.getAngle() > cpnext.getAngle()) ac -= Math.PI; cnx = Math.cos(ac); cny = Math.sin(ac); lnx = cny; lny = -cnx; da = cpnext.getAngle() - cp.getAngle(); if (da < 0.0) da += 2 * Math.PI; if (cp.isExtruded()) { if (da <= Math.PI / 2) rl = 2.0; else rl = 1.5; } else { rl = 1.0; } bases.get(cp.getEnd()).setX( bases.get(cpnext.getStart()).getX() + rl * lnx); bases.get(cp.getEnd()).setY( bases.get(cpnext.getStart()).getY() + rl * lny); bases.get(cp.getStart()).setX( bases.get(cp.getEnd()).getX() + cpy); bases.get(cp.getStart()).setY( bases.get(cp.getEnd()).getY() - cpx); } else { j = ic - 1; if (j < 0) j = lp.getNconnection() - 1; cp = lp.getConnection(j); cpnext = lp.getConnection(ic); cpnextx = cpnext.getXrad(); cpnexty = cpnext.getYrad(); ac = (cp.getAngle() + cpnext.getAngle()) / 2.0; if (cp.getAngle() > cpnext.getAngle()) ac -= Math.PI; cnx = Math.cos(ac); cny = Math.sin(ac); lnx = -cny; lny = cnx; da = cpnext.getAngle() - cp.getAngle(); if (da < 0.0) da += 2 * Math.PI; if (cp.isExtruded()) { if (da <= Math.PI / 2) rl = 2.0; else rl = 1.5; } else { rl = 1.0; } bases.get(cpnext.getStart()).setX( bases.get(cp.getEnd()).getX() + rl * lnx); bases.get(cpnext.getStart()).setY( bases.get(cp.getEnd()).getY() + rl * lny); bases.get(cpnext.getEnd()).setX( bases.get(cpnext.getStart()).getX() - cpnexty); bases.get(cpnext.getEnd()).setY( bases.get(cpnext.getStart()).getY() + cpnextx); } } } if (direction < 0) { if (icdown == icend) { icdown = -1; } else if (icdown >= 0) { if (++icdown >= lp.getNconnection()) { icdown = 0; } } direction = 1; } else { if (icup == icstart) icup = -1; else if (icup >= 0) { if (--icup < 0) { icup = lp.getNconnection() - 1; } } direction = -1; } done = icup == -1 && icdown == -1; } icnext = icend + 1; if (icnext >= lp.getNconnection()) icnext = 0; if (icend != icstart && (!(icstart == icstart1 && icnext == icstart1))) { // Move the bases just constructed (or the radius) so that // the bisector of the end points is radius distance away // from the loop center. cp = lp.getConnection(icstart); cpnext = lp.getConnection(icend); dx = bases.get(cpnext.getEnd()).getX() - bases.get(cp.getStart()).getX(); dy = bases.get(cpnext.getEnd()).getY() - bases.get(cp.getStart()).getY(); midx = bases.get(cp.getStart()).getX() + dx / 2.0; midy = bases.get(cp.getStart()).getY() + dy / 2.0; rr = Math.sqrt(dx * dx + dy * dy); mx = dx / rr; my = dy / rr; vx = xc - midx; vy = yc - midy; rr = Math.sqrt(dx * dx + dy * dy); vx /= rr; vy /= rr; dotmv = vx * mx + vy * my; nrx = dotmv * mx - vx; nry = dotmv * my - vy; rr = Math.sqrt(nrx * nrx + nry * nry); nrx /= rr; nry /= rr; // Determine which side of the bisector the center should // be. dx = bases.get(cp.getStart()).getX() - xc; dy = bases.get(cp.getStart()).getY() - yc; ac = Math.atan2(dy, dx); if (ac < 0.0) ac += 2 * Math.PI; dx = bases.get(cpnext.getEnd()).getX() - xc; dy = bases.get(cpnext.getEnd()).getY() - yc; acn = Math.atan2(dy, dx); if (acn < 0.0) acn += 2 * Math.PI; if (acn < ac) acn += 2 * Math.PI; if (acn - ac > Math.PI) sign = -1; else sign = 1; nmidx = xc + sign * radius * nrx; nmidy = yc + sign * radius * nry; if (rooted) { xc -= nmidx - midx; yc -= nmidy - midy; } else { for (ic = icstart;;) { cp = lp.getConnection(ic); i = cp.getStart(); bases.get(i).setX( bases.get(i).getX() + nmidx - midx); bases.get(i).setY( bases.get(i).getY() + nmidy - midy); i = cp.getEnd(); bases.get(i).setX( bases.get(i).getX() + nmidx - midx); bases.get(i).setY( bases.get(i).getY() + nmidy - midy); if (ic == icend) break; if (++ic >= lp.getNconnection()) ic = 0; } } } icstart = icnext; done_all_connections = icstart == icstart1; } for (ic = 0; ic < lp.getNconnection(); ic++) { cp = lp.getConnection(ic); j = ic + 1; if (j >= lp.getNconnection()) j = 0; cpnext = lp.getConnection(j); dx = bases.get(cp.getEnd()).getX() - xc; dy = bases.get(cp.getEnd()).getY() - yc; rc = Math.sqrt(dx * dx + dy * dy); ac = Math.atan2(dy, dx); if (ac < 0.0) ac += 2 * Math.PI; dx = bases.get(cpnext.getStart()).getX() - xc; dy = bases.get(cpnext.getStart()).getY() - yc; rcn = Math.sqrt(dx * dx + dy * dy); acn = Math.atan2(dy, dx); if (acn < 0.0) acn += 2 * Math.PI; if (acn < ac) acn += 2 * Math.PI; dan = acn - ac; dcp = cpnext.getAngle() - cp.getAngle(); if (dcp <= 0.0) dcp += 2 * Math.PI; if (Math.abs(dan - dcp) > Math.PI) { if (cp.isExtruded()) { warningEmition("Warning from traverse_loop. Loop " + lp.getNumber() + " has crossed regions\n"); } else if ((cpnext.getStart() - cp.getEnd()) != 1) { cp.setExtruded(true); continue set_radius; // remplacement du goto } } if (cp.isExtruded()) { construct_extruded_segment(cp, cpnext); } else { n = cpnext.getStart() - cp.getEnd(); if (n < 0) n += nbase + 1; angleinc = dan / n; for (j = 1; j < n; j++) { i = cp.getEnd() + j; if (i > nbase) i -= nbase + 1; a = ac + j * angleinc; rr = rc + (rcn - rc) * (a - ac) / dan; bases.get(i).setX(xc + rr * Math.cos(a)); bases.get(i).setY(yc + rr * Math.sin(a)); } } } break; } for (ic = 0; ic < lp.getNconnection(); ic++) { if (icroot != ic) { cp = lp.getConnection(ic); generate_region(cp); traverse_loop(cp.getLoop(), cp); } } n = 0; sx = 0.0; sy = 0.0; for (ic = 0; ic < lp.getNconnection(); ic++) { j = ic + 1; if (j >= lp.getNconnection()) j = 0; cp = lp.getConnection(ic); cpnext = lp.getConnection(j); n += 2; sx += bases.get(cp.getStart()).getX() + bases.get(cp.getEnd()).getX(); sy += bases.get(cp.getStart()).getY() + bases.get(cp.getEnd()).getY(); if (!cp.isExtruded()) { for (j = cp.getEnd() + 1; j != cpnext.getStart(); j++) { if (j > nbase) j -= nbase + 1; n++; sx += bases.get(j).getX(); sy += bases.get(j).getY(); } } } lp.setX(sx / n); lp.setY(sy / n); } /** * For the loop pointed to by lp, determine the radius of the loop that will * ensure that each base around the loop will have a separation of at least * lencut around the circle. If a segment joining two connectors will not * support this separation, then the flag, extruded, will be set in the * first of these two indicators. The radius is set in lp. * * The radius is selected by a least squares procedure where the sum of the * squares of the deviations of length from the ideal value of 1 is used as * the error function. */ private void determine_radius(Loop lp, double lencut) { if (debug) System.out.println(" Determine_radius"); double mindit, ci, dt, sumn, sumd, radius, dit; int i, j, end, start, imindit = 0; Connection cp = new Connection(), cpnext = new Connection(); double rt2_2 = 0.7071068; do { mindit = 1.0e10; for (sumd = 0.0, sumn = 0.0, i = 0; i < lp.getNconnection(); i++) { cp = lp.getConnection(i); j = i + 1; if (j >= lp.getNconnection()) j = 0; cpnext = lp.getConnection(j); end = cp.getEnd(); start = cpnext.getStart(); if (start < end) start += nbase + 1; dt = cpnext.getAngle() - cp.getAngle(); if (dt <= 0.0) dt += 2 * Math.PI; if (!cp.isExtruded()) ci = start - end; else { if (dt <= Math.PI / 2) ci = 2.0; else ci = 1.5; } sumn += dt * (1.0 / ci + 1.0); sumd += dt * dt / ci; dit = dt / ci; if (dit < mindit && !cp.isExtruded() && ci > 1.0) { mindit = dit; imindit = i; } } radius = sumn / sumd; if (radius < rt2_2) radius = rt2_2; if (mindit * radius < lencut) { lp.getConnection(imindit).setExtruded(true); } } while (mindit * radius < lencut); if (lp.getRadius() > 0.0) radius = lp.getRadius(); else lp.setRadius(radius); } /** * Determines if the connections cp and cpnext are connected */ private boolean connected_connection(Connection cp, Connection cpnext) { if (debug) System.out.println(" Connected_connection"); if (cp.isExtruded()) { return true; } else if (cp.getEnd() + 1 == cpnext.getStart()) { return true; } else { return false; } } /** * Finds the middle of a set of connected connectors. This is normally the * middle connection in the sequence except if one of the connections is the * anchor, in which case that connection will be used. * * @throws ExceptionNAViewAlgorithm */ private int find_ic_middle(int icstart, int icend, Connection anchor_connection, Connection acp, Loop lp) throws ExceptionNAViewAlgorithm { if (debug) System.out.println(" Find_ic_middle"); int count, ret, ic, i; boolean done; count = 0; ret = -1; ic = icstart; done = false; while (!done) { if (count++ > lp.getNconnection() * 2) { throw new ExceptionNAViewAlgorithm( "Infinite loop detected in find_ic_middle"); } if (anchor_connection != null && lp.getConnection(ic) == acp) { ret = ic; } done = ic == icend; if (++ic >= lp.getNconnection()) { ic = 0; } } if (ret == -1) { for (i = 1, ic = icstart; i < (count + 1) / 2; i++) { if (++ic >= lp.getNconnection()) ic = 0; } ret = ic; } return ret; } /** * Generates the coordinates for the base pairing region of a connection * given the position of the starting base pair. * * @throws ExceptionNAViewAlgorithm */ private void generate_region(Connection cp) throws ExceptionNAViewAlgorithm { if (debug) System.out.println(" Generate_region"); int l, start, end, i, mate; Region rp; rp = cp.getRegion(); l = 0; if (cp.getStart() == rp.getStart1()) { start = rp.getStart1(); end = rp.getEnd1(); } else { start = rp.getStart2(); end = rp.getEnd2(); } if (bases.get(cp.getStart()).getX() > ANUM - 100.0 || bases.get(cp.getEnd()).getX() > ANUM - 100.0) { throw new ExceptionNAViewAlgorithm( "Bad region passed to generate_region. Coordinates not defined."); } for (i = start + 1; i <= end; i++) { l++; bases.get(i).setX( bases.get(cp.getStart()).getX() + HELIX_FACTOR * l * cp.getXrad()); bases.get(i).setY( bases.get(cp.getStart()).getY() + HELIX_FACTOR * l * cp.getYrad()); mate = bases.get(i).getMate(); bases.get(mate).setX( bases.get(cp.getEnd()).getX() + HELIX_FACTOR * l * cp.getXrad()); bases.get(mate).setY( bases.get(cp.getEnd()).getY() + HELIX_FACTOR * l * cp.getYrad()); } } /** * Draws the segment of residue between the bases numbered start through * end, where start and end are presumed to be part of a base pairing * region. They are drawn as a circle which has a chord given by the ends of * two base pairing regions defined by the connections. * * @throws ExceptionNAViewAlgorithm */ private void construct_circle_segment(int start, int end) throws ExceptionNAViewAlgorithm { if (debug) System.out.println(" Construct_circle_segment"); double dx, dy, rr, midx, midy, xn, yn, nrx, nry, mx, my, a; int l, j, i; dx = bases.get(end).getX() - bases.get(start).getX(); dy = bases.get(end).getY() - bases.get(start).getY(); rr = Math.sqrt(dx * dx + dy * dy); l = end - start; if (l < 0) l += nbase + 1; if (rr >= l) { dx /= rr; dy /= rr; for (j = 1; j < l; j++) { i = start + j; if (i > nbase) i -= nbase + 1; bases.get(i).setX( bases.get(start).getX() + dx * (double) j / (double) l); bases.get(i).setY( bases.get(start).getY() + dy * (double) j / (double) l); } } else { find_center_for_arc((l - 1), rr); dx /= rr; dy /= rr; midx = bases.get(start).getX() + dx * rr / 2.0; midy = bases.get(start).getY() + dy * rr / 2.0; xn = dy; yn = -dx; nrx = midx + _h * xn; nry = midy + _h * yn; mx = bases.get(start).getX() - nrx; my = bases.get(start).getY() - nry; rr = Math.sqrt(mx * mx + my * my); a = Math.atan2(my, mx); for (j = 1; j < l; j++) { i = start + j; if (i > nbase) i -= nbase + 1; bases.get(i).setX(nrx + rr * Math.cos(a + j * angleinc)); bases.get(i).setY(nry + rr * Math.sin(a + j * angleinc)); } } } /** * Constructs the segment between cp and cpnext as a circle if possible. * However, if the segment is too large, the lines are drawn between the two * connecting regions, and bases are placed there until the connecting * circle will fit. * * @throws ExceptionNAViewAlgorithm */ private void construct_extruded_segment(Connection cp, Connection cpnext) throws ExceptionNAViewAlgorithm { if (debug) System.out.println(" Construct_extruded_segment"); double astart, aend1, aend2, aave, dx, dy, a1, a2, ac, rr, da, dac; int start, end, n, nstart, nend; boolean collision; astart = cp.getAngle(); aend2 = aend1 = cpnext.getAngle(); if (aend2 < astart) aend2 += 2 * Math.PI; aave = (astart + aend2) / 2.0; start = cp.getEnd(); end = cpnext.getStart(); n = end - start; if (n < 0) n += nbase + 1; da = cpnext.getAngle() - cp.getAngle(); if (da < 0.0) { da += 2 * Math.PI; } if (n == 2) construct_circle_segment(start, end); else { dx = bases.get(end).getX() - bases.get(start).getX(); dy = bases.get(end).getY() - bases.get(start).getY(); rr = Math.sqrt(dx * dx + dy * dy); dx /= rr; dy /= rr; if (rr >= 1.5 && da <= Math.PI / 2) { nstart = start + 1; if (nstart > nbase) nstart -= nbase + 1; nend = end - 1; if (nend < 0) nend += nbase + 1; bases.get(nstart).setX(bases.get(start).getX() + 0.5 * dx); bases.get(nstart).setY(bases.get(start).getY() + 0.5 * dy); bases.get(nend).setX(bases.get(end).getX() - 0.5 * dx); bases.get(nend).setY(bases.get(end).getY() - 0.5 * dy); start = nstart; end = nend; } do { collision = false; construct_circle_segment(start, end); nstart = start + 1; if (nstart > nbase) nstart -= nbase + 1; dx = bases.get(nstart).getX() - bases.get(start).getX(); dy = bases.get(nstart).getY() - bases.get(start).getY(); a1 = Math.atan2(dy, dx); if (a1 < 0.0) a1 += 2 * Math.PI; dac = a1 - astart; if (dac < 0.0) dac += 2 * Math.PI; if (dac > Math.PI) collision = true; nend = end - 1; if (nend < 0) nend += nbase + 1; dx = bases.get(nend).getX() - bases.get(end).getX(); dy = bases.get(nend).getY() - bases.get(end).getY(); a2 = Math.atan2(dy, dx); if (a2 < 0.0) a2 += 2 * Math.PI; dac = aend1 - a2; if (dac < 0.0) dac += 2 * Math.PI; if (dac > Math.PI) collision = true; if (collision) { ac = minf2(aave, astart + 0.5); bases.get(nstart).setX( bases.get(start).getX() + Math.cos(ac)); bases.get(nstart).setY( bases.get(start).getY() + Math.sin(ac)); start = nstart; ac = maxf2(aave, aend2 - 0.5); bases.get(nend).setX(bases.get(end).getX() + Math.cos(ac)); bases.get(nend).setY(bases.get(end).getY() + Math.sin(ac)); end = nend; n -= 2; } } while (collision && n > 1); } } /** * Given n points to be placed equidistantly and equiangularly on a polygon * which has a chord of length, b, find the distance, h, from the midpoint * of the chord for the center of polygon. Positive values mean the center * is within the polygon and the chord, whereas negative values mean the * center is outside the chord. Also, the radial angle for each polygon side * is returned in theta. * * The procedure uses a bisection algorithm to find the correct value for * the center. Two equations are solved, the angles around the center must * add to 2*Math.PI, and the sides of the polygon excluding the chord must * have a length of 1. * * @throws ExceptionNAViewAlgorithm */ private void find_center_for_arc(double n, double b) throws ExceptionNAViewAlgorithm { if (debug) System.out.println(" Find_center_for_arc"); double h, hhi, hlow, r, disc, theta, e, phi; int iter; hhi = (n + 1.0) / Math.PI; // changed to prevent div by zero if (ih) hlow = -hhi - b / (n + 1.000001 - b); if (b < 1) // otherwise we might fail below (ih) hlow = 0; iter = 0; do { h = (hhi + hlow) / 2.0; r = Math.sqrt(h * h + b * b / 4.0); // if (r<0.5) {r = 0.5; h = 0.5*Math.sqrt(1-b*b);} disc = 1.0 - 0.5 / (r * r); if (Math.abs(disc) > 1.0) { throw new ExceptionNAViewAlgorithm( "Unexpected large magnitude discriminant = " + disc + " " + r); } theta = Math.acos(disc); // theta = 2*Math.acos(Math.sqrt(1-1/(4*r*r))); phi = Math.acos(h / r); e = theta * (n + 1) + 2 * phi - 2 * Math.PI; if (e > 0.0) { hlow = h; } else { hhi = h; } } while (Math.abs(e) > 0.0001 && ++iter < MAXITER); if (iter >= MAXITER) { if (noIterationFailureYet) { warningEmition("Iteration failed in find_center_for_arc"); noIterationFailureYet = false; } h = 0.0; theta = 0.0; } _h = h; angleinc = theta; } private double minf2(double x1, double x2) { return ((x1) < (x2)) ? (x1) : (x2); } private double maxf2(double x1, double x2) { return ((x1) > (x2)) ? (x1) : (x2); } public void warningEmition(String warningMessage) throws ExceptionNAViewAlgorithm { throw (new ExceptionNAViewAlgorithm(warningMessage)); } } fr/orsay/lri/varna/models/naView/Region.java0000644000000000000000000000303711620715272020025 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.naView; public class Region { private int _start1, _end1, _start2, _end2; public int getStart1() { return _start1; } public void setStart1(int start1) { this._start1 = start1; } public int getEnd1() { return _end1; } public void setEnd1(int end1) { this._end1 = end1; } public int getStart2() { return _start2; } public void setStart2(int start2) { this._start2 = start2; } public int getEnd2() { return _end2; } public void setEnd2(int end2) { this._end2 = end2; } } fr/orsay/lri/varna/models/naView/Radloop.java0000644000000000000000000000314711620715272020204 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.models.naView; public class Radloop { private double radius; private int loopnumber; private Radloop next, prev; public double getRadius() { return radius; } public void setRadius(double radius) { this.radius = radius; } public int getLoopnumber() { return loopnumber; } public void setLoopnumber(int loopnumber) { this.loopnumber = loopnumber; } public Radloop getNext() { return next; } public void setNext(Radloop next) { this.next = next; } public Radloop getPrev() { return prev; } public void setPrev(Radloop prev) { this.prev = prev; } } fr/orsay/lri/varna/factories/0000755000000000000000000000000012275611452015201 5ustar rootrootfr/orsay/lri/varna/factories/StockholmIO.java0000644000000000000000000000463011724511530020234 0ustar rootrootpackage fr.orsay.lri.varna.factories; import java.io.BufferedReader; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; import java.io.Reader; import java.io.UnsupportedEncodingException; import java.net.MalformedURLException; import java.net.URL; import java.net.URLConnection; import java.util.ArrayList; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; public class StockholmIO { public static RNAAlignment readAlignementFromFile(String path) throws IOException { return StockholmIO.readAlignement(new BufferedReader(new FileReader(path))); } public static RNAAlignment readAlignementFromURL(String url) throws UnsupportedEncodingException, IOException { URL urlAb = new URL(url); URLConnection urlConn = urlAb.openConnection(); urlConn.setUseCaches(false); Reader r = new InputStreamReader(urlConn.getInputStream(),"UTF-8"); return readAlignement(new BufferedReader(r)); } /*public static Alignment readAlignement(Reader r) throws IOException { return readAlignement(new BufferedReader(r)); }*/ public static RNAAlignment readAlignement(BufferedReader r) throws IOException { LinkedHashMap rawSeqs = new LinkedHashMap(); RNAAlignment result = new RNAAlignment(); String line = r.readLine(); String str = ""; while(line!=null) { if (!line.startsWith("#")) { String[] data = line.split("\\s+"); if (data.length>1) { String seqName = data[0].trim(); String seq = data[1].trim(); if (!rawSeqs.containsKey(seqName)) { rawSeqs.put(seqName,new StringBuffer()); } StringBuffer val = rawSeqs.get(seqName); val.append(seq); } } else if (line.startsWith("#")) { String[] data = line.split("\\s+"); if (line.startsWith("#=GC SS_cons")) { str += data[2].trim(); } else if (line.startsWith("#=GS")) { if (data[2].trim().equals("AC")) { result.setAccession(data[1].trim(),data[3].trim()); } } } line = r.readLine(); } result.setSecStr(str); for(Map.Entry entry : rawSeqs.entrySet()) { String s = entry.getValue().toString(); result.addSequence(entry.getKey(), s); } return result; } } fr/orsay/lri/varna/factories/RNAAlignment.java0000644000000000000000000000465011724515504020327 0ustar rootrootpackage fr.orsay.lri.varna.factories; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.Comparator; import java.util.Hashtable; import java.util.Stack; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.models.rna.RNA; public class RNAAlignment { private ArrayList _lst = new ArrayList (); private Hashtable _index = new Hashtable (); private Hashtable _accession = new Hashtable (); private String _secStr = ""; public void addSequence(String id, String s) { if (!_index.containsKey(id)) { _index.put(id,_lst.size()); _lst.add(s); } _lst.set(_index.get(id),s); } public void setSecStr(String s) { _secStr = s; } public void setAccession(String id, String AC) { _accession.put(id,AC); } public ArrayList getRNAs() throws ExceptionUnmatchedClosingParentheses { ArrayList result = new ArrayList(); int[] str = RNAFactory.parseSecStr(_secStr); ArrayList ids = new ArrayList(_index.keySet()); Collections.sort(ids,new Comparator(){ public int compare(String o1, String o2) { return o1.compareToIgnoreCase(o2); }}); for (String id: ids ) { int n = _index.get(id); String seq = _lst.get(n); String nseq =""; String nstr =""; for(int i=0;i loadSecStrRNAML(Reader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax { ArrayList result = new ArrayList(); try { // System.setProperty("javax.xml.parsers.SAXParserFactory", // "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl"); SAXParserFactory saxFact = javax.xml.parsers.SAXParserFactory .newInstance(); saxFact.setValidating(false); saxFact.setXIncludeAware(false); saxFact.setNamespaceAware(false); SAXParser sp = saxFact.newSAXParser(); RNAMLParser RNAMLData = new RNAMLParser(); sp.parse(new InputSource(r), RNAMLData); /* * XMLReader xr = XMLReaderFactory.createXMLReader(); RNAMLParser * RNAMLData = new RNAMLParser(); xr.setContentHandler(RNAMLData); * xr.setErrorHandler(RNAMLData); xr.setEntityResolver(RNAMLData); * xr.parse(new InputSource(r)); */ for (RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules()) { RNA current = new RNA(); // Retrieving parsed data List seq = rnaTmp.getSequence(); // Creating empty structure of suitable size int[] str = new int[seq.size()]; for (int i = 0; i < str.length; i++) { str[i] = -1; } current.setRNA(seq, str); Vector allbpsTmp = rnaTmp.getStructure(); ArrayList allbps = new ArrayList(); for (int i = 0; i < allbpsTmp.size(); i++) { RNAMLParser.BPTemp bp = allbpsTmp.get(i); // System.err.println(bp); int bp5 = bp.pos5; int bp3 = bp.pos3; ModeleBase mb = current.getBaseAt(bp5); ModeleBase part = current.getBaseAt(bp3); ModeleBP newStyle = bp.createBPStyle(mb, part); allbps.add(newStyle); } current.applyBPs(allbps); result.add(current); } } catch (IOException ioe) { throw new ExceptionLoadingFailed( "Couldn't load file due to I/O or security policy issues.", ""); } catch (Exception ge) { ge.printStackTrace(); } return result; } public static int[] parseSecStr(String _secStr) throws ExceptionUnmatchedClosingParentheses { Hashtable> stacks = new Hashtable>(); int[] result = new int[_secStr.length()]; int i = 0; try { for (i = 0; i < _secStr.length(); i++) { result[i] = -1; char c = _secStr.charAt(i); char c2 = Character.toUpperCase(c); if (!stacks.containsKey(c2)) { stacks.put(c2, new Stack()); } switch (c) { case '<': case '{': case '(': case '[': stacks.get(c).push(i); break; case '>': { int j = stacks.get('<').pop(); result[i] = j; result[j] = i; break; } case '}': { int j = stacks.get('{').pop(); result[i] = j; result[j] = i; break; } case ')': { int j = stacks.get('(').pop(); result[i] = j; result[j] = i; break; } case ']': { int j = stacks.get('[').pop(); result[i] = j; result[j] = i; break; } case '.': break; default: { if (Character.isLetter(c) && Character.isUpperCase(c)) { stacks.get(c).push(i); } else if (Character.isLetter(c) && Character.isLowerCase(c)) { int j = stacks.get(Character.toUpperCase(c)).pop(); result[i] = j; result[j] = i; } } } } } catch (EmptyStackException e) { throw new ExceptionUnmatchedClosingParentheses(i); } return result; } public static ArrayList loadSecStrDBN(Reader r) throws ExceptionLoadingFailed, ExceptionPermissionDenied, ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax { boolean loadOk = false; ArrayList result = new ArrayList(); RNA current = new RNA(); try { BufferedReader fr = new BufferedReader(r); String line = fr.readLine(); String title = ""; String seqTmp = ""; String strTmp = ""; while ((line != null) && (strTmp.equals(""))) { line = line.trim(); if (!line.startsWith(">")) { if (seqTmp.equals("")) { seqTmp = line; } else { strTmp = line; } } else { title = line.substring(1).trim(); } line = fr.readLine(); } if (strTmp.length() != 0) { current.setRNA(seqTmp, strTmp); current.setName(title); loadOk = true; } } catch (IOException e) { throw new ExceptionLoadingFailed(e.getMessage(), ""); } if (loadOk) { result.add(current); } return result; } public static ArrayList loadSecStr(Reader r) throws ExceptionFileFormatOrSyntax { return loadSecStr(new BufferedReader(r), RNAFileType.FILE_TYPE_UNKNOWN); } public static ArrayList loadSecStr(BufferedReader r, RNAFileType fileType) throws ExceptionFileFormatOrSyntax { switch (fileType) { case FILE_TYPE_DBN: { try { ArrayList result = loadSecStrDBN(r); if (result.size() != 0) return result; } catch (Exception e) { } } break; case FILE_TYPE_CT: { try { ArrayList result = loadSecStrCT(r); if (result.size() != 0) return result; } catch (Exception e) { e.printStackTrace(); } } break; case FILE_TYPE_BPSEQ: { try { ArrayList result = loadSecStrBPSEQ(r); if (result.size() != 0) return result; } catch (Exception e) { e.printStackTrace(); } } break; case FILE_TYPE_TCOFFEE: { try { ArrayList result = loadSecStrTCoffee(r); if (result.size() != 0) return result; } catch (Exception e) { e.printStackTrace(); } } break; case FILE_TYPE_STOCKHOLM: { try { ArrayList result = loadSecStrStockholm(r); if (result.size() != 0) return result; } catch (Exception e) { e.printStackTrace(); } } break; case FILE_TYPE_RNAML: { try { ArrayList result = loadSecStrRNAML(r); if (result.size() != 0) return result; } catch (Exception e) { } } break; case FILE_TYPE_UNKNOWN: { try { r.mark(1000000); RNAFactory.RNAFileType[] types = RNAFactory.RNAFileType.values(); for (int i = 0; i < types.length; i++) { r.reset(); RNAFactory.RNAFileType t = types[i]; if (t != RNAFactory.RNAFileType.FILE_TYPE_UNKNOWN) { try { ArrayList result = loadSecStr(r, t); if (result.size() != 0) return result; } catch (Exception e) { System.err.println(e.toString()); } } } } catch (IOException e2) { } } } throw new ExceptionFileFormatOrSyntax("Couldn't parse this file as " + fileType + "."); } public static RNAFileType guessFileTypeFromExtension(String path) { if (path.toLowerCase().endsWith("ml")) { return RNAFileType.FILE_TYPE_RNAML; } else if (path.toLowerCase().endsWith("dbn") || path.toLowerCase().endsWith("faa")) { return RNAFileType.FILE_TYPE_DBN; } else if (path.toLowerCase().endsWith("ct")) { return RNAFileType.FILE_TYPE_CT; } else if (path.toLowerCase().endsWith("bpseq")) { return RNAFileType.FILE_TYPE_BPSEQ; } else if (path.toLowerCase().endsWith("rfold")) { return RNAFileType.FILE_TYPE_TCOFFEE; } else if (path.toLowerCase().endsWith("stockholm") || path.toLowerCase().endsWith("stk")) { return RNAFileType.FILE_TYPE_STOCKHOLM; } return RNAFileType.FILE_TYPE_UNKNOWN; } public static ArrayList loadSecStr(String path) throws ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax, ExceptionUnmatchedClosingParentheses, FileNotFoundException { FileReader fr = null; try { fr = new FileReader(path); RNAFileType type = guessFileTypeFromExtension(path); return loadSecStr(new BufferedReader(fr), type); } catch (ExceptionFileFormatOrSyntax e) { if (fr != null) try { fr.close(); } catch (IOException e2) { } e.setPath(path); throw e; } } public static ArrayList loadSecStrStockholm(BufferedReader r) throws IOException, ExceptionUnmatchedClosingParentheses { RNAAlignment a = StockholmIO.readAlignement(r); return a.getRNAs(); } public static ArrayList loadSecStrBPSEQ(Reader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax { boolean loadOk = false; ArrayList result = new ArrayList(); RNA current = new RNA(); try { BufferedReader fr = new BufferedReader(r); String line = fr.readLine(); ArrayList seqTmp = new ArrayList(); Hashtable> strTmp = new Hashtable>(); int bpFrom; String base; int bpTo; int minIndex = -1; boolean noWarningYet = true; String title = ""; String id = ""; String filenameStr = "Filename:"; String organismStr = "Organism:"; String ANStr = "Accession Number:"; while (line != null) { line = line.trim(); String[] tokens = line.split("\\s+"); ArrayList numbers = new ArrayList(); Hashtable numberToIndex = new Hashtable(); if ((tokens.length >= 3) && !tokens[0].contains("#") && !line.startsWith("Organism:") && !line.startsWith("Citation") && !line.startsWith("Filename:") && !line.startsWith("Accession Number:")) { base = tokens[1]; seqTmp.add(base); bpFrom = (Integer.parseInt(tokens[0])); numbers.add(bpFrom); if (minIndex < 0) minIndex = bpFrom; if (seqTmp.size() < (bpFrom - minIndex + 1)) { if (noWarningYet) { noWarningYet = false; /* * warningEmition( "Discontinuity detected between nucleotides " + * (seqTmp.size()) + " and " + (bpFrom + 1) + * "!\nFilling in missing portions with unpaired unknown 'X' nucleotides ..." * ); */ } while (seqTmp.size() < (bpFrom - minIndex + 1)) { // System.err.println("."); seqTmp.add("X"); } } for (int i = 2; i < tokens.length; i++) { bpTo = (Integer.parseInt(tokens[i])); if ((bpTo != 0) || (i != tokens.length - 1)) { if (!strTmp.containsKey(bpFrom)) strTmp.put(bpFrom, new Vector()); strTmp.get(bpFrom).add(bpTo); } } } else if (tokens[0].startsWith("#")) { int occur = line.indexOf("#"); String tmp = line.substring(occur + 1); title += tmp.trim() + " "; } else if (tokens[0].startsWith(filenameStr)) { int occur = line.indexOf(filenameStr); String tmp = line.substring(occur + filenameStr.length()); title += tmp.trim(); } else if (tokens[0].startsWith(organismStr)) { int occur = line.indexOf(organismStr); String tmp = line.substring(occur + organismStr.length()); if (title.length() != 0) { title = "/" + title; } title = tmp.trim() + title; } else if (line.contains(ANStr)) { int occur = line.indexOf(ANStr); String tmp = line.substring(occur + ANStr.length()); id = tmp.trim(); } line = fr.readLine(); } if (strTmp.size() != 0) { ArrayList seq = seqTmp; int[] str = new int[seq.size()]; for (int i = 0; i < seq.size(); i++) { str[i] = -1; } current.setRNA(seq, str, minIndex); ArrayList allbps = new ArrayList(); for (int i : strTmp.keySet()) { for (int j : strTmp.get(i)) { if (i<=j) { ModeleBase mb = current.getBaseAt(i - minIndex); ModeleBase part = current.getBaseAt(j - minIndex); ModeleBP newStyle = new ModeleBP(mb, part); allbps.add(newStyle); } } } current.applyBPs(allbps); current.setName(title); current.setID(id); loadOk = true; } } catch (NumberFormatException e) { e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (Exception e) { throw new ExceptionLoadingFailed(e.getMessage(), ""); } if (loadOk) result.add(current); return result; } public static ArrayList loadSecStrTCoffee(Reader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax { boolean loadOk = false; ArrayList result = new ArrayList(); try { BufferedReader fr = new BufferedReader(r); String line = fr.readLine(); ArrayList seqs = new ArrayList(); ArrayList ids = new ArrayList(); int numSeqs = -1; int currSeq = -1; RNA current = null; while (line != null) { if (!line.startsWith("!")) { String[] tokens = line.split("\\s+"); // This may indicate new secondary structure if (line.startsWith("#")) { currSeq = Integer.parseInt(tokens[0].substring(1)); int currSeq2 = Integer.parseInt(tokens[1]); // For TCoffee, a sec str is a matching between a seq and itself // => Disregard any alignment by filtering on the equality of sequence indices. if (currSeq == currSeq2) { current = new RNA(); current.setName(ids.get(currSeq - 1)); current.setSequence(seqs.get(currSeq - 1)); result.add(current); } else { current = null; } } // Beginning of the file... else if (current == null) { //... either this is the number of sequences... if (numSeqs < 0) { numSeqs = Integer.parseInt(tokens[0]); } //... or this is a sequence definition... else { String id = tokens[0]; String seq = tokens[2]; seqs.add(seq); ids.add(id); } } //Otherwise, this is a base-pair definition, related to the currently selected sequence else if (tokens.length == 3) { int from = Integer.parseInt(tokens[0]) - 1; int to = Integer.parseInt(tokens[1]) - 1; current.addBP(from, to); } } line = fr.readLine(); } loadOk = true; } catch (NumberFormatException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } if (!loadOk) { throw new ExceptionLoadingFailed("Parse Error", ""); } return result; } public static ArrayList loadSecStrCT(Reader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax { boolean loadOk = false; ArrayList result = new ArrayList(); RNA current = new RNA(); try { BufferedReader fr = new BufferedReader(r); String line = fr.readLine(); ArrayList seq = new ArrayList(); ArrayList lbls = new ArrayList(); Vector strTmp = new Vector(); Vector newStrands = new Vector(); int bpFrom; String base; String lbl; int bpTo; boolean noWarningYet = true; int minIndex = -1; String title = ""; while (line != null) { line = line.trim(); String[] tokens = line.split("\\s+"); if (tokens.length >= 6) { try { bpFrom = (Integer.parseInt(tokens[0])); bpTo = (Integer.parseInt(tokens[4])); if (minIndex == -1) minIndex = bpFrom; bpFrom -= minIndex; if (bpTo != 0) bpTo -= minIndex; else bpTo = -1; base = tokens[1]; lbl = tokens[5]; int before = Integer.parseInt(tokens[2]); int after = Integer.parseInt(tokens[3]); if (before==0 && !seq.isEmpty()) { newStrands.add(strTmp.size()-1); } if (bpFrom != seq.size()) { if (noWarningYet) { noWarningYet = false; /* * warningEmition( "Discontinuity detected between nucleotides " * + (seq.size()) + " and " + (bpFrom + 1) + * "!\nFilling in missing portions with unpaired unknown 'X' nucleotides ..." * ); */ } while (bpFrom > seq.size()) { seq.add("X"); strTmp.add(-1); lbls.add(""); } } seq.add(base); strTmp.add(bpTo); lbls.add(lbl); } catch (NumberFormatException e) { if (strTmp.size()!=0) e.printStackTrace(); } } if ((line.contains("ENERGY = ")) || line.contains("dG = ")) { String[] ntokens = line.split("\\s+"); if (ntokens.length >= 4) { String energy = ntokens[3]; for (int i = 4; i < ntokens.length; i++) { title += ntokens[i] + " "; } title += "(E=" + energy + " kcal/mol)"; } } line = fr.readLine(); } if (strTmp.size() != 0) { int[] str = new int[strTmp.size()]; for (int i = 0; i < strTmp.size(); i++) { str[i] = strTmp.elementAt(i).intValue(); } current.setRNA(seq, str, minIndex); current.setName(title); for (int i = 0; i < current.getSize(); i++) { current.getBaseAt(i).setLabel(lbls.get(i)); } for (int i : newStrands) { current.getBackbone().addElement(new ModeleBackboneElement(i,BackboneType.DISCONTINUOUS_TYPE)); } loadOk = true; } } catch (IOException e) { e.printStackTrace(); throw new ExceptionLoadingFailed(e.getMessage(), ""); } catch (NumberFormatException e) { e.printStackTrace(); throw new ExceptionFileFormatOrSyntax(e.getMessage(), ""); } if (loadOk) result.add(current); return result; } } fr/orsay/lri/varna/applications/0000755000000000000000000000000012275611444015711 5ustar rootrootfr/orsay/lri/varna/applications/fragseq/0000755000000000000000000000000012275611444017341 5ustar rootrootfr/orsay/lri/varna/applications/fragseq/FragSeqTree.java0000644000000000000000000000461211723130574022354 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import java.awt.Graphics; import java.awt.Rectangle; import java.awt.dnd.DragGestureEvent; import java.awt.dnd.DragGestureListener; import java.awt.dnd.DragGestureRecognizer; import java.awt.dnd.DragSource; import java.awt.dnd.MouseDragGestureRecognizer; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.util.Enumeration; import javax.swing.JComponent; import javax.swing.JTree; import javax.swing.plaf.basic.BasicTreeUI; import javax.swing.tree.AbstractLayoutCache; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.TreePath; public class FragSeqTree extends JTree implements MouseListener { private Watcher _w; public FragSeqTree(FragSeqTreeModel m) { super(m); _w = new Watcher(m ); _w.start(); } public DefaultMutableTreeNode getSelectedNode() { TreePath t = getSelectionPath(); if (t!= null) { return (DefaultMutableTreeNode) t.getLastPathComponent(); } return null; } public void mouseClicked(MouseEvent e) { int x = e.getX(); int y = e.getY(); TreePath tp = this.getPathForLocation(x, y); if (tp!=null) { DefaultMutableTreeNode n = (DefaultMutableTreeNode) tp.getLastPathComponent(); } } public void switchToPath() { FragSeqTreeModel m = (FragSeqTreeModel) getModel(); cancelEditing(); m.setRoot(m.getPathViewRoot()); Enumeration en = m.getRoot().depthFirstEnumeration(); while(en.hasMoreElements()) { FragSeqNode n = (FragSeqNode) en.nextElement(); if(m.isExpanded(n)) { expandPath(new TreePath(n.getPath())); } } } public void switchToID() { FragSeqTreeModel m = (FragSeqTreeModel) getModel(); cancelEditing(); m.setRoot(m.getIDViewRoot()); Enumeration en = m.getRoot().depthFirstEnumeration(); while(en.hasMoreElements()) { FragSeqNode n = (FragSeqNode) en.nextElement(); if(m.isExpanded(n)) { expandPath(new TreePath(n.getPath())); } } } public void mousePressed(MouseEvent e) { // TODO Auto-generated method stub } public void mouseReleased(MouseEvent e) { // TODO Auto-generated method stub } public void mouseEntered(MouseEvent e) { // TODO Auto-generated method stub } public void mouseExited(MouseEvent e) { // TODO Auto-generated method stub } } fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java0000644000000000000000000001000711722223446023310 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import java.awt.datatransfer.DataFlavor; import java.io.File; import java.io.FileNotFoundException; import java.util.ArrayList; import java.util.Collection; import java.util.Date; import java.util.Random; import java.util.regex.Pattern; import javax.swing.tree.DefaultMutableTreeNode; import fr.orsay.lri.varna.exceptions.ExceptionExportFailed; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.models.rna.RNA; public class FragSeqFileModel implements Comparable { private ArrayList _models = new ArrayList(); protected Date _lastModified; protected boolean _outOfSync = false; protected String _caption = ""; protected String _path = ""; protected String _folder = ""; protected boolean _cached = false; public static Date lastModif(String path) { return new Date(new File(path).lastModified()) ; } public FragSeqFileModel(String folder, String path) { this(folder,path,lastModif(path)); } private static Random _rnd = new Random(); public FragSeqFileModel(String folder, String path,Date lastModified) { _lastModified = lastModified; _outOfSync = false; _folder =folder; _path = path; String[] s = path.split(Pattern.quote(File.separator)); if (s.length>0) _caption = s[s.length-1]; } public void load() { ArrayList rnas = null; try { rnas = createRNAs(); for (RNA r: rnas) { this.addModel(new FragSeqRNASecStrModel(r)); int nb =_rnd.nextInt(5); for(int i=0;i getModels() { if (!_cached) { load(); } return _models; } public void addModel(FragSeqModel f) { _models.add(f); } private ArrayList createRNAs() throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax, FileNotFoundException, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed { Collection r = RNAFactory.loadSecStr(_path); for (RNA r2 : r) { r2.drawRNARadiate(); } return new ArrayList(r); } } fr/orsay/lri/varna/applications/fragseq/FragSeqTreeModel.java0000644000000000000000000001426411722224366023343 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import java.io.File; import java.io.FilenameFilter; import java.io.IOException; import java.util.ArrayList; import java.util.Enumeration; import java.util.Hashtable; import java.util.PriorityQueue; import java.util.Random; import java.util.TreeSet; import javax.swing.event.TreeExpansionEvent; import javax.swing.event.TreeWillExpandListener; import javax.swing.tree.DefaultTreeModel; import javax.swing.tree.ExpandVetoException; import javax.swing.tree.TreeNode; import javax.swing.tree.TreePath; public class FragSeqTreeModel extends DefaultTreeModel implements TreeWillExpandListener{ private FragSeqNode _rootIDs = new FragSeqNode("IDs"); private FragSeqNode _rootFolders = new FragSeqNode("Folders"); private TreeSet _folders = new TreeSet(); private Hashtable _folderPathToFolderNode = new Hashtable(); private Hashtable _idsToNode = new Hashtable(); private Hashtable> _pathToIDFileNodes = new Hashtable>(); public enum SORT_MODE{ PATH, ID } private SORT_MODE _mode = SORT_MODE.PATH; public FragSeqTreeModel() { this(new FragSeqNode("Folders")); } public FragSeqTreeModel(TreeNode t) { super(t); this.setRoot(_rootFolders); } public FragSeqNode getPathViewRoot() { return _rootFolders; } public FragSeqNode getIDViewRoot() { return _rootIDs; } public void switchToIDView() { if (_mode!=SORT_MODE.ID) { this.setRoot(this._rootIDs); } _mode=SORT_MODE.ID; } private void removeAllNodes(ArrayList toBeRemoved) { for(FragSeqNode leafNode : toBeRemoved) { FragSeqNode parent = (FragSeqNode) leafNode.getParent(); parent.remove(leafNode); if (parent.getChildCount()==0) { parent.removeFromParent(); _folderPathToFolderNode.remove(parent); if (parent.getUserObject() instanceof String) { String path = parent.getUserObject().toString(); } } else { reload(parent); } } } public FragSeqNode getNodeForId(String id) { if(!_idsToNode.containsKey(id)) { FragSeqNode idNode = new FragSeqNode(id); _idsToNode.put(id, idNode); _rootIDs.add(idNode); } FragSeqNode idNode = _idsToNode.get(id); return idNode; } public void removeFolder(String path) { ArrayList toBeRemoved = new ArrayList(); Enumeration en = _folderPathToFolderNode.get(path).children(); while(en.hasMoreElements()) { FragSeqNode n = (FragSeqNode) en.nextElement(); toBeRemoved.add(n); } removeAllNodes(toBeRemoved); _folders.remove(path); } public FragSeqNode insertGroupNode(String crit, TreeSet t) { FragSeqNode groupNode = new FragSeqNode(crit); FragSeqNode parent = getRoot(); int pos = t.headSet(crit).size(); parent.insert(groupNode, pos); reload(groupNode); return groupNode; } public void insertFileNode(FragSeqNode parent, FragSeqFileModel m) { FragSeqNode leafNode = new FragSeqNode(m); parent.add(leafNode); } public FragSeqNode addFolder(String path) { FragSeqNode groupNode = null; try { if (!_folders.contains(path)) { File dir = new File(path); if (dir.isDirectory()) { path = dir.getCanonicalPath(); _folders.add(path); groupNode = insertGroupNode(path, _folders); _folderPathToFolderNode.put(path,groupNode); for(File f:dir.listFiles(_f)) { addFile(path,f.getCanonicalPath()); } } } } catch (IOException e) { e.printStackTrace(); } return groupNode; } private void addFile(String folder, String path) { System.out.println(" => "+path); FragSeqFileModel m = new FragSeqFileModel(folder,path); addFolder(folder); insertFileNode(_folderPathToFolderNode.get(folder), m); } public FragSeqNode getRoot() { return (FragSeqNode) super.getRoot(); } public ArrayList getFolders() { ArrayList result = new ArrayList(_folders); return result; } FilenameFilter _f = new FilenameFilter(){ public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".dbn") || name.toLowerCase().endsWith(".ct") || name.toLowerCase().endsWith(".bpseq") || name.toLowerCase().endsWith(".rnaml"); }}; public FilenameFilter getFileNameFilter() { return _f; } public void setFileNameFilter(FilenameFilter f) { _f = f; } private Hashtable _isExpanded = new Hashtable(); public boolean isExpanded(FragSeqNode n) { if(_isExpanded.containsKey(n)) { return _isExpanded.get(n); } else return false; } public void treeWillExpand(TreeExpansionEvent event) throws ExpandVetoException { if (event.getSource() instanceof FragSeqTree) { FragSeqTree tree = (FragSeqTree) event.getSource(); TreePath t = event.getPath(); FragSeqNode n = (FragSeqNode) t.getLastPathComponent(); _isExpanded.put(n, true); Object o = n.getUserObject(); if (o instanceof FragSeqFileModel) { FragSeqFileModel f = (FragSeqFileModel) o; if (!f._cached) { String path = f.getPath(); if (!_pathToIDFileNodes.containsKey(path)) { _pathToIDFileNodes.put(path, new ArrayList()); } ArrayList nodesForID = _pathToIDFileNodes.get(path); for(FragSeqModel m: f.getModels()) { n.add(new FragSeqNode(m)); FragSeqNode nid = getNodeForId(m.getID()); nid.add(new FragSeqNode(m)); nodesForID.add(nid); } } } } } public void treeWillCollapse(TreeExpansionEvent event) throws ExpandVetoException { // TODO Auto-generated method stub TreePath t = event.getPath(); FragSeqNode n = (FragSeqNode) t.getLastPathComponent(); _isExpanded.put(n, false); } } fr/orsay/lri/varna/applications/fragseq/FragSeqNode.java0000644000000000000000000000047211722020426022333 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import javax.swing.tree.DefaultMutableTreeNode; public class FragSeqNode extends DefaultMutableTreeNode { public FragSeqNode(Object o) { super(o); } public boolean isLeaf() { return (this.getUserObject() instanceof FragSeqModel); } }fr/orsay/lri/varna/applications/fragseq/FragSeqModel.java0000644000000000000000000000207211721747256022524 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.datatransfer.UnsupportedFlavorException; import java.io.File; import java.io.FileFilter; import java.io.FileNotFoundException; import java.io.FilenameFilter; import java.io.IOException; import java.util.Collection; import java.util.Date; import java.util.regex.Pattern; import fr.orsay.lri.varna.exceptions.ExceptionExportFailed; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.models.rna.RNA; public abstract class FragSeqModel implements Comparable { public abstract String getID(); public int compareTo(FragSeqModel o) { // TODO Auto-generated method stub return 0; } } fr/orsay/lri/varna/applications/fragseq/FragSeqGUI.java0000644000000000000000000006562111723023512022101 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.applications.fragseq; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.GridLayout; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.datatransfer.UnsupportedFlavorException; import java.awt.dnd.DropTarget; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ComponentEvent; import java.awt.event.ComponentListener; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.WindowEvent; import java.awt.event.WindowListener; import java.io.IOException; import java.util.ArrayList; import javax.swing.BorderFactory; import javax.swing.ButtonGroup; import javax.swing.DefaultListSelectionModel; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JFileChooser; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.JSplitPane; import javax.swing.JTextPane; import javax.swing.JToolBar; import javax.swing.JTree; import javax.swing.ListSelectionModel; import javax.swing.LookAndFeel; import javax.swing.SwingUtilities; import javax.swing.TransferHandler; import javax.swing.UIManager; import javax.swing.UIManager.LookAndFeelInfo; import javax.swing.UnsupportedLookAndFeelException; import javax.swing.event.TreeModelEvent; import javax.swing.event.TreeModelListener; import javax.swing.event.TreeSelectionEvent; import javax.swing.event.TreeSelectionListener; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.ExpandVetoException; import javax.swing.tree.TreePath; import javax.swing.tree.TreeSelectionModel; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.applications.BasicINI; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.models.FullBackup; public class FragSeqGUI extends JFrame implements TreeModelListener, MouseListener,DropTargetListener, WindowListener, ComponentListener, ActionListener, TreeSelectionListener { private enum Commands { NEW_FOLDER, ADD_PANEL_UP, ADD_PANEL_DOWN, REMOVE_PANEL_UP, REMOVE_PANEL_DOWN, SORT_ID, SORT_FILENAME, REFRESH_ALL, CHANGE_LNF, TEST_XML, }; /** * */ private static final long serialVersionUID = -790155708306987257L; private String _INIFilename = "FragSeqUI.ini"; private boolean redrawOnSlide = false; private int dividerWidth = 5; private JPanel _varnaUpperPanels = new JPanel(); private JPanel _varnaLowerPanels = new JPanel(); private JPanel _listPanel = new JPanel(); private JPanel _infoPanel = new JPanel(); private FragSeqTree _sideList = null; private FragSeqTreeModel _treeModel; private JToolBar _toolbar = new JToolBar(); private JFileChooser _choice = new JFileChooser(); private JScrollPane _listScroller; private JList _selectedElems; private JSplitPane _splitLeft; private JSplitPane _splitRight; private JSplitPane _splitVARNA; private JComboBox _lnf; public FragSeqGUI() { super("VARNA Explorer"); RNAPanelDemoInit(); } private void RNAPanelDemoInit() { JFrame.setDefaultLookAndFeelDecorated(true); this.addWindowListener(this); _selectedElems = new JList(); _lnf = new JComboBox(UIManager.getInstalledLookAndFeels()); // Initializing Custom Tree Model _treeModel = new FragSeqTreeModel(); _treeModel.addTreeModelListener(this); _sideList = new FragSeqTree(_treeModel); _sideList.addMouseListener(this); _sideList.setLargeModel(true); _sideList.setEditable(true); _sideList.addTreeWillExpandListener(_treeModel); FragSeqCellRenderer renderer = new FragSeqCellRenderer(_sideList,_treeModel); //_sideList.setUI(new CustomTreeUI()); _sideList.setCellRenderer(renderer); _sideList.setCellEditor(new FragSeqCellEditor(_sideList,renderer,_treeModel)); TreeSelectionModel m = _sideList.getSelectionModel(); m.setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION); _sideList.setSelectionModel(m); m.addTreeSelectionListener(this); _sideList.setShowsRootHandles(true); _sideList.setDragEnabled(true); _sideList.setRootVisible(false); _sideList.setTransferHandler(new TransferHandler(null) { public int getSourceActions(JComponent c) { return COPY_OR_MOVE; } protected Transferable createTransferable(JComponent c) { JTree tree = (JTree) c; TreePath tp =tree.getSelectionPath(); if (tp!=null) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) tp.getLastPathComponent(); if (node.getUserObject() instanceof FragSeqRNASecStrModel) { return new Transferable(){ public DataFlavor[] getTransferDataFlavors() { DataFlavor[] dt = {FragSeqRNASecStrModel.Flavor}; return dt; } public Object getTransferData(DataFlavor df) throws UnsupportedFlavorException, IOException { if (!isDataFlavorSupported(df)) throw new UnsupportedFlavorException(df); DefaultMutableTreeNode node = (DefaultMutableTreeNode) _sideList.getSelectionPath().getLastPathComponent(); return node.getUserObject(); } public boolean isDataFlavorSupported(DataFlavor df) { return FragSeqRNASecStrModel.Flavor.equals(df); } }; } else if (node.getUserObject() instanceof FragSeqAnnotationDataModel) { return new Transferable(){ public DataFlavor[] getTransferDataFlavors() { DataFlavor[] dt = { FragSeqAnnotationDataModel.Flavor}; return dt; } public Object getTransferData(DataFlavor df) throws UnsupportedFlavorException, IOException { if (!isDataFlavorSupported(df)) throw new UnsupportedFlavorException(df); DefaultMutableTreeNode node = (DefaultMutableTreeNode) _sideList.getSelectionPath().getLastPathComponent(); return node.getUserObject(); } public boolean isDataFlavorSupported(DataFlavor df) { return FragSeqAnnotationDataModel.Flavor.equals(df); } }; } else { return null; } } return null; } }); // Various buttons JButton refreshAllFoldersButton = new JButton("Refresh All"); refreshAllFoldersButton.setActionCommand(""+Commands.REFRESH_ALL); refreshAllFoldersButton.addActionListener(this); JButton watchFolderButton = new JButton("Add folder"); watchFolderButton.setActionCommand("" +Commands.NEW_FOLDER); watchFolderButton.addActionListener(this); JButton addUpperButton = new JButton("+Up"); addUpperButton.setActionCommand(""+Commands.ADD_PANEL_UP); addUpperButton.addActionListener(this); JButton removeUpperButton = new JButton("-Up"); removeUpperButton.setActionCommand(""+Commands.REMOVE_PANEL_UP); removeUpperButton.addActionListener(this); JButton addLowerButton = new JButton("+Down"); addLowerButton.setActionCommand(""+Commands.ADD_PANEL_DOWN); addLowerButton.addActionListener(this); JButton removeLowerButton = new JButton("-Down"); removeLowerButton.setActionCommand(""+Commands.REMOVE_PANEL_DOWN); removeLowerButton.addActionListener(this); JButton changeLNFButton = new JButton("Change"); changeLNFButton.setActionCommand(""+Commands.CHANGE_LNF); changeLNFButton.addActionListener(this); JButton XMLButton = new JButton("Test XML"); XMLButton.setActionCommand(""+Commands.TEST_XML); XMLButton.addActionListener(this); _toolbar.setFloatable(false); _toolbar.add(refreshAllFoldersButton); _toolbar.addSeparator(); _toolbar.add(addUpperButton); _toolbar.add(removeUpperButton); _toolbar.add(addLowerButton); _toolbar.add(removeLowerButton); _toolbar.addSeparator(); _toolbar.add(XMLButton); _toolbar.addSeparator(); _toolbar.add(_lnf); _toolbar.add(changeLNFButton); // Scroller for File tree _listScroller = new JScrollPane(_sideList,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS); _listScroller.setPreferredSize(new Dimension(300, 200)); _listScroller.addComponentListener(this); _listPanel.setLayout(new BorderLayout()); _listPanel.add(_listScroller,BorderLayout.CENTER); _listPanel.add(_selectedElems,BorderLayout.SOUTH); _listPanel.setBorder(BorderFactory.createTitledBorder("Structures")); _listPanel.setPreferredSize(new Dimension(300, 0)); _varnaUpperPanels.setLayout(new GridLayout()); _varnaUpperPanels.setPreferredSize(new Dimension(800, 600)); _varnaLowerPanels.setLayout(new GridLayout()); _varnaLowerPanels.setPreferredSize(new Dimension(800, 000)); JRadioButton sortFileName = new JRadioButton("Directory"); sortFileName.setActionCommand("sortfilename"); sortFileName.setSelected(true); sortFileName.setOpaque(false); sortFileName.setActionCommand(""+Commands.SORT_FILENAME); sortFileName.addActionListener(this); JRadioButton sortID = new JRadioButton("ID"); sortID.setActionCommand("sortid"); sortID.setOpaque(false); sortID.setActionCommand(""+Commands.SORT_ID); sortID.addActionListener(this); ButtonGroup group = new ButtonGroup(); group.add(sortFileName); group.add(sortID); JToolBar listTools = new JToolBar(); listTools.setFloatable(false); listTools.add(watchFolderButton); listTools.addSeparator(); listTools.add(new JLabel("Sort by")); listTools.add(sortFileName); listTools.add(sortID); JPanel sidePanel = new JPanel(); sidePanel.setLayout(new BorderLayout()); sidePanel.add(listTools,BorderLayout.NORTH); sidePanel.add(_listPanel,BorderLayout.CENTER); JPanel mainVARNAPanel = new JPanel(); mainVARNAPanel.setLayout(new BorderLayout()); _splitVARNA = new JSplitPane(JSplitPane.VERTICAL_SPLIT,redrawOnSlide,_varnaUpperPanels,_varnaLowerPanels); _splitVARNA.setDividerSize(dividerWidth); _splitVARNA.setResizeWeight(1.0); _splitLeft = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,redrawOnSlide,sidePanel,_splitVARNA); _splitLeft.setResizeWeight(0.1); _splitLeft.setDividerSize(dividerWidth); _splitRight = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,redrawOnSlide,_splitLeft,_infoPanel); _splitRight.setResizeWeight(0.85); _splitRight.setDividerSize(dividerWidth); _infoPanel.setLayout(new GridLayout(0,1)); this.restoreConfig(); this.getContentPane().setLayout(new BorderLayout()); this.getContentPane().add(_splitRight, BorderLayout.CENTER); this.getContentPane().add(_toolbar, BorderLayout.NORTH); addUpperPanel(); addUpperPanel(); this.setVisible(true); } public FragSeqGUI getSelf() { return this; } public VARNAHolder createIntegratedPanel(int height) { VARNAHolder vh = new VARNAHolder(this); _varnaPanels.add(vh); return vh; } public void removeUpperPanel() { if (_varnaUpperPanels.getComponentCount()>1) { VARNAHolder vh = (VARNAHolder) _varnaUpperPanels.getComponent(_varnaUpperPanels.getComponentCount()-1); _infoPanel.remove(vh.getInfoPane()); _varnaUpperPanels.remove(vh); _splitLeft.validate(); _splitRight.validate(); } } public void addUpperPanel() { VARNAHolder vh = createIntegratedPanel(100); _varnaUpperPanels.add(vh); _infoPanel.add(vh.getInfoPane()); _splitRight.validate(); _splitLeft.validate(); } public void removeLowerPanel() { if (_varnaLowerPanels.getComponentCount()>0) { _varnaLowerPanels.remove(_varnaLowerPanels.getComponentCount()-1); if (_varnaLowerPanels.getComponentCount()==0) { _splitVARNA.setDividerLocation(1.0); _splitVARNA.validate(); _splitVARNA.repaint(); } _splitLeft.validate(); } } public void addLowerPanel() { if (_varnaLowerPanels.getComponentCount()==0) { _splitVARNA.setDividerLocation(0.7); _splitVARNA.validate(); } _varnaLowerPanels.add(createIntegratedPanel(400)); _splitLeft.validate(); } public void treeNodesChanged(TreeModelEvent e) { DefaultMutableTreeNode node; node = (DefaultMutableTreeNode) (e.getTreePath().getLastPathComponent()); /* * If the event lists children, then the changed * node is the child of the node we have already * gotten. Otherwise, the changed node and the * specified node are the same. */ try { int index = e.getChildIndices()[0]; node = (DefaultMutableTreeNode) (node.getChildAt(index)); } catch (NullPointerException exc) {} } public void addFolder(String path) { addFolder( path, true); } public void addFolder(String path, boolean shouldBeVisible) { DefaultMutableTreeNode childNode = _treeModel.addFolder(path); if ((childNode!=null) && shouldBeVisible ) { System.out.println(" Expanding: "+childNode.getUserObject()); TreePath tp = new TreePath(childNode.getPath()); _sideList.scrollPathToVisible(tp); _sideList.expandRow(_sideList.getRowForPath(tp)); _sideList.updateUI(); _sideList.validate(); } } public void treeNodesInserted(TreeModelEvent e) { System.out.println(e); } public void treeNodesRemoved(TreeModelEvent e) { // TODO Auto-generated method stub } public void treeStructureChanged(TreeModelEvent e) { // TODO Auto-generated method stub } public void mouseClicked(MouseEvent e) { // TODO Auto-generated method stub } public void mousePressed(MouseEvent e) { } int index = 0; public void mouseReleased(MouseEvent e) { // TODO Auto-generated method stub if (e.getSource() == this._sideList) { if (e.getClickCount() == 1) { /*TreePath t = _sideList.getSelectionPath(); if (t!=null) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) t.getLastPathComponent(); if (node.getUserObject() instanceof FragSeqFileModel) { int row = _sideList.getRowForPath(t); System.out.println("[A]"+row); if (!_sideList.isExpanded(row)) { try { _sideList.fireTreeWillExpand(t); _sideList.expandPath(t); } catch (ExpandVetoException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } else { try { _sideList.fireTreeWillCollapse(t); _sideList.collapsePath(t); } catch (ExpandVetoException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } } }*/ } else if (e.getClickCount() == 2) { TreePath t = _sideList.getSelectionPath(); if (t!= null) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) t.getLastPathComponent(); if (node.getUserObject() instanceof FragSeqFileModel) { if (!_sideList.isExpanded(t)) { try { _sideList.fireTreeWillExpand(t); _sideList.expandPath(t); } catch (ExpandVetoException e1) { e1.printStackTrace(); } } else { try { _sideList.fireTreeWillCollapse(t); _sideList.collapsePath(t); } catch (ExpandVetoException e1) { e1.printStackTrace(); } } } else if (node.getUserObject() instanceof FragSeqModel) { FragSeqModel model = (FragSeqModel) node.getUserObject(); // Figuring out which panel to add object to... int res; if (model instanceof FragSeqRNASecStrModel) { res = index % (_varnaUpperPanels.getComponentCount()+_varnaLowerPanels.getComponentCount()); } else { res = (index+_varnaUpperPanels.getComponentCount()+_varnaLowerPanels.getComponentCount()-1) % (_varnaUpperPanels.getComponentCount()+_varnaLowerPanels.getComponentCount()); } Component c = null; if (res<_varnaUpperPanels.getComponentCount()) { c = (VARNAHolder)_varnaUpperPanels.getComponent(res); } else { res -= _varnaUpperPanels.getComponentCount(); c = (VARNAHolder)_varnaLowerPanels.getComponent(res); } if (c instanceof VARNAHolder) { VARNAHolder h = (VARNAHolder) c; if (model instanceof FragSeqRNASecStrModel) { h.setSecStrModel((FragSeqRNASecStrModel)model); index ++; } else if (model instanceof FragSeqAnnotationDataModel) { h.setDataModel((FragSeqAnnotationDataModel)model); } } } } } } } class VARNAHolder extends JPanel { VARNAPanel vp; FragSeqRNASecStrModel _m; FragSeqAnnotationDataModel _data; JPanel _infoPanel; JTextPane _infoTxt; public VARNAHolder(DropTargetListener f) { super(); vp = new VARNAPanel(); vp.addFocusListener(new FocusListener(){ public void focusGained(FocusEvent e) { //focus(_m); } public void focusLost(FocusEvent e) { }}); vp.setPreferredSize(new Dimension(800, 400)); _infoTxt = new JTextPane(); _infoTxt.setPreferredSize(new Dimension(200,0)); _infoTxt.setContentType("text/html"); JScrollPane scroll = new JScrollPane(_infoTxt,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS); _infoPanel = new JPanel(); _infoPanel.setLayout(new BorderLayout()); _infoPanel.setPreferredSize(new Dimension(200,0)); _infoPanel.setBorder(BorderFactory.createTitledBorder("Info")); _infoPanel.add(scroll,BorderLayout.CENTER); _infoPanel.validate(); this.setLayout(new BorderLayout()); this.setPreferredSize(new Dimension(300,600)); this.setBorder(BorderFactory.createTitledBorder("None")); this.add(vp, BorderLayout.CENTER); DropTarget dt = new DropTarget(vp, f); } VARNAPanel getVARNAPanel() { return vp; } void setSecStrModel(FragSeqRNASecStrModel m) { _m = m; vp.showRNAInterpolated(m.getRNA()); setBorder(BorderFactory.createTitledBorder(m.toString())); _infoTxt.setText(m.getRNA().getHTMLDescription()); _infoPanel.setBorder(BorderFactory.createTitledBorder("Info ("+_m+")")); vp.requestFocus(); } void setDataModel(FragSeqAnnotationDataModel data) { _data = data; data.applyTo(vp.getRNA()); vp.repaint(); vp.requestFocus(); } FragSeqModel getModel() { setBorder(BorderFactory.createTitledBorder(_m.toString())); return _m; } public void setInfoTxt(String s) { _infoTxt.setText(vp.getRNA().getHTMLDescription()); _infoTxt.validate(); } public JPanel getInfoPane() { return _infoPanel; } } private ArrayList _varnaPanels = new ArrayList(); private VARNAHolder getHolder(Component vp) { if (vp instanceof VARNAHolder) { int i= _varnaPanels.indexOf(vp); if (i!=-1) { return _varnaPanels.get(i); } } if (vp instanceof VARNAPanel) { for (VARNAHolder vh: _varnaPanels) { if (vh.getVARNAPanel()==vp) return vh; } } return null; } public void mouseEntered(MouseEvent e) { // TODO Auto-generated method stub } public void mouseExited(MouseEvent e) { // TODO Auto-generated method stub } public void dragEnter(DropTargetDragEvent arg0) { // TODO Auto-generated method stub } public void dragExit(DropTargetEvent arg0) { // TODO Auto-generated method stub } public void dragOver(DropTargetDragEvent arg0) { } public void drop(DropTargetDropEvent arg0) { try { DropTarget o = (DropTarget)arg0.getSource(); if (o.getComponent() instanceof VARNAPanel) { VARNAHolder h = getHolder(o.getComponent()); if (h!=null) { System.out.println("[X]"); Transferable t = arg0.getTransferable(); if (t.isDataFlavorSupported(FragSeqRNASecStrModel.Flavor)) { Object data = t.getTransferData(FragSeqRNASecStrModel.Flavor); if (data instanceof FragSeqRNASecStrModel) { h.setSecStrModel((FragSeqRNASecStrModel) data); } } else if (t.isDataFlavorSupported(FragSeqAnnotationDataModel.Flavor)) { System.out.println("[Y]"); Object data = t.getTransferData(FragSeqAnnotationDataModel.Flavor); if (data instanceof FragSeqAnnotationDataModel) { FragSeqAnnotationDataModel d = (FragSeqAnnotationDataModel) data; h.setDataModel(d); } } } } } catch (UnsupportedFlavorException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } public void dropActionChanged(DropTargetDragEvent arg0) { // TODO Auto-generated method stub } public void windowOpened(WindowEvent e) { // TODO Auto-generated method stub } public void windowClosing(WindowEvent e) { saveConfig(); System.exit(0); } public void windowClosed(WindowEvent e) { // TODO Auto-generated method stub } public void windowIconified(WindowEvent e) { // TODO Auto-generated method stub } public void windowDeiconified(WindowEvent e) { // TODO Auto-generated method stub } public void windowActivated(WindowEvent e) { // TODO Auto-generated method stub } public void windowDeactivated(WindowEvent e) { // TODO Auto-generated method stub } private void restoreConfig() { BasicINI config = BasicINI.loadINI(_INIFilename); ArrayList vals = config.getItemList("folders"); System.out.print("[C]"+vals); for(String path:vals) { System.out.println("Loading folder "+path); addFolder(path); } _sideList.validate(); _listScroller.validate(); } private void saveConfig() { BasicINI data = new BasicINI(); int i=0; for (String folderPath: _treeModel.getFolders()) { data.addItem("folders", "val"+i, folderPath); i++; } BasicINI.saveINI(data, _INIFilename); } public void componentResized(ComponentEvent e) { _sideList.validate(); } public void componentMoved(ComponentEvent e) { // TODO Auto-generated method stub } public void componentShown(ComponentEvent e) { // TODO Auto-generated method stub } public void componentHidden(ComponentEvent e) { // TODO Auto-generated method stub } public void actionPerformed(ActionEvent e) { String cmd = e.getActionCommand(); System.out.println(cmd); if (cmd.equals(""+Commands.NEW_FOLDER)) { _choice.setDialogTitle("Watch new folder..."); _choice.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); _choice.setAcceptAllFileFilterUsed(false); try { if (_choice.showOpenDialog(getSelf()) == JFileChooser.APPROVE_OPTION) { addFolder(_choice.getSelectedFile().getCanonicalPath()); } else { System.out.println("No Selection "); } } catch (IOException e1) { e1.printStackTrace(); } } else if (cmd.equals(""+Commands.ADD_PANEL_DOWN)) { addLowerPanel(); } else if (cmd.equals(""+Commands.ADD_PANEL_UP)) { addUpperPanel(); } else if (cmd.equals(""+Commands.REMOVE_PANEL_DOWN)) { removeLowerPanel(); } else if (cmd.equals(""+Commands.REMOVE_PANEL_UP)) { removeUpperPanel(); } else if (cmd.equals(""+Commands.SORT_FILENAME)) { _sideList.switchToPath(); } else if (cmd.equals(""+Commands.SORT_ID)) { _sideList.switchToID(); } else if (cmd.equals(""+Commands.TEST_XML)) { String path = "temp.xml"; VARNAHolder vh = (VARNAHolder) _varnaUpperPanels.getComponent(0); vh.vp.toXML(path); try { FullBackup b = vh.vp.importSession(path); VARNAHolder vh2 = (VARNAHolder) _varnaUpperPanels.getComponent(1); vh2.vp.setConfig(b.config); vh2.vp.showRNAInterpolated(b.rna); vh2.vp.repaint(); } catch (ExceptionLoadingFailed e1) { e1.printStackTrace(); } } else if (cmd.equals(""+Commands.CHANGE_LNF)) { try { Object o = _lnf.getModel().getSelectedItem(); System.out.println(o); UIManager.setLookAndFeel(((LookAndFeelInfo)_lnf.getModel().getSelectedItem()).getClassName()); SwingUtilities.updateComponentTreeUI(this); this.pack(); } catch (UnsupportedLookAndFeelException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } catch (ClassNotFoundException e2) { // TODO Auto-generated catch block e2.printStackTrace(); } catch (InstantiationException e3) { // TODO Auto-generated catch block e3.printStackTrace(); } catch (IllegalAccessException e4) { // TODO Auto-generated catch block e4.printStackTrace(); } } else { JOptionPane.showMessageDialog(this, "Command '"+cmd+"' not implemented yet."); } } public void valueChanged(TreeSelectionEvent e) { int[] t = _sideList.getSelectionRows(); if (t==null) { System.out.print("null"); } else { System.out.print("["); for(int i=0;i= clickCount; } return true; } } fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java0000644000000000000000000000610011722215072025330 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import java.awt.Color; import java.awt.datatransfer.DataFlavor; import java.util.Hashtable; import java.util.Random; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; public class FragSeqAnnotationDataModel extends FragSeqModel { private String _id; private String _name; private Hashtable _values = new Hashtable(); public FragSeqAnnotationDataModel(String id, String name) { _id = id; _name = name; } public FragSeqAnnotationDataModel() { this(Long.toHexString(Double.doubleToLongBits(Math.random())),Long.toHexString(Double.doubleToLongBits(Math.random()))); } public void addValue(ChemProbModel cpm) { _values.put(cpm._baseNumber1,cpm); } static Random _rnd = new Random(); public static void addRandomAnnotations(RNA r,FragSeqAnnotationDataModel data){ int nb = r.getSize()/5+_rnd.nextInt(r.getSize()/3); Color[] colors = {Color.orange,Color.black,Color.blue.darker(),Color.green.darker(), Color.gray}; ChemProbAnnotationType[] types = ChemProbAnnotationType.values(); for(int i=0;i folders = _model.getFolders(); for (String path: folders) { _model.addFolder(path); System.out.println("Watching ["+path+"]"); } try { this.sleep(1000); } catch (InterruptedException e) { } } } public void finish() { _terminated = true; } } fr/orsay/lri/varna/applications/fragseq/FragSeqRNASecStrModel.java0000644000000000000000000000246111722172656024210 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.datatransfer.UnsupportedFlavorException; import java.io.File; import java.io.FileFilter; import java.io.FileNotFoundException; import java.io.FilenameFilter; import java.io.IOException; import java.util.ArrayList; import java.util.Collection; import java.util.Date; import java.util.regex.Pattern; import fr.orsay.lri.varna.exceptions.ExceptionExportFailed; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.models.rna.RNA; public class FragSeqRNASecStrModel extends FragSeqModel { private RNA _r =null; public FragSeqRNASecStrModel(RNA r) { _r = r; } public String toString() { return _r.getName(); } public String getID() { return _r.getID(); } public RNA getRNA() { return _r; } public static DataFlavor Flavor = new DataFlavor(FragSeqRNASecStrModel.class, "RNA Sec Str Object"); } fr/orsay/lri/varna/applications/fragseq/FragSeqCellRenderer.java0000644000000000000000000001553611722230754024032 0ustar rootrootpackage fr.orsay.lri.varna.applications.fragseq; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.File; import javax.swing.BorderFactory; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JComponent; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTree; import javax.swing.UIManager; import javax.swing.border.Border; import javax.swing.plaf.basic.BasicTreeUI; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.DefaultTreeCellRenderer; class FragSeqCellRenderer extends DefaultTreeCellRenderer { JTree _j; FragSeqTreeModel _m; private static FragSeqCellRenderer _default = new FragSeqCellRenderer(null,null); public FragSeqCellRenderer (JTree j, FragSeqTreeModel m) { _j = j; _m = m; } public JComponent baseElements(JTree tree,FragSeqTreeModel m, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) { JLabel initValue = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus); JPanel result = new JPanel(); result.setLayout(new BorderLayout()); initValue.setBorder(null); result.setBorder(null); result.setBackground(initValue.getBackground()); /*if (hasFocus) { //renderer.setBackground(Color.blue); //result.setBorder(BorderFactory.createLineBorder(Color.blue)); result.setBackground(UIManager.getColor("Tree.selectionBackground")); result.setBorder(BorderFactory.createLineBorder(initValue.getBackground())); initValue.setOpaque(true); } else { result.setBackground(Color.white); result.setBorder(BorderFactory.createLineBorder(initValue.getBackground())); }*/ DefaultMutableTreeNode t = (DefaultMutableTreeNode)value; Object o = t.getUserObject(); if (( o instanceof String)) { if (expanded) { initValue.setIcon(_default.getOpenIcon()); } else { initValue.setIcon(_default.getClosedIcon()); } result.add(initValue,BorderLayout.WEST); JButton del = new JButton(); del.setIcon(new SimpleIcon(Color.red,26,false)); Dimension d = getPreferredSize(); d.width=24; del.setPreferredSize(d); del.addActionListener(new FolderCloses((String)o,tree,m)); result.add(del,BorderLayout.EAST); } else if (( o instanceof FragSeqRNASecStrModel)) { initValue.setIcon(new SimpleIcon(Color.blue.darker())); result.add(initValue,BorderLayout.WEST); } else if (( o instanceof FragSeqFileModel)) { initValue.setIcon(_default.getLeafIcon()); FragSeqFileModel mod = (FragSeqFileModel) o; result.add(initValue,BorderLayout.WEST); if (mod.hasChanged()) { JButton refresh = new JButton("Refresh"); result.add(refresh,BorderLayout.EAST); } } else if (( o instanceof FragSeqModel)) { FragSeqModel mod = (FragSeqModel) o; initValue.setIcon(new SimpleIcon()); result.add(initValue,BorderLayout.WEST); } return result; } public Component getDefaultTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) { return super.getTreeCellRendererComponent(tree,value,sel,expanded,leaf,row,hasFocus); } public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) { return baseElements(tree,_m,value,sel,expanded,leaf,row,hasFocus); } public Dimension getPreferredSize(int row) { Dimension size = super.getPreferredSize(); size.width = _j.getWidth(); System.out.println(size); return size; } // @Override // public void setBounds(final int x, final int y, final int width, final int height) { // super.setBounds(x, y, Math.min(_j.getWidth()-x, width), height); // } public class FolderCloses implements ActionListener{ String _path; JComponent _p; FragSeqTreeModel _m; public FolderCloses(String path, JComponent p, FragSeqTreeModel m) { _path = path; _p = p; _m = m; } public void actionPerformed(ActionEvent e) { if (JOptionPane.showConfirmDialog(_p, "This folder will cease to be watched. Confirm?", "Closing folder", JOptionPane.YES_NO_OPTION)==JOptionPane.YES_OPTION) { _m.removeFolder(_path); System.out.println(_j); _j.updateUI(); } } } public class SimpleIcon implements Icon{ private int _w = 16; private int _h = 16; private BasicStroke stroke = new BasicStroke(3); private Color _r; private boolean _drawBackground = true; public SimpleIcon() { this(Color.magenta.darker()); } public SimpleIcon(Color r) { this(r,16,true); } public SimpleIcon(Color r, int dim, boolean drawBackground) { this(r,dim,dim,drawBackground); } public SimpleIcon(Color r, int width, int height,boolean drawBackground) { _r=r; _w=width; _h=height; _drawBackground=drawBackground; } public void paintIcon(Component c, Graphics g, int x, int y) { Graphics2D g2d = (Graphics2D) g.create(); if (_drawBackground) { g2d.setColor(Color.WHITE); g2d.fillRect(x +1 ,y + 1,_w -2 ,_h -2); g2d.setColor(Color.BLACK); g2d.drawRect(x +1 ,y + 1,_w -2 ,_h -2); } g2d.setColor(_r); g2d.setStroke(stroke); g2d.drawLine(x +10, y + 10, x + _w -10, y + _h -10); g2d.drawLine(x +10, y + _h -10, x + _w -10, y + 10); g2d.dispose(); } public int getIconWidth() { return _w; } public int getIconHeight() { return _h; } } } fr/orsay/lri/varna/applications/BasicINI.java0000644000000000000000000000713512541077006020137 0ustar rootrootpackage fr.orsay.lri.varna.applications; import java.io.File; import java.io.FileReader; import java.io.FileWriter; import java.io.Reader; import java.io.StreamTokenizer; import java.util.ArrayList; import java.util.Arrays; import java.util.Hashtable; import java.util.Set; public class BasicINI { private Hashtable> _data = new Hashtable>(); public void addItem(String category, String key, String val) { if (!_data.containsKey(category)) { _data.put(category, new Hashtable()); } System.out.println("[E]"+key+"->"+val); _data.get(category).put(key,val); } public String getItem(String category, String key) { String result = ""; if (_data.containsKey(category)) { if (_data.get(category).containsKey(key)) { result = _data.get(category).get(key); } } return result; } public ArrayList getItemList(String category) { ArrayList result = new ArrayList(); if (_data.containsKey(category)) { for (String key: _data.get(category).keySet()) { result.add(_data.get(category).get(key)); } } return result; } public BasicINI(){ } public static void saveINI(BasicINI data, String filename) { try { FileWriter out = new FileWriter(filename); Set cats = data._data.keySet(); String[] sortedCats = new String[cats.size()]; sortedCats = cats.toArray(sortedCats); Arrays.sort(sortedCats); for (int i=0;i vals = data._data.get(cat); Set keys = vals.keySet(); String[] sortedKeys = new String[keys.size()]; sortedKeys = keys.toArray(sortedKeys); for(int j=0;j { private Date _lastModified; private boolean _outOfSync = false; private RNA _r = null; private String _caption = ""; private String _path = ""; private String _folder = ""; public static Date lastModif(String path) { return new Date(new File(path).lastModified()) ; } public VARNAGUIModel(String folder, String path) { this(folder,path,lastModif(path)); } public VARNAGUIModel(String folder, String path,Date lastModified) { _lastModified = lastModified; _outOfSync = false; _folder =folder; _path = path; String[] s = path.split(Pattern.quote(File.separator)); if (s.length>0) _caption = s[s.length-1]; } public boolean hasChanged() { return _outOfSync; } public boolean checkForModifications() { if (!lastModif(_path).equals(_lastModified) && !_outOfSync) { _outOfSync = true; return true; } return false; } public RNA getRNA() { if (_r ==null) { try { createRNA(); } catch (ExceptionUnmatchedClosingParentheses e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (FileNotFoundException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionExportFailed e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionPermissionDenied e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionLoadingFailed e) { // TODO Auto-generated catch block e.printStackTrace(); } } return _r; } private RNA createRNA() throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax, FileNotFoundException, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed { Collection r = RNAFactory.loadSecStr(_path); if (r.size()>0) { _r = r.iterator().next(); _r.drawRNARadiate(); } else { throw new ExceptionFileFormatOrSyntax("No valid RNA defined in this file."); } return _r; } public String toString() { return _caption + (this._outOfSync?"*":""); } public String getID() { return getRNA().getID(); } public String getCaption() { return _caption; } public String getFolder() { return _folder; } public static DataFlavor Flavor = new DataFlavor(VARNAGUIModel.class, "VARNA Object"); public int compareTo(VARNAGUIModel o) { return _caption.compareTo(o._caption); } } fr/orsay/lri/varna/applications/newGUI/VARNAGUICellEditor.java0000644000000000000000000000260311720257674023103 0ustar rootrootpackage fr.orsay.lri.varna.applications.newGUI; import java.awt.Component; import java.awt.event.MouseEvent; import java.io.File; import java.util.EventObject; import javax.swing.JButton; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTree; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.DefaultTreeCellEditor; import javax.swing.tree.DefaultTreeCellRenderer; class VARNAGUICellEditor extends DefaultTreeCellEditor { VARNAGUITreeModel _m; private VARNAGUIRenderer _base; public VARNAGUICellEditor(JTree tree, DefaultTreeCellRenderer renderer, VARNAGUITreeModel m) { super(tree, renderer); _base= new VARNAGUIRenderer(tree,m); _m=m; } public Component getTreeCellEditorComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row) { JPanel renderer = (JPanel) _base.baseElements(tree,_m,value,sel,expanded,leaf,row,true); return renderer; } public boolean isCellEditable(EventObject evt) { if (evt instanceof MouseEvent) { int clickCount; // For single-click activation clickCount = 1; return ((MouseEvent)evt).getClickCount() >= clickCount; } return true; } } fr/orsay/lri/varna/applications/newGUI/VARNAGUIRenderer.java0000644000000000000000000001064711720257674022632 0ustar rootrootpackage fr.orsay.lri.varna.applications.newGUI; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.File; import javax.swing.BorderFactory; import javax.swing.JButton; import javax.swing.JComponent; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTree; import javax.swing.UIManager; import javax.swing.border.Border; import javax.swing.plaf.basic.BasicTreeUI; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.DefaultTreeCellRenderer; class VARNAGUIRenderer extends DefaultTreeCellRenderer { JTree _j; VARNAGUITreeModel _m; private static VARNAGUIRenderer _default = new VARNAGUIRenderer(null,null); public VARNAGUIRenderer (JTree j, VARNAGUITreeModel m) { _j = j; _m = m; } public JComponent baseElements(JTree tree,VARNAGUITreeModel m, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) { JLabel initValue = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus); JPanel result = new JPanel(); result.setLayout(new BorderLayout()); initValue.setBorder(null); if (hasFocus) { //renderer.setBackground(Color.blue); result.setBorder(BorderFactory.createLineBorder(Color.blue)); result.setBackground(UIManager.getColor("Tree.selectionBackground")); initValue.setOpaque(true); } else { result.setBackground(Color.white); result.setBorder(BorderFactory.createLineBorder(initValue.getBackground())); } DefaultMutableTreeNode t = (DefaultMutableTreeNode)value; Object o = t.getUserObject(); if (!( o instanceof VARNAGUIModel)) { if (expanded) { initValue.setIcon(_default.getOpenIcon()); } else { initValue.setIcon(_default.getClosedIcon()); } result.add(initValue,BorderLayout.WEST); JButton del = new JButton("X"); del.addActionListener(new FolderCloses((String)o,tree,m)); result.add(del,BorderLayout.EAST); } else { VARNAGUIModel mod = (VARNAGUIModel) o; initValue.setIcon(_default.getLeafIcon()); result.add(initValue,BorderLayout.WEST); if (mod.hasChanged()) { JButton refresh = new JButton("Refresh"); result.add(refresh,BorderLayout.EAST); } } return result; } public Component getDefaultTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) { return super.getTreeCellRendererComponent(tree,value,sel,expanded,leaf,row,hasFocus); } public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) { return baseElements(tree,_m,value,sel,expanded,leaf,row,hasFocus); } public Dimension getPreferredSize(int row) { Dimension size = super.getPreferredSize(); size.width = _j.getWidth(); System.out.println(size); return size; } // @Override // public void setBounds(final int x, final int y, final int width, final int height) { // super.setBounds(x, y, Math.min(_j.getWidth()-x, width), height); // } public class FolderCloses implements ActionListener{ String _path; JComponent _p; VARNAGUITreeModel _m; public FolderCloses(String path, JComponent p, VARNAGUITreeModel m) { _path = path; _p = p; _m = m; } public void actionPerformed(ActionEvent e) { if (JOptionPane.showConfirmDialog(_p, "This folder will cease to be watched. Confirm?", "Closing folder", JOptionPane.YES_NO_OPTION)==JOptionPane.YES_OPTION) { _m.removeFolder(_path); System.out.println(_j); _j.updateUI(); } } } } fr/orsay/lri/varna/applications/newGUI/VARNAGUITree.java0000644000000000000000000000316511720253510021741 0ustar rootrootpackage fr.orsay.lri.varna.applications.newGUI; import java.awt.Graphics; import java.awt.Rectangle; import java.awt.dnd.DragGestureEvent; import java.awt.dnd.DragGestureListener; import java.awt.dnd.DragGestureRecognizer; import java.awt.dnd.DragSource; import java.awt.dnd.MouseDragGestureRecognizer; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import javax.swing.JComponent; import javax.swing.JTree; import javax.swing.plaf.basic.BasicTreeUI; import javax.swing.tree.AbstractLayoutCache; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.TreePath; public class VARNAGUITree extends JTree implements MouseListener { private Watcher _w; public VARNAGUITree(VARNAGUITreeModel m) { super(m); _w = new Watcher(m ); _w.start(); } public DefaultMutableTreeNode getSelectedNode() { TreePath t = getSelectionPath(); if (t!= null) { return (DefaultMutableTreeNode) t.getLastPathComponent(); } return null; } public void mouseClicked(MouseEvent e) { int x = e.getX(); int y = e.getY(); TreePath tp = this.getPathForLocation(x, y); if (tp!=null) { DefaultMutableTreeNode n = (DefaultMutableTreeNode) tp.getLastPathComponent(); } } public void mousePressed(MouseEvent e) { // TODO Auto-generated method stub } public void mouseReleased(MouseEvent e) { // TODO Auto-generated method stub } public void mouseEntered(MouseEvent e) { // TODO Auto-generated method stub } public void mouseExited(MouseEvent e) { // TODO Auto-generated method stub } } fr/orsay/lri/varna/applications/newGUI/Watcher.java0000644000000000000000000000145511720253500021301 0ustar rootrootpackage fr.orsay.lri.varna.applications.newGUI; import java.io.File; import java.io.FilenameFilter; import java.util.ArrayList; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.RNA; public class Watcher extends Thread { private VARNAGUITreeModel _model; private boolean _terminated = false; public Watcher(VARNAGUITreeModel model) { _model = model; } public void run() { while (!_terminated) { ArrayList folders = _model.getFolders(); for (String path: folders) { _model.addFolder(path); System.out.println("Watching ["+path+"]"); } try { this.sleep(1000); } catch (InterruptedException e) { } } } public void finish() { _terminated = true; } } fr/orsay/lri/varna/applications/VARNAOnlineDemo.java0000644000000000000000000001663511620715272021405 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.applications; /* VARNA is a Java library for quick automated drawings RNA secondary structure Copyright (C) 2007 Yann Ponty This program is free software:you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.GridLayout; import javax.swing.JApplet; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurDemoTextField; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.models.rna.RNA; /** * An RNA 2d Panel demo applet * * @author Yann Ponty & Darty Kévin * */ public class VARNAOnlineDemo extends JApplet { /** * */ private static final long serialVersionUID = -790155708306987257L; private static final String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA"; private static final String DEFAULT_STRUCTURE = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."; private VARNAPanel _vp; private JPanel _tools = new JPanel(); private JPanel _input = new JPanel(); private JPanel _seqPanel = new JPanel(); private JPanel _structPanel = new JPanel(); private JLabel _info = new JLabel(); private JTextField _struct = new JTextField(); private JTextField _seq = new JTextField(); private JLabel _structLabel = new JLabel(" Str:"); private JLabel _seqLabel = new JLabel(" Seq:"); private static String errorOpt = "error"; private boolean _error; private Color _backgroundColor = Color.white; private int _algoCode; public VARNAOnlineDemo() { super(); try { _vp = new VARNAPanel(_seq.getText(), _struct.getText()); _vp.setErrorsOn(false); } catch (ExceptionNonEqualLength e) { _vp.errorDialog(e); } RNAPanelDemoInit(); } private void RNAPanelDemoInit() { int marginTools = 40; setBackground(_backgroundColor); _vp.setBackground(_backgroundColor); try { _vp.getRNA().setRNA(_seq.getText(), _struct.getText()); _vp.setErrorsOn(false); } catch (Exception e1) { _vp.errorDialog(e1); } Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12"); _seqLabel.setHorizontalTextPosition(JLabel.LEFT); _seqLabel.setPreferredSize(new Dimension(marginTools, 15)); _seq.setFont(textFieldsFont); _seq.setText(_vp.getRNA().getSeq()); _seqPanel.setLayout(new BorderLayout()); _seqPanel.add(_seqLabel, BorderLayout.WEST); _seqPanel.add(_seq, BorderLayout.CENTER); _structLabel.setPreferredSize(new Dimension(marginTools, 15)); _structLabel.setHorizontalTextPosition(JLabel.LEFT); _struct.setFont(textFieldsFont); _struct.setText(_vp.getRNA().getStructDBN()); _structPanel.setLayout(new BorderLayout()); _structPanel.add(_structLabel, BorderLayout.WEST); _structPanel.add(_struct, BorderLayout.CENTER); ControleurDemoTextField controleurTextField = new ControleurDemoTextField(this); _seq.addCaretListener(controleurTextField); _struct.addCaretListener(controleurTextField); _input.setLayout(new GridLayout(3, 0)); _input.add(_seqPanel); _input.add(_structPanel); _tools.setLayout(new BorderLayout()); _tools.add(_input, BorderLayout.CENTER); _tools.add(_info, BorderLayout.SOUTH); getContentPane().setLayout(new BorderLayout()); getContentPane().add(_vp, BorderLayout.CENTER); getContentPane().add(_tools, BorderLayout.SOUTH); setVisible(true); _vp.getVARNAUI().UIRadiate(); } public String[][] getParameterInfo() { String[][] info = { // Parameter Name Kind of Value Description, { "sequenceDBN", "String", "A raw RNA sequence" }, { "structureDBN", "String", "An RNA structure in dot bracket notation (DBN)" }, { errorOpt, "boolean", "To show errors" }, }; return info; } public void init() { retrieveParametersValues(); _vp.setBackground(_backgroundColor); _error = true; } private Color getSafeColor(String col, Color def) { Color result; try { result = Color.decode(col); } catch (Exception e) { try { result = Color.getColor(col, def); } catch (Exception e2) { return def; } } return result; } private String getParameterValue(String key, String def) { String tmp; tmp = getParameter(key); if (tmp == null) { return def; } else { return tmp; } } private void retrieveParametersValues() { _error = Boolean.parseBoolean(getParameterValue(errorOpt, "false")); _vp.setErrorsOn(_error); _backgroundColor = getSafeColor(getParameterValue("background", _backgroundColor.toString()), _backgroundColor); _vp.setBackground(_backgroundColor); _seq.setText(getParameterValue("sequenceDBN", "")); _struct.setText(getParameterValue("structureDBN", "")); String _algo = getParameterValue("algorithm", "radiate"); if (_algo.equals("circular")) _algoCode = RNA.DRAW_MODE_CIRCULAR; else if (_algo.equals("naview")) _algoCode = RNA.DRAW_MODE_NAVIEW; else if (_algo.equals("line")) _algoCode = RNA.DRAW_MODE_LINEAR; else _algoCode = RNA.DRAW_MODE_RADIATE; if (_seq.getText().equals("") && _struct.getText().equals("")) { _seq.setText(DEFAULT_SEQUENCE); _struct.setText(DEFAULT_STRUCTURE); } try { _vp.drawRNA(_seq.getText(), _struct.getText(), _algoCode); } catch (ExceptionNonEqualLength e) { e.printStackTrace(); } } public VARNAPanel get_varnaPanel() { return _vp; } public void set_varnaPanel(VARNAPanel surface) { _vp = surface; } public JTextField get_struct() { return _struct; } public void set_struct(JTextField _struct) { this._struct = _struct; } public JTextField get_seq() { return _seq; } public void set_seq(JTextField _seq) { this._seq = _seq; } public JLabel get_info() { return _info; } public void set_info(JLabel _info) { this._info = _info; } } fr/orsay/lri/varna/applications/FileNameExtensionFilter.java0000644000000000000000000000271511620715272023301 0ustar rootrootpackage fr.orsay.lri.varna.applications; import java.io.File; import java.util.Enumeration; import java.util.Hashtable; import javax.swing.filechooser.FileFilter; public class FileNameExtensionFilter extends FileFilter { Hashtable _exts = new Hashtable(); String _desc = ""; public FileNameExtensionFilter(String desc,String ext1) { _desc = desc; _exts.put(ext1,0); } public FileNameExtensionFilter(String desc,String ext1,String ext2) { this(desc,ext1); _exts.put(ext2,1); } public FileNameExtensionFilter(String desc,String ext1,String ext2,String ext3) { this(desc,ext1,ext2); _exts.put(ext3,2); } public FileNameExtensionFilter(String desc,String ext1,String ext2,String ext3,String ext4) { this(desc,ext1,ext2,ext3); _exts.put(ext4,3); } public boolean accept(File path) { String name = path.getName(); if (path.isDirectory()) return true; int index = name.lastIndexOf("."); if (index != -1) { String suffix = name.substring(index+1); if (_exts.containsKey(suffix)) {return true;} } return false; } @Override public String getDescription() { return _desc; } public String[] getExtensions() { String[] exts = new String[_exts.size()]; Enumeration k = _exts.keys(); int n = 0; while(k.hasMoreElements()) { exts[n] = k.nextElement(); n++; } return exts; } } fr/orsay/lri/varna/applications/VARNAEditor.java0000644000000000000000000004626312005274714020601 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.applications; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.GridLayout; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTarget; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.geom.Point2D.Double; import java.io.File; import java.text.DateFormat; import java.util.ArrayList; import java.util.Collection; import java.util.Date; import java.util.Hashtable; import java.util.List; import java.util.Set; import javax.swing.DefaultListModel; import javax.swing.DefaultListSelectionModel; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JSplitPane; import javax.swing.JTextField; import javax.swing.ListModel; import javax.swing.ListSelectionModel; import javax.swing.UIManager; import javax.swing.UnsupportedLookAndFeelException; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; import javax.swing.text.BadLocationException; import javax.swing.text.DefaultHighlighter; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.components.ReorderableJList; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener; import fr.orsay.lri.varna.models.BaseList; import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; public class VARNAEditor extends JFrame implements DropTargetListener, InterfaceVARNAListener, MouseListener { /** * */ private static final long serialVersionUID = -790155708306987257L; private static final String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA"; private static final String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."; private static final String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...))))).."; // private static final String DEFAULT_STRUCTURE1 = "((((....))))"; // private static final String DEFAULT_STRUCTURE2 = // "((((..(((....)))..))))"; private VARNAPanel _vp; private JPanel _tools = new JPanel(); private JPanel _input = new JPanel(); private JPanel _seqPanel = new JPanel(); private JPanel _strPanel = new JPanel(); private JLabel _info = new JLabel(); private JTextField _str = new JTextField(DEFAULT_STRUCTURE1); Object _hoverHighlightStr = null; ArrayList _selectionHighlightStr = new ArrayList(); private JTextField _seq = new JTextField(DEFAULT_SEQUENCE); Object _hoverHighlightSeq = null; ArrayList _selectionHighlightSeq = new ArrayList(); private JLabel _strLabel = new JLabel(" Str:"); private JLabel _seqLabel = new JLabel(" Seq:"); private JButton _deleteButton = new JButton("Delete"); private JButton _duplicateButton = new JButton("Duplicate"); private JPanel _listPanel = new JPanel(); private ReorderableJList _sideList = null; private static String errorOpt = "error"; @SuppressWarnings("unused") private boolean _error; private Color _backgroundColor = Color.white; private static int _nextID = 1; @SuppressWarnings("unused") private int _algoCode; private BackupHolder _rnaList; public VARNAEditor() { super("VARNA Editor"); RNAPanelDemoInit(); } private void RNAPanelDemoInit() { DefaultListModel dlm = new DefaultListModel(); int marginTools = 40; DefaultListSelectionModel m = new DefaultListSelectionModel(); m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); m.setLeadAnchorNotificationEnabled(false); _sideList = new ReorderableJList(); _sideList.setModel(dlm); _sideList.addMouseListener(this); _sideList.setSelectionModel(m); _sideList.setPreferredSize(new Dimension(100, 0)); _sideList.addListSelectionListener( new ListSelectionListener(){ public void valueChanged(ListSelectionEvent arg0) { //System.out.println(arg0); if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting()) { FullBackup sel = (FullBackup) _sideList.getSelectedValue(); Mapping map = Mapping.DefaultOutermostMapping(_vp.getRNA().getSize(), sel.rna.getSize()); _vp.showRNAInterpolated(sel.rna,sel.config,map); _seq.setText(sel.rna.getSeq()); _str.setText(sel.rna.getStructDBN(true)); } } }); _rnaList = new BackupHolder(dlm,_sideList); RNA _RNA1 = new RNA("User defined 1"); RNA _RNA2 = new RNA("User defined 2"); try { _vp = new VARNAPanel("0","."); _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1); _RNA1.drawRNARadiate(_vp.getConfig()); _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2); _RNA2.drawRNARadiate(_vp.getConfig()); } catch (ExceptionNonEqualLength e) { _vp.errorDialog(e); } catch (ExceptionUnmatchedClosingParentheses e2) { e2.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e3) { e3.printStackTrace(); } _vp.setPreferredSize(new Dimension(400, 400)); _rnaList.add(_vp.getConfig().clone(),_RNA2,generateDefaultName()); _rnaList.add(_vp.getConfig().clone(),_RNA1,generateDefaultName(),true); JScrollPane listScroller = new JScrollPane(_sideList); listScroller.setPreferredSize(new Dimension(150, 0)); setBackground(_backgroundColor); _vp.setBackground(_backgroundColor); Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12"); _seqLabel.setHorizontalTextPosition(JLabel.LEFT); _seqLabel.setPreferredSize(new Dimension(marginTools, 15)); _seq.setFont(textFieldsFont); _seq.setText(DEFAULT_SEQUENCE); _seq.setEditable(false); _seqPanel.setLayout(new BorderLayout()); _seqPanel.add(_seqLabel, BorderLayout.WEST); _seqPanel.add(_seq, BorderLayout.CENTER); _strLabel.setPreferredSize(new Dimension(marginTools, 15)); _strLabel.setHorizontalTextPosition(JLabel.LEFT); _str.setFont(textFieldsFont); _str.setEditable(false); _strPanel.setLayout(new BorderLayout()); _strPanel.add(_strLabel, BorderLayout.WEST); _strPanel.add(_str, BorderLayout.CENTER); _input.setLayout(new GridLayout(2, 0)); _input.add(_seqPanel); _input.add(_strPanel); _tools.setLayout(new BorderLayout()); _tools.add(_input, BorderLayout.CENTER); _tools.add(_info, BorderLayout.SOUTH); _deleteButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { _rnaList.removeSelected(); } }); _duplicateButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { _rnaList.add((VARNAConfig)_vp.getConfig().clone(),_vp.getRNA().clone(),_vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true); }}); JPanel ops = new JPanel(); ops.setLayout(new GridLayout(1,2)); ops.add(_deleteButton); ops.add(_duplicateButton); JLabel j = new JLabel("Structures",JLabel.CENTER); _listPanel.setLayout(new BorderLayout()); _listPanel.add(ops,BorderLayout.SOUTH); _listPanel.add(j,BorderLayout.NORTH); _listPanel.add(listScroller,BorderLayout.CENTER); JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,_vp); getContentPane().setLayout(new BorderLayout()); getContentPane().add(split, BorderLayout.CENTER); getContentPane().add(_tools, BorderLayout.NORTH); setVisible(true); DropTarget dt = new DropTarget(_vp, this); _vp.addRNAListener(new InterfaceVARNARNAListener(){ public void onSequenceModified(int index, String oldseq, String newseq) { _seq.setText(_vp.getRNA().getSeq()); } public void onStructureModified(Set current, Set addedBasePairs, Set removedBasePairs) { _str.setText(_vp.getRNA().getStructDBN(true)); } public void onRNALayoutChanged(Hashtable previousPositions) { } }); _vp.addSelectionListener(new InterfaceVARNASelectionListener(){ public void onHoverChanged(ModeleBase oldbase, ModeleBase newBase) { if (_hoverHighlightSeq!=null) { _seq.getHighlighter().removeHighlight(_hoverHighlightSeq); _hoverHighlightSeq = null; } if (_hoverHighlightStr!=null) { _str.getHighlighter().removeHighlight(_hoverHighlightStr); _hoverHighlightStr = null; } if (newBase!=null) { try { _hoverHighlightSeq = _seq.getHighlighter().addHighlight(newBase.getIndex(), newBase.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) ); _hoverHighlightStr = _str.getHighlighter().addHighlight(newBase.getIndex(), newBase.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) ); } catch (BadLocationException e) { e.printStackTrace(); } } } public void onSelectionChanged(BaseList selection, BaseList addedBases, BaseList removedBases) { for(Object tag: _selectionHighlightSeq) { _seq.getHighlighter().removeHighlight(tag); } _selectionHighlightSeq.clear(); for(Object tag: _selectionHighlightStr) { _str.getHighlighter().removeHighlight(tag); } _selectionHighlightStr.clear(); for (ModeleBase m: selection.getBases()) { try { _selectionHighlightSeq.add(_seq.getHighlighter().addHighlight(m.getIndex(), m.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) )); _selectionHighlightStr.add(_str.getHighlighter().addHighlight(m.getIndex(), m.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) )); } catch (BadLocationException e) { e.printStackTrace(); } } } }); _vp.addVARNAListener(this); } public static String generateDefaultName() { return "User file #"+_nextID++; } public RNA getRNA() { return (RNA)_sideList.getSelectedValue(); } public String[][] getParameterInfo() { String[][] info = { // Parameter Name Kind of Value Description, { "sequenceDBN", "String", "A raw RNA sequence" }, { "structureDBN", "String", "An RNA structure in dot bracket notation (DBN)" }, { errorOpt, "boolean", "To show errors" }, }; return info; } public void init() { _vp.setBackground(_backgroundColor); _error = true; } @SuppressWarnings("unused") private Color getSafeColor(String col, Color def) { Color result; try { result = Color.decode(col); } catch (Exception e) { try { result = Color.getColor(col, def); } catch (Exception e2) { return def; } } return result; } public VARNAPanel get_varnaPanel() { return _vp; } public void set_varnaPanel(VARNAPanel surface) { _vp = surface; } public JTextField get_seq() { return _seq; } public void set_seq(JTextField _seq) { this._seq = _seq; } public JLabel get_info() { return _info; } public void set_info(JLabel _info) { this._info = _info; } public static void main(String[] args) { VARNAEditor d = new VARNAEditor(); d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); d.pack(); d.setVisible(true); } public void dragEnter(DropTargetDragEvent arg0) { // TODO Auto-generated method stub } public void dragExit(DropTargetEvent arg0) { // TODO Auto-generated method stub } public void dragOver(DropTargetDragEvent arg0) { // TODO Auto-generated method stub } public void drop(DropTargetDropEvent dtde) { try { Transferable tr = dtde.getTransferable(); DataFlavor[] flavors = tr.getTransferDataFlavors(); for (int i = 0; i < flavors.length; i++) { if (flavors[i].isFlavorJavaFileListType()) { dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Object ob = tr.getTransferData(flavors[i]); if (ob instanceof List) { List list = (List) ob; for (int j = 0; j < list.size(); j++) { Object o = list.get(j); if (dtde.getSource() instanceof DropTarget) { DropTarget dt = (DropTarget) dtde.getSource(); Component c = dt.getComponent(); if (c instanceof VARNAPanel) { String path = o.toString(); VARNAPanel vp = (VARNAPanel) c; try{ FullBackup bck = VARNAPanel.importSession(path); _rnaList.add(bck.config, bck.rna,bck.name,true); } catch (ExceptionLoadingFailed e3) { Collection rnas = RNAFactory.loadSecStr(path); if (rnas.isEmpty()) { throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from that source."); } int id = 1; for(RNA r: rnas) { r.drawRNA(vp.getConfig()); String name = r.getName(); if (name.equals("")) { name = path.substring(path.lastIndexOf(File.separatorChar)+1); } if (rnas.size()>1) { name += " - Molecule# "+id++; } _rnaList.add(vp.getConfig().clone(),r,name,true); } } } } } } // If we made it this far, everything worked. dtde.dropComplete(true); return; } } // Hmm, the user must not have dropped a file list dtde.rejectDrop(); } catch (Exception e) { e.printStackTrace(); dtde.rejectDrop(); } } public void dropActionChanged(DropTargetDragEvent arg0) { } private class BackupHolder{ private DefaultListModel _rnaList; private ArrayList _rnas = new ArrayList(); JList _l; public BackupHolder(DefaultListModel rnaList, JList l) { _rnaList = rnaList; _l = l; } public void add(VARNAConfig c, RNA r) { add(c, r, r.getName(),false); } public void add(VARNAConfig c, RNA r,boolean select) { add(c, r, r.getName(),select); } public void add(VARNAConfig c, RNA r, String name) { add(c, r, name,false); } public void add(VARNAConfig c, RNA r, String name, boolean select) { if (select){ _l.removeSelectionInterval(0, _rnaList.size()); } if (name.equals("")) { name = generateDefaultName(); } FullBackup bck = new FullBackup(c,r,name); _rnas.add(0, r); _rnaList.add(0,bck); if (select){ _l.setSelectedIndex(0); } } public void remove(int i) { _rnas.remove(i); _rnaList.remove(i); } public DefaultListModel getModel() { return _rnaList; } public boolean contains(RNA r) { return _rnas.contains(r); } /*public int getSize() { return _rnaList.getSize(); }*/ public FullBackup getElementAt(int i) { return (FullBackup) _rnaList.getElementAt(i); } public void removeSelected() { int i = _l.getSelectedIndex(); if (i!=-1) { if (_rnaList.getSize()==1) { RNA r = new RNA(); try { r.setRNA(" ", "."); } catch (ExceptionUnmatchedClosingParentheses e1) { } catch (ExceptionFileFormatOrSyntax e1) { } _vp.showRNA(r); _vp.repaint(); } else { int newi = i+1; if (newi==_rnaList.getSize()) { newi = _rnaList.getSize()-2; } FullBackup bck = (FullBackup) _rnaList.getElementAt(newi); _l.setSelectedValue(bck,true); } _rnaList.remove(i); } } } public void onStructureRedrawn() { // TODO Auto-generated method stub } public void onUINewStructure(VARNAConfig v, RNA r) { _rnaList.add(v, r,"",true); } public void onWarningEmitted(String s) { // TODO Auto-generated method stub } public void mouseClicked(MouseEvent e) { if(e.getClickCount() == 2){ int index = _sideList.locationToIndex(e.getPoint()); ListModel dlm = _sideList.getModel(); FullBackup item = (FullBackup) dlm.getElementAt(index);; _sideList.ensureIndexIsVisible(index); Object newName = JOptionPane.showInputDialog( this, "Specify a new name for this RNA", "Rename RNA", JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if (newName!=null) { item.name = newName.toString(); this._sideList.repaint(); } } } public void mouseEntered(MouseEvent arg0) { // TODO Auto-generated method stub } public void mouseExited(MouseEvent arg0) { // TODO Auto-generated method stub } public void mousePressed(MouseEvent arg0) { // TODO Auto-generated method stub } public void mouseReleased(MouseEvent arg0) { // TODO Auto-generated method stub } public void onZoomLevelChanged() { // TODO Auto-generated method stub } public void onTranslationChanged() { // TODO Auto-generated method stub } } fr/orsay/lri/varna/applications/NussinovDemo.java0000644000000000000000000005000412031016404021165 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.applications; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.math.BigInteger; import java.util.ArrayList; import java.util.Collections; import javax.swing.BorderFactory; import javax.swing.DefaultComboBoxModel; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextArea; import javax.swing.JTextField; import javax.swing.JTextPane; import javax.swing.border.BevelBorder; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurInterpolator; import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.exceptions.MappingException; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModelBaseStyle; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;; public class NussinovDemo extends JFrame implements InterfaceVARNAListener,InterfaceVARNABasesListener { /** * */ private static final long serialVersionUID = -790155708306987257L; private static final String SEQUENCE_DUMMY = "AAAAAAAAAA"; private static final String SEQUENCE_A = "AGGCACGUCU"; private static final String SEQUENCE_B = "GAGUAGCCUC"; private static final String SEQUENCE_C = "GCAUAGCUGC"; private static final String SEQUENCE_INRIA = "GAGAAGUACUUGAAAUUGGCCUCCUC"; private static final String SEQUENCE_BIG = "AAAACAAAAACACCAUGGUGUUUUCACCCAAUUGGGUGAAAACAGAGAUCUCGAGAUCUCUGUUUUUGUUUU"; private static final String DEFAULT_STRUCTURE = ".........."; // private static final String DEFAULT_STRUCTURE1 = "((((....))))"; // private static final String DEFAULT_STRUCTURE2 = // "((((..(((....)))..))))"; private VARNAPanel _vpMaster; private InfoPanel _infos = new InfoPanel(); private JPanel _tools = new JPanel(); private JPanel _input = new JPanel(); private JPanel _seqPanel = new JPanel(); private JPanel _structPanel = new JPanel(); private JLabel _actions = new JLabel(); private JLabel _struct = new JLabel(DEFAULT_STRUCTURE); private JComboBox _seq1 = new JComboBox(); private JLabel _structLabel = new JLabel("Structure Secondaire"); private JLabel _seqLabel = new JLabel("Sequence d'ARN"); private JButton _goButton = new JButton("Repliement"); private JButton _switchButton = new JButton("Effacer"); private Color _backgroundColor = Color.white; public static Font textFieldsFont = Font.decode("MonoSpaced-BOLD-16"); public static Font labelsFont = (new JLabel()).getFont().deriveFont(16f); public static final int marginTools = 250; public static String APP_TITLE = "Nuit des Chercheurs - INRIA AMIB - Repliement d'ARN"; public static ModelBaseStyle createStyle(String txt) { ModelBaseStyle result = new ModelBaseStyle(); try { result.assignParameters(txt); } catch (ExceptionModeleStyleBaseSyntaxError e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionParameterError e) { // TODO Auto-generated catch block e.printStackTrace(); } return result; } public void applyTo(VARNAPanel vp, ModelBaseStyle mb, int[] indices) { for(int i=0;i sols = getStructs(); _infos.setInfo(sols, count(getSeq())); } public String getSeq() { return (""+_seq1.getSelectedItem()).toUpperCase(); } private boolean canBasePairAll(char a, char b) { return true; } private boolean canBasePairBasic(char a, char b) { if ((a=='G')&&(b=='C')) return true; if ((a=='C')&&(b=='G')) return true; if ((a=='U')&&(b=='A')) return true; if ((a=='A')&&(b=='U')) return true; if ((a=='G')&&(b=='U')) return true; if ((a=='U')&&(b=='G')) return true; return false; } private double basePairScoreBasic(char a, char b) { if ((a=='G')&&(b=='C')) return 1.0; if ((a=='C')&&(b=='G')) return 1.0; if ((a=='U')&&(b=='A')) return 1.0; if ((a=='A')&&(b=='U')) return 1.0; if ((a=='G')&&(b=='U')) return 1.0; if ((a=='U')&&(b=='G')) return 1.0; return Double.NEGATIVE_INFINITY; } private boolean canBasePairNussinov(char a, char b) { if ((a=='G')&&(b=='C')) return true; if ((a=='C')&&(b=='G')) return true; if ((a=='U')&&(b=='A')) return true; if ((a=='A')&&(b=='U')) return true; if ((a=='U')&&(b=='G')) return true; if ((a=='G')&&(b=='U')) return true; return false; } private double basePairScoreNussinov(char a, char b) { if ((a=='G')&&(b=='C')) return 3.0; if ((a=='C')&&(b=='G')) return 3.0; if ((a=='U')&&(b=='A')) return 2.0; if ((a=='A')&&(b=='U')) return 2.0; if ((a=='U')&&(b=='G')) return 1.0; if ((a=='G')&&(b=='U')) return 1.0; return Double.NEGATIVE_INFINITY; } private boolean canBasePairINRIA(char a, char b) { if ((a=='U')&&(b=='A')) return true; if ((a=='A')&&(b=='U')) return true; if ((a=='G')&&(b=='C')) return true; if ((a=='C')&&(b=='G')) return true; if ((a=='A')&&(b=='G')) return true; if ((a=='G')&&(b=='A')) return true; if ((a=='U')&&(b=='C')) return true; if ((a=='C')&&(b=='U')) return true; if ((a=='A')&&(b=='A')) return true; if ((a=='U')&&(b=='U')) return true; if ((a=='U')&&(b=='G')) return true; if ((a=='G')&&(b=='U')) return true; if ((a=='A')&&(b=='C')) return true; if ((a=='C')&&(b=='A')) return true; return false; } private double basePairScoreINRIA(char a, char b) { if ((a=='U')&&(b=='A')) return 3; if ((a=='A')&&(b=='U')) return 3; if ((a=='G')&&(b=='C')) return 3; if ((a=='C')&&(b=='G')) return 3; if ((a=='A')&&(b=='G')) return 2; if ((a=='G')&&(b=='A')) return 2; if ((a=='U')&&(b=='C')) return 2; if ((a=='C')&&(b=='U')) return 2; if ((a=='A')&&(b=='A')) return 2; if ((a=='U')&&(b=='U')) return 2; if ((a=='U')&&(b=='G')) return 1; if ((a=='G')&&(b=='U')) return 1; if ((a=='A')&&(b=='C')) return 1; if ((a=='C')&&(b=='A')) return 1; return Double.NEGATIVE_INFINITY; } private boolean canBasePair(char a, char b) { return canBasePairBasic(a,b); //return canBasePairNussinov(a,b); //return canBasePairINRIA(a,b); } private double basePairScore(char a, char b) { return basePairScoreBasic(a,b); //return basePairScoreNussinov(a,b); //return basePairScoreINRIA(a,b); } public double[][] fillMatrix(String seq) { int n = seq.length(); double[][] tab = new double[n][n]; for(int m=1;m<=n;m++) { for(int i=0;ii+1) { fact1 = tab[i+1][k-1]; } double fact2 = 0; if (k combine(double bonus, ArrayList part1, ArrayList part2) { ArrayList base = new ArrayList(); for(double d1: part1) { for(double d2: part2) { base.add(bonus+d1+d2); } } return base; } public static ArrayList selectBests(ArrayList base) { ArrayList result = new ArrayList(); double best = Double.NEGATIVE_INFINITY; for(double val: base) { best = Math.max(val, best); } for(double val: base) { if (val == best) result.add(val); } return result; } private ArrayList backtrack(double[][] tab, String seq) { return backtrack(tab,seq, 0, seq.length()-1); } private ArrayList backtrack(double[][] tab, String seq, int i, int j) { ArrayList result = new ArrayList(); if (i indices = new ArrayList(); indices.add(-1); for (int k=i+1;k<=j;k++) { indices.add(k); } for (int k : indices) { if (k==-1) { if (tab[i][j] == tab[i+1][j]) { for (String s:backtrack(tab, seq, i+1,j)) { result.add("."+s); } } } else { if (canBasePair(seq.charAt(i),seq.charAt(k))) { double fact1 = 0; if (k>i+1) { fact1 = tab[i+1][k-1]; } double fact2 = 0; if (ki+1) { fact1 = tab[i+1][k-1]; } BigInteger fact2 = BigInteger.ONE; if (k _cacheStructs = new ArrayList(); public ArrayList getStructs() { String seq = getSeq(); seq = seq.toUpperCase(); if (!_cache.equals(seq)) { double[][] mfe = fillMatrix(seq); _cacheStructs = backtrack(mfe,seq); _cache = seq; } return _cacheStructs; } public VARNAPanel get_varnaPanel() { return _vpMaster; } public void set_varnaPanel(VARNAPanel surface) { _vpMaster = surface; } public JLabel get_info() { return _actions; } public void set_info(JLabel _info) { this._actions = _info; } public static void main(String[] args) { NussinovDemo d = new NussinovDemo(); d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); d.pack(); d.setVisible(true); } public void onStructureRedrawn() { _vpMaster.repaint(); } public void onWarningEmitted(String s) { // TODO Auto-generated method stub } public void onLoad(String path) { // TODO Auto-generated method stub } public void onLoaded() { // TODO Auto-generated method stub } public void onUINewStructure(VARNAConfig v, RNA r) { // TODO Auto-generated method stub } static final String[] _bases = {"A","C","G","U"}; static final String[] _basesComp = {"U","G","C","A"}; public void onBaseClicked(ModeleBase mb, MouseEvent e) { } public void onZoomLevelChanged() { // TODO Auto-generated method stub } public void onTranslationChanged() { // TODO Auto-generated method stub } private class InfoPanel extends JPanel { ArrayList _sols = new ArrayList(); BigInteger _nbFolds = BigInteger.ZERO; JTextArea _text = new JTextArea(""); JTextArea _subopts = new JTextArea(""); JPanel _suboptBrowser = new JPanel(); JPanel _suboptCount = new JPanel(); int _selectedIndex = 0; JButton next = new JButton("Precedent"); JButton previous = new JButton("Suivant"); InfoPanel() { setLayout(new BorderLayout()); add(_suboptBrowser,BorderLayout.SOUTH); add(_suboptCount,BorderLayout.NORTH); next.addActionListener(new ActionListener(){ public void actionPerformed(ActionEvent arg0) { if (_sols.size()>0) { setSelectedIndex((_selectedIndex+1)%_sols.size()); } } }); previous.addActionListener(new ActionListener(){ public void actionPerformed(ActionEvent arg0) { if (_sols.size()>0) { setSelectedIndex((_selectedIndex+_sols.size()-1)%_sols.size()); } } }); next.setEnabled(false); previous.setEnabled(false); JLabel nbLab = new JLabel("#Repliements"); NussinovDemo.formatLabel(nbLab); _suboptCount.setLayout(new BorderLayout()); _suboptCount.add(nbLab,BorderLayout.WEST); _suboptCount.add(_text,BorderLayout.CENTER); JLabel cooptlab = new JLabel("#Co-optimaux"); NussinovDemo.formatLabel(cooptlab); JPanel commands = new JPanel(); commands.add(previous); commands.add(next); JPanel jp = new JPanel(); jp.setLayout(new BorderLayout()); jp.add(_subopts,BorderLayout.WEST); jp.add(commands,BorderLayout.CENTER); _suboptBrowser.setLayout(new BorderLayout()); _suboptBrowser.add(cooptlab,BorderLayout.WEST); _suboptBrowser.add(jp,BorderLayout.CENTER); } public void setSelectedIndex(int i) { _selectedIndex = i; RNA rfolded = new RNA(); try { rfolded.setRNA(getSeq(), _sols.get(i)); rfolded.drawRNARadiate(_vpMaster.getConfig()); _vpMaster.showRNAInterpolated(rfolded); } catch (ExceptionUnmatchedClosingParentheses e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e) { // TODO Auto-generated catch block e.printStackTrace(); } _struct.setText(_sols.get(i)); formatDescription(); } public void setFont(Font f) { super.setFont(f); if(_text!=null) { _text.setFont(f); _text.setOpaque(false); } if(_subopts!=null) { _subopts.setFont(f); _subopts.setOpaque(false); } } public void setInfo(ArrayList sols, BigInteger nbFolds) { _sols = sols; _nbFolds = nbFolds; formatDescription(); setSelectedIndex(0); } private void formatDescription() { _text.setText(""+_nbFolds); _subopts.setText(""+_sols.size()); next.setEnabled(_sols.size()>1); previous.setEnabled(_sols.size()>1); } } } fr/orsay/lri/varna/applications/SuperpositionDemo.java0000644000000000000000000003337512005274714022253 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.applications; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurInterpolator; import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.exceptions.MappingException; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModelBaseStyle; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;; public class SuperpositionDemo extends JFrame implements InterfaceVARNAListener { /** * */ private static final long serialVersionUID = -790155708306987257L; private static final String DEFAULT_SEQUENCE1 = "CGCGCACGCGAUAUUUCGCGUCGCGCAUUUGCGCGUAGCGCG"; private static final String DEFAULT_SEQUENCE2 = "CGCGCACGCGAUAUUUCGCGUCGCGCAUUUGCGCGUAGCGCG"; private static final String DEFAULT_STRUCTURE1 = "(((((.(((((----....----))))).(((((....)))))..)))))"; private static final String DEFAULT_STRUCTURE2 = "(((((.(((((((((....))))))))).--------------..)))))"; // private static final String DEFAULT_STRUCTURE1 = "((((....))))"; // private static final String DEFAULT_STRUCTURE2 = // "((((..(((....)))..))))"; private VARNAPanel _vpMaster; private VARNAPanel _vpSlave; private JPanel _tools = new JPanel(); private JPanel _input = new JPanel(); private JPanel _seqPanel = new JPanel(); private JPanel _struct1Panel = new JPanel(); private JPanel _struct2Panel = new JPanel(); private JLabel _info = new JLabel(); private JTextField _struct1 = new JTextField(DEFAULT_STRUCTURE1); private JTextField _struct2 = new JTextField(DEFAULT_STRUCTURE2); private JTextField _seq1 = new JTextField(DEFAULT_SEQUENCE1); private JTextField _seq2 = new JTextField(DEFAULT_SEQUENCE2); private JLabel _struct1Label = new JLabel(" Str1:"); private JLabel _struct2Label = new JLabel(" Str2:"); private JLabel _seqLabel = new JLabel(" Seq:"); private JButton _goButton = new JButton("Go"); private JButton _switchButton = new JButton("Switch"); private String _str1Backup = ""; private String _str2Backup = ""; private RNA _RNA1 = new RNA(); private RNA _RNA2 = new RNA(); private static String errorOpt = "error"; @SuppressWarnings("unused") private boolean _error; private Color _backgroundColor = Color.white; @SuppressWarnings("unused") private int _algoCode; private int _currentDisplay = 1; public static ModelBaseStyle createStyle(String txt) { ModelBaseStyle result = new ModelBaseStyle(); try { result.assignParameters(txt); } catch (ExceptionModeleStyleBaseSyntaxError e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionParameterError e) { // TODO Auto-generated catch block e.printStackTrace(); } return result; } public void applyTo(VARNAPanel vp, ModelBaseStyle mb, int[] indices) { for(int i=0;i _mainColors = new HashMap(); public Color _dominantColor = new Color(0.5f,0.5f,0.5f,0.9f); public enum RelativePosition { RP_OUTER,RP_INNER_GENERAL,RP_INNER_MOVE,RP_EDIT_START,RP_EDIT_END,RP_CONNECT_START5,RP_CONNECT_START3,RP_CONNECT_END5,RP_CONNECT_END3, RP_EDIT_TANGENT_3,RP_EDIT_TANGENT_5; }; static final Color BACKBONE_COLOR = Color.gray; static final Color CONTROL_COLOR = Color.decode("#D0D0FF"); static final Font NUMBER_FONT = new Font("Arial", Font.BOLD,18); static final Color NUMBER_COLOR = Color.gray; static final Color BASE_PAIR_COLOR = Color.blue; static final Color BASE_COLOR = Color.gray; static final Color BASE_FILL_COLOR = Color.white; static final Color BASE_FILL_3_COLOR = Color.red; static final Color BASE_FILL_5_COLOR = Color.green; static final Color MAGNET_COLOR = CONTROL_COLOR; public void setDominantColor(Color c) { _dominantColor = c; } public Color getDominantColor() { return _dominantColor; } public abstract RelativePosition getRelativePosition(double x, double y); public abstract void draw(Graphics2D g2d, boolean selected); public abstract Polygon getBoundingPolygon(); public abstract void translate(double x, double y); public abstract RelativePosition getClosestEdge(double x, double y); public abstract ArrayList getConnectedEdges(); public abstract RNATemplateElement getTemplateElement(); public void setMainColor(RelativePosition edge,Color c) { _mainColors.put(edge, c); } public abstract Shape getArea(); public void attach(GraphicalTemplateElement e, RelativePosition edgeOrig, RelativePosition edgeDest) throws ExceptionEdgeEndpointAlreadyConnected, ExceptionInvalidRNATemplate { _attachedElements.put(edgeOrig, new Couple(edgeDest,e)); } /** * Same as attach(), but without touching the underlying * RNATemplateElement objects. * This is useful if the underlying RNATemplate already contains edges * but not the graphical template. */ public void graphicalAttach(GraphicalTemplateElement e, RelativePosition edgeOrig, RelativePosition edgeDest) { _attachedElements.put(edgeOrig, new Couple(edgeDest,e)); } public void detach(RelativePosition edge) { if (_attachedElements.containsKey(edge)) { Couple c = _attachedElements.get(edge); _attachedElements.remove(edge); c.second.detach(c.first); } } public Couple getAttachedElement(RelativePosition localedge) { if (_attachedElements.containsKey(localedge)) return _attachedElements.get(localedge); return null; } public boolean hasAttachedElement(RelativePosition localedge) { return _attachedElements.containsKey(localedge); } public abstract EdgeEndPoint getEndPoint(RelativePosition r); public abstract boolean isIn(RelativePosition r); public void draw(Graphics2D g2d) { draw(g2d,false); } private HashMap> _attachedElements = new HashMap>(); private Dimension getStringDimension(Graphics2D g, String s) { FontMetrics fm = g.getFontMetrics(); Rectangle2D r = fm.getStringBounds(s, g); return (new Dimension((int) r.getWidth(), (int) fm.getAscent() - fm.getDescent())); } public void drawStringCentered(Graphics2D g2, String res, double x, double y) { Dimension d = getStringDimension(g2, res); x -= (double) d.width / 2.0; y += (double) d.height / 2.0; if (_debug) g2.drawRect((int) x, (int) y - d.height, d.width, d.height); g2.drawString(res, (int) Math.round(x), (int) Math.round(y)); } protected Stroke _boldStroke = new BasicStroke(2.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f); protected Stroke _solidStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f); private float[] dash = { 5.0f, 5.0f }; protected Stroke _dashedStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f, dash, 0); public abstract RelativePosition getConnectedEdge(RelativePosition edge); public abstract Point2D.Double getEdgePosition(RelativePosition edge); public abstract void setEdgePosition(RelativePosition edge, Point2D.Double pos); public abstract RelativePosition relativePositionFromEdgeEndPointPosition(EdgeEndPointPosition endPointPosition); public static boolean canConnect(GraphicalTemplateElement el1, RelativePosition e1,GraphicalTemplateElement el2, RelativePosition e2) { return (!el1.hasAttachedElement(e1))&&(!el2.hasAttachedElement(e2))&&(el1.isIn(e1)!=el2.isIn(e2)); } protected void drawMove(Graphics2D g2d, Point2D.Double center) { g2d.setStroke(_solidStroke); g2d.setColor(CONTROL_COLOR); g2d.fillOval((int)((center.x-Helix.MOVE_RADIUS)), (int)((center.y-Helix.MOVE_RADIUS)), (int)(2.0*Helix.MOVE_RADIUS), (int)(2.0*Helix.MOVE_RADIUS)); g2d.setColor(BACKBONE_COLOR); g2d.drawOval((int)((center.x-Helix.MOVE_RADIUS)), (int)((center.y-Helix.MOVE_RADIUS)), (int)(2.0*Helix.MOVE_RADIUS), (int)(2.0*Helix.MOVE_RADIUS)); double arrowLength = Helix.MOVE_RADIUS-2.0; double width = 3.0; drawArrow(g2d,center,new Point2D.Double(center.x+arrowLength,center.y),width); drawArrow(g2d,center,new Point2D.Double(center.x-arrowLength,center.y),width); drawArrow(g2d,center,new Point2D.Double(center.x,center.y+arrowLength),width); drawArrow(g2d,center,new Point2D.Double(center.x,center.y-arrowLength),width); } protected void drawEditStart(Graphics2D g2d, Helix h, double dx,double dy,double nx,double ny) { Point2D.Double center = h.getCenterEditStart(); drawEdit(g2d, center, dx,dy,nx,ny); } protected void drawEditEnd(Graphics2D g2d, Helix h, double dx,double dy,double nx,double ny) { Point2D.Double center = h.getCenterEditEnd(); drawEdit(g2d, center, dx,dy,nx,ny); } protected void drawEdit(Graphics2D g2d, Point2D.Double center, double dx,double dy,double nx,double ny) { g2d.setColor(CONTROL_COLOR); g2d.fillOval((int)((center.x-Helix.EDIT_RADIUS)), (int)((center.y-Helix.EDIT_RADIUS)), (int)(2.0*Helix.EDIT_RADIUS), (int)(2.0*Helix.EDIT_RADIUS)); g2d.setColor(BACKBONE_COLOR); g2d.drawOval((int)((center.x-Helix.EDIT_RADIUS)), (int)((center.y-Helix.EDIT_RADIUS)), (int)(2.0*Helix.EDIT_RADIUS), (int)(2.0*Helix.EDIT_RADIUS)); double arrowLength = Helix.EDIT_RADIUS-2.0; double width = 3.0; drawArrow(g2d,center,new Point2D.Double(center.x+nx*arrowLength,center.y+ny*arrowLength),width); drawArrow(g2d,center,new Point2D.Double(center.x-nx*arrowLength,center.y-ny*arrowLength),width); drawArrow(g2d,center,new Point2D.Double(center.x+dx*arrowLength,center.y+dy*arrowLength),width); drawArrow(g2d,center,new Point2D.Double(center.x-dx*arrowLength,center.y-dy*arrowLength),width); } protected void drawArrow(Graphics2D g2d, Point2D.Double orig, Point2D.Double dest, double width) { g2d.setStroke(_solidStroke); g2d.drawLine((int)orig.x,(int)orig.y,(int)dest.x,(int)dest.y); double dx = (orig.x-dest.x)/(orig.distance(dest)); double dy = (orig.y-dest.y)/(orig.distance(dest)); double nx = dy; double ny = -dx; g2d.drawLine((int)dest.x,(int)dest.y,(int)(dest.x-width*(-dx+nx)),(int)(dest.y-width*(-dy+ny))); g2d.drawLine((int)dest.x,(int)dest.y,(int)(dest.x-width*(-dx-nx)),(int)(dest.y-width*(-dy-ny))); } protected void drawAnchor(Graphics2D g2d, Point2D.Double p) { drawAnchor(g2d,p,CONTROL_COLOR); } protected void drawAnchor5(Graphics2D g2d, Point2D.Double p) { drawAnchor(g2d,p,BASE_FILL_5_COLOR); } protected void drawAnchor3(Graphics2D g2d, Point2D.Double p) { drawAnchor(g2d,p,BASE_FILL_3_COLOR); } protected void drawAnchor(Graphics2D g2d, Point2D.Double p, Color c) { g2d.setColor(c); g2d.fillOval((int)(p.x-Helix.EDGE_BASE_RADIUS),(int)(p.y-Helix.EDGE_BASE_RADIUS),(int)(2.0*Helix.EDGE_BASE_RADIUS),(int)(2.0*Helix.EDGE_BASE_RADIUS)); g2d.setColor(BASE_COLOR); g2d.drawOval((int)(p.x-Helix.EDGE_BASE_RADIUS),(int)(p.y-Helix.EDGE_BASE_RADIUS),(int)(2.0*Helix.EDGE_BASE_RADIUS),(int)(2.0*Helix.EDGE_BASE_RADIUS)); } protected void drawMagnet(Graphics2D g2d, Point2D.Double p) { drawAnchor(g2d, p, MAGNET_COLOR); g2d.setColor(BASE_COLOR); g2d.drawOval((int)(p.x-Helix.EDGE_BASE_RADIUS),(int)(p.y-Helix.EDGE_BASE_RADIUS),(int)(2.0*Helix.EDGE_BASE_RADIUS),(int)(2.0*Helix.EDGE_BASE_RADIUS)); g2d.drawOval((int)(p.x-2),(int)(p.y-2),(int)(2.0*2),(int)(2.0*2)); } protected void drawBase(Graphics2D g2d, Point2D.Double p) { g2d.setColor(BASE_FILL_COLOR); g2d.fillOval((int)(p.x-Helix.BASE_RADIUS),(int)(p.y-Helix.BASE_RADIUS),(int)(2.0*Helix.BASE_RADIUS),(int)(2.0*Helix.BASE_RADIUS)); g2d.setColor(BASE_COLOR); g2d.drawOval((int)(p.x-Helix.BASE_RADIUS),(int)(p.y-Helix.BASE_RADIUS),(int)(2.0*Helix.BASE_RADIUS),(int)(2.0*Helix.BASE_RADIUS)); } public boolean equals(Object b) { if (b instanceof GraphicalTemplateElement) { return b==this; } else return false; } } fr/orsay/lri/varna/applications/templateEditor/TemplateEdits.java0000644000000000000000000001213411620715272024300 0ustar rootrootpackage fr.orsay.lri.varna.applications.templateEditor; import java.awt.geom.Point2D; import javax.swing.undo.AbstractUndoableEdit; import javax.swing.undo.CannotRedoException; import javax.swing.undo.CannotUndoException; import javax.swing.undo.UndoableEdit; public class TemplateEdits { public static final double MAX_DISTANCE= 15.0; public static class ElementAddTemplateEdit extends AbstractUndoableEdit { private GraphicalTemplateElement _h; private TemplatePanel _p; public ElementAddTemplateEdit(GraphicalTemplateElement h,TemplatePanel p) { _h = h; _p = p; } public void undo() throws CannotUndoException { _p.removeElement(_h); _p.repaint(); } public void redo() throws CannotRedoException { _p.addElement(_h); _p.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Graphical element added"; } }; public static class ElementRemoveTemplateEdit extends AbstractUndoableEdit { private GraphicalTemplateElement _h; private TemplatePanel _p; public ElementRemoveTemplateEdit(GraphicalTemplateElement h,TemplatePanel p) { _h = h; _p = p; } public void undo() throws CannotUndoException { _p.addElement(_h); _p.repaint(); } public void redo() throws CannotRedoException { _p.removeElement(_h); _p.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Graphical element removed"; } }; public static class ElementAttachTemplateEdit extends AbstractUndoableEdit { Connection _c; private TemplatePanel _p; public ElementAttachTemplateEdit(Connection c, TemplatePanel p) { _c = c; _p = p; } public void undo() throws CannotUndoException { _p.removeConnection(_c); _p.repaint(); } public void redo() throws CannotRedoException { _c = _p.addConnection(_c._h1,_c._edge1,_c._h2,_c._edge2); _p.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Graphical elements attached"; } }; public static class ElementDetachTemplateEdit extends AbstractUndoableEdit { Connection _c; private TemplatePanel _p; public ElementDetachTemplateEdit(Connection c, TemplatePanel p) { _c = c; _p = p; } public void undo() throws CannotUndoException { _c = _p.addConnection(_c._h1,_c._edge1,_c._h2,_c._edge2); _p.repaint(); } public void redo() throws CannotRedoException { _p.removeConnection(_c); _p.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Graphical elements detached"; } }; public static class ElementEdgeMoveTemplateEdit extends AbstractUndoableEdit { private GraphicalTemplateElement _ur; GraphicalTemplateElement.RelativePosition _edge; private double _ox; private double _oy; private double _nx; private double _ny; private TemplatePanel _p; public ElementEdgeMoveTemplateEdit(GraphicalTemplateElement ur, GraphicalTemplateElement.RelativePosition edge, double nx, double ny, TemplatePanel p) { _ur = ur; _edge = edge; _ox = ur.getEdgePosition(edge).x; _oy = ur.getEdgePosition(edge).y; _nx = nx; _ny = ny; _p = p; } public void undo() throws CannotUndoException { _ur.setEdgePosition(_edge,new Point2D.Double(_ox,_oy)); _p.repaint(); } public void redo() throws CannotRedoException { _ur.setEdgePosition(_edge,new Point2D.Double(_nx,_ny)); _p.repaint(); } public boolean canUndo() { return true; } public boolean canRedo() { return true; } public String getPresentationName() { return "Edge moved "+_edge; } public boolean addEdit(UndoableEdit anEdit) { if (anEdit instanceof ElementEdgeMoveTemplateEdit) { ElementEdgeMoveTemplateEdit e = (ElementEdgeMoveTemplateEdit) anEdit; if (e._edge==_edge) { Point2D.Double po1 = new Point2D.Double(_ox,_oy); Point2D.Double pn1 = new Point2D.Double(_nx,_ny); Point2D.Double po2 = new Point2D.Double(e._ox,e._oy); Point2D.Double pn2 = new Point2D.Double(e._nx,e._ny); if ((_ur==e._ur)&&(pn1.equals(po2))&&(po1.distance(pn2) _RNAComponents; private ArrayList _RNAConnections; private Hashtable,Connection> _helixToConnection; private TemplateEditorPanelUI _ui; private RNATemplate _template; private static Color[] BackgroundColors = {Color.blue,Color.red,Color.cyan,Color.green,Color.lightGray,Color.magenta,Color.PINK}; private int _nextBackgroundColor = 0; private static double scaleFactorDefault = 0.7; private double scaleFactor = scaleFactorDefault; private TemplateEditor _editor; public double getScaleFactor() { return scaleFactor; } public void setScaleFactor(double scaleFactor) { this.scaleFactor = scaleFactor; } public Color nextBackgroundColor() { Color c = BackgroundColors[_nextBackgroundColor++]; _nextBackgroundColor = _nextBackgroundColor % BackgroundColors.length; return new Color(c.getRed(),c.getBlue(),c.getGreen(),50); } public TemplatePanel(TemplateEditor parent) { _editor = parent; init(); } public RNATemplate getTemplate() { return _template; } List getRNAComponents() { return _RNAComponents; } private void init() { _ui = new TemplateEditorPanelUI(this); _RNAComponents = new ArrayList(); _RNAConnections = new ArrayList(); _helixToConnection = new Hashtable,Connection>(); _template = new RNATemplate(); setBackground(Color.WHITE); MouseControler mc = new MouseControler(this,_ui); addMouseListener(mc); addMouseMotionListener(mc); addMouseWheelListener(mc); _solidStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f); float[] dash = { 5.0f, 5.0f }; _dashedStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f, dash, 0); } public void addUndoableEditListener(UndoManager manager) { _ui.addUndoableEditListener(manager); } public TemplateEditorPanelUI getTemplateUI() { return _ui; } public void flip(Helix h) { h.toggleFlipped(); } public void addElement(GraphicalTemplateElement h) { _RNAComponents.add(h); } public void removeElement(GraphicalTemplateElement h) { _RNAComponents.remove(h); try { _template.removeElement(h.getTemplateElement()); } catch (ExceptionInvalidRNATemplate e) { //e.printStackTrace(); } } private GraphicalTemplateElement _selected = null; public GraphicalTemplateElement getSelected() { return _selected; } public void setSelected(GraphicalTemplateElement sel) { _selected = sel; if (_selected instanceof Helix) { _editor.flipButtonEnable(); } else { _editor.flipButtonDisable(); } } Helix.RelativePosition _relpos = Helix.RelativePosition.RP_OUTER; public void setSelectedEdge(Helix.RelativePosition rel) { _relpos = rel; } public void unselectEdge(Helix.RelativePosition rel) { _relpos = rel; } Point2D.Double _mousePos = new Point2D.Double(); public void setPointerPos(Point2D.Double p) { _mousePos = p; } public void Unselect() { _editor.flipButtonDisable(); _selected = null; } public GraphicalTemplateElement getElement(RNATemplateElement t) { for(GraphicalTemplateElement t2: _RNAComponents) if (t==t2.getTemplateElement()) return t2; return null; } public GraphicalTemplateElement getElementAt(double x, double y) { return getElementAt(x, y, null); } public GraphicalTemplateElement getElementAt(double x, double y, GraphicalTemplateElement excluded) { GraphicalTemplateElement h = null; for (int i=0; i<_RNAComponents.size();i++) { GraphicalTemplateElement h2 = _RNAComponents.get(i); if (( (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_END3) || (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_END5) || (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_START3) || (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_START5)) && (excluded!=h2)) { h = h2; } } if (h==null) { h = getElementCloseTo(x, y, excluded);}; return h; } public GraphicalTemplateElement getElementCloseTo(double x, double y) { return getElementCloseTo(x, y, null); } public GraphicalTemplateElement getElementCloseTo(double x, double y, GraphicalTemplateElement excluded) { GraphicalTemplateElement h = null; for (int i=0; i<_RNAComponents.size();i++) { GraphicalTemplateElement h2 = _RNAComponents.get(i); if ((h2.getRelativePosition(x, y) != Helix.RelativePosition.RP_OUTER) && (excluded!=h2)) { h = h2; } } return h; } public void addConnection(Connection c) { _RNAConnections.add(c); _helixToConnection.put(new Couple(c._h1,c._edge1), c); _helixToConnection.put(new Couple(c._h2,c._edge2), c); try { c._h1.attach(c._h2, c._edge1, c._edge2); c._h2.attach(c._h1, c._edge2, c._edge1); } catch (ExceptionInvalidRNATemplate e) { System.out.println(e.toString());// TODO Auto-generated catch block } } public Connection addConnection(GraphicalTemplateElement h1, GraphicalTemplateElement.RelativePosition edge1,GraphicalTemplateElement h2, GraphicalTemplateElement.RelativePosition edge2) { if ((h1!=h2)&&(getPartner(h1,edge1)==null)&&(getPartner(h2,edge2)==null)) { Connection c = new Connection(h1,edge1,h2,edge2); addConnection(c); return c; } return null; } /** * When there is already a connection in the underlying RNATemplate * and we want to create one at the graphical level. */ public void addGraphicalConnection(GraphicalTemplateElement h1, GraphicalTemplateElement.RelativePosition edge1,GraphicalTemplateElement h2, GraphicalTemplateElement.RelativePosition edge2) { //System.out.println("Connecting " + h1 + " " + edge1 + " to " + h2 + " " + edge2); Connection c = new Connection(h1,edge1,h2,edge2); _RNAConnections.add(c); _helixToConnection.put(new Couple(c._h1,c._edge1), c); _helixToConnection.put(new Couple(c._h2,c._edge2), c); c._h1.graphicalAttach(c._h2, c._edge1, c._edge2); c._h2.graphicalAttach(c._h1, c._edge2, c._edge1); } public void removeConnection(Connection c) { _RNAConnections.remove(c); _helixToConnection.remove(new Couple(c._h1,c._edge1)); _helixToConnection.remove(new Couple(c._h2,c._edge2)); System.out.println("[A]"+c); c._h1.detach(c._edge1); } public boolean isInCycle(GraphicalTemplateElement el, GraphicalTemplateElement.RelativePosition edge) { Stack > p = new Stack>(); Hashtable,Integer> alreadySeen = new Hashtable,Integer>(); p.add(new Couple(el,edge)); while(!p.empty()) { Couple c2 = p.pop(); if (alreadySeen.containsKey(c2)) { return true; } else { alreadySeen.put(c2, new Integer(1)); } GraphicalTemplateElement.RelativePosition next = c2.first.getConnectedEdge(c2.second); Couple otherEnd = new Couple(c2.first,next); if (!alreadySeen.containsKey(otherEnd)) { p.push(otherEnd); } else { Couple child = getPartner(c2.first,c2.second); if (child!=null) { p.push(child); } } } return false; } private static Color[] _colors = {Color.gray,Color.pink,Color.cyan,Color.RED,Color.green,Color.orange}; public static Color getIndexedColor(int n) { return _colors[n%_colors.length]; } public HashMap,Integer> buildConnectedComponents() { HashMap,Integer> alreadySeen = new HashMap,Integer>(); int numConnectedComponents = 0; for (GraphicalTemplateElement el : this._RNAComponents) { for (GraphicalTemplateElement.RelativePosition edge : el.getConnectedEdges()) { Couple c = new Couple(el,edge); if (!alreadySeen.containsKey(c)) { Stack > p = new Stack>(); p.add(c); p.add(new Couple(el,el.getConnectedEdge(edge))); while(!p.empty()) { Couple c2 = p.pop(); if (!alreadySeen.containsKey(c2)) { //System.out.println(" "+numConnectedComponents+" "+c2); c2.first.setMainColor(c2.second, getIndexedColor(numConnectedComponents)); alreadySeen.put(c2, new Integer(numConnectedComponents)); GraphicalTemplateElement.RelativePosition next = c2.first.getConnectedEdge(c2.second); Couple otherEnd = new Couple(c2.first,next); p.push(otherEnd); Couple child = getPartner(c2.first,c2.second); if (child!=null) { p.push(child); } } } numConnectedComponents += 1; } } } return alreadySeen; } public boolean isInCycle(Connection c) { return isInCycle(c._h1,c._edge1); } public Couple getPartner(GraphicalTemplateElement h, GraphicalTemplateElement.RelativePosition edge) { Connection c = getConnection(h, edge); if (c != null) { if ((c._h1==h)&&(c._edge1==edge)) { return new Couple(c._h2,c._edge2); } else { return new Couple(c._h1,c._edge1); } } else { return null; } } public Connection getConnection(GraphicalTemplateElement h, Helix.RelativePosition edge) { Couple target = new Couple(h,edge); if (_helixToConnection.containsKey(target)) { return _helixToConnection.get(target); } else { return null; } } private boolean isConnected(Helix h, GraphicalTemplateElement.RelativePosition edge) { Couple partner = getPartner(h,edge); return partner!=null; } // Aspects graphiques private static final Color CYCLE_COLOR = Color.red; private static final Color NON_EXISTANT_COLOR = Color.gray.brighter(); private static final Color CONTROL_COLOR = Color.gray.darker(); private static final Color BACKGROUND_COLOR = Color.white; private Stroke _solidStroke; private Stroke _dashedStroke; private void drawConnections(Graphics2D g2d, Connection c) { GraphicalTemplateElement h1 = c._h1; GraphicalTemplateElement.RelativePosition edge1 = c._edge1; Point2D.Double p1 = h1.getEdgePosition(edge1); GraphicalTemplateElement h2 = c._h2; GraphicalTemplateElement.RelativePosition edge2 = c._edge2; Point2D.Double p2 = h2.getEdgePosition(edge2); if (isInCycle(c)) { g2d.setColor(CYCLE_COLOR); } else { g2d.setColor(GraphicalTemplateElement.BACKBONE_COLOR); } g2d.drawLine((int)p1.x,(int)p1.y,(int)p2.x,(int)p2.y); } public void paintComponent(Graphics g) { //rescale(); // Debug code to show drawing area // g.setColor(Color.red); // g.fillRect(0,0,getWidth(),getHeight()); // g.setColor(Color.white); // g.fillRect(10,10,getWidth()-20,getHeight()-20); g.setColor(Color.white); g.fillRect(0,0,getWidth(),getHeight()); Graphics2D g2d = (Graphics2D) g; g2d.scale(scaleFactor, scaleFactor); g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); removeAll(); //super.paintComponent(g2d); buildConnectedComponents(); if (_selected!=null) { if (_relpos != GraphicalTemplateElement.RelativePosition.RP_OUTER) { Point2D.Double p = _selected.getEdgePosition(_relpos); g2d.setStroke(_solidStroke); g2d.drawLine((int)_mousePos.x, (int)_mousePos.y, (int)p.x, (int)p.y); } } for (int i=0;i<_RNAConnections.size();i++) { Connection c = _RNAConnections.get(i); drawConnections(g2d,c); } for (int i=0;i<_RNAComponents.size();i++) { GraphicalTemplateElement elem = _RNAComponents.get(i); //g2d.setColor(elem.getDominantColor()); //g2d.fill(elem.getArea()); if (_selected == elem) { elem.draw(g2d,true); } else { elem.draw(g2d,false); } } } /** * Get the bounding rectangle of the RNA components, always including the origin (0,0). */ public Rectangle getBoundingRectange() { int minX = 0; int maxX = 0; int minY = 0; int maxY = 0; for(int i=0;i graphical template element mapping Map map = new HashMap(); // First, we load elements { Iterator iter = template.classicIterator(); while (iter.hasNext()) { RNATemplateElement templateElement = iter.next(); if (templateElement instanceof RNATemplateHelix) { RNATemplateHelix templateHelix = (RNATemplateHelix) templateElement; Helix graphicalHelix = new Helix(templateHelix); graphicalHelix.setDominantColor(nextBackgroundColor()); _RNAComponents.add(graphicalHelix); map.put(templateHelix, graphicalHelix); } else if (templateElement instanceof RNATemplateUnpairedSequence) { RNATemplateUnpairedSequence templateSequence = (RNATemplateUnpairedSequence) templateElement; UnpairedRegion graphicalSequence = new UnpairedRegion(templateSequence); graphicalSequence.setDominantColor(nextBackgroundColor()); _RNAComponents.add(graphicalSequence); map.put(templateSequence, graphicalSequence); } } } // Now, we load edges { Iterator iter = template.makeEdgeList().iterator(); while (iter.hasNext()) { EdgeEndPoint v1 = iter.next(); EdgeEndPoint v2 = v1.getOtherEndPoint(); GraphicalTemplateElement gte1 = map.get(v1.getElement()); GraphicalTemplateElement gte2 = map.get(v2.getElement()); RelativePosition rp1 = gte1.relativePositionFromEdgeEndPointPosition(v1.getPosition()); RelativePosition rp2 = gte2.relativePositionFromEdgeEndPointPosition(v2.getPosition()); addGraphicalConnection(gte1, rp1, gte2, rp2); } } zoomFit(); //repaint(); } /** * Load a template from an XML file. */ public void loadFromXmlFile(File filename) { try { RNATemplate newTemplate = RNATemplate.fromXMLFile(filename); loadTemplate(newTemplate); } catch (ExceptionXmlLoading e) { e.printStackTrace(); JOptionPane.showMessageDialog(this, e.getMessage(), "Template loading error", JOptionPane.ERROR_MESSAGE); } } private void zoomFinish() { rescale(); repaint(); } public void zoomIn() { scaleFactor *= 1.2; zoomFinish(); } public void zoomOut() { scaleFactor /= 1.2; zoomFinish(); } public void zoomReset() { scaleFactor = scaleFactorDefault; zoomFinish(); } public void zoomFit() { if (_RNAComponents.isEmpty()) { zoomReset(); } else { Rectangle rect = getBoundingRectange(); double areaW = (rect.width + 100); double areaH = (rect.height + 100); // make it cover at least the space visible in the window scaleFactor = 1; scaleFactor = Math.min(scaleFactor, _editor.getJp().getViewport().getSize().width / areaW); scaleFactor = Math.min(scaleFactor, _editor.getJp().getViewport().getSize().height / areaH); zoomFinish(); } } public void translateView(Point trans) { int newX = _editor.getJp().getHorizontalScrollBar().getValue() - trans.x; int newY = _editor.getJp().getVerticalScrollBar().getValue() - trans.y; newX = Math.max(0, Math.min(newX, _editor.getJp().getHorizontalScrollBar().getMaximum())); newY = Math.max(0, Math.min(newY, _editor.getJp().getVerticalScrollBar().getMaximum())); _editor.getJp().getHorizontalScrollBar().setValue(newX); _editor.getJp().getVerticalScrollBar().setValue(newY); } } fr/orsay/lri/varna/applications/templateEditor/TemplateEditorPanelUI.java0000644000000000000000000000736312243516344025705 0ustar rootrootpackage fr.orsay.lri.varna.applications.templateEditor; import java.awt.geom.Point2D; import javax.swing.undo.UndoManager; import javax.swing.undo.UndoableEditSupport; import fr.orsay.lri.varna.applications.templateEditor.GraphicalTemplateElement.RelativePosition; import fr.orsay.lri.varna.models.templates.RNATemplate; public class TemplateEditorPanelUI { private UndoableEditSupport _undoableEditSupport; private TemplatePanel _tp; private Tool selectedTool = Tool.CREATE_HELIX; public enum Tool { SELECT, CREATE_HELIX, CREATE_UNPAIRED } public TemplateEditorPanelUI(TemplatePanel tp) { _tp = tp; _undoableEditSupport = new UndoableEditSupport(tp); } public Tool getSelectedTool() { return selectedTool; } public void setSelectedTool(Tool selectedTool) { this.selectedTool = selectedTool; } /* Generic undoable event firing for edge movement */ public void undoableEdgeMove(GraphicalTemplateElement h, GraphicalTemplateElement.RelativePosition edge,double nx, double ny) { _undoableEditSupport.postEdit(new TemplateEdits.ElementEdgeMoveTemplateEdit( h,edge,nx,ny,_tp)); h.setEdgePosition(edge, new Point2D.Double(nx,ny)); _tp.repaint(); } public void setEdge5UI(GraphicalTemplateElement h, double nx, double ny) { undoableEdgeMove(h,GraphicalTemplateElement.RelativePosition.RP_CONNECT_START5, nx,ny); } public void setEdge3UI(UnpairedRegion h, double nx, double ny) { undoableEdgeMove(h,GraphicalTemplateElement.RelativePosition.RP_CONNECT_END3, nx,ny); } public void setEdge5TangentUI(UnpairedRegion h, double nx, double ny) { undoableEdgeMove(h,GraphicalTemplateElement.RelativePosition.RP_EDIT_TANGENT_5, nx,ny); } public void setEdge3TangentUI(UnpairedRegion h, double nx, double ny) { undoableEdgeMove(h,GraphicalTemplateElement.RelativePosition.RP_EDIT_TANGENT_3, nx,ny); } public void moveUnpairedUI(UnpairedRegion u, double nx, double ny) { undoableEdgeMove(u,GraphicalTemplateElement.RelativePosition.RP_INNER_MOVE, nx,ny); } public void moveHelixUI(Helix h, double nx, double ny) { undoableEdgeMove(h,GraphicalTemplateElement.RelativePosition.RP_INNER_MOVE, nx,ny); } public void setHelixPosUI(Helix h, double nx, double ny) { undoableEdgeMove(h,GraphicalTemplateElement.RelativePosition.RP_EDIT_START, nx,ny); } public void setHelixExtentUI(Helix h, double nx, double ny) { undoableEdgeMove(h,GraphicalTemplateElement.RelativePosition.RP_EDIT_END, nx,ny); } public void addElementUI(GraphicalTemplateElement h) { _undoableEditSupport.postEdit(new TemplateEdits.ElementAddTemplateEdit( h,_tp)); _tp.addElement(h); } public void removeElementUI(GraphicalTemplateElement h) { _undoableEditSupport.postEdit(new TemplateEdits.ElementRemoveTemplateEdit( h,_tp)); _tp.removeElement(h); } public void addUndoableEditListener(UndoManager manager) { _undoableEditSupport.addUndoableEditListener(manager); } public void addConnectionUI(GraphicalTemplateElement h1, GraphicalTemplateElement.RelativePosition e1, GraphicalTemplateElement h2, GraphicalTemplateElement.RelativePosition e2) { if (GraphicalTemplateElement.canConnect(h1, e1,h2, e2)) { Connection c = _tp.addConnection(h1,e1,h2,e2); _undoableEditSupport.postEdit(new TemplateEdits.ElementAttachTemplateEdit(c,_tp)); } } public void removeConnectionUI(Connection c) { _undoableEditSupport.postEdit(new TemplateEdits.ElementDetachTemplateEdit(c,_tp)); _tp.removeConnection(c); } public void flipHelixUI(Helix h) { _undoableEditSupport.postEdit(new TemplateEdits.HelixFlipTemplateEdit(h,_tp)); _tp.flip(h); _tp.repaint(); } public RNATemplate getTemplate() { return _tp.getTemplate(); } } fr/orsay/lri/varna/applications/templateEditor/UnpairedRegion.java0000644000000000000000000003354012243521352024447 0ustar rootrootpackage fr.orsay.lri.varna.applications.templateEditor; import java.awt.Graphics2D; import java.awt.Polygon; import java.awt.Shape; import java.awt.geom.CubicCurve2D; import java.awt.geom.GeneralPath; import java.awt.geom.Point2D; import java.awt.geom.Point2D.Double; import java.util.ArrayList; import fr.orsay.lri.varna.applications.templateEditor.GraphicalTemplateElement.RelativePosition; import fr.orsay.lri.varna.exceptions.ExceptionEdgeEndpointAlreadyConnected; import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate; import fr.orsay.lri.varna.models.geom.CubicBezierCurve; import fr.orsay.lri.varna.models.templates.RNATemplate; import fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint; public class UnpairedRegion extends GraphicalTemplateElement{ private RNATemplateUnpairedSequence _e; public static final double DEFAULT_VECTOR_LENGTH = 35; public static final double DEFAULT_VECTOR_DISTANCE = 35; private Point2D.Double[] sequenceBasesCoords = null; public UnpairedRegion(double x, double y, RNATemplate tmp) { _e = tmp.new RNATemplateUnpairedSequence(""); _e.setVertex5(new Point2D.Double(x,y)); _e.setVertex3(new Point2D.Double(x+DEFAULT_VECTOR_DISTANCE,y)); _e.setInTangentVectorLength(DEFAULT_VECTOR_LENGTH); _e.setInTangentVectorAngle(-Math.PI/2.0); _e.setOutTangentVectorLength(DEFAULT_VECTOR_LENGTH); _e.setOutTangentVectorAngle(-Math.PI/2.0); updateLength(); } /** * Build an UnpairedRegion object from a RNATemplateUnpairedSequence * object. The RNATemplateUnpairedSequence must be connected to * an helix on both sides. */ public UnpairedRegion(RNATemplateUnpairedSequence templateSequence) { _e = templateSequence; } public Point2D.Double getEdge5() { RelativePosition r = RelativePosition.RP_CONNECT_START5; Couple c = getAttachedElement(r); return (isAnchored5()? c.second.getEdgePosition(c.first): _e.getVertex5()); } public Point2D.Double getEdge3() { RelativePosition r = RelativePosition.RP_CONNECT_END3; Couple c = getAttachedElement(r); return (isAnchored3()? c.second.getEdgePosition(c.first): _e.getVertex3()); } public Point2D.Double getCenter() { Point2D.Double p1 = getEdge5(); Point2D.Double p2 = getEdge3(); return new Point2D.Double((p1.x+p2.x)/2.,(p1.y+p2.y)/2.); } public void setEdge5(Point2D.Double d) { _e.setVertex5(d); updateLength(); } public void setEdge3(Point2D.Double d) { _e.setVertex3(d); updateLength(); } public void setCenter(Point2D.Double d) { Point2D.Double p1 = getEdge5(); Point2D.Double p2 = getEdge3(); double dx = p1.x-p2.x; double dy = p1.y-p2.y; _e.setVertex3(new Point2D.Double(d.x-dx/2.,d.y-dy/2.)); _e.setVertex5(new Point2D.Double(d.x+dx/2.,d.y+dy/2.)); invalidateCoords(); } public boolean isAnchored5() { return (_e.getIn().getOtherElement()!=null); } public boolean isAnchored3() { return (_e.getOut().getOtherElement()!=null); } public static Shape bezToShape(CubicBezierCurve c) { GeneralPath p = new GeneralPath(); int nb = 9; double[] tab = new double[nb]; for (int i=0;i> v = new ArrayList>(); v.add(new Couple(p.distance(p5),RelativePosition.RP_CONNECT_START5)); v.add(new Couple(p.distance(p3),RelativePosition.RP_CONNECT_END3)); v.add(new Couple(p.distance(t5),RelativePosition.RP_EDIT_TANGENT_5)); v.add(new Couple(p.distance(t3),RelativePosition.RP_EDIT_TANGENT_3)); v.add(new Couple(p.distance(ct),RelativePosition.RP_INNER_MOVE)); double dist = java.lang.Double.MAX_VALUE; RelativePosition r = RelativePosition.RP_OUTER; for (Couple c : v) { if (c.first c = getAttachedElement(edge); getEndPoint(edge).disconnect(); } // Call the parent class detach function, which will also take care to disconnect this other endpoint of this edge super.detach(edge); } public void setEdgePosition(RelativePosition edge, Point2D.Double pos) { switch(edge) { case RP_CONNECT_START5: setEdge5(pos); break; case RP_INNER_MOVE: setCenter(pos); break; case RP_CONNECT_END3: setEdge3(pos); break; case RP_EDIT_TANGENT_5: updateControl5(pos); break; case RP_EDIT_TANGENT_3: updateControl3(pos); break; } } public ArrayList getConnectedEdges() { ArrayList result = new ArrayList(); result.add(RelativePosition.RP_CONNECT_START5); result.add(RelativePosition.RP_CONNECT_END3); return result; } public RNATemplateElement getTemplateElement() { return _e; } public RelativePosition relativePositionFromEdgeEndPointPosition( EdgeEndPointPosition pos) { switch (pos) { case IN1: return RelativePosition.RP_CONNECT_START5; case OUT1: return RelativePosition.RP_CONNECT_END3; default: return null; } } } fr/orsay/lri/varna/applications/templateEditor/TemplateEditor.java0000644000000000000000000004157612243552312024466 0ustar rootrootpackage fr.orsay.lri.varna.applications.templateEditor; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.ComponentOrientation; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTarget; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.Reader; import java.net.MalformedURLException; import java.net.URL; import java.net.URLConnection; import java.util.ArrayList; import java.util.List; import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JDialog; import javax.swing.JFileChooser; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.JToggleButton; import javax.swing.JToolBar; import javax.swing.UIManager; import javax.swing.UIManager.LookAndFeelInfo; import javax.swing.filechooser.FileFilter; import javax.swing.undo.UndoManager; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.applications.FileNameExtensionFilter; import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration; import fr.orsay.lri.varna.models.templates.Benchmark; import fr.orsay.lri.varna.models.templates.DrawRNATemplateCurveMethod; import fr.orsay.lri.varna.models.templates.DrawRNATemplateMethod; import fr.orsay.lri.varna.models.templates.RNATemplate; import fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException; import fr.orsay.lri.varna.models.templates.RNATemplateMapping; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement; public class TemplateEditor extends JFrame implements KeyListener, ActionListener,DropTargetListener { private TemplatePanel _sk; private VARNAPanel _vp; private File currentFilePath = null; private JButton saveButton; private JScrollPane jp; private UndoManager manager; private JButton flipButton; private JComboBox ellipseMethodList; private JComboBox applyMethodList; /*private JRadioButton ellipseButtons[]; private JRadioButton methodButtons[]; */ public TemplateEditor() { init(); clearCurrentFilePath(); } public JScrollPane getJp() { return jp; } private void init() { try { _vp = new VARNAPanel(" ","."); } catch (ExceptionNonEqualLength e) { e.printStackTrace(); } _vp.setNumPeriod(0); JPanel p = new JPanel(); p.setLayout(new GridLayout(1,2)); JToolBar systemBar = new JToolBar(); JToolBar optionsBar = new JToolBar(); JButton newButton = new JButton("New",UIManager.getIcon("FileView.fileIcon")); newButton.setActionCommand("new"); newButton.addActionListener(this); newButton.addKeyListener(this); JButton loadButton = new JButton("Open...",UIManager.getIcon("FileView.directoryIcon")); loadButton.setActionCommand("open"); loadButton.addActionListener(this); loadButton.addKeyListener(this); saveButton = new JButton("Save",UIManager.getIcon("FileView.floppyDriveIcon")); saveButton.setActionCommand("save"); saveButton.addActionListener(this); saveButton.addKeyListener(this); saveButton.setEnabled(false); JButton saveAsButton = new JButton("Save As...",UIManager.getIcon("FileView.floppyDriveIcon")); saveAsButton.setActionCommand("save as"); saveAsButton.addActionListener(this); saveAsButton.addKeyListener(this); JButton undoButton = new JButton("Undo"); undoButton.setActionCommand("undo"); undoButton.addActionListener(this); undoButton.addKeyListener(this); JButton redoButton = new JButton("Redo"); redoButton.setActionCommand("redo"); redoButton.addActionListener(this); redoButton.addKeyListener(this); JButton benchmarkButton = new JButton("Benchmark"); benchmarkButton.setActionCommand("benchmark"); benchmarkButton.addActionListener(this); benchmarkButton.addKeyListener(this); DrawRNATemplateMethod applyMethods[] = DrawRNATemplateMethod.values(); applyMethodList = new JComboBox(applyMethods); applyMethodList.setSelectedItem(DrawRNATemplateMethod.getDefault()); DrawRNATemplateCurveMethod ellipseMethods[] = DrawRNATemplateCurveMethod.values(); ellipseMethodList = new JComboBox(ellipseMethods); ellipseMethodList.setSelectedItem(DrawRNATemplateCurveMethod.getDefault()); JButton applyButton = new JButton("Apply"); applyButton.setActionCommand("apply"); applyButton.addActionListener(this); applyButton.addKeyListener(this); JButton retrieveButton = new JButton("Retrieve Templates"); retrieveButton.setActionCommand("retrieve"); retrieveButton.addActionListener(this); flipButton = new JButton("Flip helix"); flipButton.setActionCommand("flip"); flipButton.addActionListener(this); flipButton.addKeyListener(this); flipButton.setEnabled(false); systemBar.add(newButton); systemBar.add(loadButton); systemBar.add(saveButton); systemBar.add(saveAsButton); systemBar.addSeparator(); systemBar.addSeparator(); systemBar.addSeparator(); systemBar.add(benchmarkButton); systemBar.addKeyListener(this); optionsBar.setLayout(new FlowLayout(FlowLayout.LEFT)); optionsBar.add(new JLabel("Single-Stranded ")); optionsBar.add(this.ellipseMethodList); optionsBar.addSeparator(); optionsBar.add(new JLabel("Layout ")); optionsBar.add(this.applyMethodList); optionsBar.addSeparator(); optionsBar.add(applyButton); optionsBar.addSeparator(); optionsBar.add(retrieveButton); optionsBar.doLayout(); /*optionsBar.add(new JLabel("Curves:")); for (int i=0; i res = new ArrayList(); String s = b.readLine(); while(s!=null) { res.add(s); s = b.readLine(); } } catch (MalformedURLException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } } fr/orsay/lri/varna/applications/templateEditor/MouseControler.java0000644000000000000000000002263112243521106024510 0ustar rootrootpackage fr.orsay.lri.varna.applications.templateEditor; import java.awt.Point; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.awt.geom.Point2D; public class MouseControler implements MouseListener, MouseMotionListener, MouseWheelListener { private int _granularity = 8; private final int HYSTERESIS_DISTANCE = 10; TemplatePanel _sp; GraphicalTemplateElement _elem; TemplateEditorPanelUI _ui; private GraphicalTemplateElement.RelativePosition _currentMode = Helix.RelativePosition.RP_OUTER; private boolean movingView = false; private Point2D.Double _clickedPos = new Point2D.Double(); private Point _clickedPosScreen = new Point(); public MouseControler(TemplatePanel sp, TemplateEditorPanelUI ui) { _sp = sp; _elem = null; _ui = ui; } public void mouseWheelMoved(MouseWheelEvent e) { if (e.getWheelRotation() == -1) { _sp.zoomIn(); } else { _sp.zoomOut(); } e.consume(); } public void mouseClicked(MouseEvent arg0) { } public void mouseEntered(MouseEvent arg0) { // TODO Auto-generated method stub } public void mouseExited(MouseEvent arg0) { // TODO Auto-generated method stub } /** * Get mouse position in logical coordinates, ie. those used in the template XML file. * It differs from the screen coordinates relative to panel because of the scaling factor. */ public Point2D.Double getLogicalMouseCoords(MouseEvent event) { return new Point2D.Double(event.getX()/_sp.getScaleFactor(), event.getY()/_sp.getScaleFactor()); } public void mousePressed(MouseEvent arg0) { movingView = false; _clickedPos = new Point2D.Double(arg0.getX(), arg0.getY()); _clickedPosScreen.x = arg0.getXOnScreen(); _clickedPosScreen.y = arg0.getYOnScreen(); // middle-click if (arg0.getButton() == MouseEvent.BUTTON2) { movingView = true; } else { Point2D.Double logicalMousePos = getLogicalMouseCoords(arg0); GraphicalTemplateElement elem = _sp.getElementAt(logicalMousePos.getX(), logicalMousePos.getY()); _sp.Unselect(); if (elem==null) { if (arg0.getButton()==MouseEvent.BUTTON1 && _ui.getSelectedTool() == TemplateEditorPanelUI.Tool.CREATE_HELIX) { _currentMode = Helix.RelativePosition.RP_EDIT_START; } else if ((arg0.getButton()==MouseEvent.BUTTON1 && _ui.getSelectedTool() == TemplateEditorPanelUI.Tool.CREATE_UNPAIRED)) { // Create a new unpaired region UnpairedRegion n = new UnpairedRegion(logicalMousePos.getX(),logicalMousePos.getY(),_sp.getTemplate()); n.setDominantColor(_sp.nextBackgroundColor()); _ui.addElementUI(n); _sp.setSelected(n); _sp.repaint(); _elem = n; _currentMode = GraphicalTemplateElement.RelativePosition.RP_EDIT_START; } } else if (arg0.getButton()==MouseEvent.BUTTON1) { _currentMode = elem.getRelativePosition(logicalMousePos.getX(), logicalMousePos.getY()); _sp.setSelected(elem); _elem = elem; switch (_currentMode) { case RP_EDIT_START: case RP_EDIT_END: case RP_EDIT_TANGENT_5: case RP_EDIT_TANGENT_3: break; case RP_INNER_MOVE: break; case RP_INNER_GENERAL: _currentMode = Helix.RelativePosition.RP_INNER_MOVE; break; case RP_CONNECT_END3: case RP_CONNECT_END5: case RP_CONNECT_START5: case RP_CONNECT_START3: { Couple al = _sp.getPartner(elem, _currentMode); boolean isConnected = (al!=null); if (isConnected) { Connection c = _sp.getConnection(elem, _currentMode); _ui.removeConnectionUI(c); GraphicalTemplateElement p1 = c._h1; GraphicalTemplateElement p2 = c._h2; boolean p1IsHelix = (p1 instanceof Helix); boolean p1IsUnpaired = (p1 instanceof UnpairedRegion); boolean p2IsHelix = (p2 instanceof Helix); boolean p2IsUnpaired = (p2 instanceof UnpairedRegion); boolean p1StillAttached = (p1 == elem); if ((p1IsUnpaired && p2IsHelix)) { p1StillAttached = false; } if (p1StillAttached) { _elem = p2; _currentMode = c._edge2; } else if (!p1StillAttached) { _elem=p1; _currentMode = c._edge1; } } if (_elem instanceof Helix) { _sp.setPointerPos(new Point2D.Double(logicalMousePos.getX(),logicalMousePos.getY())); _sp.setSelectedEdge(_currentMode); } _sp.setSelected(_elem); } break; case RP_OUTER: _sp.Unselect(); _elem = null; } _sp.repaint(); } } } public void mouseReleased(MouseEvent arg0) { movingView = false; Point2D.Double logicalMousePos = getLogicalMouseCoords(arg0); if (_elem!=null) { switch (_currentMode) { case RP_EDIT_START: case RP_EDIT_END: { if (_elem instanceof Helix) { Helix h = (Helix) _elem; if (h.getPos().distance(h.getExtent())<10.0) { _ui.removeElementUI(_elem); _sp.Unselect(); } } } break; case RP_INNER_MOVE: break; case RP_CONNECT_END3: case RP_CONNECT_END5: case RP_CONNECT_START5: case RP_CONNECT_START3: { GraphicalTemplateElement t = _sp.getElementAt(logicalMousePos.getX(), logicalMousePos.getY(),_elem); if (t!=null) { GraphicalTemplateElement.RelativePosition edge = t.getClosestEdge(logicalMousePos.getX(), logicalMousePos.getY()); _ui.addConnectionUI(_elem,_currentMode,t,edge); } _sp.setSelectedEdge(Helix.RelativePosition.RP_OUTER); } break; } _elem = null; _sp.rescale(); } _sp.setSelectedEdge(Helix.RelativePosition.RP_OUTER); _currentMode = Helix.RelativePosition.RP_OUTER; _sp.repaint(); } private Point2D.Double projectPoint(double x, double y, Point2D.Double ref) { Point2D.Double result = new Point2D.Double(); double nx = x-ref.x; double ny = y-ref.y; double tmp = Double.MIN_VALUE; for (int i=0;i tmp) { tmp = norm; result.x = ref.x+dx*norm; result.y = ref.y+dy*norm; } } return result; } public void mouseDragged(MouseEvent arg0) { if (movingView) { Point trans = new Point( arg0.getXOnScreen() - _clickedPosScreen.x, arg0.getYOnScreen() - _clickedPosScreen.y); _sp.translateView(trans); _clickedPosScreen.x = arg0.getXOnScreen(); _clickedPosScreen.y = arg0.getYOnScreen(); } else { Point2D.Double logicalMousePos = getLogicalMouseCoords(arg0); if (_elem == null) { switch (_currentMode) { case RP_EDIT_START: { if (_clickedPos.distance(arg0.getX(),arg0.getY())>HYSTERESIS_DISTANCE) { System.out.println("Creating Helix..."); Helix h1 = new Helix(logicalMousePos.getX(),logicalMousePos.getY(),_sp.getTemplate(),_sp.getRNAComponents()); h1.setDominantColor(_sp.nextBackgroundColor()); _ui.addElementUI(h1); _sp.setSelected(h1); _sp.repaint(); _elem = h1; } } break; } } else { if (_elem instanceof Helix) { Helix h = (Helix) _elem; switch (_currentMode) { case RP_EDIT_START: { Point2D.Double d = projectPoint(logicalMousePos.getX(),logicalMousePos.getY(),h.getPos()); _ui.setHelixExtentUI(h, d.x,d.y); } break; case RP_EDIT_END: { Point2D.Double d = projectPoint( logicalMousePos.getX(),logicalMousePos.getY(),h.getExtent()); _ui.setHelixPosUI(h, d.x,d.y); } break; case RP_INNER_MOVE: _ui.moveHelixUI(h, logicalMousePos.getX(),logicalMousePos.getY()); break; case RP_CONNECT_END3: case RP_CONNECT_END5: case RP_CONNECT_START5: case RP_CONNECT_START3: _sp.setPointerPos(new Point2D.Double(logicalMousePos.getX(),logicalMousePos.getY())); _sp.repaint(); break; } } else if (_elem instanceof UnpairedRegion) { UnpairedRegion ur = (UnpairedRegion) _elem; Point2D.Double p = new Point2D.Double(logicalMousePos.getX(),logicalMousePos.getY()); switch (_currentMode) { case RP_EDIT_TANGENT_5: { _ui.setEdge5TangentUI(ur,logicalMousePos.getX(),logicalMousePos.getY()); _sp.repaint(); break; } case RP_EDIT_TANGENT_3: { _ui.setEdge3TangentUI(ur,logicalMousePos.getX(),logicalMousePos.getY()); _sp.repaint(); break; } case RP_INNER_MOVE: { _ui.moveUnpairedUI(ur,logicalMousePos.getX(),logicalMousePos.getY()); _sp.repaint(); break; } case RP_CONNECT_START5: _ui.setEdge5UI(ur,logicalMousePos.getX(),logicalMousePos.getY()); break; case RP_CONNECT_END3: _ui.setEdge3UI(ur,logicalMousePos.getX(),logicalMousePos.getY()); break; } _sp.repaint(); } } } } public void mouseMoved(MouseEvent arg0) { // TODO Auto-generated method stub } } fr/orsay/lri/varna/applications/templateEditor/Helix.java0000644000000000000000000004647512003616456022624 0ustar rootrootpackage fr.orsay.lri.varna.applications.templateEditor; import java.awt.Graphics2D; import java.awt.Polygon; import java.awt.Shape; import java.awt.geom.Point2D; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.models.templates.RNATemplate; import fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix; import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint; public class Helix extends GraphicalTemplateElement{ RNATemplateHelix _h; public Helix(double x, double y, RNATemplate tmp, List existingRNAElements) { this(x,y,getNextAutomaticCaption(existingRNAElements),tmp); } public Helix(double x, double y, String cap, RNATemplate tmp) { _h = tmp.new RNATemplateHelix(cap); _h.setStartPosition(new Point2D.Double(x,y)); _h.setEndPosition(new Point2D.Double(x,y)); _h.setLength(1); _h.setCaption(cap); } public Helix(RNATemplateHelix templateHelix) { _h = templateHelix; } private static String getNextAutomaticCaption(List existingRNAElements) { // Find which captions are already used Set captions = new HashSet(); for (GraphicalTemplateElement element: existingRNAElements) { if (element instanceof Helix) { Helix helix = (Helix) element; if (helix.getCaption() != null) { captions.add(helix.getCaption()); } } } // Find a non-conflicting name for this helix for (int i=1;;i++) { String candidateCaption = "H" + i; if (! captions.contains(candidateCaption)) { return candidateCaption; } } } public void toggleFlipped() { _h.setFlipped(!_h.isFlipped()); updateAttachedUnpairedRegions(); } /** * When an helix is moved/resized/etc... it is necessary to update * the positions of endpoints from unpaired regions that are attached * to the helix. This function updates the endpoints positions of * attached unpaired regions. */ public void updateAttachedUnpairedRegions() { for (RelativePosition rpos: getConnectedEdges()) { Couple c = getAttachedElement(rpos); if (c != null && c.second instanceof UnpairedRegion) { UnpairedRegion unpairedRegion = (UnpairedRegion) c.second; Point2D.Double pos = getEdgePosition(rpos); if (c.first == RelativePosition.RP_CONNECT_START5) { unpairedRegion.setEdge5(pos); } else if (c.first == RelativePosition.RP_CONNECT_END3) { unpairedRegion.setEdge3(pos); } } } } public double getPosX() { return _h.getStartPosition().x; } public String getCaption() { return _h.getCaption(); } public double getPosY() { return _h.getStartPosition().y; } public RNATemplateHelix getTemplateElement() { return _h; } public void setX(double x) { _h.getStartPosition().x = x; } public void setY(double y) { _h.getStartPosition().y = y; } public void setPos(Point2D.Double p) { _h.setStartPosition(p); updateLength(); } public void setPos(double x, double y) { setPos(new Point2D.Double(x,y)); } public Point2D.Double getPos() { return _h.getStartPosition(); } public void moveCenter(double x, double y) { Point2D.Double center = new Point2D.Double((_h.getStartPosition().x+_h.getEndPosition().x)/2.0,(_h.getStartPosition().y+_h.getEndPosition().y)/2.0); double dx = x-center.x; double dy = y-center.y; _h.setStartPosition(new Point2D.Double(_h.getStartPosition().x+dx,_h.getStartPosition().y+dy)); _h.setEndPosition(new Point2D.Double(_h.getEndPosition().x+dx,_h.getEndPosition().y+dy)); } public void setExtent(double x, double y) { setExtent(new Point2D.Double(x,y)); } private void updateLength() { _h.setLength(getNbBP()); } public void setExtent(Point2D.Double p) { _h.setEndPosition(p); updateLength(); } public double getExtentX() { return _h.getEndPosition().x; } public Point2D.Double getExtent() { return _h.getEndPosition(); } public double getExtentY() { return _h.getEndPosition().y; } public static final double BASE_PAIR_DISTANCE = RNA.BASE_PAIR_DISTANCE; public static final double LOOP_DISTANCE = RNA.LOOP_DISTANCE; public static final double SELECTION_RADIUS = 15.0; public Point2D.Double getAbsStart5() { double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition())); double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition())); double nx = dy; double ny = -dx; Point2D.Double start5 = new Point2D.Double((getPosX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()-Helix.BASE_PAIR_DISTANCE*ny/2.0)); return start5; } public Point2D.Double getAbsStart3() { double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition())); double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition())); double nx = dy; double ny = -dx; Point2D.Double start3 = new Point2D.Double((getPosX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()+Helix.BASE_PAIR_DISTANCE*ny/2.0)); return start3; } public Point2D.Double getAbsEnd5() { double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition())); double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition())); double nx = dy; double ny = -dx; Point2D.Double end5 = new Point2D.Double((getExtentX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()-Helix.BASE_PAIR_DISTANCE*ny/2.0)); return end5; } public Point2D.Double getAbsEnd3() { double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition())); double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition())); double nx = dy; double ny = -dx; Point2D.Double end3 = new Point2D.Double((getExtentX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()+Helix.BASE_PAIR_DISTANCE*ny/2.0)); return end3; } public Point2D.Double getStart5() { if (_h.isFlipped()) return getAbsStart3(); else return getAbsStart5(); } public Point2D.Double getStart3() { if (_h.isFlipped()) return getAbsStart5(); else return getAbsStart3(); } public Point2D.Double getEnd5() { if (_h.isFlipped()) return getAbsEnd3(); else return getAbsEnd5(); } public Point2D.Double getEnd3() { if (_h.isFlipped()) return getAbsEnd5(); else return getAbsEnd3(); } public Polygon getBoundingPolygon() { double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition())); double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition())); double nx = dy; double ny = -dx; Point2D.Double start5 = new Point2D.Double((getPosX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()+Helix.BASE_PAIR_DISTANCE*ny/2.0)); Point2D.Double end5 = new Point2D.Double((getExtentX()+Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()+Helix.BASE_PAIR_DISTANCE*ny/2.0)); Point2D.Double start3 = new Point2D.Double((getPosX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getPosY()-Helix.BASE_PAIR_DISTANCE*ny/2.0)); Point2D.Double end3 = new Point2D.Double((getExtentX()-Helix.BASE_PAIR_DISTANCE*nx/2.0),(getExtentY()-Helix.BASE_PAIR_DISTANCE*ny/2.0)); Polygon p = new Polygon(); p.addPoint((int)start5.x, (int)start5.y); p.addPoint((int)end5.x, (int)end5.y); p.addPoint((int)end3.x, (int)end3.y); p.addPoint((int)start3.x, (int)start3.y); return p; } public Point2D.Double getCenter() { return new Point2D.Double((int)((_h.getStartPosition().x+_h.getEndPosition().x)/2.0), (int)((_h.getStartPosition().y+_h.getEndPosition().y)/2.0)); } public Point2D.Double getCenterEditStart() { double dist = _h.getStartPosition().distance(_h.getEndPosition()); double dx = (_h.getEndPosition().x-_h.getStartPosition().x)/(dist); double dy = (_h.getEndPosition().y-_h.getStartPosition().y)/(dist); return new Point2D.Double((int)(_h.getStartPosition().x+(dist-10.0)*dx), (int)(_h.getStartPosition().y+(dist-10.0)*dy)); } public Point2D.Double getCenterEditEnd() { double dist = _h.getStartPosition().distance(_h.getEndPosition()); double dx = (_h.getEndPosition().x-_h.getStartPosition().x)/(dist); double dy = (_h.getEndPosition().y-_h.getStartPosition().y)/(dist); return new Point2D.Double((int)(_h.getStartPosition().x+(10.0)*dx), (int)(_h.getStartPosition().y+(10.0)*dy)); } public Shape getSelectionBox() { double dx = (_h.getStartPosition().x-_h.getEndPosition().x)/(_h.getStartPosition().distance(_h.getEndPosition())); double dy = (_h.getStartPosition().y-_h.getEndPosition().y)/(_h.getStartPosition().distance(_h.getEndPosition())); double nx = dy; double ny = -dx; Polygon hbox = getBoundingPolygon(); Polygon p = new Polygon(); Point2D.Double start5 = new Point2D.Double(hbox.xpoints[0]+SELECTION_RADIUS*(dx+nx),hbox.ypoints[0]+SELECTION_RADIUS*(dy+ny)); Point2D.Double end5 = new Point2D.Double(hbox.xpoints[1]+SELECTION_RADIUS*(-dx+nx),hbox.ypoints[1]+SELECTION_RADIUS*(-dy+ny)); Point2D.Double end3 = new Point2D.Double(hbox.xpoints[2]+SELECTION_RADIUS*(-dx-nx),hbox.ypoints[2]+SELECTION_RADIUS*(-dy-ny));; Point2D.Double start3 = new Point2D.Double(hbox.xpoints[3]+SELECTION_RADIUS*(dx-nx),hbox.ypoints[3]+SELECTION_RADIUS*(dy-ny));; p.addPoint((int)start5.x, (int)start5.y); p.addPoint((int)end5.x, (int)end5.y); p.addPoint((int)end3.x, (int)end3.y); p.addPoint((int)start3.x, (int)start3.y); return p; } public Shape getArea() { return getSelectionBox(); } public static final double EDIT_RADIUS = 10.0; public static final double MOVE_RADIUS = 13.0; public static final double BASE_RADIUS = 8.0; public static final double EDGE_BASE_RADIUS = 7.0; public RelativePosition getRelativePosition(double x, double y) { Point2D.Double current = new Point2D.Double(x,y); Shape p = getSelectionBox(); if (p.contains(current)) { if (getCenterEditStart().distance(current) getConnectedEdges() { ArrayList result = new ArrayList(); result.add(RelativePosition.RP_CONNECT_START5); result.add(RelativePosition.RP_CONNECT_START3); result.add(RelativePosition.RP_CONNECT_END5); result.add(RelativePosition.RP_CONNECT_END3); return result; } public String toString() { return "Helix " + getCaption(); } public RelativePosition relativePositionFromEdgeEndPointPosition( EdgeEndPointPosition pos) { switch (pos) { case IN1: return RelativePosition.RP_CONNECT_START5; case OUT1: return RelativePosition.RP_CONNECT_END5; case IN2: return RelativePosition.RP_CONNECT_END3; case OUT2: return RelativePosition.RP_CONNECT_START3; default: return null; } } } fr/orsay/lri/varna/applications/templateEditor/Couple.java0000644000000000000000000000115711620715272022766 0ustar rootrootpackage fr.orsay.lri.varna.applications.templateEditor; public class Couple { public T first; public U second; private static final int HASH_PRIME = 1000003; public Couple(T a, U b) { first = a; second = b; } public boolean equals( Object c) { if (!(c instanceof Couple)) { return false; } Couple cc = (Couple) c; return (cc.first.equals(first) && (cc.second.equals(second))); } public int hashCode() { return HASH_PRIME*first.hashCode()+second.hashCode(); } public String toString() { return "("+first+","+second+")"; } } fr/orsay/lri/varna/applications/NussinovDesignDemo.java0000644000000000000000000006151612031333132022331 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.applications; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseEvent; import java.math.BigInteger; import java.util.ArrayList; import java.util.Collections; import javax.swing.BorderFactory; import javax.swing.DefaultComboBoxModel; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSplitPane; import javax.swing.JTextArea; import javax.swing.JTextField; import javax.swing.JTextPane; import javax.swing.border.BevelBorder; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurInterpolator; import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.exceptions.MappingException; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModelBaseStyle; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;; public class NussinovDesignDemo extends JFrame implements InterfaceVARNAListener,InterfaceVARNABasesListener, ItemListener { /** * */ private static final long serialVersionUID = -790155708306987257L; private static final String SEQUENCE_A = "AGGCACGUCU"; private static final String SEQUENCE_B = "GAGUAGCCUC"; private static final String SEQUENCE_C = "GCAUAGCUGC"; private static final String SEQUENCE_INRIA = "CGAUUGCAUCGCAAGU"; private static final String TARGET_STRUCTURE_1 = "(((((((..)))))))"; private static final String TARGET_STRUCTURE_2 = "(((())))(((())))"; private static final String TARGET_STRUCTURE_3 = "(.((.((..).)).))"; private static final String TARGET_STRUCTURE_4 = "((((((())))(((())(()))))))"; private static final String TARGET_STRUCTURE_5 = "(((())))(((())))(((())))(((())))(((())))(((())))"; private static final String SEQUENCE_BIG = "AAAACAAAAACACCAUGGUGUUUUCACCCAAUUGGGUGAAAACAGAGAUCUCGAGAUCUCUGUUUUUGUUUU"; private static final String DEFAULT_STRUCTURE = ".........."; // private static final String DEFAULT_STRUCTURE1 = "((((....))))"; // private static final String DEFAULT_STRUCTURE2 = // "((((..(((....)))..))))"; private VARNAPanel _vpMaster; private VARNAPanel _vpTarget; private InfoPanel _infos = new InfoPanel(); private JPanel _tools = new JPanel(); private JPanel _input = new JPanel(); private JPanel _seqPanel = new JPanel(); private JPanel _structPanel = new JPanel(); private JLabel _actions = new JLabel(); private JComboBox _struct = new JComboBox(); private JLabel _seq1 = new JLabel(); private JLabel _structLabel = new JLabel("Structure Secondaire Cible"); private JLabel _seqLabel = new JLabel("Sequence d'ARN"); private JButton _switchButton = new JButton("Reset"); private Color _backgroundColor = Color.white; private Color _targetColor = new Color(200,200,250); private Color _okColor = new Color(100,100,250); private Color _koColor = new Color(250,200,200); public static ModelBaseStyle createStyle(String txt) { ModelBaseStyle result = new ModelBaseStyle(); try { result.assignParameters(txt); } catch (ExceptionModeleStyleBaseSyntaxError e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionParameterError e) { // TODO Auto-generated catch block e.printStackTrace(); } return result; } public void applyTo(VARNAPanel vp, ModelBaseStyle mb, int[] indices) { for(int i=0;i sols = getStructs(); _infos.setInfo(sols, count(getSeq())); if ((sols.size()==1)&&(sols.get(0).equals(_struct.getSelectedItem().toString()))) { this._vpMaster.setTitle("Flicitations !"); /*JOptionPane.showMessageDialog(null, "Vous avez trouv une squence pour cette structure !!!\n Saurez vous faire le design de molcules plus complexes ?", "Flicitations !", JOptionPane.INFORMATION_MESSAGE);*/ } else { this._vpMaster.setTitle("Meilleur repliement - Squence courante"); } } public void setTarget(String target) { RNA r = new RNA(); try { _vpTarget.drawRNA(String.format("%"+target.length()+"s", ""),target); createDummySeq(); showSolution(); onStructureRedrawn(); } catch (ExceptionNonEqualLength e) { // TODO Auto-generated catch block e.printStackTrace(); } } private void createDummySeq() { RNA r = _vpTarget.getRNA(); String seq = new String(); for (int i=0;ii+1) { fact1 = tab[i+1][k-1]; } double fact2 = 0; if (k combine(double bonus, ArrayList part1, ArrayList part2) { ArrayList base = new ArrayList(); for(double d1: part1) { for(double d2: part2) { base.add(bonus+d1+d2); } } return base; } public static ArrayList selectBests(ArrayList base) { ArrayList result = new ArrayList(); double best = Double.NEGATIVE_INFINITY; for(double val: base) { best = Math.max(val, best); } for(double val: base) { if (val == best) result.add(val); } return result; } private ArrayList backtrack(double[][] tab, String seq) { return backtrack(tab,seq, 0, seq.length()-1); } private ArrayList backtrack(double[][] tab, String seq, int i, int j) { ArrayList result = new ArrayList(); if (i indices = new ArrayList(); indices.add(-1); for (int k=i+1;k<=j;k++) { indices.add(k); } for (int k : indices) { if (k==-1) { if (tab[i][j] == tab[i+1][j]) { for (String s:backtrack(tab, seq, i+1,j)) { result.add("."+s); } } } else { if (canBasePair(seq.charAt(i),seq.charAt(k))) { double fact1 = 0; if (k>i+1) { fact1 = tab[i+1][k-1]; } double fact2 = 0; if (ki+1) { fact1 = tab[i+1][k-1]; } BigInteger fact2 = BigInteger.ONE; if (k _cacheStructs = new ArrayList(); public ArrayList getStructs() { String seq = getSeq(); seq = seq.toUpperCase(); if (!_cache.equals(seq)) { double[][] mfe = fillMatrix(seq); _cacheStructs = backtrack(mfe,seq); _cache = seq; } return _cacheStructs; } public VARNAPanel get_varnaPanel() { return _vpMaster; } public void set_varnaPanel(VARNAPanel surface) { _vpMaster = surface; } public JLabel get_info() { return _actions; } public void set_info(JLabel _info) { this._actions = _info; } public static void main(String[] args) { NussinovDesignDemo d = new NussinovDesignDemo(); d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); d.pack(); d.setVisible(true); } public void onStructureRedrawn() { _vpMaster.repaint(); } public void onWarningEmitted(String s) { // TODO Auto-generated method stub } public void onLoad(String path) { // TODO Auto-generated method stub } public void onLoaded() { // TODO Auto-generated method stub } public void onUINewStructure(VARNAConfig v, RNA r) { // TODO Auto-generated method stub } static final String[] _bases = {"A","C","G","U"}; static final String[] _basesComp = {"U","G","C","A"}; public void onBaseClicked(ModeleBase mb, MouseEvent e) { int index = -1; for(int i =0;i<_bases.length;i++) { if (mb.getContent().equalsIgnoreCase(_bases[i])) { index = i; } } index = (index+1)%_bases.length; mb.setContent(_bases[index].toUpperCase()); ArrayList partners =_vpTarget.getRNA().getAllPartners(mb.getIndex()); if (partners.size()!=0) { ModeleBase mbPartner = _vpMaster.getRNA().getBaseAt(partners.get(0).getIndex()); mbPartner.setContent(_basesComp[index].toUpperCase()); } _vpMaster.repaint(); _seq1.setText(_vpMaster.getRNA().getSeq()); new Temporizer(_vpMaster.getRNA().getSeq()).start(); } private class Temporizer extends Thread{ String _seq; public Temporizer(String seq) { _seq = seq; } public void run() { try { this.sleep(1000); if (_vpMaster.getRNA().getSeq().equalsIgnoreCase(_seq)) { showSolution(); } } catch (InterruptedException e) { // TODO Auto-generated catch block e.printStackTrace(); } } } public void onZoomLevelChanged() { // TODO Auto-generated method stub } public void onTranslationChanged() { // TODO Auto-generated method stub } public void itemStateChanged(ItemEvent arg0) { // TODO Auto-generated method stub System.out.println(); } public class InfoPanel extends JPanel { ArrayList _sols = new ArrayList(); BigInteger _nbFolds = BigInteger.ZERO; JTextArea _text = new JTextArea(""); JTextArea _subopts = new JTextArea(""); JPanel _suboptBrowser = new JPanel(); JPanel _suboptCount = new JPanel(); int _selectedIndex = 0; JButton next = new JButton("Precedent"); JButton previous = new JButton("Suivant"); InfoPanel() { this.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5)); setLayout(new BorderLayout()); add(_suboptBrowser,BorderLayout.SOUTH); add(_suboptCount,BorderLayout.NORTH); next.addActionListener(new ActionListener(){ public void actionPerformed(ActionEvent arg0) { if (_sols.size()>0) { setSelectedIndex((_selectedIndex+1)%_sols.size()); } } }); previous.addActionListener(new ActionListener(){ public void actionPerformed(ActionEvent arg0) { if (_sols.size()>0) { setSelectedIndex((_selectedIndex+_sols.size()-1)%_sols.size()); } } }); next.setEnabled(false); previous.setEnabled(false); JLabel nbLab = new JLabel("#Repliements"); NussinovDemo.formatLabel(nbLab); _suboptCount.setLayout(new BorderLayout()); _suboptCount.add(nbLab,BorderLayout.WEST); _suboptCount.add(_text,BorderLayout.CENTER); JLabel cooptlab = new JLabel("#Co-optimaux"); NussinovDemo.formatLabel(cooptlab); JPanel commands = new JPanel(); commands.add(previous); commands.add(next); JPanel jp = new JPanel(); jp.setLayout(new BorderLayout()); jp.add(_subopts,BorderLayout.WEST); jp.add(commands,BorderLayout.CENTER); _suboptBrowser.setLayout(new BorderLayout()); _suboptBrowser.add(cooptlab,BorderLayout.WEST); _suboptBrowser.add(jp,BorderLayout.CENTER); } /*public void setSelectedIndex(int i) { _selectedIndex = i; RNA rfolded = new RNA(); try { rfolded.setRNA(getSeq(), _sols.get(i)); rfolded.drawRNARadiate(_vpMaster.getConfig()); _vpMaster.showRNAInterpolated(rfolded); } catch (ExceptionUnmatchedClosingParentheses e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e) { // TODO Auto-generated catch block e.printStackTrace(); } //_struct.setText(_sols.get(i)); formatDescription(); }*/ public void setSelectedIndex(int i) { _selectedIndex = i; RNA rfolded = new RNA(); try { rfolded.setRNA(getSeq(), _sols.get(i)); RNA target = _vpTarget.getRNA(); for(ModeleBase mb: rfolded.get_listeBases()) { ModeleBase mbref = target.getBaseAt(mb.getIndex()); if (mb.getElementStructure()==mbref.getElementStructure()) { mb.getStyleBase().setBaseInnerColor(_okColor); mb.getStyleBase().setBaseNameColor(Color.white); } } for(ModeleBase mb: target.get_listeBases()) { ModeleBase mbref = rfolded.getBaseAt(mb.getIndex()); if (mb.getElementStructure()==mbref.getElementStructure()) { mb.getStyleBase().setBaseInnerColor(_okColor); } else { mb.getStyleBase().setBaseInnerColor(Color.white); } } rfolded.drawRNARadiate(_vpMaster.getConfig()); _vpMaster.showRNAInterpolated(rfolded); _vpTarget.repaint(); } catch (ExceptionUnmatchedClosingParentheses e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e) { // TODO Auto-generated catch block e.printStackTrace(); } //_struct.setSelectedItem(_sols.get(i)); formatDescription(); } public void setFont(Font f) { super.setFont(f); if(_text!=null) { _text.setFont(f); _text.setOpaque(false); } if(_subopts!=null) { _subopts.setFont(f); _subopts.setOpaque(false); } } public void setInfo(ArrayList sols, BigInteger nbFolds) { _sols = sols; _nbFolds = nbFolds; formatDescription(); setSelectedIndex(0); } private void formatDescription() { _text.setText(""+_nbFolds); _subopts.setText(""+_sols.size()); next.setEnabled(_sols.size()>1); previous.setEnabled(_sols.size()>1); } } } fr/orsay/lri/varna/applications/VARNAcmd.java0000644000000000000000000003761012416277112020113 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.applications; import java.awt.Graphics2D; import java.awt.geom.AffineTransform; import java.awt.geom.Rectangle2D; import java.awt.image.BufferedImage; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Comparator; import java.util.Hashtable; import java.util.Vector; import javax.imageio.IIOImage; import javax.imageio.ImageIO; import javax.imageio.ImageWriteParam; import javax.imageio.ImageWriter; import javax.imageio.stream.FileImageOutputStream; import javax.swing.JFrame; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.exceptions.ExceptionExportFailed; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.interfaces.InterfaceParameterLoader; import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.VARNAConfigLoader; import fr.orsay.lri.varna.models.rna.RNA; public class VARNAcmd implements InterfaceParameterLoader { public class ExitCode extends Exception{ /** * */ private static final long serialVersionUID = -3011196062868355584L; private int _c; private String _msg; public ExitCode(int c,String msg){ _c = c; _msg = msg; } public int getExitCode(){ return _c; } public String getExitMessage(){ return _msg; } } private Hashtable _optsValues = new Hashtable(); private Hashtable _basicOptsInv = new Hashtable(); private String _inFile = ""; private String _outFile = ""; int _baseWidth = 400; double _scale = 1.0; float _quality = 0.9f; private String[] _basicOptions = { VARNAConfigLoader.algoOpt, VARNAConfigLoader.bpStyleOpt, VARNAConfigLoader.bondColorOpt, VARNAConfigLoader.backboneColorOpt, VARNAConfigLoader.periodNumOpt, VARNAConfigLoader.baseInnerColorOpt, VARNAConfigLoader.baseOutlineColorOpt, }; public VARNAcmd(Vector args) throws ExitCode { for (int j = 0; j < _basicOptions.length; j++) { _basicOptsInv.put(_basicOptions[j], _basicOptions[j]); } int i = 0; while (i < args.size()) { String opt = args.elementAt(i); if (opt.charAt(0) != '-') { errorExit("Missing or unknown option \"" + opt + "\""); } if (opt.equals("-h")) { displayLightHelpExit(); } if (opt.equals("-x")) { displayDetailledHelpExit(); } else { if (i + 1 >= args.size()) { errorExit("Missing argument for option \"" + opt + "\""); } String val = args.get(i + 1); if (opt.equals("-i")) { _inFile = val; } else if (opt.equals("-o")) { _outFile = val; } else if (opt.equals("-quality")) { _quality = Float.parseFloat(val); } else if (opt.equals("-resolution")) { _scale = Float.parseFloat(val); } else { addOption(opt, val); } } i += 2; } } public void addOption(String key, String value) { if (key.equals("-i")) { _inFile = value; } else if (key.equals("-o")) { _outFile = value; } else { _optsValues.put(key.substring(1), value); } } private String getDescription() { return "VARNA v" + VARNAConfig.MAJOR_VERSION + "." + VARNAConfig.MINOR_VERSION + " Assisted drawing of RNA secondary structure (Command Line version)"; } private String indent(int k) { String result = ""; for (int i = 0; i < k; i++) { result += " "; } return result; } private String complete(String s, int k) { String result = s; while (result.length() < k) { result += " "; } return result; } Vector matrix = new Vector(); private void addLine(String opt, String val) { String[] line = { opt, val }; matrix.add(line); } private static int MAX_WIDTH = 100; @SuppressWarnings("unchecked") private void printMatrix(int ind) { String[][] values = new String[matrix.size()][]; matrix.toArray(values); Arrays.sort(values, new Comparator() { public int compare(Object o1, Object o2) { String[] tab1 = (String[]) o1; String[] tab2 = (String[]) o2; return tab1[0].compareTo(tab2[0]); } }); int maxSize = 0; for (int i = 0; i < values.length; i++) { String[] elem = values[i]; maxSize = Math.max(maxSize, elem[0].length()); } maxSize += ind + 2; for (int i = 0; i < values.length; i++) { String[] elem = values[i]; String opt = elem[0]; String msg = elem[1]; opt = complete("", ind) + "-" + complete(opt, maxSize - ind); System.out.println(opt + msg.substring(0, Math.min(MAX_WIDTH - opt.length(), msg.length()))); if (opt.length() + msg.length() >= MAX_WIDTH) { int off = MAX_WIDTH - opt.length(); while (off < msg.length()) { String nmsg = msg.substring(off, Math.min(off + MAX_WIDTH - opt.length(), msg.length())); System.out.println(complete("", opt.length())+nmsg); off += MAX_WIDTH - opt.length(); } } } matrix = new Vector(); } private void printUsage() { System.out .println("Usage: java -cp . [-i InFile|-sequenceDBN XXX -structureDBN YYY] -o OutFile [Options]"); System.out.println("Where:"); System.out.println(indent(1) + "OutFile\tSupported formats: {JPEG,PNG,EPS,XFIG,SVG}"); System.out .println(indent(1) + "InFile\tSecondary structure file: Supported formats: {BPSEQ,CT,RNAML,DBN}"); } private void printHelpOptions() { System.out.println("\nMain options:"); addLine("h", "Displays a short description of main options and exits"); addLine("x", "Displays a detailled description of all options"); printMatrix(2); } private void printMainOptions(String[][] info) { System.out.println("\nMain options:"); addLine("h", "Displays a short description of main options and exits"); addLine("x", "Displays a detailled description of all options"); for (int i = 0; i < info.length; i++) { String key = info[i][0]; if (_basicOptsInv.containsKey(key)) { addLine(key, info[i][2]); } } printMatrix(2); } private void printAdvancedOptions(String[][] info) { System.out.println("\nAdvanced options:"); for (int i = 0; i < info.length; i++) { String key = info[i][0]; if (!_basicOptsInv.containsKey(key)) { addLine(key, info[i][2]); } } addLine("quality", "Sets quality (non-vector file formats only)"); addLine("resolution", "Sets resolution (non-vector file formats only)"); printMatrix(2); } private void displayLightHelpExit() throws ExitCode { String[][] info = VARNAConfigLoader.getParameterInfo(); System.out.println(getDescription()); printUsage(); printMainOptions(info); throw(new ExitCode(1,"")); } private void displayDetailledHelpExit() throws ExitCode { String[][] info = VARNAConfigLoader.getParameterInfo(); System.out.println(getDescription()); printUsage(); printMainOptions(info); printAdvancedOptions(info); throw(new ExitCode(1,"")); } private void errorExit(String msg) throws ExitCode { System.out.println(getDescription()); System.out.println("Error: " + msg + "\n"); printUsage(); printHelpOptions(); throw(new ExitCode(1,"")); } public String getParameterValue(String key, String def) { if (_optsValues.containsKey(key)) { return _optsValues.get(key); } return def; } public String formatOutputPath(String base,int index, int total) { String result = base; if (total>1) { int indexDot = base.lastIndexOf('.'); String pref; String ext; if (indexDot!=-1) { pref = base.substring(0,indexDot); ext = base.substring(indexDot); } else{ pref=base; ext=""; } result = pref+"-"+index+ext; } System.err.println("Output file: "+result); return result; } public void run() throws IOException, ExitCode { VARNAConfigLoader VARNAcfg = new VARNAConfigLoader(this); ArrayList vpl; ArrayList confs = new ArrayList(); try { if (!_inFile.equals("")) { Collection rnas = RNAFactory.loadSecStr(_inFile); if (rnas.isEmpty()) { FullBackup f = null; try{ f = VARNAPanel.importSession(new FileInputStream(_inFile), _inFile); confs.add(f); } catch(Exception e) { e.printStackTrace(); } if (f==null) { throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from file '"+_inFile+"'."); } } else{ for (RNA r: rnas) { confs.add(new FullBackup(r,_inFile)); } } } else { RNA r = new RNA(); r.setRNA(this.getParameterValue("sequenceDBN", ""), this.getParameterValue( "structureDBN", "")); confs.add(new FullBackup(r,"From Params")); } if (!_outFile.equals("")) { int index = 1; for (FullBackup r: confs) { VARNAcfg.setRNA(r.rna); vpl = VARNAcfg.createVARNAPanels(); if (vpl.size() > 0) { VARNAPanel _vp = vpl.get(0); if (r.hasConfig()) { _vp.setConfig(r.config); } RNA _rna = _vp.getRNA(); Rectangle2D.Double bbox = _vp.getRNA().getBBox(); //System.out.println(_vp.getRNA().getBBox()); if (_outFile.toLowerCase().endsWith(".jpeg") || _outFile.toLowerCase().endsWith(".jpg") || _outFile.toLowerCase().endsWith(".png")) { _vp.setTitleFontSize((int)(_scale*_vp.getTitleFont().getSize())); _vp.setSize((int)(_baseWidth*_scale), (int)((_scale*_baseWidth*bbox.height)/((double)bbox.width))); } if (_outFile.toLowerCase().endsWith(".eps")) { _rna.saveRNAEPS(formatOutputPath(_outFile,index, confs.size()), _vp.getConfig()); } else if (_outFile.toLowerCase().endsWith(".xfig") || _outFile.toLowerCase().endsWith(".fig")) { _rna.saveRNAXFIG(formatOutputPath(_outFile,index, confs.size()), _vp.getConfig()); } else if (_outFile.toLowerCase().endsWith(".svg")) { _rna.saveRNASVG(formatOutputPath(_outFile,index, confs.size()), _vp.getConfig()); } else if (_outFile.toLowerCase().endsWith(".jpeg") || _outFile.toLowerCase().endsWith(".jpg")) { this.saveToJPEG(formatOutputPath(_outFile,index, confs.size()), _vp); } else if (_outFile.toLowerCase().endsWith(".png")) { this.saveToPNG(formatOutputPath(_outFile,index, confs.size()), _vp); } else if (_outFile.toLowerCase().endsWith(".varna")) { _vp.saveSession(formatOutputPath(_outFile,index, confs.size())); } else { errorExit("Unknown extension for output file \"" + _outFile + "\""); } } index++; } } // No output file => Open GUI else { VARNAGUI d = new VARNAGUI(); d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); d.pack(); d.setVisible(true); for (FullBackup b: confs) { RNA r = b.rna; VARNAcfg.setRNA(r); vpl = VARNAcfg.createVARNAPanels(); if (vpl.size() > 0) { VARNAPanel _vp = vpl.get(0); VARNAConfig cfg = _vp.getConfig(); if (b.hasConfig()) { cfg = b.config; } RNA rna = _vp.getRNA(); d.addRNA(rna, cfg); } } } } catch (ExceptionWritingForbidden e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionJPEGEncoding e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionParameterError e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionModeleStyleBaseSyntaxError e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionNonEqualLength e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionUnmatchedClosingParentheses e) { e.printStackTrace(); System.exit(1); } catch (ExceptionExportFailed e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionPermissionDenied e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionLoadingFailed e) { e.printStackTrace(); throw(new ExitCode(1,"")); } catch (ExceptionFileFormatOrSyntax e) { e.setPath(_inFile); e.printStackTrace(); throw(new ExitCode(1,"")); } catch (FileNotFoundException e) { throw(new ExitCode(1,"Error: Missing input file \""+_inFile+"\".")); } if (!_outFile.equals("")) throw(new ExitCode(0,"")); } public void saveToJPEG(String filename, VARNAPanel vp) throws ExceptionJPEGEncoding, ExceptionExportFailed { BufferedImage myImage = new BufferedImage((int) Math.round(vp .getWidth() ), (int) Math.round(vp.getHeight() ), BufferedImage.TYPE_INT_RGB); Graphics2D g2 = myImage.createGraphics(); vp.paintComponent(g2); try { FileImageOutputStream out = new FileImageOutputStream(new File(filename)); ImageWriter writer = ImageIO.getImageWritersByFormatName("jpeg").next(); ImageWriteParam params = writer.getDefaultWriteParam(); params.setCompressionMode(ImageWriteParam.MODE_EXPLICIT); params.setCompressionQuality(_quality); writer.setOutput(out); IIOImage myIIOImage = new IIOImage(myImage, null, null); writer.write(null, myIIOImage, params); out.close(); } catch (IOException e) { throw new ExceptionExportFailed(e.getMessage(), filename); } } public void saveToPNG(String filename, VARNAPanel vp) throws ExceptionExportFailed { BufferedImage myImage = new BufferedImage((int) Math.round(vp .getWidth()), (int) Math.round(vp.getHeight() ), BufferedImage.TYPE_INT_RGB); Graphics2D g2 = myImage.createGraphics(); vp.paintComponent(g2); g2.dispose(); try { ImageIO.write(myImage, "PNG", new File(filename)); } catch (IOException e) { e.printStackTrace(); } } public static void main(String[] argv) { Vector opts = new Vector(); for (int i = 0; i < argv.length; i++) { opts.add(argv[i]); } try { VARNAcmd app = new VARNAcmd(opts); app.run(); } catch (IOException e) { e.printStackTrace(); } catch (ExitCode e) { System.err.println(e.getExitMessage()); System.exit(e.getExitCode()); } } } fr/orsay/lri/varna/utils/0000755000000000000000000000000012275611452014362 5ustar rootrootfr/orsay/lri/varna/utils/XMLUtils.java0000644000000000000000000001037112050236700016676 0ustar rootrootpackage fr.orsay.lri.varna.utils; import java.awt.Color; import java.awt.Font; import java.util.ArrayList; import java.util.Formatter; import javax.xml.transform.sax.TransformerHandler; import org.xml.sax.Attributes; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; public class XMLUtils { public static String toHTMLNotation(Color c) { Formatter f = new Formatter(); f.format("#%02X%02X%02X", c.getRed(),c.getGreen(),c.getBlue()); return f.toString(); } public static void toXML(TransformerHandler hd, Font f) throws SAXException { toXML(hd, f,""); } public static String XML_BASELIST_ELEMENT_NAME = "baselist"; public static String XML_FONT_ELEMENT_NAME = "font"; public static String XML_ROLE_NAME = "role"; public static String XML_NAME_NAME = "name"; public static String XML_FAMILY_NAME = "family"; public static String XML_STYLE_NAME = "style"; public static String XML_SIZE_NAME = "size"; public static void toXML(TransformerHandler hd, Font f, String role) throws SAXException { AttributesImpl atts = new AttributesImpl(); if (!role.equals("")) atts.addAttribute("","",XML_ROLE_NAME,"CDATA",""+role); atts.addAttribute("","",XML_NAME_NAME,"CDATA",""+f.getName()); //atts.addAttribute("","",XML_FAMILY_NAME,"CDATA",""+f.getFamily()); atts.addAttribute("","",XML_STYLE_NAME,"CDATA",""+f.getStyle()); atts.addAttribute("","",XML_SIZE_NAME,"CDATA",""+f.getSize2D()); hd.startElement("","",XML_FONT_ELEMENT_NAME,atts); hd.endElement("","",XML_FONT_ELEMENT_NAME); } public static Font getFont(String qName, Attributes attributes) { if (qName.equals(XMLUtils.XML_FONT_ELEMENT_NAME)){ int style = Integer.parseInt(attributes.getValue(XMLUtils.XML_STYLE_NAME)); String name = (attributes.getValue(XMLUtils.XML_NAME_NAME)); double size = Double.parseDouble(attributes.getValue(XMLUtils.XML_SIZE_NAME)); Font f = new Font(name, style, (int)size); return f.deriveFont((float)size); } return null; } public static void toXML(TransformerHandler hd, ModeleBase mb) throws SAXException { ArrayList m = new ArrayList(); m.add(mb); toXML(hd, m); } public static void toXML(TransformerHandler hd, ArrayList m) throws SAXException { AttributesImpl atts = new AttributesImpl(); String result = ""; for (ModeleBase mb: m) { if (!result.equals("")) result+= ","; result += mb.getIndex(); } hd.startElement("","",XML_BASELIST_ELEMENT_NAME,atts); exportCDATAString(hd, result); hd.endElement("","",XML_BASELIST_ELEMENT_NAME); } public static ArrayList toModeleBaseArray(String baselist, RNA rna) { ArrayList result = new ArrayList(); String[] data = baselist.trim().split(","); for(int i=0;i _sequence = new ArrayList(); public Vector _sequenceIDs = new Vector(); public Vector _structure = new Vector(); public Vector _helices = new Vector(); public ArrayList getSequence() { return _sequence; } public Vector getStructure() { return _structure; } }; private Hashtable _molecules = new Hashtable(); private boolean _inSequenceIDs, _inLength, _inSequence, _inHelix, _inStrAnnotation, _inBP, _inBP5, _inBP3, _inEdge5, _inEdge3, _inPosition, _inBondOrientation, _inMolecule; private StringBuffer _buffer; private String _currentModel = ""; private int _id5, _id3, _length; String _edge5, _edge3, _orientation, _helixID; public RNAMLParser() { super(); _inSequenceIDs = false; _inSequence = false; _inStrAnnotation = false; _inBP = false; _inBP5 = false; _inBP3 = false; _inPosition = false; _inEdge5 = false; _inEdge3 = false; _inBondOrientation = false; _inHelix = false; _inMolecule = false; } public InputSource createSourceFromURL(String path) { URL url = null; try { url = new URL(path); URLConnection connexion = url.openConnection(); connexion.setUseCaches(false); InputStream r = connexion.getInputStream(); InputStreamReader inr = new InputStreamReader(r); return new InputSource(inr); } catch (Exception e) { e.printStackTrace(); } return new InputSource(new StringReader("")); } public InputSource resolveEntity(String publicId, String systemId) { // System.out.println("[crade]"); if (systemId.endsWith("rnaml.dtd")) { String resourceName = "/rnaml.dtd"; URL url = ClassLoader.getSystemResource(resourceName); if (url!=null) { try { InputStream stream = url.openStream(); if (stream != null) { return new InputSource(stream ); } } catch (IOException e) { e.printStackTrace(); } } } return new InputSource(new StringReader("")); } public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException { if (qName.equals("numbering-table")) { _inSequenceIDs = true; _buffer = new StringBuffer(); } else if (qName.equals("helix")) { _inHelix = true; _buffer = new StringBuffer(); _helixID = attributes.getValue("id"); } else if (qName.equals("seq-data")) { _inSequence = true; _buffer = new StringBuffer(); } else if (qName.equals("length")) { _inLength = true; _buffer = new StringBuffer(); } else if (qName.equals("str-annotation")) { _inStrAnnotation = true; } else if (qName.equals("base-pair")) { _inBP = true; } else if (qName.equals("base-id-5p")) { if (_inBP || _inHelix) { _inBP5 = true; } } else if (qName.equals("base-id-3p")) { if (_inBP || _inHelix) { _inBP3 = true; } } else if (qName.equals("edge-5p")) { _inEdge5 = true; _buffer = new StringBuffer(); } else if (qName.equals("edge-3p")) { _inEdge3 = true; _buffer = new StringBuffer(); } else if (qName.equals("position")) { _inPosition = true; _buffer = new StringBuffer(); } else if (qName.equals("bond-orientation")) { _inBondOrientation = true; _buffer = new StringBuffer(); } else if (qName.equals("molecule")) { _inMolecule = true; String id = (attributes.getValue("id")); // System.err.println("Molecule#"+id); _molecules.put(id, new RNATmp()); _currentModel = id; } else { // We don't care too much about the rest ... } } public void endElement(String uri, String localName, String qName) throws SAXException { if (qName.equals("numbering-table")) { _inSequenceIDs = false; String content = _buffer.toString(); content = content.trim(); String[] tokens = content.split("\\s+"); Vector results = new Vector(); for (int i = 0; i < tokens.length; i++) { try { results.add(new Integer(Integer.parseInt(tokens[i]))); } catch (NumberFormatException e) { e.printStackTrace(); } } _molecules.get(_currentModel)._sequenceIDs = results; _buffer = null; } else if (qName.equals("seq-data")) { _inSequence = false; String content = _buffer.toString(); content = content.trim(); String[] tokens = content.split("\\s+"); ArrayList results = new ArrayList(); for (int i = 0; i < tokens.length; i++) { for (int j = 0; j < tokens[i].length(); j++) results.add("" + tokens[i].charAt(j)); } // System.err.println(" Seq: "+results); _molecules.get(_currentModel)._sequence = results; _buffer = null; } else if (qName.equals("bond-orientation")) { _inBondOrientation = false; String content = _buffer.toString(); content = content.trim(); _orientation = content; _buffer = null; } else if (qName.equals("str-annotation")) { _inStrAnnotation = false; } else if (qName.equals("base-pair")) { if (_inMolecule) { _inBP = false; BPTemp bp = new BPTemp(_id5, _id3, _edge5, _edge3, _orientation); _molecules.get(_currentModel)._structure.add(bp); // System.err.println(" "+bp); } } else if (qName.equals("helix")) { _inHelix = false; if (_inMolecule) { HelixTemp h = new HelixTemp(_id5, _id3, _length, _helixID); _molecules.get(_currentModel)._helices.add(h); } } else if (qName.equals("base-id-5p")) { _inBP5 = false; } else if (qName.equals("base-id-3p")) { _inBP3 = false; } else if (qName.equals("length")) { _inLength = false; String content = _buffer.toString(); content = content.trim(); _length = Integer.parseInt(content); _buffer = null; } else if (qName.equals("position")) { String content = _buffer.toString(); content = content.trim(); int pos = Integer.parseInt(content); if (_inBP5) { _id5 = pos; } if (_inBP3) { _id3 = pos; } _buffer = null; } else if (qName.equals("edge-5p")) { _inEdge5 = false; String content = _buffer.toString(); content = content.trim(); _edge5 = content; _buffer = null; } else if (qName.equals("edge-3p")) { _inEdge3 = false; String content = _buffer.toString(); content = content.trim(); _edge3 = content; _buffer = null; } else if (qName.equals("molecule")) { _inMolecule = false; } else { // We don't care too much about the rest ... } } public void characters(char[] ch, int start, int length) throws SAXException { String lecture = new String(ch, start, length); if (_buffer != null) _buffer.append(lecture); } public void startDocument() throws SAXException { } public void endDocument() throws SAXException { postProcess(); } // Discarding stacking interactions... private void discardStacking() { Vector result = new Vector(); for (int i = 0; i < _molecules.get(_currentModel)._structure.size(); i++) { BPTemp bp = _molecules.get(_currentModel)._structure.get(i); if (bp.orientation.equals("c") || bp.orientation.equals("t")) { result.add(bp); } } _molecules.get(_currentModel)._structure = result; } public static boolean isSelfCrossing(int[] str) { Stack intervals = new Stack(); intervals.add(new Point(0, str.length - 1)); while (!intervals.empty()) { Point p = intervals.pop(); if (p.x <= p.y) { if (str[p.x] == -1) { intervals.push(new Point(p.x + 1, p.y)); } else { int i = p.x; int j = p.y; int k = str[i]; if ((k <= i) || (k > j)) { return true; } else { intervals.push(new Point(i + 1, k - 1)); intervals.push(new Point(k + 1, j)); } } } } return false; } @SuppressWarnings("unused") private void debugPrintArray(Object[] str) { StringBuffer s = new StringBuffer("["); for (int i = 0; i < str.length; i++) { if (i != 0) { s.append(","); } s.append(str[i]); } s.append("]"); System.out.println(s.toString()); } /** * Computes and returns a maximal planar subset of the current structure. * * @param str * A sequence of base-pairing positions * @return A sequence of non-crossing base-pairing positions */ public static int[] planarize(int[] str) { if (!isSelfCrossing(str)) { return str; } int length = str.length; int[] result = new int[length]; for (int i = 0; i < result.length; i++) { result[i] = -1; } short[][] tab = new short[length][length]; short[][] backtrack = new short[length][length]; int theta = 3; for (int i = 0; i < result.length; i++) { for (int j = i; j < Math.min(i + theta, result.length); j++) { tab[i][j] = 0; backtrack[i][j] = -1; } } for (int n = theta; n < length; n++) { for (int i = 0; i < length - n; i++) { int j = i + n; tab[i][j] = tab[i + 1][j]; backtrack[i][j] = -1; int k = str[i]; if ((k != -1) && (k <= j) && (i < k)) { int tmp = 1; if (i + 1 <= k - 1) { tmp += tab[i + 1][k - 1]; } if (k + 1 <= j) { tmp += tab[k + 1][j]; } if (tmp > tab[i][j]) { tab[i][j] = (short) tmp; backtrack[i][j] = (short) k; } } } } Stack intervals = new Stack(); intervals.add(new Point(0, length - 1)); while (!intervals.empty()) { Point p = intervals.pop(); if (p.x <= p.y) { if (backtrack[p.x][p.y] == -1) { result[p.x] = -1; intervals.push(new Point(p.x + 1, p.y)); } else { int i = p.x; int j = p.y; int k = backtrack[p.x][p.y]; result[i] = k; result[k] = i; intervals.push(new Point(i + 1, k - 1)); intervals.push(new Point(k + 1, j)); } } } return result; } public static void planarize(ArrayList input, ArrayList planar, ArrayList others, int length) { // System.err.println("Planarize: Length:"+length); Hashtable> index2BPs = new Hashtable>(); for (ModeleBP msbp : input) { int i = msbp.getPartner5().getIndex(); if (!index2BPs.containsKey(i)) { index2BPs.put(i, new ArrayList()); } index2BPs.get(i).add(msbp); } // System.err.println(index2BPs); short[][] tab = new short[length][length]; short[][] backtrack = new short[length][length]; int theta = 3; for (int i = 0; i < length; i++) { for (int j = i; j < Math.min(i + theta, length); j++) { tab[i][j] = 0; backtrack[i][j] = -1; } } for (int n = theta; n < length; n++) { for (int i = 0; i < length - n; i++) { int j = i + n; tab[i][j] = tab[i + 1][j]; backtrack[i][j] = -1; if (index2BPs.containsKey(i)) { ArrayList vi = index2BPs.get(i); // System.err.print("."); for (int numBP = 0; numBP < vi.size(); numBP++) { ModeleBP mb = vi.get(numBP); int k = mb.getPartner3().getIndex(); if ((k != -1) && (k <= j) && (i < k)) { int tmp = 1; if (i + 1 <= k - 1) { tmp += tab[i + 1][k - 1]; } if (k + 1 <= j) { tmp += tab[k + 1][j]; } if (tmp > tab[i][j]) { tab[i][j] = (short) tmp; backtrack[i][j] = (short) numBP; } } } } } } // System.err.println("DP table: "+tab[0][length-1]); // Backtracking Stack intervals = new Stack(); intervals.add(new Point(0, length - 1)); while (!intervals.empty()) { Point p = intervals.pop(); if (p.x <= p.y) { if (backtrack[p.x][p.y] == -1) { intervals.push(new Point(p.x + 1, p.y)); } else { int i = p.x; int j = p.y; int nb = backtrack[p.x][p.y]; ModeleBP mb = index2BPs.get(i).get(nb); int k = mb.getPartner3().getIndex(); planar.add(mb); intervals.push(new Point(i + 1, k - 1)); intervals.push(new Point(k + 1, j)); } } } // Remaining base pairs for (int i : index2BPs.keySet()) { ArrayList vi = index2BPs.get(i); for (ModeleBP mb : vi) { if (!planar.contains(mb)) { others.add(mb); } } } } private void postProcess() { for (RNATmp r : _molecules.values()) { // First, check if base numbers were specified if (r._sequenceIDs.size() == 0) { Vector results = new Vector(); for (int i = 0; i < r._sequence.size(); i++) { results.add(new Integer(i + 1)); } r._sequenceIDs = results; } // System.err.println("IDs: "+_sequenceIDs); // System.err.println("Before remapping: "+_structure); // Then, build inverse mapping ID => index Hashtable ID2Index = new Hashtable(); for (int i = 0; i < r._sequenceIDs.size(); i++) { ID2Index.put(r._sequenceIDs.get(i), i); } // Translate BP coordinates into indices for (BPTemp bp : r._structure) { bp.pos3 = bp.pos3 - 1; bp.pos5 = bp.pos5 - 1; } // System.err.println("After remapping: "+_structure); discardStacking(); // System.err.println(" Discard stacking (length="+r._sequence.size()+") => "+r._structure); // Eliminate redundancy Hashtable> index2BPs = new Hashtable>(); for (BPTemp msbp : r._structure) { int i = msbp.pos5; if (!index2BPs.containsKey(i)) { index2BPs.put(i, new Hashtable()); } if (!index2BPs.get(i).contains(msbp.pos3)) { index2BPs.get(i).put(msbp.pos3,msbp); } } // Adding helices... for (int i = 0; i < r._helices.size(); i++) { HelixTemp h = r._helices.get(i); for (int j = 0; j < h.length; j++) { // System.err.println("Looking for residues: "+(h.pos5+j-1)+" and "+(h.pos3-j-1)); int a = (h.pos5 + j - 1); int b = (h.pos3 - j - 1); BPTemp bp = new BPTemp(a, (b), "+", "+", "c"); if (!index2BPs.containsKey(a)) { index2BPs.put(a, new Hashtable()); } if (!index2BPs.get(a).contains(b)) { index2BPs.get(a).put(b,bp); } } } Vector newStructure = new Vector(); for (int i : index2BPs.keySet()) { for (int j : index2BPs.get(i).keySet()) { BPTemp bp = index2BPs.get(i).get(j); newStructure.add(bp); } } r._structure = newStructure; // System.err.println("After Helices => "+_structure); // System.err.println("After Postprocess => "+_structure); } } public ArrayList getMolecules() { return new ArrayList(_molecules.values()); } }fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java0000644000000000000000000000315512050477312021404 0ustar rootroot/** * File written by Raphael Champeimont * UMR 7238 Genomique des Microorganismes */ package fr.orsay.lri.varna.utils; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.File; import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; import java.util.ArrayList; import java.util.List; public class TranslateFormatRNaseP { public static void main(String[] args) throws Exception { File templatesDir = new File(new File(System.getProperty("user.dir")), "templates"); File infile = new File(new File(templatesDir, "RNaseP_bact_a"), "a_bacterial_rnas.gb"); File outfile = new File(new File(templatesDir, "RNaseP_bact_a"), "alignment.fasta"); BufferedReader inbuf = new BufferedReader(new FileReader(infile)); String line = inbuf.readLine(); String seqname; List seqnames = new ArrayList(); List sequences = new ArrayList(); while (line != null) { if (line.length() != 0) { if (line.startsWith("LOCUS")) { String parts[] = line.split("\\s+"); seqname = parts[1]; seqnames.add(seqname); sequences.add(""); } if (line.startsWith(" ")) { String parts[] = line.split("\\s+"); for (int i=2; i" + seqnames.get(i) + "\n"); outbuf.write(sequences.get(i) + "\n"); } outbuf.close(); } } fr/orsay/lri/varna/utils/VARNASessionParser.java0000644000000000000000000004224212541142644020617 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.utils; import java.awt.Color; import java.awt.Font; import java.awt.Point; import java.awt.geom.Point2D; import java.io.InputStream; import java.io.InputStreamReader; import java.io.StringReader; import java.net.URL; import java.net.URLConnection; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.ArrayList; import java.util.Collections; import java.util.Hashtable; import java.util.List; import java.util.Stack; import java.util.TreeSet; import java.util.Vector; import org.xml.sax.Attributes; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.helpers.DefaultHandler; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation.AnchorType; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.ModeleBP.Edge; import fr.orsay.lri.varna.models.rna.ModeleBP.Stericity; import fr.orsay.lri.varna.models.rna.ModeleBPStyle; import fr.orsay.lri.varna.models.rna.ModeleBackbone; import fr.orsay.lri.varna.models.rna.ModeleBackboneElement; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleBasesComparison; import fr.orsay.lri.varna.models.rna.ModelBaseStyle; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.models.rna.VARNAPoint; public class VARNASessionParser extends DefaultHandler { StringBuffer _buffer = null; ModeleBaseNucleotide mbn = null; ModeleBasesComparison mbc = null; ModeleBP mbp = null; ModeleBPStyle mbps = null; ModelBaseStyle msb = null; TextAnnotation ta = null; ModeleBackbone backbone = null; HighlightRegionAnnotation hra = null; RNA rna = null; Font f = null; VARNAConfig config = null; public VARNASessionParser() { super(); } public InputSource createSourceFromURL(String path) { URL url = null; try { url = new URL(path); URLConnection connexion = url.openConnection(); connexion.setUseCaches(false); InputStream r = connexion.getInputStream(); InputStreamReader inr = new InputStreamReader(r); return new InputSource(inr); } catch(Exception e) { e.printStackTrace(); } return new InputSource(new StringReader("")); } public InputSource resolveEntity(String publicId, String systemId) { return new InputSource(new StringReader("")); } private TreeSet _context = new TreeSet(); private void addToContext(String s) { _context.add(s); } private void removeFromContext(String s) { _context.remove(s); } private boolean contextContains(String s) { return _context.contains(s); } public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException { if (qName.equals(VARNAPanel.XML_ELEMENT_NAME)) { } else if (qName.equals(VARNAConfig.XML_ELEMENT_NAME)){ config = new VARNAConfig(); config.loadFromXMLAttributes(attributes); } else if (qName.equals(RNA.XML_ELEMENT_NAME)){ rna = new RNA(); int mode = Integer.parseInt(attributes.getValue(RNA.XML_VAR_DRAWN_MODE_NAME)); rna.setDrawMode(mode); } else if (qName.equals(ModeleBackbone.XML_ELEMENT_NAME)){ backbone = new ModeleBackbone(); rna.setBackbone(backbone); } else if (qName.equals(ModeleBackboneElement.XML_ELEMENT_NAME)){ if (backbone!=null){ int index = Integer.parseInt(attributes.getValue(ModeleBackboneElement.XML_VAR_INDEX_NAME)); ModeleBackboneElement.BackboneType type = ModeleBackboneElement.BackboneType.getType( (attributes.getValue(ModeleBackboneElement.XML_VAR_TYPE_NAME))); Color c = null; if (type == ModeleBackboneElement.BackboneType.CUSTOM_COLOR) { c = Color.decode(attributes.getValue(TextAnnotation.XML_VAR_COLOR_NAME)); backbone.addElement(new ModeleBackboneElement(index, c)); } else { backbone.addElement(new ModeleBackboneElement(index, type)); } } } else if (qName.equals(ModeleBackbone.XML_ELEMENT_NAME)){ backbone = new ModeleBackbone(); } else if (qName.equals(ModeleBaseNucleotide.XML_ELEMENT_NAME)){ if (rna!=null){ mbn = new ModeleBaseNucleotide(rna.getSize()); if (mbn.getIndex()!=Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_INDEX_NAME))) throw new SAXException("Index mismatch for Base"); mbn.setBaseNumber(Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_NUMBER_NAME))); mbn.setLabel(attributes.getValue(ModeleBase.XML_VAR_LABEL_NAME)); mbn.setColorie(Boolean.parseBoolean(attributes.getValue(ModeleBase.XML_VAR_CUSTOM_DRAWN_NAME))); mbn.setValue(Double.parseDouble(attributes.getValue(ModeleBase.XML_VAR_VALUE_NAME))); rna.addBase(mbn); } } else if (qName.equals(XMLUtils.XML_FONT_ELEMENT_NAME)){ f = XMLUtils.getFont(qName,attributes); if (contextContains(TextAnnotation.XML_ELEMENT_NAME)) { ta.setFont(f); f=null; } else if (contextContains(VARNAConfig.XML_ELEMENT_NAME)) { String role = attributes.getValue(XMLUtils.XML_ROLE_NAME); if (role.equals(VARNAConfig.XML_VAR_TITLE_FONT)) { config._titleFont = XMLUtils.getFont(qName, attributes); } else if (role.equals(VARNAConfig.XML_VAR_NUMBERS_FONT)) { config._numbersFont = XMLUtils.getFont(qName, attributes); } else if (role.equals(VARNAConfig.XML_VAR_FONT_BASES)) { config._fontBasesGeneral = XMLUtils.getFont(qName, attributes); } } } else if (qName.equals(ModeleBaseNucleotide.XML_VAR_CONTENT_NAME)){ _buffer = new StringBuffer(); } else if (qName.equals(ModeleBasesComparison.XML_VAR_FIRST_CONTENT_NAME)){ _buffer = new StringBuffer(); } else if (qName.equals(ModeleBasesComparison.XML_VAR_SECOND_CONTENT_NAME)){ _buffer = new StringBuffer(); } else if (qName.equals(ModeleBasesComparison.XML_ELEMENT_NAME)){ if (rna!=null){ mbc = new ModeleBasesComparison(rna.getSize()); if (mbc.getIndex()!=Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_INDEX_NAME))) throw new SAXException("Index mismatch for Base"); mbc.setBaseNumber(Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_NUMBER_NAME))); mbc.setLabel(attributes.getValue(ModeleBase.XML_VAR_LABEL_NAME)); mbc.set_appartenance(Integer.parseInt(attributes.getValue(ModeleBasesComparison.XML_VAR_MEMBERSHIP_NAME))); mbc.setColorie(Boolean.parseBoolean(attributes.getValue(ModeleBase.XML_VAR_CUSTOM_DRAWN_NAME))); mbc.setValue(Double.parseDouble(attributes.getValue(ModeleBase.XML_VAR_VALUE_NAME))); rna.addBase(mbc); } } else if (qName.equals(RNA.XML_VAR_NAME_NAME)) { if (rna!=null){ _buffer = new StringBuffer(); } } else if (qName.equals(ModeleBP.XML_ELEMENT_NAME)) { Edge e5 = Edge.valueOf(attributes.getValue(ModeleBP.XML_VAR_EDGE5_NAME)); Edge e3 = Edge.valueOf(attributes.getValue(ModeleBP.XML_VAR_EDGE3_NAME)); Stericity s = Stericity.valueOf(attributes.getValue(ModeleBP.XML_VAR_STERICITY_NAME)); int i5 = Integer.parseInt(attributes.getValue(ModeleBP.XML_VAR_PARTNER5_NAME)); int i3 = Integer.parseInt(attributes.getValue(ModeleBP.XML_VAR_PARTNER3_NAME)); boolean inSecStr = Boolean.parseBoolean(attributes.getValue(ModeleBP.XML_VAR_SEC_STR_NAME)); mbp = new ModeleBP(rna.getBaseAt(i5),rna.getBaseAt(i3),e5,e3,s); if (inSecStr) rna.addBP(i5,i3,mbp); else rna.addBPAux(i5,i3,mbp); } else if (qName.equals(ChemProbAnnotation.XML_ELEMENT_NAME)) { int i5 = Integer.parseInt(attributes.getValue(ChemProbAnnotation.XML_VAR_INDEX5_NAME)); int i3 = Integer.parseInt(attributes.getValue(ChemProbAnnotation.XML_VAR_INDEX3_NAME)); ChemProbAnnotation cpa = new ChemProbAnnotation(rna.getBaseAt(i5),rna.getBaseAt(i3)); cpa.setColor(Color.decode(attributes.getValue(ChemProbAnnotation.XML_VAR_COLOR_NAME))); cpa.setIntensity(Double.parseDouble(attributes.getValue(ChemProbAnnotation.XML_VAR_INTENSITY_NAME))); cpa.setType(ChemProbAnnotationType.valueOf(attributes.getValue(ChemProbAnnotation.XML_VAR_TYPE_NAME))); cpa.setOut(Boolean.parseBoolean(attributes.getValue(ChemProbAnnotation.XML_VAR_OUTWARD_NAME))); rna.addChemProbAnnotation(cpa); } else if (qName.equals(TextAnnotation.XML_VAR_TEXT_NAME)){ _buffer = new StringBuffer(); } else if (qName.equals(VARNAConfig.XML_VAR_TITLE)){ _buffer = new StringBuffer(); } else if (qName.equals(VARNAConfig.XML_VAR_CM_CAPTION)){ _buffer = new StringBuffer(); } else if (qName.equals(TextAnnotation.XML_ELEMENT_NAME)) { AnchorType t = AnchorType.valueOf(attributes.getValue(TextAnnotation.XML_VAR_TYPE_NAME)); ta = new TextAnnotation(""); ta.setColor(Color.decode(attributes.getValue(TextAnnotation.XML_VAR_COLOR_NAME))); ta.setAngleInDegres(Double.parseDouble(attributes.getValue(TextAnnotation.XML_VAR_ANGLE_NAME))); ta.setType(t); } else if (qName.equals(HighlightRegionAnnotation.XML_ELEMENT_NAME)) { hra = new HighlightRegionAnnotation(); rna.addHighlightRegion(hra); hra.setOutlineColor(Color.decode(attributes.getValue(HighlightRegionAnnotation.XML_VAR_OUTLINE_NAME))); hra.setFillColor(Color.decode(attributes.getValue(HighlightRegionAnnotation.XML_VAR_FILL_NAME))); hra.setRadius(Double.parseDouble(attributes.getValue(HighlightRegionAnnotation.XML_VAR_RADIUS_NAME))); } else if (qName.equals(XMLUtils.XML_BASELIST_ELEMENT_NAME)) { _buffer = new StringBuffer(); } else if (qName.equals(VARNAPoint.XML_ELEMENT_NAME)) { Point2D.Double vp = new Point2D.Double(); vp.x = Double.parseDouble(attributes.getValue(VARNAPoint.XML_VAR_X_NAME)); vp.y = Double.parseDouble(attributes.getValue(VARNAPoint.XML_VAR_Y_NAME)); String role = attributes.getValue(VARNAPoint.XML_VAR_ROLE_NAME); if (contextContains(ModeleBaseNucleotide.XML_ELEMENT_NAME)) { if (role != null) { if (role.equals(ModeleBase.XML_VAR_POSITION_NAME)) { if (mbn!=null) { mbn.setCoords(vp); } else throw new SAXException("No Base model for this position Point"); } else if (role.equals(ModeleBase.XML_VAR_CENTER_NAME)) { if (mbn!=null) { mbn.setCenter(vp); } else throw new SAXException("No Base model for this center Point"); } } } if (contextContains(ModeleBasesComparison.XML_ELEMENT_NAME)) { if (role != null) { if (role.equals(ModeleBase.XML_VAR_POSITION_NAME)) { if (mbc!=null) { mbc.setCoords(vp); } else throw new SAXException("No Base model for this position Point"); } else if (role.equals(ModeleBase.XML_VAR_CENTER_NAME)) { if (mbc!=null) { mbc.setCenter(vp); } else throw new SAXException("No Base model for this center Point"); } } } if (contextContains(TextAnnotation.XML_ELEMENT_NAME)) { if (ta!=null) ta.setAncrage(vp.x,vp.y); else throw new SAXException("No TextAnnotation model for this Point"); } } else if (qName.equals(ModelBaseStyle.XML_ELEMENT_NAME)) { msb = new ModelBaseStyle(); msb.setBaseOutlineColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_OUTLINE_NAME))); msb.setBaseInnerColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_INNER_NAME))); msb.setBaseNameColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_NAME_NAME))); msb.setBaseNumberColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_NUMBER_NAME))); if (mbn!=null) { mbn.setStyleBase(msb); } else if (mbc!=null) { mbc.setStyleBase(msb); } msb = null; } else if (qName.equals(ModeleBPStyle.XML_ELEMENT_NAME)) { mbps = new ModeleBPStyle(); boolean customColor = Boolean.parseBoolean(attributes.getValue(ModeleBPStyle.XML_VAR_CUSTOM_STYLED_NAME)); if (customColor) mbps.setCustomColor(Color.decode(attributes.getValue(ModeleBPStyle.XML_VAR_COLOR_NAME))); mbps.setThickness(Double.parseDouble(attributes.getValue(ModeleBPStyle.XML_VAR_THICKNESS_NAME))); mbps.setBent(Double.parseDouble(attributes.getValue(ModeleBPStyle.XML_VAR_BENT_NAME))); if (mbp!=null) { mbp.setStyle(mbps); } mbps = null; } addToContext(qName); } public void endElement(String uri, String localName, String qName) throws SAXException { if (qName.equals(ModeleBaseNucleotide.XML_VAR_CONTENT_NAME)){ if (_buffer==null){ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME); } if (mbn==null){ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME); } String val = _buffer.toString(); mbn.setContent(val); } else if (qName.equals(ModeleBasesComparison.XML_VAR_FIRST_CONTENT_NAME)){ if (_buffer==null){ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME); } if (mbc==null){ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME); } String val = _buffer.toString(); mbc.setBase1(val.trim().charAt(0)); } else if (qName.equals(ModeleBasesComparison.XML_VAR_SECOND_CONTENT_NAME)){ if (_buffer==null){ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME); } if (mbc==null){ throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME); } String val = _buffer.toString(); mbc.setBase2(val.trim().charAt(0)); } else if (qName.equals(ModeleBaseNucleotide.XML_ELEMENT_NAME)){ mbn = null; } else if (qName.equals(ModeleBP.XML_ELEMENT_NAME)) { mbp = null; } else if (qName.equals(HighlightRegionAnnotation.XML_ELEMENT_NAME)) { hra = null; } else if (qName.equals(TextAnnotation.XML_VAR_TEXT_NAME)) { String text = _buffer.toString(); ta.setText(text); _buffer = null; } else if (qName.equals(RNA.XML_VAR_NAME_NAME)) { if (rna!=null){ rna.setName(_buffer.toString()); _buffer = null; } } else if (qName.equals(VARNAConfig.XML_VAR_CM_CAPTION)){ config._colorMapCaption = _buffer.toString(); _buffer = null; } else if (qName.equals(TextAnnotation.XML_ELEMENT_NAME)) { rna.addAnnotation(ta); ta = null; } else if (qName.equals(XMLUtils.XML_BASELIST_ELEMENT_NAME)) { String result = _buffer.toString(); ArrayList al = XMLUtils.toModeleBaseArray(result, rna); if (contextContains(TextAnnotation.XML_ELEMENT_NAME)) { switch(ta.getType()) { case POSITION: break; case BASE: ta.setAncrage(al.get(0)); break; case HELIX: case LOOP: try { ta.setAncrage(al, ta.getType()); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } break; default: } } if (contextContains(HighlightRegionAnnotation.XML_ELEMENT_NAME)) { hra.setBases(al); } _buffer = null; } removeFromContext(qName); } public void characters(char[] ch, int start, int length) throws SAXException { String lecture = new String(ch, start, length); if (_buffer != null) _buffer.append(lecture); } public void startDocument() throws SAXException { } public void endDocument() throws SAXException { } public RNA getRNA() { return rna; } public VARNAConfig getVARNAConfig() { return config; } }fr/orsay/lri/varna/exceptions/0000755000000000000000000000000012275611446015406 5ustar rootrootfr/orsay/lri/varna/exceptions/ExceptionXMLGeneration.java0000644000000000000000000000056711620715270022605 0ustar rootrootpackage fr.orsay.lri.varna.exceptions; /** * Thrown by XML-generating algorithms when they fail. * * @author Raphael Champeimont */ public class ExceptionXMLGeneration extends Exception { private static final long serialVersionUID = 8867910395701431387L; public ExceptionXMLGeneration(String message) { super(message); } public ExceptionXMLGeneration() { } } fr/orsay/lri/varna/exceptions/MappingException.java0000644000000000000000000000365411620715270021524 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; public class MappingException extends Exception { private static final long serialVersionUID = 1L; public static final int MULTIPLE_PARTNERS_DEFINITION_ATTEMPT = 1; public static final int BAD_ALIGNMENT_INPUT = 2; public static final int CUSTOM_MESSAGE = 3; private String _errorMessage; private int _type; public MappingException(String errorMessage) { _errorMessage = errorMessage; _type = CUSTOM_MESSAGE; } public MappingException(int type) { _type = type; } public String getMessage() { switch (_type) { case MULTIPLE_PARTNERS_DEFINITION_ATTEMPT: return "Mapping error: Attempt to define multiple partners for a base-pair"; case BAD_ALIGNMENT_INPUT: return "Mapping error: Bad input alignment"; case CUSTOM_MESSAGE: return _errorMessage; default: return "Mapping error: Type is unknown."; } } } fr/orsay/lri/varna/exceptions/ExceptionWritingForbidden.java0000644000000000000000000000304111620715270023357 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Used when writing file problems append due to security policy * * @author darty * */ public class ExceptionWritingForbidden extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; public ExceptionWritingForbidden(String errorMessage) { _errorMessage = errorMessage; } public String getError() { return _errorMessage; } public String getMessage() { return "Writing is not allowed within current security policy."; } } fr/orsay/lri/varna/exceptions/ExceptionJPEGEncoding.java0000644000000000000000000000270611620715270022322 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Specific problems with JPEG encoding */ public class ExceptionJPEGEncoding extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; public ExceptionJPEGEncoding(String errorMessage) { _errorMessage = errorMessage; } public String getError() { return _errorMessage; } public String getMessage() { return "JPEG encoding failed!"; } } fr/orsay/lri/varna/exceptions/ExceptionExportFailed.java0000644000000000000000000000310011620715270022501 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Exception for export problems * * @author darty * */ public class ExceptionExportFailed extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; private String _path; public ExceptionExportFailed(String errorMessage, String path) { _errorMessage = errorMessage; _path = path; } public String getError() { return _errorMessage; } public String getMessage() { return "Export failed, File " + _path + " cannot be created or overwritten !\n"; } }fr/orsay/lri/varna/exceptions/ExceptionLoadingFailed.java0000644000000000000000000000306311620715270022605 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Exception for file load problems * * @author darty * */ public class ExceptionLoadingFailed extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; private String _path; public ExceptionLoadingFailed(String errorMessage, String path) { _errorMessage = errorMessage; _path = path; } public String getError() { return _errorMessage; } public String getMessage() { return "Loading failed!\n File '" + _path + "' cannot be read !"; } } fr/orsay/lri/varna/exceptions/ExceptionEdgeEndpointAlreadyConnected.java0000644000000000000000000000101111620715270025604 0ustar rootrootpackage fr.orsay.lri.varna.exceptions; /** * Thrown by an EdgeEndPoint when it is already connected and you try * to connect it. * * @author Raphael Champeimont */ public class ExceptionEdgeEndpointAlreadyConnected extends ExceptionInvalidRNATemplate { private static final long serialVersionUID = 3978166870034913842L; public ExceptionEdgeEndpointAlreadyConnected(String message) { super(message); } public ExceptionEdgeEndpointAlreadyConnected() { super("Edge endpoint is already connected"); } } fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax.java0000644000000000000000000000337711620715270023673 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Exception for any problem with the format or the syntax of a file loaded * * @author darty * */ public class ExceptionFileFormatOrSyntax extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _path; private String _errorMessage; public ExceptionFileFormatOrSyntax(String errorMessage, String path) { _path = path; _errorMessage = errorMessage; } public ExceptionFileFormatOrSyntax(String path) { _path = path; } public String getError() { return _errorMessage; } public String getMessage() { return "Unknown format or syntax error in file ' " + _path + " '. \nLoading cancelled !"; } public void setPath(String path) { _path = path; } } fr/orsay/lri/varna/exceptions/ExceptionInvalidRNATemplate.java0000644000000000000000000000072211620715270023545 0ustar rootrootpackage fr.orsay.lri.varna.exceptions; /** * This exception is thrown when we discover that a template is invalid * (it contains impossible connections between elements). * * @author Raphael Champeimont */ public class ExceptionInvalidRNATemplate extends Exception { private static final long serialVersionUID = 3866618355319087333L; public ExceptionInvalidRNATemplate(String message) { super(message); } public ExceptionInvalidRNATemplate() { } } fr/orsay/lri/varna/exceptions/ExceptionPermissionDenied.java0000644000000000000000000000312311620715270023361 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Exception for permission denied problems due to security * * @author darty * */ public class ExceptionPermissionDenied extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; public ExceptionPermissionDenied(String errorMessage) { _errorMessage = errorMessage; } public String getError() { return _errorMessage; } public String getMessage() { return "Permission denied for security reason !\n" + "Consider using the VARNA panel class in a signed context.\n"; } } fr/orsay/lri/varna/exceptions/ExceptionNonEqualLength.java0000644000000000000000000000302311620715270023003 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Exception for different rna lenghts * * @author darty * */ public class ExceptionNonEqualLength extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; public ExceptionNonEqualLength(String errorMessage) { _errorMessage = errorMessage; } public String getError() { return _errorMessage; } public String getMessage() { return "Both RNA have not the same length, cannot resolve secondary structure."; } } fr/orsay/lri/varna/exceptions/ExceptionModeleStyleBaseSyntaxError.java0000644000000000000000000000270211620715270025364 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Exception for problems with the script about modele style base creation * * @author darty * */ public class ExceptionModeleStyleBaseSyntaxError extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _details; public ExceptionModeleStyleBaseSyntaxError(String details) { _details = details; } public String getMessage() { return _details; } } fr/orsay/lri/varna/exceptions/ExceptionUnmatchedClosingParentheses.java0000644000000000000000000000337211620715270025557 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; import java.text.ParseException; /** * Exception used when a rna has not the same number of opening and clothing * parentheses * * @author darty * */ public class ExceptionUnmatchedClosingParentheses extends ParseException { /** * */ private static final long serialVersionUID = 1L; public ExceptionUnmatchedClosingParentheses(String s, int errorOffset) { super(s, errorOffset); } public ExceptionUnmatchedClosingParentheses(int errorOffset) { super("", errorOffset); } public String getMessage() { return "Unbalanced parentheses expression, cannot resolve secondary structure.\n" + "Bad secondary structure (DBN format):Unmatched closing parentheses ')' at " + getErrorOffset(); } } fr/orsay/lri/varna/exceptions/ExceptionDrawingAlgorithm.java0000644000000000000000000000065311620715270023367 0ustar rootrootpackage fr.orsay.lri.varna.exceptions; /** * Exceptions of this class, or of a derived class, * are thrown by the RNA drawing algorithms. * * @author Raphael Champeimont */ public class ExceptionDrawingAlgorithm extends Exception { private static final long serialVersionUID = -8705033963886770829L; public ExceptionDrawingAlgorithm(String message) { super(message); } public ExceptionDrawingAlgorithm() { } } fr/orsay/lri/varna/exceptions/ExceptionNAViewAlgorithm.java0000644000000000000000000000264211620715270023125 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; public class ExceptionNAViewAlgorithm extends ExceptionDrawingAlgorithm { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; public ExceptionNAViewAlgorithm(String errorMessage) { _errorMessage = errorMessage; } public String getError() { return _errorMessage; } public String getMessage() { return _errorMessage; } } fr/orsay/lri/varna/exceptions/ExceptionParameterError.java0000644000000000000000000000316111620715270023054 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.exceptions; /** * Exception for parameter problems * * @author darty * */ public class ExceptionParameterError extends Exception { /** * */ private static final long serialVersionUID = 1L; private String _errorMessage; private String _details; public ExceptionParameterError(String errorMessage, String details) { _errorMessage = errorMessage; _details = details; } public ExceptionParameterError(String details) { _errorMessage = ""; _details = details; } public String getError() { return _errorMessage; } public String getMessage() { return _details; } }fr/orsay/lri/varna/exceptions/ExceptionXmlLoading.java0000644000000000000000000000056711620715270022167 0ustar rootrootpackage fr.orsay.lri.varna.exceptions; /** * Thrown by algorithms that load data from XML when they fail. * * @author Raphael Champeimont */ public class ExceptionXmlLoading extends Exception { private static final long serialVersionUID = -6267373620339074008L; public ExceptionXmlLoading(String message) { super(message); } public ExceptionXmlLoading() { } }fr/orsay/lri/varna/interfaces/0000755000000000000000000000000012275611432015343 5ustar rootrootfr/orsay/lri/varna/interfaces/InterfaceParameterLoader.java0000644000000000000000000000224511620715270023077 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.interfaces; public interface InterfaceParameterLoader { public String getParameterValue(String key, String def); } fr/orsay/lri/varna/interfaces/InterfaceVARNABasesListener.java0000644000000000000000000000076112000316136023353 0ustar rootrootpackage fr.orsay.lri.varna.interfaces; import java.awt.event.MouseEvent; import java.awt.geom.Point2D; import java.util.ArrayList; import java.util.Hashtable; import java.util.Set; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.ModeleBase; public interface InterfaceVARNABasesListener { /** * Reacts to click over base * @param mb The base which has just been clicked */ public void onBaseClicked(ModeleBase mb, MouseEvent e); } fr/orsay/lri/varna/interfaces/InterfaceVARNAListener.java0000644000000000000000000000275212005274612022406 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.interfaces; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.RNA; /** * Observable design pattern * * @author darty * */ public abstract interface InterfaceVARNAListener { public abstract void onWarningEmitted(String s); public abstract void onStructureRedrawn(); public abstract void onUINewStructure(VARNAConfig v, RNA r); public abstract void onZoomLevelChanged(); public abstract void onTranslationChanged(); } fr/orsay/lri/varna/interfaces/InterfaceVARNASelectionListener.java0000644000000000000000000000155611621223320024246 0ustar rootrootpackage fr.orsay.lri.varna.interfaces; import fr.orsay.lri.varna.models.BaseList; import fr.orsay.lri.varna.models.rna.ModeleBase; public interface InterfaceVARNASelectionListener { /** * Specifies an action that should be performed upon changing the hovered base. * @param oldbase Previously hovered base (possibly null). * @param newBase Newly hovered base (possibly null). */ public void onHoverChanged(ModeleBase oldbase, ModeleBase newBase); /** * Specifies the action to be performed upon changing the selection. * @param selection The list of bases currently selected * @param addedBases The list of bases added since previous selection event * @param removedBases The list of bases removed since previous selection event */ public void onSelectionChanged(BaseList selection, BaseList addedBases, BaseList removedBases); } fr/orsay/lri/varna/interfaces/InterfaceVARNARNAListener.java0000644000000000000000000000216512005271464022747 0ustar rootrootpackage fr.orsay.lri.varna.interfaces; import java.awt.geom.Point2D; import java.util.ArrayList; import java.util.Hashtable; import java.util.Set; import fr.orsay.lri.varna.models.rna.ModeleBP; public interface InterfaceVARNARNAListener { /** * Reacts to changes being made at the sequence level. * @param index The sequence index where a change of base content is observed * @param oldseq Previous base content * @param newseq New base content */ public void onSequenceModified(int index, String oldseq, String newseq); /** * Reacts to modification of the structure (Base-pair addition/removal). * @param current Current list of base-pairs (can be also accessed within the current RNA object). * @param addedBasePairs Newly created base-pairs * @param removedBasePairs Newly removed base-pairs */ public void onStructureModified(Set current, Set addedBasePairs, Set removedBasePairs); /** * Reacts to displacement of * @param previousPositions */ public void onRNALayoutChanged(Hashtable previousPositions); } fr/orsay/lri/varna/interfaces/InterfaceVARNAObservable.java0000644000000000000000000000233211620715270022701 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.interfaces; /** * Observable design pattern * * @author darty * */ public abstract class InterfaceVARNAObservable { public abstract void addVARNAListener(InterfaceVARNAListener rl); }fr/orsay/lri/varna/controlers/0000755000000000000000000000000012275611450015412 5ustar rootrootfr/orsay/lri/varna/controlers/ControleurSelectionHighlight.java0000644000000000000000000000467111620715272024117 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.util.ArrayList; import java.util.Collection; import java.util.Vector; import javax.swing.JMenuItem; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.rna.ModeleBase; public class ControleurSelectionHighlight implements ChangeListener { private Collection _selection; private VARNAPanel _target; private JMenuItem _parent; public ControleurSelectionHighlight(int elem, VARNAPanel v, JMenuItem parent) { ArrayList sel = new ArrayList(); sel.add(elem); _selection = v.getRNA().getBasesAt(sel); _target = v; _parent = parent; } public ControleurSelectionHighlight(Vector sel, VARNAPanel v, JMenuItem parent) { this(new ArrayList(sel), v, parent); } public ControleurSelectionHighlight(ArrayList sel, VARNAPanel v, JMenuItem parent) { this(v.getRNA().getBasesAt(sel),v,parent); } public ControleurSelectionHighlight(Collection sel, VARNAPanel v, JMenuItem parent) { _selection = sel; _target = v; _parent = parent; } public void stateChanged(ChangeEvent e) { if (_parent.isSelected()) { _target.saveSelection(); _target.setSelection(_selection); } else { _target.restoreSelection(); } } } fr/orsay/lri/varna/controlers/ControleurClicMovement.java0000644000000000000000000005417312007503160022720 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Component; import java.awt.Point; import java.awt.Rectangle; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.Point2D; import java.util.ArrayList; import java.util.Collection; import java.util.Vector; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.event.PopupMenuEvent; import javax.swing.event.PopupMenuListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleBasesComparison; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.RNA; /** * Controller of the mouse click * * @author darty * */ public class ControleurClicMovement implements MouseListener, MouseMotionListener, PopupMenuListener { private VARNAPanel _vp; private boolean _presenceMenuSelection; private JMenu _submenuSelection; public Point _spawnPoint; public Point _initialPoint; public Point _prevPoint; public Point _currentPoint; public static final double MIN_SELECTION_DISTANCE = 40.0; public static final double HYSTERESIS_DISTANCE = 10.0; private ModeleBase _selectedBase = null; public enum MouseStates { NONE, MOVE_ELEMENT, MOVE_OR_SELECT_ELEMENT, SELECT_ELEMENT, SELECT_REGION_OR_UNSELECT, SELECT_REGION, CREATE_BP, POPUP_MENU, MOVE_ANNOTATION, }; private MouseStates _currentState = MouseStates.NONE; public ControleurClicMovement(VARNAPanel _vuep) { _vp = _vuep; _vp.getPopup().addPopupMenuListener(this); _presenceMenuSelection = false; } public void mouseClicked(MouseEvent arg0) { } public void mouseEntered(MouseEvent arg0) { } public void mouseExited(MouseEvent arg0) { } public void mousePressed(MouseEvent arg0) { _vp.requestFocus(); boolean button1 = (arg0.getButton() == MouseEvent.BUTTON1); boolean button2 = (arg0.getButton() == MouseEvent.BUTTON2); boolean button3 = (arg0.getButton() == MouseEvent.BUTTON3); boolean shift = arg0.isShiftDown(); boolean ctrl = arg0.isControlDown(); boolean alt = arg0.isAltDown(); _vp.removeSelectedAnnotation(); if (button1 && !ctrl && !alt && !shift) { if (_vp.isModifiable()) { _currentState = MouseStates.MOVE_OR_SELECT_ELEMENT; if (_vp.getRealCoords() != null && _vp.getRealCoords().length != 0 && _vp.getRNA().get_listeBases().size() != 0) { _selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false); TextAnnotation selectedAnnotation = _vp.getNearestAnnotation(arg0.getX(), arg0.getY()); _initialPoint = new Point(arg0.getX(),arg0.getY()); _currentPoint = new Point(_initialPoint); _prevPoint = new Point(_initialPoint); if (_selectedBase != null) { if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE) { _vp.highlightSelectedBase(_selectedBase); } else { if (!_vp.getSelectionIndices().contains(_selectedBase.getIndex())) { _vp.highlightSelectedBase(_selectedBase); } else { // Otherwise, keep current selection as it is and move it } } } else { if (selectedAnnotation != null) { _currentState = MouseStates.MOVE_ANNOTATION; _vp.set_selectedAnnotation(selectedAnnotation); _vp.highlightSelectedAnnotation(); } else { _vp.clearSelection(); _selectedBase = null; _currentState = MouseStates.SELECT_REGION_OR_UNSELECT; _initialPoint = new Point(arg0.getX(),arg0.getY()); _prevPoint = new Point(_initialPoint); _currentPoint = new Point(_initialPoint); } } } } } else if (button1 && ctrl && !alt && !shift) { _selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false); if (_selectedBase != null) { _vp.clearSelection(); _currentState = MouseStates.CREATE_BP; _vp.highlightSelectedBase(_selectedBase); _vp.setOriginLink(_vp.logicToPanel(_selectedBase.getCoords())); _initialPoint = new Point(arg0.getX(),arg0.getY()); _currentPoint = new Point(_initialPoint); } } else if (button1 && !ctrl && !alt && shift) { _currentState = MouseStates.SELECT_ELEMENT; _initialPoint = new Point(arg0.getX(),arg0.getY()); _currentPoint = new Point(_initialPoint); } else if (button3) { _currentState = MouseStates.POPUP_MENU; if (_presenceMenuSelection) { _vp.getPopupMenu().removeSelectionMenu(); } if ((_vp.getRealCoords() != null) && _vp.getRNA().get_listeBases().size() != 0) { updateNearestBase(arg0); // on insere dans le menu les nouvelles options addMenu(arg0); if (_vp.get_selectedAnnotation() != null) _vp.highlightSelectedAnnotation(); } // affichage du popup menu if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_LINEAR) { _vp.getPopup().get_rotation().setEnabled(false); } else { _vp.getPopup().get_rotation().setEnabled(true); } _vp.getPopup().updateDialog(); _vp.getPopup().show(_vp, arg0.getX(), arg0.getY()); } _vp.repaint(); } public void mouseDragged(MouseEvent me) { if ((_currentState == MouseStates.MOVE_OR_SELECT_ELEMENT)||(_currentState == MouseStates.MOVE_ELEMENT)) { _vp.lockScrolling(); _currentState = MouseStates.MOVE_ELEMENT; // si on deplace la souris et qu'une base est selectionnée if (_selectedBase != null) { if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE) { _vp.highlightSelectedStem(_selectedBase); // dans le cas radiale on deplace une helice _vp.getVARNAUI().UIMoveHelixAtom(_selectedBase.getIndex(), _vp.panelToLogicPoint(new Point2D.Double(me.getX(), me.getY()))); } else { // dans le cas circulaire naview ou line on deplace une base _currentPoint = new Point(me.getX(), me.getY()); moveSelection(_prevPoint,_currentPoint); _prevPoint = new Point(_currentPoint); } _vp.repaint(); } } else if (_currentState == MouseStates.MOVE_ANNOTATION) { if (_vp.get_selectedAnnotation()!=null) { Point2D.Double p = _vp.panelToLogicPoint(new Point2D.Double(me.getX(), me.getY())); _vp.get_selectedAnnotation().setAncrage(p.x,p.y); _vp.repaint(); } } else if ((_currentState == MouseStates.SELECT_ELEMENT)||(_currentState == MouseStates.SELECT_REGION_OR_UNSELECT)) { if (_initialPoint.distance(me.getX(),me.getY())>HYSTERESIS_DISTANCE) _currentState = MouseStates.SELECT_REGION; } else if (_currentState == MouseStates.SELECT_REGION) { _currentPoint = new Point(me.getX(),me.getY()); int minx = Math.min(_currentPoint.x, _initialPoint.x); int miny = Math.min(_currentPoint.y, _initialPoint.y); int maxx = Math.max(_currentPoint.x, _initialPoint.x); int maxy = Math.max(_currentPoint.y, _initialPoint.y); _vp.setSelectionRectangle(new Rectangle(minx,miny,maxx-minx,maxy-miny)); } else if (_currentState == MouseStates.CREATE_BP) { if (_initialPoint.distance(me.getX(),me.getY())>HYSTERESIS_DISTANCE) { ModeleBase newSelectedBase = _vp.getNearestBase(me.getX(),me.getY(),false,false); _vp.setHoverBase(newSelectedBase); if (newSelectedBase==null) { _vp.setDestinationLink(new Point2D.Double(me.getX(),me.getY())); _vp.clearSelection(); _vp.addToSelection(_selectedBase.getIndex()); } else { ModeleBase mborig = _selectedBase; _vp.clearSelection(); _vp.addToSelection(newSelectedBase.getIndex()); _vp.addToSelection(mborig.getIndex()); _vp.setDestinationLink(_vp.logicToPanel(newSelectedBase.getCoords())); } _vp.repaint(); } } } public void mouseReleased(MouseEvent arg0) { if (arg0.getButton() == MouseEvent.BUTTON1) { _vp.fireBaseClicked(_selectedBase, arg0); //System.out.println(""+_currentState); if (_currentState == MouseStates.MOVE_ELEMENT) { _vp.clearSelection(); _selectedBase = null; _vp.unlockScrolling(); _vp.removeSelectedAnnotation(); } else if (_currentState == MouseStates.SELECT_REGION_OR_UNSELECT) { _vp.clearSelection(); _selectedBase = null; _vp.removeSelectedAnnotation(); } else if (_currentState == MouseStates.SELECT_ELEMENT) { if (_vp.getRealCoords() != null && _vp.getRealCoords().length != 0 && _vp.getRNA().get_listeBases().size() != 0) { int selectedIndex = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),false,false); if (selectedIndex !=-1) { _vp.toggleSelection(selectedIndex); } } _selectedBase = null; } else if (_currentState == MouseStates.SELECT_REGION) { _vp.removeSelectionRectangle(); } else if (_currentState == MouseStates.CREATE_BP) { if (_initialPoint.distance(arg0.getX(),arg0.getY())>HYSTERESIS_DISTANCE) { int selectedIndex = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),false,false); if (selectedIndex>=0) { ModeleBase mb = _vp.getNearestBase(arg0.getX(),arg0.getY(),false,false); ModeleBase mborig = _selectedBase; ModeleBP msbp = new ModeleBP(mb,mborig); if (mb!=mborig) { _vp.getVARNAUI().UIAddBP(mb.getIndex(),mborig.getIndex(),msbp); } } } _vp.removeLink(); _vp.clearSelection(); _vp.repaint(); } else { _vp.clearSelection(); } } _currentState = MouseStates.NONE; _vp.repaint(); } private void addMenu(MouseEvent arg0) { // creation du menu _submenuSelection = new JMenu("Selection"); addCurrent(); // ajout des option sur base addMenuBase(); // ajout des option sur paire de base if (_vp.getRNA().get_listeBases().get(_vp.getNearestBase()) .getElementStructure() != -1) { addMenuBasePair(); } // detection renflement detectBulge(); // detection 3' detect3Prime(); // detection 5' detect5Prime(); // detection boucle detectLoop(); // detection d'helice detectHelix(); // detection tige detectStem(); // Ajout de toutes bases addAllBase(); // detection d'annotation detectAnnotation(arg0); _vp.getPopup().addSelectionMenu(_submenuSelection); _presenceMenuSelection = true; } private void detectAnnotation(MouseEvent arg0) { if (_vp.getListeAnnotations().size() != 0) { double dist = Double.MAX_VALUE; double d2; Point2D.Double position; for (TextAnnotation textAnnot : _vp.getListeAnnotations()) { // calcul de la distance position = textAnnot.getCenterPosition(); position = _vp.transformCoord(position); d2 = Math.sqrt(Math.pow((position.x - arg0.getX()), 2) + Math.pow((position.y - arg0.getY()), 2)); // si la valeur est inferieur au minimum actuel if (dist > d2) { _vp.set_selectedAnnotation(textAnnot); dist = d2; } } _submenuSelection.addSeparator(); _vp.getPopup().addAnnotationMenu(_submenuSelection,true); } } private void detectBulge() { int indiceB = _vp.getNearestBase(); ArrayList indices = _vp.getRNA().findBulge(indiceB); if ((indices.size() > 0) && (_vp.getRNA().getHelixCountOnLoop(_vp.getNearestBase()) == 2)) { JMenu submenuBulge = new JMenu("Bulge"); submenuBulge.addChangeListener(new ControleurSelectionHighlight( new Vector(indices), _vp, submenuBulge)); submenuBulge.setActionCommand("bulge"); if (!_vp.isModifiable()) submenuBulge.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuBulge); _submenuSelection.add(submenuBulge); } } private void detectHelix() { int indiceH = _vp.getNearestBase(); ArrayList indices = _vp.getRNA().findHelix(indiceH); if (indices.size() != 0) { // ajout menu helice JMenu submenuHelix = new JMenu("Helix"); submenuHelix.addChangeListener(new ControleurSelectionHighlight( new Vector(indices), _vp, submenuHelix)); submenuHelix.setActionCommand("helix"); if (!_vp.isModifiable()) submenuHelix.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuHelix); submenuHelix.addSeparator(); _vp.getPopupMenu().addAnnotationMenu(submenuHelix); _submenuSelection.add(submenuHelix); } } private void detectStem() { int indiceS = _vp.getNearestBase(); ArrayList indices = _vp.getRNA().findStem(indiceS); if (indices.size() > 0) { JMenu submenuStem = new JMenu("Stem"); submenuStem.addChangeListener(new ControleurSelectionHighlight( new Vector(indices), _vp, submenuStem)); submenuStem.setActionCommand("stem"); if (!_vp.isModifiable()) submenuStem.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuStem); _submenuSelection.add(submenuStem); } } private void detect3Prime() { // detection 3' int indice3 = _vp.getNearestBase(); ArrayList indices = _vp.getRNA().find3Prime(indice3); if (indices.size() != 0) { JMenu submenu3Prime = new JMenu("3'"); submenu3Prime.addChangeListener(new ControleurSelectionHighlight( new Vector(indices), _vp, submenu3Prime)); submenu3Prime.setActionCommand("3'"); if (!_vp.isModifiable()) submenu3Prime.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenu3Prime); _submenuSelection.add(submenu3Prime); } } private void detect5Prime() { int indice5 = _vp.getNearestBase(); ArrayList indices = _vp.getRNA().find5Prime(indice5); if (indices.size() != 0) { JMenu submenu5Prime = new JMenu("5'"); submenu5Prime.addChangeListener(new ControleurSelectionHighlight( new Vector(indices), _vp, submenu5Prime)); submenu5Prime.setActionCommand("5'"); if (!_vp.isModifiable()) submenu5Prime.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenu5Prime); _submenuSelection.add(submenu5Prime); } } private void detectLoop() { int indexL = _vp.getNearestBase(); if (_vp.getRNA().get_listeBases().get(indexL).getElementStructure() == -1) { ArrayList listLoop = _vp.getRNA().findLoop(indexL); JMenu submenuLoop = new JMenu("Loop"); submenuLoop.addChangeListener(new ControleurSelectionHighlight( listLoop, _vp, submenuLoop)); submenuLoop.setActionCommand("loop1"); if (!_vp.isModifiable()) submenuLoop.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuLoop); submenuLoop.addSeparator(); _vp.getPopupMenu().addAnnotationMenu(submenuLoop); _submenuSelection.add(submenuLoop); } else { ArrayList listLoop1 = _vp.getRNA().findLoopForward(indexL); if (listLoop1.size() > 0) { JMenu submenuLoop1 = new JMenu("Forward loop"); submenuLoop1 .addChangeListener(new ControleurSelectionHighlight( listLoop1, _vp, submenuLoop1)); submenuLoop1.setActionCommand("loop1"); if (!_vp.isModifiable()) submenuLoop1.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuLoop1); submenuLoop1.addSeparator(); _vp.getPopupMenu().addAnnotationMenu(submenuLoop1); _submenuSelection.add(submenuLoop1); } ArrayList listLoop2 = _vp.getRNA() .findLoopBackward(indexL); if (listLoop2.size() > 0) { JMenu submenuLoop2 = new JMenu("Backward loop"); submenuLoop2 .addChangeListener(new ControleurSelectionHighlight( listLoop2, _vp, submenuLoop2)); submenuLoop2.setActionCommand("loop2"); if (!_vp.isModifiable()) submenuLoop2.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuLoop2); submenuLoop2.addSeparator(); _vp.getPopupMenu().addAnnotationMenu(submenuLoop2); _submenuSelection.add(submenuLoop2); } } } private void addCurrent() { Collection mbs = _vp.getSelection().getBases(); if (mbs.size()>0) { JMenu submenuAll = new JMenu("Current"); submenuAll.addChangeListener(new ControleurSelectionHighlight( mbs, _vp, submenuAll)); submenuAll.setActionCommand("current"); if (!_vp.isModifiable()) submenuAll.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuAll); _submenuSelection.add(submenuAll); } } private void addMenuBase() { JMenu submenuBase = new JMenu(); ModeleBase mb = _vp.getRNA().get_listeBases().get(_vp.getNearestBase()); if (mb instanceof ModeleBasesComparison) { submenuBase.setText("Base #" + (mb.getBaseNumber()) + ":" + ((ModeleBasesComparison) mb).getBases()); } else { submenuBase.setText("Base #" + (mb.getBaseNumber()) + ":" + ((ModeleBaseNucleotide) mb).getBase()); } submenuBase.addChangeListener(new ControleurSelectionHighlight(mb .getIndex(), _vp, submenuBase)); submenuBase.setActionCommand("base"); // option disponible seulement en mode modifiable if (!_vp.isModifiable()) submenuBase.setEnabled(false); JMenuItem baseChar = new JMenuItem("Edit base"); baseChar.setActionCommand("baseChar"); baseChar.addActionListener(_vp.getPopupMenu().get_controleurMenu()); submenuBase.add(baseChar); _vp.getPopupMenu().addColorOptions(submenuBase); submenuBase.addSeparator(); _vp.getPopupMenu().addAnnotationMenu(submenuBase); _submenuSelection.add(submenuBase); } private void addAllBase() { ArrayList indices = _vp.getRNA().findAll(); JMenu submenuAll = new JMenu("All"); submenuAll.addChangeListener(new ControleurSelectionHighlight( new Vector(indices), _vp, submenuAll)); submenuAll.setActionCommand("all"); if (!_vp.isModifiable()) submenuAll.setEnabled(false); _vp.getPopupMenu().addColorOptions(submenuAll); _submenuSelection.add(submenuAll); } private void addMenuBasePair() { int indiceBP = _vp.getNearestBase(); ArrayList indices = _vp.getRNA().findPair(indiceBP); ModeleBase base = _vp.getRNA() .get_listeBases().get(_vp.getNearestBase()); if (base.getElementStructure() != -1) { JMenu submenuBasePair = new JMenu(); ModeleBase partner = _vp .getRNA().get_listeBases().get( base.getElementStructure()); submenuBasePair .addChangeListener(new ControleurSelectionHighlight( indices, _vp, submenuBasePair)); submenuBasePair.setText("Base pair #(" + (Math.min(base.getBaseNumber(), partner .getBaseNumber())) + "," + (Math.max(base.getBaseNumber(), partner .getBaseNumber())) + ")"); submenuBasePair.setActionCommand("bp"); // option disponible seulement en mode modifiable if (!_vp.isModifiable()) submenuBasePair.setEnabled(false); JMenuItem basepair = new JMenuItem("Edit BP"); basepair.setActionCommand("basepair"); basepair.addActionListener(_vp.getPopupMenu() .get_controleurMenu()); _vp.getPopupMenu().addColorOptions(submenuBasePair); Component[] comps = submenuBasePair.getMenuComponents(); int offset = -1; for (int i = 0; i < comps.length; i++) { Component c = comps[i]; if (c instanceof JMenuItem) { JMenuItem jmi = (JMenuItem) c; if (jmi.getActionCommand().contains(",BPColor")) { offset = i; } } } if (offset != -1) { submenuBasePair.insert(basepair, offset); } else { submenuBasePair.add(basepair); } _submenuSelection.add(submenuBasePair); } } private void updateNearestBase(MouseEvent arg0) { int i = _vp.getNearestBaseIndex(arg0.getX(),arg0.getY(),true,false); if (i!=-1) _vp.setNearestBase(i); } public void mouseMoved(MouseEvent arg0) { _selectedBase = _vp.getNearestBase(arg0.getX(),arg0.getY()); TextAnnotation selectedAnnotation = _vp.getNearestAnnotation(arg0.getX(),arg0.getY()); _vp.setHoverBase(_selectedBase); if (_selectedBase != null) { } else if (selectedAnnotation!=null) { _vp.set_selectedAnnotation(selectedAnnotation); _vp.highlightSelectedAnnotation(); _vp.repaint(); } _vp.setLastSelectedPosition(new Point2D.Double(arg0.getX(),arg0.getY())); } private void moveSelection(Point prev, Point cur) { Point2D.Double p1 = _vp.panelToLogicPoint(new Point2D.Double(prev.x,prev.y)); Point2D.Double p2 = _vp.panelToLogicPoint(new Point2D.Double(cur.x,cur.y)); double dx = (p2.x - p1.x); double dy = (p2.y - p1.y); if (_vp.isModifiable()) { double ndx = dx; double ndy = dy; if (_vp.getRNA().get_drawMode() == RNA.DRAW_MODE_LINEAR) { ndy=0.0; } _vp.getVARNAUI().UIShiftBaseCoord(_vp.getSelectionIndices(), ndx, ndy); _vp.fireLayoutChanged(); } } public void popupMenuCanceled(PopupMenuEvent arg0) { } public void popupMenuWillBecomeInvisible(PopupMenuEvent arg0) { _vp.resetAnnotationHighlight(); _selectedBase = null; } public void popupMenuWillBecomeVisible(PopupMenuEvent arg0) { } }fr/orsay/lri/varna/controlers/ControleurJCheckBoxMenuItem.java0000644000000000000000000000274111620715272023602 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import fr.orsay.lri.varna.VARNAPanel; /** * Controller of check box menu items to repaint if item state changes * * @author darty * */ public class ControleurJCheckBoxMenuItem implements ItemListener { private VARNAPanel _vp; public ControleurJCheckBoxMenuItem(VARNAPanel v) { _vp = v; } public void itemStateChanged(ItemEvent e) { _vp.repaint(); } } fr/orsay/lri/varna/controlers/ControleurVARNAPanelKeys.java0000644000000000000000000002400512441747356023030 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Point; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.geom.Point2D; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.views.VueUI; /** * VARNAPanel Shortcuts Controller * * @author darty * */ public class ControleurVARNAPanelKeys implements KeyListener, FocusListener { private VARNAPanel _vp; public ControleurVARNAPanelKeys(VARNAPanel vp) { _vp = vp; } public void mouseClicked(MouseEvent e) { } public void mouseEntered(MouseEvent e) { // prise du focus //_vp.requestFocus(); } public void mouseExited(MouseEvent e) { } public void mousePressed(MouseEvent e) { } public void mouseReleased(MouseEvent e) { } public void keyPressed(KeyEvent e) { boolean controlDown = (e.getModifiersEx() & (KeyEvent.CTRL_DOWN_MASK)) == KeyEvent.CTRL_DOWN_MASK; boolean shiftDown = (e.getModifiersEx() & (KeyEvent.SHIFT_DOWN_MASK)) == KeyEvent.SHIFT_DOWN_MASK; boolean altDown = (e.getModifiersEx() & (KeyEvent.ALT_DOWN_MASK)) == KeyEvent.ALT_DOWN_MASK; VueUI ui = _vp.getVARNAUI(); try { switch (e.getKeyCode()) { case (KeyEvent.VK_A): if (controlDown) { ui.UIAbout(); } break; case (KeyEvent.VK_B): if (controlDown) { ui.UISetBorder(); } else if (altDown) { ui.UIToggleDrawBackbone(); } break; case (KeyEvent.VK_C): if (shiftDown && controlDown) { ui.UISetColorMapCaption(); } break; case (KeyEvent.VK_D): if (controlDown) { if (shiftDown) { ui.UIPickGapsBasesColor(); } else { ui.UIToggleColorGapsBases(); } } break; case (KeyEvent.VK_E): if (controlDown) { ui.UIToggleShowNonPlanar(); } break; case (KeyEvent.VK_F): if (controlDown) { ui.UIToggleFlatExteriorLoop(); } break; case (KeyEvent.VK_G): if (controlDown) { ui.UISetBackground(); } else if (!shiftDown && altDown) { ui.UIToggleGaspinMode(); } break; case (KeyEvent.VK_H): if (controlDown && !shiftDown) { ui.UISetBPHeightIncrement(); } else if (controlDown && shiftDown) { Point2D.Double p = _vp.getLastSelectedPosition(); ui.UIAnnotationsAddPosition((int)p.x,(int)p.y); } break; case (KeyEvent.VK_J): if (controlDown) { if (shiftDown) { ui.UIPickSpecialBasesColor(); } else { ui.UIToggleColorSpecialBases(); } } break; case (KeyEvent.VK_K): if (controlDown && shiftDown) { ui.UILoadColorMapValues(); } else if (controlDown) { ui.UISetBackboneColor(); } break; case (KeyEvent.VK_L): if (shiftDown && controlDown) { ui.UIToggleColorMap(); } else if (controlDown) { ui.UISetColorMapStyle(); } else if (shiftDown) { ui.UISetColorMapValues(); } break; case (KeyEvent.VK_M): if (controlDown) { ui.UISetNumPeriod(); } else if (shiftDown && altDown) { ui.UIToggleModifiable(); } break; case (KeyEvent.VK_N): if (controlDown) { ui.UIManualInput(); } break; case (KeyEvent.VK_O): if (controlDown) { ui.UIFile(); } break; case (KeyEvent.VK_P): if (controlDown && shiftDown) { ui.UISetBPStyle(); } else if (controlDown && !shiftDown) { ui.UIPrint(); } break; case (KeyEvent.VK_Q): if (controlDown && !shiftDown && !altDown) { _vp.getVARNAUI().UIAutoAnnotateHelices(); } else if (controlDown && shiftDown && !altDown) { _vp.getVARNAUI().UIAutoAnnotateTerminalLoops(); } else if (!controlDown && shiftDown && altDown) { _vp.getVARNAUI().UIAutoAnnotateInteriorLoops(); } else if (controlDown && !shiftDown && altDown) { _vp.getVARNAUI().UIAutoAnnotateStrandEnds(); } break; case (KeyEvent.VK_R): if (controlDown) { if (shiftDown) { ui.UIReset(); } else { ui.UIGlobalRotation(); } } break; case (KeyEvent.VK_S): if (controlDown) { if (shiftDown) { ui.UISetSpaceBetweenBases(); } else { ui.UISaveAs(); } } break; case (KeyEvent.VK_T): if (controlDown) { if (shiftDown) { ui.UISetTitleFont(); } else if (altDown) { ui.UISetTitleColor(); } else { ui.UISetTitle(); } } break; case (KeyEvent.VK_U): if (controlDown && !shiftDown && !altDown) { _vp.getVARNAUI().UIBaseTypeColor(); } else if (!controlDown && shiftDown && !altDown) { _vp.getVARNAUI().UIBasePairTypeColor(); } else if (!controlDown && !shiftDown && altDown) { _vp.getVARNAUI().UIBaseAllColor(); } break; case (KeyEvent.VK_W): if (controlDown) { ui.UIToggleShowNCBP(); } break; case (KeyEvent.VK_X): if (controlDown) { ui.UIExport(); } break; case (KeyEvent.VK_Y): if (controlDown) { ui.UIRedo(); } break; case (KeyEvent.VK_Z): if (controlDown && !shiftDown) { ui.UIUndo(); } else if (controlDown && shiftDown) { ui.UIRedo(); } else if (!controlDown && !shiftDown) { ui.UICustomZoom(); } break; case (KeyEvent.VK_1): if (controlDown) { ui.UILine(); } break; case (KeyEvent.VK_2): if (controlDown) { ui.UICircular(); } break; case (KeyEvent.VK_3): if (controlDown) { ui.UIRadiate(); } break; case (KeyEvent.VK_4): if (controlDown) { ui.UINAView(); } break; case (KeyEvent.VK_5): if (controlDown) { ui.UIVARNAView(); } break; case (KeyEvent.VK_6): if (controlDown) { ui.UIMOTIFView(); } break; // Navigation control keys (Zoom in/out, arrow keys ...) case (KeyEvent.VK_DOWN): if (_vp.getZoom() > 1) { _vp.setTranslation(new Point(_vp.getTranslation().x,_vp.getTranslation().y-5)); _vp.checkTranslation(); } break; case (KeyEvent.VK_UP): if (_vp.getZoom() > 1) { _vp.setTranslation(new Point(_vp.getTranslation().x,_vp.getTranslation().y+5)); _vp.checkTranslation(); } break; case (KeyEvent.VK_LEFT): if (_vp.getZoom() > 1) { _vp.setTranslation(new Point(_vp.getTranslation().x+5,_vp.getTranslation().y)); _vp.checkTranslation(); } break; case (KeyEvent.VK_RIGHT): if (_vp.getZoom() > 1) { _vp.setTranslation(new Point(_vp.getTranslation().x-5,_vp.getTranslation().y)); _vp.checkTranslation(); } break; case (KeyEvent.VK_EQUALS): case (KeyEvent.VK_PLUS): ui.UIZoomIn(); break; case (KeyEvent.VK_MINUS): ui.UIZoomOut(); break; } } catch (Exception e1) { _vp.errorDialog(e1); } _vp.repaint(); } /** * if ((e.getKeyCode() == KeyEvent.VK_PLUS)||(e.getKeyChar() == '+')) { * _vp.getVARNAUI().UIZoomIn(); } else if (e.getKeyCode() == * KeyEvent.VK_MINUS) { _vp.getVARNAUI().UIZoomOut(); } // 1 pour Redraw * Radiate else if (e.getKeyChar() == KeyEvent.VK_1) { * _vp.getVARNAUI().UIRadiate(); } // 2 pour Redraw Circular else if * (e.getKeyChar() == KeyEvent.VK_2) { _vp.getVARNAUI().UICircular(); } // 3 * pour Redraw NAView else if (e.getKeyChar() == KeyEvent.VK_3) { * _vp.getVARNAUI().UINAView(); } * * // 4 for RNA on a line else if (e.getKeyChar() == KeyEvent.VK_4) { * _vp.getVARNAUI().UILine(); } // 5 fun arn random coord else if * (e.isControlDown() && e.getKeyChar() == KeyEvent.VK_9) { for (int i = 0; * i < _vp.getRNA().get_listeBases().size(); i++) { * _vp.getRNA().get_listeBases().get(i).set_coords( new * Point2D.Double(_vp.getWidth() * Math.random(), _vp.getHeight() * * Math.random())); _vp.getRNA().get_listeBases().get(i).set_center( new * Point2D.Double(_vp.getWidth() / 2 Math.random(), _vp.getHeight() / 2 * Math.random())); } } // 6 fun random arn structure else if * (e.isControlDown() & e.getKeyChar() == KeyEvent.VK_8) { try { * _vp.drawRNA(_vp.getRNA().getListeBasesToString(), getRandomRNA(), _vp * .getRNA().get_drawMode()); } catch (ExceptionNonEqualLength e1) { * _vp.errorDialog(e1); } } _vp.repaint(); } **/ public String getRandomRNA() { int pile = 0, j, i = 0; double l; String fun = ""; while (i < 2000) { if (Math.random() > 0.5) { j = 0; l = Math.random() * 10; while (j < l) { fun += '.'; i++; j++; } } else { if (Math.random() > 0.5 && pile > 0) { j = 0; l = Math.random() * 5; while (j < l && pile > 0) { fun += ')'; pile--; j++; i++; } } else { j = 0; l = Math.random() * 5; while (j < l) { fun += '('; pile++; j++; i++; } } } } while (pile > 0) { fun += ')'; pile--; } return fun; } public void keyReleased(KeyEvent e) { } public void keyTyped(KeyEvent e) { } public void focusGained(FocusEvent arg0) { _vp.repaint(); } public void focusLost(FocusEvent arg0) { _vp.repaint(); } }fr/orsay/lri/varna/controlers/ControleurDemoTextField.java0000644000000000000000000001147611620715272023040 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Color; import java.util.ArrayList; import java.util.Stack; import javax.swing.event.CaretEvent; import javax.swing.event.CaretListener; import javax.swing.text.BadLocationException; import javax.swing.text.DefaultHighlighter; import javax.swing.text.Highlighter; import fr.orsay.lri.varna.applications.VARNAOnlineDemo; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; /** * It controls the sequence and structure text fields and changes their color if * they have different lengths or unbalanced parentheses. * * @author darty * */ public class ControleurDemoTextField implements CaretListener { private VARNAOnlineDemo _vod; private String _oldSeq, _oldStruct; private Highlighter _hilit; private Highlighter.HighlightPainter _painter; private final Color COLORERROR = Color.RED; private final Color COLORWARNING = Color.ORANGE; public ControleurDemoTextField(VARNAOnlineDemo VOD) { _vod = VOD; _oldSeq = _vod.get_seq().getText(); _oldStruct = _vod.get_struct().getText(); _hilit = new DefaultHighlighter(); _painter = new DefaultHighlighter.DefaultHighlightPainter(Color.BLACK); _vod.get_struct().setHighlighter(_hilit); } // if there is any change public void caretUpdate(CaretEvent e) { if (_oldStruct != _vod.get_struct().getText() || _oldSeq != _vod.get_seq().getText()) { ArrayList infos = new ArrayList(); _vod.get_info().removeAll(); _hilit.removeAllHighlights(); _oldStruct = _vod.get_struct().getText(); _oldSeq = _vod.get_seq().getText(); int nbPO = 0, nbPF = 0; // compte les parentheses ouvrantes et fermantes Stack p = new Stack(); boolean pb = false; for (int i = 0; i < _vod.get_struct().getText().length(); i++) { if (_vod.get_struct().getText().charAt(i) == '(') { nbPO++; p.push(i); } else if (_vod.get_struct().getText().charAt(i) == ')') { nbPF++; if (p.size() == 0) { try { _hilit.addHighlight(i, i + 1, _painter); } catch (BadLocationException e1) { _vod.get_varnaPanel().errorDialog(e1); } pb = true; } else p.pop(); } } // si le nombre de parentheses ouvrantes/fermantes est different if (pb || p.size() > 0) { // colorie en rouge if (pb) { infos.add("too many closing parentheses"); } if (p.size() > 0) { int indice; while (!p.isEmpty()) { indice = p.pop(); try { _hilit.addHighlight(indice, indice + 1, _painter); } catch (BadLocationException e1) { _vod.get_varnaPanel().errorDialog(e1); } } infos.add("too many opening parentheses"); } _vod.get_info().setForeground(COLORERROR); _vod.get_seq().setForeground(COLORERROR); _vod.get_struct().setForeground(COLORERROR); } else { try { // redraw the new RNA _vod.get_varnaPanel().drawRNA(_vod.get_seq().getText(), _vod.get_struct().getText(), _vod.get_varnaPanel().getRNA().get_drawMode()); } catch (ExceptionNonEqualLength e1) { _vod.get_varnaPanel().errorDialog(e1); } // verifie la longueur de la structure et de la sequence if (_vod.get_seq().getText().length() != _vod.get_struct() .getText().length()) { // colorie en orange infos.add("different lenghts"); _vod.get_seq().setForeground(COLORWARNING); _vod.get_struct().setForeground(COLORWARNING); } else { // sinon colorie en noir _vod.get_seq().setForeground(Color.black); _vod.get_struct().setForeground(Color.black); } } _vod.get_varnaPanel().getVARNAUI().UIReset(); String info = new String(); if (infos.size() != 0) { info += infos.get(0); for (int i = 1; i < infos.size(); i++) { info += ", " + infos.get(i); } info += "."; } _vod.get_info().setText(info); } } }fr/orsay/lri/varna/controlers/ControleurBlinkingThread.java0000644000000000000000000000466511620715272023232 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import fr.orsay.lri.varna.VARNAPanel; public class ControleurBlinkingThread extends Thread { public static final long DEFAULT_FREQUENCY = 50; private long _period; private VARNAPanel _parent; private double _minVal, _maxVal, _val, _incr; private boolean _increasing = true; private boolean _active = false; public ControleurBlinkingThread(VARNAPanel vp) { this(vp, DEFAULT_FREQUENCY, 0, 1.0, 0.0, 0.2); } public ControleurBlinkingThread(VARNAPanel vp, long period, double minVal, double maxVal, double val, double incr) { _parent = vp; _period = period; _minVal = minVal; _maxVal = maxVal; _incr = incr; } public void setActive(boolean b) { if (_active == b) {} else { _active = b; if (_active) { interrupt(); } } } public boolean getActive() { return _active; } public double getVal() { return _val; } public void run() { while (true) { try { if (_active) { sleep(_period); if (_increasing) { _val = Math.min(_val + _incr, _maxVal); if (_val == _maxVal) { _increasing = false; } } else { _val = Math.max(_val - _incr, _minVal); if (_val == _minVal) { _increasing = true; } } _parent.repaint(); } else { sleep(10000); } } catch (InterruptedException e) { } } } } fr/orsay/lri/varna/controlers/ControleurVueAnnotation.java0000644000000000000000000000435311620715272023131 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import javax.swing.JColorChooser; import javax.swing.event.CaretEvent; import javax.swing.event.CaretListener; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.views.VueAnnotation; /** * Annotation View Controller * * @author Darty@lri.fr * */ public class ControleurVueAnnotation implements CaretListener, ChangeListener, ActionListener { private VueAnnotation _vueAnnot; /** * Creates a ControleurVueAnnotation * * @param vueAnnot */ public ControleurVueAnnotation(VueAnnotation vueAnnot) { _vueAnnot = vueAnnot; } public void caretUpdate(CaretEvent arg0) { _vueAnnot.update(); } public void stateChanged(ChangeEvent arg0) { _vueAnnot.update(); } public void actionPerformed(ActionEvent arg0) { if (arg0.getActionCommand().equals("setcolor")) { Color c = JColorChooser.showDialog(_vueAnnot.get_vp(), "Pick a color", _vueAnnot.getTextAnnotation().getColor()); if (c != null) { _vueAnnot.updateColor(c); } } _vueAnnot.update(); } } fr/orsay/lri/varna/controlers/ControleurDraggedMolette.java0000644000000000000000000000614711726145412023231 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Point; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import fr.orsay.lri.varna.VARNAPanel; /** * Controller of the mouse for scroll wheel click and dragged events * * @author darty * */ public class ControleurDraggedMolette implements MouseListener, MouseMotionListener { private VARNAPanel _vp; /** * true if the right button is pressed
* false if not */ private static Boolean _rightButtonClick; /** * The vector which contains the direction of the mouse movement */ private static Point _direction; /** * The position of the cursor before the mouse drag */ private static Point _avant; /** * The position of the cursor after the mouse drag */ private static Point _apres; public ControleurDraggedMolette(VARNAPanel vp) { _vp = vp; _rightButtonClick = false; _avant = _apres = _direction = new Point(); } public void mouseDragged(MouseEvent e) { // si le bon boutton a été pressé if (_rightButtonClick) { _apres = e.getPoint(); _direction = new Point(_apres.x - _avant.x, _apres.y - _avant.y); _vp.setTranslation(new Point(_vp.getTranslation().x + _direction.x, _vp.getTranslation().y + _direction.y)); _avant = _apres; _vp.checkTranslation(); _vp.repaint(); } } public void mouseMoved(MouseEvent e) { } public void mouseClicked(MouseEvent e) { } public void mouseEntered(MouseEvent e) { } public void mouseExited(MouseEvent e) { } public void mousePressed(MouseEvent e) { // lors du clic, la position du curseur est enregistrée _avant = e.getPoint(); // si le boutton molette est pressé ou si le boutton gauche et shift // sont pressés if (e.getButton() == MouseEvent.BUTTON2) { _rightButtonClick = true; } else { _rightButtonClick = false; } } public void mouseReleased(MouseEvent e) { // si le boutton molette est relaché ou si le boutton gauche et shift // sont relachés if (e.getButton() == MouseEvent.BUTTON2) _rightButtonClick = false; } } fr/orsay/lri/varna/controlers/ControleurBorder.java0000644000000000000000000000333711620715272021555 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Dimension; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.views.VueBorder; public class ControleurBorder implements ChangeListener { private VueBorder _vb; public ControleurBorder(VueBorder vb) { _vb = vb; } public void stateChanged(ChangeEvent e) { if (_vb.getDimension().getHeight() < _vb.get_vp().getHeight() && _vb.getDimension().getWidth() < _vb.get_vp().getWidth()) { _vb.get_vp().setBorderSize(_vb.getDimension()); _vb.get_vp().setMinimumSize( new Dimension(_vb.get_vp().getBorderSize().width * 2, _vb .get_vp().getBorderSize().height * 2)); _vb.get_vp().repaint(); } } } fr/orsay/lri/varna/controlers/ControleurGlobalRescale.java0000644000000000000000000000331612020067514023026 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.VARNAEdits; import fr.orsay.lri.varna.views.VueGlobalRescale; import fr.orsay.lri.varna.views.VueGlobalRotation; public class ControleurGlobalRescale implements ChangeListener { private VueGlobalRescale _vGR; private double _oldScale; private VARNAPanel _vp; public ControleurGlobalRescale(VueGlobalRescale vGR, VARNAPanel vp) { _vGR = vGR; _oldScale = 1.0; _vp = vp; } public void stateChanged(ChangeEvent e) { _vp.getVARNAUI().UIGlobalRescale(_vGR.getScale()/_oldScale); _oldScale = _vGR.getScale(); } } fr/orsay/lri/varna/controlers/ControleurGlobalRotation.java0000644000000000000000000000324111620715272023252 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.VARNAEdits; import fr.orsay.lri.varna.views.VueGlobalRotation; public class ControleurGlobalRotation implements ChangeListener { private VueGlobalRotation _vGR; private double _oldAngle; private VARNAPanel _vp; public ControleurGlobalRotation(VueGlobalRotation vGR, VARNAPanel vp) { _vGR = vGR; _oldAngle = 0; _vp = vp; } public void stateChanged(ChangeEvent e) { _vp.getVARNAUI().UIGlobalRotation(_vGR.getAngle() - _oldAngle); _oldAngle = _vGR.getAngle(); } } fr/orsay/lri/varna/controlers/ControleurNumPeriod.java0000644000000000000000000000270211620715272022235 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.views.VueNumPeriod; public class ControleurNumPeriod implements ChangeListener { private VueNumPeriod _vnp; public ControleurNumPeriod(VueNumPeriod vnp) { _vnp = vnp; } public void stateChanged(ChangeEvent e) { _vnp.get_vp().setNumPeriod(_vnp.getNumPeriod()); _vnp.get_vp().repaint(); } } fr/orsay/lri/varna/controlers/ControleurBaseSpecialColorEditor.java0000644000000000000000000000706411722471072024662 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import fr.orsay.lri.varna.components.BaseSpecialColorEditor; import fr.orsay.lri.varna.models.BaseList; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.views.VueBases; public class ControleurBaseSpecialColorEditor implements ActionListener { private BaseSpecialColorEditor _specialColorEditor; private int _selectedRow; private int _selectedCol; private Color _selectedColor; private String _selectedColTitle; public ControleurBaseSpecialColorEditor(BaseSpecialColorEditor specialColorEditor) { _specialColorEditor = specialColorEditor; } /** * Handles events from the editor button and from the dialog's OK button. */ public void actionPerformed(ActionEvent e) { if (BaseSpecialColorEditor.getEDIT().equals(e.getActionCommand())) { // The user has clicked the cell, so // bring up the dialog. _specialColorEditor.getButton().setBackground( _specialColorEditor.getCurrentColor()); _specialColorEditor.getColorChooser().setColor( _specialColorEditor.getCurrentColor()); _specialColorEditor.getDialog().setVisible(true); // Make the renderer reappear. _specialColorEditor.callFireEditingStopped(); } else { // User pressed dialog's "OK" button. _specialColorEditor.setCurrentColor(_specialColorEditor .getColorChooser().getColor()); _selectedRow = _specialColorEditor.get_vueBases().getTable() .getSelectedRow(); _selectedCol = _specialColorEditor.get_vueBases().getTable() .getSelectedColumn(); _selectedColor = _specialColorEditor.getCurrentColor(); _selectedColTitle = _specialColorEditor.get_vueBases() .getSpecialTableModel().getColumnName(_selectedCol); BaseList lb = _specialColorEditor.get_vueBases().getDataAt(_selectedRow); for(ModeleBase mb: lb.getBases()) { applyColor(_selectedColTitle, _selectedColor,mb); } _specialColorEditor.get_vueBases().get_vp().repaint(); } } private void applyColor(String titreCol, Color couleur, ModeleBase mb) { if (titreCol.equals("Inner Color")) { mb.getStyleBase() .setBaseInnerColor(couleur); } else if (titreCol.equals("Outline Color")) { mb.getStyleBase() .setBaseOutlineColor(couleur); } else if (titreCol.equals("Name Color")) { mb.getStyleBase() .setBaseNameColor(couleur); } else if (titreCol.equals("Number Color")) { mb.getStyleBase() .setBaseNumberColor(couleur); } } } fr/orsay/lri/varna/controlers/ControleurMenu.java0000644000000000000000000005363212441661074021251 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.File; import java.text.ParseException; import java.util.ArrayList; import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JOptionPane; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.exceptions.ExceptionExportFailed; import fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.views.VueBPThickness; import fr.orsay.lri.varna.views.VueMenu; /** * This listener controls menu items * * @author darty * */ public class ControleurMenu implements InterfaceVARNAListener, ActionListener { private VARNAPanel _vp; @SuppressWarnings("unused") private VueMenu _vm; private String _type; private String _color; private Object _source; /** * Creates the menu listener * * @param _varnaPanel * The VARNAPanel */ public ControleurMenu(VARNAPanel _varnaPanel, VueMenu _vueMenu) { _vp = _varnaPanel; _vm = _vueMenu; _vp.getRNA().addVARNAListener(this); } public void actionPerformed(ActionEvent e) { String[] temp = e.getActionCommand().split(","); _source = e.getSource(); _type = temp[0]; if (temp.length > 1) _color = temp[1]; else _color = ""; // selon l'option choisie dans le menu: if (!optionRedraw()) if (!optionExport()) if (!optionImport()) if (!optionRNADisplay()) if (!optionTitle()) if (!optionColorMap()) if (!optionView()) if (!optionBase()) if (!optionBasePair()) if (!optionLoop()) if (!option3prime()) if (!option5prime()) if (!optionHelix()) if (!optionStem()) if (!optionBulge()) if (!optionAnnotation()) if (!optionEditRNA()) _vp.errorDialog(new Exception("Uknown action command '"+_type+"'")); } private boolean optionEditRNA() { if (_type.equals("editallbps")) { _vp.getVARNAUI().UIEditAllBasePairs(); } else if (_type.equals("editallbases")) { _vp.getVARNAUI().UIEditAllBases(); } else return false; return true; } private boolean optionAnnotation() { if (!_type.contains("annotation")) return false; // a partir du menu principale (gestion des annotations) if (_type.equals("annotationsaddPosition")) { _vp.getVARNAUI().UIAnnotationsAddPosition(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y); } else if (_type.equals("annotationsaddBase")) { _vp.getVARNAUI().UIAnnotationsAddBase(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y); } else if (_type.equals("annotationsaddLoop")) { _vp.getVARNAUI().UIAnnotationsAddLoop(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y); } else if (_type.equals("annotationsaddChemProb")) { _vp.getVARNAUI().UIAnnotationsAddChemProb(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y); } else if (_type.equals("annotationsaddRegion")) { _vp.getVARNAUI().UIAnnotationsAddRegion(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y); } else if (_type.equals("annotationsaddHelix")) { _vp.getVARNAUI().UIAnnotationsAddHelix(_vp.getPopup().getSpawnPoint().x,_vp.getPopup().getSpawnPoint().y); } else if (_type.equals("annotationsautohelices")) { _vp.getVARNAUI().UIAutoAnnotateHelices(); } else if (_type.equals("annotationsautointerior")) { _vp.getVARNAUI().UIAutoAnnotateInteriorLoops(); } else if (_type.equals("annotationsautoterminal")) { _vp.getVARNAUI().UIAutoAnnotateTerminalLoops(); } else if (_type.equals("annotationsautohelices")) { _vp.getVARNAUI().UIAutoAnnotateHelices(); } else if (_type.equals("annotationsremove")) { _vp.getVARNAUI().UIAnnotationsRemove(); } else if (_type.equals("annotationsautoextremites")) { _vp.getVARNAUI().UIAutoAnnotateStrandEnds(); } else if (_type.equals("annotationsedit")) { _vp.getVARNAUI().UIAnnotationsEdit(); // a partir du menu selection (annotation la plus proche) } else if (_type.equals("Selectionannotationremove")) { _vp.getVARNAUI().UIAnnotationRemoveFromAnnotation(_vp.get_selectedAnnotation()); } else if (_type.equals("Selectionannotationedit")) { _vp.getVARNAUI().UIAnnotationEditFromAnnotation(_vp.get_selectedAnnotation()); // a partir d'une structure(base, loop, helix) dans l'arn // (annotation li� a la structure) } else if (_type.endsWith("annotationadd")||_type.contains("annotationremove")||_type.contains("annotationedit")) { try { TextAnnotation.AnchorType type = trouverAncrage(); ArrayList listeIndex = new ArrayList(); switch(type) { case BASE: listeIndex.add(_vp.getNearestBase()); case LOOP: if (_type.startsWith("loop1")) listeIndex = _vp.getRNA().findLoopForward(_vp.getNearestBase()); else if (_type.startsWith("loop2")) listeIndex = _vp.getRNA().findLoopBackward(_vp.getNearestBase()); else listeIndex = _vp.getRNA().findLoop(_vp.getNearestBase()); break; case HELIX: listeIndex = _vp.getRNA().findHelix(_vp.getNearestBase()); break; } if (_type.endsWith("annotationadd")) { _vp.getVARNAUI().UIAnnotationAddFromStructure(type,listeIndex); } else if (_type.contains("annotationremove")) { _vp.getVARNAUI().UIAnnotationRemoveFromStructure(trouverAncrage(),listeIndex); } else if (_type.contains("annotationedit")) { _vp.getVARNAUI().UIAnnotationEditFromStructure(trouverAncrage(),listeIndex); } } catch (Exception e2) { e2.printStackTrace(); } } else return false; return true; } private TextAnnotation.AnchorType trouverAncrage() { if (_type.contains("loop")) return TextAnnotation.AnchorType.LOOP; if (_type.contains("helix")) return TextAnnotation.AnchorType.HELIX; if (_type.contains("base")) return TextAnnotation.AnchorType.BASE; errorDialog(new Exception("probleme d'identification de l'ancrage")); return TextAnnotation.AnchorType.POSITION; } private boolean option5prime() { return colorBases(); } private boolean option3prime() { return colorBases(); } private boolean optionBulge() { return colorBases(); } private boolean optionStem() { return colorBases(); } private boolean optionHelix() { return colorBases(); } private boolean colorBases() { // System.out.println(_type); ArrayList listBase = new ArrayList(); String phrase = "Choose new " + _type; if (_color.equals("InnerColor")) { phrase += " inner color"; Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_INNER_COLOR_DEFAULT); if (c != null) { listBase = listSwitchType(_type); for (int i = 0; i < listBase.size(); i++) { _vp.getRNA().get_listeBases().get(listBase.get(i)) .getStyleBase().setBaseInnerColor(c); } _vp.repaint(); } } else if (_color.equals("OutlineColor")) { phrase += " outline color"; Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_OUTLINE_COLOR_DEFAULT); if (c != null) { listBase = listSwitchType(_type); for (int i = 0; i < listBase.size(); i++) { _vp.getRNA().get_listeBases().get(listBase.get(i)) .getStyleBase().setBaseOutlineColor(c); } _vp.repaint(); } } else if (_color.equals("NameColor")) { phrase += " name color"; Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NAME_COLOR_DEFAULT); if (c != null) { listBase = listSwitchType(_type); for (int i = 0; i < listBase.size(); i++) { _vp.getRNA().get_listeBases().get(listBase.get(i)) .getStyleBase().setBaseNameColor(c); } _vp.repaint(); } } else if (_color.equals("NumberColor")) { phrase += " number color"; Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NUMBER_COLOR_DEFAULT); if (c != null) { listBase = listSwitchType(_type); for (int i = 0; i < listBase.size(); i++) { _vp.getRNA().get_listeBases().get(listBase.get(i)) .getStyleBase().setBaseNumberColor(c); } _vp.repaint(); } } else if (_color.equals("BPColor")) { phrase += " base-pair color"; Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NUMBER_COLOR_DEFAULT); if (c != null) { listBase = listSwitchType(_type); for (int i = 0; i < listBase.size(); i++) { for (ModeleBP msbp:_vp.getRNA().getBPsAt(listBase.get(i))) { if (msbp!=null) { msbp.getStyle().setCustomColor(c); } } } _vp.repaint(); } } else if (_color.equals("BPColor")) { phrase += " base-pair color"; Color c = JColorChooser.showDialog(_vp, phrase, VARNAConfig.BASE_NUMBER_COLOR_DEFAULT); if (c != null) { listBase = listSwitchType(_type); for (int i = 0; i < listBase.size(); i++) { ModeleBase mb = _vp.getRNA().get_listeBases().get( listBase.get(i)); if (mb.getElementStructure() != -1) { mb.getStyleBP().getStyle().setCustomColor(c); } } _vp.repaint(); } } else if (_color.equals("BPThickness")) { listBase = listSwitchType(_type); // System.out.println(listBase.size()); ArrayList styleBPs = new ArrayList(); for (int i = 0; i < listBase.size(); i++) { ModeleBase mb = _vp.getRNA().get_listeBases().get( listBase.get(i)); if (mb.getElementStructure() != -1) { styleBPs.add(mb.getStyleBP()); } } VueBPThickness vbpt = new VueBPThickness(_vp, styleBPs); if (JOptionPane.showConfirmDialog(_vp, vbpt.getPanel(), "Set base pair(s) thickness", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { vbpt.restoreThicknesses(); _vp.repaint(); } } else return false; return true; } private ArrayList listSwitchType(String _type) { if (_type.equals("helix")) return _vp.getRNA().findHelix(_vp.getNearestBase()); if (_type.equals("current")) { return _vp.getSelectionIndices(); } if (_type.equals("allBases")) { return _vp.getRNA().findAll(); } if (_type.equals("loop1")) { return _vp.getRNA().findLoopForward(_vp.getNearestBase()); } if (_type.equals("loop2")) { return _vp.getRNA().findLoopBackward(_vp.getNearestBase()); } if (_type.equals("stem")) return _vp.getRNA().findStem(_vp.getNearestBase()); if (_type.equals("base")) { ArrayList list = new ArrayList(); list.add(_vp.getNearestBase()); return list; } if (_type.equals("basepair") || _type.equals("bpcolor") || _type.equals("bp")) { ArrayList list = new ArrayList(); int i = _vp.getNearestBase(); list.add(i); ModeleBase mb = _vp.getRNA().get_listeBases().get(i); int j = mb.getElementStructure(); if (mb.getElementStructure() != -1) { list.add(i); list.add(j); } return list; } if (_type.equals("5'")) return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase()); if (_type.equals("3'")) return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase()); if (_type.equals("bulge")) return _vp.getRNA().findNonPairedBaseGroup(_vp.getNearestBase()); if (_type.equals("all")) return _vp.getRNA().findAll(); return new ArrayList(); } private boolean optionLoop() { return colorBases(); } private boolean optionBase() { if (_type.equals("baseChar")) { _vp.getVARNAUI().UISetBaseCharacter(); return true; } else { return colorBases(); } } private boolean optionBasePair() { if (_type.equals("basepair")) { _vp.getVARNAUI().UIEditBasePair(); return true; } else if (_type.equals("bpcolor")) { _vp.getVARNAUI().UIColorBasePair(); return true; } else if (_type.equals("thickness")) { _vp.getVARNAUI().UIThicknessBasePair(); return true; } return false; } private boolean optionView() { if (_type.equals("background")) { _vp.getVARNAUI().UISetBackground(); } else if (_type.equals("shownc")) { _vp.getVARNAUI().UIToggleShowNCBP(); } else if (_type.equals("showbackbone")) { _vp.getVARNAUI().UIToggleDrawBackbone(); } else if (_type.equals("shownp")) { _vp.getVARNAUI().UIToggleShowNonPlanar(); } else if (_type.equals("spaceBetweenBases")) { _vp.getVARNAUI().UISetSpaceBetweenBases(); } else if (_type.equals("bpheightincrement")) { _vp.getVARNAUI().UISetBPHeightIncrement(); } else if (_type.equals("borderSize")) { _vp.getVARNAUI().UISetBorder(); } else if (_type.startsWith("zoom")) { if (_type.equals("zoom")) { _vp.getVARNAUI().UICustomZoom(); } else { String factor = _type.substring("zoom".length()); double pc = Integer.parseInt(factor); pc /= 100.0; _vp.setZoom(new Double(pc)); _vp.repaint(); } } else if (_type.equals("rotation")) { _vp.getVARNAUI().UIGlobalRotation(); } else if (_type.equals("rescale")) { _vp.getVARNAUI().UIGlobalRescale(); } else return false; return true; } private boolean optionTitle() { if (_type.equals("titleDisplay")) { _vp.getVARNAUI().UISetTitleFont(); } else if (_type.equals("setTitle")) { _vp.getVARNAUI().UISetTitle(); } else if (_type.equals("titleColor")) { _vp.getVARNAUI().UISetTitleColor(); } else return false; return true; } private boolean optionColorMap() { if (_type.equals("toggleshowcolormap")) { _vp.getVARNAUI().UIToggleColorMap(); } else if (_type.equals("colormapcaption")) { _vp.getVARNAUI().UISetColorMapCaption(); } else if (_type.equals("colormapstyle")) { _vp.getVARNAUI().UISetColorMapStyle(); } else if (_type.equals("colormaploadvalues")) { _vp.getVARNAUI().UILoadColorMapValues(); } else if (_type.equals("colormapvalues")) { _vp.getVARNAUI().UISetColorMapValues(); } else return false; return true; } private boolean optionRNADisplay() { // les options d'affichages generales if (_type.equals("gaspin")) { _vp.getVARNAUI().UIToggleGaspinMode(); } else if (_type.equals("backbone")) { _vp.getVARNAUI().UISetBackboneColor(); } else if (_type.equals("bonds")) { Color c = JColorChooser.showDialog(_vp, "Choose new bonds color", _vp.getBackground()); if (c != null) { _vp.setDefaultBPColor(c); _vp.repaint(); } } else if (_type.equals("basecolorforBP")) { if (_source != null) { if (_source instanceof JCheckBoxMenuItem) { JCheckBoxMenuItem check = (JCheckBoxMenuItem) _source; _vp.setUseBaseColorsForBPs(check.getState()); _vp.repaint(); } } } else if (_type.equals("bpstyle")) { _vp.getVARNAUI().UISetBPStyle(); } else if (_type.equals("specialbasecolored")) { _vp.getVARNAUI().UIToggleColorSpecialBases(); } else if (_type.equals("showwarnings")) { _vp.getVARNAUI().UIToggleShowWarnings(); } else if (_type.equals("dashbasecolored")) { _vp.getVARNAUI().UIToggleColorGapsBases(); } else if (_type.equals("numPeriod")) { _vp.getVARNAUI().UISetNumPeriod(); } else if (_type.equals("eachKind")) { if (_vp.getRNA().get_listeBases() != null) { _vp.getVARNAUI().UIBaseTypeColor(); } else { _vp.emitWarning("No base"); } } else if (_type.equals("eachCouple")) { if (_vp.getRNA().get_listeBases() != null && _vp.getRNA().get_listeBases().size() != 0) { _vp.getVARNAUI().UIBasePairTypeColor(); } else { _vp.emitWarning("No base"); } } else if (_type.equals("eachBase")) { if (_vp.getRNA().get_listeBases() != null && _vp.getRNA().get_listeBases().size() != 0) { _vp.getVARNAUI().UIBaseAllColor(); } else { _vp.emitWarning("No base"); } } else if (_type.equals("specialBasesColor")) { _vp.getVARNAUI().UIPickSpecialBasesColor(); } else if (_type.equals("dashBasesColor")) { _vp.getVARNAUI().UIPickGapsBasesColor(); } else return colorBases(); return true; } private boolean optionImport() { if (_type.equals("userInput")) { try { _vp.getVARNAUI().UIManualInput(); } catch (ParseException e1) { errorDialog(e1); } catch (ExceptionNonEqualLength e2) { errorDialog(e2); } } else if (_type.equals("file")) { try { _vp.getVARNAUI().UIFile(); } catch (ExceptionNonEqualLength e1) { errorDialog(e1); } } else if (_type.equals("print")) { _vp.getVARNAUI().UIPrint(); } else if (_type.equals("about")) { _vp.getVARNAUI().UIAbout(); } else return false; return true; } private boolean optionRedraw() { if (_type.equals("reset")) { _vp.getVARNAUI().UIReset(); } else if (_type.equals("circular")) { _vp.getVARNAUI().UICircular(); } else if (_type.equals("radiate")) { _vp.getVARNAUI().UIRadiate(); } else if (_type.equals("naview")) { _vp.getVARNAUI().UINAView(); } else if (_type.equals("varnaview")) { _vp.getVARNAUI().UIVARNAView(); } else if (_type.equals("motifview")) { _vp.getVARNAUI().UIMOTIFView(); } else if (_type.equals("line")) { _vp.getVARNAUI().UILine(); } else if (_type.equals("flat")) { _vp.getVARNAUI().UIToggleFlatExteriorLoop(); } else return false; return true; } private boolean optionExport() { if (_type.equals("saveas")) { try { _vp.getVARNAUI().UISaveAs(); } catch (ExceptionExportFailed e1) { errorDialog(e1); } catch (ExceptionPermissionDenied e1) { errorDialog(e1); } } else if (_type.equals("dbn")) { try { _vp.getVARNAUI().UISaveAsDBN(); } catch (ExceptionExportFailed e) { errorDialog(e); } catch (ExceptionPermissionDenied e) { errorDialog(e); } } else if (_type.equals("bpseq")) { try { _vp.getVARNAUI().UISaveAsBPSEQ(); } catch (ExceptionExportFailed e) { errorDialog(e); } catch (ExceptionPermissionDenied e) { errorDialog(e); } } else if (_type.equals("ct")) { try { _vp.getVARNAUI().UISaveAsCT(); } catch (ExceptionExportFailed e) { errorDialog(e); } catch (ExceptionPermissionDenied e) { errorDialog(e); } } else if (_type.equals("eps")) { try { _vp.getVARNAUI().UIExportEPS(); } catch (ExceptionWritingForbidden e1) { errorDialog(e1); } catch (ExceptionExportFailed e) { errorDialog(e); } } else if (_type.equals("xfig")) { try { _vp.getVARNAUI().UIExportXFIG(); } catch (ExceptionWritingForbidden e1) { errorDialog(e1); } catch (ExceptionExportFailed e) { errorDialog(e); } } else if (_type.equals("svg")) { try { _vp.getVARNAUI().UIExportSVG(); } catch (ExceptionWritingForbidden e1) { errorDialog(e1); } catch (ExceptionExportFailed e) { errorDialog(e); } } else if (_type.equals("jpeg")) { try { _vp.getVARNAUI().UIExportJPEG(); } catch (ExceptionJPEGEncoding e1) { errorDialog(e1); } catch (ExceptionExportFailed e1) { errorDialog(e1); } } else if (_type.equals("png")) { try { _vp.getVARNAUI().UIExportPNG(); } catch (ExceptionExportFailed e1) { errorDialog(e1); } } else return false; return true; } /** * Return the extension of a file, it means the string after the last dot of * the file name * * @param f * The file * @return null if the file name have no dot
* ext if the file name contains a dot */ public String getExtension(File f) { String s = f.getName(); return getExtension(s); } /** * Return the extension of a string, it means the string after the last dot * of the path * * @param s * The strnig o the path * @return null if the path have no dot
* ext if the path contains a dot */ public String getExtension(String s) { String ext = null; int i = s.lastIndexOf('.'); if (i > 0 && i < s.length() - 1) { ext = s.substring(i + 1).toLowerCase(); } return ext; } /** * Open an error message dialog with the exception message * * @param e1 * The Exception */ public void errorDialog(Exception e1) { if (_vp.isErrorsOn()) JOptionPane.showMessageDialog(_vp, e1.getMessage(), "VARNA Error", JOptionPane.ERROR_MESSAGE); } public void onStructureRedrawn() { // TODO Auto-generated method stub } public void onWarningEmitted(String s) { if (_vp.isErrorsOn()) JOptionPane.showMessageDialog(_vp,s, "VARNA Warning", JOptionPane.ERROR_MESSAGE); } public void onLoad(String path) { // TODO Auto-generated method stub } public void onLoaded() { // TODO Auto-generated method stub } public void onUINewStructure(VARNAConfig v, RNA r) { // TODO Auto-generated method stub } public void onZoomLevelChanged() { // TODO Auto-generated method stub } public void onTranslationChanged() { // TODO Auto-generated method stub } } fr/orsay/lri/varna/controlers/ControleurScriptParser.java0000644000000000000000000003562712337233436022773 0ustar rootrootpackage fr.orsay.lri.varna.controlers; import java.awt.Color; import java.io.StreamTokenizer; import java.io.StringReader; import java.util.ArrayList; import java.util.Hashtable; import java.util.Vector; import javax.swing.JOptionPane; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.models.rna.RNA; public class ControleurScriptParser { private static String SCRIPT_ERROR_PREFIX = "Error"; private static class Command{ Function _f; Vector _argv; public Command(Function f, Vector argv) { _f = f; _argv = argv; } }; private static abstract class Argument{ ArgumentType _t; public Argument(ArgumentType t) { _t = t; } public ArgumentType getType() { return _t; } public abstract String toString(); }; private static class NumberArgument extends Argument{ Number _val; public NumberArgument(Number val) { super(ArgumentType.NUMBER_TYPE); _val = val; } public Number getNumber() { return _val; } public String toString() { return _val.toString(); } }; private static class ColorArgument extends Argument{ Color _val; public ColorArgument(Color val) { super(ArgumentType.COLOR_TYPE); _val = val; } public Color getColor() { return _val; } public String toString() { return _val.toString(); } }; private static class BooleanArgument extends Argument{ boolean _val; public BooleanArgument(boolean val) { super(ArgumentType.BOOLEAN_TYPE); _val = val; } public boolean getBoolean() { return _val; } public String toString() { return ""+_val; } }; private static class StringArgument extends Argument{ String _val; public StringArgument(String val) { super(ArgumentType.STRING_TYPE); _val = val; } public String toString() { return _val.toString(); } }; private static class ArrayArgument extends Argument{ Vector _val; public ArrayArgument(Vector val) { super(ArgumentType.ARRAY_TYPE); _val = val; } public int getSize() { return _val.size(); } public Argument getArgument(int i) { return _val.get(i); } public String toString() { return _val.toString(); } }; private enum ArgumentType{ STRING_TYPE, NUMBER_TYPE, BOOLEAN_TYPE, ARRAY_TYPE, COLOR_TYPE }; private enum Function{ ADD_CHEM_PROB("addchemprob",new ArgumentType[] {ArgumentType.NUMBER_TYPE,ArgumentType.NUMBER_TYPE,ArgumentType.STRING_TYPE,ArgumentType.NUMBER_TYPE,ArgumentType.COLOR_TYPE,ArgumentType.BOOLEAN_TYPE}), ERASE_SEQ("eraseseq",new ArgumentType[] {}), RESET_CHEM_PROB("resetchemprob",new ArgumentType[] {}), SET_COLOR_MAP_MIN("setcolormapminvalue",new ArgumentType[]{ArgumentType.NUMBER_TYPE}), SET_COLOR_MAP_MAX("setcolormapmaxvalue",new ArgumentType[]{ArgumentType.NUMBER_TYPE}), SET_COLOR_MAP("setcolormap",new ArgumentType[]{ArgumentType.STRING_TYPE}), SET_CUSTOM_COLOR_MAP("setcustomcolormap",new ArgumentType[]{ArgumentType.ARRAY_TYPE}), SET_SEQ("setseq",new ArgumentType[]{ArgumentType.STRING_TYPE}), SET_STRUCT("setstruct",new ArgumentType[]{ArgumentType.STRING_TYPE}), SET_STRUCT_SMOOTH("setstructsmooth",new ArgumentType[] {ArgumentType.STRING_TYPE}), SET_TITLE("settitle",new ArgumentType[] {ArgumentType.STRING_TYPE}), SET_RNA("setrna",new ArgumentType[]{ArgumentType.STRING_TYPE,ArgumentType.STRING_TYPE}), SET_RNA_SMOOTH("setrnasmooth",new ArgumentType[]{ArgumentType.STRING_TYPE,ArgumentType.STRING_TYPE}), SET_SELECTION("setselection",new ArgumentType[]{ArgumentType.ARRAY_TYPE}), SET_VALUES("setvalues",new ArgumentType[]{ArgumentType.ARRAY_TYPE}), TOGGLE_SHOW_COLOR_MAP("toggleshowcolormap",new ArgumentType[]{}), REDRAW("redraw",new ArgumentType[] {ArgumentType.STRING_TYPE}), UNKNOWN("N/A",new ArgumentType[] {}); String _funName; ArgumentType[] _args; Function(String funName, ArgumentType[] args) { _funName = funName; _args = args; } ArgumentType[] getPrototype() { return this._args; } String getFunName() { return this._funName; } }; private static Hashtable _name2Fun = new Hashtable(); private static Hashtable _fun2Prot = new Hashtable(); private static void initFunctions() { if (_name2Fun.size()>0) { return; } Function[] funs = Function.values(); for(int i=0;i cmds = parseScript(cmdtxt); for(int i=0;i vals = new ArrayList(); for (int j=0;j parseArguments(StreamTokenizer st, boolean parType) throws Exception { Vector result = new Vector(); while((st.ttype!=')' && parType) || (st.ttype!=']' && !parType)) { st.nextToken(); //System.out.println(""+ (parType?"Par.":"Bra.")+" "+(char)st.ttype); switch(st.ttype) { case(StreamTokenizer.TT_NUMBER): { result.add(new NumberArgument(st.nval)); } break; case(StreamTokenizer.TT_WORD): { Color c = parseColor(st.sval); if (c!=null) { result.add(new ColorArgument(c)); } else { Boolean b = parseBoolean(st.sval); if (b!=null) { result.add(new BooleanArgument(b)); } else { result.add(new StringArgument(st.sval)); } } } break; case('"'): { result.add(new StringArgument(st.sval)); } break; case('['): { result.add(new ArrayArgument(parseArguments(st, false))); } break; case('('): { result.add(new ArrayArgument(parseArguments(st, true))); } break; case(')'): { if (parType) return result; else throw new Exception(SCRIPT_ERROR_PREFIX+": Opening "+(parType?"parenthesis":"bracket")+" matched with a closing "+(!parType?"parenthesis":"bracket")); } case(']'): { if (!parType) return result; else throw new Exception(SCRIPT_ERROR_PREFIX+": Opening "+(parType?"parenthesis":"bracket")+" matched with a closing "+(!parType?"parenthesis":"bracket")); } case(','): break; case(StreamTokenizer.TT_EOF): { throw new Exception(SCRIPT_ERROR_PREFIX+": Unmatched opening "+(parType?"parenthesis":"bracket")); } } } return result; } private static Command parseCommand(String cmd) throws Exception { int cut = cmd.indexOf("("); if (cut==-1) { throw new Exception(SCRIPT_ERROR_PREFIX+": Syntax error"); } String fun = cmd.substring(0,cut); Function f = getFunction(fun); if (f==Function.UNKNOWN) { throw new Exception(SCRIPT_ERROR_PREFIX+": Unknown function \""+fun+"\""); } StreamTokenizer st = new StreamTokenizer(new StringReader(cmd.substring(cut+1))); st.eolIsSignificant(false); st.parseNumbers(); st.quoteChar('\"'); st.ordinaryChar('='); st.ordinaryChar(','); st.ordinaryChar('['); st.ordinaryChar(']'); st.ordinaryChar('('); st.ordinaryChar(')'); st.wordChars('#', '#'); Vector argv = parseArguments(st,true); checkArgs(f,argv); Command result = new Command(f,argv); return result; } private static boolean checkArgs(Function f, Vector argv) throws Exception { ArgumentType[] argtypes = getPrototype(f); if (argtypes.length!=argv.size()) throw new Exception(SCRIPT_ERROR_PREFIX+": Wrong number of argument for function \""+f+"\"."); for (int i=0;i parseScript(String cmd) throws Exception { initFunctions(); Vector cmds = new Vector(); String[] data = cmd.split(";"); for (int i=0;i> clusterIndices(int numIndices, int[] mappedIndices) throws MappingException { int[] indices = new int[numIndices]; for (int i = 0; i < numIndices; i++) { indices[i] = i; } return clusterIndices(indices, mappedIndices); } /** * Builds and returns an interval array, alternating unmatched regions and * matched indices. Namely, returns a vector of vector such that the vectors * found at odd positions contain those indices that are NOT associated with * any other base in the current mapping. On the other hand, vectors found * at even positions contain only one mapped index.
* Ex: If indices=[1,2,3,4,5] and mappedIndices= * [2,5] then the function will return * [[1],[2],[3,4],[5],[]]. * * @param indices * The total list of indices * @param mappedIndices * Matched indices, should be a subset of indices * @return A clustered array * @throws MappingException * If one of the parameters is an empty array */ private Vector> clusterIndices(int[] indices, int[] mappedIndices) throws MappingException { if ((mappedIndices.length == 0) || (indices.length == 0)) { throw new MappingException( "Mapping Error: Cannot cluster indices in an empty mapping"); } Vector> res = new Vector>(); Arrays.sort(indices); Arrays.sort(mappedIndices); int i, j = 0, k; Vector tmp = new Vector(); for (i = 0; (i < indices.length) && (j < mappedIndices.length); i++) { if (indices[i] == mappedIndices[j]) { res.add(tmp); tmp = new Vector(); tmp.add(indices[i]); res.add(tmp); tmp = new Vector(); j++; } else { tmp.add(indices[i]); } } k = i; for (i = k; (i < indices.length); i++) { tmp.add(indices[i]); } res.add(tmp); return res; } public void run() { while (true) { TargetsHolder d = _d.get(); _running = true; try{ nextTarget(d.target,d.conf,d.mapping); } catch(Exception e) { System.err.println(e); e.printStackTrace(); } _running = false; } } /** * Compute the centroid of the RNA bases that have their indexes * in the given array. */ private static Point2D.Double computeCentroid(ArrayList rnaBases, int[] indexes) { double centroidX = 0, centroidY = 0; for (int i=0; i= maxnumsteps) { // If things go bad (for example f''(x) keeps being 0) // we need to give up after what we consider to be too many steps. // In practice this can happen only in pathological cases // like f being constant, which is very unlikely. result = x_n_plus_1; break; } x_n = x_n_plus_1; } // We now have either found the min or the max at x = result. // If we have the max at x we know the min is at x+pi. if (f(result + Math.PI) < f(result)) { result = result + Math.PI; } return result; } } /** * We suppose we have two lists of points. The coordinates of the first * list of points are X1 and Y1, and X2 and Y2 for the second list. * We suppose that the centroids of [X1,Y1] and [X2,Y2] are both (0,0). * This function computes the rotation to apply to the second set of * points such that the RMSD (Root mean square deviation) between them * is minimum. The returned angle is in radians. */ private static double minimizeRotateRMSD(double[] X1, double[] Y1, double[] X2, double[] Y2) { MinimizeRMSD minimizer = new MinimizeRMSD(X1, Y1, X2, Y2); return minimizer.computeOptimalTheta(); } /** * Move rna2 using a rotation so that it would move as little as possible * (in the sense that we minimize the RMSD) when transforming * it to rna1 using the given mapping. */ public static void moveNearOtherRNA(RNA rna1, RNA rna2, Mapping mapping) { int[] rna1MappedElems = mapping.getSourceElems(); int[] rna2MappedElems = mapping.getTargetElems(); ArrayList rna1Bases = rna1.get_listeBases(); ArrayList rna2Bases = rna2.get_listeBases(); int n = rna1MappedElems.length; // If there is less than 2 points, it is useless to rotate the RNA. if (n < 2) return; // We can now assume that n >= 2. // Compute the centroids of both RNAs Point2D.Double rna1MappedElemsCentroid = computeCentroid(rna1Bases, rna1MappedElems); Point2D.Double rna2MappedElemsCentroid = computeCentroid(rna2Bases, rna2MappedElems); // Compute the optimal rotation // We first compute coordinates for both RNAs, changing the origins // to be the centroids. double[] X1 = new double[rna1MappedElems.length]; double[] Y1 = new double[rna1MappedElems.length]; double[] X2 = new double[rna2MappedElems.length]; double[] Y2 = new double[rna2MappedElems.length]; for (int i=0; i currBases = current.get_listeBases(); ArrayList destBases = _target.get_listeBases(); Vector> intArrSource = new Vector>(); Vector> intArrTarget = new Vector>(); // Building interval arrays intArrSource = clusterIndices(currBases.size(), _mapping .getSourceElems()); intArrTarget = clusterIndices(destBases.size(), _mapping .getTargetElems()); // Duplicating source and target coordinates Point2D.Double[] initPosSource = new Point2D.Double[currBases .size()]; Point2D.Double[] finalPosTarget = new Point2D.Double[destBases .size()]; for (int i = 0; i < currBases.size(); i++) { Point2D tmp = currBases.get(i).getCoords(); initPosSource[i] = new Point2D.Double(tmp.getX(), tmp.getY()); } for (int i = 0; i < destBases.size(); i++) { Point2D tmp = destBases.get(i).getCoords(); finalPosTarget[i] = new Point2D.Double(tmp.getX(), tmp.getY()); } /** * Assigning final (Source) and initial (Target) coordinates */ Point2D.Double[] finalPosSource = new Point2D.Double[initPosSource.length]; Point2D.Double[] initPosTarget = new Point2D.Double[finalPosTarget.length]; // Final position of source model for (int i = 0; i < finalPosSource.length; i++) { if (_mapping.getPartner(i) != Mapping.UNKNOWN) { Point2D dest; dest = finalPosTarget[_mapping.getPartner(i)]; finalPosSource[i] = new Point2D.Double(dest.getX(), dest .getY()); } } for (int i = 0; i < intArrSource.size(); i += 2) { int matchedNeighborLeft, matchedNeighborRight; if (i == 0) { matchedNeighborLeft = intArrSource.get(1).get(0); matchedNeighborRight = intArrSource.get(1).get(0); } else if (i == intArrSource.size() - 1) { matchedNeighborLeft = intArrSource.get( intArrSource.size() - 2).get(0); matchedNeighborRight = intArrSource.get( intArrSource.size() - 2).get(0); } else { matchedNeighborLeft = intArrSource.get(i - 1).get(0); matchedNeighborRight = intArrSource.get(i + 1).get(0); } Vector v = intArrSource.get(i); for (int j = 0; j < v.size(); j++) { int index = v.get(j); finalPosSource[index] = computeDestination( initPosSource[matchedNeighborLeft], initPosSource[matchedNeighborRight], initPosSource[index], j + 1, v.size() + 1, finalPosSource[matchedNeighborLeft], finalPosSource[matchedNeighborRight]); } } for (int i = 0; i < initPosTarget.length; i++) { if (_mapping.getAncestor(i) != Mapping.UNKNOWN) { Point2D dest; dest = initPosSource[_mapping.getAncestor(i)]; initPosTarget[i] = new Point2D.Double(dest.getX(), dest.getY()); } } for (int i = 0; i < intArrTarget.size(); i += 2) { int matchedNeighborLeft, matchedNeighborRight; if (i == 0) { matchedNeighborLeft = intArrTarget.get(1).get(0); matchedNeighborRight = intArrTarget.get(1).get(0); } else if (i == intArrTarget.size() - 1) { matchedNeighborLeft = intArrTarget.get( intArrTarget.size() - 2).get(0); matchedNeighborRight = intArrTarget.get( intArrTarget.size() - 2).get(0); } else { matchedNeighborLeft = intArrTarget.get(i - 1).get(0); matchedNeighborRight = intArrTarget.get(i + 1).get(0); } Vector v = intArrTarget.get(i); for (int j = 0; j < v.size(); j++) { int index = v.get(j); initPosTarget[index] = computeDestination( finalPosTarget[matchedNeighborLeft], finalPosTarget[matchedNeighborRight], finalPosTarget[index], j + 1, v.size() + 1, initPosTarget[matchedNeighborLeft], initPosTarget[matchedNeighborRight]); } } boolean firstHalf = true; for (int i = 0; i < _numSteps; i++) { if (i == _numSteps / 2) { _vpn.showRNA(_target); current = _target; currBases = current.get_listeBases(); firstHalf = false; if (_conf!=null) {_vpn.setConfig(_conf);} for (int j = 0; j < initPosSource.length; j++) { source.setCoord(j, initPosSource[j]); } } for (int j = 0; j < currBases.size(); j++) { ModeleBase m = currBases.get(j); Point2D mpc, mnc; if (firstHalf) { mpc = initPosSource[j]; mnc = finalPosSource[j]; } else { mpc = initPosTarget[j]; mnc = finalPosTarget[j]; } m.setCoords(new Point2D.Double(((_numSteps - 1 - i) * mpc.getX() + (i) * mnc.getX()) / (_numSteps - 1), ((_numSteps - 1 - i) * mpc.getY() + i * mnc.getY()) / (_numSteps - 1))); } _vpn.repaint(); sleep(_timeDelay); } } } catch (InterruptedException e) { e.printStackTrace(); } catch (MappingException e) { e.printStackTrace(); }catch (Exception e) { e.printStackTrace(); } _vpn.showRNA(_target); _vpn.repaint(); } private class TargetsHolder { public RNA target; public VARNAConfig conf; public Mapping mapping; public TargetsHolder(RNA t, VARNAConfig c, Mapping m) { target = t; conf = c; mapping = m; } } private class Targets { LinkedList _d = new LinkedList(); public synchronized void add(TargetsHolder d) { _d.addLast(d); notify(); } public synchronized TargetsHolder get() { while(_d.size()==0) { try { wait(); } catch (InterruptedException e) { e.printStackTrace(); } } TargetsHolder x = _d.getLast(); _d.clear(); return x; } } } fr/orsay/lri/varna/controlers/ControleurTableAnnotations.java0000644000000000000000000001175211620715272023605 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import javax.swing.JTable; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.views.VueAnnotation; import fr.orsay.lri.varna.views.VueChemProbAnnotation; import fr.orsay.lri.varna.views.VueHighlightRegionEdit; /** * Mouse action and motion listener for AnnotationTableModel * * @author Darty@lri.fr * */ public class ControleurTableAnnotations implements MouseListener, MouseMotionListener { public static final int REMOVE = 0, EDIT = 1; private JTable _table; private VARNAPanel _vp; private int _type; /** * * @param table * @param vp * @param type * : REMOVE = 0, EDIT = 1 */ public ControleurTableAnnotations(JTable table, VARNAPanel vp, int type) { _table = table; _vp = vp; _type = type; } public void mouseClicked(MouseEvent arg0) { switch (_type) { case EDIT: edit(); break; case REMOVE: remove(); break; default: break; } } /** * if remove case */ private void remove() { _vp.set_selectedAnnotation(null); Object o = _table.getValueAt(_table.getSelectedRow(), 0); if (o instanceof TextAnnotation) { if (!_vp.removeAnnotation((TextAnnotation) o)) _vp.errorDialog(new Exception("Impossible de supprimer")); _table.setValueAt("Deleted!", _table.getSelectedRow(), 0); } else if (o instanceof ChemProbAnnotation) { _vp.getRNA().removeChemProbAnnotation((ChemProbAnnotation) o); _table.setValueAt("Deleted!", _table.getSelectedRow(), 0); } else if (o instanceof HighlightRegionAnnotation) { _vp.getRNA().removeHighlightRegion((HighlightRegionAnnotation) o); _table.setValueAt("Deleted!", _table.getSelectedRow(), 0); } _vp.repaint(); } /** * if edit case */ private void edit() { Object o = _table.getValueAt(_table .getSelectedRow(), 0); if (o instanceof TextAnnotation) { TextAnnotation textAnnot = (TextAnnotation) o; VueAnnotation vueAnnotation; vueAnnotation = new VueAnnotation(_vp, textAnnot, false); vueAnnotation.show(); }else if (o instanceof HighlightRegionAnnotation) { HighlightRegionAnnotation annot = (HighlightRegionAnnotation) o; HighlightRegionAnnotation an = annot.clone(); VueHighlightRegionEdit vueAnnotation = new VueHighlightRegionEdit(_vp,annot); if (!vueAnnotation.show()) { annot.setBases(an.getBases()); annot.setFillColor(an.getFillColor()); annot.setOutlineColor(an.getOutlineColor()); annot.setRadius(an.getRadius()); } }else if (o instanceof ChemProbAnnotation) { ChemProbAnnotation annot = (ChemProbAnnotation) o; ChemProbAnnotation an = annot.clone(); VueChemProbAnnotation vueAnnotation = new VueChemProbAnnotation(_vp,annot); if (!vueAnnotation.show()) { annot.setColor(an.getColor()); annot.setIntensity(an.getIntensity()); annot.setType(an.getType()); annot.setOut(an.isOut()); } } } public void mouseEntered(MouseEvent arg0) { } public void mouseExited(MouseEvent arg0) { _vp.set_selectedAnnotation(null); _vp.repaint(); } public void mousePressed(MouseEvent arg0) { } public void mouseReleased(MouseEvent arg0) { } public void mouseDragged(MouseEvent arg0) { } /** * update selected annotation */ public void mouseMoved(MouseEvent arg0) { if (_table.rowAtPoint(arg0.getPoint()) < 0) return; Object o = _table.getValueAt(_table.rowAtPoint(arg0.getPoint()), 0); if (o.getClass().equals(TextAnnotation.class) && o != _vp.get_selectedAnnotation()) { _vp.set_selectedAnnotation((TextAnnotation) o); _vp.repaint(); } } } fr/orsay/lri/varna/controlers/ControleurSpaceBetweenBases.java0000644000000000000000000000302112050247762023653 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.views.VueSpaceBetweenBases; public class ControleurSpaceBetweenBases implements ChangeListener { private VueSpaceBetweenBases _vsbb; public ControleurSpaceBetweenBases(VueSpaceBetweenBases vsbb) { _vsbb = vsbb; } public void stateChanged(ChangeEvent e) { _vsbb.get_vp().setSpaceBetweenBases(_vsbb.getSpace()); _vsbb.get_vp().drawRNA(); _vsbb.get_vp().repaint(); } } fr/orsay/lri/varna/controlers/ControleurMolette.java0000644000000000000000000000333512243424014021740 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.controlers; import java.awt.Point; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import fr.orsay.lri.varna.VARNAPanel; /** * Listener which control the zoom-in and zoom-out with mouse wheel. * * @author DARTY Kevin */ public class ControleurMolette implements MouseWheelListener { private VARNAPanel _vp; public ControleurMolette(VARNAPanel vuep) { _vp = vuep; } public void mouseWheelMoved(MouseWheelEvent e) { if (_vp.isFocusOwner()) { // Roulement vers le haut => zoom in if (e.getWheelRotation() == -1) { _vp.getVARNAUI().UIZoomIn(); } // Roulement vers le bas => zoom out else { _vp.getVARNAUI().UIZoomOut(); } } } } fr/orsay/lri/varna/VARNAPanel.java0000644000000000000000000045231512464223262015724 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2012 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.9. VARNA version 3.9 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.9 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ /* GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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END OF TERMS AND CONDITIONS */ package fr.orsay.lri.varna; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Point; import java.awt.Rectangle; import java.awt.RenderingHints; import java.awt.Shape; import java.awt.Stroke; import java.awt.event.MouseEvent; import java.awt.geom.AffineTransform; import java.awt.geom.GeneralPath; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.ObjectInputStream; import java.io.ObjectOutputStream; import java.io.PrintWriter; import java.io.Reader; import java.text.NumberFormat; import java.util.ArrayList; import java.util.Collection; import java.util.Hashtable; import java.util.Set; import java.util.zip.ZipEntry; import java.util.zip.ZipInputStream; import java.util.zip.ZipOutputStream; import javax.print.attribute.HashPrintRequestAttributeSet; import javax.print.attribute.PrintRequestAttributeSet; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollBar; import javax.swing.undo.UndoManager; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import javax.xml.parsers.SAXParser; import javax.xml.parsers.SAXParserFactory; import javax.xml.transform.OutputKeys; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerConfigurationException; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.sax.SAXTransformerFactory; import javax.xml.transform.sax.TransformerHandler; import javax.xml.transform.stream.StreamResult; import org.w3c.dom.DOMImplementation; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.helpers.AttributesImpl; import fr.orsay.lri.varna.controlers.ControleurBlinkingThread; import fr.orsay.lri.varna.controlers.ControleurClicMovement; import fr.orsay.lri.varna.controlers.ControleurDraggedMolette; import fr.orsay.lri.varna.controlers.ControleurInterpolator; import fr.orsay.lri.varna.controlers.ControleurMolette; import fr.orsay.lri.varna.controlers.ControleurVARNAPanelKeys; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener; import fr.orsay.lri.varna.models.BaseList; import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.models.export.SwingGraphics; import fr.orsay.lri.varna.models.export.VueVARNAGraphics; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.ModeleBackbone; import fr.orsay.lri.varna.models.rna.ModeleBackboneElement.BackboneType; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleBasesComparison; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.RNA; import fr.orsay.lri.varna.utils.RNAMLParser; import fr.orsay.lri.varna.utils.VARNASessionParser; import fr.orsay.lri.varna.views.VueMenu; import fr.orsay.lri.varna.views.VueUI; /** * The RNA 2D Panel is a lightweight component that allows for an automatic * basic drawing of an RNA secondary structures. The drawing algorithms do not * ensure a non-overlapping drawing of helices, thus it is possible to "spin the * helices" through a click-and-drag approach. A typical usage of the class from * within the constructor of a JFrame would be the following:
* *   VARNAPanel _rna = new VARNAPanel("CCCCAUAUGGGGACC","((((....))))...");
*   this.getContentPane().add(_rna); * * * @version 3.4 * @author Yann Ponty & Kevin Darty * */ public class VARNAPanel extends JPanel { /** * */ private static final long serialVersionUID = 8194421570308956001L; private RNA _RNA = new RNA(); private boolean _debug = false; private VARNAConfig _conf = new VARNAConfig(); private ArrayList _VARNAListeners = new ArrayList(); private ArrayList _selectionListeners = new ArrayList(); private ArrayList _RNAListeners = new ArrayList(); private ArrayList _basesListeners = new ArrayList(); UndoManager _manager; // private boolean _foldMode = true; private Point2D.Double[] _realCoords = new Point2D.Double[0]; private Point2D.Double[] _realCenters = new Point2D.Double[0]; private double _scaleFactor = 1.0; private Point2D.Double _offsetPanel = new Point2D.Double(); private Point2D.Double _offsetRNA = new Point2D.Double(); private double _offX; private double _offY; private ControleurBlinkingThread _blink; private BaseList _selectedBases = new BaseList("selection"); private ArrayList _backupSelection = new ArrayList(); private Integer _nearestBase = null; private Point2D.Double _lastSelectedCoord = new Point2D.Double(0.0, 0.0); private Point2D.Double _linkOrigin = null; private Point2D.Double _linkDestination = null; private Rectangle _selectionRectangle = null; private boolean _highlightAnnotation = false; private int _titleHeight; private Dimension _border = new Dimension(0, 0); private boolean _drawBBox = false; private boolean _drawBorder = false; // private Point _positionRelativeSouris; private Point _translation; private boolean _horsCadre; private boolean _premierAffichage; private ControleurInterpolator _interpolator; /** * If comparison mode is TRUE (ON), then the application will be used to * display a super-structure resulting on an RNA secondary structure * comparison. Else, the application is used by default. */ private VueMenu _popup = new VueMenu(this); private VueUI _UI = new VueUI(this); private TextAnnotation _selectedAnnotation; /** * Creates an RNA 2D panel with initially displays the empty structure. * * @throws ExceptionNonEqualLength * */ public VARNAPanel() { init(); drawRNA(); } /** * Creates an RNA 2D panel, and creates and displays an RNA coupled with its * secondary structure formatted as a well-balanced parenthesis with dots * word (DBN format). * * @param seq * The raw nucleotide sequence * @param str * The secondary structure in DBN format * @throws ExceptionNonEqualLength */ public VARNAPanel(String seq, String str) throws ExceptionNonEqualLength { this(seq, str, RNA.DRAW_MODE_RADIATE); } /** * Creates a VARNAPanel instance, and creates and displays an RNA coupled * with its secondary structure formatted as a well-balanced parenthesis * with dots word (DBN format). Allows the user to choose the drawing * algorithm to be used. * * @param seq * The raw nucleotide sequence * @param str * The secondary structure in DBN format * @param drawMode * The drawing mode * @throws ExceptionNonEqualLength * @see RNA#DRAW_MODE_RADIATE * @see RNA#DRAW_MODE_CIRCULAR * @see RNA#DRAW_MODE_NAVIEW */ public VARNAPanel(String seq, String str, int drawMode) throws ExceptionNonEqualLength { this(seq, str, drawMode, ""); } public VARNAPanel(Reader r) throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax { this(r, RNA.DRAW_MODE_RADIATE); } public VARNAPanel(Reader r, int drawMode) throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax { this(r, drawMode, ""); } public VARNAPanel(Reader r, int drawMode, String title) throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax { init(); drawRNA(r, drawMode); setTitle(title); } public void setOriginLink(Point2D.Double p) { _linkOrigin = (p); } public void setDestinationLink(Point2D.Double p) { _linkDestination = (p); } public void removeLink() { _linkOrigin = null; _linkDestination = null; } /** * Creates a VARNAPanel instance, and displays an RNA. * * @param r * The RNA to be displayed within this panel */ public VARNAPanel(RNA r) { showRNA(r); init(); } /** * Creates a VARNAPanel instance, and creates and displays an RNA coupled * with its secondary structure formatted as a well-balanced parenthesis * with dots word (DBN format). Allows the user to choose the drawing * algorithm to be used. Additionally, sets the panel's title. * * @param seq * The raw nucleotide sequence * @param str * The secondary structure in DBN format * @param drawMode * The drawing mode * @param title * The panel title * @throws ExceptionNonEqualLength * @see RNA#DRAW_MODE_CIRCULAR * @see RNA#DRAW_MODE_RADIATE * @see RNA#DRAW_MODE_NAVIEW */ public VARNAPanel(String seq, String str, int drawMode, String title) throws ExceptionNonEqualLength { drawRNA(seq, str, drawMode); init(); setTitle(title); // VARNASecDraw._vp = this; } public VARNAPanel(String seq1, String struct1, String seq2, String struct2, int drawMode, String title) { _conf._comparisonMode = true; drawRNA(seq1, struct1, seq2, struct2, drawMode); init(); setTitle(title); } private void init() { setBackground(VARNAConfig.DEFAULT_BACKGROUND_COLOR); _manager = new UndoManager(); _manager.setLimit(10000); _UI.addUndoableEditListener(_manager); _blink = new ControleurBlinkingThread(this, ControleurBlinkingThread.DEFAULT_FREQUENCY, 0, 1.0, 0.0, 0.2); _blink.start(); _premierAffichage = true; _translation = new Point(0, 0); _horsCadre = false; this.setFont(_conf._fontBasesGeneral); // ajout des controleurs au VARNAPanel ControleurClicMovement controleurClicMovement = new ControleurClicMovement( this); this.addMouseListener(controleurClicMovement); this.addMouseMotionListener(controleurClicMovement); this.addMouseWheelListener(new ControleurMolette(this)); ControleurDraggedMolette ctrlDraggedMolette = new ControleurDraggedMolette( this); this.addMouseMotionListener(ctrlDraggedMolette); this.addMouseListener(ctrlDraggedMolette); ControleurVARNAPanelKeys ctrlKey = new ControleurVARNAPanelKeys(this); this.addKeyListener(ctrlKey); this.addFocusListener(ctrlKey); _interpolator = new ControleurInterpolator(this); _interpolator.start(); } public void undo() { if (_manager.canUndo()) _manager.undo(); } public void redo() { if (_manager.canRedo()) _manager.redo(); } /** * Sets the new style of the title font. * * @param newStyle * An int that describes the new font style ("PLAIN","BOLD", * "BOLDITALIC", or "ITALIC") */ public void setTitleFontStyle(int newStyle) { _conf._titleFont = _conf._titleFont.deriveFont(newStyle); updateTitleHeight(); } /** * Sets the new size of the title font. * * @param newSize * The new size of the title font */ public void setTitleFontSize(float newSize) { //System.err.println("Applying title size "+newSize); _conf._titleFont = _conf._titleFont.deriveFont(newSize); updateTitleHeight(); } /** * Sets the new font family to be used for the title. Available fonts are * system-specific, yet it seems that "Arial", "Dialog", and "MonoSpaced" * are almost always available. * * @param newFamily * New font family used for the title */ public void setTitleFontFamily(String newFamily) { _conf._titleFont = new Font(newFamily, _conf._titleFont.getStyle(), _conf._titleFont.getSize()); updateTitleHeight(); } /** * Sets the color to be used for the title. * * @param newColor * A color used to draw the title */ public void setTitleFontColor(Color newColor) { _conf._titleColor = newColor; updateTitleHeight(); } /** * Sets the font size for displaying bases * * @param size * Font size for base caption */ public void setBaseFontSize(Float size) { _conf._fontBasesGeneral = _conf._fontBasesGeneral.deriveFont(size); } /** * Sets the font size for displaying base numbers * * @param size * Font size for base caption */ public void setNumbersFontSize(Float size) { _conf._numbersFont = _conf._numbersFont.deriveFont(size); } /** * Sets the font style for displaying bases * * @param style * An int that describes the new font style ("PLAIN","BOLD", * "BOLDITALIC", or "ITALIC") */ public void setBaseFontStyle(int style) { _conf._fontBasesGeneral = _conf._fontBasesGeneral.deriveFont(style); } private void updateTitleHeight() { if (!getTitle().equals("")) { _titleHeight = (int) (_conf._titleFont.getSize() * 1.5); } else { _titleHeight = 0; } if (Math.abs(this.getZoom() - 1) < .02) { _translation.y = (int) (-getTitleHeight() / 2.0); } } /** * Sets the panel's title, giving a short description of the RNA secondary * structure. * * @param title * The new title */ public void setTitle(String title) { _RNA.setName(title); updateTitleHeight(); } /** * Sets the distance between consecutive base numbers. Please notice that : *
    *
  • The first and last base are always numbered
    • *
  • The numbering is based on the base numbers, not on the indices. So * base numbers may appear more frequently than expected if bases are * skipped
    • *
  • The periodicity is measured starting from 0. This means that for a * period of 10 and bases numbered from 1 to 52, the base numbers * [1,10,20,30,40,50,52] will be drawn.
    • *
* * @param n * New numbering period */ public void setNumPeriod(int n) { _conf._numPeriod = n; } /** * Returns the current numbering period. Please notice that : *
    *
  • The first and last base are always numbered
    • *
  • The numbering is based on the base numbers, not on the indices. So * base numbers may appear more frequently than expected if bases are * skipped
    • *
  • The periodicity is measured starting from 0. This means that for a * period of 10 and bases numbered from 1 to 52, the base numbers * [1,10,20,30,40,50,52] will be drawn.
    • *
* * @return Current numbering period */ public int getNumPeriod() { return _conf._numPeriod; } private void setScaleFactor(double d) { _scaleFactor = d; } private double getScaleFactor() { return _scaleFactor; } private void setAutoFit(boolean fit) { _conf._autoFit = fit; repaint(); } public void lockScrolling() { setAutoFit(false); setAutoCenter(false); } public void unlockScrolling() { setAutoFit(true); setAutoCenter(true); } private void drawStringOutline(VueVARNAGraphics g2D, String res, double x, double y, double margin) { Dimension d = g2D.getStringDimension(res); x -= (double) d.width / 2.0; y += (double) d.height / 2.0; g2D.setColor(Color.GRAY); g2D.setSelectionStroke(); g2D.drawRect((x - margin), (y - d.height - margin), (d.width + 2.0 * margin), (d.height + 2.0 * margin)); } private void drawSymbol(VueVARNAGraphics g2D, double posx, double posy, double normx, double normy, double radius, boolean isCIS, ModeleBP.Edge e) { Color bck = g2D.getColor(); switch (e) { case WC: if (isCIS) { g2D.setColor(bck); g2D.fillCircle((posx - (radius) / 2.0), (posy - (radius) / 2.0), radius); g2D.drawCircle((posx - (radius) / 2.0), (posy - (radius) / 2.0), radius); } else { g2D.setColor(Color.white); g2D.fillCircle(posx - (radius) / 2.0, (posy - (radius) / 2.0), (radius)); g2D.setColor(bck); g2D.drawCircle((posx - (radius) / 2.0), (posy - (radius) / 2.0), (radius)); } break; case HOOGSTEEN: { GeneralPath p2 = new GeneralPath(); radius /= 1.05; p2.moveTo((float) (posx - radius * normx / 2.0 - radius * normy / 2.0), (float) (posy - radius * normy / 2.0 + radius * normx / 2.0)); p2.lineTo((float) (posx + radius * normx / 2.0 - radius * normy / 2.0), (float) (posy + radius * normy / 2.0 + radius * normx / 2.0)); p2.lineTo((float) (posx + radius * normx / 2.0 + radius * normy / 2.0), (float) (posy + radius * normy / 2.0 - radius * normx / 2.0)); p2.lineTo((float) (posx - radius * normx / 2.0 + radius * normy / 2.0), (float) (posy - radius * normy / 2.0 - radius * normx / 2.0)); p2.closePath(); if (isCIS) { g2D.setColor(bck); g2D.fill(p2); g2D.draw(p2); } else { g2D.setColor(Color.white); g2D.fill(p2); g2D.setColor(bck); g2D.draw(p2); } } break; case SUGAR: { double ix = radius * normx / 2.0; double iy = radius * normy / 2.0; double jx = radius * normy / 2.0; double jy = -radius * normx / 2.0; GeneralPath p2 = new GeneralPath(); p2.moveTo((float) (posx - ix + jx), (float) (posy - iy + jy)); p2.lineTo((float) (posx + ix + jx), (float) (posy + iy + jy)); p2.lineTo((float) (posx - jx), (float) (posy - jy)); p2.closePath(); if (isCIS) { g2D.setColor(bck); g2D.fill(p2); g2D.draw(p2); } else { g2D.setColor(Color.white); g2D.fill(p2); g2D.setColor(bck); g2D.draw(p2); } } break; } g2D.setColor(bck); } private void drawBasePairArc(VueVARNAGraphics g2D, int i, int j, Point2D.Double orig, Point2D.Double dest, double scaleFactor, ModeleBP style, double newRadius) { double distance, coef; if (j - i == 1) coef = getBPHeightIncrement() * 1.75; else coef = getBPHeightIncrement(); distance = dest.x - orig.x; switch (_conf._mainBPStyle) { case LW: { double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0) * scaleFactor; if (style.isCanonical()) { if (style.isCanonicalGC()) { if ((orig.x != dest.x) || (orig.y != dest.y)) { g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance - scaleFactor * _RNA.BASE_RADIUS / 3.0), (distance * coef - scaleFactor * _RNA.BASE_RADIUS / 3.0), 0, 180); g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance + scaleFactor * _RNA.BASE_RADIUS / 3.0), (distance * coef + scaleFactor * _RNA.BASE_RADIUS / 3.0), 0, 180); } } else if (style.isCanonicalAU()) { g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0, 180); } else if (style.isWobbleUG()) { Point2D.Double midtop = new Point2D.Double( (dest.x + orig.x) / 2., dest.y - distance * coef / 2. - scaleFactor * _RNA.BASE_RADIUS / 2.0); g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0, 180); drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle, false, ModeleBP.Edge.WC); } else { Point2D.Double midtop = new Point2D.Double( (dest.x + orig.x) / 2., dest.y - distance * coef / 2. - scaleFactor * _RNA.BASE_RADIUS / 2.0); g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0, 180); drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle, style.isCIS(), style.getEdgePartner5()); } } else { ModeleBP.Edge p1 = style.getEdgePartner5(); ModeleBP.Edge p2 = style.getEdgePartner3(); Point2D.Double midtop = new Point2D.Double( (dest.x + orig.x) / 2., dest.y - distance * coef / 2. - scaleFactor * _RNA.BASE_RADIUS / 2.0); g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0, 180); if (p1 == p2) { drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle, false, style.getEdgePartner5()); } else { drawSymbol(g2D, midtop.x - scaleFactor * _RNA.BASE_RADIUS, midtop.y, 1., 0., radiusCircle, style.isCIS(), p1); drawSymbol(g2D, midtop.x + scaleFactor * _RNA.BASE_RADIUS, midtop.y, -1., 0., radiusCircle, style.isCIS(), p2); } } } break; case LW_ALT: { double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0) * scaleFactor; double distFromBaseCenter = DISTANCE_FACT*scaleFactor; orig = new Point2D.Double(orig.x,orig.y-(distFromBaseCenter+newRadius)); dest = new Point2D.Double(dest.x,dest.y-(distFromBaseCenter+newRadius)); if (style.isCanonical()) { if (style.isCanonicalGC()) { if ((orig.x != dest.x) || (orig.y != dest.y)) { g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance - scaleFactor * _RNA.BASE_RADIUS / 3.0), (distance * coef - scaleFactor * _RNA.BASE_RADIUS / 3.0), 0, 180); g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance + scaleFactor * _RNA.BASE_RADIUS / 3.0), (distance * coef + scaleFactor * _RNA.BASE_RADIUS / 3.0), 0, 180); } } else if (style.isCanonicalAU()) { g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0, 180); } } else { ModeleBP.Edge p1 = style.getEdgePartner5(); ModeleBP.Edge p2 = style.getEdgePartner3(); Point2D.Double midtop = new Point2D.Double( (dest.x + orig.x) / 2., dest.y - distance * coef / 2. - scaleFactor * _RNA.BASE_RADIUS / 2.0); g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0, 180); drawSymbol(g2D, orig.x, orig.y-radiusCircle*.95, 1., 0., radiusCircle, style.isCIS(), p1); drawSymbol(g2D, dest.x, dest.y-radiusCircle*.95, -1., 0., radiusCircle, style.isCIS(), p2); } } break; default: g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0, 180); break; } } public static double DISTANCE_FACT = 2.; private void drawBasePair(VueVARNAGraphics g2D, Point2D.Double orig, Point2D.Double dest, ModeleBP style, double newRadius, double scaleFactor) { double dx = dest.x - orig.x; double dy = dest.y - orig.y; double dist = Math.sqrt((dest.x - orig.x) * (dest.x - orig.x) + (dest.y - orig.y) * (dest.y - orig.y)); dx /= dist; dy /= dist; double nx = -dy; double ny = dx; orig = new Point2D.Double(orig.x + newRadius * dx, orig.y + newRadius * dy); dest = new Point2D.Double(dest.x - newRadius * dx, dest.y - newRadius * dy); switch (_conf._mainBPStyle) { case LW: { double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0) * scaleFactor; if (style.isCanonical()) { if (style.isCanonicalGC()) { if ((orig.x != dest.x) || (orig.y != dest.y)) { nx *= scaleFactor * _RNA.BASE_RADIUS / 4.0; ny *= scaleFactor * _RNA.BASE_RADIUS / 4.0; g2D.drawLine((orig.x + nx), (orig.y + ny), (dest.x + nx), (dest.y + ny)); g2D.drawLine((orig.x - nx), (orig.y - ny), (dest.x - nx), (dest.y - ny)); } } else if (style.isCanonicalAU()) { g2D.drawLine(orig.x, orig.y, dest.x, dest.y); } else if (style.isWobbleUG()) { double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; g2D.drawLine(orig.x, orig.y, dest.x, dest.y); drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, false, ModeleBP.Edge.WC); } else { double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; g2D.drawLine(orig.x, orig.y, dest.x, dest.y); drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(), style.getEdgePartner5()); } } else { ModeleBP.Edge p1 = style.getEdgePartner5(); ModeleBP.Edge p2 = style.getEdgePartner3(); double cx = (dest.x + orig.x) / 2.0; double cy = (dest.y + orig.y) / 2.0; g2D.drawLine(orig.x, orig.y, dest.x, dest.y); if (p1 == p2) { drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(), p1); } else { double vdx = (dest.x - orig.x); double vdy = (dest.y - orig.y); vdx /= 6.0; vdy /= 6.0; drawSymbol(g2D, cx + vdx, cy + vdy, -nx, -ny, radiusCircle, style.isCIS(), p2); drawSymbol(g2D, cx - vdx, cy - vdy, nx, ny, radiusCircle, style.isCIS(), p1); } } } break; case LW_ALT: { double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0) * scaleFactor; double distFromBaseCenter = DISTANCE_FACT*scaleFactor; Point2D.Double norig = new Point2D.Double(orig.x+(distFromBaseCenter+.5*newRadius)*dx,orig.y+(distFromBaseCenter+.5*newRadius)*dy); Point2D.Double ndest = new Point2D.Double(dest.x-(distFromBaseCenter+.5*newRadius)*dx,dest.y-(distFromBaseCenter+.5*newRadius)*dy); if (style.isCanonical()) { if (style.isCanonicalGC()) { if ((norig.x != ndest.x) || (norig.y != ndest.y)) { nx *= scaleFactor * _RNA.BASE_RADIUS / 4.0; ny *= scaleFactor * _RNA.BASE_RADIUS / 4.0; g2D.drawLine((norig.x + nx), (norig.y + ny), (ndest.x + nx), (ndest.y + ny)); g2D.drawLine((norig.x - nx), (norig.y - ny), (ndest.x - nx), (ndest.y - ny)); } } else if (style.isCanonicalAU()) { g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y); } else if (style.isWobbleUG()) { double cx = (ndest.x + norig.x) / 2.0; double cy = (ndest.y + norig.y) / 2.0; g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y); drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, false, ModeleBP.Edge.WC); } else { double cx = (ndest.x + norig.x) / 2.0; double cy = (ndest.y + norig.y) / 2.0; g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y); drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(), style.getEdgePartner5()); } } else { ModeleBP.Edge p1 = style.getEdgePartner5(); ModeleBP.Edge p2 = style.getEdgePartner3(); double cx = (ndest.x + norig.x) / 2.0; double cy = (ndest.y + norig.y) / 2.0; g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y); if (p1 == p2) { drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(), p1); } else { double fac = .4; drawSymbol(g2D, ndest.x - fac*radiusCircle*dx, ndest.y - fac*radiusCircle*dy, -nx, -ny, radiusCircle, style.isCIS(), p2); drawSymbol(g2D, norig.x + fac*radiusCircle*dx, norig.y + fac*radiusCircle*dy, nx, ny, radiusCircle, style.isCIS(), p1); } } } break; case SIMPLE: g2D.drawLine(orig.x, orig.y, dest.x, dest.y); break; case RNAVIZ: double xcenter = (orig.x + dest.x) / 2.0; double ycenter = (orig.y + dest.y) / 2.0; double radius = Math.max(4.0 * scaleFactor, 1.0); g2D.fillCircle((xcenter - radius), (ycenter - radius), (2.0 * radius)); break; case NONE: break; } } private Color getHighlightedVersion(Color c1, Color c2) { int r1 = c1.getRed(); int g1 = c1.getGreen(); int b1 = c1.getBlue(); int r2 = c2.getRed(); int g2 = c2.getGreen(); int b2 = c2.getBlue(); double val = _blink.getVal(); int nr = Math.max(0, Math.min((int) ((r1 * val + r2 * (1.0 - val))), 255)); int ng = Math.max(0, Math.min((int) ((g1 * val + g2 * (1.0 - val))), 255)); int nb = Math.max(0, Math.min((int) ((b1 * val + b2 * (1.0 - val))), 255)); return new Color(nr, ng, nb); } private Color highlightFilter(int index, Color initialColor, Color c1, Color c2, boolean localView) { if (_selectedBases.contains(_RNA.getBaseAt(index)) && localView) { return getHighlightedVersion(c1, c2); } else return initialColor; } private Point2D.Double computeExcentricUnitVector(int i, Point2D.Double[] points, Point2D.Double[] centers) { double dist = points[i].distance(centers[i]); Point2D.Double byCenter = new Point2D.Double( (points[i].x - centers[i].x) / dist, (points[i].y - centers[i].y) / dist); if ((i > 0) && (i < points.length - 1)) { Point2D.Double p0 = points[i - 1]; Point2D.Double p1 = points[i]; Point2D.Double p2 = points[i + 1]; double dist1 = p2.distance(p1); Point2D.Double v1 = new Point2D.Double((p2.x - p1.x) / dist1, (p2.y - p1.y) / dist1); Point2D.Double vn1 = new Point2D.Double(v1.y, -v1.x); double dist2 = p1.distance(p0); Point2D.Double v2 = new Point2D.Double((p1.x - p0.x) / dist2, (p1.y - p0.y) / dist2); Point2D.Double vn2 = new Point2D.Double(v2.y, -v2.x); Point2D.Double vn = new Point2D.Double((vn1.x + vn2.x) / 2.0, (vn1.y + vn2.y) / 2.0); double D = vn.distance(new Point2D.Double(0.0, 0.0)); vn.x /= D; vn.y /= D; if (byCenter.x * vn.x + byCenter.y * vn.y < 0) { vn.x = -vn.x; vn.y = -vn.y; } return vn; } else if (((i==0) || (i==points.length-1)) && (points.length>1)) { int a = (i==0)?0:points.length-1; int b = (i==0)?1:points.length-2; double D = points[a].distance(points[b]); return new Point2D.Double( (points[a].x - points[b].x) / D, (points[a].y - points[b].y) / D); } else { return byCenter; } } private void drawBase(VueVARNAGraphics g2D, int i, Point2D.Double[] points, Point2D.Double[] centers, double newRadius, double _scaleFactor, boolean localView) { Point2D.Double p = points[i]; ModeleBase mb = _RNA.get_listeBases().get(i); g2D.setFont(_conf._fontBasesGeneral); Color baseInnerColor = highlightFilter(i, _RNA.getBaseInnerColor(i, _conf), Color.white, _RNA.getBaseInnerColor(i, _conf), localView); Color baseOuterColor = highlightFilter(i, _RNA.getBaseOuterColor(i, _conf), _RNA.getBaseOuterColor(i, _conf), Color.white, localView); Color baseNameColor = highlightFilter(i, _RNA.getBaseNameColor(i, _conf), _RNA.getBaseNameColor(i, _conf), Color.white, localView); if ( RNA.whiteLabelPreferrable(baseInnerColor)) { baseNameColor=Color.white; } if (mb instanceof ModeleBaseNucleotide) { ModeleBaseNucleotide mbn = (ModeleBaseNucleotide) mb; String res = mbn.getBase(); if (_hoveredBase == mb && localView) { g2D.setColor(_conf._hoverColor); g2D.fillCircle(p.getX() - 1.5 * newRadius, p.getY() - 1.5 * newRadius, 3.0 * newRadius); g2D.setColor(_conf._hoverColor.darker()); g2D.drawCircle(p.getX() - 1.5 * newRadius, p.getY() - 1.5 * newRadius, 3.0 * newRadius); g2D.setPlainStroke(); } if (_conf._fillBases) { // Filling inner circle g2D.setColor(baseInnerColor); g2D.fillCircle(p.getX() - newRadius, p.getY() - newRadius, 2.0 * newRadius); } if (_conf._drawOutlineBases) { // Drawing outline g2D.setColor(baseOuterColor); g2D.setStrokeThickness(_conf._baseThickness * _scaleFactor); g2D.drawCircle(p.getX() - newRadius, p.getY() - newRadius, 2.0 * newRadius); } // Drawing label g2D.setColor(baseNameColor); g2D.drawStringCentered(String.valueOf(res), p.getX(), p.getY()); } else if (mb instanceof ModeleBasesComparison) { ModeleBasesComparison mbc = (ModeleBasesComparison) mb; // On lui donne l'aspect voulue (on a un trait droit) g2D.setPlainStroke(); // On doit avoir un trait droit, sans arrondit g2D.setStrokeThickness(_conf._baseThickness * _scaleFactor); // On dessine l'étiquette, rectangle aux bords arrondies. g2D.setColor(baseInnerColor); g2D.fillRoundRect((p.getX() - 1.5 * newRadius), (p.getY() - newRadius), (3.0 * newRadius), (2.0 * newRadius), 10 * _scaleFactor, 10 * _scaleFactor); /* Dessin du rectangle exterieur (bords) */ g2D.setColor(baseOuterColor); g2D.drawRoundRect((p.getX() - 1.5 * newRadius), (p.getY() - newRadius), (3 * newRadius), (2 * newRadius), 10 * _scaleFactor, 10 * _scaleFactor); // On le dessine au centre de l'étiquette. g2D.drawLine((p.getX()), (p.getY() + newRadius) - 1, (p.getX()), (p.getY() - newRadius) + 1); /* Dessin du nom de la base (A,C,G,U,etc...) */ // On créer le texte des étiquettes String label1 = String.valueOf(mbc.getBase1()); String label2 = String.valueOf(mbc.getBase2()); // On leur donne une couleur g2D.setColor(getRNA().get_listeBases().get(i).getStyleBase() .get_base_name_color()); // Et on les dessine. g2D.drawStringCentered(label1, p.getX() - (.75 * newRadius), p.getY()); g2D.drawStringCentered(label2, p.getX() + (.75 * newRadius), p.getY()); } // Drawing base number if (_RNA.isNumberDrawn(mb, getNumPeriod())) { Point2D.Double vn = computeExcentricUnitVector(i, points, centers); g2D.setColor(mb.getStyleBase().get_base_number_color()); g2D.setFont(_conf._numbersFont); double factorMin = Math.min(.5, _conf._distNumbers); double factorMax = Math.min(_conf._distNumbers - 1.5, _conf._distNumbers); g2D.drawLine(p.x + vn.x * ((1 + factorMin) * newRadius), p.y + vn.y * ((1 + factorMin) * newRadius), p.x + vn.x * ((1 + factorMax) * newRadius), p.y + vn.y * ((1 + factorMax) * newRadius)); g2D.drawStringCentered(mb.getLabel(), p.x + vn.x * ((1 + _conf._distNumbers) * newRadius), p.y + vn.y * ((1 + _conf._distNumbers) * newRadius)); } } void drawChemProbAnnotation(VueVARNAGraphics g2D, ChemProbAnnotation cpa, Point2D.Double anchor, double scaleFactor) { g2D.setColor(cpa.getColor()); g2D.setStrokeThickness(RNA.CHEM_PROB_ARROW_THICKNESS * scaleFactor * cpa.getIntensity()); g2D.setPlainStroke(); Point2D.Double v = cpa.getDirVector(); Point2D.Double vn = cpa.getNormalVector(); Point2D.Double base = new Point2D.Double( (anchor.x + _RNA.CHEM_PROB_DIST * scaleFactor * v.x), (anchor.y + _RNA.CHEM_PROB_DIST * scaleFactor * v.y)); Point2D.Double edge = new Point2D.Double( (base.x + _RNA.CHEM_PROB_BASE_LENGTH * cpa.getIntensity() * scaleFactor * v.x), (base.y + _RNA.CHEM_PROB_BASE_LENGTH * cpa.getIntensity() * scaleFactor * v.y)); switch (cpa.getType()) { case ARROW: { Point2D.Double arrowTip1 = new Point2D.Double( (base.x + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_ARROW_WIDTH * vn.x + _RNA.CHEM_PROB_ARROW_HEIGHT * v.x)), (base.y + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_ARROW_WIDTH * vn.y + _RNA.CHEM_PROB_ARROW_HEIGHT * v.y))); Point2D.Double arrowTip2 = new Point2D.Double( (base.x + cpa.getIntensity() * scaleFactor * (-_RNA.CHEM_PROB_ARROW_WIDTH * vn.x + _RNA.CHEM_PROB_ARROW_HEIGHT * v.x)), (base.y + cpa.getIntensity() * scaleFactor * (-_RNA.CHEM_PROB_ARROW_WIDTH * vn.y + _RNA.CHEM_PROB_ARROW_HEIGHT * v.y))); g2D.drawLine(base.x, base.y, edge.x, edge.y); g2D.drawLine(base.x, base.y, arrowTip1.x, arrowTip1.y); g2D.drawLine(base.x, base.y, arrowTip2.x, arrowTip2.y); } break; case PIN: { Point2D.Double side1 = new Point2D.Double( (edge.x - cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.x)), (edge.y - cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.y))); Point2D.Double side2 = new Point2D.Double( (edge.x - cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.x)), (edge.y - cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.y))); Point2D.Double side3 = new Point2D.Double( (edge.x + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.x)), (edge.y + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.y))); Point2D.Double side4 = new Point2D.Double( (edge.x + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.x)), (edge.y + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.y))); GeneralPath p2 = new GeneralPath(); p2.moveTo((float) side1.x, (float) side1.y); p2.lineTo((float) side2.x, (float) side2.y); p2.lineTo((float) side3.x, (float) side3.y); p2.lineTo((float) side4.x, (float) side4.y); p2.closePath(); g2D.fill(p2); g2D.drawLine(base.x, base.y, edge.x, edge.y); } break; case TRIANGLE: { Point2D.Double arrowTip1 = new Point2D.Double( (edge.x + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.x)), (edge.y + cpa.getIntensity() * scaleFactor * (_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.y))); Point2D.Double arrowTip2 = new Point2D.Double( (edge.x + cpa.getIntensity() * scaleFactor * (-_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.x)), (edge.y + cpa.getIntensity() * scaleFactor * (-_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.y))); GeneralPath p2 = new GeneralPath(); p2.moveTo((float) base.x, (float) base.y); p2.lineTo((float) arrowTip1.x, (float) arrowTip1.y); p2.lineTo((float) arrowTip2.x, (float) arrowTip2.y); p2.closePath(); g2D.fill(p2); } break; case DOT: { Double radius = scaleFactor * _RNA.CHEM_PROB_DOT_RADIUS * cpa.getIntensity(); Point2D.Double center = new Point2D.Double((base.x + radius * v.x), (base.y + radius * v.y)); g2D.fillCircle((center.x - radius), (center.y - radius), (2 * radius)); } break; } } Point2D.Double buildCaptionPosition(ModeleBase mb, double scaleFactor, double heightEstimate) { double radius = 2.0; if (_RNA.isNumberDrawn(mb, getNumPeriod())) { radius += _conf._distNumbers; } Point2D.Double center = mb.getCenter(); Point2D.Double p = mb.getCoords(); double realDistance = _RNA.BASE_RADIUS * radius + heightEstimate; return new Point2D.Double(center.getX() + (p.getX() - center.getX()) * ((p.distance(center) + realDistance) / p.distance(center)), center.getY() + (p.getY() - center.getY()) * ((p.distance(center) + realDistance) / p .distance(center))); } private void renderAnnotations(VueVARNAGraphics g2D, double offX, double offY, double rnaBBoxX, double rnaBBoxY, double scaleFactor) { for (TextAnnotation textAnnotation : _RNA.getAnnotations()) { g2D.setColor(textAnnotation.getColor()); g2D.setFont(textAnnotation .getFont() .deriveFont( (float) (2.0 * textAnnotation.getFont().getSize() * scaleFactor))); Point2D.Double position = textAnnotation.getCenterPosition(); if (textAnnotation.getType() == TextAnnotation.AnchorType.BASE) { ModeleBase mb = (ModeleBase) textAnnotation.getAncrage(); double fontHeight = Math.ceil(textAnnotation.getFont() .getSize()); position = buildCaptionPosition(mb, scaleFactor, fontHeight); } position = transformCoord(position, offX, offY, rnaBBoxX, rnaBBoxY, scaleFactor); g2D.drawStringCentered(textAnnotation.getTexte(), position.x, position.y); if ((_selectedAnnotation == textAnnotation) && (_highlightAnnotation)) { drawStringOutline(g2D, textAnnotation.getTexte(), position.x, position.y, 5); } } for (ChemProbAnnotation cpa : _RNA.getChemProbAnnotations()) { Point2D.Double anchor = transformCoord(cpa.getAnchorPosition(), offX, offY, rnaBBoxX, rnaBBoxY, scaleFactor); drawChemProbAnnotation(g2D, cpa, anchor, scaleFactor); } } public Rectangle2D.Double getExtendedRNABBox() { // We get the logical bounding box Rectangle2D.Double rnabbox = _RNA.getBBox(); rnabbox.y -= _conf._distNumbers * _RNA.BASE_RADIUS; rnabbox.height += 2.0 * _conf._distNumbers * _RNA.BASE_RADIUS; rnabbox.x -= _conf._distNumbers * _RNA.BASE_RADIUS; rnabbox.width += 2.0 * _conf._distNumbers * _RNA.BASE_RADIUS; if (_RNA.hasVirtualLoops()) { rnabbox.y -= RNA.VIRTUAL_LOOP_RADIUS; rnabbox.height += 2.0 * RNA.VIRTUAL_LOOP_RADIUS; rnabbox.x -= RNA.VIRTUAL_LOOP_RADIUS; rnabbox.width += 2.0 * RNA.VIRTUAL_LOOP_RADIUS; } return rnabbox; } public void drawBackbone(VueVARNAGraphics g2D, Point2D.Double[] newCoords, double newRadius, double _scaleFactor) { // Drawing backbone if (getDrawBackbone()) { g2D.setStrokeThickness(1.5 * _scaleFactor); g2D.setColor(_conf._backboneColor); ModeleBackbone bck = _RNA.getBackbone(); for (int i = 1; i < _RNA.get_listeBases().size(); i++) { Point2D.Double p1 = newCoords[i - 1]; Point2D.Double p2 = newCoords[i]; double dist = p1.distance(p2); int a = _RNA.getBaseAt(i - 1).getElementStructure(); int b = _RNA.getBaseAt(i).getElementStructure(); boolean consecutivePair = (a == i) && (b == i - 1); if ((dist > 0)) { Point2D.Double vbp = new Point2D.Double(); vbp.x = (p2.x - p1.x) / dist; vbp.y = (p2.y - p1.y) / dist; BackboneType bt = bck.getTypeBefore(i); if (bt!=BackboneType.DISCONTINUOUS_TYPE) { if (bt==BackboneType.MISSING_PART_TYPE) { g2D.setSelectionStroke(); } else { g2D.setPlainStroke(); } g2D.setColor(bck.getColorBefore(i, _conf._backboneColor)); if (consecutivePair && (_RNA.getDrawMode() != RNA.DRAW_MODE_LINEAR) && (_RNA.getDrawMode() != RNA.DRAW_MODE_CIRCULAR)) { int dir = 0; if (i + 1 < newCoords.length) { dir = (_RNA.testDirectionality(i - 1, i, i + 1) ? -1 : 1); } else if (i - 2 >= 0) { dir = (_RNA.testDirectionality(i - 2, i - 1, i) ? -1 : 1); } Point2D.Double vn = new Point2D.Double(dir * vbp.y, -dir * vbp.x); Point2D.Double centerSeg = new Point2D.Double( (p1.x + p2.x) / 2.0, (p1.y + p2.y) / 2.0); double distp1CenterSeq = p1.distance(centerSeg); double centerDist = Math .sqrt((RNA.VIRTUAL_LOOP_RADIUS * _scaleFactor * RNA.VIRTUAL_LOOP_RADIUS * _scaleFactor) - distp1CenterSeq * distp1CenterSeq); Point2D.Double centerLoop = new Point2D.Double( centerSeg.x + centerDist * vn.x, centerSeg.y + centerDist * vn.y); double radius = centerLoop.distance(p1); double a1 = 360. * (Math.atan2(-(p1.y - centerLoop.y), (p1.x - centerLoop.x))) / (2. * Math.PI); double a2 = 360. * (Math.atan2(-(p2.y - centerLoop.y), (p2.x - centerLoop.x))) / (2. * Math.PI); double angle = (a2 - a1); if (-dir * angle < 0) { angle += -dir * 360.; } // if (angle<0.) angle += 360.; // angle = -dir*(360-dir*angle); g2D.drawArc(centerLoop.x + .8 * newRadius * vn.x, centerLoop.y + .8 * newRadius * vn.y, 2 * radius, 2 * radius, a1, angle); } else { g2D.drawLine((newCoords[i - 1].x + newRadius * vbp.x), (newCoords[i - 1].y + newRadius * vbp.y), (newCoords[i].x - newRadius * vbp.x), (newCoords[i].y - newRadius * vbp.y)); } } } } } } public Point2D.Double logicToPanel(Point2D.Double logicPoint) { return new Point2D.Double(_offX + (getScaleFactor() * (logicPoint.x - _offsetRNA.x)), _offY + (getScaleFactor() * (logicPoint.y - _offsetRNA.y))); } public Rectangle2D.Double renderRNA(VueVARNAGraphics g2D, Rectangle2D.Double bbox) { return renderRNA(g2D, bbox, false, true); } private double computeScaleFactor(Rectangle2D.Double bbox, boolean localView, boolean autoCenter) { Rectangle2D.Double rnabbox = getExtendedRNABBox(); double scaleFactor = Math.min((double) bbox.width / (double) rnabbox.width, (double) bbox.height / (double) rnabbox.height); // Use it to get an estimate of the font size for numbers ... float newFontSize = Math.max(1, (int) ((1.7 * _RNA.BASE_RADIUS) * scaleFactor)); // ... and increase bounding box accordingly rnabbox.y -= newFontSize; rnabbox.height += newFontSize; if (_conf._drawColorMap) { rnabbox.height += getColorMapHeight(); } rnabbox.x -= newFontSize; rnabbox.width += newFontSize; // Now, compute the final scaling factor and corresponding font size scaleFactor = Math.min((double) bbox.width / (double) rnabbox.width, (double) bbox.height / (double) rnabbox.height); if (localView) { if (_conf._autoFit) setScaleFactor(scaleFactor); scaleFactor = getScaleFactor(); } return scaleFactor; } public synchronized Rectangle2D.Double renderRNA(VueVARNAGraphics g2D, Rectangle2D.Double bbox, boolean localView, boolean autoCenter) { Rectangle2D.Double rnaMultiBox = new Rectangle2D.Double(0, 0, 1, 1); double scaleFactor = computeScaleFactor(bbox, localView, autoCenter); float newFontSize = Math.max(1, (int) ((1.7 * _RNA.BASE_RADIUS) * scaleFactor)); double newRadius = Math.max(1.0, (scaleFactor * _RNA.BASE_RADIUS)); setBaseFontSize(newFontSize); setNumbersFontSize(newFontSize); double offX = bbox.x; double offY = bbox.y; Rectangle2D.Double rnabbox = getExtendedRNABBox(); if (_RNA.getSize() != 0) { Point2D.Double offsetRNA = new Point2D.Double(rnabbox.x, rnabbox.y); if (autoCenter) { offX = (bbox.x + (bbox.width - Math.round(rnabbox.width * scaleFactor)) / 2.0); offY = (bbox.y + (bbox.height - Math.round(rnabbox.height * scaleFactor)) / 2.0); if (localView) { _offX = offX; _offY = offY; _offsetPanel = new Point2D.Double(_offX, _offY); _offsetRNA = new Point2D.Double(rnabbox.x, rnabbox.y); } } if (localView) { offX = _offX; offY = _offY; offsetRNA = _offsetRNA; } // Re-scaling once and for all Point2D.Double[] newCoords = new Point2D.Double[_RNA .get_listeBases().size()]; Point2D.Double[] newCenters = new Point2D.Double[_RNA .get_listeBases().size()]; for (int i = 0; i < _RNA.get_listeBases().size(); i++) { ModeleBase mb = _RNA.getBaseAt(i); newCoords[i] = new Point2D.Double(offX + (scaleFactor * (mb.getCoords().x - offsetRNA.x)), offY + (scaleFactor * (mb.getCoords().y - offsetRNA.y))); Point2D.Double centerBck = _RNA.getCenter(i); // si la base est dans un angle entre une boucle et une helice if (_RNA.get_drawMode() == RNA.DRAW_MODE_NAVIEW || _RNA.get_drawMode() == RNA.DRAW_MODE_RADIATE) { if ((mb.getElementStructure() != -1) && i < _RNA.get_listeBases().size() - 1 && i > 1) { ModeleBase b1 = _RNA.get_listeBases().get(i - 1); ModeleBase b2 = _RNA.get_listeBases().get(i + 1); int j1 = b1.getElementStructure(); int j2 = b2.getElementStructure(); if ((j1 == -1) ^ (j2 == -1)) { // alors la position du nombre associé doit etre Point2D.Double a1 = b1.getCoords(); Point2D.Double a2 = b2.getCoords(); Point2D.Double c1 = b1.getCenter(); Point2D.Double c2 = b2.getCenter(); centerBck.x = mb.getCoords().x + (c1.x - a1.x) / c1.distance(a1) + (c2.x - a2.x) / c2.distance(a2); centerBck.y = mb.getCoords().y + (c1.y - a1.y) / c1.distance(a1) + (c2.y - a2.y) / c2.distance(a2); } } } newCenters[i] = new Point2D.Double(offX + (scaleFactor * (centerBck.x - offsetRNA.x)), offY + (scaleFactor * (centerBck.y - offsetRNA.y))); } // Keep track of coordinates for mouse interactions if (localView) { _realCoords = newCoords; _realCenters = newCenters; } g2D.setStrokeThickness(1.5 * scaleFactor); g2D.setPlainStroke(); g2D.setFont(_conf._fontBasesGeneral); // Drawing region highlights Annotation drawRegionHighlightsAnnotation(g2D, _realCoords, _realCenters, scaleFactor); drawBackbone(g2D, newCoords, newRadius, scaleFactor); // Drawing base-pairs // pour chaque base for (int i = 0; i < _RNA.get_listeBases().size(); i++) { int j = _RNA.get_listeBases().get(i).getElementStructure(); // si c'est une parenthese ouvrante (premiere base du // couple) if (j > i) { ModeleBP msbp = _RNA.get_listeBases().get(i).getStyleBP(); // System.err.println(msbp); if (msbp.isCanonical() || _conf._drawnNonCanonicalBP) { if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) { g2D.setStrokeThickness(_RNA.getBasePairThickness( msbp, _conf) * 2.0 * scaleFactor * _conf._bpThickness); } else { g2D.setStrokeThickness(_RNA.getBasePairThickness( msbp, _conf) * 1.5 * scaleFactor); } g2D.setColor(_RNA.getBasePairColor(msbp, _conf)); if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) { drawBasePairArc(g2D, i, j, newCoords[i], newCoords[j], scaleFactor, msbp, newRadius); } else { drawBasePair(g2D, newCoords[i], newCoords[j], msbp, newRadius, scaleFactor); } } } } // Liaisons additionelles (non planaires) if (_conf._drawnNonPlanarBP) { ArrayList bpaux = _RNA.getStructureAux(); for (int k = 0; k < bpaux.size(); k++) { ModeleBP msbp = bpaux.get(k); if (msbp.isCanonical() || _conf._drawnNonCanonicalBP) { int i = msbp.getPartner5().getIndex(); int j = msbp.getPartner3().getIndex(); if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) { g2D.setStrokeThickness(_RNA.getBasePairThickness( msbp, _conf) * 2.5 * scaleFactor * _conf._bpThickness); g2D.setPlainStroke(); } else { g2D.setStrokeThickness(_RNA.getBasePairThickness( msbp, _conf) * 1.5 * scaleFactor); g2D.setPlainStroke(); } g2D.setColor(_RNA.getBasePairColor(msbp, _conf)); if (j > i) { if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) { drawBasePairArc(g2D, i, j, newCoords[i], newCoords[j], scaleFactor, msbp, newRadius); } else { drawBasePair(g2D, newCoords[i], newCoords[j], msbp, newRadius, scaleFactor); } } } } } // Drawing bases g2D.setPlainStroke(); for (int i = 0; i < Math.min(_RNA.get_listeBases().size(), newCoords.length); i++) { drawBase(g2D, i, newCoords, newCenters, newRadius, scaleFactor, localView); } rnaMultiBox = new Rectangle2D.Double(offX, offY, (scaleFactor * rnabbox.width) - 1, (scaleFactor * rnabbox.height) - 1); if (localView) { // Drawing bbox if (_debug || _drawBBox) { g2D.setColor(Color.RED); g2D.setSelectionStroke(); g2D.drawRect(rnaMultiBox.x, rnaMultiBox.y, rnaMultiBox.width, rnaMultiBox.height); } // Draw color map if (_conf._drawColorMap) { drawColorMap(g2D, scaleFactor, rnabbox); } if (_debug || _drawBBox) { g2D.setColor(Color.GRAY); g2D.setSelectionStroke(); g2D.drawRect(0, 0, getWidth() - 1, getHeight() - getTitleHeight() - 1); } } // Draw annotations renderAnnotations(g2D, offX, offY, offsetRNA.x, offsetRNA.y, scaleFactor); // Draw additional debug shape if (_RNA._debugShape != null) { Color c = new Color(255, 0, 0, 50); g2D.setColor(c); AffineTransform at = new AffineTransform(); at.translate(offX - scaleFactor * rnabbox.x, offY - scaleFactor * rnabbox.y); at.scale(scaleFactor, scaleFactor); Shape s = at.createTransformedShape(_RNA._debugShape); if (s instanceof GeneralPath) { g2D.fill((GeneralPath) s); } } } else { g2D.setColor(VARNAConfig.DEFAULT_MESSAGE_COLOR); g2D.setFont(VARNAConfig.DEFAULT_MESSAGE_FONT); rnaMultiBox = new Rectangle2D.Double(0,0,10,10); g2D.drawStringCentered("No RNA here", bbox.getCenterX(),bbox.getCenterY()); } return rnaMultiBox; } public void centerViewOn(double x, double y) { Rectangle2D.Double r = _RNA.getBBox(); _target = new Point2D.Double(x, y); Point2D.Double q = logicToPanel(_target); Point p = new Point((int) (-q.x), (int) (-q.y)); setTranslation(p); repaint(); } Point2D.Double _target = new Point2D.Double(0, 0); Point2D.Double _target2 = new Point2D.Double(0, 0); public ModeleBase getBaseAt(Point2D.Double po) { ModeleBase mb = null; Point2D.Double p = panelToLogicPoint(po); double dist = Double.MAX_VALUE; for (ModeleBase tmp : _RNA.get_listeBases()) { double ndist = tmp.getCoords().distance(p); if (dist > ndist) { mb = tmp; dist = ndist; } } return mb; } public void setColorMapValues(Double[] values) { _RNA.setColorMapValues(values, _conf._cm, true); _conf._drawColorMap = true; repaint(); } public void setColorMapMaxValue(double d) { _conf._cm.setMaxValue(d); } public void setColorMapMinValue(double d) { _conf._cm.setMinValue(d); } public ModeleColorMap getColorMap() { return _conf._cm; } public void setColorMap(ModeleColorMap cm) { //_RNA.adaptColorMapToValues(cm); _conf._cm = cm; repaint(); } public void setColorMapCaption(String caption) { _conf._colorMapCaption = caption; repaint(); } public String getColorMapCaption() { return _conf._colorMapCaption; } public void drawColorMap(boolean draw) { _conf._drawColorMap = draw; } private double getColorMapHeight() { double result = VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE + _conf._colorMapHeight; if (!_conf._colorMapCaption.equals("")) result += VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE; return result; } private void drawColorMap(VueVARNAGraphics g2D, double scaleFactor, Rectangle2D.Double rnabbox) { double v1 = _conf._cm.getMinValue(); double v2 = _conf._cm.getMaxValue(); double x, y; g2D.setPlainStroke(); double xSpaceAvail = 0; double ySpaceAvail = Math .min((getHeight() - rnabbox.height * scaleFactor - getTitleHeight()) / 2.0, scaleFactor * (_conf._colorMapHeight + VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE)); if ((int) ySpaceAvail == 0) { xSpaceAvail = Math.min( (getWidth() - rnabbox.width * scaleFactor) / 2, scaleFactor * (_conf._colorMapWidth) + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH); } double xBase = (xSpaceAvail + _offX + scaleFactor * (rnabbox.width - _conf._colorMapWidth - _conf._colorMapXOffset)); double hcaption = VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE; double yBase = (ySpaceAvail + _offY + scaleFactor * (rnabbox.height - _conf._colorMapHeight - _conf._colorMapYOffset - hcaption)); for (int i = 0; i < _conf._colorMapWidth; i++) { double ratio = (((double) i) / ((double) _conf._colorMapWidth)); double val = v1 + (v2 - v1) * ratio; g2D.setColor(_conf._cm.getColorForValue(val)); x = (xBase + scaleFactor * i); y = yBase; g2D.fillRect(x, y, scaleFactor * VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH, (scaleFactor * _conf._colorMapHeight)); } g2D.setColor(VARNAConfig.DEFAULT_COLOR_MAP_OUTLINE); g2D.drawRect(xBase, yBase, (VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH - 1 + scaleFactor * _conf._colorMapWidth), ((scaleFactor * _conf._colorMapHeight))); g2D.setFont(getFont() .deriveFont( (float) (scaleFactor * VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE))); g2D.setColor(VARNAConfig.DEFAULT_COLOR_MAP_FONT_COLOR); NumberFormat nf = NumberFormat.getInstance(); nf.setMaximumFractionDigits(2); nf.setMinimumFractionDigits(0); g2D.drawStringCentered(nf.format(_conf._cm.getMinValue()), xBase, yBase + scaleFactor * (_conf._colorMapHeight+(VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7))); g2D.drawStringCentered(nf.format(_conf._cm.getMaxValue()), xBase + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH + scaleFactor * _conf._colorMapWidth, yBase + scaleFactor * (_conf._colorMapHeight+(VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7))); if (!_conf._colorMapCaption.equals("")) g2D.drawStringCentered( "" + _conf._colorMapCaption, xBase + scaleFactor * _conf._colorMapWidth / 2.0, yBase + scaleFactor * (VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7 + _conf._colorMapHeight)); } public Point2D.Double panelToLogicPoint(Point2D.Double p) { return new Point2D.Double( ((p.x - getOffsetPanel().x) / getScaleFactor()) + getRNAOffset().x, ((p.y - getOffsetPanel().y) / getScaleFactor()) + getRNAOffset().y); } public Point2D.Double transformCoord(Point2D.Double coordDebut, double offX, double offY, double rnaBBoxX, double rnaBBoxY, double scaleFactor) { return new Point2D.Double(offX + (scaleFactor * (coordDebut.x - rnaBBoxX)), offY + (scaleFactor * (coordDebut.y - rnaBBoxY))); } public void eraseSequence() { _RNA.eraseSequence(); } public Point2D.Double transformCoord(Point2D.Double coordDebut) { Rectangle2D.Double rnabbox = getExtendedRNABBox(); return new Point2D.Double(_offX + (getScaleFactor() * (coordDebut.x - rnabbox.x)), _offY + (getScaleFactor() * (coordDebut.y - rnabbox.y))); } public void paintComponent(Graphics g) { paintComponent(g, false); } public void paintComponent(Graphics g, boolean transparentBackground) { if (_premierAffichage) { // _border = new Dimension(0, 0); _translation.x = 0; _translation.y = (int) (-getTitleHeight() / 2.0); _popup.buildPopupMenu(); this.add(_popup); _premierAffichage = false; } Graphics2D g2 = (Graphics2D) g; Stroke dflt = g2.getStroke(); VueVARNAGraphics g2D = new SwingGraphics(g2); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); this.removeAll(); super.paintComponent(g2); renderComponent(g2D, transparentBackground, getScaleFactor()); if (isFocusOwner()) { g2.setStroke(new BasicStroke(1.5f)); g2.setColor(Color.decode("#C0C0C0")); g2.drawRect(0, 0, getWidth() - 1, getHeight() - 1); } g2.setStroke(dflt); /* * PSExport e = new PSExport(); SecStrProducerGraphics export = new * SecStrProducerGraphics(e); renderRNA(export, getExtendedRNABBox()); * try { export.saveToDisk("./out.ps"); } catch * (ExceptionWritingForbidden e1) { e1.printStackTrace(); } */ } /** * Draws current RNA structure in a given Graphics "device". * * @param g2D * A graphical device * @param transparentBackground * Whether the background should be transparent, or drawn. */ public synchronized void renderComponent(VueVARNAGraphics g2D, boolean transparentBackground, double scaleFactor) { updateTitleHeight(); if (_debug || _drawBorder) { g2D.setColor(Color.BLACK); g2D.setPlainStroke(); g2D.drawRect(getLeftOffset(), getTopOffset(), getInnerWidth(), getInnerHeight()); } if (!transparentBackground) { super.setBackground(_conf._backgroundColor); } else { super.setBackground(new Color(0, 0, 0, 120)); } if (getMinimumSize().height < getSize().height && getMinimumSize().width < getSize().width) { // Draw Title if (!getTitle().equals("")) { g2D.setColor(_conf._titleColor); g2D.setFont(_conf._titleFont); g2D.drawStringCentered(getTitle(), this.getWidth() / 2, this.getHeight() - getTitleHeight() / 2.0); } // Draw RNA renderRNA(g2D, getClip(), true, _conf._autoCenter); } if (_selectionRectangle != null) { g2D.setColor(Color.BLACK); g2D.setSelectionStroke(); g2D.drawRect(_selectionRectangle.x, _selectionRectangle.y, _selectionRectangle.width, _selectionRectangle.height); } if ((_linkOrigin != null) && (_linkDestination != null)) { g2D.setColor(_conf._bondColor); g2D.setPlainStroke(); g2D.setStrokeThickness(3.0 * scaleFactor); Point2D.Double linkOrigin = (_linkOrigin); Point2D.Double linkDestination = (_linkDestination); g2D.drawLine(linkOrigin.x, linkOrigin.y, linkDestination.x, linkDestination.y); for (int i : getSelection().getIndices()) drawBase(g2D, i, _realCoords, _realCenters, scaleFactor * _RNA.BASE_RADIUS, scaleFactor, true); } if (_debug) { g2D.setStrokeThickness(3.0 * scaleFactor); g2D.setColor(Color.black); Point2D.Double t = this.logicToPanel(_target); g2D.drawLine(t.x - 3, t.y - 3, t.x + 3, t.y + 3); g2D.drawLine(t.x - 3, t.y + 3, t.x + 3, t.y - 3); g2D.setColor(Color.red); t = this.logicToPanel(_target2); g2D.drawLine(t.x - 3, t.y - 3, t.x + 3, t.y + 3); g2D.drawLine(t.x - 3, t.y + 3, t.x + 3, t.y - 3); } } public void drawRegionHighlightsAnnotation(VueVARNAGraphics g2D, Point2D.Double[] realCoords, Point2D.Double[] realCenters, double scaleFactor) { g2D.setStrokeThickness(2.0 * scaleFactor); g2D.setPlainStroke(); for (HighlightRegionAnnotation r : _RNA.getHighlightRegion()) { GeneralPath s = r.getShape(realCoords, realCenters, scaleFactor); g2D.setColor(r.getFillColor()); g2D.fill(s); g2D.setColor(r.getOutlineColor()); g2D.draw(s); } } private Rectangle2D.Double getClip() { return new Rectangle2D.Double(getLeftOffset(), getTopOffset(), this.getInnerWidth(), this.getInnerHeight()); } public Rectangle2D.Double getViewClip() { return new Rectangle2D.Double(this.getLeftOffset(), this.getTopOffset(), this.getInnerWidth(), this.getInnerHeight()); } /** * Returns the color used to draw backbone bounds. * * @return The color used to draw backbone bounds */ public Color getBackboneColor() { return _conf._backboneColor; } /** * Sets the color to be used for drawing backbone interactions. * * @param backbone_color * The new color for the backbone bounds */ public void setBackboneColor(Color backbone_color) { _conf._backboneColor = backbone_color; } /** * Returns the color used to display hydrogen bonds (base pairings) * * @return The color of hydrogen bonds */ public Color getBondColor() { return _conf._bondColor; } /** * Returns the title of this panel * * @return The title */ public String getTitle() { return _RNA.getName(); } /** * Sets the new color to be used for hydrogen bonds (base pairings) * * @param bond_color * The new color for hydrogen bonds */ public void setDefaultBPColor(Color bond_color) { _conf._bondColor = bond_color; } /** * Sets the size of the border, i.e. the empty space between the end of the * drawing area and the actual border. * * @param b * The new border size */ public void setBorderSize(Dimension b) { _border = b; } /** * Returns the size of the border, i.e. the empty space between the end of * the drawing area * * @return The border size */ public Dimension getBorderSize() { return _border; } /** * Sets the RNA to be displayed within this Panel. This method does not use * a drawing algorithm to reassigns base coordinates, rather assuming that * the RNA was previously drawn. * * @param r * An already drawn RNA to display in this panel */ public synchronized void showRNA(RNA r) { fireUINewStructure(r); _RNA = r; } /** * Sets the RNA secondary structure to be drawn in this panel, using the * default layout algorithm. In addition to the raw nucleotides sequence, * the secondary structure is given in the so-called "Dot-bracket notation" * (DBN) format. This format is a well-parenthesized word over the alphabet * '(',')','.'.
* Ex:((((((((....))))..(((((...))).))))))
* Returns true if the sequence/structure couple could be * parsed into a valid secondary structure, and false * otherwise. * * @param seq * The raw nucleotides sequence * @param str * The secondary structure * @throws ExceptionNonEqualLength */ public void drawRNA(String seq, String str) throws ExceptionNonEqualLength { drawRNA(seq, str, _RNA.get_drawMode()); } /** * Sets the RNA secondary structure to be drawn in this panel, using a given * layout algorithm. * * @param r * The new secondary structure * @param drawMode * The drawing algorithm */ public void drawRNA(RNA r, int drawMode) { r.setDrawMode(drawMode); drawRNA(r); } /** * Redraws the current RNA. This reassigns base coordinates to their default * value using the current drawing algorithm. */ public void drawRNA() { try { _RNA.drawRNA(_RNA.get_drawMode(), _conf); } catch (ExceptionNAViewAlgorithm e) { errorDialog(e); e.printStackTrace(); } repaint(); } /** * Sets the RNA secondary structure to be drawn in this panel, using the * current drawing algorithm. * * @param r * The new secondary structure */ public void drawRNA(RNA r) { if (r != null) { _RNA = r; drawRNA(); } } /** * Sets the RNA secondary structure to be drawn in this panel, using a given * layout algorithm. In addition to the raw nucleotides sequence, the * secondary structure is given in the so-called "Dot-bracket notation" * (DBN) format. This format is a well-parenthesized word over the alphabet * '(',')','.'.
* Ex: ((((((((....))))..(((((...))).))))))
* Returns true if the sequence/structure couple could be * parsed into a valid secondary structure, and false * otherwise. * * @param seq * The raw nucleotides sequence * @param str * The secondary structure * @param drawMode * The drawing algorithm * @throws ExceptionNonEqualLength */ public void drawRNA(String seq, String str, int drawMode) throws ExceptionNonEqualLength { _RNA.setDrawMode(drawMode); try { _RNA.setRNA(seq, str); drawRNA(); } catch (ExceptionUnmatchedClosingParentheses e) { errorDialog(e); } catch (ExceptionFileFormatOrSyntax e1) { errorDialog(e1); } } public void drawRNA(Reader r, int drawMode) throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax { _RNA.setDrawMode(drawMode); Collection rnas = RNAFactory.loadSecStr(r); if (rnas.isEmpty()) { throw new ExceptionFileFormatOrSyntax( "No RNA could be parsed from that source."); } _RNA = rnas.iterator().next(); drawRNA(); } /** * Draws a secondary structure of RNA using the default drawing algorithm * and displays it, using an interpolated transition between the previous * one and the new one. Extra bases, resulting from a size difference * between the two successive RNAs, are assumed to initiate from the middle * of the sequence. In other words, both prefixes and suffixes of the RNAs * are assumed to match, and what remains is an insertion. * * @param seq * Sequence * @param str * Structure in dot bracket notation * @throws ExceptionNonEqualLength * If len(seq)!=len(str) */ public void drawRNAInterpolated(String seq, String str) throws ExceptionNonEqualLength { drawRNAInterpolated(seq, str, _RNA.get_drawMode()); } /** * Draws a secondary structure of RNA using a given algorithm and displays * it, using an interpolated transition between the previous one and the new * one. Extra bases, resulting from a size difference between the two * successive RNAs, are assumed to initiate from the middle of the sequence. * In other words, both prefixes and suffixes of the RNAs are assumed to * match, and what remains is an insertion. * * @param seq * Sequence * @param str * Structure in dot bracket notation * @param drawMode * The drawing algorithm to be used for the initial placement * @throws ExceptionNonEqualLength * If len(seq)!=len(str) */ public void drawRNAInterpolated(String seq, String str, int drawMode) { drawRNAInterpolated(seq, str, drawMode, Mapping.DefaultOutermostMapping(_RNA.get_listeBases().size(), str.length())); } /** * Draws a secondary structure of RNA using the default drawing algorithm * and displays it, using an interpolated transition between the previous * one and the new one. Here, a mapping between those bases of the new * structure and the previous one is explicitly provided. * * @param seq * Sequence * @param str * Structure in dot bracket notation * @param m * A mapping between the currently rendered structure and its * successor (seq,str) * @throws ExceptionNonEqualLength * If len(seq)!=len(str) */ public void drawRNAInterpolated(String seq, String str, Mapping m) { drawRNAInterpolated(seq, str, _RNA.get_drawMode(), m); } /** * Draws a secondary structure of RNA using a given drawing algorithm and * displays it, using an interpolated transition between the previous one * and the new one. Here, a mapping between those bases of the new structure * and the previous one is provided. * * @param seq * Sequence * @param str * Structure in dot bracket notation * @param drawMode * The drawing algorithm to be used for the initial placement * @param m * A mapping between the currently rendered structure and its * successor (seq,str) */ public void drawRNAInterpolated(String seq, String str, int drawMode, Mapping m) { RNA target = new RNA(); try { target.setRNA(seq, str); drawRNAInterpolated(target, drawMode, m); } catch (ExceptionUnmatchedClosingParentheses e) { errorDialog(e); } catch (ExceptionFileFormatOrSyntax e) { errorDialog(e); } } /** * Draws a secondary structure of RNA using the default drawing algorithm * and displays it, using an interpolated transition between the previous * one and the new one. Here, a mapping between those bases of the new * structure and the previous one is explicitly provided. * * @param target * Secondary structure */ public void drawRNAInterpolated(RNA target) { drawRNAInterpolated(target, target.get_drawMode(), Mapping.DefaultOutermostMapping(_RNA.get_listeBases().size(), target.getSize())); } /** * Draws a secondary structure of RNA using the default drawing algorithm * and displays it, using an interpolated transition between the previous * one and the new one. Here, a mapping between those bases of the new * structure and the previous one is explicitly provided. * * @param target * Secondary structure * @param m * A mapping between the currently rendered structure and its * successor (seq,str) */ public void drawRNAInterpolated(RNA target, Mapping m) { drawRNAInterpolated(target, target.get_drawMode(), m); } /** * Draws a secondary structure of RNA using a given drawing algorithm and * displays it, using an interpolated transition between the previous one * and the new one. Here, a mapping between those bases of the new structure * and the previous one is provided. * * @param target * Secondary structure of RNA * @param drawMode * The drawing algorithm to be used for the initial placement * @param m * A mapping between the currently rendered structure and its * successor (seq,str) */ public void drawRNAInterpolated(RNA target, int drawMode, Mapping m) { try { target.drawRNA(drawMode, _conf); _conf._drawColorMap = false; _interpolator.addTarget(target, m); } catch (ExceptionNAViewAlgorithm e) { errorDialog(e); e.printStackTrace(); } } /** * Returns the current algorithm used for drawing the structure * * @return The current drawing algorithm */ public int getDrawMode() { return this._RNA.getDrawMode(); } public void showRNA(RNA t, VARNAConfig cfg) { showRNA(t); if (cfg != null) { this.setConfig(cfg); } repaint(); } /** * Checks whether an interpolated transition bewteen two RNAs is occurring. * * @return True if an interpolated transition is occurring, false otherwise */ public boolean isInterpolationInProgress() { if (_interpolator == null) { return false; } else return _interpolator.isInterpolationInProgress(); } /** * Simply displays (does not redraw) a secondary structure , using an * interpolated transition between the previous one and the new one. A * default mapping between those bases of the new structure and the previous * one is used. * * @param target * Secondary structure of RNA */ public void showRNAInterpolated(RNA target) { showRNAInterpolated(target, Mapping.DefaultOutermostMapping(_RNA .get_listeBases().size(), target.getSize())); } /** * Simply displays (does not redraw) a secondary structure , using an * interpolated transition between the previous one and the new one. Here, a * mapping between bases of the new structure and the previous one is given. * * @param target * Secondary structure of RNA * @param m * A mapping between the currently rendered structure and its * successor (seq,str) * @throws ExceptionNonEqualLength * If len(seq)!=len(str) */ public void showRNAInterpolated(RNA target, Mapping m) { showRNAInterpolated(target, null, m); } public void showRNAInterpolated(RNA target, VARNAConfig cfg, Mapping m) { _interpolator.addTarget(target, cfg, m); } /** * When comparison mode is ON, sets the two RNA secondary structure to be * drawn in this panel, using a given layout algorithm. In addition to the * raw nucleotides sequence, the secondary structure is given in the * so-called "Dot-bracket notation" (DBN) format. This format is a * well-parenthesized word over the alphabet '(',')','.'.
* Ex: ((((((((....))))..(((((...))).))))))
* * @param firstSeq * The first RNA raw nucleotides sequence * @param firstStruct * The first RNA secondary structure * @param secondSeq * The second RNA raw nucleotides sequence * @param secondStruct * The second RNA secondary structure * @param drawMode * The drawing algorithm */ public void drawRNA(String firstSeq, String firstStruct, String secondSeq, String secondStruct, int drawMode) { _RNA.setDrawMode(drawMode); /** * Checking the sequences and structures validities... */ // This is a comparison, so the two RNA alignment past in parameters // must // have the same sequence and structure length. if (firstSeq.length() == secondSeq.length() && firstStruct.length() == secondStruct.length()) { // First RNA if (firstSeq.length() != firstStruct.length()) { if (_conf._showWarnings) { emitWarning("First sequence length " + firstSeq.length() + " differs from that of it's secondary structure " + firstStruct.length() + ". \nAdapting first sequence length ..."); } if (firstSeq.length() < firstStruct.length()) { while (firstSeq.length() < firstStruct.length()) { firstSeq += " "; } } else { firstSeq = firstSeq.substring(0, firstStruct.length()); } } // Second RNA if (secondSeq.length() != secondStruct.length()) { if (_conf._showWarnings) { emitWarning("Second sequence length " + secondSeq.length() + " differs from that of it's secondary structure " + secondStruct.length() + ". \nAdapting second sequence length ..."); } if (secondSeq.length() < secondStruct.length()) { while (secondSeq.length() < secondStruct.length()) { secondSeq += " "; } } else { secondSeq = secondSeq.substring(0, secondStruct.length()); } } int RNALength = firstSeq.length(); String string_superStruct = new String(""); String string_superSeq = new String(""); /** * In this array, we'll have for each indexes of each characters of * the final super-structure, the RNA number which is own it. */ ArrayList array_rnaOwn = new ArrayList(); /** * Generating super-structure sequences and structures... */ firstStruct = firstStruct.replace('-', '.'); secondStruct = secondStruct.replace('-', '.'); // First of all, we make the structure for (int i = 0; i < RNALength; i++) { // If both characters are the same, so it'll be in the super // structure if (firstStruct.charAt(i) == secondStruct.charAt(i)) { string_superStruct = string_superStruct + firstStruct.charAt(i); array_rnaOwn.add(0); } // Else if one of the characters is an opening parenthese, so // it'll be an opening parenthese in the super structure else if (firstStruct.charAt(i) == '(' || secondStruct.charAt(i) == '(') { string_superStruct = string_superStruct + '('; array_rnaOwn.add((firstStruct.charAt(i) == '(') ? 1 : 2); } // Else if one of the characters is a closing parenthese, so // it'll be a closing parenthese in the super structure else if (firstStruct.charAt(i) == ')' || secondStruct.charAt(i) == ')') { string_superStruct = string_superStruct + ')'; array_rnaOwn.add((firstStruct.charAt(i) == ')') ? 1 : 2); } else { string_superStruct = string_superStruct + '.'; array_rnaOwn.add(-1); } } // Next, we make the sequence taking the characters at the same // index in the first and second sequence for (int i = 0; i < RNALength; i++) { string_superSeq = string_superSeq + firstSeq.charAt(i) + secondSeq.charAt(i); } // Now, we need to create the super-structure RNA with the owning // bases array // in order to color bases outer depending on the owning statement // of each bases. if (!string_superSeq.equals("") && !string_superStruct.equals("")) { try { _RNA.setRNA(string_superSeq, string_superStruct, array_rnaOwn); } catch (ExceptionUnmatchedClosingParentheses e) { errorDialog(e); } catch (ExceptionFileFormatOrSyntax e) { errorDialog(e); } } else { emitWarning("ERROR : The super-structure is NULL."); } switch (_RNA.get_drawMode()) { case RNA.DRAW_MODE_RADIATE: _RNA.drawRNARadiate(_conf); break; case RNA.DRAW_MODE_CIRCULAR: _RNA.drawRNACircle(_conf); break; case RNA.DRAW_MODE_LINEAR: _RNA.drawRNALine(_conf); break; case RNA.DRAW_MODE_NAVIEW: try { _RNA.drawRNANAView(_conf); } catch (ExceptionNAViewAlgorithm e) { errorDialog(e); } break; default: break; } } } /** * Returns the currently selected base index, obtained through a mouse-left * click * * @return Selected base * * public int getSelectedBaseIndex() { return _selectedBase; } * * /** Returns the currently selected base, obtained through a * mouse-left click * * @return Selected base * * public ModeleBase getSelectedBase() { return * _RNA.get_listeBases().get(_selectedBase); } * * /** Sets the selected base index * * @param base * New selected base index * * public void setSelectedBase(int base) { _selectedBase = base; * } */ /** * Returns the coordinates of the currently displayed RNA * * @return Coordinates array */ public Point2D.Double[] getRealCoords() { return _realCoords; } /** * Sets the coordinates of the currently displayed RNA * * @param coords * New coordinates */ public void setRealCoords(Point2D.Double[] coords) { _realCoords = coords; } /** * Returns the popup menu used for user mouse iteractions * * @return Popup menu */ public VueMenu getPopup() { return _popup; } /** * Sets the color used to display hydrogen bonds (base pairings) * * @param bond_color * The color of hydrogen bonds */ public void setBondColor(Color bond_color) { _conf._bondColor = bond_color; } /** * Returns the color used to draw the title * * @return The color used to draw the title */ public Color getTitleColor() { return _conf._titleColor; } /** * Sets the color used to draw the title * * @param title_color * The new color used to draw the title */ public void setTitleColor(Color title_color) { _conf._titleColor = title_color; } /** * Returns the height taken by the title * * @return The height taken by the title */ private int getTitleHeight() { return _titleHeight; } /** * Sets the height taken by the title * * @param title_height * The height taken by the title */ @SuppressWarnings("unused") private void setTitleHeight(int title_height) { _titleHeight = title_height; } /** * Returns the current state of auto centering mode. * * @return True if autocentered, false otherwise */ public boolean isAutoCentered() { return _conf._autoCenter; } /** * Sets the current state of auto centering mode. * * @param center * New auto-centered state */ public void setAutoCenter(boolean center) { _conf._autoCenter = center; } /** * Returns the font currently used for rendering the title. * * @return Current title font */ public Font getTitleFont() { return _conf._titleFont; } /** * Sets the font used for rendering the title. * * @param font * New title font */ public void setTitleFont(Font font) { _conf._titleFont = font; updateTitleHeight(); } /** * For the LINE_MODE drawing algorithm, sets the base pair height increment, * i.e. the vertical distance between two nested arcs. * * @return The current base pair increment */ public double getBPHeightIncrement() { return _RNA._bpHeightIncrement; } /** * Sets the base pair height increment, i.e. the vertical distance between * two arcs to be used in LINE_MODE. * * @param inc * New height increment */ public void setBPHeightIncrement(double inc) { _RNA._bpHeightIncrement = inc; } /** * Returns the shifting of the origin of the Panel in zoom mode * * @return The logical coordinate of the top-left panel point */ public Point2D.Double getOffsetPanel() { return _offsetPanel; } /** * Returns the vector bringing the logical coordinate of left-top-most point * in the panel to the left-top-most point of the RNA. * * @return The logical coordinate of the top-left panel point */ private Point2D.Double getRNAOffset() { return _offsetRNA; } /** * Returns this panel's UI menu * * @return Applet's UI popupmenu */ public VueMenu getPopupMenu() { return _popup; } /** * Returns the atomic zoom factor step, or increment. * * @return Atomic zoom factor increment */ public double getZoomIncrement() { return _conf._zoomAmount; } /** * Sets the atomic zoom factor step, or increment. * * @param amount * Atomic zoom factor increment */ public void setZoomIncrement(Object amount) { setZoomIncrement(Float.valueOf(amount.toString())); } /** * Sets the atomic zoom factor step, or increment. * * @param amount * Atomic zoom factor increment */ public void setZoomIncrement(double amount) { _conf._zoomAmount = amount; } /** * Returns the current zoom factor * * @return Current zoom factor */ public double getZoom() { return _conf._zoom; } /** * Sets the current zoom factor * * @param _zoom * New zoom factor */ public void setZoom(Object _zoom) { double d = Float.valueOf(_zoom.toString()); if (_conf._zoom != d) { _conf._zoom = d; fireZoomLevelChanged(d); } } /** * Returns the translation used for zooming in and out * * @return A vector describing the translation */ public Point getTranslation() { return _translation; } /** * Sets the translation used for zooming in and out * * @param trans * A vector describing the new translation */ public void setTranslation(Point trans) { _translation = trans; checkTranslation(); fireTranslationChanged(); } /** * Returns the current RNA model * * @return Current RNA model */ public RNA getRNA() { return _RNA; } /** * Checks whether the drawn RNA is too large to be displayed, allowing for * shifting mouse interactions. * * @return true if the RNA is too large to be displayed, false otherwise */ public boolean isOutOfFrame() { return _horsCadre; } /** * Pops up an error Dialog displaying an exception in an human-readable way. * * @param error * The exception to display within the Dialog */ public void errorDialog(Exception error) { errorDialog(error, this); } /** * Pops up an error Dialog displaying an exception in an human-readable way * if errors are set to be displayed. * * @see #setErrorsOn(boolean) * @param error * The exception to display within the Dialog * @param c * Parent component for the dialog box */ public void errorDialog(Exception error, Component c) { if (isErrorsOn()) { JOptionPane.showMessageDialog(c, error.getMessage(), "VARNA Error", JOptionPane.ERROR_MESSAGE); } } /** * Pops up an error Dialog displaying an exception in an human-readable way. * * @param error * The exception to display within the Dialog * @param c * Parent component for the dialog box */ public static void errorDialogStatic(Exception error, Component c) { if (c != null) { JOptionPane.showMessageDialog(c, error.getMessage(), "VARNA Critical Error", JOptionPane.ERROR_MESSAGE); } else { System.err.println("Error: " + error.getMessage()); } } /** * Displays a warning message through a modal dialog if warnings are set to * be displayed. * * @see #setShowWarnings(boolean) * @param warning * A message expliciting the warning */ public void emitWarning(String warning) { if (_conf._showWarnings) JOptionPane.showMessageDialog(this, warning, "VARNA Warning", JOptionPane.WARNING_MESSAGE); } public static void emitWarningStatic(Exception e, Component c) { emitWarningStatic(e.getMessage(), c); } public static void emitWarningStatic(String warning, Component c) { if (c != null) { JOptionPane.showMessageDialog(c, warning, "VARNA Warning", JOptionPane.WARNING_MESSAGE); } else { System.err.println("Error: " + warning); } } /** * Toggles modifications on and off * * @param modifiable * Modification status */ public void setModifiable(boolean modifiable) { _conf._modifiable = modifiable; } /** * Returns current modification status * * @return current modification status */ public boolean isModifiable() { return _conf._modifiable; } /** * Resets the visual aspects (Zoom factor, shift) for the Panel. */ public void reset() { this.setBorderSize(new Dimension(0, 0)); this.setTranslation(new Point(0, (int) (-getTitleHeight() / 2.0))); this.setZoom(VARNAConfig.DEFAULT_ZOOM); this.setZoomIncrement(VARNAConfig.DEFAULT_AMOUNT); } /** * Returns the color used to draw non-standard bases * * @return The color used to draw non-standard bases */ public Color getNonStandardBasesColor() { return _conf._specialBasesColor; } /** * Sets the color used to draw non-standard bases * * @param basesColor * The color used to draw non-standard bases */ public void setNonStandardBasesColor(Color basesColor) { _conf._specialBasesColor = basesColor; } /** * Checks if the current translation doesn't "kick" the whole RNA out of the * panel, and corrects the situation if necessary. */ public void checkTranslation() { // verification pour un zoom < 1 if (this.getZoom() <= 1) { // verification sortie gauche if (this.getTranslation().x < -(int) ((this.getWidth() - this .getInnerWidth()) / 2.0)) { this.setTranslation(new Point(-(int) ((this.getWidth() - this .getInnerWidth()) / 2.0), this.getTranslation().y)); } // verification sortie droite if (this.getTranslation().x > (int) ((this.getWidth() - this .getInnerWidth()) / 2.0)) { this.setTranslation(new Point((int) ((this.getWidth() - this .getInnerWidth()) / 2.0), this.getTranslation().y)); } // verification sortie bas if (this.getTranslation().y > (int) ((this.getHeight() - getTitleHeight() * 2 - this.getInnerHeight()) / 2.0)) { this.setTranslation(new Point(this.getTranslation().x, (int) ((this.getHeight() - getTitleHeight() * 2 - this .getInnerHeight()) / 2.0))); } // verification sortie haut if (this.getTranslation().y < -(int) ((this.getHeight() - this .getInnerHeight()) / 2.0)) { this.setTranslation(new Point( this.getTranslation().x, -(int) ((this.getHeight() - this.getInnerHeight()) / 2.0))); } } else { // zoom > 1 Rectangle r2 = getZoomedInTranslationBox(); int LBoundX = r2.x; int UBoundX = r2.x + r2.width; int LBoundY = r2.y; int UBoundY = r2.y + r2.height; if (this.getTranslation().x < LBoundX) { this.setTranslation(new Point(LBoundX, getTranslation().y)); } else if (this.getTranslation().x > UBoundX) { this.setTranslation(new Point(UBoundX, getTranslation().y)); } if (this.getTranslation().y < LBoundY) { this.setTranslation(new Point(getTranslation().x, LBoundY)); } else if (this.getTranslation().y > UBoundY) { this.setTranslation(new Point(getTranslation().x, UBoundY)); } } } public Rectangle getZoomedInTranslationBox() { int LBoundX = -(int) ((this.getInnerWidth()) / 2.0); int UBoundX = (int) ((this.getInnerWidth()) / 2.0); int LBoundY = -(int) ((this.getInnerHeight()) / 2.0); int UBoundY = (int) ((this.getInnerHeight()) / 2.0); return new Rectangle(LBoundX, LBoundY, UBoundX - LBoundX, UBoundY - LBoundY); } /** * Returns the "real pixels" x-coordinate of the RNA. * * @return X-coordinate of the translation */ public int getLeftOffset() { return _border.width + ((this.getWidth() - 2 * _border.width) - this.getInnerWidth()) / 2 + _translation.x; } /** * Returns the "real pixels" width of the drawing surface for our RNA. * * @return Width of the drawing surface for our RNA */ public int getInnerWidth() { // Largeur du dessin return (int) Math.round((this.getWidth() - 2 * _border.width) * _conf._zoom); } /** * Returns the "real pixels" y-coordinate of the RNA. * * @return Y-coordinate of the translation */ public int getTopOffset() { return _border.height + ((this.getHeight() - 2 * _border.height) - this .getInnerHeight()) / 2 + _translation.y; } /** * Returns the "real pixels" height of the drawing surface for our RNA. * * @return Height of the drawing surface for our RNA */ public int getInnerHeight() { // Hauteur du dessin return (int) Math.round((this.getHeight()) * _conf._zoom - 2 * _border.height - getTitleHeight()); } /** * Checks if the current mode is the "comparison" mode * * @return True if comparison, false otherwise */ public boolean isComparisonMode() { return _conf._comparisonMode; } /** * Rotates the RNA coordinates by a certain angle * * @param angleDegres * Rotation angle, in degrees */ public void globalRotation(Double angleDegres) { _RNA.globalRotation(angleDegres); fireLayoutChanged(); repaint(); } /** * Returns the index of the currently selected base, defaulting to the * closest base to the last mouse-click. * * @return Index of the currently selected base */ public Integer getNearestBase() { return _nearestBase; } /** * Sets the index of the currently selected base. * * @param base * Index of the new selected base */ public void setNearestBase(Integer base) { _nearestBase = base; } /** * Returns the color used to draw 'Gaps' bases in comparison mode * * @return Color used for 'Gaps' */ public Color getGapsBasesColor() { return _conf._dashBasesColor; } /** * Sets the color to use for 'Gaps' bases in comparison mode * * @param c * Color used for 'Gaps' */ public void setGapsBasesColor(Color c) { _conf._dashBasesColor = c; } @SuppressWarnings("unused") private void imprimer() { // PrintPanel canvas; // canvas = new PrintPanel(); PrintRequestAttributeSet attributes; attributes = new HashPrintRequestAttributeSet(); try { PrinterJob job = PrinterJob.getPrinterJob(); // job.setPrintable(this); if (job.printDialog(attributes)) { job.print(attributes); } } catch (PrinterException exception) { errorDialog(exception); } } /** * Checks whether errors are to be displayed * * @return Error display status */ public boolean isErrorsOn() { return _conf._errorsOn; } /** * Sets whether errors are to be displayed * * @param on * New error display status */ public void setErrorsOn(boolean on) { _conf._errorsOn = on; } /** * Returns the view associated with user interactions * * @return A view associated with user interactions */ public VueUI getVARNAUI() { return _UI; } /** * Toggles on/off using base inner color for drawing base-pairs * * @param on * True for using base inner color for drawing base-pairs, false * for classic mode */ public void setUseBaseColorsForBPs(boolean on) { _conf._useBaseColorsForBPs = on; } /** * Returns true if current base color is used as inner color for drawing * base-pairs * * @return True for using base inner color for drawing base-pairs, false for * classic mode */ public boolean getUseBaseColorsForBPs() { return _conf._useBaseColorsForBPs; } /** * Toggles on/off using a special color used for drawing "non-standard" * bases * * @param on * True for using a special color used for drawing "non-standard" * bases, false for classic mode */ public void setColorNonStandardBases(boolean on) { _conf._colorSpecialBases = on; } /** * Returns true if a special color is used as inner color for non-standard * base * * @return True for using a special color used for drawing "non-standard" * bases, false for classic mode */ public boolean getColorSpecialBases() { return _conf._colorSpecialBases; } /** * Toggles on/off using a special color used for drawing "Gaps" bases in * comparison mode * * @param on * True for using a special color used for drawing "Gaps" bases * in comparison mode, false for classic mode */ public void setColorGapsBases(boolean on) { _conf._colorDashBases = on; } /** * Returns true if a special color is used for drawing "Gaps" bases in * comparison mode * * @return True for using a special color used for drawing "Gaps" bases in * comparison mode, false for classic mode */ public boolean getColorGapsBases() { return _conf._colorDashBases; } /** * Toggles on/off displaying warnings * * @param on * True to display warnings, false otherwise */ public void setShowWarnings(boolean on) { _conf._showWarnings = on; } /** * Get current warning display status * * @return True to display warnings, false otherwise */ public boolean getShowWarnings() { return _conf._showWarnings; } /** * Toggles on/off displaying non-canonical base-pairs * * @param on * True to display NC base-pairs, false otherwise */ public void setShowNonCanonicalBP(boolean on) { _conf._drawnNonCanonicalBP = on; } /** * Return the current display status for non-canonical base-pairs * * @return True if NC base-pairs are displayed, false otherwise */ public boolean getShowNonCanonicalBP() { return _conf._drawnNonCanonicalBP; } /** * Toggles on/off displaying "non-planar" base-pairs * * @param on * True to display "non-planar" base-pairs, false otherwise */ public void setShowNonPlanarBP(boolean on) { _conf._drawnNonPlanarBP = on; } /** * Return the current display status for non-planar base-pairs * * @return True if non-planars base-pairs are displayed, false otherwise */ public boolean getShowNonPlanarBP() { return _conf._drawnNonPlanarBP; } /** * Sets the base-pair representation style * * @param st * The new base-pair style */ public void setBPStyle(VARNAConfig.BP_STYLE st) { _conf._mainBPStyle = st; } /** * Returns the base-pair representation style * * @return The current base-pair style */ public VARNAConfig.BP_STYLE getBPStyle() { return _conf._mainBPStyle; } /** * Returns the current VARNA Panel configuration. The returned instance * should not be modified directly, but rather through the getters/setters * from the VARNAPanel class. * * @return Current configuration */ public VARNAConfig getConfig() { return _conf; } /** * Sets the background color * * @param c * New background color */ public void setBackground(Color c) { if (_conf != null) { if (c != null) { _conf._backgroundColor = c; _conf._drawBackground = (!c .equals(VARNAConfig.DEFAULT_BACKGROUND_COLOR)); } else { _conf._backgroundColor = VARNAConfig.DEFAULT_BACKGROUND_COLOR; _conf._drawBackground = false; } } } /** * Starts highlighting the selected base. */ public void highlightSelectedBase(ModeleBase m) { ArrayList v = new ArrayList(); int sel = m.getIndex(); if (sel != -1) { v.add(sel); } setSelection(v); } /** * Starts highlighting the selected base. */ public void highlightSelectedStem(ModeleBase m) { ArrayList v = new ArrayList(); int sel = m.getIndex(); if (sel != -1) { ArrayList r = _RNA.findStem(sel); v.addAll(r); } setSelection(v); } public BaseList getSelection() { return _selectedBases; } public ArrayList getSelectionIndices() { return _selectedBases.getIndices(); } public void setSelection(ArrayList indices) { setSelection(_RNA.getBasesAt(indices)); } public void setSelection(Collection mbs) { BaseList bck = new BaseList(_selectedBases); _selectedBases.clear(); _selectedBases.addBases(mbs); _blink.setActive(true); fireSelectionChanged(bck, _selectedBases); } public ArrayList getBasesInRectangleDiff(Rectangle recIn, Rectangle recOut) { ArrayList result = new ArrayList(); for (int i = 0; i < _realCoords.length; i++) { if (recIn.contains(_realCoords[i]) ^ recOut.contains(_realCoords[i])) result.add(i); } return result; } public ArrayList getBasesInRectangle(Rectangle rec) { ArrayList result = new ArrayList(); for (int i = 0; i < _realCoords.length; i++) { if (rec.contains(_realCoords[i])) result.add(i); } return result; } public void setSelectionRectangle(Rectangle rec) { ArrayList result = new ArrayList(); if (_selectionRectangle != null) { result = getBasesInRectangleDiff(_selectionRectangle, rec); } else { result = getBasesInRectangle(rec); } _selectionRectangle = new Rectangle(rec); toggleSelection(result); repaint(); } public void removeSelectionRectangle() { _selectionRectangle = null; } public void addToSelection(Collection indices) { for (int i : indices) { addToSelection(i); } } public void addToSelection(int i) { BaseList bck = new BaseList(_selectedBases); ModeleBase mb = _RNA.getBaseAt(i); _selectedBases.addBase(mb); _blink.setActive(true); fireSelectionChanged(bck, _selectedBases); } public void removeFromSelection(int i) { BaseList bck = new BaseList(_selectedBases); ModeleBase mb = _RNA.getBaseAt(i); _selectedBases.removeBase(mb); if (_selectedBases.size() == 0) { _blink.setActive(false); } else { _blink.setActive(true); } fireSelectionChanged(bck, _selectedBases); } public boolean isInSelection(int i) { return _selectedBases.contains(_RNA.getBaseAt(i)); } public void toggleSelection(int i) { if (isInSelection(i)) removeFromSelection(i); else addToSelection(i); } public void toggleSelection(Collection indices) { for (int i : indices) { toggleSelection(i); } } /** * Stops highlighting bases */ public void clearSelection() { BaseList bck = new BaseList(_selectedBases); _selectedBases.clear(); _blink.setActive(false); repaint(); fireSelectionChanged(bck, _selectedBases); } public void saveSelection() { _backupSelection.clear(); _backupSelection.addAll(_selectedBases.getBases()); } public void restoreSelection() { setSelection(_backupSelection); } /** * Stops highlighting bases */ public void resetAnnotationHighlight() { _highlightAnnotation = false; repaint(); } /** * Toggles on/off a rectangular outline of the bounding box. * * @param on * True to draw the bounding box, false otherwise */ public void drawBBox(boolean on) { _drawBBox = on; } /** * Toggles on/off a rectangular outline of the border. * * @param on * True to draw the bounding box, false otherwise */ public void drawBorder(boolean on) { _drawBorder = on; } public void setBaseInnerColor(Color c) { _RNA.setBaseInnerColor(c); } public void setBaseNumbersColor(Color c) { _RNA.setBaseNumbersColor(c); } public void setBaseNameColor(Color c) { _RNA.setBaseNameColor(c); } public void setBaseOutlineColor(Color c) { _RNA.setBaseOutlineColor(c); } public ArrayList getListeAnnotations() { return _RNA.getAnnotations(); } public void resetListeAnnotations() { _RNA.clearAnnotations(); repaint(); } public void addAnnotation(TextAnnotation textAnnotation) { _RNA.addAnnotation(textAnnotation); repaint(); } public boolean removeAnnotation(TextAnnotation textAnnotation) { boolean done = _RNA.removeAnnotation(textAnnotation); repaint(); return done; } public TextAnnotation get_selectedAnnotation() { return _selectedAnnotation; } public void set_selectedAnnotation(TextAnnotation annotation) { _selectedAnnotation = annotation; } public void removeSelectedAnnotation() { _highlightAnnotation = false; _selectedAnnotation = null; } public void highlightSelectedAnnotation() { _highlightAnnotation = true; } public boolean getFlatExteriorLoop() { return _conf._flatExteriorLoop; } public void setFlatExteriorLoop(boolean on) { _conf._flatExteriorLoop = on; } public void setLastSelectedPosition(Point2D.Double p) { _lastSelectedCoord.x = p.x; _lastSelectedCoord.y = p.y; } public Point2D.Double getLastSelectedPosition() { return _lastSelectedCoord; } public void setSequence(String s) { _RNA.setSequence(s); repaint(); } public void setColorMapVisible(boolean b) { _conf._drawColorMap = b; repaint(); } public boolean getColorMapVisible() { return _conf._drawColorMap; } public void removeColorMap() { _conf._drawColorMap = false; repaint(); } public void saveSession(String path) { /* * FileOutputStream fos = null; ObjectOutputStream out = null; try { fos * = new FileOutputStream(path); out = new ObjectOutputStream(fos); * out.writeObject(new FullBackup(_conf, _RNA, _conf._title)); * out.close(); } catch (Exception ex) { ex.printStackTrace(); } */ toXML(path); } public FullBackup loadSession(String path) throws ExceptionLoadingFailed { FullBackup bck = importSession(path); Mapping map = Mapping.DefaultOutermostMapping(getRNA().getSize(), bck.rna.getSize()); showRNAInterpolated(bck.rna, map); _conf = bck.config; repaint(); return bck; } public static String VARNA_SESSION_EXTENSION = "varna"; public static FullBackup importSession(String path) throws ExceptionLoadingFailed { try { FileInputStream fis = new FileInputStream(path); // ZipInputStream zis = new // ZipInputStream(new BufferedInputStream(fis)); // zis.getNextEntry(); FullBackup h = importSession(fis, path); // zis.close(); return h; } catch (FileNotFoundException e) { throw (new ExceptionLoadingFailed("File not found.", path)); } catch (IOException e) { // TODO Auto-generated catch block throw (new ExceptionLoadingFailed( "I/O error while loading session.", path)); } } public static FullBackup importSession(InputStream fis, String path) throws ExceptionLoadingFailed { System.setProperty("javax.xml.parsers.SAXParserFactory", "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl"); SAXParserFactory saxFact = javax.xml.parsers.SAXParserFactory .newInstance(); saxFact.setValidating(false); saxFact.setXIncludeAware(false); saxFact.setNamespaceAware(false); try { SAXParser sp = saxFact.newSAXParser(); VARNASessionParser sessionData = new VARNASessionParser(); sp.parse(fis, sessionData); FullBackup res = new FullBackup(sessionData.getVARNAConfig(), sessionData.getRNA(), "test"); return res; } catch (ParserConfigurationException e) { throw new ExceptionLoadingFailed("Bad XML parser configuration", path); } catch (SAXException e) { throw new ExceptionLoadingFailed("XML parser Exception", path); } catch (IOException e) { throw new ExceptionLoadingFailed("I/O error", path); } } public void loadFile(String path) { loadFile(path, false); } public boolean getDrawBackbone() { return _conf._drawBackbone; } public void setDrawBackbone(boolean b) { _conf._drawBackbone = b; } public void addHighlightRegion(HighlightRegionAnnotation n) { _RNA.addHighlightRegion(n); } public void removeHighlightRegion(HighlightRegionAnnotation n) { _RNA.removeHighlightRegion(n); } public void addHighlightRegion(int i, int j) { _RNA.addHighlightRegion(i, j); } public void addHighlightRegion(int i, int j, Color fill, Color outline, double radius) { _RNA.addHighlightRegion(i, j, fill, outline, radius); } public void loadRNA(String path) { loadRNA(path, false); } public void loadRNA(String path, boolean interpolate) { try { Collection rnas = RNAFactory.loadSecStr(path); if (rnas.isEmpty()) { throw new ExceptionFileFormatOrSyntax( "No RNA could be parsed from that source."); } RNA rna = rnas.iterator().next(); try { rna.drawRNA(_conf); } catch (ExceptionNAViewAlgorithm e) { e.printStackTrace(); } if (!interpolate) { showRNA(rna); } else { this.showRNAInterpolated(rna); } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e) { e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } } public void loadFile(String path, boolean interpolate) { try { loadSession(path); } catch (Exception e1) { loadRNA(path, interpolate); } } public void setConfig(VARNAConfig cfg) { _conf = cfg; } public void toggleDrawOutlineBases() { _conf._drawOutlineBases = !_conf._drawOutlineBases; } public void toggleFillBases() { _conf._fillBases = !_conf._fillBases; } public void setDrawOutlineBases(boolean drawn) { _conf._drawOutlineBases = drawn; } public void setFillBases(boolean drawn) { _conf._fillBases = drawn; } public void readValues(Reader r) { this._RNA.readValues(r, _conf._cm); } public void addVARNAListener(InterfaceVARNAListener v) { _VARNAListeners.add(v); } public void fireLayoutChanged() { for (InterfaceVARNAListener v : _VARNAListeners) { v.onStructureRedrawn(); } } public void fireUINewStructure(RNA r) { for (InterfaceVARNAListener v : _VARNAListeners) { v.onUINewStructure(_conf, r); } } public void fireZoomLevelChanged(double d) { for (InterfaceVARNAListener v : _VARNAListeners) { v.onZoomLevelChanged(); } } public void fireTranslationChanged() { for (InterfaceVARNAListener v2 : _VARNAListeners) { v2.onTranslationChanged(); } } public void addSelectionListener(InterfaceVARNASelectionListener v) { _selectionListeners.add(v); } public void fireSelectionChanged(BaseList mold, BaseList mnew) { BaseList addedBases = mnew.removeAll(mold); BaseList removedBases = mold.removeAll(mnew); for (InterfaceVARNASelectionListener v2 : _selectionListeners) { v2.onSelectionChanged(mnew, addedBases, removedBases); } } public void fireHoverChanged(ModeleBase mold, ModeleBase mnew) { for (InterfaceVARNASelectionListener v2 : _selectionListeners) { v2.onHoverChanged(mold, mnew); } } public void addRNAListener(InterfaceVARNARNAListener v) { _RNAListeners.add(v); } public void addVARNABasesListener(InterfaceVARNABasesListener l) { _basesListeners.add(l); } public void fireSequenceChanged(int index, String oldseq, String newseq) { for (InterfaceVARNARNAListener v2 : _RNAListeners) { v2.onSequenceModified(index, oldseq, newseq); } } public void fireStructureChanged(Set current, Set addedBasePairs, Set removedBasePairs) { for (InterfaceVARNARNAListener v2 : _RNAListeners) { v2.onStructureModified(current, addedBasePairs, removedBasePairs); } } public void fireLayoutChanged( Hashtable movedPositions) { for (InterfaceVARNARNAListener v2 : _RNAListeners) { v2.onRNALayoutChanged(movedPositions); } } public void fireBaseClicked(ModeleBase mb, MouseEvent me) { if (mb != null) { for (InterfaceVARNABasesListener v2 : _basesListeners) { v2.onBaseClicked(mb, me); } } } public double getOrientation() { return _RNA.getOrientation(); } public ModeleBase _hoveredBase = null; public void setHoverBase(ModeleBase m) { if (m != _hoveredBase) { ModeleBase bck = _hoveredBase; _hoveredBase = m; repaint(); fireHoverChanged(bck, m); } } public void toXML(String path) { FileOutputStream fis; try { fis = new FileOutputStream(path); // ZipOutputStream zis = new ZipOutputStream(new // BufferedOutputStream(fis)); // ZipEntry entry = new ZipEntry("VARNASession"); // zis.putNextEntry(entry); PrintWriter pw = new PrintWriter(fis); toXML(pw); pw.flush(); // zis.closeEntry(); // zis.close(); fis.close(); } catch (FileNotFoundException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } public void toXML(PrintWriter out) { try { // out = new PrintWriter(System.out); StreamResult streamResult = new StreamResult(out); SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory .newInstance(); // SAX2.0 ContentHandler. TransformerHandler hd = tf.newTransformerHandler(); Transformer serializer = hd.getTransformer(); serializer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1"); serializer .setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "users.dtd"); serializer.setOutputProperty(OutputKeys.INDENT, "yes"); hd.setResult(streamResult); hd.startDocument(); toXML(hd); hd.endDocument(); } catch (TransformerConfigurationException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (SAXException e) { // TODO Auto-generated catch block e.printStackTrace(); } } public static String XML_ELEMENT_NAME = "VARNASession"; public void toXML(TransformerHandler hd) throws SAXException { AttributesImpl atts = new AttributesImpl(); hd.startElement("", "", XML_ELEMENT_NAME, atts); _RNA.toXML(hd); _conf.toXML(hd); hd.endElement("", "", XML_ELEMENT_NAME); } public TextAnnotation getNearestAnnotation(int x, int y) { TextAnnotation t = null; if (getListeAnnotations().size() != 0) { double dist = Double.MAX_VALUE; double d2; Point2D.Double position; for (TextAnnotation textAnnot : getListeAnnotations()) { // calcul de la distance position = textAnnot.getCenterPosition(); position = transformCoord(position); d2 = Math.sqrt(Math.pow((position.x - x), 2) + Math.pow((position.y - y), 2)); // si la valeur est inferieur au minimum actuel if ((dist > d2) && (d2 < getScaleFactor() * ControleurClicMovement.MIN_SELECTION_DISTANCE)) { t = textAnnot; dist = d2; } } } return t; } public ModeleBase getNearestBase(int x, int y, boolean always, boolean onlyPaired) { int i = getNearestBaseIndex(x, y, always, onlyPaired); if (i == -1) return null; return getRNA().get_listeBases().get(i); } public ModeleBase getNearestBase(int x, int y) { return getNearestBase(x, y, false, false); } public int getNearestBaseIndex(int x, int y, boolean always, boolean onlyPaired) { double d2, dist = Double.MAX_VALUE; int mb = -1; for (int i = 0; i < getRealCoords().length; i++) { if (!onlyPaired || (getRNA().get_listeBases().get(i).getElementStructure() != -1)) { d2 = Math.sqrt(Math.pow((getRealCoords()[i].x - x), 2) + Math.pow((getRealCoords()[i].y - y), 2)); if ((dist > d2) && ((d2 < getScaleFactor() * ControleurClicMovement.MIN_SELECTION_DISTANCE) || always)) { dist = d2; mb = i; } } } return mb; } public void globalRescale(double factor) { _RNA.rescale(factor); fireLayoutChanged(); repaint(); } public void setSpaceBetweenBases(double sp) { _conf._spaceBetweenBases = sp; } public double getSpaceBetweenBases() { return _conf._spaceBetweenBases; } } fr/orsay/lri/varna/views/0000755000000000000000000000000012275611446014362 5ustar rootrootfr/orsay/lri/varna/views/VueBPThickness.java0000644000000000000000000000713611621171216020057 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import java.util.ArrayList; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.ModeleBP; public class VueBPThickness implements ChangeListener { private VARNAPanel _vp; ArrayList _msbp; private JSlider _thicknessSlider; private JPanel panel; private ArrayList _backupThicknesses = new ArrayList(); private double FACTOR = 10.0; public VueBPThickness(VARNAPanel vp, ArrayList msbp) { _vp = vp; _msbp = msbp; backupThicknesses(); _thicknessSlider = new JSlider(JSlider.HORIZONTAL, 1, 100, (int) (msbp.get(0).getStyle().getThickness( VARNAConfig.DEFAULT_BP_THICKNESS) * FACTOR)); _thicknessSlider.setMajorTickSpacing(10); _thicknessSlider.setPaintTicks(true); _thicknessSlider.setPaintLabels(false); _thicknessSlider.setPreferredSize(new Dimension(500, 50)); JLabel thicknessLabel = new JLabel(String.valueOf(msbp.get(0).getStyle() .getThickness(VARNAConfig.DEFAULT_BP_THICKNESS))); thicknessLabel.setPreferredSize(new Dimension(50, thicknessLabel .getPreferredSize().height)); _thicknessSlider.addChangeListener(new ControleurSliderLabel( thicknessLabel, 1.0 / FACTOR)); _thicknessSlider.addChangeListener(this); panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JLabel labelZ = new JLabel("Thickness:"); panel.add(labelZ); panel.add(_thicknessSlider); panel.add(thicknessLabel); } private void backupThicknesses() { for (int i = 0; i < _msbp.size(); i++) { this._backupThicknesses.add(_msbp.get(i).getStyle().getThickness( VARNAConfig.DEFAULT_BP_THICKNESS)); } } public void restoreThicknesses() { for (int i = 0; i < _msbp.size(); i++) { _msbp.get(i).getStyle().setThickness(_backupThicknesses.get(i)); } } public JPanel getPanel() { return panel; } public double getThickness() { return (double) _thicknessSlider.getValue() / FACTOR; } public VARNAPanel get_vp() { return _vp; } public void stateChanged(ChangeEvent e) { for (int i = 0; i < _msbp.size(); i++) { _msbp.get(i).getStyle().setThickness( ((double) _thicknessSlider.getValue()) / FACTOR); } _vp.repaint(); } } fr/orsay/lri/varna/views/VueRNAList.java0000644000000000000000000001242211724511664017161 0ustar rootrootpackage fr.orsay.lri.varna.views; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyVetoException; import java.beans.VetoableChangeListener; import java.util.ArrayList; import java.util.Collection; import java.util.Vector; import javax.swing.JButton; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.event.TableModelEvent; import javax.swing.event.TableModelListener; import javax.swing.table.AbstractTableModel; import javax.swing.table.TableColumn; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.components.ColorRenderer; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.models.rna.RNA; public class VueRNAList extends JPanel implements TableModelListener, ActionListener { private JTable table; private ValueTableModel _tm; private ArrayList data; private ArrayList columns; private ArrayList included; public VueRNAList( ArrayList rnas) { super(new BorderLayout()); data = rnas; init(); } public ArrayList getSelectedRNAs() { ArrayList result = new ArrayList(); for (int i = 0; i < data.size(); i++) { if (included.get(i)) { result.add(data.get(i)); } } return result; } private void init() { Object[] col = {"Num","Selected","Name","ID","Length"}; columns = new ArrayList(); for (int i = 0; i < col.length; i++) { columns.add(col[i]); } included = new ArrayList(); for (int i = 0; i < data.size(); i++) { included.add(new Boolean(true)); } _tm = new ValueTableModel(); table = new JTable(_tm); table.setDefaultRenderer(Color.class, new ColorRenderer(true)); table.setPreferredScrollableViewportSize(new Dimension(600, 300)); table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); TableColumn c0 = table.getColumnModel().getColumn(0); c0.setPreferredWidth(30); TableColumn c1 = table.getColumnModel().getColumn(1); c1.setPreferredWidth(30); TableColumn c2 = table.getColumnModel().getColumn(2); c2.setPreferredWidth(200); TableColumn c3 = table.getColumnModel().getColumn(3); c3.setPreferredWidth(200); TableColumn c4 = table.getColumnModel().getColumn(4); c4.setPreferredWidth(30); table.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS); table.getModel().addTableModelListener(this); JScrollPane scrollPane = new JScrollPane(table); this.add(scrollPane,BorderLayout.CENTER); JPanel jp = new JPanel(); JPanel jpl = new JPanel(); JPanel jpr = new JPanel(); jp.setLayout(new BorderLayout()); jp.add(jpl,BorderLayout.WEST); jp.add(jpr,BorderLayout.EAST); jp.add(new JLabel("Please select which model(s) should be imported." ),BorderLayout.SOUTH); JButton selectAll = new JButton("Select All"); selectAll.addActionListener(this); selectAll.setActionCommand("all"); JButton deselectAll = new JButton("Deselect All"); deselectAll.addActionListener(this); deselectAll.setActionCommand("none"); jpl.add(selectAll); jpr.add(deselectAll); add(scrollPane,BorderLayout.CENTER); add(jp,BorderLayout.SOUTH); } private class ValueTableModel extends AbstractTableModel { public String getColumnName(int col) { return columns.get(col).toString(); } public int getRowCount() { return data.size(); } public int getColumnCount() { return columns.size(); } public Object getValueAt(int row, int col) { RNA r = data.get(row); if (col==0) { return new Integer(row+1); } else if (col==1) { return new Boolean(included.get(row)); } else if (col==2) { return new String(r.getName()); } else if (col==3) { return new String(r.getID()); } else if (col==4) { return new Integer(r.getSize()); } return "N/A"; } public boolean isCellEditable(int row, int col) { if (col==1) return true; return false; } public void setValueAt(Object value, int row, int col) { if (col==1) { included.set(row, (Boolean)value); fireTableCellUpdated(row, col); } } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } } public void tableChanged(TableModelEvent e) { if (e.getType() == TableModelEvent.UPDATE) { table.repaint(); } } public void actionPerformed(ActionEvent e) { if (e.getActionCommand().equals("none")) { for(int i=0;i data = new ArrayList(); private Hashtable revdata = new Hashtable(); private JTable table; private BaseTableModel specialTableModel; public VueBases(VARNAPanel vp, int mode) { super(new GridLayout(1, 0)); _vp = vp; switch (mode) { case (KIND_MODE): _mode = KIND_MODE; kindMode(); break; case (ALL_MODE): _mode = ALL_MODE; allMode(); break; case (COUPLE_MODE): _mode = COUPLE_MODE; coupleMode(); break; default: break; } } private BaseList locateOrAddList(String caption) { if (!revdata.containsKey(caption)) { BaseList mbl = new BaseList(caption); revdata.put(caption,mbl); data.add(mbl); } return revdata.get(caption); } private void coupleMode() { String pairString; for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) { int j = _vp.getRNA().get_listeBases().get(i).getElementStructure(); if (j > i) { String tmp1 = (_vp.getRNA().get_listeBases().get(i).getContent()); String tmp2 = (_vp.getRNA().get_listeBases().get(j).getContent()); pairString = tmp1 +"-"+ tmp2; BaseList bl = locateOrAddList(pairString); bl.addBase(_vp.getRNA().get_listeBases().get(i)); bl.addBase(_vp.getRNA().get_listeBases().get(j)); } } createView(); } private void allMode() { for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) { ModeleBase mb = _vp.getRNA().get_listeBases().get(i); BaseList bl = locateOrAddList(""+i); bl.addBase(mb); } createView(); } private void kindMode() { for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) { ModeleBase mb = _vp.getRNA().get_listeBases().get(i); String tmp1 = (mb.getContent()); BaseList bl = locateOrAddList(tmp1); bl.addBase(mb); } createView(); } private void createView() { specialTableModel = new BaseTableModel(data); table = new JTable(specialTableModel); table.setPreferredScrollableViewportSize(new Dimension(500, 300)); // TODO: Find equivalent in JRE 1.5 //table.setFillsViewportHeight(true); // Create the scroll pane and add the table to it. JScrollPane scrollPane = new JScrollPane(table); // Set up renderer and editor for the Favorite Color column. table.setDefaultRenderer(Color.class, new ColorRenderer(true)); table.setDefaultEditor(Color.class, new BaseSpecialColorEditor(this)); specialTableModel.addTableModelListener(new TableModelListener(){ public void tableChanged(TableModelEvent e) { _vp.repaint(); } }); // Add the scroll pane to this panel. add(scrollPane); UIvueBases(); } /** * Create the GUI and show it. For thread safety, this method should be * invoked from the event-dispatching thread. */ public void UIvueBases() { // Create and set up the content pane. JComponent newContentPane = this; newContentPane.setOpaque(true); // content panes must be opaque JOptionPane.showMessageDialog(_vp, newContentPane, "Base Colors Edition", JOptionPane.PLAIN_MESSAGE); } public int getMode() { return _mode; } public BaseList getDataAt(int i) { return data.get(i); } public ArrayList getData() { return data; } public VARNAPanel get_vp() { return _vp; } public JTable getTable() { return table; } public void setTable(JTable table) { this.table = table; } public BaseTableModel getSpecialTableModel() { return specialTableModel; } public void setSpecialTableModel(BaseTableModel specialTableModel) { this.specialTableModel = specialTableModel; } } fr/orsay/lri/varna/views/VueLoadColorMapValues.java0000644000000000000000000000563111620715272021401 0ustar rootrootpackage fr.orsay.lri.varna.views; import java.awt.CardLayout; import java.awt.Dimension; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.Reader; import java.net.MalformedURLException; import java.net.URL; import java.net.URLConnection; import javax.swing.ButtonGroup; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JFileChooser; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JTextField; import fr.orsay.lri.varna.VARNAPanel; public class VueLoadColorMapValues extends JPanel implements ActionListener { /** * */ private static final long serialVersionUID = -1648400107478203724L; VARNAPanel _vp; public VueLoadColorMapValues(VARNAPanel vp) { _vp = vp; init(); } JRadioButton urlCB = new JRadioButton("URL"); JRadioButton fileCB = new JRadioButton("File"); JPanel urlAux = new JPanel(); JPanel fileAux = new JPanel(); CardLayout l = new CardLayout(); JPanel input = new JPanel(); JTextField urlTxt = new JTextField(); JTextField fileTxt = new JTextField(); JButton load = new JButton("Choose file"); private void init() { setLayout(new GridLayout(2,1)); JPanel choice = new JPanel(); urlCB.addActionListener(this); fileCB.addActionListener(this); ButtonGroup group = new ButtonGroup(); group.add(urlCB); group.add(fileCB); choice.add(new JLabel("Choose input source:")); choice.add(urlCB); choice.add(fileCB); input.setLayout(l); urlTxt.setPreferredSize(new Dimension(300,30)); fileTxt.setPreferredSize(new Dimension(300,30)); urlAux.add(urlTxt); fileAux.add(fileTxt); fileAux.add(load); input.add(fileAux,"file"); input.add(urlAux,"url"); group.setSelected(fileCB.getModel(), true); load.addActionListener(this); this.add(choice); this.add(input); } public void actionPerformed(ActionEvent e) { if (e.getSource() instanceof JRadioButton) { if (urlCB.isSelected()) { l.show(input, "url"); } else { l.show(input, "file"); } } else if (e.getSource() instanceof JButton) { JFileChooser fc = new JFileChooser(); if (fc.showSaveDialog(_vp) == JFileChooser.APPROVE_OPTION) { this.fileTxt.setText(fc.getSelectedFile().getAbsolutePath()); } } } public Reader getReader() throws IOException { if (urlCB.isSelected()) { URL url = new URL(urlTxt.getText()); URLConnection connexion = url.openConnection(); connexion.setUseCaches(false); InputStream r = connexion.getInputStream(); return new InputStreamReader(r); } else { return new FileReader(fileTxt.getText()); } } } fr/orsay/lri/varna/views/VueGlobalRescale.java0000644000000000000000000000472412020071042020367 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurGlobalRescale; import fr.orsay.lri.varna.controlers.ControleurGlobalRotation; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; public class VueGlobalRescale { private VARNAPanel _vp; private JSlider rescaleSlider; private JPanel panel; public VueGlobalRescale(VARNAPanel vp) { _vp = vp; rescaleSlider = new JSlider(JSlider.HORIZONTAL, 1, 500, 100); rescaleSlider.setMajorTickSpacing(100); rescaleSlider.setPaintTicks(true); rescaleSlider.setPaintLabels(true); rescaleSlider.setPreferredSize(new Dimension(500, 50)); JLabel rescaleLabel = new JLabel(String.valueOf(0)); rescaleLabel.setPreferredSize(new Dimension(50, rescaleLabel .getPreferredSize().height)); rescaleSlider.addChangeListener(new ControleurSliderLabel( rescaleLabel, false)); rescaleSlider.addChangeListener(new ControleurGlobalRescale(this,vp)); panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JLabel labelZ = new JLabel("Scale (%):"); panel.add(labelZ); panel.add(rescaleSlider); panel.add(rescaleLabel); } public JPanel getPanel() { return panel; } public double getScale() { return rescaleSlider.getValue()/100.0; } public VARNAPanel get_vp() { return _vp; } } fr/orsay/lri/varna/views/VueStyleBP.java0000644000000000000000000000456611620715272017235 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.FlowLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JPanel; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.VARNAConfig; public class VueStyleBP implements ActionListener { private VARNAPanel _vp; private JComboBox _cmb; private JPanel panel; public VueStyleBP(VARNAPanel vp) { _vp = vp; VARNAConfig.BP_STYLE[] styles = VARNAConfig.BP_STYLE.values(); VARNAConfig.BP_STYLE bck = vp.getConfig()._mainBPStyle; _cmb = new JComboBox(styles); for (int i = 0; i < styles.length; i++) { if (styles[i] == bck) _cmb.setSelectedIndex(i); } _cmb.addActionListener(this); panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JLabel labelZ = new JLabel("Base pair style: "); panel.add(labelZ); panel.add(_cmb); } public JPanel getPanel() { return panel; } public VARNAConfig.BP_STYLE getStyle() { return (VARNAConfig.BP_STYLE) _cmb.getSelectedItem(); } public VARNAPanel get_vp() { return _vp; } public void actionPerformed(ActionEvent e) { VARNAConfig.BP_STYLE newSel = (VARNAConfig.BP_STYLE) _cmb .getSelectedItem(); _vp.setBPStyle(newSel); _vp.repaint(); } } fr/orsay/lri/varna/views/VueNumPeriod.java0000644000000000000000000000504112050247230017572 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurNumPeriod; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; public class VueNumPeriod { private VARNAPanel _vp; private JPanel panel; private JSlider numPeriodSlider; public VueNumPeriod(VARNAPanel vp) { _vp = vp; panel = new JPanel(); int maxPeriod = _vp.getRNA().get_listeBases().size(); numPeriodSlider = new JSlider(JSlider.HORIZONTAL, 1, maxPeriod, Math .min(_vp.getNumPeriod(), maxPeriod)); // Turn on labels at major tick marks. numPeriodSlider.setMajorTickSpacing(10); numPeriodSlider.setMinorTickSpacing(5); numPeriodSlider.setPaintTicks(true); numPeriodSlider.setPaintLabels(true); JLabel numLabel = new JLabel(String.valueOf(_vp.getNumPeriod())); numLabel.setPreferredSize(new Dimension(50, numLabel.getPreferredSize().height)); numPeriodSlider.addChangeListener(new ControleurSliderLabel(numLabel, false)); numPeriodSlider.addChangeListener(new ControleurNumPeriod(this)); panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JLabel labelS = new JLabel("NumPeriod:"); panel.add(labelS); panel.add(numPeriodSlider); panel.add(numLabel); } public VARNAPanel get_vp() { return _vp; } public JPanel getPanel() { return panel; } public int getNumPeriod() { return numPeriodSlider.getValue(); } } fr/orsay/lri/varna/views/VueListeAnnotations.java0000644000000000000000000000765311620715272021211 0ustar rootroot/* * VARNA is a tool for the automated drawing, visualization and annotation * of the secondary structure of RNA, designed as a companion software for * web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise * and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat * 490 Universit Paris-Sud 91405 Orsay Cedex France * * This file is part of VARNA version 3.1. VARNA version 3.1 is free * software: you can redistribute it and/or modify it under the terms of the * GNU General Public License as published by the Free Software Foundation, * either version 3 of the License, or (at your option) any later version. * * VARNA version 3.1 is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General * Public License for more details. * * You should have received a copy of the GNU General Public License along * with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.GridLayout; import java.util.ArrayList; import javax.swing.JComponent; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.components.AnnotationTableModel; import fr.orsay.lri.varna.controlers.ControleurTableAnnotations; /** * a view for all annoted texts on the VARNAPanel * * @author Darty@lri.fr * */ public class VueListeAnnotations extends JPanel { /** * */ private static final long serialVersionUID = 1L; /** * if this view is for removing annoted texts */ public static final int REMOVE = 0; /** * if this view is for editing annoted texts */ public static final int EDIT = 1; private VARNAPanel _vp; private ArrayList data; private JTable table; private int type; private AnnotationTableModel specialTableModel; /** * creates the view * * @param vp * @param type * (REMOVE or EDIT) */ public VueListeAnnotations(VARNAPanel vp, int type) { super(new GridLayout(1, 0)); this.type = type; _vp = vp; data = new ArrayList(); data.addAll(_vp.getListeAnnotations()); data.addAll(_vp.getRNA().getHighlightRegion()); data.addAll(_vp.getRNA().getChemProbAnnotations()); createView(); } private void createView() { specialTableModel = new AnnotationTableModel(data); table = new JTable(specialTableModel); ControleurTableAnnotations ctrl = new ControleurTableAnnotations(table, _vp, type); table.addMouseListener(ctrl); table.addMouseMotionListener(ctrl); // table.setPreferredScrollableViewportSize(new Dimension(500, 100)); // TODO: Find equivalent in JRE 1.5 // table.setFillsViewportHeight(true); // Create the scroll pane and add the table to it. JScrollPane scrollPane = new JScrollPane(table); add(scrollPane); UIvueListeAnnotations(); } /** * Create the GUI and show it. For thread safety, this method should be * invoked from the event-dispatching thread. */ public void UIvueListeAnnotations() { JComponent newContentPane = this; newContentPane.setOpaque(true); JOptionPane.showMessageDialog(_vp, newContentPane, "Annotation edition", JOptionPane.PLAIN_MESSAGE); } public ArrayList getData() { return data; } public void setData(ArrayList data) { this.data = data; } public VARNAPanel get_vp() { return _vp; } public JTable getTable() { return table; } public void setTable(JTable table) { this.table = table; } public AnnotationTableModel getSpecialTableModel() { return specialTableModel; } public void setSpecialTableModel(AnnotationTableModel specialTableModel) { this.specialTableModel = specialTableModel; } } fr/orsay/lri/varna/views/VueGlobalRotation.java0000644000000000000000000000465312020071100020604 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurGlobalRotation; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; public class VueGlobalRotation { private VARNAPanel _vp; private JSlider rotationSlider; private JPanel panel; public VueGlobalRotation(VARNAPanel vp) { _vp = vp; rotationSlider = new JSlider(JSlider.HORIZONTAL, -360, 360, 0); rotationSlider.setMajorTickSpacing(60); rotationSlider.setPaintTicks(true); rotationSlider.setPaintLabels(true); rotationSlider.setPreferredSize(new Dimension(500, 50)); JLabel rotationLabel = new JLabel(String.valueOf(0)); rotationLabel.setPreferredSize(new Dimension(50, rotationLabel .getPreferredSize().height)); rotationSlider.addChangeListener(new ControleurSliderLabel( rotationLabel, false)); rotationSlider.addChangeListener(new ControleurGlobalRotation(this,vp)); panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JLabel labelZ = new JLabel("Rotation (degrees):"); panel.add(labelZ); panel.add(rotationSlider); panel.add(rotationLabel); } public JPanel getPanel() { return panel; } public double getAngle() { return rotationSlider.getValue(); } public VARNAPanel get_vp() { return _vp; } } fr/orsay/lri/varna/views/VueAnnotation.java0000644000000000000000000002444611722636140020023 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; import java.awt.geom.Point2D.Double; import javax.swing.JButton; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSlider; import javax.swing.JTextArea; import javax.swing.border.Border; import javax.swing.plaf.basic.BasicBorders; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; import fr.orsay.lri.varna.controlers.ControleurVueAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation; /** * annoted text view for edition * * @author Darty@lri.fr * */ public class VueAnnotation { private VARNAPanel _vp; private JSlider ySlider, xSlider; private JButton colorButton; private JTextArea textArea; private JPanel panel; private TextAnnotation textAnnotation, textAnnotationSave; private VueFont vueFont; private ControleurVueAnnotation _controleurVueAnnotation; private boolean newAnnotation, limited; private Double position; private JSlider rotationSlider; /** * creates a view for a new annoted text * * @param vp * @param limited * if true, lets custom position and angle. */ public VueAnnotation(VARNAPanel vp, boolean limited) { this( vp, (int) (vp.getExtendedRNABBox().x + vp.getExtendedRNABBox().width / 2.0), (int) (vp.getExtendedRNABBox().y + vp.getExtendedRNABBox().height / 2.0), limited); } /** * creates a view for a new annoted text, without limited option * * @param vp */ public VueAnnotation(VARNAPanel vp) { this(vp, false); } /** * creates a view for a new annoted text at a given position, without * limited option * * @param vp */ public VueAnnotation(VARNAPanel vp, int x, int y) { this(vp, x, y, false); } /** * creates a view for a new annoted text at a given position, without * limited option * * @param vp */ public VueAnnotation(VARNAPanel vp, int x, int y, boolean limited) { this(vp, new TextAnnotation("", x, y), false, true); } /** * creates a view for an annoted text, without limited option * * @param vp * @param textAnnot */ public VueAnnotation(VARNAPanel vp, TextAnnotation textAnnot, boolean newAnnotation) { this(vp, textAnnot, (textAnnot.getType()!=TextAnnotation.AnchorType.POSITION), newAnnotation); } /** * creates a view for an annoted text * * * @param vp * @param textAnnot * @param reduite * if true, lets custom position and angle. * @param newAnnotation * if true, deleted if cancelled. */ public VueAnnotation(VARNAPanel vp, TextAnnotation textAnnot, boolean reduite, boolean newAnnotation) { this.limited = reduite; this.newAnnotation = newAnnotation; _vp = vp; textAnnotation = textAnnot; textAnnotationSave = textAnnotation.clone(); if (!_vp.getListeAnnotations().contains(textAnnot)) { _vp.addAnnotation(textAnnotation); } _controleurVueAnnotation = new ControleurVueAnnotation(this); position = textAnnotation.getCenterPosition(); /* * if (textAnnotation.getType() != TextAnnotation.POSITION) { position = * _vp.transformCoord(position); } */ JPanel py = new JPanel(); JPanel px = new JPanel(); panel = new JPanel(); panel.setLayout(new GridLayout(0, 1)); py.setLayout(new FlowLayout(FlowLayout.LEFT)); px.setLayout(new FlowLayout(FlowLayout.LEFT)); ySlider = new JSlider(JSlider.HORIZONTAL, 0, (int) (_vp .getExtendedRNABBox().height), Math.max(0, Math.min((int) (_vp .getExtendedRNABBox().height), (int) (position.y - _vp .getExtendedRNABBox().y)))); // Turn on labels at major tick marks. ySlider.setMajorTickSpacing(500); ySlider.setMinorTickSpacing(100); ySlider.setPaintTicks(true); ySlider.setPaintLabels(true); ySlider.setPreferredSize(new Dimension(400, ySlider.getPreferredSize().height)); JLabel yValueLabel = new JLabel(String.valueOf((int) position.y - _vp.getExtendedRNABBox().y)); yValueLabel.setPreferredSize(new Dimension(50, yValueLabel .getPreferredSize().height)); ySlider .addChangeListener(new ControleurSliderLabel(yValueLabel, false)); ySlider.addChangeListener(_controleurVueAnnotation); xSlider = new JSlider(JSlider.HORIZONTAL, 0, (int) (_vp .getExtendedRNABBox().width), Math.max(0, Math.min((int) _vp .getExtendedRNABBox().width, (int) (position.x - _vp .getExtendedRNABBox().x)))); // Turn on labels at major tick marks. xSlider.setMajorTickSpacing(500); xSlider.setMinorTickSpacing(100); xSlider.setPaintTicks(true); xSlider.setPaintLabels(true); xSlider.setPreferredSize(new Dimension(400, xSlider.getPreferredSize().height)); JLabel xValueLabel = new JLabel(String.valueOf((int) position.x - _vp.getExtendedRNABBox().x)); xValueLabel.setPreferredSize(new Dimension(50, xValueLabel .getPreferredSize().height)); xSlider .addChangeListener(new ControleurSliderLabel(xValueLabel, false)); xSlider.addChangeListener(_controleurVueAnnotation); JLabel labelY = new JLabel("Y:"); JLabel labelX = new JLabel("X:"); py.add(labelY); py.add(ySlider); py.add(yValueLabel); px.add(labelX); px.add(xSlider); px.add(xValueLabel); /*if (!limited) { panel.add(px); panel.add(py); }*/ JPanel panelTexte = new JPanel(); panelTexte.setLayout(new BorderLayout()); textArea = new JTextArea(textAnnotation.getTexte()); textArea.addCaretListener(_controleurVueAnnotation); textArea.setPreferredSize(panelTexte.getSize()); Border border = new BasicBorders.FieldBorder(Color.black, Color.black, Color.black, Color.black); textArea.setBorder(border); JLabel labelTexte = new JLabel("Text:"); panelTexte.add(textArea, BorderLayout.CENTER); panelTexte.add(labelTexte, BorderLayout.NORTH); panel.add(panelTexte); vueFont = new VueFont(textAnnot.getFont()); vueFont.getBoxPolice().addActionListener(_controleurVueAnnotation); vueFont.getSizeSlider().addChangeListener(_controleurVueAnnotation); vueFont.getStylesBox().addActionListener(_controleurVueAnnotation); colorButton = new JButton("Set color"); colorButton.setActionCommand("setcolor"); colorButton.setForeground(textAnnot.getColor()); colorButton.addActionListener(_controleurVueAnnotation); JPanel fontAndColor = new JPanel(); fontAndColor.add(vueFont.getPanel()); fontAndColor.add(colorButton); panel.add(fontAndColor); JPanel rotationPanel = new JPanel(); rotationSlider = new JSlider(JSlider.HORIZONTAL, -360, 360, (int) textAnnotation.getAngleInDegres()); rotationSlider.setMajorTickSpacing(60); rotationSlider.setPaintTicks(true); rotationSlider.setPaintLabels(true); rotationSlider.setPreferredSize(new Dimension(500, 50)); JLabel rotationLabel = new JLabel(String.valueOf(0)); rotationLabel.setPreferredSize(new Dimension(50, rotationLabel .getPreferredSize().height)); rotationSlider.addChangeListener(new ControleurSliderLabel( rotationLabel, false)); rotationSlider.addChangeListener(_controleurVueAnnotation); JLabel labelZ = new JLabel("Rotation (degrees):"); rotationPanel.add(labelZ); rotationPanel.add(rotationSlider); rotationPanel.add(rotationLabel); /* * if (!limited) { panel.add(rotationPanel); } */ if (limited) { ySlider.setEnabled(false); xSlider.setEnabled(false); rotationSlider.setEnabled(false); } textArea.requestFocusInWindow(); } private void applyFont() { textAnnotation.setFont(vueFont.getFont()); } /** * update the annoted text on the VARNAPanel */ public void update() { applyFont(); if (textAnnotation.getType() == TextAnnotation.AnchorType.POSITION) textAnnotation.setAncrage((double) xSlider.getValue() + _vp.getExtendedRNABBox().x, ySlider.getValue() + _vp.getExtendedRNABBox().y); textAnnotation.setText(textArea.getText()); textAnnotation.setAngleInDegres(rotationSlider.getValue()); _vp.clearSelection(); _vp.repaint(); } public JPanel getPanel() { return panel; } /** * * @return the annoted text */ public TextAnnotation getTextAnnotation() { return textAnnotation; } public VARNAPanel get_vp() { return _vp; } /** * shows the dialog which add it to the VARNAPanel for previsualization. *

* if validate, just update the annoted text *

* if cancelled : remove the annoted text if it was a new one, otherwise * cancel modifications *

* */ public void show() { _vp.set_selectedAnnotation(textAnnotation); _vp.highlightSelectedAnnotation(); if (JOptionPane.showConfirmDialog(_vp, getPanel(), "Add/edit annotation", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE) == JOptionPane.OK_OPTION) { update(); } else { if (newAnnotation) { _vp.set_selectedAnnotation(null); if (!_vp.removeAnnotation(textAnnotation)) _vp.errorDialog(new Exception("Impossible de supprimer")); } else { textAnnotation.copy(textAnnotationSave); } } _vp.resetAnnotationHighlight(); _vp.set_selectedAnnotation(null); _vp.repaint(); } public boolean isLimited() { return limited; } public void setLimited(boolean limited) { this.limited = limited; } public boolean isNewAnnotation() { return this.newAnnotation; } public void updateColor(Color c) { colorButton.setForeground(c); textAnnotation.setColor(c); } } fr/orsay/lri/varna/views/VueUI.java0000644000000000000000000013554512441661060016227 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Color; import java.awt.Dimension; import java.awt.Graphics2D; import java.awt.Image; import java.awt.Point; import java.awt.Toolkit; import java.awt.geom.AffineTransform; import java.awt.geom.Point2D; import java.awt.image.BufferedImage; import java.awt.image.FilteredImageSource; import java.awt.image.ImageFilter; import java.awt.image.ImageProducer; import java.awt.image.RGBImageFilter; import java.io.File; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; import java.text.ParseException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.HashSet; import java.util.Hashtable; import java.util.Vector; import javax.imageio.IIOImage; import javax.imageio.ImageIO; import javax.imageio.ImageWriteParam; import javax.imageio.ImageWriter; import javax.imageio.stream.FileImageOutputStream; import javax.swing.JColorChooser; import javax.swing.JFileChooser; import javax.swing.JOptionPane; import javax.swing.filechooser.FileFilter; import javax.swing.undo.UndoManager; import javax.swing.undo.UndoableEditSupport; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.applications.FileNameExtensionFilter; import fr.orsay.lri.varna.applications.VARNAPrinter; import fr.orsay.lri.varna.applications.templateEditor.Couple; import fr.orsay.lri.varna.applications.templateEditor.TemplateEdits; import fr.orsay.lri.varna.applications.templateEditor.TemplatePanel; import fr.orsay.lri.varna.exceptions.ExceptionExportFailed; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden; import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.VARNAEdits; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.annotations.TextAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleBasesComparison; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.RNA; public class VueUI { private VARNAPanel _vp; private File _fileChooserDirectory = null; private UndoableEditSupport _undoableEditSupport; public VueUI(VARNAPanel vp) { _vp = vp; _undoableEditSupport = new UndoableEditSupport(_vp); } public void addUndoableEditListener(UndoManager manager) { _undoableEditSupport.addUndoableEditListener(manager); } public void UIToggleColorMap() { if (_vp.isModifiable()) { _vp.setColorMapVisible(!_vp.getColorMapVisible()); _vp.repaint(); } } public void UIToggleDrawBackbone() { if (_vp.isModifiable()) { _vp.setDrawBackbone(!_vp.getDrawBackbone()); _vp.repaint(); } } public Hashtable backupAllCoords() { Hashtable tmp = new Hashtable(); for(int i=0;i<_vp.getRNA().getSize();i++) { tmp.put(i, _vp.getRNA().getCoords(i)); } return tmp; } public void UIToggleFlatExteriorLoop() { if (_vp.isModifiable() && _vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(RNA.DRAW_MODE_RADIATE,_vp,!_vp.getFlatExteriorLoop())); _vp.setFlatExteriorLoop(!_vp.getFlatExteriorLoop()); _vp.reset(); _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_RADIATE); _vp.repaint(); _vp.fireLayoutChanged(bck); } } public void UIRadiate() { if (_vp.isModifiable()) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(RNA.DRAW_MODE_RADIATE,_vp)); _vp.reset(); _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_RADIATE); _vp.repaint(); _vp.fireLayoutChanged(bck); } } public void UIMOTIFView() { if (_vp.isModifiable()) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(RNA.DRAW_MODE_MOTIFVIEW,_vp)); _vp.reset(); _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_MOTIFVIEW); _vp.repaint(); _vp.fireLayoutChanged(bck); } } public void UILine() { if (_vp.isModifiable()) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(RNA.DRAW_MODE_LINEAR,_vp)); _vp.reset(); _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_LINEAR); _vp.repaint(); _vp.fireLayoutChanged(bck); } } public void UICircular() { if (_vp.isModifiable()) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(RNA.DRAW_MODE_CIRCULAR,_vp)); _vp.reset(); _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_CIRCULAR); _vp.repaint(); _vp.fireLayoutChanged(bck); } } public void UINAView() { if (_vp.isModifiable()) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(RNA.DRAW_MODE_NAVIEW,_vp)); _vp.reset(); _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_NAVIEW); _vp.repaint(); _vp.fireLayoutChanged(bck); } } public void UIVARNAView() { if (_vp.isModifiable()) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(RNA.DRAW_MODE_VARNA_VIEW,_vp)); _vp.reset(); _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_VARNA_VIEW); _vp.repaint(); _vp.fireLayoutChanged(bck); } } public void UIReset() { if (_vp.isModifiable()) { Hashtable bck = backupAllCoords(); _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(_vp.getRNA().get_drawMode(),_vp)); _vp.reset(); _vp.drawRNA(_vp.getRNA(), _vp.getRNA().get_drawMode()); _vp.repaint(); _vp.fireLayoutChanged(bck); } } private void savePath(JFileChooser jfc) { _fileChooserDirectory = jfc.getCurrentDirectory(); } private void loadPath(JFileChooser jfc) { if (_fileChooserDirectory != null) { jfc.setCurrentDirectory(_fileChooserDirectory); } } public void UIChooseRNAs(ArrayList rnas) { if (rnas.size()>5) { VueRNAList vl = new VueRNAList(rnas); if( JOptionPane.showConfirmDialog(_vp, vl, "Select imported sequence/structures", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { for(RNA r: vl.getSelectedRNAs()) { try { r.drawRNA(_vp.getConfig()); } catch (ExceptionNAViewAlgorithm e) { e.printStackTrace(); } _vp.showRNA(r); } _vp.repaint(); } } else { for(RNA r: rnas) { try { r.drawRNA(_vp.getConfig()); } catch (ExceptionNAViewAlgorithm e) { e.printStackTrace(); } _vp.showRNA(r); } _vp.repaint(); } } public void UIFile() throws ExceptionNonEqualLength { if (_vp.isModifiable()) { JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode(JFileChooser.OPEN_DIALOG); fc.setDialogTitle("Open..."); loadPath(fc); if (fc.showOpenDialog(_vp) == JFileChooser.APPROVE_OPTION) { try { savePath(fc); String path = fc.getSelectedFile().getAbsolutePath(); if (!path.toLowerCase().endsWith(".varna")) { ArrayList rnas = RNAFactory.loadSecStr(path); if (rnas.isEmpty()) { throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from that source."); } else { UIChooseRNAs(rnas); } } else { FullBackup bck = _vp.loadSession(path); } } catch (ExceptionExportFailed e1) { _vp.errorDialog(e1); } catch (ExceptionPermissionDenied e1) { _vp.errorDialog(e1); } catch (ExceptionLoadingFailed e1) { _vp.errorDialog(e1); } catch (ExceptionFileFormatOrSyntax e1) { _vp.errorDialog(e1); } catch (ExceptionUnmatchedClosingParentheses e1) { _vp.errorDialog(e1); } catch (FileNotFoundException e) { _vp.errorDialog(e); } } } } public void UISetColorMapStyle() { VueColorMapStyle cms = new VueColorMapStyle(_vp); if (JOptionPane.showConfirmDialog(_vp, cms, "Choose color map style", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { _vp.setColorMap(cms.getColorMap()); } else { cms.cancelChanges(); } } public void UILoadColorMapValues() { VueLoadColorMapValues cms = new VueLoadColorMapValues(_vp); if (JOptionPane.showConfirmDialog(_vp, cms, "Load base values", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { try { _vp.setColorMapVisible(true); _vp.readValues(cms.getReader()); } catch (IOException e) { _vp.errorDialog(e); } } } public void UISetColorMapValues() { VueBaseValues cms = new VueBaseValues(_vp); if (JOptionPane.showConfirmDialog(_vp, cms, "Choose base values", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { } else { cms.cancelChanges(); } } public void UIManualInput() throws ParseException, ExceptionNonEqualLength { if (_vp.isModifiable()) { VueManualInput manualInput = new VueManualInput(_vp); if (JOptionPane.showConfirmDialog(_vp, manualInput.getPanel(), "Input sequence/structure", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { if (_vp.getRNA().getSize() == 0) { } try { RNA r = new RNA(); VARNAConfig cfg = new VARNAConfig(); r.setRNA(manualInput.getTseq().getText(),manualInput.getTstr().getText()); r.drawRNA(_vp.getRNA().get_drawMode(), cfg); _vp.drawRNAInterpolated(r); _vp.repaint(); } catch (ExceptionFileFormatOrSyntax e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ExceptionNAViewAlgorithm e) { // TODO Auto-generated catch block e.printStackTrace(); } } } } public void UISetTitle() { if (_vp.isModifiable()) { String res = JOptionPane.showInputDialog(_vp, "Input title", _vp .getTitle()); if (res != null) { _vp.setTitle(res); _vp.repaint(); } } } public void UISetColorMapCaption() { if (_vp.isModifiable()) { String res = JOptionPane.showInputDialog(_vp, "Input new color map caption", _vp.getColorMapCaption()); if (res != null) { _vp.setColorMapCaption(res); _vp.repaint(); } } } public void UISetBaseCharacter() { if (_vp.isModifiable()) { int i = _vp.getNearestBase(); if (_vp.isComparisonMode()) { String res = JOptionPane.showInputDialog(_vp, "Input base", ((ModeleBasesComparison) _vp.getRNA().get_listeBases() .get(i)).getBases()); if (res != null) { ModeleBasesComparison mb = (ModeleBasesComparison) _vp.getRNA().get_listeBases().get(i); String bck = mb.getBase1()+"|"+mb.getBase2(); mb.setBase1(((res.length()>0)?res.charAt(0):' ')); mb.setBase2(((res.length()>1)?res.charAt(1):' ')); _vp.repaint(); _vp.fireSequenceChanged(i, bck, res); } } else { String res = JOptionPane.showInputDialog(_vp, "Input base", ((ModeleBaseNucleotide) _vp.getRNA().get_listeBases() .get(i)).getBase()); if (res != null) { ModeleBaseNucleotide mb = (ModeleBaseNucleotide) _vp.getRNA().get_listeBases().get(i); String bck = mb.getBase(); mb.setBase(res); _vp.repaint(); _vp.fireSequenceChanged(i, bck, res); } } } } FileNameExtensionFilter _varnaFilter = new FileNameExtensionFilter( "VARNA Session File", "varna", "VARNA"); FileNameExtensionFilter _bpseqFilter = new FileNameExtensionFilter( "BPSeq (CRW) File", "bpseq", "BPSEQ"); FileNameExtensionFilter _ctFilter = new FileNameExtensionFilter( "Connect (MFold) File", "ct", "CT"); FileNameExtensionFilter _dbnFilter = new FileNameExtensionFilter( "Dot-bracket notation (Vienna) File", "dbn", "DBN", "faa", "FAA"); FileNameExtensionFilter _jpgFilter = new FileNameExtensionFilter( "JPEG Picture", "jpeg", "jpg", "JPG", "JPEG"); FileNameExtensionFilter _pngFilter = new FileNameExtensionFilter( "PNG Picture", "png", "PNG"); FileNameExtensionFilter _epsFilter = new FileNameExtensionFilter( "EPS File", "eps", "EPS"); FileNameExtensionFilter _svgFilter = new FileNameExtensionFilter( "SVG Picture", "svg", "SVG"); FileNameExtensionFilter _xfigFilter = new FileNameExtensionFilter( "XFig Diagram", "fig", "xfig", "FIG", "XFIG"); public void UIExport() throws ExceptionExportFailed, ExceptionPermissionDenied, ExceptionWritingForbidden, ExceptionJPEGEncoding { ArrayList v = new ArrayList(); v.add(_epsFilter); v.add(_svgFilter); v.add(_xfigFilter); v.add(_jpgFilter); v.add(_pngFilter); String dest = UIChooseOutputFile(v); if (dest != null) { String extLower = dest.substring(dest.lastIndexOf('.')) .toLowerCase(); // System.out.println(extLower); if (extLower.equals(".eps")) { _vp.getRNA().saveRNAEPS(dest, _vp.getConfig()); } else if (extLower.equals(".svg")) { _vp.getRNA().saveRNASVG(dest, _vp.getConfig()); } else if (extLower.equals(".fig") || extLower.equals("xfig")) { _vp.getRNA().saveRNAXFIG(dest, _vp.getConfig()); } else if (extLower.equals(".png")) { saveToPNG(dest); } else if (extLower.equals("jpg") || extLower.equals("jpeg")) { saveToJPEG(dest); } } } public void UIExportJPEG() throws ExceptionJPEGEncoding, ExceptionExportFailed { String dest = UIChooseOutputFile(_jpgFilter); if (dest != null) { saveToJPEG(dest); } } public void UIPrint() { VARNAPrinter.printComponent(_vp); } public void UIExportPNG() throws ExceptionExportFailed { String dest = UIChooseOutputFile(_pngFilter); if (dest != null) { saveToPNG(dest); } } public void UIExportXFIG() throws ExceptionExportFailed, ExceptionWritingForbidden { String dest = UIChooseOutputFile(_xfigFilter); if (dest != null) { _vp.getRNA().saveRNAXFIG(dest, _vp.getConfig()); } } public void UIExportEPS() throws ExceptionExportFailed, ExceptionWritingForbidden { String dest = UIChooseOutputFile(_epsFilter); if (dest != null) { _vp.getRNA().saveRNAEPS(dest, _vp.getConfig()); } } public void UIExportSVG() throws ExceptionExportFailed, ExceptionWritingForbidden { String dest = UIChooseOutputFile(_svgFilter); if (dest != null) { _vp.getRNA().saveRNASVG(dest, _vp.getConfig()); } } public void UISaveAsDBN() throws ExceptionExportFailed, ExceptionPermissionDenied { String name = _vp.getVARNAUI().UIChooseOutputFile(_dbnFilter); if (name != null) _vp.getRNA().saveAsDBN(name, _vp.getTitle()); } public void UISaveAsCT() throws ExceptionExportFailed, ExceptionPermissionDenied { String name = _vp.getVARNAUI().UIChooseOutputFile(_ctFilter); if (name != null) _vp.getRNA().saveAsCT(name, _vp.getTitle()); } public void UISaveAsBPSEQ() throws ExceptionExportFailed, ExceptionPermissionDenied { String name = _vp.getVARNAUI().UIChooseOutputFile(_bpseqFilter); if (name != null) _vp.getRNA().saveAsBPSEQ(name, _vp.getTitle()); } public void UISaveAs() throws ExceptionExportFailed, ExceptionPermissionDenied { ArrayList v = new ArrayList(); v.add(_bpseqFilter); v.add(_dbnFilter); v.add(_ctFilter); v.add(_varnaFilter); String dest = UIChooseOutputFile(v); if (dest != null) { String extLower = dest.substring(dest.lastIndexOf('.')) .toLowerCase(); if (extLower.endsWith("bpseq")) { _vp.getRNA().saveAsBPSEQ(dest, _vp.getTitle()); } else if (extLower.endsWith("ct")) { _vp.getRNA().saveAsCT(dest, _vp.getTitle()); } else if (extLower.endsWith("dbn") || extLower.endsWith("faa")) { _vp.getRNA().saveAsDBN(dest, _vp.getTitle()); } else if (extLower.endsWith("varna")) { _vp.saveSession(dest); } } } public String UIChooseOutputFile(FileNameExtensionFilter filtre) { ArrayList v = new ArrayList(); v.add(filtre); return UIChooseOutputFile(v); } /** * Opens a save dialog with right extensions and return the absolute path * * @param filtre * Allowed extensions * @return null if the user doesn't approve the save dialog,
* absolutePath if the user approve the save dialog */ public String UIChooseOutputFile(ArrayList filtre) { JFileChooser fc = new JFileChooser(); loadPath(fc); String absolutePath = null; // applique le filtre for (int i = 0; i < filtre.size(); i++) { fc.addChoosableFileFilter(filtre.get(i)); } // en mode open dialog pour voir les autres fichiers avec la meme // extension fc.setFileSelectionMode(JFileChooser.OPEN_DIALOG); fc.setDialogTitle("Save..."); // Si l'utilisateur a valider if (fc.showSaveDialog(_vp) == JFileChooser.APPROVE_OPTION) { savePath(fc); absolutePath = fc.getSelectedFile().getAbsolutePath(); String extension = _vp.getPopupMenu().get_controleurMenu() .getExtension(fc.getSelectedFile()); FileFilter f = fc.getFileFilter(); if (f instanceof FileNameExtensionFilter) { ArrayList listeExtension = new ArrayList(); listeExtension.addAll(Arrays .asList(((FileNameExtensionFilter) f).getExtensions())); // si l'extension du fichier ne fait pas partie de la liste // d'extensions acceptées if (!listeExtension.contains(extension)) { absolutePath += "." + listeExtension.get(0); } } } return absolutePath; } public void UISetBorder() { VueBorder border = new VueBorder(_vp); Dimension oldBorder = _vp.getBorderSize(); _vp.drawBBox(true); _vp.drawBorder(true); _vp.repaint(); if (JOptionPane.showConfirmDialog(_vp, border.getPanel(), "Set new border size", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { _vp.setBorderSize(oldBorder); } _vp.drawBorder(false); _vp.drawBBox(false); _vp.repaint(); } public void UISetBackground() { Color c = JColorChooser.showDialog(_vp, "Choose new background color", _vp.getBackground()); if (c != null) { _vp.setBackground(c); _vp.repaint(); } } public void UIZoomIn() { double _actualZoom = _vp.getZoom(); double _actualAmount = _vp.getZoomIncrement(); Point _actualTranslation = _vp.getTranslation(); double newZoom = Math.min(VARNAConfig.MAX_ZOOM, _actualZoom * _actualAmount); double ratio = newZoom / _actualZoom; Point newTrans = new Point((int) (_actualTranslation.x * ratio), (int) (_actualTranslation.y * ratio)); _vp.setZoom(newZoom); _vp.setTranslation(newTrans); // verification que la translation ne pose pas de problemes _vp.checkTranslation(); //System.out.println("Zoom in"); _vp.repaint(); } public void UIZoomOut() { double _actualZoom = _vp.getZoom(); double _actualAmount = _vp.getZoomIncrement(); Point _actualTranslation = _vp.getTranslation(); double newZoom = Math.max(_actualZoom / _actualAmount, VARNAConfig.MIN_ZOOM); double ratio = newZoom / _actualZoom; Point newTrans = new Point((int) (_actualTranslation.x * ratio), (int) (_actualTranslation.y * ratio)); _vp.setZoom(newZoom); _vp.setTranslation(newTrans); // verification que la translation ne pose pas de problemes _vp.checkTranslation(); _vp.repaint(); } public void UICustomZoom() { VueZoom zoom = new VueZoom(_vp); double oldZoom = _vp.getZoom(); double oldZoomAmount = _vp.getZoomIncrement(); _vp.drawBBox(true); _vp.repaint(); if (JOptionPane.showConfirmDialog(_vp, zoom.getPanel(), "Set zoom", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { _vp.setZoom(oldZoom); _vp.setZoomIncrement(oldZoomAmount); } _vp.drawBBox(false); _vp.repaint(); } public void UIGlobalRescale() { if (_vp.isModifiable()) { if (_vp.getRNA().get_listeBases().size() > 0) { VueGlobalRescale rescale = new VueGlobalRescale(_vp); if (JOptionPane.showConfirmDialog(_vp, rescale.getPanel(), "Rescales the whole RNA (No redraw)", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { UIGlobalRescale(1./rescale.getScale()); } _vp.drawBBox(false); _vp.repaint(); } } } public void UIGlobalRescale(double d) { if (_vp.isModifiable()) { if (_vp.getRNA().get_listeBases().size() > 0) { _vp.globalRescale(d); _undoableEditSupport.postEdit(new VARNAEdits.RescaleRNAEdit(d,_vp)); } } } public void UIGlobalRotation() { if (_vp.isModifiable()) { if (_vp.getRNA().get_listeBases().size() > 0) { _vp.drawBBox(true); _vp.repaint(); VueGlobalRotation rotation = new VueGlobalRotation(_vp); if (JOptionPane.showConfirmDialog(_vp, rotation.getPanel(), "Rotates the whole RNA", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { UIGlobalRotation(-rotation.getAngle()); } _vp.drawBBox(false); _vp.repaint(); } } } public void UIGlobalRotation(double d) { if (_vp.isModifiable()) { if (_vp.getRNA().get_listeBases().size() > 0) { _vp.globalRotation(d); _undoableEditSupport.postEdit(new VARNAEdits.RotateRNAEdit(d,_vp)); } } } public void UISetBPStyle() { if (_vp.getRNA().get_listeBases().size() > 0) { VueStyleBP bpstyle = new VueStyleBP(_vp); VARNAConfig.BP_STYLE bck = _vp.getBPStyle(); if (JOptionPane.showConfirmDialog(_vp, bpstyle.getPanel(), "Set main base pair style", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { _vp.setBPStyle(bck); _vp.repaint(); } } } public void UISetTitleColor() { if (_vp.isModifiable()) { Color c = JColorChooser.showDialog(_vp, "Choose new title color", _vp.getTitleColor()); if (c != null) { _vp.setTitleColor(c); _vp.repaint(); } } } public void UISetBackboneColor() { if (_vp.isModifiable()) { Color c = JColorChooser.showDialog(_vp, "Choose new backbone color", _vp.getBackboneColor()); if (c != null) { _vp.setBackboneColor(c); _vp.repaint(); } } } public void UISetTitleFont() { if (_vp.isModifiable()) { VueFont font = new VueFont(_vp); if (JOptionPane.showConfirmDialog(_vp, font.getPanel(), "New Title font", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { _vp.setTitleFont(font.getFont()); _vp.repaint(); } } } public void UISetSpaceBetweenBases() { if (_vp.isModifiable()) { VueSpaceBetweenBases vsbb = new VueSpaceBetweenBases(_vp); Double oldSpace = _vp.getSpaceBetweenBases(); if (JOptionPane.showConfirmDialog(_vp, vsbb.getPanel(), "Set the space between each base", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { _vp.setSpaceBetweenBases(oldSpace); _vp.drawRNA(_vp.getRNA()); _vp.repaint(); } } } public void UISetBPHeightIncrement() { if (_vp.isModifiable()) { VueBPHeightIncrement vsbb = new VueBPHeightIncrement(_vp); Double oldSpace = _vp.getBPHeightIncrement(); if (JOptionPane.showConfirmDialog(_vp, vsbb.getPanel(), "Set the vertical increment in linear mode", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { _vp.setBPHeightIncrement(oldSpace); _vp.drawRNA(_vp.getRNA()); _vp.repaint(); } } } public void UISetNumPeriod() { if (_vp.getRNA().get_listeBases().size() != 0) { int oldNumPeriod = _vp.getNumPeriod(); VueNumPeriod vnp = new VueNumPeriod(_vp); if (JOptionPane.showConfirmDialog(_vp, vnp.getPanel(), "Set new numbering period", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { _vp.setNumPeriod(oldNumPeriod); _vp.repaint(); } } } public void UIEditBasePair() { if (_vp.isModifiable()) { ModeleBase mb = _vp.getRNA().get_listeBases().get( _vp.getNearestBase()); if (mb.getElementStructure() != -1) { ModeleBP msbp = mb.getStyleBP(); ModeleBP.Edge bck5 = msbp.getEdgePartner5(); ModeleBP.Edge bck3 = msbp.getEdgePartner3(); ModeleBP.Stericity bcks = msbp.getStericity(); VueBPType vbpt = new VueBPType(_vp, msbp); if (JOptionPane.showConfirmDialog(_vp, vbpt.getPanel(), "Set base pair L/W type", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { msbp.setEdge5(bck5); msbp.setEdge3(bck3); msbp.setStericity(bcks); _vp.repaint(); } } } } public void UIColorBasePair() { if (_vp.isModifiable()) { ModeleBase mb = _vp.getRNA().get_listeBases().get( _vp.getNearestBase()); if (mb.getElementStructure() != -1) { ModeleBP msbp = mb.getStyleBP(); Color c = JColorChooser.showDialog(_vp, "Choose custom base pair color", msbp.getStyle().getColor(_vp .getConfig()._bondColor)); if (c != null) { msbp.getStyle().setCustomColor(c); _vp.repaint(); } } } } public void UIThicknessBasePair() { if (_vp.isModifiable()) { ModeleBase mb = _vp.getRNA().get_listeBases().get( _vp.getNearestBase()); if (mb.getElementStructure() != -1) { ModeleBP msbp = mb.getStyleBP(); ArrayList bases = new ArrayList(); bases.add(msbp); VueBPThickness vbpt = new VueBPThickness(_vp, bases); if (JOptionPane.showConfirmDialog(_vp, vbpt.getPanel(), "Set base pair(s) thickness", JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) { vbpt.restoreThicknesses(); _vp.repaint(); } } } } public void saveToPNG(String filename) throws ExceptionExportFailed { VueJPEG jpeg = new VueJPEG(true, false); if (JOptionPane.showConfirmDialog(_vp, jpeg.getPanel(), "Set resolution", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { Double scale = jpeg.getScaleSlider().getValue() / 100.0; BufferedImage myImage = new BufferedImage((int) Math.round(_vp .getWidth() * scale), (int) Math.round(_vp.getHeight() * scale), BufferedImage.TRANSLUCENT); Graphics2D g2 = myImage.createGraphics(); AffineTransform AF = new AffineTransform(); AF.setToScale(scale, scale); g2.setTransform(AF); _vp.paintComponent(g2,!_vp.getConfig()._drawBackground); g2.dispose(); try { ImageIO.write(myImage, "PNG", new File(filename)); } catch (IOException e) { e.printStackTrace(); } } } public void saveToJPEG(String filename) throws ExceptionJPEGEncoding, ExceptionExportFailed { VueJPEG jpeg = new VueJPEG(true, true); if (JOptionPane.showConfirmDialog(_vp, jpeg.getPanel(), "Set resolution/quality", JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) { Double scale; if (jpeg.getScaleSlider().getValue() == 0) scale = 1. / 100.; else scale = jpeg.getScaleSlider().getValue() / 100.; BufferedImage myImage = new BufferedImage((int) Math.round(_vp .getWidth() * scale), (int) Math.round(_vp.getHeight() * scale), BufferedImage.TYPE_INT_RGB); Graphics2D g2 = myImage.createGraphics(); AffineTransform AF = new AffineTransform(); AF.setToScale(scale, scale); g2.setTransform(AF); _vp.paintComponent(g2); try { FileImageOutputStream out = new FileImageOutputStream(new File(filename)); ImageWriter writer = ImageIO.getImageWritersByFormatName("jpeg").next(); ImageWriteParam params = writer.getDefaultWriteParam(); params.setCompressionMode(ImageWriteParam.MODE_EXPLICIT); params.setCompressionQuality(jpeg.getQualitySlider().getValue() / 100.0f); writer.setOutput(out); IIOImage myIIOImage = new IIOImage(myImage, null, null); writer.write(null, myIIOImage, params); out.close(); } catch (IOException e) { throw new ExceptionExportFailed(e.getMessage(), filename); } } } public void UIToggleShowNCBP() { if (_vp.isModifiable()) { _vp.setShowNonCanonicalBP(!_vp.getShowNonCanonicalBP()); _vp.repaint(); } } public void UIToggleColorSpecialBases() { _vp.setColorNonStandardBases(!_vp.getColorSpecialBases()); _vp.repaint(); } public void UIToggleColorGapsBases() { _vp.setColorGapsBases(!_vp.getColorGapsBases()); _vp.repaint(); } public void UIToggleShowNonPlanar() { if (_vp.isModifiable()) { _vp.setShowNonPlanarBP(!_vp.getShowNonPlanarBP()); _vp.repaint(); } } public void UIToggleShowWarnings() { _vp.setShowWarnings(!_vp.getShowWarnings()); _vp.repaint(); } public void UIPickSpecialBasesColor() { Color c = JColorChooser.showDialog(_vp, "Choose new special bases color", _vp .getNonStandardBasesColor()); if (c != null) { _vp.setNonStandardBasesColor(c); _vp.setColorNonStandardBases(true); _vp.repaint(); } } public void UIPickGapsBasesColor() { Color c = JColorChooser.showDialog(_vp, "Choose new gaps bases color", _vp.getGapsBasesColor()); if (c != null) { _vp.setGapsBasesColor(c); _vp.setColorGapsBases(true); _vp.repaint(); } } public void UIBaseTypeColor() { if (_vp.isModifiable()) { new VueBases(_vp, VueBases.KIND_MODE); } } public void UIToggleModifiable() { _vp.setModifiable(!_vp.isModifiable()); } public void UIBasePairTypeColor() { if (_vp.isModifiable()) { new VueBases(_vp, VueBases.COUPLE_MODE); } } public void UIBaseAllColor() { if (_vp.isModifiable()) { new VueBases(_vp, VueBases.ALL_MODE); } } public void UIAbout() { VueAboutPanel about = new VueAboutPanel(); JOptionPane.showMessageDialog(_vp, about, "About VARNA " + VARNAConfig.MAJOR_VERSION + "." + VARNAConfig.MINOR_VERSION, JOptionPane.PLAIN_MESSAGE); about.gracefulStop(); } public void UIAutoAnnotateHelices() { if (_vp.isModifiable()) { _vp.getRNA().autoAnnotateHelices(); _vp.repaint(); } } public void UIAutoAnnotateStrandEnds() { if (_vp.isModifiable()) { _vp.getRNA().autoAnnotateStrandEnds(); _vp.repaint(); } } public void UIAutoAnnotateInteriorLoops() { if (_vp.isModifiable()) { _vp.getRNA().autoAnnotateInteriorLoops(); _vp.repaint(); } } public void UIAutoAnnotateTerminalLoops() { if (_vp.isModifiable()) { _vp.getRNA().autoAnnotateTerminalLoops(); _vp.repaint(); } } public void UIAnnotationRemoveFromAnnotation(TextAnnotation textAnnotation) { if (_vp.isModifiable()) { _vp.set_selectedAnnotation(null); _vp.getListeAnnotations().remove(textAnnotation); _vp.repaint(); } } public void UIAnnotationEditFromAnnotation(TextAnnotation textAnnotation) { VueAnnotation vue; if (textAnnotation.getType() == TextAnnotation.AnchorType.POSITION) vue = new VueAnnotation(_vp, textAnnotation, false); else vue = new VueAnnotation(_vp, textAnnotation, true, false); vue.show(); } public void UIAnnotationAddFromStructure(TextAnnotation.AnchorType type, ArrayList listeIndex) throws Exception { TextAnnotation textAnnot; ArrayList listeBase; VueAnnotation vue; switch (type) { case BASE: textAnnot = new TextAnnotation("", _vp.getRNA().get_listeBases() .get(listeIndex.get(0))); vue = new VueAnnotation(_vp, textAnnot, true); vue.show(); break; case LOOP: listeBase = new ArrayList(); for (Integer i : listeIndex) { listeBase.add(_vp.getRNA().get_listeBases().get(i)); } textAnnot = new TextAnnotation("", listeBase, type); vue = new VueAnnotation(_vp, textAnnot, true); vue.show(); break; case HELIX: listeBase = new ArrayList(); for (Integer i : listeIndex) { listeBase.add(_vp.getRNA().get_listeBases().get(i)); } textAnnot = new TextAnnotation("", listeBase, type); vue = new VueAnnotation(_vp, textAnnot, true); vue.show(); break; default: _vp.errorDialog(new Exception("Unknown structure type")); break; } } public void UIAnnotationEditFromStructure(TextAnnotation.AnchorType type, ArrayList listeIndex) { if (_vp.isModifiable()) { ModeleBase mb = _vp.getRNA().get_listeBases() .get(listeIndex.get(0)); TextAnnotation ta = _vp.getRNA().getAnnotation(type, mb); if (ta != null) UIAnnotationEditFromAnnotation(ta); } } public void UIAnnotationRemoveFromStructure(TextAnnotation.AnchorType type, ArrayList listeIndex) { if (_vp.isModifiable()) { ModeleBase mb = _vp.getRNA().get_listeBases() .get(listeIndex.get(0)); TextAnnotation ta = _vp.getRNA().getAnnotation(type, mb); if (ta != null) UIAnnotationRemoveFromAnnotation(ta); } } public void UIAnnotationsAddPosition(int x, int y) { if (_vp.isModifiable()) { Point2D.Double p = _vp.panelToLogicPoint(new Point2D.Double(x, y)); VueAnnotation annotationAdd = new VueAnnotation(_vp, (int) p.x, (int) p.y); annotationAdd.show(); } } public void UIAnnotationsAddBase(int x, int y) { if (_vp.isModifiable()) { ModeleBase mb = _vp.getBaseAt(new Point2D.Double(x, y)); if(mb!=null) { _vp.highlightSelectedBase(mb); TextAnnotation textAnnot = new TextAnnotation("", mb); VueAnnotation annotationAdd = new VueAnnotation(_vp, textAnnot,true); annotationAdd.show(); } } } public void UIAnnotationsAddLoop(int x, int y) { if (_vp.isModifiable()) { try { ModeleBase mb = _vp.getBaseAt(new Point2D.Double(x, y)); if(mb!=null) { Vector v = _vp.getRNA().getLoopBases(mb.getIndex()); ArrayList mbs = _vp.getRNA().getBasesAt(v); TextAnnotation textAnnot; textAnnot = new TextAnnotation("", mbs,TextAnnotation.AnchorType.LOOP); _vp.setSelection(mbs); VueAnnotation annotationAdd = new VueAnnotation(_vp, textAnnot,true); annotationAdd.show(); } } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } } private ArrayList extractMaxContiguousPortion(ArrayList m) { ModeleBase[] tab = new ModeleBase[_vp.getRNA().getSize()]; for(int i=0;i best = new ArrayList(); ArrayList current = new ArrayList(); for(int i=0;ibest.size()) best = current; current = new ArrayList(); } } if (current.size()>best.size()) { best = current; } return best; } public void UIAnnotationsAddRegion(int x, int y) { if (_vp.isModifiable()) { ArrayList mb = _vp.getSelection().getBases(); if (mb.size()==0) { ModeleBase m = _vp.getBaseAt(new Point2D.Double(x, y)); mb.add(m); } mb = extractMaxContiguousPortion(extractMaxContiguousPortion(mb)); _vp.setSelection(mb); HighlightRegionAnnotation regionAnnot = new HighlightRegionAnnotation(mb); _vp.addHighlightRegion(regionAnnot); VueHighlightRegionEdit annotationAdd = new VueHighlightRegionEdit(_vp,regionAnnot); if (!annotationAdd.show()) { _vp.removeHighlightRegion(regionAnnot); } _vp.clearSelection(); } } public void UIAnnotationsAddChemProb(int x, int y) { if (_vp.isModifiable() && _vp.getRNA().getSize()>1) { Point2D.Double p = _vp.panelToLogicPoint(new Point2D.Double(x, y)); ModeleBase m1 = _vp.getBaseAt(new Point2D.Double(x, y)); ModeleBase best = null; if (m1.getIndex()-1>=0) { best = _vp.getRNA().getBaseAt(m1.getIndex()-1);} if (m1.getIndex()+1<_vp.getRNA().getSize()) { ModeleBase m2 = _vp.getRNA().getBaseAt(m1.getIndex()+1); if (best==null) { best = m2; } else { if (best.getCoords().distance(p)>m2.getCoords().distance(p)) { best = m2; } } } ArrayList tab = new ArrayList(); tab.add(m1); tab.add(best); _vp.setSelection(tab); ChemProbAnnotation regionAnnot = new ChemProbAnnotation(m1,best); _vp.getRNA().addChemProbAnnotation(regionAnnot); VueChemProbAnnotation annotationAdd = new VueChemProbAnnotation(_vp,regionAnnot); if (!annotationAdd.show()) { _vp.getRNA().removeChemProbAnnotation(regionAnnot); } _vp.clearSelection(); } } public void UIAnnotationsAddHelix(int x, int y) { if (_vp.isModifiable()) { try { ModeleBase mb = _vp.getBaseAt(new Point2D.Double(x, y)); if(mb!=null) { ArrayList v = _vp.getRNA().findHelix(mb.getIndex()); ArrayList mbs = _vp.getRNA().getBasesAt(v); TextAnnotation textAnnot; textAnnot = new TextAnnotation("", mbs,TextAnnotation.AnchorType.HELIX); _vp.setSelection(mbs); VueAnnotation annotationAdd = new VueAnnotation(_vp, textAnnot,true); annotationAdd.show(); } } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } } public void UIToggleGaspinMode() { if (_vp.isModifiable()) { _vp.toggleDrawOutlineBases(); _vp.toggleFillBases(); _vp.repaint(); } } public void UIAnnotationsAdd() { if (_vp.isModifiable()) { VueAnnotation annotationAdd = new VueAnnotation(_vp); annotationAdd.show(); } } public void UIEditAllBasePairs() { if (_vp.isModifiable()) { new VueBPList(_vp); } } public void UIEditAllBases() { if (_vp.isModifiable()) { new VueBases(_vp,VueBases.ALL_MODE); } } public void UIAnnotationsRemove() { if (_vp.isModifiable()) { new VueListeAnnotations(_vp, VueListeAnnotations.REMOVE); } } public void UIAnnotationsEdit() { if (_vp.isModifiable()) { new VueListeAnnotations(_vp, VueListeAnnotations.EDIT); } } public void UIAddBP(int i, int j, ModeleBP ms) { if (_vp.isModifiable()) { _vp.getRNA().addBP(i, j, ms); _undoableEditSupport.postEdit(new VARNAEdits.AddBPEdit(i,j,ms,_vp)); _vp.repaint(); HashSet tmp = new HashSet(); tmp.add(ms); _vp.fireStructureChanged(new HashSet(_vp.getRNA().getAllBPs()), tmp, new HashSet()); } } public void UIRemoveBP(ModeleBP ms) { if (_vp.isModifiable()) { _undoableEditSupport.postEdit(new VARNAEdits.RemoveBPEdit(ms.getIndex5(),ms.getIndex3(),ms,_vp)); _vp.getRNA().removeBP(ms); _vp.repaint(); HashSet tmp = new HashSet(); tmp.add(ms); _vp.fireStructureChanged(new HashSet(_vp.getRNA().getAllBPs()), new HashSet(), tmp); } } public void UIShiftBaseCoord(ArrayList indices, double dx, double dy) { if (_vp.isModifiable()) { Hashtable backupPos = new Hashtable(); for (int index:indices) { ModeleBase mb = _vp.getRNA().getBaseAt(index); Point2D.Double d = mb.getCoords(); backupPos.put(index,d); _vp.getRNA().setCoord(index, d.x+dx,d.y+dy); _vp.getRNA().setCenter(index, mb.getCenter().x+dx,mb.getCenter().y+dy); } _undoableEditSupport.postEdit(new VARNAEdits.BasesShiftEdit(indices,dx,dy,_vp)); _vp.repaint(); _vp.fireLayoutChanged(backupPos); } } public void UIShiftBaseCoord(ArrayList indices, Point2D.Double dv) { UIShiftBaseCoord(indices, dv.x,dv.y); } public void UIMoveSingleBase(int index, double nx, double ny) { if (_vp.isModifiable()) { ModeleBase mb = _vp.getRNA().getBaseAt(index); Point2D.Double d = mb.getCoords(); Hashtable backupPos = new Hashtable(); backupPos.put(index,d); _undoableEditSupport.postEdit(new VARNAEdits.SingleBaseMoveEdit(index,nx,ny,_vp)); _vp.getRNA().setCoord(index, nx,ny); _vp.repaint(); _vp.fireLayoutChanged(backupPos); } } public void UIMoveSingleBase(int index, Point2D.Double dv) { UIMoveSingleBase(index, dv.x,dv.y); } public void UISetBaseCenter(int index, double x, double y) { UISetBaseCenter(index, new Point2D.Double(x, y)); } public void UISetBaseCenter(int index, Point2D.Double p) { if (_vp.isModifiable()) { _vp.getRNA().setCenter(index, p); } } public void UIUndo() { _vp.undo(); } public void UIRedo() { _vp.redo(); } /** * Move a helix of the rna * * @param index * :the index of the selected base * @param newPos * :the new xy coordinate, within the logical system of coordinates */ public void UIMoveHelixAtom(int index, Point2D.Double newPos) { if (_vp.isModifiable() && (index >= 0) && (index < _vp.getRNA().get_listeBases().size())) { int indexTo = _vp.getRNA().get_listeBases().get(index) .getElementStructure(); Point h = _vp.getRNA().getHelixInterval(index); Point ml = _vp.getRNA().getMultiLoop(h.x); int i = ml.x; if (indexTo != -1) { if (i == 0) { if (shouldFlip(index, newPos)) { UIFlipHelix(h); _undoableEditSupport.postEdit(new VARNAEdits.HelixFlipEdit(h,_vp)); } } else { UIRotateHelixAtom(index, newPos); } } _vp.fireLayoutChanged(); } } /** * Flip an helix around its supporting base */ public void UIFlipHelix(Point h) { int hBeg=h.x; int hEnd=h.y; Point2D.Double A = _vp.getRNA().getCoords(hBeg); Point2D.Double B = _vp.getRNA().getCoords(hEnd); Point2D.Double AB = new Point2D.Double(B.x - A.x, B.y - A.y); double normAB = Math.sqrt(AB.x * AB.x + AB.y * AB.y); // Creating a coordinate system centered on A and having // unit x-vector Ox. Point2D.Double O = A; Point2D.Double Ox = new Point2D.Double(AB.x / normAB, AB.y / normAB); Hashtable old = new Hashtable(); for (int i = hBeg + 1; i < hEnd; i++) { Point2D.Double P = _vp.getRNA().getCoords(i); Point2D.Double nP = RNA.project(O, Ox, P); old.put(i, nP); } _vp.getRNA().flipHelix(h); _vp.fireLayoutChanged(old); } /** * Tests if an helix needs to be flipped. */ boolean shouldFlip(int index, Point2D.Double P) { Point h = _vp.getRNA().getHelixInterval(index); Point2D.Double A = _vp.getRNA().getCoords(h.x); Point2D.Double B = _vp.getRNA().getCoords(h.y); Point2D.Double C = _vp.getRNA().getCoords(h.x + 1); // Creating a vector that is orthogonal to AB Point2D.Double hAB = new Point2D.Double(B.y - A.y, -(B.x - A.x)); Point2D.Double AC = new Point2D.Double(C.x - A.x, C.y - A.y); Point2D.Double AP = new Point2D.Double(P.x - A.x, P.y - A.y); double signC = (hAB.x * AC.x + hAB.y * AC.y); double signP = (hAB.x * AP.x + hAB.y * AP.y); // Now, the product signC*signP is negative iff the mouse and the first // base inside // the helix are on different sides of the end of the helix => Flip the // helix! return (signC * signP < 0.0); } public void UIRotateHelixAtom(int index, Point2D.Double newPos) { Point h = _vp.getRNA().getHelixInterval(index); Point ml = _vp.getRNA().getMultiLoop(h.x); int i = ml.x; int prevIndex = h.x; int nextIndex = h.y; while (i <= ml.y) { int j = _vp.getRNA().get_listeBases().get(i) .getElementStructure(); if ((j != -1) && (i < h.x)) { prevIndex = i; } if ((j != -1) && (i > h.y) && (nextIndex == h.y)) { nextIndex = i; } if ((j > i) && (j < ml.y)) { i = _vp.getRNA().get_listeBases().get(i) .getElementStructure(); } else { i++; } } Point2D.Double oldPos = _vp.getRNA().getCoords(index); Point2D.Double limitLoopLeft, limitLoopRight, limitLeft, limitRight, helixStart, helixStop; boolean isDirect = _vp.getRNA().testDirectionality(ml.x, ml.y, h.x); if (isDirect) { limitLoopLeft = _vp.getRNA().getCoords(ml.y); limitLoopRight = _vp.getRNA().getCoords(ml.x); limitLeft = _vp.getRNA().getCoords(prevIndex); limitRight = _vp.getRNA().getCoords(nextIndex); helixStart = _vp.getRNA().getCoords(h.x); helixStop = _vp.getRNA().getCoords(h.y); } else { limitLoopLeft = _vp.getRNA().getCoords(ml.x); limitLoopRight = _vp.getRNA().getCoords(ml.y); limitLeft = _vp.getRNA().getCoords(nextIndex); limitRight = _vp.getRNA().getCoords(prevIndex); helixStart = _vp.getRNA().getCoords(h.y); helixStop = _vp.getRNA().getCoords(h.x); } Point2D.Double center = _vp.getRNA().get_listeBases().get( h.x).getCenter(); double base = (RNA.computeAngle(center, limitLoopRight) + RNA.computeAngle( center, limitLoopLeft)) / 2.0; double pLimR = RNA.computeAngle(center, limitLeft) - base; double pHelR = RNA.computeAngle(center, helixStart) - base; double pNew = RNA.computeAngle(center, newPos) - base; double pOld = RNA.computeAngle(center, oldPos) - base; double pHelL = RNA.computeAngle(center, helixStop) - base; double pLimL = RNA.computeAngle(center, limitRight) - base; while (pLimR < 0.0) pLimR += 2.0 * Math.PI; while (pHelR < pLimR) pHelR += 2.0 * Math.PI; while ((pNew < pHelR)) pNew += 2.0 * Math.PI; while ((pOld < pHelR)) pOld += 2.0 * Math.PI; while ((pHelL < pOld)) pHelL += 2.0 * Math.PI; while ((pLimL < pHelL)) pLimL += 2.0 * Math.PI; double minDelta = normalizeAngle((pLimR - pHelR) + 0.25); double maxDelta = normalizeAngle((pLimL - pHelL) - 0.25); while (maxDelta < minDelta) maxDelta += 2.0 * Math.PI; double delta = normalizeAngle(pNew - pOld); while (delta < minDelta) delta += 2.0 * Math.PI; if (delta > maxDelta) { double distanceMax = delta - maxDelta; double distanceMin = minDelta - (delta - 2.0 * Math.PI); if (distanceMin < distanceMax) { delta = minDelta; } else { delta = maxDelta; } } double corrected = RNA.correctHysteresis((delta+base+(pHelR+pHelL)/2.)); delta = corrected-(base+(pHelR+pHelL)/2.); _undoableEditSupport.postEdit(new VARNAEdits.HelixRotateEdit(delta,base,pLimL,pLimR,h,ml,_vp)); UIRotateEverything(delta, base, pLimL, pLimR, h, ml); } public void UIRotateEverything(double delta, double base, double pLimL, double pLimR, Point h, Point ml) { Hashtable backupPos = new Hashtable(); _vp.getRNA().rotateEverything(delta, base, pLimL, pLimR, h, ml,backupPos); _vp.fireLayoutChanged(backupPos); } private double normalizeAngle(double angle) { return normalizeAngle(angle, 0.0); } private double normalizeAngle(double angle, double base) { while (angle < base) { angle += 2.0 * Math.PI; } while (angle >= (2.0 * Math.PI) - base) { angle -= 2.0 * Math.PI; } return angle; } } fr/orsay/lri/varna/views/VueMenu.java0000644000000000000000000004143412441747202016612 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Color; import java.awt.Component; import java.awt.Container; import java.awt.Font; import java.awt.Point; import java.awt.event.KeyEvent; import java.util.ArrayList; import javax.swing.JCheckBoxMenuItem; import javax.swing.JComponent; import javax.swing.JLabel; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; import javax.swing.JSeparator; import javax.swing.KeyStroke; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurMenu; import fr.orsay.lri.varna.models.rna.RNA; public class VueMenu extends JPopupMenu { /** * */ private static final long serialVersionUID = 1L; private VARNAPanel _vp; private ControleurMenu _controlerMenu; private JCheckBoxMenuItem _itemOptionSpecialBaseColored = new JCheckBoxMenuItem( "Custom colored", false); private JCheckBoxMenuItem _itemShowWarnings = new JCheckBoxMenuItem( "Show warnings", false); private JCheckBoxMenuItem _itemDrawBackbone = new JCheckBoxMenuItem( "Draw backbone", true); private JCheckBoxMenuItem _itemOptionGapsBaseColored = new JCheckBoxMenuItem( "Custom colored", false); private JCheckBoxMenuItem _itemOptionBondsColored = new JCheckBoxMenuItem( "Use base color for base-pairs", false); private JCheckBoxMenuItem _itemShowNCBP = new JCheckBoxMenuItem( "Show non-canonical BPs", true); private JCheckBoxMenuItem _itemShowOnlyPlanar = new JCheckBoxMenuItem( "Hide tertiary BPs", false); private JCheckBoxMenuItem _itemFlatExteriorLoop = new JCheckBoxMenuItem( "Flat exterior loop", false); private JCheckBoxMenuItem _itemShowColorMap = new JCheckBoxMenuItem( "Show color map", false); private JMenuItem _dashBasesColor; private ArrayList _disabled = new ArrayList(); private JMenuItem _rotation; private JMenuItem _bpHeightIncrement; private Point _spawnOrigin = new Point(-1,-1); public VueMenu(VARNAPanel vp) { _vp = vp; _controlerMenu = new ControleurMenu(_vp, this); } private void addTitle(String title, boolean keep) { JSeparator sep = new JSeparator(); JLabel titleItem = new JLabel(" " + title); // titleItem.setAlignmentX(0.5f); Font previousFont = titleItem.getFont(); Font futureFont = previousFont.deriveFont(Font.BOLD).deriveFont( (float) previousFont.getSize() + 1.0f); titleItem.setFont(futureFont); Color current = titleItem.getForeground(); Color future = current.brighter().brighter(); // titleItem.setBackground(future); titleItem.setForeground(future); add(titleItem); add(sep); if (!keep) { _disabled.add(sep); _disabled.add(titleItem); } } private void configMenuItem(JMenuItem mi, String command, String keyStroke, Container par) { configMenuItem(mi,command,keyStroke,par,false); } private void configMenuItem(JMenuItem mi, String command, String keyStroke, Container par, boolean disabled) { mi.setActionCommand(command); mi.addActionListener(_controlerMenu); if (keyStroke!=null) if (!keyStroke.equals("")) mi.setAccelerator(KeyStroke.getKeyStroke(keyStroke)); if (disabled) { _disabled.add(mi);} par.add(mi); } private JMenuItem createMenuItem(String caption, String command, String keyStroke, Container par, boolean disabled) { JMenuItem mi = new JMenuItem(caption); configMenuItem(mi, command,keyStroke, par, disabled); return mi; } private JMenuItem createMenuItem(String caption, String command, String keyStroke, Container par) { return createMenuItem(caption, command, keyStroke, par,false); } public void updateDialog() { for (int i = 0; i < _disabled.size(); i++) { JComponent j = _disabled.get(i); j.setVisible(_vp.isModifiable()); } _itemOptionSpecialBaseColored.setState(_vp.getColorSpecialBases()); _itemShowWarnings.setState(_vp.getShowWarnings()); _itemOptionGapsBaseColored.setState(_vp.getColorGapsBases()); _itemOptionGapsBaseColored.setEnabled(_vp.isComparisonMode()); _dashBasesColor.setEnabled(_vp.isComparisonMode()); _rotation.setEnabled(_vp.getDrawMode() != RNA.DRAW_MODE_LINEAR); _bpHeightIncrement.setEnabled(_vp.getDrawMode() == RNA.DRAW_MODE_LINEAR); _itemOptionBondsColored.setState(_vp.getUseBaseColorsForBPs()); _itemShowNCBP.setState(_vp.getShowNonCanonicalBP()); _itemShowOnlyPlanar.setState(!_vp.getShowNonPlanarBP()); _itemShowColorMap.setState(_vp.getColorMapVisible()); _itemFlatExteriorLoop.setState(_vp.getFlatExteriorLoop()); _itemFlatExteriorLoop.setEnabled(_vp.getDrawMode() == RNA.DRAW_MODE_RADIATE); } /** * Builds the popup menu */ public void buildPopupMenu() { addTitle("File", true); fileMenu(); exportMenu(); createMenuItem("Print...", "print", "control P", this); addSeparator(); addTitle("Display", true); viewMenu(); displayMenu(); JSeparator sep = new JSeparator(); add(sep); _disabled.add(sep); addTitle("Edit", false); editRNAMenu(); redrawMenu(); colorClassesMenu(); annotationMenu(); _disabled.add(_itemShowNCBP); _disabled.add(_itemShowOnlyPlanar); aboutMenu(); } private void annotationMenu() { JMenu submenuAnnotations = new JMenu("Annotations"); JMenu addAnnotations = new JMenu("New"); createMenuItem("Here", "annotationsaddPosition", "", addAnnotations); createMenuItem("Base", "annotationsaddBase", "", addAnnotations); createMenuItem("Loop", "annotationsaddLoop", "", addAnnotations); createMenuItem("Helix", "annotationsaddHelix", "", addAnnotations); JSeparator sep = new JSeparator(); addAnnotations.add(sep); createMenuItem("Region", "annotationsaddRegion", "", addAnnotations); createMenuItem("Chem. prob.", "annotationsaddChemProb", "", addAnnotations); submenuAnnotations.add(addAnnotations); createMenuItem("Edit from list...", "annotationsedit", "", submenuAnnotations); createMenuItem("Remove from list...", "annotationsremove", "", submenuAnnotations); submenuAnnotations.addSeparator(); createMenuItem("Auto 5'/3'", "annotationsautoextremites", "control alt Q", submenuAnnotations); createMenuItem("Auto helices", "annotationsautohelices", "control Q", submenuAnnotations); createMenuItem("Auto interior loops", "annotationsautointerior", "alt shift Q", submenuAnnotations); createMenuItem("Auto terminal loops", "annotationsautoterminal", "control shift Q", submenuAnnotations); add(submenuAnnotations); } private void fileMenu() { createMenuItem("New...", "userInput", "control N", this,true); createMenuItem("Open...", "file", "control O", this,true); createMenuItem("Save...", "saveas", "control S", this,true); JMenu submenuSave = new JMenu("Save as"); createMenuItem("DBN (Vienna)", "dbn", "", submenuSave); createMenuItem("BPSEQ", "bpseq", "", submenuSave); createMenuItem("CT", "ct", "", submenuSave); add(submenuSave); } private void exportMenu() { // Export menu JMenu submenuExport = new JMenu("Export"); createMenuItem("SVG", "svg", "", submenuExport); createMenuItem("XFIG", "xfig", "", submenuExport); submenuExport.addSeparator(); createMenuItem("EPS", "eps", "", submenuExport); submenuExport.addSeparator(); createMenuItem("PNG", "png", "", submenuExport); createMenuItem("JPEG", "jpeg", "", submenuExport); add(submenuExport); } private void displayMenu() { // SubMenu Base-pairs JMenu subMenuBasePairs = new JMenu("Base Pairs"); createMenuItem("BP style...", "bpstyle", "control shift P", subMenuBasePairs); configMenuItem(_itemShowNCBP, "shownc", "control W", subMenuBasePairs); configMenuItem(_itemShowOnlyPlanar, "shownp", "control E", subMenuBasePairs); // SubMenu Non standard Bases JMenu subMenuNSBases = new JMenu("Non-standard bases"); configMenuItem(_itemOptionSpecialBaseColored, "specialbasecolored", "control J", subMenuNSBases); createMenuItem("Color", "specialBasesColor", "control shift J", subMenuNSBases); // SubMenu Gaps Bases JMenu subMenuGapsBases = new JMenu("'Gaps' bases"); configMenuItem(_itemOptionGapsBaseColored, "dashbasecolored", "control D", subMenuGapsBases); _dashBasesColor = createMenuItem("Color", "dashBasesColor", "control shift D", subMenuGapsBases); // Removable separator JSeparator sep = new JSeparator(); _disabled.add(sep); // Style menu JMenu submenuStyle = new JMenu("RNA style"); createMenuItem("Toggle draw bases", "gaspin", "alt G", submenuStyle,true); submenuStyle.add(subMenuBasePairs); submenuStyle.addSeparator(); submenuStyle.add(subMenuNSBases); submenuStyle.add(subMenuGapsBases); submenuStyle.add(sep); createMenuItem("Backbone color", "backbone", "control K", submenuStyle,true); configMenuItem(_itemDrawBackbone, "showbackbone", "alt B", submenuStyle); // Submenu Title JMenu submenuTitle = new JMenu("Title"); createMenuItem("Set Title", "setTitle", "control T", submenuTitle, true); createMenuItem("Font", "titleDisplay", "control shift T", submenuTitle, true); createMenuItem("Color", "titleColor", "control alt T", submenuTitle, true); _disabled.add(submenuTitle); // Color map menu JMenu submenuColorMap = new JMenu("Color map"); configMenuItem(_itemShowColorMap, "toggleshowcolormap", "control shift L", submenuColorMap, false); createMenuItem("Caption", "colormapcaption", "control shift C", submenuColorMap,true); createMenuItem("Style...", "colormapstyle", "control L", submenuColorMap,false); submenuColorMap.addSeparator(); createMenuItem("Edit values...", "colormapvalues", "shift L", submenuColorMap,true); createMenuItem("Load values...", "colormaploadvalues", "control shift K", submenuColorMap,true); _disabled.add(submenuColorMap); // Menu Misc JMenu submenuMisc = new JMenu("Misc"); createMenuItem("Num. period.", "numPeriod", "control M", submenuMisc); createMenuItem("Background color", "background", "control G", submenuMisc); submenuMisc.add(submenuTitle); // Main menu add(submenuStyle); add(submenuColorMap); add(submenuMisc); } private void editRNAMenu() { createMenuItem("Bases...","editallbases","",this,true); createMenuItem("BasePairs...","editallbps","",this,true); } private void redrawMenu() { JMenu submenuRedraw = new JMenu("Redraw"); _disabled.add(submenuRedraw); JMenu submenuAlgorithms = new JMenu("Algorithm"); _disabled.add(submenuAlgorithms); createMenuItem("Linear","line","control 1",submenuAlgorithms,true); createMenuItem("Circular","circular","control 2",submenuAlgorithms,true); createMenuItem("Radiate","radiate","control 3",submenuAlgorithms,true); createMenuItem("NAView","naview","control 4",submenuAlgorithms,true); //createMenuItem("VARNAView","varnaview","control 5",submenuAlgorithms,true); //createMenuItem("MOTIFView","motifview","control 6",submenuAlgorithms,true); submenuRedraw.add(submenuAlgorithms); // Sets the height increment in LINEAR_MODE type of drawing _bpHeightIncrement = createMenuItem("BP height increment","bpheightincrement","control H",submenuRedraw); configMenuItem(_itemFlatExteriorLoop, "flat", "control F", submenuRedraw, true); // Item pour le r�glage de l'espace entre chaques bases createMenuItem("Space between bases","spaceBetweenBases","control shift S",submenuRedraw,true); createMenuItem("Reset","reset","control shift R",submenuRedraw,true); add(submenuRedraw); } @SuppressWarnings("unused") private void warningMenu() { // Menu showWarning configMenuItem(_itemShowWarnings, "showwarnings", "", this, true); } private void viewMenu() { // View menu JMenu submenuView = new JMenu("View"); // Zoom submenu JMenu zoomDisplay = new JMenu("Zoom"); createMenuItem("25%","zoom25","",zoomDisplay); createMenuItem("50%","zoom50","",zoomDisplay); createMenuItem("100%","zoom100","",zoomDisplay); createMenuItem("150%","zoom150","",zoomDisplay); createMenuItem("200%","zoom200","",zoomDisplay); createMenuItem("Custom","zoom","control Z",zoomDisplay); submenuView.add(zoomDisplay); _rotation = createMenuItem("Rotation...","rotation","control R",submenuView); createMenuItem("Rescale...","rescale","",submenuView); submenuView.addSeparator(); createMenuItem("Border size","borderSize","control B",submenuView); add(submenuView); } JMenu _subMenuBases; private Component _selectionMenuIndex = null; public void addSelectionMenu(JMenuItem s) { _selectionMenuIndex = s; _disabled.add(s); insert(s, getComponentCount() - 2); } public void removeSelectionMenu() { if (_selectionMenuIndex != null) { this.remove(_selectionMenuIndex); _selectionMenuIndex = null; } } private void colorClassesMenu() { // Menu Bases _subMenuBases = new JMenu("Colors"); _disabled.add(_subMenuBases); createMenuItem("By Base","eachKind","control U",_subMenuBases,true); createMenuItem("By BP","eachCouple","shift U",_subMenuBases,true); createMenuItem("By Position","eachBase","alt U",_subMenuBases,true); add(_subMenuBases); } /** * add default color options to a menu */ public void addColorOptions(JMenu submenu) { createMenuItem("Fill Color",submenu.getActionCommand() + ",InnerColor","",submenu,true); createMenuItem("Stroke Color",submenu.getActionCommand() + ",OutlineColor","",submenu,true); createMenuItem("Label Color",submenu.getActionCommand() + ",NameColor","",submenu,true); submenu.addSeparator(); createMenuItem("BP Color",submenu.getActionCommand() + ",BPColor","",submenu,true); createMenuItem("BP Thickness",submenu.getActionCommand() + ",BPThickness","",submenu,true); submenu.addSeparator(); createMenuItem("Number Color",submenu.getActionCommand() + ",NumberColor","",submenu,true); } private void aboutMenu() { addSeparator(); createMenuItem("About VARNA", "about", "control A", this); } public void addAnnotationMenu(JMenu menu) { addAnnotationMenu(menu, false); } public void addAnnotationMenu(JMenu menu, boolean existingAnnot) { String title = "Annotation"; if (existingAnnot) { String debut = ""; String texte = _vp.get_selectedAnnotation().getTexte(); if (texte.length() < 5) debut = texte; else debut = texte.substring(0, 5) + "..."; title = "Annotation: " + debut; } JMenu menuAnnotation = new JMenu(title); if (!existingAnnot) createMenuItem("Add",menu.getActionCommand() + "annotationadd","",menuAnnotation,true); createMenuItem("Edit",menu.getActionCommand() + "annotationedit","",menuAnnotation,true); createMenuItem("Remove",menu.getActionCommand() + "annotationremove","",menuAnnotation,true); menu.add(menuAnnotation); } public static long getSerialVersionUID() { return serialVersionUID; } public VARNAPanel get_vp() { return _vp; } public ControleurMenu get_controleurMenu() { return _controlerMenu; } public JCheckBoxMenuItem get_itemOptionSpecialBaseColored() { return _itemOptionSpecialBaseColored; } public JCheckBoxMenuItem get_itemShowWarnings() { return _itemShowWarnings; } public JCheckBoxMenuItem get_itemOptionDashBaseColored() { return _itemOptionGapsBaseColored; } public void set_controleurMenu(ControleurMenu menu) { _controlerMenu = menu; } public void set_itemOptionSpecialBaseColored( JCheckBoxMenuItem optionSpecialBaseColored) { _itemOptionSpecialBaseColored = optionSpecialBaseColored; } public void set_itemShowWarnings(JCheckBoxMenuItem showWarnings) { _itemShowWarnings = showWarnings; } public void set_itemOptionDashBaseColored( JCheckBoxMenuItem optionDashBaseColored) { _itemOptionGapsBaseColored = optionDashBaseColored; } public JMenuItem get_rotation() { return _rotation; } public void set_rotation(JMenuItem _rotation) { this._rotation = _rotation; } public JCheckBoxMenuItem get_itemOptionBondsColored() { return _itemOptionBondsColored; } public void set_itemOptionBondsColored(JCheckBoxMenuItem optionBondsColored) { _itemOptionBondsColored = optionBondsColored; } public void show(Component invoker,int x,int y) { _spawnOrigin = new Point(x,y); super.show(invoker,x,y); } public Point getSpawnPoint() { return _spawnOrigin ; } }fr/orsay/lri/varna/views/VueJPEG.java0000644000000000000000000000517511620715272016435 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; public class VueJPEG { private JSlider qualitySlider; private JSlider scaleSlider; private JPanel panel; // Turn on labels at major tick marks. // public VueJPEG() { // } public VueJPEG(boolean showQuality, boolean showScale) { qualitySlider = new JSlider(JSlider.HORIZONTAL, 10, 100, 75); qualitySlider.setMajorTickSpacing(5); qualitySlider.setPaintTicks(true); qualitySlider.setPaintLabels(true); qualitySlider.setPreferredSize(new Dimension(400, 50)); scaleSlider = new JSlider(JSlider.HORIZONTAL, 0, 600, 100); scaleSlider.setPreferredSize(new Dimension(400, 50)); scaleSlider.setMajorTickSpacing(100); scaleSlider.setPaintTicks(true); scaleSlider.setPaintLabels(true); panel = new JPanel(); JPanel pup = new JPanel(); JPanel pdown = new JPanel(); int nbPanels = 0; if (showQuality) nbPanels++; if (showScale) nbPanels++; panel.setLayout(new GridLayout(nbPanels, 1)); pup.setLayout(new FlowLayout(FlowLayout.LEFT)); pdown.setLayout(new FlowLayout(FlowLayout.LEFT)); JLabel lseq = new JLabel("Resolution:"); JLabel lstr = new JLabel("Quality:"); pup.add(lseq); pup.add(scaleSlider); pdown.add(lstr); pdown.add(qualitySlider); if (showQuality) { panel.add(pup); } if (showScale) { panel.add(pdown); } } public JSlider getQualitySlider() { return qualitySlider; } public JSlider getScaleSlider() { return scaleSlider; } public JPanel getPanel() { return panel; } } fr/orsay/lri/varna/views/VueZoom.java0000644000000000000000000001005611620715272016626 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; import fr.orsay.lri.varna.controlers.ControleurZoom; import fr.orsay.lri.varna.models.VARNAConfig; public class VueZoom implements ChangeListener { private VARNAPanel _vp; private JSlider zoomSlider, zoomAmountSlider; private JPanel panel; public VueZoom(VARNAPanel vp) { _vp = vp; JPanel pup = new JPanel(); JPanel pdown = new JPanel(); panel = new JPanel(); panel.setLayout(new GridLayout(2, 1)); pup.setLayout(new FlowLayout(FlowLayout.LEFT)); pdown.setLayout(new FlowLayout(FlowLayout.LEFT)); zoomSlider = new JSlider(JSlider.HORIZONTAL, (int) (VARNAConfig.MIN_ZOOM * 100), (int) (VARNAConfig.MAX_ZOOM * 100), (int) (_vp.getZoom() * 100)); // Turn on labels at major tick marks. zoomSlider.setMajorTickSpacing(2000); zoomSlider.setMinorTickSpacing(500); zoomSlider.setPaintTicks(true); zoomSlider.setPaintLabels(true); zoomSlider.setPreferredSize(new Dimension(250, zoomSlider .getPreferredSize().height)); zoomSlider.addChangeListener(new ControleurZoom(this)); JLabel zoomValueLabel = new JLabel(String.valueOf(_vp.getZoom())); zoomValueLabel.setPreferredSize(new Dimension(50, zoomValueLabel .getPreferredSize().height)); zoomSlider.addChangeListener(new ControleurSliderLabel(zoomValueLabel, true)); zoomAmountSlider = new JSlider(JSlider.HORIZONTAL, (int) (VARNAConfig.MIN_AMOUNT * 100), (int) (VARNAConfig.MAX_AMOUNT * 100), (int) (_vp .getZoomIncrement() * 100)); // Turn on labels at major tick marks. zoomAmountSlider.setMajorTickSpacing(50); zoomAmountSlider.setMinorTickSpacing(10); zoomAmountSlider.setPaintTicks(true); zoomAmountSlider.setPaintLabels(true); zoomAmountSlider.setPreferredSize(new Dimension(200, zoomAmountSlider .getPreferredSize().height)); JLabel zoomAmountValueLabel = new JLabel(String.valueOf(_vp .getZoomIncrement())); zoomAmountValueLabel.setPreferredSize(new Dimension(50, zoomAmountValueLabel.getPreferredSize().height)); zoomAmountSlider.addChangeListener(new ControleurSliderLabel( zoomAmountValueLabel, true)); zoomAmountSlider.addChangeListener(this); JLabel labelZ = new JLabel("Zoom:"); JLabel labelA = new JLabel("Increment:"); pup.add(labelZ); pup.add(zoomSlider); pup.add(zoomValueLabel); pdown.add(labelA); pdown.add(zoomAmountSlider); pdown.add(zoomAmountValueLabel); panel.add(pup); panel.add(pdown); } public JPanel getPanel() { return panel; } public double getZoom() { return zoomSlider.getValue() / 100.0; } public double getZoomAmount() { return zoomAmountSlider.getValue() / 100.0; } public VARNAPanel get_vp() { return _vp; } public void stateChanged(ChangeEvent e) { _vp.setZoomIncrement(getZoomAmount()); } } fr/orsay/lri/varna/views/PrintTest.java0000644000000000000000000001243311620715272017157 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.BorderLayout; import java.awt.Container; import java.awt.Font; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Shape; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.font.FontRenderContext; import java.awt.font.TextLayout; import java.awt.geom.AffineTransform; import java.awt.geom.GeneralPath; import java.awt.geom.Line2D; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; import javax.print.attribute.HashPrintRequestAttributeSet; import javax.print.attribute.PrintRequestAttributeSet; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JOptionPane; import javax.swing.JPanel; /** * This program demonstrates how to print 2D graphics */ public class PrintTest { @SuppressWarnings("deprecation") public static void main(String[] args) { JFrame frame = new PrintTestFrame(); frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); frame.show(); } } /** * This frame shows a panel with 2D graphics and buttons to print the graphics * and to set up the page format. */ @SuppressWarnings("serial") class PrintTestFrame extends JFrame { public PrintTestFrame() { setTitle("PrintTest"); setSize(WIDTH, HEIGHT); Container contentPane = getContentPane(); canvas = new PrintPanel(); contentPane.add(canvas, BorderLayout.CENTER); attributes = new HashPrintRequestAttributeSet(); JPanel buttonPanel = new JPanel(); JButton printButton = new JButton("Print"); buttonPanel.add(printButton); printButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { try { PrinterJob job = PrinterJob.getPrinterJob(); job.setPrintable(canvas); if (job.printDialog(attributes)) { job.print(attributes); } } catch (PrinterException exception) { JOptionPane.showMessageDialog(PrintTestFrame.this, exception); } } }); JButton pageSetupButton = new JButton("Page setup"); buttonPanel.add(pageSetupButton); pageSetupButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { PrinterJob job = PrinterJob.getPrinterJob(); job.pageDialog(attributes); } }); contentPane.add(buttonPanel, BorderLayout.NORTH); } private PrintPanel canvas; private PrintRequestAttributeSet attributes; private static final int WIDTH = 300; private static final int HEIGHT = 300; } /** * This panel generates a 2D graphics image for screen display and printing. */ @SuppressWarnings("serial") class PrintPanel extends JPanel implements Printable { public void paintComponent(Graphics g) { super.paintComponent(g); Graphics2D g2 = (Graphics2D) g; drawPage(g2); } public int print(Graphics g, PageFormat pf, int page) throws PrinterException { if (page >= 1) return Printable.NO_SUCH_PAGE; Graphics2D g2 = (Graphics2D) g; g2.translate(pf.getImageableX(), pf.getImageableY()); g2.draw(new Rectangle2D.Double(0, 0, pf.getImageableWidth(), pf .getImageableHeight())); drawPage(g2); return Printable.PAGE_EXISTS; } /** * This method draws the page both on the screen and the printer graphics * context. * * @param g2 * the graphics context */ public void drawPage(Graphics2D g2) { FontRenderContext context = g2.getFontRenderContext(); Font f = new Font("Serif", Font.PLAIN, 72); GeneralPath clipShape = new GeneralPath(); TextLayout layout = new TextLayout("Hello", f, context); AffineTransform transform = AffineTransform.getTranslateInstance(0, 72); Shape outline = layout.getOutline(transform); clipShape.append(outline, false); layout = new TextLayout("World", f, context); transform = AffineTransform.getTranslateInstance(0, 144); outline = layout.getOutline(transform); clipShape.append(outline, false); g2.draw(clipShape); g2.clip(clipShape); final int NLINES = 50; Point2D p = new Point2D.Double(0, 0); for (int i = 0; i < NLINES; i++) { double x = (2 * getWidth() * i) / NLINES; double y = (2 * getHeight() * (NLINES - 1 - i)) / NLINES; Point2D q = new Point2D.Double(x, y); g2.draw(new Line2D.Double(p, q)); } } }fr/orsay/lri/varna/views/VueManualInput.java0000644000000000000000000000500011620715272020130 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.Font; import java.awt.GridLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; import fr.orsay.lri.varna.VARNAPanel; public class VueManualInput { private VARNAPanel _vp; private JPanel panel; private JTextField tseq, tstr; public VueManualInput(VARNAPanel vp) { _vp = vp; buildView(); } private void buildView() { panel = new JPanel(); JPanel pup = new JPanel(); JPanel pdown = new JPanel(); panel.setLayout(new GridLayout(2, 1)); pup.setLayout(new FlowLayout(FlowLayout.LEFT)); pdown.setLayout(new FlowLayout(FlowLayout.LEFT)); Font _textFieldsFont = Font.decode("MonoSpaced-PLAIN-12"); JLabel lseq = new JLabel("Sequence:"); tseq = new JTextField(_vp.getRNA().getListeBasesToString()); JLabel lstr = new JLabel("Structure:"); tstr = new JTextField(_vp.getRNA().getStructDBN()); tstr .setPreferredSize(new Dimension(400, tstr.getPreferredSize().height)); tseq .setPreferredSize(new Dimension(400, tseq.getPreferredSize().height)); tstr.setFont(_textFieldsFont); tseq.setFont(_textFieldsFont); pup.add(lseq); pup.add(tseq); pdown.add(lstr); pdown.add(tstr); panel.add(pup); panel.add(pdown); } public JPanel getPanel() { return panel; } public void setPanel(JPanel panel) { this.panel = panel; } public JTextField getTseq() { return tseq; } public JTextField getTstr() { return tstr; } } fr/orsay/lri/varna/views/VueBPList.java0000644000000000000000000001364211716337170017046 0ustar rootrootpackage fr.orsay.lri.varna.views; import java.awt.Color; import java.awt.Dimension; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyVetoException; import java.beans.VetoableChangeListener; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.Vector; import javax.swing.DefaultCellEditor; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.event.TableModelEvent; import javax.swing.event.TableModelListener; import javax.swing.table.AbstractTableModel; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.components.ActionEditor; import fr.orsay.lri.varna.components.ActionRenderer; import fr.orsay.lri.varna.components.ColorRenderer; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.models.rna.ModeleBP; import fr.orsay.lri.varna.models.rna.RNA; public class VueBPList extends JPanel implements TableModelListener, ActionListener { private JTable table; private BPTableModel _tm; private VARNAPanel _vp; private ArrayList data; private ArrayList _backup; private ArrayList columns; public enum Actions{ ACTION_DELETE, ACTION_EDIT_STYLE; public String toString() { switch(this) { case ACTION_DELETE: return "Delete"; case ACTION_EDIT_STYLE: return "Edit Style"; } return "N/A"; } }; public VueBPList(VARNAPanel vp) { super(new GridLayout(1, 0)); _vp = vp; init(); } private void init() { Object[] col = {"Sec.Str.","5' partner","3' partner","5' edge","3' edge","Orientation","Remove"}; columns = new ArrayList(); for (int i = 0; i < col.length; i++) { columns.add(col[i]); } _backup = new ArrayList(); data = new ArrayList(); for (ModeleBP ms: _vp.getRNA().getAllBPs()) { data.add(ms); } Collections.sort(data); _tm = new BPTableModel(); table = new JTable(_tm); table.setDefaultRenderer(Color.class, new ColorRenderer(true)); table.setDefaultRenderer(Actions.class, new ActionRenderer()); table.setDefaultEditor(ModeleBP.Edge.class, new DefaultCellEditor(new JComboBox(ModeleBP.Edge.values()))); table.setDefaultEditor(ModeleBP.Stericity.class, new DefaultCellEditor(new JComboBox(ModeleBP.Stericity.values()))); table.setDefaultEditor(Actions.class, new ActionEditor(this)); table.setPreferredScrollableViewportSize(new Dimension(500, 500)); table.getModel().addTableModelListener(this); table.setRowHeight(25); JScrollPane scrollPane = new JScrollPane(table); add(scrollPane); setOpaque(true); // content panes must be opaque this.doLayout(); JOptionPane.showMessageDialog(_vp, this, "Base pairs Edition", JOptionPane.PLAIN_MESSAGE); } public void cancelChanges() { for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) { ModeleBase mb = _vp.getRNA().get_listeBases().get(i); mb.setValue(_backup.get(i)); } _vp.getRNA().rescaleColorMap(_vp.getColorMap()); } private class BPTableModel extends AbstractTableModel { /** * */ private static final long serialVersionUID = 1L; public String getColumnName(int col) { return columns.get(col).toString(); } public int getRowCount() { return data.size(); } public int getColumnCount() { return columns.size(); } public Object getValueAt(int row, int col) { ModeleBP mb = data.get(row); if (col==0) { return new Boolean(mb.getPartner3().getElementStructure()==mb.getPartner5().getIndex()); } else if (col==1) { return new String(""+mb.getPartner5().getBaseNumber()+"-"+mb.getPartner5().getContent()); } else if (col==2) { return new String(""+mb.getPartner3().getBaseNumber()+"-"+mb.getPartner3().getContent()); } else if (col==3) { return mb.getEdgePartner5(); } else if (col==4) { return mb.getEdgePartner3(); } else if (col==5) { return mb.getStericity(); } else if (col==6) { return Actions.ACTION_DELETE; } return "N/A"; } public boolean isCellEditable(int row, int col) { if ( col == 3 || col ==4 || col ==5 || col ==6) return true; return false; } public void setValueAt(Object value, int row, int col) { if ( col == 3 || col ==4 || col ==5) { ModeleBP mb = data.get(row); if ( col == 3) { mb.setEdge5((ModeleBP.Edge)value); } else if ( col == 4) { mb.setEdge3((ModeleBP.Edge)value); } else if ( col == 5) { mb.setStericity((ModeleBP.Stericity)value); } fireTableCellUpdated(row, col); _vp.repaint(); } } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } } public void tableChanged(TableModelEvent e) { if (e.getType() == TableModelEvent.UPDATE) { table.repaint(); } } public void actionPerformed(ActionEvent arg0) { //System.out.println(""+arg0.toString()); String[] data2 = arg0.getActionCommand().split("-"); int row = Integer.parseInt(data2[data2.length-1]); if (data2[0].equals("Delete")) { ModeleBP ms = data.get(row); _vp.getVARNAUI().UIRemoveBP(ms); data.remove(row); _tm.fireTableRowsDeleted(row, row); } } } fr/orsay/lri/varna/views/VueFont.java0000644000000000000000000000667111620715272016620 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Font; import java.awt.GraphicsEnvironment; import javax.swing.JComboBox; import javax.swing.JPanel; import javax.swing.JSlider; import fr.orsay.lri.varna.VARNAPanel; public class VueFont { private VARNAPanel _vp; private Font font; private JComboBox stylesBox; private JComboBox boxPolice; private JPanel panel; private JSlider sizeSlider; public VueFont(VARNAPanel vp) { _vp = vp; init(); buildViewVPTitle(); } public VueFont(Font f) { font = f; init(); buildViewFont(); } private void init() { GraphicsEnvironment ge = GraphicsEnvironment .getLocalGraphicsEnvironment(); String[] polices = ge.getAvailableFontFamilyNames(); boxPolice = new JComboBox(polices); sizeSlider = new JSlider(JSlider.HORIZONTAL, 4, 88, 14); // Turn on labels at major tick marks. sizeSlider.setMajorTickSpacing(10); sizeSlider.setMinorTickSpacing(5); sizeSlider.setPaintTicks(true); sizeSlider.setPaintLabels(true); String[] styles = { "Plain", "Italic", "Bold" }; stylesBox = new JComboBox(styles); panel = new JPanel(); panel.add(boxPolice); panel.add(sizeSlider); panel.add(stylesBox); } private void buildViewFont() { boxPolice.setSelectedItem(font.getFamily()); sizeSlider.setValue(font.getSize()); stylesBox.setSelectedItem(styleIntToString(font.getStyle())); } private void buildViewVPTitle() { boxPolice.setSelectedItem(_vp.getTitleFont().getFamily()); sizeSlider.setValue(_vp.getTitleFont().getSize()); stylesBox.setSelectedItem(styleIntToString(_vp.getTitleFont() .getStyle())); } public String styleIntToString(int styleInt) { switch (styleInt) { case Font.PLAIN:// Plain return "Plain"; case Font.ITALIC:// Italic return "Italic"; case Font.BOLD:// Bold return "Bold"; default:// Plain return "Plain"; } } public JComboBox getStylesBox() { return stylesBox; } public JComboBox getBoxPolice() { return boxPolice; } public JPanel getPanel() { return panel; } public JSlider getSizeSlider() { return sizeSlider; } public Font getFont() { int style; switch (getStylesBox().getSelectedIndex()) { case 0:// Plain style = Font.PLAIN; break; case 1:// Italic style = Font.ITALIC; break; case 2:// Bold style = Font.BOLD; break; default:// Plain style = Font.PLAIN; break; } return new Font((String) getBoxPolice().getSelectedItem(), style, getSizeSlider().getValue()); } } fr/orsay/lri/varna/views/VueSpaceBetweenBases.java0000644000000000000000000000477212050247166021235 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; import fr.orsay.lri.varna.controlers.ControleurSpaceBetweenBases; public class VueSpaceBetweenBases { private VARNAPanel _vp; private JPanel panel; private JSlider spaceSlider; public VueSpaceBetweenBases(VARNAPanel vp) { _vp = vp; panel = new JPanel(); spaceSlider = new JSlider(JSlider.HORIZONTAL, 10, 200, Integer .valueOf(String.valueOf(Math.round(_vp.getSpaceBetweenBases() * 100)))); // Turn on labels at major tick marks. spaceSlider.setMajorTickSpacing(30); spaceSlider.setPaintTicks(true); spaceSlider.setPaintLabels(true); JLabel spaceLabel = new JLabel(String.valueOf(100.0 * _vp.getSpaceBetweenBases())); spaceLabel.setPreferredSize(new Dimension(50, spaceLabel .getPreferredSize().height)); spaceSlider.addChangeListener(new ControleurSliderLabel(spaceLabel, false)); spaceSlider.addChangeListener(new ControleurSpaceBetweenBases(this)); panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JLabel labelS = new JLabel("Space:"); panel.add(labelS); panel.add(spaceSlider); panel.add(spaceLabel); } public VARNAPanel get_vp() { return _vp; } public JPanel getPanel() { return panel; } public Double getSpace() { return spaceSlider.getValue() / 100.0; } } fr/orsay/lri/varna/views/VueBorder.java0000644000000000000000000000736111620715272017124 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JSlider; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurBorder; import fr.orsay.lri.varna.controlers.ControleurSliderLabel; public class VueBorder { private VARNAPanel _vp; private JSlider borderHeightSlider, borderWidthSlider; private JPanel panel; public VueBorder(VARNAPanel vp) { _vp = vp; JPanel pup = new JPanel(); JPanel pdown = new JPanel(); panel = new JPanel(); panel.setLayout(new GridLayout(2, 1)); pup.setLayout(new FlowLayout(FlowLayout.LEFT)); pdown.setLayout(new FlowLayout(FlowLayout.LEFT)); borderHeightSlider = new JSlider(JSlider.HORIZONTAL, 0, _vp.getHeight() / 2 - 10, _vp.getBorderSize().height); // Turn on labels at major tick marks. borderHeightSlider.setMajorTickSpacing(50); borderHeightSlider.setMinorTickSpacing(10); borderHeightSlider.setPaintTicks(true); borderHeightSlider.setPaintLabels(true); JLabel borderHeightLabel = new JLabel(String.valueOf(_vp .getBorderSize().height)); borderHeightLabel.setPreferredSize(new Dimension(50, borderHeightLabel .getPreferredSize().height)); borderHeightSlider.addChangeListener(new ControleurSliderLabel( borderHeightLabel, false)); borderHeightSlider.addChangeListener(new ControleurBorder(this)); borderWidthSlider = new JSlider(JSlider.HORIZONTAL, 0, _vp.getWidth() / 2 - 10, _vp.getBorderSize().width); // Turn on labels at major tick marks. borderWidthSlider.setMajorTickSpacing(50); borderWidthSlider.setMinorTickSpacing(10); borderWidthSlider.setPaintTicks(true); borderWidthSlider.setPaintLabels(true); JLabel borderWidthLabel = new JLabel(String .valueOf(_vp.getBorderSize().width)); borderWidthLabel.setPreferredSize(new Dimension(50, borderWidthLabel .getPreferredSize().height)); borderWidthSlider.addChangeListener(new ControleurSliderLabel( borderWidthLabel, false)); borderWidthSlider.addChangeListener(new ControleurBorder(this)); JLabel labelW = new JLabel("Width:"); JLabel labelH = new JLabel("Height:"); pup.add(labelW); pup.add(borderWidthSlider); pup.add(borderWidthLabel); pdown.add(labelH); pdown.add(borderHeightSlider); pdown.add(borderHeightLabel); panel.add(pup); panel.add(pdown); } public JPanel getPanel() { return panel; } public Dimension getDimension() { return new Dimension(borderWidthSlider.getValue(), borderHeightSlider .getValue()); } public int getHeight() { return borderHeightSlider.getValue(); } public int getWidth() { return borderWidthSlider.getValue(); } public VARNAPanel get_vp() { return _vp; } } fr/orsay/lri/varna/views/VueChemProbAnnotation.java0000644000000000000000000001145511620715272021440 0ustar rootroot package fr.orsay.lri.varna.views; import java.awt.Color; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.ArrayList; import javax.swing.JButton; import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSlider; import javax.swing.JSpinner; import javax.swing.SpinnerNumberModel; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; public class VueChemProbAnnotation implements ChangeListener, ActionListener, ItemListener { private VARNAPanel _vp; private JPanel panel; private ChemProbAnnotation _an; private static int CONTROL_HEIGHT = 50; private static int TITLE_WIDTH = 70; private static int CONTROL_WIDTH = 200; private JButton color = new JButton(); JSpinner intensity; JComboBox outward = new JComboBox(new String[]{"Inward","Outward"}); JComboBox type = new JComboBox(ChemProbAnnotation.ChemProbAnnotationType.values()); public VueChemProbAnnotation(VARNAPanel vp, ChemProbAnnotation an) { _an = an; _vp = vp; panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JPanel outlinep = new JPanel(); JLabel l1 = new JLabel("Color: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); color.setContentAreaFilled(false); color.setOpaque(true); color.setPreferredSize(new Dimension(CONTROL_WIDTH,CONTROL_HEIGHT)); color.setBackground(_an.getColor()); color.addActionListener(this); color.setActionCommand("outline"); outlinep.add(l1); outlinep.add(color); JPanel radiusp = new JPanel(); l1 = new JLabel("Intensity: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); SpinnerNumberModel jm = new SpinnerNumberModel(_an.getIntensity(),0.01,10.0,0.01); intensity = new JSpinner(jm); radiusp.add(l1); radiusp.add(intensity); intensity.addChangeListener(this); JPanel dirp = new JPanel(); l1 = new JLabel("Direction: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); outward.addItemListener(this); dirp.add(l1); dirp.add(outward); JPanel typep = new JPanel(); l1 = new JLabel("Type: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); type.addItemListener(this); typep.add(l1); typep.add(type); JPanel jp = new JPanel(); jp.setLayout(new GridLayout(4,1)); jp.add(outlinep); jp.add(radiusp); jp.add(dirp); jp.add(typep); panel.add(jp); } public JPanel getPanel() { return panel; } public VARNAPanel get_vp() { return _vp; } HighlightRegionAnnotation _backup = null; public boolean show() { boolean accept = false; intensity.setValue(_an.getIntensity()); color.setBackground(_an.getColor()); type.setSelectedItem(_an.getType()); outward.setSelectedItem((_an.isOut()?"Inward":"Outward")); if (JOptionPane.showConfirmDialog(_vp, getPanel(), "Edit chemical probing annotation", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE) == JOptionPane.OK_OPTION) { accept = true; } _vp.repaint(); return accept; } public void stateChanged(ChangeEvent e) { if (e.getSource().equals(intensity)) { Object val = intensity.getValue(); if (val instanceof Double) { _an.setIntensity(((Double)val).doubleValue()); _vp.repaint(); } } } public void actionPerformed(ActionEvent e) { if (e.getActionCommand().equals("outline")) { Color c = JColorChooser.showDialog(getPanel(), "Choose new outline color", _an.getColor()); if (c!= null) { _an.setColor(c); } } color.setBackground(_an.getColor()); _vp.repaint(); } public void itemStateChanged(ItemEvent e) { if (e.getSource()==outward) { _an.setOut(!e.getItem().equals("Outward")); _vp.repaint(); } else if ((e.getSource()==type)&&(e.getItem() instanceof ChemProbAnnotation.ChemProbAnnotationType)) { ChemProbAnnotation.ChemProbAnnotationType t = (ChemProbAnnotation.ChemProbAnnotationType) e.getItem(); _an.setType(t); _vp.repaint(); } } } fr/orsay/lri/varna/views/VueColorMapStyle.java0000644000000000000000000001206012464222220020425 0ustar rootrootpackage fr.orsay.lri.varna.views; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Cursor; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.RenderingHints; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.util.Arrays; import java.util.Comparator; import javax.swing.BoxLayout; import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JDialog; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.components.GradientEditorPanel; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.models.rna.ModeleColorMap.NamedColorMapTypes; public class VueColorMapStyle extends JPanel implements ActionListener, ItemListener, PropertyChangeListener { private VARNAPanel _vp; private GradientEditorPanel _gp; private JComboBox _cb; private JTextField _code; private ModeleColorMap _backup; public VueColorMapStyle(VARNAPanel vp) { super(); _vp = vp; init(); } private void init() { JLabel gradientCaption = new JLabel("Click gradient to add new color..."); _gp = new GradientEditorPanel(_vp.getColorMap().clone()); _backup = _vp.getColorMap(); _gp.setPreferredSize(new Dimension(300,70)); _gp.addPropertyChangeListener(this); JPanel codePanel = new JPanel(); JLabel codeCaption = new JLabel("Param. code: "); _code = new JTextField(""); _code.setFont(Font.decode("Monospaced-PLAIN-12")); _code.setEditable(false); _code.addFocusListener(new FocusListener(){ public void focusGained(FocusEvent arg0) { _code.setSelectionStart(0); _code.setSelectionEnd(_code.getText().length()); } public void focusLost(FocusEvent arg0) { } }); NamedColorMapTypes[] palettes = ModeleColorMap.NamedColorMapTypes.values(); Arrays.sort(palettes,new Comparator(){ public int compare(ModeleColorMap.NamedColorMapTypes arg0, ModeleColorMap.NamedColorMapTypes arg1) { return arg0.getId().compareTo(arg1.getId()); } }); Object[] finalArray = new Object[palettes.length+1]; int selected = -1; for (int i=0;i 0) return NO_SUCH_PAGE; Graphics2D g2 = (Graphics2D) g; g2.setPaint(Color.blue); g2.setFont(new Font("Serif", Font.PLAIN, 64)); g2.drawString(phrase, 96, 144); return PAGE_EXISTS; } public static void main(String args[]) { PrinterJob tache = PrinterJob.getPrinterJob(); tache.setPrintable(new Imprimer( "Ceci est un teste d'impression en java!")); // printDialog affiche la fenetre de sélection de l’imprimante, // etc... // il retourne true si on clique sur "Ok", false si on clique sur // "Annuler" //System.out.println(PrinterJob.getPrinterJob()); if (!tache.printDialog()) return; try { tache.print(); } catch (Exception e) { System.err.println("impossible d'imprimer"); } } }fr/orsay/lri/varna/views/VueBaseValues.java0000644000000000000000000000724611620715272017743 0ustar rootrootpackage fr.orsay.lri.varna.views; import java.awt.Color; import java.awt.Dimension; import java.awt.GridLayout; import java.beans.PropertyChangeEvent; import java.beans.PropertyVetoException; import java.beans.VetoableChangeListener; import java.util.ArrayList; import java.util.Vector; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.event.TableModelEvent; import javax.swing.event.TableModelListener; import javax.swing.table.AbstractTableModel; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.components.ColorRenderer; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.ModeleColorMap; import fr.orsay.lri.varna.models.rna.RNA; public class VueBaseValues extends JPanel implements TableModelListener { private JTable table; private ValueTableModel _tm; private VARNAPanel _vp; private ArrayList data; private ArrayList _backup; private ArrayList columns; public VueBaseValues(VARNAPanel vp) { super(new GridLayout(1, 0)); _vp = vp; init(); } private void init() { Object[] col = {"Number","Base","Value","Preview"}; columns = new ArrayList(); for (int i = 0; i < col.length; i++) { columns.add(col[i]); } _backup = new ArrayList(); data = new ArrayList(); for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) { ModeleBase mb = _vp.getRNA().get_listeBases().get(i); data.add(mb); _backup.add(mb.getValue()); } _tm = new ValueTableModel(); table = new JTable(_tm); table.setDefaultRenderer(Color.class, new ColorRenderer(true)); table.setPreferredScrollableViewportSize(new Dimension(300, 300)); table.getModel().addTableModelListener(this); JScrollPane scrollPane = new JScrollPane(table); this.add(scrollPane); } public void cancelChanges() { for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) { ModeleBase mb = _vp.getRNA().get_listeBases().get(i); mb.setValue(_backup.get(i)); } _vp.getRNA().rescaleColorMap(_vp.getColorMap()); } private class ValueTableModel extends AbstractTableModel { public String getColumnName(int col) { return columns.get(col).toString(); } public int getRowCount() { return data.size(); } public int getColumnCount() { return columns.size(); } public Object getValueAt(int row, int col) { ModeleBase mb = data.get(row); if (col==0) { return new Integer(mb.getBaseNumber()); } else if (col==1) { return new String(mb.getContent()); } else if (col==2) { return new Double(mb.getValue()); } else if (col==3) { return _vp.getColorMap().getColorForValue(mb.getValue()); } return "N/A"; } public boolean isCellEditable(int row, int col) { if (getColumnName(col).equals("Value")) return true; return false; } public void setValueAt(Object value, int row, int col) { if (getColumnName(col).equals("Value")) { data.get(row).setValue(((Double)value)); _vp.getRNA().rescaleColorMap(_vp.getColorMap()); _vp.repaint(); fireTableCellUpdated(row, col); } } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } } public void tableChanged(TableModelEvent e) { if (e.getType() == TableModelEvent.UPDATE) { table.repaint(); } } } fr/orsay/lri/varna/views/VueHighlightRegionEdit.java0000644000000000000000000001360011620715272021561 0ustar rootrootpackage fr.orsay.lri.varna.views; import java.awt.Color; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.ArrayList; import javax.swing.JButton; import javax.swing.JColorChooser; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSlider; import javax.swing.JSpinner; import javax.swing.SpinnerNumberModel; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; public class VueHighlightRegionEdit implements ChangeListener, ActionListener { private VARNAPanel _vp; private JSlider _fromSlider; private JSlider _toSlider; private JPanel panel; private HighlightRegionAnnotation _an; private static int CONTROL_HEIGHT = 50; private static int TITLE_WIDTH = 70; private static int CONTROL_WIDTH = 200; private JButton fillShow = new JButton(); private JButton outlineShow = new JButton(); JSpinner rad; public VueHighlightRegionEdit(VARNAPanel vp, HighlightRegionAnnotation an) { _an = an; _vp = vp; _toSlider = new JSlider(JSlider.HORIZONTAL, 0,vp.getRNA().getSize()-1,0); _toSlider.setMajorTickSpacing(10); _toSlider.setPaintTicks(true); _toSlider.setPaintLabels(true); _toSlider.setPreferredSize(new Dimension(CONTROL_WIDTH, CONTROL_HEIGHT)); _fromSlider = new JSlider(JSlider.HORIZONTAL, 0,vp.getRNA().getSize()-1,0); _fromSlider.setMajorTickSpacing(10); _fromSlider.setPaintTicks(true); _fromSlider.setPaintLabels(true); _fromSlider.setPreferredSize(new Dimension(CONTROL_WIDTH, CONTROL_HEIGHT)); _fromSlider.addChangeListener(this); _toSlider.addChangeListener(this); panel = new JPanel(); panel.setLayout(new FlowLayout(FlowLayout.LEFT)); JPanel fromp = new JPanel(); JLabel l1 = new JLabel("From: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); fromp.add(l1); fromp.add(_fromSlider); JPanel top = new JPanel(); l1 = new JLabel("To: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); top.add(l1); top.add(_toSlider); JPanel outlinep = new JPanel(); l1 = new JLabel("Outline color: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); outlineShow.setContentAreaFilled(false); outlineShow.setOpaque(true); outlineShow.setPreferredSize(new Dimension(CONTROL_WIDTH,CONTROL_HEIGHT)); outlineShow.setBackground(an.getOutlineColor()); outlineShow.addActionListener(this); outlineShow.setActionCommand("outline"); outlinep.add(l1); outlinep.add(outlineShow); JPanel fillp = new JPanel(); l1 = new JLabel("Fill color: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); fillShow.setContentAreaFilled(false); fillShow.setOpaque(true); fillShow.setPreferredSize(new Dimension(CONTROL_WIDTH,CONTROL_HEIGHT)); fillShow.setBackground(an.getFillColor()); fillShow.addActionListener(this); fillShow.setActionCommand("fill"); fillp.add(l1); fillp.add(fillShow); JPanel radiusp = new JPanel(); l1 = new JLabel("Radius: "); l1.setPreferredSize(new Dimension(TITLE_WIDTH,CONTROL_HEIGHT)); SpinnerNumberModel jm = new SpinnerNumberModel(_an.getRadius(),1.0,50.0,0.1); rad = new JSpinner(jm); rad.setPreferredSize(new Dimension(CONTROL_WIDTH,CONTROL_HEIGHT)); radiusp.add(l1); radiusp.add(rad); rad.addChangeListener(this); JPanel jp = new JPanel(); jp.setLayout(new GridLayout(5,1)); jp.add(fromp); jp.add(top); jp.add(outlinep); jp.add(fillp); jp.add(radiusp); panel.add(jp); } public JPanel getPanel() { return panel; } public double getAngle() { return _toSlider.getValue(); } public VARNAPanel get_vp() { return _vp; } HighlightRegionAnnotation _backup = null; public boolean show() { boolean accept = false; int from = _an.getMinIndex(); int to = _an.getMaxIndex(); _fromSlider.setValue(from); _toSlider.setValue(to ); if (JOptionPane.showConfirmDialog(_vp, getPanel(), "Edit region annotation", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE) == JOptionPane.OK_OPTION) { accept = true; } _vp.repaint(); return accept; } public void stateChanged(ChangeEvent e) { if ((e.getSource()==_toSlider)||(e.getSource()==_fromSlider)) { int from = _fromSlider.getValue(); int to = _toSlider.getValue(); if (from>to) { if (e.getSource().equals(_fromSlider)) { _toSlider.setValue(from); } else if (e.getSource().equals(_toSlider)) { _fromSlider.setValue(to); } } from = _fromSlider.getValue(); to = _toSlider.getValue(); _an.setBases(_vp.getRNA().getBasesBetween(from, to)); _vp.repaint(); } else if (e.getSource().equals(rad)) { Object val = rad.getValue(); if (val instanceof Double) { _an.setRadius(((Double)val).doubleValue()); } } } public void actionPerformed(ActionEvent e) { if (e.getActionCommand().equals("outline")) { Color c = JColorChooser.showDialog(getPanel(), "Choose new outline color", _an.getOutlineColor()); if (c!= null) { _an.setOutlineColor(c); } } else if (e.getActionCommand().equals("fill")) { Color c = JColorChooser.showDialog(getPanel(), "Choose new fill color", _an.getFillColor()); if (c!= null) { _an.setFillColor(c); } } outlineShow.setBackground(_an.getOutlineColor()); fillShow.setBackground(_an.getFillColor()); _vp.repaint(); } } fr/orsay/lri/varna/views/VueAboutPanel.java0000644000000000000000000001204711620715272017736 0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ package fr.orsay.lri.varna.views; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.util.ArrayList; import javax.swing.BorderFactory; import javax.swing.JPanel; import javax.swing.JTextArea; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.models.VARNAConfig; public class VueAboutPanel extends JPanel { /** * */ private static final long serialVersionUID = 4525998278180950602L; private AboutAnimator _anim; private JPanel _textPanel; private JTextArea _textArea; public VueAboutPanel() { init(); } private void init() { try { setBorder(BorderFactory.createEtchedBorder()); setLayout(new BorderLayout()); setBackground(Color.WHITE); String message = "VARNA " + VARNAConfig.MAJOR_VERSION + "." + VARNAConfig.MINOR_VERSION + "\n" + "\n" + "Created by: Kevin Darty, Alain Denise and Yann Ponty\n" + "Contact: ponty@lri.fr\n" + "\n" + "VARNA is freely distributed under the terms of the GNU GPL 3.0 license.\n" + "\n" + "Supported by the BRASERO project (ANR-06-BLAN-0045)\n"; _textArea = new JTextArea(); _textArea.setText(message); _textArea.setEditable(false); _textPanel = new JPanel(); _textPanel.setBackground(Color.WHITE); _textPanel.setLayout(new BorderLayout()); _textPanel.setBorder(BorderFactory.createMatteBorder(0, 15, 0, 15, getBackground())); _textPanel.add(_textArea); VARNAPanel vp = new VARNAPanel("GGGGAAAACCCC", "((((....))))"); vp.setModifiable(false); vp.setPreferredSize(new Dimension(100, 100)); // vp.setBorder(BorderFactory.createLineBorder(Color.gray)); _anim = new AboutAnimator(vp); _anim .addRNA("GGGGAAGGGGAAAACCCCAACCCC", "((((..((((....))))..))))"); _anim.addRNA("GGGGAAGGGGAAGGGGAAAACCCCAACCCCAACCCC", "((((..((((..((((....))))..))))..))))"); _anim .addRNA( "GGGGAGGGGAAAACCCCAGGGGAGGGGAAAACCCCAGGGGAAAACCCCAGGGGAAAACCCCACCCCAGGGGAAAACCCCACCCC", "((((.((((....)))).((((.((((....)))).((((....)))).((((....)))).)))).((((....)))).))))"); _anim .addRNA( "GGGGGGGGAAAACCCCAGGGGAAAACCCCAGGGGGGGGAAAACCCCAGGGGAAAACCCCAGGGGAAAACCCCAGGGGAAAACCCCGGGGAAAACCCCACCCCAGGGGAAAACCCCAGGGGAAAACCCCCCCC", "((((((((....)))).((((....)))).((((((((....)))).((((....)))).((((....)))).((((....))))((((....)))).)))).((((....)))).((((....))))))))"); _anim.addRNA("GGGGAAAACCCC", "((((....))))"); _anim.addRNA("GGGGAAGGGGAAAACCCCAGGGGAAAACCCCACCCC", "((((..((((....)))).((((....)))).))))"); _anim.addRNA("GGGGAGGGGAAAACCCCAGGGGAAAACCCCAGGGGAAAACCCCACCCC", "((((.((((....)))).((((....)))).((((....)))).))))"); _anim .addRNA( "GGGGAGGGGAAAAAAACCCCAGGGGAAAAAAACCCCAGGGGAAAAAAACCCCACCCC", "((((.((((.......)))).((((.......)))).((((.......)))).))))"); _anim.start(); add(vp, BorderLayout.WEST); add(_textPanel, BorderLayout.CENTER); } catch (ExceptionNonEqualLength e) { } } public void gracefulStop() { _anim.gracefulStop(); } private class AboutAnimator extends Thread { VARNAPanel _vp; ArrayList _structures = new ArrayList(); ArrayList _sequences = new ArrayList(); int _period = 2000; boolean _over = false; public AboutAnimator(VARNAPanel vp) { super(); _vp = vp; } public void addRNA(String seq, String str) { _sequences.add(seq); _structures.add(str); } public void gracefulStop() { _over = true; } public void run() { try { int i = 0; while (!_over) { sleep(_period); String seq = _sequences.get(i); String str = _structures.get(i); _vp.drawRNAInterpolated(seq, str); sleep(500); i = (i + 1) % _sequences.size(); } } catch (InterruptedException e) { e.printStackTrace(); } catch (ExceptionNonEqualLength e) { e.printStackTrace(); } } } } rnaml.dtd0000644000000000000000000005277111441741446011404 0ustar rootroot META-INF/0000755000000000000000000000000012655733661010732 5ustar rootrootMETA-INF/MANIFEST.MF0000644000000000000000000022725712541143162012364 0ustar rootrootManifest-Version: 1.0 Ant-Version: Apache Ant 1.8.4 Application-Library-Allowable-Codebase: 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0ustar rootroot/* VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1. If not, see http://www.gnu.org/licenses. */ import java.awt.Component; import java.awt.GridLayout; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTarget; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.io.FileReader; import java.io.IOException; import java.util.ArrayList; import java.util.List; import javax.swing.JApplet; import javax.swing.JOptionPane; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.controlers.ControleurScriptParser; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionParameterError; import fr.orsay.lri.varna.interfaces.InterfaceParameterLoader; import fr.orsay.lri.varna.models.VARNAConfigLoader; import fr.orsay.lri.varna.models.rna.RNA; public class VARNA extends JApplet implements InterfaceParameterLoader,DropTargetListener { ArrayList _vpl = null; /** * */ private static final long serialVersionUID = -2598221520127067670L; public VARNA() { super(); } public void init() { try { VARNAConfigLoader VARNAcfg = new VARNAConfigLoader(this); try { _vpl = VARNAcfg.createVARNAPanels(); for (int i=0;i<_vpl.size();i++) { new DropTarget(_vpl.get(i), this); } } catch (IOException e) { JOptionPane.showMessageDialog(this, e.getMessage(), "VARNA Error", JOptionPane.ERROR_MESSAGE); } catch (ExceptionFileFormatOrSyntax e) { JOptionPane.showMessageDialog(this, e.getMessage(), "VARNA Error", JOptionPane.ERROR_MESSAGE); } catch (ExceptionLoadingFailed e) { JOptionPane.showMessageDialog(this, e.getMessage(), "VARNA Error", JOptionPane.ERROR_MESSAGE); } setLayout(new GridLayout(VARNAcfg.getNbColumns(), VARNAcfg .getNbRows())); for (int i = 0; i < _vpl.size(); i++) { getContentPane().add(_vpl.get(i)); } getContentPane().setVisible(true); getContentPane().repaint(); } catch (ExceptionParameterError e) { VARNAPanel.errorDialogStatic(e, this); } catch (ExceptionModeleStyleBaseSyntaxError e) { VARNAPanel.errorDialogStatic(e, this); } catch (ExceptionNonEqualLength e) { VARNAPanel.errorDialogStatic(e, this); } } public String getParameterValue(String key, String def) { if (getParameter(key) == null) { return def; } else { return getParameter(key); } } public String[][] getParameterInfo() { return VARNAConfigLoader.getParameterInfo(); } public ArrayList getPanels() { return _vpl; } public String getSelection() { return getSelection(0); } public String getSelection(int panel) { String result = "["; VARNAPanel v = _vpl.get(panel); List l = v.getSelectionIndices(); for(int i=0;i0) {result += ",";} result += n; } result += "]"; return result; } public void runScript(String script) { if (_vpl.size()>0) { VARNAPanel _vp = _vpl.get(0); try { ControleurScriptParser.executeScript(_vp, script); } catch (Exception e) { e.printStackTrace(); } } } public void setRNA(String seq, String str) { if (_vpl.size()>0) { try { _vpl.get(0).drawRNA(seq, str); } catch (ExceptionNonEqualLength e) { e.printStackTrace(); } } } public void setSmoothedRNA(String seq, String str) { if (_vpl.size()>0) { try { _vpl.get(0).drawRNAInterpolated(seq, str); _vpl.get(0).repaint(); } catch (ExceptionNonEqualLength e) { // TODO Auto-generated catch block e.printStackTrace(); } } } public void dragEnter(DropTargetDragEvent arg0) { } public void dragExit(DropTargetEvent arg0) { } public void dragOver(DropTargetDragEvent arg0) { } public void drop(DropTargetDropEvent dtde) { try { Transferable tr = dtde.getTransferable(); DataFlavor[] flavors = tr.getTransferDataFlavors(); for (int i = 0; i < flavors.length; i++) { if (flavors[i].isFlavorJavaFileListType()) { dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); List list = (List) tr.getTransferData(flavors[i]); for (int j = 0; j < list.size(); j++) { Object o = list.get(j); if (dtde.getSource() instanceof DropTarget) { DropTarget dt = (DropTarget) dtde.getSource(); Component c = dt.getComponent(); if (c instanceof VARNAPanel) { VARNAPanel vp = (VARNAPanel) c; String path = o.toString(); vp.loadFile(path,true); vp.repaint(); } } } dtde.dropComplete(true); return; } } dtde.rejectDrop(); } catch (Exception e) { e.printStackTrace(); dtde.rejectDrop(); } } public void dropActionChanged(DropTargetDragEvent arg0) { } } VARNA.js0000644000000000000000000000637012337237460010776 0ustar rootroot/** * @author ponty */ function addChemProb(appletid,numFrom,numTo,type,intensity,color,orientation) { var applet = document.getElementById(appletid); var script = "addChemProb("+numFrom+","+numTo+",\""+type+"\","+intensity+","+color+","+orientation+")"; applet.runScript(script); }; function resetChemProb(appletid) { var applet = document.getElementById(appletid); var script = "resetChemProb()"; applet.runScript(script); }; function setTitle(appletid,ntitle) { var applet = document.getElementById(appletid); var script = "setTitle(\""+ntitle+"\")"; applet.runScript(script); }; function setSeq(appletid,nseq) { var applet = document.getElementById(appletid); var script = "setSeq(\""+nseq+"\")"; applet.runScript(script); }; function eraseSeq(appletid) { var applet = document.getElementById(appletid); var script = "eraseSeq()"; applet.runScript(script); }; function setStruct(appletid,nstr) { var applet = document.getElementById(appletid); var script = "setStruct(\""+nstr+"\")"; applet.runScript(script); }; function setStructSmooth(appletid,nstr) { var applet = document.getElementById(appletid); var script = "setStructSmooth(\""+nstr+"\")"; applet.runScript(script); }; function setRNA(appletid,nseq,nstr) { var applet = document.getElementById(appletid); var script = "setRNA(\""+nseq+"\",\""+nstr+"\")"; applet.runScript(script); }; function setRNASmooth(appletid,nseq,nstr) { var applet = document.getElementById(appletid); var script = "setRNASmooth(\""+nseq+"\",\""+nstr+"\")"; applet.runScript(script); }; function redraw(appletid,nalgo) { var applet = document.getElementById(appletid); var script = "redraw(\""+nalgo+"\")"; applet.runScript(script); }; function setColorMapValues(appletid,values) { var applet = document.getElementById(appletid); var txt = ""; for(var i=0;i0) txt += ", "; txt += values[i]; } var script = "setValues(["+txt+"])"; applet.runScript(script); }; function setColorMapMinValue(appletid,value) { var applet = document.getElementById(appletid); var script = "setColorMapMinValue("+value+")"; applet.runScript(script); }; function setColorMapMaxValue(appletid,value) { var applet = document.getElementById(appletid); var script = "setColorMapMaxValue("+value+")"; applet.runScript(script); }; function setColorMap(appletid,val) { var applet = document.getElementById(appletid); var script = "setColorMap("+val+")"; applet.runScript(script); }; function setCustomColorMap(appletid,val) { var applet = document.getElementById(appletid); var script = "setCustomColorMap("+val+")"; 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Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat 490 Universit Paris-Sud 91405 Orsay Cedex France The latest version of this software can be found at: http://varna.lri.fr %%%%%%%%%%%%%%%%%%%%%%%%% INVOKING THE GUI VERSION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% A basic editor demonstrating the features of VARNA can be spawned through the following command: java -jar VARNAv3-1.jar applis.VARNAGUI %%%%%%%%%%%%%%%%%%%%%% INVOKING COMMAND LINE VERSION %%%%%%%%%%%%%%%%%%%%%%%%%%%% VARNA can also be used as a standalone application for producing pictures. For such an application, the VARNAcmd class was coded, and should be invoked in the following way: java -jar VARNAv3-1.jar applis.VARNAcmd [-i inputFile|-sequenceDBN XXX -structureDBN YYY] -o outFile [opts] Where: * inFile: An input file using one of the supported formats (Vienna, CT, BPSeq or RNAML). * XXX: An RNA sequence. * YYY: A dot-bracket representation of this RNA. * outFile: An output file whose format is guessed from the extension. Many additional options are supported, matching the syntax of the Applet's parameters. Namely, if param is a valid parameter for the VARNA Applet, then -param is an option that has the exact same arguments and effects in the standalone, command-line version. %%%%%%%%%%%%%%%%%%%%%% LEGAL STUFF AND USUAL DISCLAIMER %%%%%%%%%%%%%%%%%%%%%%%%%% This file is part of VARNA version 3.1. VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with VARNA version 3.1 (See LICENSE.txt file). If not, see http://www.gnu.org/licenses.