addLayoutComponent(Component, Object).ThermoResult.Frame object using the stored fields.JInternalFrame object using the stored fields.ThermoResult.MethodType enum from the current
instance of RegisterMethods.getMinimumSize method to return the preferred
size - these text areas should never be any smaller than their preferred
size.getPreferredSize method in order to produce
better resizing behaviour.Frame object.JInternalFrame object.MethodType enum, initialized with
all the (non-final) methods from the RegisterMethods class.parameter and
methodName.Observable class and overriding
its setChanged method so it is no longer protected.Frame or
JInternalFrame, together with whether it is maximized,
iconified or hidden.Frame
object.JInternalFrame object.public static enum MeltingLayout.Size extends java.lang.Enum<MeltingLayout.Size>
| Modifier and Type | Method and Description |
|---|---|
static MeltingLayout.Size |
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static MeltingLayout.Size[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final MeltingLayout.Size MAXIMUM
public static final MeltingLayout.Size PREFERRED
public static final MeltingLayout.Size MINIMUM
public static MeltingLayout.Size[] values()
for (MeltingLayout.Size c : MeltingLayout.Size.values()) System.out.println(c);
public static MeltingLayout.Size valueOf(java.lang.String name)
name - the name of the enum constant to be returned.java.lang.IllegalArgumentException - if this enum type has no constant
with the specified namejava.lang.NullPointerException - if the argument is nullpublic static enum ArgsMessage.ArgumentType extends java.lang.Enum<ArgsMessage.ArgumentType>
| Modifier and Type | Method and Description |
|---|---|
static ArgsMessage.ArgumentType |
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static ArgsMessage.ArgumentType[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final ArgsMessage.ArgumentType MANDATORY
public static final ArgsMessage.ArgumentType GENERAL
public static ArgsMessage.ArgumentType[] values()
for (ArgsMessage.ArgumentType c : ArgsMessage.ArgumentType.values()) System.out.println(c);
public static ArgsMessage.ArgumentType valueOf(java.lang.String name)
name - the name of the enum constant to be returned.java.lang.IllegalArgumentException - if this enum type has no constant
with the specified namejava.lang.NullPointerException - if the argument is nullpublic class MeltingObservable
extends java.util.Observable
Observable class and overriding
its setChanged method so it is no longer protected.| Constructor and Description |
|---|
MeltingObservable() |
| Modifier and Type | Method and Description |
|---|---|
void |
setChanged()
Notifies the program that the observable has changed.
|
public class MeltingLayout
extends java.lang.Object
implements java.awt.LayoutManager2, java.io.Serializable
| Modifier and Type | Class and Description |
|---|---|
static class |
MeltingLayout.ComponentGroupType
The two possible component groups: Label group and Input group.
|
static class |
MeltingLayout.Size
Different types of sizes that we might want to find: maximum size,
preferred size and minimum size.
|
| Modifier and Type | Field and Description |
|---|---|
static MeltingLayout.ComponentGroupType |
INPUT_GROUP
Component group type: input group.
|
static MeltingLayout.ComponentGroupType |
LABEL_GROUP
Component group type: label group.
|
| Constructor and Description |
|---|
MeltingLayout(java.awt.Container parent)
Constructs a new MELTING layout with no gaps between components.
|
MeltingLayout(java.awt.Container parent,
int hgap,
int vgap)
Constructs a MELTING layout with the specified gaps between components.
|
| Modifier and Type | Method and Description |
|---|---|
void |
addLayoutComponent(java.awt.Component component,
java.lang.Object constraints)
Adds a component to the layout, specifying that it belongs either to the
label group or to the input group, according to the constraint given.
|
void |
addLayoutComponent(java.lang.String name,
java.awt.Component component)
Deprecated.
Only here because the interface demands it. Replaced by
addLayoutComponent(Component, Object). |
void |
checkContainer(java.awt.Container target)
Checks that a supplied container is the parent container for this layout.
|
float |
getLayoutAlignmentX(java.awt.Container parent)
Returns the alignment along the x axis.
|
float |
getLayoutAlignmentY(java.awt.Container parent)
Returns the alignment along the y axis.
|
void |
invalidateLayout(java.awt.Container parent)
Invalidates the layout, indicating that any cached information should be
discarded.
|
void |
layoutContainer(java.awt.Container target)
Lays out the container argument using this MELTING layout.
|
java.awt.Dimension |
maximumLayoutSize(java.awt.Container parent)
Returns the maximum size for the specified container.
|
java.awt.Dimension |
minimumLayoutSize(java.awt.Container parent)
Returns the minimum size for the specified container.
|
java.awt.Dimension |
preferredLayoutSize(java.awt.Container parent)
Returns the preferred size for the specified container.
|
void |
removeLayoutComponent(java.awt.Component component)
Removes the specified component from this MELTING layout.
|
public static final MeltingLayout.ComponentGroupType LABEL_GROUP
public static final MeltingLayout.ComponentGroupType INPUT_GROUP
public MeltingLayout(java.awt.Container parent)
parent - the parent Container.public MeltingLayout(java.awt.Container parent,
int hgap,
int vgap)
hgap and the vertical gap
is specified by vgap.parent - the parent Container.hgap - the horizontal gap.vgap - the vertical gap.public void addLayoutComponent(java.awt.Component component,
java.lang.Object constraints)
Container.add method with the same argument types.addLayoutComponent in interface java.awt.LayoutManager2component - the component to be added.constraints - an object that specifies whether the new component
should be added to the label group, or whether it
should be added to the input group.java.lang.IllegalArgumentException - if the constraint object is not an
integer, or if it does not refer to one of the two groups.@Deprecated
public void addLayoutComponent(java.lang.String name,
java.awt.Component component)
addLayoutComponent(Component, Object).addLayoutComponent in interface java.awt.LayoutManagerpublic void removeLayoutComponent(java.awt.Component component)
remove or
removeAll methods. Most applications do not call this method
directly.removeLayoutComponent in interface java.awt.LayoutManagercomponent - the component to be removed.public java.awt.Dimension preferredLayoutSize(java.awt.Container parent)
preferredLayoutSize in interface java.awt.LayoutManagerparent - The container to return the preferred size for.public java.awt.Dimension minimumLayoutSize(java.awt.Container parent)
minimumLayoutSize in interface java.awt.LayoutManagerparent - The container to return the minimum size for.public java.awt.Dimension maximumLayoutSize(java.awt.Container parent)
maximumLayoutSize in interface java.awt.LayoutManager2parent - The container to return the maximum size for.public void layoutContainer(java.awt.Container target)
The method moves through each label group-input group pair (a 'component line') and decides whether it has space to put the label group and the input group on the same line. If it does, then the left hand edge of the input group is aligned with the left hand edges of all other appended input groups. Otherwise, the input group is placed on a new line. In both cases, the input group is resized in order to take up all available space, or left alone if there is not enough space.
layoutContainer in interface java.awt.LayoutManagertarget - The container in which to do the layout.public float getLayoutAlignmentX(java.awt.Container parent)
getLayoutAlignmentX in interface java.awt.LayoutManager2parent - The parent container.public float getLayoutAlignmentY(java.awt.Container parent)
getLayoutAlignmentY in interface java.awt.LayoutManager2parent - The parent container.public void invalidateLayout(java.awt.Container parent)
invalidateLayout in interface java.awt.LayoutManager2parent - The parent container.public void checkContainer(java.awt.Container target)
public class MeltingGui
extends javax.swing.JFrame
implements java.util.Observer
javax.swing.JFrame.AccessibleJFramejava.awt.Window.AccessibleAWTWindow, java.awt.Window.TypeaccessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabledCROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSORBOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT| Constructor and Description |
|---|
MeltingGui()
Sets up the GUI and displays the main MELTING frame.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args)
Starts up the new frame, and creates an instance of MELTING on it.
|
void |
update(java.util.Observable observable,
java.lang.Object message)
Receives command line options and sends out the MELTING results.
|
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, updateaddNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecoratedaddPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFrontadd, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic MeltingGui()
public void update(java.util.Observable observable,
java.lang.Object message)
update in interface java.util.Observerpublic static void main(java.lang.String[] args)
args - - Arguments from the command line.public class MeltingCalculator
extends java.lang.Object
| Constructor and Description |
|---|
MeltingCalculator(java.lang.String[] argsOption)
Creates the calculator.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
fetchMeltingResults()
Computes and returns the results from MELTING.
|
ThermoResult |
getResults()
Returns the results from MELTING.
|
void |
setArgsOption(java.lang.String[] argsOption)
Sets the command-line arguments.
|
public MeltingCalculator(java.lang.String[] argsOption)
argsOption - Command line options for the calculator.public void setArgsOption(java.lang.String[] argsOption)
argsOption - The command-line arguments.public ThermoResult fetchMeltingResults() throws java.lang.RuntimeException
java.lang.RuntimeExceptionpublic ThermoResult getResults()
public class ResultsPanel
extends javax.swing.JPanel
javax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponentaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
ResultsPanel()
Create and set up the panel.
|
| Modifier and Type | Method and Description |
|---|---|
void |
disableEnthalpyEntropy()
Disables the enthalpy and entropy output fields.
|
void |
displayMeltingResults(ThermoResult results)
Displays the results from the MELTING program.
|
void |
enableEnthalpyEntropy()
Enables the enthalpy and entropy output fields.
|
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic final void disableEnthalpyEntropy()
public final void enableEnthalpyEntropy()
public void displayMeltingResults(ThermoResult results)
results - The ThermoResultpublic class SequenceDialog extends InputFieldArray<MeltingTextArea> implements DialogInterface
javax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponentwidgetsaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
SequenceDialog()
Creates the dialog.
|
| Modifier and Type | Method and Description |
|---|---|
void |
complementarySelectAll()
Selects all the text in the "Complementary sequence" text box.
|
java.lang.String |
getCommandLineFlags()
Gets the command-line flags corresponding to the chosen sequence and
complementary sequence.
|
java.lang.String |
getComplementaryText()
Gets the complementary sequence text.
|
java.lang.String |
getSequenceText()
Gets the sequence text.
|
void |
selectAllSequence()
Selects all the text in the "Sequence" text box.
|
disable, disableAll, enable, enableAll, getValue, selectAll, setValuegetAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic java.lang.String getSequenceText()
public java.lang.String getComplementaryText()
public void selectAllSequence()
public void complementarySelectAll()
public java.lang.String getCommandLineFlags()
getCommandLineFlags in interface DialogInterfacepublic class ComboBoxDialog extends javax.swing.JPanel implements DialogInterface
DialogInterfacejavax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponentaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
ComboBoxDialog(java.lang.String comboBoxLabelText,
ComboBoxOption[] comboBoxOptions,
java.lang.String commandLineTag)
Sets up the dialog.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getCommandLineFlags()
Returns the command-line flags corresponding to the user's choice on the
combo box.
|
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic ComboBoxDialog(java.lang.String comboBoxLabelText,
ComboBoxOption[] comboBoxOptions,
java.lang.String commandLineTag)
comboBoxLabelText - The text for the label on the dialog.comboBoxOptions - The combo box options to put in the combo box.commandLineTag - The command line tag corresponding to this combo
box.public java.lang.String getCommandLineFlags()
getCommandLineFlags in interface DialogInterfacepublic class HybridizationDialog extends InputField<HybridizationWidget> implements DialogInterface
javax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponentwidgetsaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
HybridizationDialog()
Set up the dialog.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getCommandLineFlags()
Returns the command-line flags corresponding to the user's choice of
hybridization type.
|
getValue, selectAll, setDisabled, setEnabled, setValuedisable, disableAll, enable, enableAll, getValue, selectAll, setValuegetAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic java.lang.String getCommandLineFlags()
getCommandLineFlags in interface DialogInterface| Package | Description |
|---|---|
| meltinggui.dialogs |
| Class and Description |
|---|
| DialogInterface
An interface that represents a dialog on the GUI.
|
| Package | Description |
|---|---|
| meltinggui.dialogs |
| Modifier and Type | Class and Description |
|---|---|
class |
ComboBoxDialog
A dialog with a label and a combo box with various options on it.
|
class |
HybridizationDialog |
class |
IonConcentrationDialog
A dialog allowing the user to specify the concentration of ions in the
solution.
|
class |
OligomerConcentrationDialog
A dialog for specifying the oligomer concentration.
|
class |
SequenceDialog
Dialog for specifying the sequence and complementary sequence.
|
| Interface | Description |
|---|---|
| DialogInterface |
An interface that represents a dialog on the GUI.
|
| Class | Description |
|---|---|
| ComboBoxDialog |
A dialog with a label and a combo box with various options on it.
|
| HybridizationDialog | |
| IonConcentrationDialog |
A dialog allowing the user to specify the concentration of ions in the
solution.
|
| OligomerConcentrationDialog |
A dialog for specifying the oligomer concentration.
|
| ResultsPanel |
A panel to display the melting temperature, enthalpy and entropy results.
|
| SequenceDialog |
Dialog for specifying the sequence and complementary sequence.
|
public interface DialogInterface
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getCommandLineFlags()
Gets the command-line flags from the dialog.
|
public class OligomerConcentrationDialog extends InputField<MeltingTextField> implements DialogInterface
javax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponentwidgetsaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
OligomerConcentrationDialog()
Sets up the dialog.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getCommandLineFlags()
Gets the command-line flags.
|
getValue, selectAll, setDisabled, setEnabled, setValuedisable, disableAll, enable, enableAll, getValue, selectAll, setValuegetAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic OligomerConcentrationDialog()
public java.lang.String getCommandLineFlags()
getCommandLineFlags in interface DialogInterfacepublic class IonConcentrationDialog extends javax.swing.JComboBox implements DialogInterface
javax.swing.JComboBox.AccessibleJComboBox, javax.swing.JComboBox.KeySelectionManagerjavax.swing.JComponent.AccessibleJComponentactionCommand, dataModel, isEditable, keySelectionManager, lightWeightPopupEnabled, maximumRowCount, renderer, selectedItemReminderaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
IonConcentrationDialog()
Set up the dialog.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getCommandLineFlags()
Gets the command line flags the user would have typed in were they using
the command line.
|
actionPerformed, actionPropertyChanged, addActionListener, addItem, addItemListener, addPopupMenuListener, configureEditor, configurePropertiesFromAction, contentsChanged, createActionPropertyChangeListener, createDefaultKeySelectionManager, fireActionEvent, fireItemStateChanged, firePopupMenuCanceled, firePopupMenuWillBecomeInvisible, firePopupMenuWillBecomeVisible, getAccessibleContext, getAction, getActionCommand, getActionListeners, getEditor, getItemAt, getItemCount, getItemListeners, getKeySelectionManager, getMaximumRowCount, getModel, getPopupMenuListeners, getPrototypeDisplayValue, getRenderer, getSelectedIndex, getSelectedItem, getSelectedObjects, getUI, getUIClassID, hidePopup, insertItemAt, installAncestorListener, intervalAdded, intervalRemoved, isEditable, isLightWeightPopupEnabled, isPopupVisible, paramString, processKeyEvent, removeActionListener, removeAllItems, removeItem, removeItemAt, removeItemListener, removePopupMenuListener, selectedItemChanged, selectWithKeyChar, setAction, setActionCommand, setEditable, setEditor, setEnabled, setKeySelectionManager, setLightWeightPopupEnabled, setMaximumRowCount, setModel, setPopupVisible, setPrototypeDisplayValue, setRenderer, setSelectedIndex, setSelectedItem, setUI, showPopup, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic java.lang.String getCommandLineFlags()
getCommandLineFlags in interface DialogInterfacepublic class FrameScreenPosition
extends java.lang.Object
implements java.io.Serializable
Frame or
JInternalFrame, together with whether it is maximized,
iconified or hidden.| Constructor and Description |
|---|
FrameScreenPosition()
Constructor with no arguments does nothing.
|
FrameScreenPosition(java.awt.Frame frame)
Instantiates the class and fills in the fields from a
Frame
object. |
FrameScreenPosition(javax.swing.JInternalFrame internalFrame)
Instantiates the class and fills in the fields from a
JInternalFrame object. |
| Modifier and Type | Method and Description |
|---|---|
void |
getScreenPosition(java.awt.Frame frame)
Fills in the fields from the current screen position of a
Frame object. |
void |
getScreenPosition(javax.swing.JInternalFrame internalFrame)
Fills in the fields from the current screen position of a
JInternalFrame object. |
void |
setScreenPosition(java.awt.Frame frame)
Sets up a
Frame object using the stored fields. |
void |
setScreenPosition(javax.swing.JInternalFrame internalFrame)
Sets up a
JInternalFrame object using the stored fields. |
public FrameScreenPosition()
public FrameScreenPosition(java.awt.Frame frame)
Frame
object.public FrameScreenPosition(javax.swing.JInternalFrame internalFrame)
JInternalFrame object.public void getScreenPosition(java.awt.Frame frame)
Frame object.frame - The frame to fill in the fields from.public void getScreenPosition(javax.swing.JInternalFrame internalFrame)
JInternalFrame object.internalFrame - The frame to fill in the fields from.public void setScreenPosition(java.awt.Frame frame)
Frame object using the stored fields.frame - The frame to set the screen position of.public void setScreenPosition(javax.swing.JInternalFrame internalFrame)
JInternalFrame object using the stored fields.internalFrame - The internal frame to set the screen position of.| Package | Description |
|---|---|
| meltinggui.frames |
| Class and Description |
|---|
| ErrorFrame
A frame with a text area for displaying error messages.
|
| MeltingFrame
The frame that opens when the user runs the GUI.
|
| OuterFrame |
public class OuterFrame
extends javax.swing.JFrame
javax.swing.JFrame.AccessibleJFramejava.awt.Window.AccessibleAWTWindow, java.awt.Window.TypeaccessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabledCROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSORBOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT| Constructor and Description |
|---|
OuterFrame()
Sets up the GUI and displays the main MELTING frame.
|
| Modifier and Type | Method and Description |
|---|---|
void |
addObserver(java.util.Observer observer)
Adds an observer to the melting frame.
|
void |
clearErrors() |
void |
displayMeltingResults(ThermoResult results)
Displays MELTING results on the MELTING frame.
|
void |
logException(java.lang.Exception exception)
Logs an exception on to the error frame.
|
void |
restoreScreenPositions()
Sets up the screen positions of the frames.
|
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, updateaddNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecoratedaddPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFrontadd, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic OuterFrame()
public void addObserver(java.util.Observer observer)
observer - The observer.public void displayMeltingResults(ThermoResult results)
results - The results from MELTING.public void logException(java.lang.Exception exception)
exception - The exception.public void restoreScreenPositions()
public void clearErrors()
| Package | Description |
|---|---|
| meltinggui.frames |
| Modifier and Type | Method and Description |
|---|---|
void |
GuiScreenPositions.setScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Sets the screen positions of the frames from the stored fields.
|
| Constructor and Description |
|---|
GuiScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Fills in the fields from the frames themselves.
|
| Package | Description |
|---|---|
| meltinggui.frames |
| Modifier and Type | Method and Description |
|---|---|
void |
GuiScreenPositions.setScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Sets the screen positions of the frames from the stored fields.
|
| Constructor and Description |
|---|
GuiScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Fills in the fields from the frames themselves.
|
| Package | Description |
|---|---|
| meltinggui.frames |
| Modifier and Type | Method and Description |
|---|---|
void |
GuiScreenPositions.setScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Sets the screen positions of the frames from the stored fields.
|
| Constructor and Description |
|---|
GuiScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Fills in the fields from the frames themselves.
|
| Class | Description |
|---|---|
| ErrorFrame |
A frame with a text area for displaying error messages.
|
| FrameScreenPosition |
The location on the screen of a
Frame or
JInternalFrame, together with whether it is maximized,
iconified or hidden. |
| GuiScreenPositions |
The locations on the screen of the GUI and all the components it contains.
|
| MeltingFrame |
The frame that opens when the user runs the GUI.
|
| OuterFrame |
public class GuiScreenPositions
extends java.lang.Object
implements java.io.Serializable
| Constructor and Description |
|---|
GuiScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Fills in the fields from the frames themselves.
|
| Modifier and Type | Method and Description |
|---|---|
void |
setScreenPositions(OuterFrame outerFrame,
MeltingFrame meltingFrame,
ErrorFrame errorFrame)
Sets the screen positions of the frames from the stored fields.
|
public GuiScreenPositions(OuterFrame outerFrame, MeltingFrame meltingFrame, ErrorFrame errorFrame)
outerFrame - The outer frame to get the screen position from.meltingFrame - The MELTING frame.errorFrame - The error frame.public void setScreenPositions(OuterFrame outerFrame, MeltingFrame meltingFrame, ErrorFrame errorFrame)
outerFrame - The outer frame to set the screen position for.meltingFrame - The MELTING frame.errorFrame - The error frame.public class ErrorFrame
extends javax.swing.JInternalFrame
javax.swing.JInternalFrame.AccessibleJInternalFrame, javax.swing.JInternalFrame.JDesktopIconjavax.swing.JComponent.AccessibleJComponentclosable, CONTENT_PANE_PROPERTY, desktopIcon, FRAME_ICON_PROPERTY, frameIcon, GLASS_PANE_PROPERTY, iconable, IS_CLOSED_PROPERTY, IS_ICON_PROPERTY, IS_MAXIMUM_PROPERTY, IS_SELECTED_PROPERTY, isClosed, isIcon, isMaximum, isSelected, LAYERED_PANE_PROPERTY, maximizable, MENU_BAR_PROPERTY, resizable, ROOT_PANE_PROPERTY, rootPane, rootPaneCheckingEnabled, title, TITLE_PROPERTYaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOWBOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT| Constructor and Description |
|---|
ErrorFrame()
Set up the widgets on the frame.
|
| Modifier and Type | Method and Description |
|---|---|
void |
clearErrors() |
void |
logException(java.lang.Exception exception)
Logs an exception into the exception log text area.
|
addImpl, addInternalFrameListener, createRootPane, dispose, doDefaultCloseAction, fireInternalFrameEvent, getAccessibleContext, getContentPane, getDefaultCloseOperation, getDesktopIcon, getDesktopPane, getFocusCycleRootAncestor, getFocusOwner, getFrameIcon, getGlassPane, getInternalFrameListeners, getJMenuBar, getLastCursor, getLayer, getLayeredPane, getMenuBar, getMostRecentFocusOwner, getNormalBounds, getRootPane, getTitle, getUI, getUIClassID, getWarningString, hide, isClosable, isClosed, isFocusCycleRoot, isIcon, isIconifiable, isMaximizable, isMaximum, isResizable, isRootPaneCheckingEnabled, isSelected, moveToBack, moveToFront, pack, paintComponent, paramString, remove, removeInternalFrameListener, reshape, restoreSubcomponentFocus, setClosable, setClosed, setContentPane, setCursor, setDefaultCloseOperation, setDesktopIcon, setFocusCycleRoot, setFrameIcon, setGlassPane, setIcon, setIconifiable, setJMenuBar, setLayer, setLayer, setLayeredPane, setLayout, setMaximizable, setMaximum, setMenuBar, setNormalBounds, setResizable, setRootPane, setRootPaneCheckingEnabled, setSelected, setTitle, setUI, show, toBack, toFront, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic class MeltingFrame
extends javax.swing.JInternalFrame
javax.swing.JInternalFrame.AccessibleJInternalFrame, javax.swing.JInternalFrame.JDesktopIconjavax.swing.JComponent.AccessibleJComponentclosable, CONTENT_PANE_PROPERTY, desktopIcon, FRAME_ICON_PROPERTY, frameIcon, GLASS_PANE_PROPERTY, iconable, IS_CLOSED_PROPERTY, IS_ICON_PROPERTY, IS_MAXIMUM_PROPERTY, IS_SELECTED_PROPERTY, isClosed, isIcon, isMaximum, isSelected, LAYERED_PANE_PROPERTY, maximizable, MENU_BAR_PROPERTY, resizable, ROOT_PANE_PROPERTY, rootPane, rootPaneCheckingEnabled, title, TITLE_PROPERTYaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOWBOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT| Constructor and Description |
|---|
MeltingFrame()
Creates the new frame.
|
| Modifier and Type | Method and Description |
|---|---|
void |
addObserver(java.util.Observer observer)
Adds an observer to the melting frame observable.
|
void |
displayMeltingResults(ThermoResult results)
Displays the MELTING results.
|
void |
sendMeltingArgs()
Calculates and displays the MELTING results.
|
addImpl, addInternalFrameListener, createRootPane, dispose, doDefaultCloseAction, fireInternalFrameEvent, getAccessibleContext, getContentPane, getDefaultCloseOperation, getDesktopIcon, getDesktopPane, getFocusCycleRootAncestor, getFocusOwner, getFrameIcon, getGlassPane, getInternalFrameListeners, getJMenuBar, getLastCursor, getLayer, getLayeredPane, getMenuBar, getMostRecentFocusOwner, getNormalBounds, getRootPane, getTitle, getUI, getUIClassID, getWarningString, hide, isClosable, isClosed, isFocusCycleRoot, isIcon, isIconifiable, isMaximizable, isMaximum, isResizable, isRootPaneCheckingEnabled, isSelected, moveToBack, moveToFront, pack, paintComponent, paramString, remove, removeInternalFrameListener, reshape, restoreSubcomponentFocus, setClosable, setClosed, setContentPane, setCursor, setDefaultCloseOperation, setDesktopIcon, setFocusCycleRoot, setFrameIcon, setGlassPane, setIcon, setIconifiable, setJMenuBar, setLayer, setLayer, setLayeredPane, setLayout, setMaximizable, setMaximum, setMenuBar, setNormalBounds, setResizable, setRootPane, setRootPaneCheckingEnabled, setSelected, setTitle, setUI, show, toBack, toFront, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic void addObserver(java.util.Observer observer)
observer - The new observer.public void sendMeltingArgs()
public void displayMeltingResults(ThermoResult results)
results - The results from the MELTING program.| Package | Description |
|---|---|
| meltinggui |
| Class and Description |
|---|
| ArgsMessage.ArgumentType
The different possible types of arguments that can be sent.
|
| MeltingLayout.ComponentGroupType
The two possible component groups: Label group and Input group.
|
| MeltingLayout.Size
Different types of sizes that we might want to find: maximum size,
preferred size and minimum size.
|
| Package | Description |
|---|---|
| meltinggui |
| Modifier and Type | Method and Description |
|---|---|
static MeltingLayout.Size |
MeltingLayout.Size.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static MeltingLayout.Size[] |
MeltingLayout.Size.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
| Package | Description |
|---|---|
| meltinggui |
| Modifier and Type | Method and Description |
|---|---|
ArgsMessage.ArgumentType |
ArgsMessage.getArgumentType()
Gets the type of the message.
|
static ArgsMessage.ArgumentType |
ArgsMessage.ArgumentType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static ArgsMessage.ArgumentType[] |
ArgsMessage.ArgumentType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
| Constructor and Description |
|---|
ArgsMessage(ArgsMessage.ArgumentType argumentType,
String commandLineText)
Fills in the argument type and command-line arguments.
|
| Package | Description |
|---|---|
| meltinggui |
| Modifier and Type | Field and Description |
|---|---|
static MeltingLayout.ComponentGroupType |
MeltingLayout.INPUT_GROUP
Component group type: input group.
|
static MeltingLayout.ComponentGroupType |
MeltingLayout.LABEL_GROUP
Component group type: label group.
|
| Modifier and Type | Method and Description |
|---|---|
static MeltingLayout.ComponentGroupType |
MeltingLayout.ComponentGroupType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static MeltingLayout.ComponentGroupType[] |
MeltingLayout.ComponentGroupType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static enum MeltingLayout.ComponentGroupType extends java.lang.Enum<MeltingLayout.ComponentGroupType>
| Enum Constant and Description |
|---|
INPUT_GROUP |
LABEL_GROUP |
| Modifier and Type | Method and Description |
|---|---|
static MeltingLayout.ComponentGroupType |
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static MeltingLayout.ComponentGroupType[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final MeltingLayout.ComponentGroupType LABEL_GROUP
public static final MeltingLayout.ComponentGroupType INPUT_GROUP
public static MeltingLayout.ComponentGroupType[] values()
for (MeltingLayout.ComponentGroupType c : MeltingLayout.ComponentGroupType.values()) System.out.println(c);
public static MeltingLayout.ComponentGroupType valueOf(java.lang.String name)
name - the name of the enum constant to be returned.java.lang.IllegalArgumentException - if this enum type has no constant
with the specified namejava.lang.NullPointerException - if the argument is null| Class | Description |
|---|---|
| ArgsMessage |
A message that GUI components can send the main program, containing MELTING
arguments that it can use to get results.
|
| MeltingCalculator |
Class intended to provide an interface between the GUI and the MELTING
program itself.
|
| MeltingGui |
The Main class for the Melting GUI.
|
| MeltingLayout |
A layout manager designed for use with label/text pairs.
|
| MeltingObservable |
Class created with the sole intention of extending the
{@link java.util.Observable
Observable class and overriding
its setChanged method so it is no longer protected. |
| Enum | Description |
|---|---|
| ArgsMessage.ArgumentType |
The different possible types of arguments that can be sent.
|
| MeltingLayout.ComponentGroupType |
The two possible component groups: Label group and Input group.
|
| MeltingLayout.Size |
Different types of sizes that we might want to find: maximum size,
preferred size and minimum size.
|
public class MeltingLayoutTest extends JFrame
JFrame.AccessibleJFrameFrame.AccessibleAWTFrameWindow.AccessibleAWTWindow, Window.TypeContainer.AccessibleAWTContainerComponent.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategyaccessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabledCROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSORBOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENTDISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSEABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH| Constructor and Description |
|---|
MeltingLayoutTest() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(String[] args) |
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, updateaddNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecoratedaddPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFrontadd, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycleclone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitgetFont, postEventpublic static void main(String[] args)
public class ArgsMessage
extends java.lang.Object
| Modifier and Type | Class and Description |
|---|---|
static class |
ArgsMessage.ArgumentType
The different possible types of arguments that can be sent.
|
| Constructor and Description |
|---|
ArgsMessage(ArgsMessage.ArgumentType argumentType,
java.lang.String commandLineText)
Fills in the argument type and command-line arguments.
|
| Modifier and Type | Method and Description |
|---|---|
ArgsMessage.ArgumentType |
getArgumentType()
Gets the type of the message.
|
java.lang.String |
getCommandLineText()
Gets the command-line arguments.
|
public ArgsMessage(ArgsMessage.ArgumentType argumentType, java.lang.String commandLineText)
argumentType - The type of arguments being sent.commandLineText - The command-line arguments being sent.public ArgsMessage.ArgumentType getArgumentType()
public java.lang.String getCommandLineText()
public class MeltingComboBox extends javax.swing.JComboBox implements InputWidgetInterface
InputWidgetInterfacejavax.swing.JComboBox.AccessibleJComboBox, javax.swing.JComboBox.KeySelectionManagerjavax.swing.JComponent.AccessibleJComponentactionCommand, dataModel, editor, isEditable, keySelectionManager, lightWeightPopupEnabled, maximumRowCount, renderer, selectedItemReminderaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
MeltingComboBox(ComboBoxOption[] suppliedOptions)
Fills in the combo box options, and sets up the combo box model.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getValue()
Gets the command-line text corrseponding to the selected option.
|
void |
selectAll()
Does nothing.
|
void |
setValue(java.lang.String newValue)
Does nothing.
|
actionPerformed, actionPropertyChanged, addActionListener, addItem, addItemListener, addPopupMenuListener, configureEditor, configurePropertiesFromAction, contentsChanged, createActionPropertyChangeListener, createDefaultKeySelectionManager, fireActionEvent, fireItemStateChanged, firePopupMenuCanceled, firePopupMenuWillBecomeInvisible, firePopupMenuWillBecomeVisible, getAccessibleContext, getAction, getActionCommand, getActionListeners, getEditor, getItemAt, getItemCount, getItemListeners, getKeySelectionManager, getMaximumRowCount, getModel, getPopupMenuListeners, getPrototypeDisplayValue, getRenderer, getSelectedIndex, getSelectedItem, getSelectedObjects, getUI, getUIClassID, hidePopup, insertItemAt, installAncestorListener, intervalAdded, intervalRemoved, isEditable, isLightWeightPopupEnabled, isPopupVisible, paramString, processKeyEvent, removeActionListener, removeAllItems, removeItem, removeItemAt, removeItemListener, removePopupMenuListener, selectedItemChanged, selectWithKeyChar, setAction, setActionCommand, setEditable, setEditor, setEnabled, setKeySelectionManager, setLightWeightPopupEnabled, setMaximumRowCount, setModel, setPopupVisible, setPrototypeDisplayValue, setRenderer, setSelectedIndex, setSelectedItem, setUI, showPopup, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic MeltingComboBox(ComboBoxOption[] suppliedOptions)
suppliedOptions - The combo box options supplied parameters to the
constructor.public java.lang.String getValue()
getValue in interface InputWidgetInterfacepublic void setValue(java.lang.String newValue)
setValue in interface InputWidgetInterfacenewValue - public void selectAll()
selectAll in interface InputWidgetInterface| Package | Description |
|---|---|
| meltinggui.dialogs | |
| meltinggui.widgets |
| Class and Description |
|---|
| ComboBoxOption
An option on a combo box used to select additional MELTING options.
|
| InputField
A widget for enter in a value, together with a label to tell you what to
enter.
|
| InputFieldArray
A vertical array of widgets, each with a label describing what to type in
it.
|
| InputWidgetInterface
Represents a generic input widget on the frame.
|
| Class and Description |
|---|
| ComboBoxOption
An option on a combo box used to select additional MELTING options.
|
| InputField
A widget for enter in a value, together with a label to tell you what to
enter.
|
| InputFieldArray
A vertical array of widgets, each with a label describing what to type in
it.
|
| InputWidgetInterface
Represents a generic input widget on the frame.
|
| MeltingComboBox
A combo box where the user can specify a particular option.
|
public class ComboBoxOption
extends java.lang.Object
| Constructor and Description |
|---|
ComboBoxOption(java.lang.String optionText,
java.lang.String commandLineText)
Constructor setting the text to be displayed in the combo box and the text
that would be written to the cmomand line.
|
| Modifier and Type | Method and Description |
|---|---|
ComboBoxOption |
copy()
Copies this combo box option to another combo box option.
|
java.lang.String |
getCommandLineText()
Gets the command-line text.
|
java.lang.String |
getOptionText()
Gets the option text.
|
void |
setCommandLineText(java.lang.String commandLineText)
Sets the command-line text.
|
void |
setOptionText(java.lang.String optionText)
Sets the option text.
|
public ComboBoxOption(java.lang.String optionText,
java.lang.String commandLineText)
public void setOptionText(java.lang.String optionText)
optionText - Text displayed on the combo box option.public java.lang.String getOptionText()
public void setCommandLineText(java.lang.String commandLineText)
commandLineText - Text that would be written to the command line.public java.lang.String getCommandLineText()
public ComboBoxOption copy()
| Package | Description |
|---|---|
| meltinggui.widgets |
| Modifier and Type | Class and Description |
|---|---|
class |
HybridizationWidget
A dialog where the user can specify a particular hybridization type.
|
| Package | Description |
|---|---|
| meltinggui.dialogs | |
| meltinggui.widgets |
| Constructor and Description |
|---|
ComboBoxDialog(String comboBoxLabelText,
ComboBoxOption[] comboBoxOptions,
String commandLineTag)
Sets up the dialog.
|
| Modifier and Type | Method and Description |
|---|---|
ComboBoxOption |
ComboBoxOption.copy()
Copies this combo box option to another combo box option.
|
| Constructor and Description |
|---|
MeltingComboBox(ComboBoxOption[] suppliedOptions)
Fills in the combo box options, and sets up the combo box model.
|
| Package | Description |
|---|---|
| meltinggui.dialogs | |
| meltinggui.widgets |
| Modifier and Type | Class and Description |
|---|---|
class |
HybridizationDialog |
class |
OligomerConcentrationDialog
A dialog for specifying the oligomer concentration.
|
| Modifier and Type | Class and Description |
|---|---|
class |
InputField<W extends Component & InputWidgetInterface>
A widget for enter in a value, together with a label to tell you what to
enter.
|
class |
InputFieldArray<W extends Component & InputWidgetInterface>
A vertical array of widgets, each with a label describing what to type in
it.
|
| Modifier and Type | Class and Description |
|---|---|
class |
HybridizationWidget
A dialog where the user can specify a particular hybridization type.
|
class |
InputField<W extends Component & InputWidgetInterface>
A widget for enter in a value, together with a label to tell you what to
enter.
|
class |
MeltingComboBox
A combo box where the user can specify a particular option.
|
class |
MeltingTextArea
A text area for use with the MELTING program.
|
class |
MeltingTextField
A text box for use with the MELTING program.
|
class |
OutputField
A label together with a non-editable text box for displaying results.
|
| Package | Description |
|---|---|
| meltinggui.dialogs | |
| meltinggui.widgets |
| Modifier and Type | Class and Description |
|---|---|
class |
HybridizationDialog |
class |
OligomerConcentrationDialog
A dialog for specifying the oligomer concentration.
|
| Modifier and Type | Class and Description |
|---|---|
class |
OutputField
A label together with a non-editable text box for displaying results.
|
| Package | Description |
|---|---|
| meltinggui.dialogs | |
| meltinggui.widgets |
| Modifier and Type | Class and Description |
|---|---|
class |
HybridizationDialog |
class |
OligomerConcentrationDialog
A dialog for specifying the oligomer concentration.
|
class |
SequenceDialog
Dialog for specifying the sequence and complementary sequence.
|
| Modifier and Type | Class and Description |
|---|---|
class |
InputField<W extends Component & InputWidgetInterface>
A widget for enter in a value, together with a label to tell you what to
enter.
|
class |
OutputField
A label together with a non-editable text box for displaying results.
|
public class HybridizationWidget extends MeltingComboBox
javax.swing.JComboBox.AccessibleJComboBox, javax.swing.JComboBox.KeySelectionManagerjavax.swing.JComponent.AccessibleJComponentactionCommand, dataModel, editor, isEditable, keySelectionManager, lightWeightPopupEnabled, maximumRowCount, renderer, selectedItemReminderaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
HybridizationWidget()
Sets up and creates the hybridization dialog.
|
getValue, selectAll, setValueactionPerformed, actionPropertyChanged, addActionListener, addItem, addItemListener, addPopupMenuListener, configureEditor, configurePropertiesFromAction, contentsChanged, createActionPropertyChangeListener, createDefaultKeySelectionManager, fireActionEvent, fireItemStateChanged, firePopupMenuCanceled, firePopupMenuWillBecomeInvisible, firePopupMenuWillBecomeVisible, getAccessibleContext, getAction, getActionCommand, getActionListeners, getEditor, getItemAt, getItemCount, getItemListeners, getKeySelectionManager, getMaximumRowCount, getModel, getPopupMenuListeners, getPrototypeDisplayValue, getRenderer, getSelectedIndex, getSelectedItem, getSelectedObjects, getUI, getUIClassID, hidePopup, insertItemAt, installAncestorListener, intervalAdded, intervalRemoved, isEditable, isLightWeightPopupEnabled, isPopupVisible, paramString, processKeyEvent, removeActionListener, removeAllItems, removeItem, removeItemAt, removeItemListener, removePopupMenuListener, selectedItemChanged, selectWithKeyChar, setAction, setActionCommand, setEditable, setEditor, setEnabled, setKeySelectionManager, setLightWeightPopupEnabled, setMaximumRowCount, setModel, setPopupVisible, setPrototypeDisplayValue, setRenderer, setSelectedIndex, setSelectedItem, setUI, showPopup, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle| Interface | Description |
|---|---|
| InputWidgetInterface |
Represents a generic input widget on the frame.
|
| Class | Description |
|---|---|
| ComboBoxOption |
An option on a combo box used to select additional MELTING options.
|
| HybridizationWidget |
A dialog where the user can specify a particular hybridization type.
|
| InputField<W extends java.awt.Component & InputWidgetInterface> |
A widget for enter in a value, together with a label to tell you what to
enter.
|
| InputFieldArray<W extends java.awt.Component & InputWidgetInterface> |
A vertical array of widgets, each with a label describing what to type in
it.
|
| MeltingComboBox |
A combo box where the user can specify a particular option.
|
| MeltingTextArea |
A text area for use with the MELTING program.
|
| MeltingTextField |
A text box for use with the MELTING program.
|
| OutputField |
A label together with a non-editable text box for displaying results.
|
public interface InputWidgetInterface
public class OutputField extends InputField<MeltingTextField> implements InputWidgetInterface
javax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponentwidgetsaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
OutputField(java.lang.String labelText)
Creates and sets up the field.
|
getValue, selectAll, setDisabled, setEnabled, setValuedisable, disableAll, enable, enableAll, getValue, selectAll, setValuegetAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycleclone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitgetValue, selectAll, setValuepublic class MeltingTextField extends javax.swing.JTextField implements InputWidgetInterface
InputWidgetInterfacejavax.swing.JTextField.AccessibleJTextFieldjavax.swing.text.JTextComponent.AccessibleJTextComponent, javax.swing.text.JTextComponent.DropLocation, javax.swing.text.JTextComponent.KeyBindingjavax.swing.JComponent.AccessibleJComponentaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOWBOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT| Constructor and Description |
|---|
MeltingTextField()
Creates a new MELTING text field with the default number of 16 columns.
|
MeltingTextField(int columns)
Creates a new MELTING text field with a given number of columns.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getValue()
Returns the text from the field.
|
void |
selectAll()
Selects all the text in the field.
|
void |
setValue(java.lang.String newValue)
Sets the text in the field.
|
actionPropertyChanged, addActionListener, configurePropertiesFromAction, createActionPropertyChangeListener, createDefaultModel, fireActionPerformed, getAccessibleContext, getAction, getActionListeners, getActions, getColumns, getColumnWidth, getHorizontalAlignment, getHorizontalVisibility, getPreferredSize, getScrollOffset, getUIClassID, isValidateRoot, paramString, postActionEvent, removeActionListener, scrollRectToVisible, setAction, setActionCommand, setColumns, setDocument, setFont, setHorizontalAlignment, setScrollOffsetaddCaretListener, addInputMethodListener, addKeymap, copy, cut, fireCaretUpdate, getCaret, getCaretColor, getCaretListeners, getCaretPosition, getDisabledTextColor, getDocument, getDragEnabled, getDropLocation, getDropMode, getFocusAccelerator, getHighlighter, getInputMethodRequests, getKeymap, getKeymap, getMargin, getNavigationFilter, getPreferredScrollableViewportSize, getPrintable, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getSelectedText, getSelectedTextColor, getSelectionColor, getSelectionEnd, getSelectionStart, getText, getText, getToolTipText, getUI, isEditable, loadKeymap, modelToView, moveCaretPosition, paste, print, print, print, processInputMethodEvent, read, removeCaretListener, removeKeymap, removeNotify, replaceSelection, restoreComposedText, saveComposedText, select, setCaret, setCaretColor, setCaretPosition, setComponentOrientation, setDisabledTextColor, setDragEnabled, setDropMode, setEditable, setFocusAccelerator, setHighlighter, setKeymap, setMargin, setNavigationFilter, setSelectedTextColor, setSelectionColor, setSelectionEnd, setSelectionStart, setText, setUI, updateUI, viewToModel, writeaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic MeltingTextField()
public MeltingTextField(int columns)
columns - The number of columns in the text field.public void setValue(java.lang.String newValue)
setValue in interface InputWidgetInterfacenewValue - The new text for the field.public java.lang.String getValue()
getValue in interface InputWidgetInterfacepublic void selectAll()
selectAll in interface InputWidgetInterfaceselectAll in class javax.swing.text.JTextComponentpublic class MeltingTextArea extends javax.swing.JTextArea implements InputWidgetInterface
InputWidgetInterfacejavax.swing.JTextArea.AccessibleJTextAreajavax.swing.text.JTextComponent.AccessibleJTextComponent, javax.swing.text.JTextComponent.DropLocation, javax.swing.text.JTextComponent.KeyBindingjavax.swing.JComponent.AccessibleJComponentaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
MeltingTextArea()
Creates a new MELTING text area with the default number of 4 rows and
32 columns.
|
MeltingTextArea(int rows,
int columns)
Creates a new MELTING text area with a given number of columns.
|
| Modifier and Type | Method and Description |
|---|---|
java.awt.Dimension |
getMinimumSize()
Override the
getMinimumSize method to return the preferred
size - these text areas should never be any smaller than their preferred
size. |
java.awt.Dimension |
getPreferredSize()
We override the
getPreferredSize method in order to produce
better resizing behaviour. |
java.lang.String |
getValue()
Returns the text from the area.
|
void |
selectAll()
Selects all the text in the area.
|
void |
setValue(java.lang.String newValue)
Sets the text in the area.
|
append, createDefaultModel, getAccessibleContext, getColumns, getColumnWidth, getLineCount, getLineEndOffset, getLineOfOffset, getLineStartOffset, getLineWrap, getPreferredScrollableViewportSize, getRowHeight, getRows, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getTabSize, getUIClassID, getWrapStyleWord, insert, paramString, replaceRange, setColumns, setFont, setLineWrap, setRows, setTabSize, setWrapStyleWordaddCaretListener, addInputMethodListener, addKeymap, copy, cut, fireCaretUpdate, getActions, getCaret, getCaretColor, getCaretListeners, getCaretPosition, getDisabledTextColor, getDocument, getDragEnabled, getDropLocation, getDropMode, getFocusAccelerator, getHighlighter, getInputMethodRequests, getKeymap, getKeymap, getMargin, getNavigationFilter, getPrintable, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getSelectedText, getSelectedTextColor, getSelectionColor, getSelectionEnd, getSelectionStart, getText, getText, getToolTipText, getUI, isEditable, loadKeymap, modelToView, moveCaretPosition, paste, print, print, print, processInputMethodEvent, read, removeCaretListener, removeKeymap, removeNotify, replaceSelection, restoreComposedText, saveComposedText, select, setCaret, setCaretColor, setCaretPosition, setComponentOrientation, setDisabledTextColor, setDocument, setDragEnabled, setDropMode, setEditable, setFocusAccelerator, setHighlighter, setKeymap, setMargin, setNavigationFilter, setSelectedTextColor, setSelectionColor, setSelectionEnd, setSelectionStart, setText, setUI, updateUI, viewToModel, writeaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getNextFocusableComponent, getPopupLocation, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic MeltingTextArea()
public MeltingTextArea(int rows,
int columns)
rows - The number of rows in the text area.columns - The number of columns in the text area.public void setValue(java.lang.String newValue)
setValue in interface InputWidgetInterfacenewValue - The new text for the area.public java.lang.String getValue()
getValue in interface InputWidgetInterfacepublic void selectAll()
selectAll in interface InputWidgetInterfaceselectAll in class javax.swing.text.JTextComponentpublic java.awt.Dimension getPreferredSize()
getPreferredSize method in order to produce
better resizing behaviour.getPreferredSize in class javax.swing.JTextAreapublic java.awt.Dimension getMinimumSize()
getMinimumSize method to return the preferred
size - these text areas should never be any smaller than their preferred
size.getMinimumSize in class javax.swing.JComponentpublic class InputField<W extends java.awt.Component & InputWidgetInterface> extends InputFieldArray<W> implements InputWidgetInterface
javax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponentwidgetsaccessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
InputField(java.lang.String labelText,
java.lang.Class<W> clazz)
Creates the widgets, and sets them up.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getValue()
Gets the value from the widget.
|
void |
selectAll()
Selects all the text in the widget.
|
void |
setDisabled()
Disables the widget.
|
void |
setEnabled()
Enables the widget.
|
void |
setValue(java.lang.String newValue)
Sets the value in the widget.
|
disable, disableAll, enable, enableAll, getValue, selectAll, setValuegetAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic InputField(java.lang.String labelText,
java.lang.Class<W> clazz)
labelText - The text to type in the label.clazz - The widget type.public java.lang.String getValue()
getValue in interface InputWidgetInterfacepublic void setValue(java.lang.String newValue)
setValue in interface InputWidgetInterfacenewText - The new value in the widget.public void selectAll()
selectAll in interface InputWidgetInterfacepublic void setDisabled()
public void setEnabled()
public class InputFieldArray<W extends java.awt.Component & InputWidgetInterface>
extends javax.swing.JPanel
javax.swing.JPanel.AccessibleJPaneljavax.swing.JComponent.AccessibleJComponent| Modifier and Type | Field and Description |
|---|---|
java.util.List<W> |
widgets
The widgets on the array.
|
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW| Constructor and Description |
|---|
InputFieldArray(java.lang.String[] labelText,
java.lang.Class<W> clazz)
Create the widgets and set them up.
|
| Modifier and Type | Method and Description |
|---|---|
void |
disable(int index)
Disables a widget.
|
void |
disableAll()
Disables all widgets.
|
void |
enable(int index)
Enables a widget.
|
void |
enableAll()
Enables all widgets.
|
java.lang.String |
getValue(int index)
Get the value from a particular widget.
|
void |
selectAll(int index)
Selects all the text in a particular widget.
|
void |
setValue(int index,
java.lang.String newValue)
Sets the value in a particular widget.
|
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCyclepublic java.util.List<W extends java.awt.Component & InputWidgetInterface> widgets
public InputFieldArray(java.lang.String[] labelText,
java.lang.Class<W> clazz)
labelText - Array of strings holding the text for each label.public java.lang.String getValue(int index)
index - The index of that widget.public void setValue(int index,
java.lang.String newValue)
index - The index of that widget.newValue - The new value for the widget.public void selectAll(int index)
index - The index of that widget.public void disable(int index)
index - The index of the widget to disable.public void disableAll()
public void enable(int index)
index - The index of the widget to enable.public void enableAll()
public class NearestNeighborMode extends java.lang.Object implements MeltingComputationMethod
| Constructor and Description |
|---|
NearestNeighborMode() |
| Modifier and Type | Method and Description |
|---|---|
static double |
computesHairpinTemperature(Environment environment)
computes the melting temperature of a hairpin loop (when there is more than 4 CNG repeats in a sequence)
|
static double |
computesMeltingTemperature(Environment environment)
computes the melting temperature for for the Environment 'environment'.
|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
RegisterMethods |
getRegister()
This method is called to get the RegisterMethod of the implemented class.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
void |
setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
Creates the Environment object and set up the variables of the chosen model.
|
public ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodpublic boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodpublic void setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
MeltingComputationMethodsetUpVariables in interface MeltingComputationMethodoptions - containing all the options (default options and options entered by the user)public RegisterMethods getRegister()
MeltingComputationMethodgetRegister in interface MeltingComputationMethodpublic static double computesHairpinTemperature(Environment environment)
environment - public static double computesMeltingTemperature(Environment environment)
environment - | Class | Description |
|---|---|
| NearestNeighborMode |
This class represents the nearest neighbor model.
|
| Class and Description |
|---|
| EntropyCorrection
This class represents a specific type of ion correction which corrects the entropy value.
|
| Class and Description |
|---|
| EntropyCorrection
This class represents a specific type of ion correction which corrects the entropy value.
|
| Class and Description |
|---|
| EntropyCorrection
This class represents a specific type of ion correction which corrects the entropy value.
|
| Class and Description |
|---|
| DNADMSOCorrections
This class represents the DMSO correction.
|
| Package | Description |
|---|---|
| melting.otherCorrections.dmsoCorrections |
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01DMSOCorrection
This class represents the DMSO correction model ahs01.
|
class |
Cullen76DMSOCorrection
This class represents the DMSO correction model cul76.
|
class |
Escara80DMSOCorrection
This class represents the DMSO correction model esc80.
|
class |
Musielski81DMSOCorrection
This class represents the DMSO correction model mus81.
|
| Package | Description |
|---|---|
| melting.ionCorrection.magnesiumCorrections | |
| melting.ionCorrection.mixedNaMgCorrections | |
| melting.ionCorrection.sodiumCorrections |
| Modifier and Type | Class and Description |
|---|---|
class |
Tan06MagnesiumCorrection
This class represents the magnesium correction model tanmg06.
|
class |
Tan07MagnesiumCorrection
This class represents the magnesium correction model tanmg07.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Tan07MixedNaMgCorrection
This class represents the mixed (Na,Mg) correction model tanmix07.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01SodiumCorrection
This class represents the sodium correction model ahs01.
|
class |
Santalucia98_04SodiumCorrection
This class represents the sodium correction model san04.
|
class |
Tan06SodiumCorrection
This class represents the sodium correction model tanna06.
|
class |
Tan07SodiumCorrection
This class represents the sodium correction model tanna07.
|
| Class | Description |
|---|---|
| DNADMSOCorrections |
This class represents the DMSO correction.
|
| EntropyCorrection |
This class represents a specific type of ion correction which corrects the entropy value.
|
public abstract class DNADMSOCorrections extends java.lang.Object implements CorrectionMethod
| Constructor and Description |
|---|
DNADMSOCorrections() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResult(Environment environment,
double parameter) |
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitcorrectMeltingResultspublic boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResult(Environment environment, double parameter)
public abstract class EntropyCorrection extends java.lang.Object implements CorrectionMethod
| Constructor and Description |
|---|
EntropyCorrection() |
| Modifier and Type | Method and Description |
|---|---|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodprotected double correctEntropy(Environment environment)
environment - public class MeltingFormatter
extends java.util.logging.Formatter
| Constructor and Description |
|---|
MeltingFormatter() |
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
format(java.util.logging.LogRecord record) |
public class Tanaka04 extends DecomposedInitiation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Tanaka04() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
computesHybridizationInitiationgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Freier86 extends CricksNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Freier86() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
computesHybridizationInitiationgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class AllawiSantalucia97 extends DecomposedInitiation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
AllawiSantalucia97() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
computesHybridizationInitiationgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Sugimoto96 extends CricksNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Sugimoto96() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
computesHybridizationInitiationgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class GlobalInitiation extends CricksNNMethod
collector, fileName| Constructor and Description |
|---|
GlobalInitiation() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
computeThermodynamics, isMissingParametersgetCollector, getData, getDataFileName, initialiseFileName, isApplicable, loadData, loadFilepublic ThermoResult computesHybridizationInitiation(Environment environment)
CricksNNMethodcomputesHybridizationInitiation in class CricksNNMethodpublic class Turner06 extends CricksNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Turner06() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public ThermoResult computesHybridizationInitiation(Environment environment)
CricksNNMethodcomputesHybridizationInitiation in class CricksNNMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia04 extends CricksNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Santalucia04() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public ThermoResult computesHybridizationInitiation(Environment environment)
CricksNNMethodcomputesHybridizationInitiation in class CricksNNMethodpublic java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.patternModels.cricksPair |
| Class and Description |
|---|
| CricksNNMethod
This class represents the NN nearest neighbor model (adds the thermodynamic energy (enthalpy and entropy) for each Crick's pair composing the duplex).
|
| DecomposedInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
| GlobalInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
public class Breslauer86 extends GlobalInitiation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Breslauer86() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
computesHybridizationInitiationgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class DecomposedInitiation extends CricksNNMethod
collector, fileName| Constructor and Description |
|---|
DecomposedInitiation() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
computeThermodynamics, isMissingParametersgetCollector, getData, getDataFileName, initialiseFileName, isApplicable, loadData, loadFilepublic ThermoResult computesHybridizationInitiation(Environment environment)
CricksNNMethodcomputesHybridizationInitiation in class CricksNNMethod| Package | Description |
|---|---|
| melting.patternModels.cricksPair |
| Modifier and Type | Class and Description |
|---|---|
class |
Breslauer86
This class represents the nearest neighbor model bre86.
|
class |
Santalucia96
This class represents the nearest neighbor model san96.
|
| Package | Description |
|---|---|
| melting.patternModels.cricksPair |
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantalucia97
This class represents the nearest neighbor model all97.
|
class |
Tanaka04
This class represents the nearest neighbor model tan04.
|
| Package | Description |
|---|---|
| melting.patternModels.cricksPair |
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantalucia97
This class represents the nearest neighbor model all97.
|
class |
Breslauer86
This class represents the nearest neighbor model bre86.
|
class |
DecomposedInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
class |
Freier86
This class represents the nearest neighbor model fre86.
|
class |
GlobalInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
class |
Santalucia04
This class represents the nearest neighbor model san04.
|
class |
Santalucia96
This class represents the nearest neighbor model san96.
|
class |
Sugimoto95
This class represents the nearest neighbor model sug95.
|
class |
Sugimoto96
This class represents the nearest neighbor model sug96.
|
class |
Tanaka04
This class represents the nearest neighbor model tan04.
|
class |
Turner06
This class represents the nearest neighbor model tur06.
|
class |
Xia98
This class represents the nearest neighbor model xia98.
|
public abstract class CricksNNMethod extends PatternComputation
collector, fileName| Constructor and Description |
|---|
CricksNNMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, initialiseFileName, isApplicable, loadData, loadFilepublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public ThermoResult computesHybridizationInitiation(Environment environment)
environment - | Class | Description |
|---|---|
| AllawiSantalucia97 |
This class represents the nearest neighbor model all97.
|
| Breslauer86 |
This class represents the nearest neighbor model bre86.
|
| CricksNNMethod |
This class represents the NN nearest neighbor model (adds the thermodynamic energy (enthalpy and entropy) for each Crick's pair composing the duplex).
|
| DecomposedInitiation |
This class represents one model to compute the initiation enthalpy and entropy.
|
| Freier86 |
This class represents the nearest neighbor model fre86.
|
| GlobalInitiation |
This class represents one model to compute the initiation enthalpy and entropy.
|
| Santalucia04 |
This class represents the nearest neighbor model san04.
|
| Santalucia96 |
This class represents the nearest neighbor model san96.
|
| Sugimoto95 |
This class represents the nearest neighbor model sug95.
|
| Sugimoto96 |
This class represents the nearest neighbor model sug96.
|
| Tanaka04 |
This class represents the nearest neighbor model tan04.
|
| Turner06 |
This class represents the nearest neighbor model tur06.
|
| Xia98 |
This class represents the nearest neighbor model xia98.
|
public class Xia98 extends CricksNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Xia98() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public ThermoResult computesHybridizationInitiation(Environment environment)
CricksNNMethodcomputesHybridizationInitiation in class CricksNNMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Sugimoto95 extends CricksNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Sugimoto95() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
computesHybridizationInitiationgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia96 extends GlobalInitiation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
|
collector, fileName| Constructor and Description |
|---|
Santalucia96() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class CricksNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class CricksNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public ThermoResult computesHybridizationInitiation(Environment environment)
CricksNNMethodcomputesHybridizationInitiation in class GlobalInitiationpublic java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia05Inosine extends InosineNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for inosine
|
collector, fileName| Constructor and Description |
|---|
Santalucia05Inosine() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class InosineNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class InosineNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.patternModels.wobble |
| Class and Description |
|---|
| InosineNNMethod
This class represents the inosine model.
|
public class Turner99Wobble extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for GU base pairs
|
collector, fileName| Constructor and Description |
|---|
Turner99Wobble() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.protected ThermoResult getGUThermoResult(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.patternModels.wobble |
| Modifier and Type | Class and Description |
|---|---|
class |
Santalucia05Inosine
This class represents the inosine model san05.
|
class |
Znosko07Inosine
This class represents the inosine model zno07.
|
public class Znosko07Inosine extends InosineNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for inosine
|
collector, fileName| Constructor and Description |
|---|
Znosko07Inosine() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class InosineNNMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class InosineNNMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Serra12Wobble extends PatternComputation implements NamedMethod
10/02/13
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for GU base pairs
|
collector, fileName| Constructor and Description |
|---|
Serra12Wobble() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.protected ThermoResult getGUThermoResult(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| InosineNNMethod |
This class represents the inosine model.
|
| Santalucia05Inosine |
This class represents the inosine model san05.
|
| Serra12Wobble |
This class represents the GU base pair model ser12.
|
| Turner99Wobble |
This class represents the GU base pair model tur99.
|
| Znosko07Inosine |
This class represents the inosine model zno07.
|
public abstract class InosineNNMethod extends PatternComputation
collector, fileName| Constructor and Description |
|---|
InosineNNMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, initialiseFileName, isApplicable, loadData, loadFilepublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplexpublic class AllawiSantaluciaPeyret97_98_99tanmm extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for tandem mismatches
|
collector, fileName| Constructor and Description |
|---|
AllawiSantaluciaPeyret97_98_99tanmm() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
getCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| AllawiSantaluciaPeyret97_98_99tanmm |
This class represents the tandem mismatches model allsanpey.
|
| Turner99_06tanmm |
This class represents the tandem mismatches model tur06.
|
public class Turner99_06tanmm extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for tandem mismatches
|
collector, fileName| Constructor and Description |
|---|
Turner99_06tanmm() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Bommarito00SingleDanglingEnd extends SingleDanglingEndMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single dangling end
|
collector, fileName| Constructor and Description |
|---|
Bommarito00SingleDanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class SingleDanglingEndMethodpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class SingleDanglingEndMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class SingleDanglingEndMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.patternModels.singleDanglingEnds |
| Class and Description |
|---|
| SingleDanglingEndMethod
This class represents the single dangling end model.
|
| Package | Description |
|---|---|
| melting.patternModels.singleDanglingEnds |
| Modifier and Type | Class and Description |
|---|---|
class |
Bommarito00SingleDanglingEnd
This class represents the single dangling end model bom00.
|
class |
Serra06_08SingleDanglingEnd
This class represents the single dangling end model ser08.
|
| Class | Description |
|---|---|
| Bommarito00SingleDanglingEnd |
This class represents the single dangling end model bom00.
|
| Serra06_08SingleDanglingEnd |
This class represents the single dangling end model ser08.
|
| SingleDanglingEndMethod |
This class represents the single dangling end model.
|
public class Serra06_08SingleDanglingEnd extends SingleDanglingEndMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single dangling end
|
collector, fileName| Constructor and Description |
|---|
Serra06_08SingleDanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class SingleDanglingEndMethodpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class SingleDanglingEndMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class SingleDanglingEndMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class SingleDanglingEndMethod extends PatternComputation
collector, fileName| Constructor and Description |
|---|
SingleDanglingEndMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, initialiseFileName, loadData, loadFilepublic boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplexpublic class Serra06DoubleDanglingEnd extends SecondDanglingEndMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for second dangling end
|
collector, fileName| Constructor and Description |
|---|
Serra06DoubleDanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositions, isApplicable, loadDatagetCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class SecondDanglingEndMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class SecondDanglingEndMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class SecondDanglingEndMethod extends PatternComputation
collector, fileName| Constructor and Description |
|---|
SecondDanglingEndMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
getCollector, getData, getDataFileName, initialiseFileName, loadFilepublic boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplex| Package | Description |
|---|---|
| melting.patternModels.secondDanglingEnds |
| Class and Description |
|---|
| SecondDanglingEndMethod
This class represents the second dangling end model.
|
| Package | Description |
|---|---|
| melting.patternModels.secondDanglingEnds |
| Modifier and Type | Class and Description |
|---|---|
class |
Serra05DoubleDanglingEnd
This class represents the second dangling end model ser05.
|
class |
Serra06DoubleDanglingEnd
This class represents the second dangling end model ser06.
|
| Class | Description |
|---|---|
| SecondDanglingEndMethod |
This class represents the second dangling end model.
|
| Serra05DoubleDanglingEnd |
This class represents the second dangling end model ser05.
|
| Serra06DoubleDanglingEnd |
This class represents the second dangling end model ser06.
|
public class Serra05DoubleDanglingEnd extends SecondDanglingEndMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for second dangling end
|
collector, fileName| Constructor and Description |
|---|
Serra05DoubleDanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositions, isApplicable, loadDatagetCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class SecondDanglingEndMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class SecondDanglingEndMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia04SingleBulgeLoop extends Santalucia04LongBulgeLoop implements NamedMethod
defaultFileName, formulaEnthalpy, formulaEntropycollector, fileName| Constructor and Description |
|---|
Santalucia04SingleBulgeLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
correctPositions, initialiseFileName, isApplicablegetCollector, getData, getDataFileName, loadFilepublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class Santalucia04LongBulgeLoopsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class Santalucia04LongBulgeLoopsequences - which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)public java.lang.String getName()
getName in interface NamedMethodgetName in class Santalucia04LongBulgeLooppublic class Turner99_06SingleBulgeLoop extends Turner99_06LongBulgeLoop implements NamedMethod
defaultFileName, formulaEnthalpycollector, fileName| Constructor and Description |
|---|
Turner99_06SingleBulgeLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
protected boolean |
isClosingPenaltyNecessary()
to check if a penalty for the closing base pairs is necessary.
|
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
correctPositions, initialiseFileName, isApplicablegetCollector, getData, getDataFileName, loadFilepublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class Turner99_06LongBulgeLoopsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class Turner99_06LongBulgeLoopsequences - which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)protected boolean isClosingPenaltyNecessary()
Turner99_06LongBulgeLoopisClosingPenaltyNecessary in class Turner99_06LongBulgeLooppublic java.lang.String getName()
getName in interface NamedMethodgetName in class Turner99_06LongBulgeLooppublic abstract class GlobalSingleBulgeLoopMethod extends PatternComputation
collector, fileName| Constructor and Description |
|---|
GlobalSingleBulgeLoopMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, initialiseFileName, isApplicable, loadData, loadFilepublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplexpublic class Tanaka04SingleBulgeLoop extends GlobalSingleBulgeLoopMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single bulge loop
|
collector, fileName| Constructor and Description |
|---|
Tanaka04SingleBulgeLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class GlobalSingleBulgeLoopMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class GlobalSingleBulgeLoopMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.patternModels.singleBulge |
| Class and Description |
|---|
| GlobalSingleBulgeLoopMethod
This class represents one single bulge loop model.
|
| Package | Description |
|---|---|
| melting.patternModels.singleBulge |
| Modifier and Type | Class and Description |
|---|---|
class |
Serra07SingleBulgeLoop
This class represents the single bulge loop model ser07.
|
class |
Tanaka04SingleBulgeLoop
This class represents the single bulge loop model tan04.
|
public class Serra07SingleBulgeLoop extends GlobalSingleBulgeLoopMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single bulge loop
|
collector, fileName| Constructor and Description |
|---|
Serra07SingleBulgeLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class GlobalSingleBulgeLoopMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class GlobalSingleBulgeLoopMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| GlobalSingleBulgeLoopMethod |
This class represents one single bulge loop model.
|
| Santalucia04SingleBulgeLoop |
This class represents the single bulge loop model san04.
|
| Serra07SingleBulgeLoop |
This class represents the single bulge loop model ser07.
|
| Tanaka04SingleBulgeLoop |
This class represents the single bulge loop model tan04.
|
| Turner99_06SingleBulgeLoop |
This class represents the single bulge loop model tur06.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
| Class and Description |
|---|
| PatternComputation
This class represents the different pattern models.
|
public class Znosko07mm extends ZnoskoMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
|
formulaEnthalpycollector, fileName| Constructor and Description |
|---|
Znosko07mm() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
correctPositions, isApplicable, isMissingParametersgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class ZnoskoMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class ZnoskoMethod extends PatternComputation
| Modifier and Type | Field and Description |
|---|---|
protected static java.lang.String |
formulaEnthalpy
String formulaEnthalpy : enthalpy formula
|
collector, fileName| Constructor and Description |
|---|
ZnoskoMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, initialiseFileName, loadData, loadFileprotected static java.lang.String formulaEnthalpy
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplexpublic class Watkins11mm extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
Default name for the xml file containing the thermodynamic parameters for
a single mismatch in a DNA/RNA duplex.
|
collector, fileName| Constructor and Description |
|---|
Watkins11mm() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static final java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.patternModels.singleMismatch |
| Class and Description |
|---|
| ZnoskoMethod
This class represents the single mismatch model from Znosco et al, 2007, 2008.
|
| Package | Description |
|---|---|
| melting.patternModels.singleMismatch |
| Modifier and Type | Class and Description |
|---|---|
class |
Znosko07mm
This class represents the single mismatch model zno07.
|
class |
Znosko08mm
This class represents the single mismatch model zno08.
|
| Class | Description |
|---|---|
| AllawiSantaluciaPeyret97_98_99mm |
This class represents the single mismatch model allsanpey.
|
| Turner06mm |
This class represents the single mismatch model tur06.
|
| Watkins11mm |
This class represents the DNA/RNA single mismatch model wat11.
|
| Znosko07mm |
This class represents the single mismatch model zno07.
|
| Znosko08mm |
This class represents the single mismatch model zno08.
|
| ZnoskoMethod |
This class represents the single mismatch model from Znosco et al, 2007, 2008.
|
public class Turner06mm extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
|
collector, fileName| Constructor and Description |
|---|
Turner06mm() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Znosko08mm extends ZnoskoMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
|
formulaEnthalpycollector, fileName| Constructor and Description |
|---|
Znosko08mm() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
correctPositions, isMissingParametersgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class ZnoskoMethodpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class ZnoskoMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class AllawiSantaluciaPeyret97_98_99mm extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
|
collector, fileName| Constructor and Description |
|---|
AllawiSantaluciaPeyret97_98_99mm() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Modifier and Type | Class and Description |
|---|---|
class |
Broda05CNGRepeats
This class represents the CNG repeats model bro05.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantalucia97
This class represents the nearest neighbor model all97.
|
class |
Breslauer86
This class represents the nearest neighbor model bre86.
|
class |
CricksNNMethod
This class represents the NN nearest neighbor model (adds the thermodynamic energy (enthalpy and entropy) for each Crick's pair composing the duplex).
|
class |
DecomposedInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
class |
Freier86
This class represents the nearest neighbor model fre86.
|
class |
GlobalInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
class |
Santalucia04
This class represents the nearest neighbor model san04.
|
class |
Santalucia96
This class represents the nearest neighbor model san96.
|
class |
Sugimoto95
This class represents the nearest neighbor model sug95.
|
class |
Sugimoto96
This class represents the nearest neighbor model sug96.
|
class |
Tanaka04
This class represents the nearest neighbor model tan04.
|
class |
Turner06
This class represents the nearest neighbor model tur06.
|
class |
Xia98
This class represents the nearest neighbor model xia98.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Santalucia04InternalLoop
This class represents the internal loop model san04.
|
class |
Turner06InternalLoop
This class represents the internal loop model tur06.
|
class |
Znosko071x2Loop
This class represents the 1x2 internal loop model zno07.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Santalucia04LongBulgeLoop
This class represents the long bulge loop model san04.
|
class |
Turner99_06LongBulgeLoop
This class represents the long bulge loop model tur06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Sugimoto02DNADanglingEnd
This class represents the long dangling end model sugdna02 (for long poly A only).
|
class |
Sugimoto02RNADanglingEnd
This class represents the long dangling end model sugrna02 (for long poly A only).
|
class |
SugimotoLongDanglingEndMethod
This class represents the long dangling end model (for long poly A only)from Sugimoto et al. 2002.
|
| Modifier and Type | Class and Description |
|---|---|
class |
SecondDanglingEndMethod
This class represents the second dangling end model.
|
class |
Serra05DoubleDanglingEnd
This class represents the second dangling end model ser05.
|
class |
Serra06DoubleDanglingEnd
This class represents the second dangling end model ser06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
GlobalSingleBulgeLoopMethod
This class represents one single bulge loop model.
|
class |
Santalucia04SingleBulgeLoop
This class represents the single bulge loop model san04.
|
class |
Serra07SingleBulgeLoop
This class represents the single bulge loop model ser07.
|
class |
Tanaka04SingleBulgeLoop
This class represents the single bulge loop model tan04.
|
class |
Turner99_06SingleBulgeLoop
This class represents the single bulge loop model tur06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Bommarito00SingleDanglingEnd
This class represents the single dangling end model bom00.
|
class |
Serra06_08SingleDanglingEnd
This class represents the single dangling end model ser08.
|
class |
SingleDanglingEndMethod
This class represents the single dangling end model.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantaluciaPeyret97_98_99mm
This class represents the single mismatch model allsanpey.
|
class |
Turner06mm
This class represents the single mismatch model tur06.
|
class |
Watkins11mm
This class represents the DNA/RNA single mismatch model wat11.
|
class |
Znosko07mm
This class represents the single mismatch model zno07.
|
class |
Znosko08mm
This class represents the single mismatch model zno08.
|
class |
ZnoskoMethod
This class represents the single mismatch model from Znosco et al, 2007, 2008.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Asanuma05Azobenzene
This class represents the azobenzene (X_C or X_T) model asa05.
|
class |
McTigue04LockedAcid
This class represents the locked nucleic acid (AL, GL, CL or TL) model mct04.
|
class |
Sugimoto01Hydroxyadenine
This class represents the hydroxyadenine (A*) model sug01.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantaluciaPeyret97_98_99tanmm
This class represents the tandem mismatches model allsanpey.
|
class |
Turner99_06tanmm
This class represents the tandem mismatches model tur06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
InosineNNMethod
This class represents the inosine model.
|
class |
Santalucia05Inosine
This class represents the inosine model san05.
|
class |
Serra12Wobble
This class represents the GU base pair model ser12.
|
class |
Turner99Wobble
This class represents the GU base pair model tur99.
|
class |
Znosko07Inosine
This class represents the inosine model zno07.
|
| Package | Description |
|---|---|
| melting.patternModels.singleBulge |
| Class and Description |
|---|
| Santalucia04LongBulgeLoop
This class represents the long bulge loop model san04.
|
| Turner99_06LongBulgeLoop
This class represents the long bulge loop model tur06.
|
public class Turner99_06LongBulgeLoop extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long bulge loop
|
protected static java.lang.String |
formulaEnthalpy
String formulaEnthalpy : enthalpy formula
|
collector, fileName| Constructor and Description |
|---|
Turner99_06LongBulgeLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
protected boolean |
isClosingPenaltyNecessary()
to check if a penalty for the closing base pairs is necessary.
|
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
protected static java.lang.String formulaEnthalpy
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.protected boolean isClosingPenaltyNecessary()
protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplexpublic java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.patternModels.singleBulge |
| Modifier and Type | Class and Description |
|---|---|
class |
Turner99_06SingleBulgeLoop
This class represents the single bulge loop model tur06.
|
| Package | Description |
|---|---|
| melting.patternModels.singleBulge |
| Modifier and Type | Class and Description |
|---|---|
class |
Santalucia04SingleBulgeLoop
This class represents the single bulge loop model san04.
|
| Class | Description |
|---|---|
| Santalucia04LongBulgeLoop |
This class represents the long bulge loop model san04.
|
| Turner99_06LongBulgeLoop |
This class represents the long bulge loop model tur06.
|
public class Santalucia04LongBulgeLoop extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long bulge loop
|
protected static java.lang.String |
formulaEnthalpy
String formulaEnthalpy : enthalpy formula
|
protected static java.lang.String |
formulaEntropy
String formulaEntropy : entropy formula
|
collector, fileName| Constructor and Description |
|---|
Santalucia04LongBulgeLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
protected static java.lang.String formulaEnthalpy
protected static java.lang.String formulaEntropy
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplexpublic java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| PatternComputation |
This class represents the different pattern models.
|
public class Owczarzy11TandemLockedAcid extends LockedAcidNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
|
collector, fileName| Constructor and Description |
|---|
Owczarzy11TandemLockedAcid() |
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
computeThermodynamics, isApplicable, isMissingParametersgetCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)public java.lang.String getName()
getName in interface NamedMethodgetName in class LockedAcidNNMethodpublic class McTigue04LockedAcid extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
|
collector, fileName| Constructor and Description |
|---|
McTigue04LockedAcid() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
getCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Owczarzy11LockedAcid extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
|
collector, fileName| Constructor and Description |
|---|
Owczarzy11LockedAcid() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Sugimoto01Hydroxyadenine extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for hydroxyadenine mismatch
|
collector, fileName| Constructor and Description |
|---|
Sugimoto01Hydroxyadenine() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
getCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Owczarzy11SingleMismatchLockedAcid extends LockedAcidNNMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
|
collector, fileName| Constructor and Description |
|---|
Owczarzy11SingleMismatchLockedAcid() |
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
computeThermodynamics, isApplicable, isMissingParametersgetCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodgetName in class LockedAcidNNMethodpublic void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)| Class | Description |
|---|---|
| Asanuma05Azobenzene |
This class represents the azobenzene (X_C or X_T) model asa05.
|
| LockedAcidNNMethod |
This class represents the locked nucleic acid (AL, GL, CL or TL) model owc11.
|
| McTigue04LockedAcid |
This class represents the locked nucleic acid (AL, GL, CL or TL) model mct04.
|
| Owczarzy11LockedAcid |
This class represents the locked nucleic acid (AL, GL, CL or TL) model owc11.
|
| Owczarzy11SingleMismatchLockedAcid |
This class represents the locked nucleic acid (AL, GL, CL or TL) model owc11.
|
| Owczarzy11TandemLockedAcid |
This class represents the locked nucleic acid (AL, GL, CL or TL) model owc11.
|
| Sugimoto01Hydroxyadenine |
This class represents the hydroxyadenine (A*) model sug01.
|
public class Asanuma05Azobenzene extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName |
collector, fileName| Constructor and Description |
|---|
Asanuma05Azobenzene() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class LockedAcidNNMethod extends PatternComputation implements NamedMethod
collector, fileName| Constructor and Description |
|---|
LockedAcidNNMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
abstract java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, initialiseFileName, loadData, loadFilepublic boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public abstract java.lang.String getName()
getName in interface NamedMethodpublic class Broda05CNGRepeats extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for CNG repeats
|
collector, fileName| Constructor and Description |
|---|
Broda05CNGRepeats() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| Broda05CNGRepeats |
This class represents the CNG repeats model bro05.
|
public class Turner06InternalLoop extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for internal loop
|
collector, fileName| Constructor and Description |
|---|
Turner06InternalLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Znosko071x2Loop extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for internal loop
|
collector, fileName| Constructor and Description |
|---|
Znosko071x2Loop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia04InternalLoop extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for internal loop
|
collector, fileName| Constructor and Description |
|---|
Santalucia04InternalLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
getCollector, getData, getDataFileName, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodloadData in class PatternComputationoptions - which contains the current options. (default options and options entered by the user)public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| Santalucia04InternalLoop |
This class represents the internal loop model san04.
|
| Turner06InternalLoop |
This class represents the internal loop model tur06.
|
| Znosko071x2Loop |
This class represents the 1x2 internal loop model zno07.
|
public class Sugimoto02DNADanglingEnd extends SugimotoLongDanglingEndMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long dangling end
(just long poly A)
|
collector, fileName| Constructor and Description |
|---|
Sugimoto02DNADanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class SugimotoLongDanglingEndMethodpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class SugimotoLongDanglingEndMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class SugimotoLongDanglingEndMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class SugimotoLongDanglingEndMethod extends PatternComputation
collector, fileName| Constructor and Description |
|---|
SugimotoLongDanglingEndMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, initialiseFileName, loadData, loadFilepublic boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplex| Package | Description |
|---|---|
| melting.patternModels.longDanglingEnds |
| Class and Description |
|---|
| SugimotoLongDanglingEndMethod
This class represents the long dangling end model (for long poly A only)from Sugimoto et al. 2002.
|
| Package | Description |
|---|---|
| melting.patternModels.longDanglingEnds |
| Modifier and Type | Class and Description |
|---|---|
class |
Sugimoto02DNADanglingEnd
This class represents the long dangling end model sugdna02 (for long poly A only).
|
class |
Sugimoto02RNADanglingEnd
This class represents the long dangling end model sugrna02 (for long poly A only).
|
| Class | Description |
|---|---|
| Sugimoto02DNADanglingEnd |
This class represents the long dangling end model sugdna02 (for long poly A only).
|
| Sugimoto02RNADanglingEnd |
This class represents the long dangling end model sugrna02 (for long poly A only).
|
| SugimotoLongDanglingEndMethod |
This class represents the long dangling end model (for long poly A only)from Sugimoto et al.
|
public class Sugimoto02RNADanglingEnd extends SugimotoLongDanglingEndMethod implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long dangling end
(just long poly A)
|
collector, fileName| Constructor and Description |
|---|
Sugimoto02RNADanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class SugimotoLongDanglingEndMethodpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class SugimotoLongDanglingEndMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class SugimotoLongDanglingEndMethodsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.public java.lang.String getName()
getName in interface NamedMethodpublic abstract class PatternComputation extends java.lang.Object implements PatternComputationMethod
| Modifier and Type | Field and Description |
|---|---|
protected DataCollect |
collector
DataCollect collector : contains the data HasMap with the thermodynamic parameters for the pattern computation.
|
protected java.lang.String |
fileName
String fileName : name of the xml file containing the thermodynamic parameters.
|
| Constructor and Description |
|---|
PatternComputation() |
| Modifier and Type | Method and Description |
|---|---|
abstract ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
DataCollect |
getCollector()
This method is called to get the DataCollect of the implemented class.
|
static java.lang.String |
getData()
This method is called to get the HasMap of DataCollect containing the thermodynamic parameters
|
java.lang.String |
getDataFileName(java.lang.String methodName) |
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
void |
loadFile(java.lang.String name,
DataCollect collector)
To load the thermodynamic parameters from the file "name" and stock them in the map of a DataCollect object.
|
protected DataCollect collector
protected java.lang.String fileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodpublic abstract ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodsequences - which contains the sequences entered by the user.public DataCollect getCollector()
PatternComputationMethodgetCollector in interface PatternComputationMethodpublic void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodoptions - which contains the current options. (default options and options entered by the user)public void loadFile(java.lang.String name,
DataCollect collector)
PatternComputationMethodloadFile in interface PatternComputationMethodname - : the file name where to find the thermodynamic parameterscollector - : The object which stocks the different thermodynamic parameters in a map.public java.lang.String getDataFileName(java.lang.String methodName)
getDataFileName in interface PatternComputationMethodmethodName - : method or model name entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodmethodName - : method or model name entered by the user.public static java.lang.String getData()
public class FileReader
extends java.lang.Object
| Constructor and Description |
|---|
FileReader() |
| Modifier and Type | Method and Description |
|---|---|
static java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,Thermodynamics>> |
getLoadedData()
This method is called to get the loadedData of FileReader.
|
static java.util.HashMap<java.lang.String,Thermodynamics> |
readFile(java.io.File file)
stocks the thermodynamic parameters from the file in a HashMap.
|
public static java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,Thermodynamics>> getLoadedData()
public static java.util.HashMap<java.lang.String,Thermodynamics> readFile(java.io.File file) throws javax.xml.parsers.ParserConfigurationException, org.xml.sax.SAXException
File - file : file containing the thermodynamic parameters to load.javax.xml.parsers.ParserConfigurationExceptionorg.xml.sax.SAXException - If an IOException is catch, a FileException is thrown.public class NucleotidSequences
extends java.lang.Object
| Modifier | Constructor and Description |
|---|---|
protected |
NucleotidSequences(java.lang.String hybridizationType,
NucleotidSequences sequences)
Creates a new NucleotidSequences object from a reference nucleotiDSequences object.
|
|
NucleotidSequences(java.lang.String sequence,
java.lang.String complementary)
Creates a NucleotidSequences object from two String.
|
| Modifier and Type | Method and Description |
|---|---|
static NucleotidSequences |
buildSymetricSequences(java.lang.String seq1,
java.lang.String seq2)
creates a NucleotidSequences with two symmetric sequences String created from the
seq1 String an seq2 String.
|
double |
calculateNumberOfTerminal(java.lang.String base1,
java.lang.String base2,
int pos1,
int pos2)
calculates the number of base pairs (base1, base2) at the postions pos1 and pos2 in the duplex of NucleotidSequences.
|
static boolean |
checkSequence(java.lang.String sequence)
Checks if the String sequence is composed of nucleic acids known by MELTING.
|
int |
computesInternalLoopLength(int pos1,
int pos2)
computes the number of nucleic acids in the internal loop between the positions pos1 + 1 and
pos2 - 1 in the duplex ArrayList of the NucleotidSequences object.
|
double |
computesPercentGC()
computes the percentage of GC base pairs in the duplex of NucleotidSequences.
|
double |
computesPercentMismatching()
Computes the percentage of mismatching base pairs in the duplex of NucleotidSequences.
|
static java.lang.String |
convertToPyr_Pur(java.lang.String sequence)
converts a sequence into a String composed of purine and pyrimidine.
|
java.lang.String[] |
correctSequences(java.lang.String sequence,
java.lang.String complementary)
removes the unnecessary "-" in the String sequence and complementary of NucleotidSequences.
|
static java.lang.String[] |
decodeSequences(java.lang.String sequence,
java.lang.String complementary)
decodes the String sequence and complementary of NucleotidSequences.
|
java.lang.String[] |
encodeSequences(java.lang.String sequence,
java.lang.String complementary)
encodes the String sequence and complementary of the NucleotidSequences object.
|
java.lang.String |
getComplementary()
This method is called to get the encoded complementary String of NucleotidSequences.
|
java.lang.String |
getComplementary(int pos1,
int pos2)
This method is called to get a substring between two positions of the complementary String.
|
java.lang.String |
getComplementary(int pos1,
int pos2,
java.lang.String hybridizationType)
This method is called to get a substring of the complementary String between the positions pos1 and pos2 in the duplex.
|
java.lang.String |
getComplementaryNNPair(int pos)
to get the two nucleic acids which are from the complementary sequence (3'5') in the Crick's pair at the position "pos" in the duplex.
|
java.lang.String |
getComplementaryNNPairUnlocked(int pos)
to get the two unlocked nucleic acids which are from the complementary sequence (3'5') in the Crick's pair at the position "pos" in the duplex.
|
static java.lang.String |
getComplementarySequence(java.lang.String sequence,
java.lang.String hybridization)
This method is called when we want to get the complementary of NucleotidSequences with the
type of hybridization "hybridization".
|
java.lang.String |
getComplementaryTo(java.lang.String sequence,
int pos1,
int pos2)
This method is called to get the complementary sequence to the sequence String between the positions pos1 and pos2.
|
static java.lang.String |
getDanglingSens(java.lang.String seq1,
java.lang.String seq2)
this method is called to get the sens of the dangling end for the sequences seq1 and seq2
|
java.util.ArrayList<BasePair> |
getDuplex()
This method is called to get the duplex of NucleotidSequences.
|
static java.util.ArrayList<BasePair> |
getDuplexFrom(java.lang.String sequence,
java.lang.String complementary)
This method is called to get the duplex of NucleotidSequences.
|
int |
getDuplexLength()
This method is called to get the length of the ArrayList duplex of NucleotidSequences.
|
NucleotidSequences |
getEquivalentSequences(java.lang.String hybridizationType)
This method is called when the same NucleotidSequences is required but with the sequences converted in the new
hybridization type "hybridizationType"
|
java.lang.String |
getInternalLoopType(int pos1,
int pos2)
gives the type of the internal loop at the positions pos1 + 1 and pos2 - 1 in the duplex ArrayList of the NucleotidSequences object.
|
static java.lang.String |
getInversedSequence(java.lang.String sequence)
creates the inverse String of the sequence
|
java.lang.String[] |
getLoopFistMismatch(int pos1)
This method is called to get the first mismatch of the internal loop at the positions pos1 + 1 and pos2 - 1
in the duplex ArrayList of the NucleotidSequences object.
|
SpecificAcidNames |
getModifiedAcidName(BasePair pair)
This method is called to get the name of a specific nucleic acid in the base pair (BasePair object).
|
static java.util.HashMap<java.lang.String,SpecificAcidNames> |
getModifiedAcidNames()
This method is called to get the modifiedAcidNames of NucleotidSequences.
|
java.lang.String[] |
getNNPairWithoutHydroxyA(int pos)
to get the two nucleic acids from each sequence in the Crick's pair at the position "pos" in the duplex.
|
double |
getNumberTerminal5TA(int pos1,
int pos2)
calculates the number of terminal 5'T3'A in the subduplex between pos1 and pos2
|
java.lang.String |
getSequence()
This method is called to get the encoded sequence String of NucleotidSequences.
|
java.lang.String |
getSequence(int pos1,
int pos2)
This method is called to get a substring between two positions of the sequence String.
|
java.lang.String |
getSequence(int pos1,
int pos2,
java.lang.String hybridizationType)
This method is called to get a substring of the sequence String between the positions pos1 and pos2 in the duplex.
|
java.lang.String |
getSequenceContaining(java.lang.String pattern,
int pos1,
int pos2)
this method is called to get the String sequence or complementary of NucleotidSequences.
|
java.lang.String |
getSequenceNNPair(int pos)
to get the two nucleic acids which are from the sequence (5'3') in the Crick's pair at the position "pos" in the duplex.
|
java.lang.String |
getSequenceNNPairUnlocked(int pos)
to get the two unlocked nucleic acids which are from the sequence (5'3') in the Crick's pair at the position "pos" in the duplex.
|
java.lang.String |
getSequenceSens(java.lang.String sequence,
int pos1,
int pos2)
To get the orientation of the subsequence sequence.
|
java.lang.String[] |
getSingleBulgeNeighbors(int pos1)
This method is called to get the base pairs adjacent to the single bulge loop (unpaired nucleic acid) at the position pos1 in the duplex ArrayList
|
static void |
initialiseModifiedAcidHashmap()
initialises the modifiedAcidNames of NucleotidSequences.
|
boolean |
isAPyrimidineInThePosition(int pos)
to check if there is at least one pyrimidine in the base pair at the position pos of the duplex ArrayList.
|
boolean |
isAsymetricInternalLoop(int pos1,
int pos2)
to check if the internal loop between the positions pos1 + 1 and pos2 - 1 in the duplex ArrayList
is asymetric.
|
boolean |
isBasePair(java.lang.String base1,
java.lang.String base2,
int pos)
To check if the base pair at the position pos in the duplex is (base1, base2) or (base2, base1).
|
boolean |
isBulgeLoop(int pos1,
int pos2)
to check if the pattern between the positions pos1 and pos2 in the duplex is a single or long bulge loop.
|
boolean |
isCNGPattern(int pos1,
int pos2)
to check if the pattern between the positions pos1 and pos2 in the duplex is a CNG repeat pattern.
|
boolean |
isDanglingEnd(int pos1,
int pos2)
to check if there is at least one dangling end between the positions pos1 and pos2 in the duplex.
|
boolean |
isGUSequences(int pos1,
int pos2)
to check if the pattern between the positions pos1 and pos2 in the duplex is only composed of GU base pairs.
|
boolean |
isMismatch(int pos1,
int pos2)
to check if the pattern between the positions pos1 and pos2 in the duplex is a single mismatch, tandem mismatch or internal loop.
|
boolean |
isMismatchPair(int pos)
to check if the base pair at the position pos in the duplex is a mismatch.
|
boolean |
isNoGapInSequence(int pos1,
int pos2)
to chack if there is no gap (an unpaired nucleic acid) in the duplex between theb positions pos1 and pos2
|
boolean |
isOneGCBasePair()
To check if there is at least one GC base pair in the duplex of NucleotidSequences.
|
boolean |
isPerfectMatchSequence(int pos1,
int pos2)
to check to check if the sequences between the positions pos1 and pos2 in the duplex are perfectly
matching sequences.
|
boolean |
isRegisteredNucleicAcid(int pos)
to check if the nucleic acids in the base pair at the position pos in the duplex are existing nucleic acids.
|
static boolean |
isSelfComplementarySequence(java.lang.String sequence)
To check if a sequence is self complementary.
|
boolean |
isSymmetric(int pos1,
int pos2)
To check if the String sequence and String complementary are symmetric between the positions pos1 and pos2
in the duplex ArrayList of the NucleotidSequences object.
|
boolean |
isTandemMismatchDeltaPPenaltyNecessary(int pos)
to check if there is an AG or GA base pair adjacent to an UC or CU base pair or a CC base pair
adjacent to an AA base pair.
|
boolean |
isTandemMismatchGGPenaltyNecessary(int pos)
To check if there is a GG base pair adjacent to a AA base pair or a base pair containing a pyrimidine ("C", "T" or "U").
|
int[] |
removeTerminalUnpairedNucleotides()
find the real starting and ending positions of the duplex.
|
public NucleotidSequences(java.lang.String sequence,
java.lang.String complementary)
sequence - : the sequence (5'3')complementary - : the complementary sequence (3'5')protected NucleotidSequences(java.lang.String hybridizationType,
NucleotidSequences sequences)
hybridizationType - : hybridization type of the duplex.sequences - : the reference nucleotidSequences object.public NucleotidSequences getEquivalentSequences(java.lang.String hybridizationType)
hybridizationType - : the new hybridization type of the sequencespublic java.lang.String[] encodeSequences(java.lang.String sequence,
java.lang.String complementary)
sequence - : the sequence (5'3')complementary - : the complementary sequence (3'5')public java.lang.String[] correctSequences(java.lang.String sequence,
java.lang.String complementary)
sequence - : the sequence (5'3')complementary - : the complementary sequence (3'5')public java.lang.String getComplementaryTo(java.lang.String sequence,
int pos1,
int pos2)
sequence - : substring of one of the sequences (sequence 5'3' or the complementary 3'5')pos1 - : starting position of the subsequence in the duplexpos2 - : ending position of the subsequence in the duplexpublic java.lang.String getSequenceContaining(java.lang.String pattern,
int pos1,
int pos2)
pattern - pos1 - : starting position of the pattern in the duplexpos2 - : ending position of the pattern in the duplexpublic boolean isCNGPattern(int pos1,
int pos2)
pos1 - : starting position of the pattern in the duplexpos2 - : ending position of the pattern in the duplexpublic boolean isPerfectMatchSequence(int pos1,
int pos2)
pos1 - : starting position of the pattern in the duplexpos2 - : ending position of the pattern in the duplexpublic boolean isDanglingEnd(int pos1,
int pos2)
pos1 - : starting position of the pattern in the duplexpos2 - : ending position of the pattern in the duplexpublic boolean isGUSequences(int pos1,
int pos2)
pos1 - : starting position of the pattern in the duplexpos2 - : ending position of the pattern in the duplexpublic boolean isMismatchPair(int pos)
pos - : the position of the base pair to test in the duplex ArrayListpublic boolean isMismatch(int pos1,
int pos2)
pos1 - : starting position of the pattern in the duplexpos2 - : ending position of the pattern in the duplexpublic boolean isBulgeLoop(int pos1,
int pos2)
pos1 - : starting position of the pattern in the duplexpos2 - : ending position of the pattern in the duplexpublic boolean isRegisteredNucleicAcid(int pos)
pos - : position of the nucleic acid in the duplexpublic SpecificAcidNames getModifiedAcidName(BasePair pair)
pair - public boolean isAPyrimidineInThePosition(int pos)
pos - : position of the base pair in the duplexpublic boolean isTandemMismatchGGPenaltyNecessary(int pos)
pos - : position of the Crick' pair in the duplexpublic boolean isTandemMismatchDeltaPPenaltyNecessary(int pos)
pos - : positions of the Crick's pair in the duplexpublic boolean isNoGapInSequence(int pos1,
int pos2)
pos1 - : starting position of the subsequence in the duplexpos2 - : ending position of the subsequence in the duplexpublic boolean isSymmetric(int pos1,
int pos2)
pos1 - : starting position of the subduplex in the duplex ArrayList of NucleotidSequences object.pos2 - : ending position of the subduplex in the duplex ArrayList of NucleotidSequences object.public java.lang.String getInternalLoopType(int pos1,
int pos2)
pos1 - : position preceding the starting position of the internal looppos2 - : position following the ending position of the internal looppublic java.lang.String[] getLoopFistMismatch(int pos1)
pos1 - : the position preceding the internal loop.public java.lang.String[] getSingleBulgeNeighbors(int pos1)
pos1 - : position preceding the unpaired nucleic acid in the single bulge loop.public boolean isAsymetricInternalLoop(int pos1,
int pos2)
pos1 - : position preceding the starting position of the internal looppos2 - : position following the ending position of the internal looppublic java.lang.String getSequence(int pos1,
int pos2,
java.lang.String hybridizationType)
pos1 - : starting position of the subsequencepos2 - : ending position of the subsequencehybridizationType - : type of sequence ("dna" or "rna")public java.lang.String getComplementary(int pos1,
int pos2,
java.lang.String hybridizationType)
pos1 - : starting position of the subsequencepos2 - : ending position of the subsequencehybridizationType - : type of sequence ("dna" or "rna")public int computesInternalLoopLength(int pos1,
int pos2)
pos1 - : position preceding the starting position of the internal looppos2 - : position following the ending position of the internal looppublic java.util.ArrayList<BasePair> getDuplex()
public java.lang.String getSequenceSens(java.lang.String sequence,
int pos1,
int pos2)
sequence - : a substring of sequence String or complementary String.pos1 - : the starting position of the substring in the sequence String or complementary Stringpos2 - : the ending position of the substring in the sequence String or complementary Stringpublic double computesPercentGC()
public double computesPercentMismatching()
public boolean isOneGCBasePair()
public int getDuplexLength()
public java.lang.String getSequence()
public java.lang.String getComplementary()
public java.lang.String getSequence(int pos1,
int pos2)
pos1 - : starting position of the subsequencepos2 - : ending position of the subsequencepublic java.lang.String getComplementary(int pos1,
int pos2)
pos1 - : starting position of the subsequencepos2 - : ending position of the subsequencepublic java.lang.String getSequenceNNPair(int pos)
pos - : position of the crick's pair in the duplex.public java.lang.String getComplementaryNNPair(int pos)
pos - : position of the crick's pair in the duplex.public java.lang.String getSequenceNNPairUnlocked(int pos)
pos - : position of the crick's pair in the duplex.public java.lang.String getComplementaryNNPairUnlocked(int pos)
pos - : position of the crick's pair in the duplex.public java.lang.String[] getNNPairWithoutHydroxyA(int pos)
pos - : position of the crick's pair in the duplex.public double calculateNumberOfTerminal(java.lang.String base1,
java.lang.String base2,
int pos1,
int pos2)
base1 - base2 - pos1 - : starting position of the subsequence in the duplex of NucleotidSequences.pos2 - : ending position of the subsequence in the duplex of NucleotidSequences.public double getNumberTerminal5TA(int pos1,
int pos2)
pos1 - : starting position of the subsequence in the duplex of NucleotidSequences.pos2 - : ending position of the subsequence in the duplex of NucleotidSequences.public int[] removeTerminalUnpairedNucleotides()
public boolean isBasePair(java.lang.String base1,
java.lang.String base2,
int pos)
base1 - base2 - pos - : position of the base pair in the duplexpublic static java.util.ArrayList<BasePair> getDuplexFrom(java.lang.String sequence, java.lang.String complementary)
sequence - : sequence (5'3')complementary - : complementary sequence (3'5')public static java.lang.String[] decodeSequences(java.lang.String sequence,
java.lang.String complementary)
sequence - : sequence (5'3')complementary - : complementary sequence (3'5')public static NucleotidSequences buildSymetricSequences(java.lang.String seq1, java.lang.String seq2)
seq1 - : sequence (5'3')seq2 - : complementary sequence (3'5')public static java.lang.String getInversedSequence(java.lang.String sequence)
sequence - to inversepublic static boolean isSelfComplementarySequence(java.lang.String sequence)
sequence - public static java.lang.String convertToPyr_Pur(java.lang.String sequence)
sequence - to convert in purine-pyrimidine sequence.public static java.util.HashMap<java.lang.String,SpecificAcidNames> getModifiedAcidNames()
public static void initialiseModifiedAcidHashmap()
public static java.lang.String getComplementarySequence(java.lang.String sequence,
java.lang.String hybridization)
sequence - hybridization - : type of hybridizationpublic static boolean checkSequence(java.lang.String sequence)
sequence - public static java.lang.String getDanglingSens(java.lang.String seq1,
java.lang.String seq2)
seq1 - : String terminal pattern of the sequence (5'3')seq2 - : String terminal pattern of the complementary sequence (3'5')public class BasePair
extends java.lang.Object
| Constructor and Description |
|---|
BasePair(int pos)
To create a BasePair, we need to give the position in the sequence where starts the String TopAcid or BottomAcid.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getBottomAcid()
This method is called to get the nucleic acid "BottomAcid" of BasePair..
|
static java.util.ArrayList<java.lang.String> |
getExistingNucleicAcids()
This method is called to get the existingNucleicAcids of BasePair.
|
int |
getLengthAcid()
This method is called to get the length of the nucleic acid.
|
int |
getPosition()
This method is called to get the position of BasePair in the duplex.
|
java.lang.String |
getTopAcid()
This method is called to get the nucleic acid "TopAcid" of BasePair.
|
static void |
initialiseNucleicAcidList()
initialises the existingNucleicAcids of BasePair.
|
boolean |
isBasePairEqualTo(java.lang.String base1,
java.lang.String base2)
Check if the two nucleic acids of the base pair are (base1, base2) or (base2, base1).
|
boolean |
isBasePairStrictlyEqualTo(java.lang.String base1,
java.lang.String base2)
Check if the two nucleic acids of the base pair are (base1, base2).
|
boolean |
isBottomBasePyrimidine()
Check if the nucleic acid represented by BottomAcid is a pyrimidine.
|
boolean |
isComplementaryBasePair()
To check if the two nucleic acids in the base pair are complementary.
|
boolean |
isComplementaryLockedPair()
To check if the two nucleic acids in the base pair are complementary when one of them is a locked nucleic acid.
|
boolean |
isFrequentNucleicAcidTopBase()
Check if the Nucleic acid TopAcid is a frequent nucleic acid.
|
boolean |
isTopBasePyrimidine()
Check if the nucleic acid represented by TopAcid is a pyrimidine.
|
boolean |
isUnpaired()
To check if the nucleic acids in the base pair are paired.
|
boolean |
isWatsonCrickBottomBase()
Check if the Nucleic acid BottomAcid is a frequent nucleic acid.
|
void |
setBottomAcid(java.lang.String bottomAcid)
To change the BottomAcid Value of BasePair.
|
void |
setTopAcid(java.lang.String topAcid)
To change the TopAcid Value of BasePair..
|
public BasePair(int pos)
pos - : the position of the base pair in the sequence. It is the starting position of the String
TopAcid or BottomAcid in the String sequence.public java.lang.String getTopAcid()
public void setTopAcid(java.lang.String topAcid)
public java.lang.String getBottomAcid()
public void setBottomAcid(java.lang.String bottomAcid)
public boolean isComplementaryBasePair()
public boolean isComplementaryLockedPair()
public boolean isFrequentNucleicAcidTopBase()
public boolean isWatsonCrickBottomBase()
public boolean isTopBasePyrimidine()
public boolean isBottomBasePyrimidine()
public boolean isBasePairEqualTo(java.lang.String base1,
java.lang.String base2)
base1 - : first base (the nucleic acid is represented by a String)base2 - : second base (the nucleic acid is represented by a String)public boolean isBasePairStrictlyEqualTo(java.lang.String base1,
java.lang.String base2)
base1 - : first base (the nucleic acid is represented by a String)base2 - : second base (the nucleic acid is represented by a String)public int getLengthAcid()
public boolean isUnpaired()
public static void initialiseNucleicAcidList()
public static java.util.ArrayList<java.lang.String> getExistingNucleicAcids()
public int getPosition()
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| Class and Description |
|---|
| BasePair
This class represents a base pair of nucleic acids.
|
| NucleotidSequences
This class represents a pair of nucleic acid sequences.
|
| SpecificAcidNames
This enum represents the name of the specific or modified nucleic acid, which can be inosine, locked nucleic acid, hydroxyadenine and azobenzene
|
| Modifier and Type | Method and Description |
|---|---|
NucleotidSequences |
Environment.getSequences()
This method is called to get the sequences NucleotidSequences of Environment.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
PatternComputationMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
PatternComputationMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
| Modifier and Type | Method and Description |
|---|---|
abstract ThermoResult |
PatternComputation.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
PatternComputation.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Broda05CNGRepeats.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Broda05CNGRepeats.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Breslauer86.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Freier86.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Xia98.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto96.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto95.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
CricksNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Tanaka04.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantalucia97.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia96.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Breslauer86.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Freier86.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Xia98.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Sugimoto96.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Sugimoto95.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner06.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
CricksNNMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Tanaka04.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
AllawiSantalucia97.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia96.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Znosko071x2Loop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Znosko071x2Loop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner06InternalLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04InternalLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Turner99_06LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Turner99_06LongBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04LongBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Sugimoto02RNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SugimotoLongDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto02DNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Sugimoto02RNADanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
SugimotoLongDanglingEndMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Sugimoto02DNADanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Serra05DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SecondDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Serra05DoubleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra06DoubleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
SecondDanglingEndMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Tanaka04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99_06SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
GlobalSingleBulgeLoopMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra07SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Tanaka04SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner99_06SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
GlobalSingleBulgeLoopMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra07SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Bommarito00SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06_08SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SingleDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Bommarito00SingleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra06_08SingleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
SingleDanglingEndMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Znosko08mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
ZnoskoMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Watkins11mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
ZnoskoMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Watkins11mm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner06mm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99mm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Sugimoto01Hydroxyadenine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Asanuma05Azobenzene.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
McTigue04LockedAcid.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Sugimoto01Hydroxyadenine.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Asanuma05Azobenzene.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
McTigue04LockedAcid.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Turner99_06tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Turner99_06tanmm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99tanmm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Santalucia05Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
InosineNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra12Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Turner99Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Serra12Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Santalucia05Inosine.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
InosineNNMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner99Wobble.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Znosko07Inosine.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra12Wobble.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
static NucleotidSequences |
NucleotidSequences.buildSymetricSequences(String seq1,
String seq2)
creates a NucleotidSequences with two symmetric sequences String created from the
seq1 String an seq2 String.
|
NucleotidSequences |
NucleotidSequences.getEquivalentSequences(String hybridizationType)
This method is called when the same NucleotidSequences is required but with the sequences converted in the new
hybridization type "hybridizationType"
|
| Constructor and Description |
|---|
NucleotidSequences(String hybridizationType,
NucleotidSequences sequences)
Creates a new NucleotidSequences object from a reference nucleotiDSequences object.
|
| Package | Description |
|---|---|
| melting.sequences |
| Modifier and Type | Method and Description |
|---|---|
ArrayList<BasePair> |
NucleotidSequences.getDuplex()
This method is called to get the duplex of NucleotidSequences.
|
static ArrayList<BasePair> |
NucleotidSequences.getDuplexFrom(String sequence,
String complementary)
This method is called to get the duplex of NucleotidSequences.
|
| Modifier and Type | Method and Description |
|---|---|
SpecificAcidNames |
NucleotidSequences.getModifiedAcidName(BasePair pair)
This method is called to get the name of a specific nucleic acid in the base pair (BasePair object).
|
| Package | Description |
|---|---|
| melting.sequences |
| Modifier and Type | Method and Description |
|---|---|
SpecificAcidNames |
NucleotidSequences.getModifiedAcidName(BasePair pair)
This method is called to get the name of a specific nucleic acid in the base pair (BasePair object).
|
static SpecificAcidNames |
SpecificAcidNames.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static SpecificAcidNames[] |
SpecificAcidNames.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
| Modifier and Type | Method and Description |
|---|---|
static HashMap<String,SpecificAcidNames> |
NucleotidSequences.getModifiedAcidNames()
This method is called to get the modifiedAcidNames of NucleotidSequences.
|
public enum SpecificAcidNames extends java.lang.Enum<SpecificAcidNames>
| Enum Constant and Description |
|---|
azobenzene |
hydroxyadenine |
inosine |
lockedNucleicAcid |
| Modifier and Type | Method and Description |
|---|---|
static SpecificAcidNames |
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static SpecificAcidNames[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final SpecificAcidNames inosine
public static final SpecificAcidNames lockedNucleicAcid
public static final SpecificAcidNames hydroxyadenine
public static final SpecificAcidNames azobenzene
public static SpecificAcidNames[] values()
for (SpecificAcidNames c : SpecificAcidNames.values()) System.out.println(c);
public static SpecificAcidNames valueOf(java.lang.String name)
name - the name of the enum constant to be returned.java.lang.IllegalArgumentException - if this enum type has no constant
with the specified namejava.lang.NullPointerException - if the argument is null| Class | Description |
|---|---|
| BasePair |
This class represents a base pair of nucleic acids.
|
| NucleotidSequences |
This class represents a pair of nucleic acid sequences.
|
| Enum | Description |
|---|---|
| SpecificAcidNames |
This enum represents the name of the specific or modified nucleic acid, which can be inosine, locked nucleic acid, hydroxyadenine and azobenzene
|
public class ThermoResult extends Thermodynamics
enthalpy, entropy| Constructor and Description |
|---|
ThermoResult(double enthalpy,
double entropy,
double Tm)
creates a ThermoResult object initialised with the double enthalpy, double entropy and double Tm.
|
| Modifier and Type | Method and Description |
|---|---|
MeltingComputationMethod |
getCalculMethod()
Gets the calculation method of the
ThermoResult. |
double |
getEnergyValueInJ(double energyValue)
converts the energyValy double in cal/mol into an energy value in J/mol.
|
double |
getSaltIndependentEntropy()
This method is called to get the SaltIndependentEntropy of ThermoResult.
|
double |
getTm()
This method is called to get the Tm of ThermoResult.
|
void |
setCalculMethod(MeltingComputationMethod calculMethod)
Changes the calculation method in the
ThermoResult. |
void |
setSaltIndependentEntropy(double saltIndependentEntropy)
This method is called to change the SaltIndependentEntropy of ThermoResult.
|
void |
setTm(double tm)
This method is called to change the Tm of ThermoResult.
|
getEnthalpy, getEntropy, setEnthalpy, setEntropypublic ThermoResult(double enthalpy,
double entropy,
double Tm)
enthalpy - : the enthalpy valueentropy - : the entropy valueTm - : the melting temperaturepublic double getTm()
public void setTm(double tm)
tm - : the new melting temperaturepublic double getSaltIndependentEntropy()
public void setSaltIndependentEntropy(double saltIndependentEntropy)
SaltIndependentEntropy - : the new salt independent concentration.public MeltingComputationMethod getCalculMethod()
ThermoResult.public void setCalculMethod(MeltingComputationMethod calculMethod)
ThermoResult.calculMethod - : the new calculation method.public double getEnergyValueInJ(double energyValue)
energyValue - : a thermodynamic energy value in cal/mol (enthalpy or entropy)public class OptionSyntaxError
extends java.lang.RuntimeException
| Constructor and Description |
|---|
OptionSyntaxError() |
OptionSyntaxError(java.lang.String message) |
OptionSyntaxError(java.lang.String message,
java.lang.Throwable cause) |
OptionSyntaxError(java.lang.Throwable cause) |
public class ThermodynamicParameterError
extends java.lang.RuntimeException
| Constructor and Description |
|---|
ThermodynamicParameterError() |
ThermodynamicParameterError(java.lang.String message) |
ThermodynamicParameterError(java.lang.String message,
java.lang.Throwable cause) |
ThermodynamicParameterError(java.lang.Throwable cause) |
public ThermodynamicParameterError()
public ThermodynamicParameterError(java.lang.String message,
java.lang.Throwable cause)
public ThermodynamicParameterError(java.lang.Throwable cause)
public ThermodynamicParameterError(java.lang.String message)
public class SequenceException
extends java.lang.RuntimeException
| Constructor and Description |
|---|
SequenceException() |
SequenceException(java.lang.String message) |
SequenceException(java.lang.String message,
java.lang.Throwable cause) |
SequenceException(java.lang.Throwable cause) |
public class NoExistingOutputFileException
extends java.lang.RuntimeException
| Constructor and Description |
|---|
NoExistingOutputFileException() |
NoExistingOutputFileException(java.lang.String message) |
NoExistingOutputFileException(java.lang.String message,
java.lang.Throwable cause) |
NoExistingOutputFileException(java.lang.Throwable cause) |
public NoExistingOutputFileException()
public NoExistingOutputFileException(java.lang.String message,
java.lang.Throwable cause)
public NoExistingOutputFileException(java.lang.Throwable cause)
public NoExistingOutputFileException(java.lang.String message)
public class NucleicAcidNotKnownException
extends java.lang.RuntimeException
| Constructor and Description |
|---|
NucleicAcidNotKnownException() |
NucleicAcidNotKnownException(java.lang.String message) |
NucleicAcidNotKnownException(java.lang.String message,
java.lang.Throwable cause) |
NucleicAcidNotKnownException(java.lang.Throwable cause) |
public NucleicAcidNotKnownException()
public NucleicAcidNotKnownException(java.lang.String message,
java.lang.Throwable cause)
public NucleicAcidNotKnownException(java.lang.Throwable cause)
public NucleicAcidNotKnownException(java.lang.String message)
| Exception | Description |
|---|---|
| FileException |
This class represents an exception raised by a parameters file or another Melting file.
|
| MethodNotApplicableException |
This class represents an exception for a method or model which is not applicable.
|
| NoExistingMethodException |
This class represents an exception for a method or model which doesn't exist.
|
| NoExistingOutputFileException |
This class represents an exception for an output file which doesn't exist.
|
| NucleicAcidNotKnownException |
This class represents an exception for a nucleic acid which is not known by Melting.
|
| OptionSyntaxError |
This class represents an exception raised by an option syntax error.
|
| SequenceException |
This class represents a problem within the sequences.
|
| ThermodynamicParameterError |
This class represents a problem with the thermodynamic parameters.
|
public class FileException
extends java.lang.RuntimeException
| Constructor and Description |
|---|
FileException() |
FileException(java.lang.String message) |
FileException(java.lang.String message,
java.lang.Throwable cause) |
FileException(java.lang.Throwable cause) |
public class MethodNotApplicableException
extends java.lang.RuntimeException
| Constructor and Description |
|---|
MethodNotApplicableException() |
MethodNotApplicableException(java.lang.String message) |
MethodNotApplicableException(java.lang.String message,
java.lang.Throwable cause) |
MethodNotApplicableException(java.lang.Throwable cause) |
public MethodNotApplicableException(java.lang.String message)
public MethodNotApplicableException()
public MethodNotApplicableException(java.lang.String message,
java.lang.Throwable cause)
public MethodNotApplicableException(java.lang.Throwable cause)
public class NoExistingMethodException
extends java.lang.RuntimeException
| Constructor and Description |
|---|
NoExistingMethodException() |
NoExistingMethodException(java.lang.String message) |
NoExistingMethodException(java.lang.String message,
java.lang.Throwable cause) |
NoExistingMethodException(java.lang.Throwable cause) |
public NoExistingMethodException()
public NoExistingMethodException(java.lang.String message,
java.lang.Throwable cause)
public NoExistingMethodException(java.lang.Throwable cause)
public NoExistingMethodException(java.lang.String message)
public class Environment
extends java.lang.Object
| Constructor and Description |
|---|
Environment(java.util.HashMap<java.lang.String,java.lang.String> options)
creates an Environment object from the different options (default options and options entered by the user).
|
| Modifier and Type | Method and Description |
|---|---|
void |
addResult(double enthalpy,
double entropy)
increments the ThermoResult enthalpy and ThermoResult entropy of Environment.
|
java.util.HashMap<java.lang.String,java.lang.Double> |
getConcentrations()
This method is called to get the concentrations of Environment.
|
double |
getDMSO()
This method is called to get the DMSO concentration.
|
double |
getDNTP()
This method is called to get the dNTP concentration.
|
int |
getFactor()
This method is called to get the factor of Environment.
|
double |
getFormamide()
This method is called to get the formamide concentration.
|
java.lang.String |
getHybridization()
This method is called to get the hybridization of Environment.
|
double |
getK()
This method is called to get the potassium concentration.
|
double |
getMg()
This method is called to get the magnesium concentration.
|
double |
getNa()
This method is called to get the sodium concentration.
|
double |
getNucleotides()
This method is called to get the oligomerConcentration of Environment.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getOptions()
This method is called to get the HashMap options of Environment.
|
ThermoResult |
getResult()
This method is called to get the ThermoResult of Environment.
|
NucleotidSequences |
getSequences()
This method is called to get the sequences NucleotidSequences of Environment.
|
double |
getTris()
This method is called to get the Tris buffer concentration.
|
boolean |
isSelfComplementarity()
To check if the sequences are self complementary.
|
void |
setFactor(int factor)
changes the factor value of Environment.
|
void |
setMg(double Mg)
changes the magnesium concentration in the environment
|
void |
setNa(double na)
changes the sodium concentration in the environment
|
void |
setResult(double temperature)
changes the melting temperature of ThermoResult.
|
void |
setResult(ThermoResult result)
changes the result ThermoResult of Environment.
|
void |
setSelfComplementarity(boolean b)
changes the boolean value of the isSelfComplementarity boolean.
|
void |
sortSquences(java.lang.String hybridization,
java.lang.String firstSequence,
java.lang.String secondSequence)
sorts the sequences in function of the type of hybridization : In case of DNA/RNA type of hybridization, the sequence (5'3') must be a DNA sequence
and the complementary sequence (3'5') a RNA sequence.
|
public Environment(java.util.HashMap<java.lang.String,java.lang.String> options)
options - : contains the options (default options and options entered by the user)public void sortSquences(java.lang.String hybridization,
java.lang.String firstSequence,
java.lang.String secondSequence)
hybridization - : type of hybridization. Precise the nature of each sequence (DNA, RNA or mRNA)firstSequence - : sequence (5'3')secondSequence - : complementary sequence (3'5')public int getFactor()
public void setFactor(int factor)
factor - : new factor valuepublic ThermoResult getResult()
public NucleotidSequences getSequences()
public double getNucleotides()
public boolean isSelfComplementarity()
public void setSelfComplementarity(boolean b)
b - public java.lang.String getHybridization()
public java.util.HashMap<java.lang.String,java.lang.String> getOptions()
public double getNa()
public double getMg()
public void setMg(double Mg)
Mg - : new magnesium concentrationpublic double getTris()
public double getK()
public java.util.HashMap<java.lang.String,java.lang.Double> getConcentrations()
public double getDMSO()
public double getFormamide()
public void setNa(double na)
Na - : new sodium concentrationpublic void addResult(double enthalpy,
double entropy)
enthalpy - : enthalpy incrementation valueentropy - : entropy incrementation valuepublic void setResult(double temperature)
temperature - : new melting temperaturepublic void setResult(ThermoResult result)
result - : new ThermoResult object.public double getDNTP()
public class OptionManagement
extends java.lang.Object
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
approximativeMode
Option name for the choice of approximative computation method.
|
static java.lang.String |
azobenzeneMethod
Option name for the choice of azobenzene computation method.
|
static java.lang.String |
CNGMethod
Option name for the choice of CNG repeats computation method.
|
static java.lang.String |
complementarySequence
Option name for the complementary sequence (3'5').
|
static java.lang.String |
dataPathway
Option name for the default melting data files pathway.
|
static java.lang.String |
dataPathwayValue
String dataPathwayValue : default Melting data file pathway.
|
static java.lang.String |
DMSOCorrection
Option name for the choice of DMSO correction computation method.
|
static java.lang.String |
doubleDanglingEndMethod
Option name for the choice of double dangling end computation method.
|
static java.lang.String |
factor
Option name for the oligomer concentration correction factor.
|
static java.lang.String |
formamideCorrection
Option name for the choice of formamide correction computation method.
|
static java.lang.String |
globalMethod
Option name for the choice of computation method (approximative "-A" or nearest neighbor "-NN").
|
static java.lang.String |
hybridization
Option name for the type of hybridization.
|
static java.lang.String |
hydroxyadenineMethod
Option name for the choice of hydroxyadenine computation method.
|
static java.lang.String |
inosineMethod
Option name for the choice of inosine computation method.
|
static java.lang.String |
internalLoopMethod
Option name for the choice of internal loop computation method.
|
static java.lang.String |
ionCorrection
Option name for the choice of ion correction method.
|
static java.lang.String |
legalInformation
Option name for the melting legal information.
|
static java.lang.String |
lockedAcidMethod
Option name for the choice of locked nucleic acid computation method.
|
static java.lang.String |
lockedAcidSingleMismatchMethod
Option name for the choice of locked nucleic acid with single mismatch computation method.
|
static java.lang.String |
longBulgeLoopMethod
Option name for the choice of long bulge loop computation method.
|
static java.lang.String |
longDanglingEndMethod
Option name for the choice of long dangling end computation method.
|
static java.lang.String |
meltingHelp
Option name for the melting help documentation.
|
static java.lang.String |
meltingHelpAlt
Alternative option name for the melting help documentation.
|
static java.lang.String |
NaEquivalentMethod
Option name for the choice of sodium equivalence method.
|
static java.lang.String |
NN_Path
Option name for the data file pathway.
|
static java.lang.String |
NNMethod
Option name for the choice of nearest neighbor computation method.
|
static java.lang.String |
nucleotides
Option name for the oligomer concentration (mol/L).
|
static java.lang.String |
outPutFile
Option name to print the melting results in an output file.
|
static java.lang.String |
selfComplementarity
Option name to precise the self complementarity of the sequences.
|
static java.lang.String |
sequence
Option name for the sequence (5'3').
|
static java.lang.String |
singleBulgeLoopMethod
Option name for the choice of single bulge loop computation method.
|
static java.lang.String |
singleDanglingEndMethod
Option name for the choice of single dangling end computation method.
|
static java.lang.String |
singleMismatchMethod
Option name for the choice of single mismatch computation method.
|
static java.lang.String |
solutioncomposition
Option name for the different ion and agent concentrations (mol/L).
|
static java.lang.String |
tandemLockedAcidMethod
Option name for the choice of tandem locked nucleic acid computation method.
|
static java.lang.String |
tandemMismatchMethod
Option name for the choice of tandem mismatches computation method.
|
static java.lang.String |
threshold
Option name for the threshold value.
|
static java.lang.String |
verboseMode
Option name to activate the verbose mode.
|
static java.lang.String |
versionNumber
Option name for the current melting version number.
|
static java.lang.String |
wobbleBaseMethod
Option name for the choice of GU base pairs computation method.
|
| Constructor and Description |
|---|
OptionManagement()
creates an OptionManagement object.
|
| Modifier and Type | Method and Description |
|---|---|
Environment |
createEnvironment(java.lang.String[] args)
collects the options entered by the user and creates an Environment from them.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getDNADefaultOptions()
This method is called to get the DNADefaultOptions of OptionManagement.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getHybridDefaultOptions()
This method is called to get the hybridDefaultOptions of OptionManagement.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getMRNADefaultOptions()
This method is called to get the mRNADefaultOptions of OptionManagement.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getRNADefaultOptions()
This method is called to get the RNADefaultOptions of OptionManagement.
|
void |
initialiseLogger()
initialises the meltingLogger.
|
boolean |
isMeltingInformationOption(java.lang.String[] args)
to check if the user just wants to know some information about melting.
|
static void |
logError(java.lang.String errorText)
Logs an error to the melting logger.
|
static void |
logError(java.lang.String errorText,
java.lang.Throwable throwable)
Logs an error message to the melting logger, along with the error itself.
|
static void |
logFileName(java.lang.String fileName)
Logs a file name to the melting logger.
|
static void |
logInfo(java.lang.String infoText)
Logs information to the melting logger.
|
static void |
logMessage(java.lang.String messageText)
Logs a message to the melting logger.
|
static void |
logMethodName(java.lang.String methodName)
Logs the name of a method to the melting logger.
|
static void |
logTemperatureEquation(java.lang.String temperatureEquation)
Logs a temperature equation to the melting logger.
|
static void |
logWarning(java.lang.String warningText)
Logs a warning to the melting logger.
|
void |
readMeltingHelp()
displays Melting help documentation.
|
void |
readOptions(java.lang.String[] args)
if at least one of the options entered by the user is an option to display some information about Melting,
the requested information is displayed.
|
public static final java.lang.String meltingHelp
public static final java.lang.String meltingHelpAlt
public static final java.lang.String legalInformation
public static final java.lang.String dataPathway
public static final java.lang.String versionNumber
public static final java.lang.String globalMethod
public static final java.lang.String approximativeMode
public static final java.lang.String NNMethod
public static final java.lang.String singleMismatchMethod
public static final java.lang.String wobbleBaseMethod
public static final java.lang.String tandemMismatchMethod
public static final java.lang.String internalLoopMethod
public static final java.lang.String singleDanglingEndMethod
public static final java.lang.String doubleDanglingEndMethod
public static final java.lang.String longDanglingEndMethod
public static final java.lang.String singleBulgeLoopMethod
public static final java.lang.String longBulgeLoopMethod
public static final java.lang.String CNGMethod
public static final java.lang.String inosineMethod
public static final java.lang.String hydroxyadenineMethod
public static final java.lang.String azobenzeneMethod
public static final java.lang.String lockedAcidMethod
public static final java.lang.String tandemLockedAcidMethod
public static final java.lang.String lockedAcidSingleMismatchMethod
public static final java.lang.String sequence
public static final java.lang.String complementarySequence
public static final java.lang.String solutioncomposition
public static final java.lang.String nucleotides
public static final java.lang.String hybridization
public static final java.lang.String ionCorrection
public static final java.lang.String NaEquivalentMethod
public static final java.lang.String DMSOCorrection
public static final java.lang.String formamideCorrection
public static final java.lang.String verboseMode
public static final java.lang.String threshold
public static final java.lang.String NN_Path
public static final java.lang.String outPutFile
public static final java.lang.String selfComplementarity
public static final java.lang.String factor
public static java.lang.String dataPathwayValue
public OptionManagement()
public void readMeltingHelp()
public void initialiseLogger()
public java.util.HashMap<java.lang.String,java.lang.String> getDNADefaultOptions()
public java.util.HashMap<java.lang.String,java.lang.String> getRNADefaultOptions()
public java.util.HashMap<java.lang.String,java.lang.String> getHybridDefaultOptions()
public java.util.HashMap<java.lang.String,java.lang.String> getMRNADefaultOptions()
public boolean isMeltingInformationOption(java.lang.String[] args)
args - : contains the options entered by the userpublic void readOptions(java.lang.String[] args)
args - : contains the option entered by the userpublic Environment createEnvironment(java.lang.String[] args)
args - : contains the options entered by the userpublic static void logError(java.lang.String errorText)
errorText - The text of the error.public static void logError(java.lang.String errorText,
java.lang.Throwable throwable)
errorText - The text of the error.throwable - The error itself.public static void logWarning(java.lang.String warningText)
warningText - The text of the warning.public static void logInfo(java.lang.String infoText)
infoText - The information to log.public static void logMessage(java.lang.String messageText)
messageText - The text of the message.public static void logMethodName(java.lang.String methodName)
methodName - The method name.public static void logFileName(java.lang.String fileName)
fileName - The file name to log.public static void logTemperatureEquation(java.lang.String temperatureEquation)
temperatureEquation - The temperature equation to log.| Package | Description |
|---|---|
| melting | |
| melting.approximativeMethods | |
| melting.configuration | |
| melting.methodInterfaces | |
| melting.nearestNeighborModel |
| Class and Description |
|---|
| OptionManagement
This class contains all the methods necessary to manage the options entered by the user.
|
| Class and Description |
|---|
| RegisterMethods
This class registers all the methods and models implemented by Melting.
|
| Class and Description |
|---|
| MethodText
The text representations corresponding to a method used in melting
temperature computation.
|
| RegisterMethods.MethodType
Represents a particular type of method (e.g., approximative method,
double dangling end method, Mg/Na mix correction method).
|
| Class and Description |
|---|
| RegisterMethods
This class registers all the methods and models implemented by Melting.
|
| Class and Description |
|---|
| RegisterMethods
This class registers all the methods and models implemented by Melting.
|
| Package | Description |
|---|---|
| melting |
| Modifier and Type | Method and Description |
|---|---|
static ThermoResult |
Main.getMeltingResults(String[] args,
OptionManagement optionManager)
Compute the entropy, enthalpy and melting temperature, and return
these results.
|
| Package | Description |
|---|---|
| melting.approximativeMethods | |
| melting.methodInterfaces | |
| melting.nearestNeighborModel |
| Modifier and Type | Field and Description |
|---|---|
protected RegisterMethods |
ApproximativeMode.register
RegisterMethods register : registers all the pattern computation methods implemented by Melting
|
| Modifier and Type | Method and Description |
|---|---|
RegisterMethods |
ApproximativeMode.getRegister() |
| Modifier and Type | Method and Description |
|---|---|
RegisterMethods |
MeltingComputationMethod.getRegister()
This method is called to get the RegisterMethod of the implemented class.
|
| Modifier and Type | Method and Description |
|---|---|
RegisterMethods |
NearestNeighborMode.getRegister() |
public class MethodText
extends java.lang.Object
| Constructor and Description |
|---|
MethodText(java.lang.String methodName,
java.lang.String methodCommandLineFlag)
Sets up the method name and command line flag.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getMethodCommandLineFlag()
Gets the method command line flag.
|
java.lang.String |
getMethodName()
Gets the method name.
|
public class RegisterMethods
extends java.lang.Object
| Modifier and Type | Class and Description |
|---|---|
static class |
RegisterMethods.MethodType
Represents a particular type of method (e.g., approximative method,
double dangling end method, Mg/Na mix correction method).
|
| Constructor and Description |
|---|
RegisterMethods()
creates a RegisterMethods object with the different initialised HasMaps.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeOtherMeltingCorrections(Environment environment)
corrects the melting temperature if other agents are present in the solution (formamide, DMSO, ...)
|
CorrectionMethod |
getCorrectionMethod(java.lang.String optionName,
java.lang.String methodName)
This method is called to get the CorrectionMethod which represents the method 'methodName'
entered with the option 'optionName'.
|
CorrectionMethod |
getIonCorrectionMethod(Environment environment)
This method is called to get the CorrectionMethod which represents the method or model
used for the ion correction in the environment 'environment'.
|
MeltingComputationMethod |
getMeltingComputationMethod(java.util.HashMap<java.lang.String,java.lang.String> optionSet)
This method is called to get the MeltingComputationMethod which represents the method or model
for the enthalpy, entropy and melting temperature computation in the HashMap 'optionSet'.
|
RegisterMethods.MethodType |
getMethodType()
Gets an instance of the
MethodType enum from the current
instance of RegisterMethods. |
SodiumEquivalentMethod |
getNaEqMethod(java.util.HashMap<java.lang.String,java.lang.String> optionSet)
This method is called to get the SodiumEquivalentMethod which represents the method or model
for the sodium equivalence in the HashMap 'optionSet'.
|
PatternComputationMethod |
getPatternComputationMethod(java.lang.String optionName,
java.lang.String methodName)
This method is called to get the PatternComputationMethod which represents the method 'methodName'
entered with the option 'optionName'.
|
static RegisterMethods.MethodType |
makeMethodList()
Creates an instance of the
MethodType enum, initialized with
all the (non-final) methods from the RegisterMethods class. |
public RegisterMethods()
public PatternComputationMethod getPatternComputationMethod(java.lang.String optionName, java.lang.String methodName)
optionName - : option namemethodName - : method or model namepublic SodiumEquivalentMethod getNaEqMethod(java.util.HashMap<java.lang.String,java.lang.String> optionSet)
optionSet - : contains the options (default options and options entered by the user)public CorrectionMethod getIonCorrectionMethod(Environment environment)
environment - public MeltingComputationMethod getMeltingComputationMethod(java.util.HashMap<java.lang.String,java.lang.String> optionSet)
optionSet - : contains the options (default options and options entered by the user)public CorrectionMethod getCorrectionMethod(java.lang.String optionName, java.lang.String methodName)
optionName - : option namemethodName - : method or model namepublic ThermoResult computeOtherMeltingCorrections(Environment environment)
environment - public RegisterMethods.MethodType getMethodType()
MethodType enum from the current
instance of RegisterMethods.MethodType enum, with non-final
values filled in.public static RegisterMethods.MethodType makeMethodList()
MethodType enum, initialized with
all the (non-final) methods from the RegisterMethods class.MethodType enum, with non-final
values filled in.| Class | Description |
|---|---|
| MethodText |
The text representations corresponding to a method used in melting
temperature computation.
|
| OptionManagement |
This class contains all the methods necessary to manage the options entered by the user.
|
| RegisterMethods |
This class registers all the methods and models implemented by Melting.
|
| Enum | Description |
|---|---|
| RegisterMethods.MethodType |
Represents a particular type of method (e.g., approximative method,
double dangling end method, Mg/Na mix correction method).
|
public static enum RegisterMethods.MethodType extends java.lang.Enum<RegisterMethods.MethodType>
| Modifier and Type | Method and Description |
|---|---|
java.util.ArrayList<MethodText> |
getMethodTextList()
Gets a list of the text representations of methods of this type.
|
static RegisterMethods.MethodType |
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static RegisterMethods.MethodType[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final RegisterMethods.MethodType NA_EQUATION
public static final RegisterMethods.MethodType APPROXIMATIVE
public static final RegisterMethods.MethodType CRICKS
public static final RegisterMethods.MethodType SINGLE_MISMATCH
public static final RegisterMethods.MethodType TANDEM_MISMATCH
public static final RegisterMethods.MethodType WOBBLE
public static final RegisterMethods.MethodType INTERNAL_LOOP
public static final RegisterMethods.MethodType SINGLE_BULGE_LOOP
public static final RegisterMethods.MethodType LONG_BULGE_LOOP
public static final RegisterMethods.MethodType SINGLE_DANGLING_END
public static final RegisterMethods.MethodType DOUBLE_DANGLING_END
public static final RegisterMethods.MethodType LONG_DANGLING_END
public static final RegisterMethods.MethodType INOSINE
public static final RegisterMethods.MethodType CNG_REPEATS
public static final RegisterMethods.MethodType AZOBENZENE
public static final RegisterMethods.MethodType LOCKED_ACID
public static final RegisterMethods.MethodType TANDEM_LOCKED_ACID
public static final RegisterMethods.MethodType LOCKED_ACID_SINGLE_MISMATCH
public static final RegisterMethods.MethodType HYDROXYADENOSINE
public static final RegisterMethods.MethodType ION_CORRECTION
public static final RegisterMethods.MethodType DMSO_CORRECTION
public static final RegisterMethods.MethodType FORMAMIDE_CORRECTION
public static final RegisterMethods.MethodType OTHER_CORRECTION
public static RegisterMethods.MethodType[] values()
for (RegisterMethods.MethodType c : RegisterMethods.MethodType.values()) System.out.println(c);
public static RegisterMethods.MethodType valueOf(java.lang.String name)
name - the name of the enum constant to be returned.java.lang.IllegalArgumentException - if this enum type has no constant
with the specified namejava.lang.NullPointerException - if the argument is nullpublic java.util.ArrayList<MethodText> getMethodTextList()
public class Owczarzy08MagnesiumCorrection extends java.lang.Object implements CorrectionMethod, NamedMethod
| Modifier and Type | Field and Description |
|---|---|
protected double |
a |
protected double |
b |
protected double |
c |
protected double |
d |
protected double |
e |
protected double |
f |
protected double |
g |
protected static java.lang.String |
temperatureCorrection
temperature formula
|
| Constructor and Description |
|---|
Owczarzy08MagnesiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
protected double |
correctTemperature(Environment environment)
corrects the computed melting temperature depending on the environment.
|
protected void |
displayVariable()
logs the a, d and g variables.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
protected double a
protected double b
protected double c
protected double d
protected double e
protected double f
protected double g
protected static java.lang.String temperatureCorrection
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodprotected double correctTemperature(Environment environment)
environment - protected void displayVariable()
public java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.ionCorrection.mixedNaMgCorrections |
| Class and Description |
|---|
| Owczarzy08MagnesiumCorrection
This class represents the magnesium correction model owc08.
|
public class Tan06MagnesiumCorrection extends EntropyCorrection implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
protected static java.lang.String |
aFormula |
protected static java.lang.String |
bFormula |
protected static java.lang.String |
entropyCorrection
String entropyCorrection : formula for the entropy correction
|
protected static java.lang.String |
gFormula
String gFormula : function associated with the electrostatic folding free energy per base stack.
|
| Constructor and Description |
|---|
Tan06MagnesiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
static double |
computeFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
correctMeltingResultsprotected static java.lang.String entropyCorrection
protected static java.lang.String aFormula
protected static java.lang.String bFormula
protected static java.lang.String gFormula
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodisApplicable in class EntropyCorrectionprotected double correctEntropy(Environment environment)
EntropyCorrectioncorrectEntropy in class EntropyCorrectionpublic static double computeFreeEnergyPerBaseStack(Environment environment)
environment - public java.lang.String getName()
getName in interface NamedMethodpublic class Tan07MagnesiumCorrection extends EntropyCorrection implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
protected static java.lang.String |
aFormula |
protected static java.lang.String |
bFormula |
protected static java.lang.String |
entropyCorrection
String entropyCorrection : formula for the entropy correction
|
protected static java.lang.String |
gFormula
String gFormula : function associated with the electrostatic folding free energy per base stack.
|
| Constructor and Description |
|---|
Tan07MagnesiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
static double |
computeFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
correctMeltingResultsprotected static java.lang.String entropyCorrection
protected static java.lang.String aFormula
protected static java.lang.String bFormula
protected static java.lang.String gFormula
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodisApplicable in class EntropyCorrectionprotected double correctEntropy(Environment environment)
EntropyCorrectioncorrectEntropy in class EntropyCorrectionpublic static double computeFreeEnergyPerBaseStack(Environment environment)
environment - public java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.ionCorrection.mixedNaMgCorrections |
| Modifier and Type | Class and Description |
|---|---|
class |
Owczarzy08MixedNaMgCorrection
This class represents the mixed (Na,Mg) correction model owcmix08.
|
| Class | Description |
|---|---|
| Owczarzy08MagnesiumCorrection |
This class represents the magnesium correction model owc08.
|
| Tan06MagnesiumCorrection |
This class represents the magnesium correction model tanmg06.
|
| Tan07MagnesiumCorrection |
This class represents the magnesium correction model tanmg07.
|
public class Ahsen01_NaEquivalent extends SodiumEquivalent implements NamedMethod
| Constructor and Description |
|---|
Ahsen01_NaEquivalent() |
| Modifier and Type | Method and Description |
|---|---|
double |
computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
This method is called to convert an initial sodium concentration in a new equivalent sodium concentration
which takes in account the other cation concentrations.
|
java.lang.String |
getName()
Gets the full name of the method.
|
getSodiumEquivalent, isApplicablepublic double computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
SodiumEquivalentMethodcomputeSodiumEquivalent in interface SodiumEquivalentMethodNa - : sodium concentration entered by the userMg - : magnesium concentration entered by the userK - : potassium concentration entered by the userTris - : Tris buffer concentration entered by the user.dNTP - : dNTP concentration entered by the userpublic java.lang.String getName()
getName in interface NamedMethodpublic class Mitsuhashi96NaEquivalent extends SodiumEquivalent implements NamedMethod
| Constructor and Description |
|---|
Mitsuhashi96NaEquivalent() |
| Modifier and Type | Method and Description |
|---|---|
double |
computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
This method is called to convert an initial sodium concentration in a new equivalent sodium concentration
which takes in account the other cation concentrations.
|
java.lang.String |
getName()
Gets the full name of the method.
|
getSodiumEquivalent, isApplicablepublic double computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
SodiumEquivalentMethodcomputeSodiumEquivalent in interface SodiumEquivalentMethodNa - : sodium concentration entered by the userMg - : magnesium concentration entered by the userK - : potassium concentration entered by the userTris - : Tris buffer concentration entered by the user.dNTP - : dNTP concentration entered by the userpublic java.lang.String getName()
getName in interface NamedMethodpublic class Peyret00_NaEquivalent extends SodiumEquivalent implements NamedMethod
| Constructor and Description |
|---|
Peyret00_NaEquivalent() |
| Modifier and Type | Method and Description |
|---|---|
double |
computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
This method is called to convert an initial sodium concentration in a new equivalent sodium concentration
which takes in account the other cation concentrations.
|
java.lang.String |
getName()
Gets the full name of the method.
|
getSodiumEquivalent, isApplicablepublic double computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
SodiumEquivalentMethodcomputeSodiumEquivalent in interface SodiumEquivalentMethodNa - : sodium concentration entered by the userMg - : magnesium concentration entered by the userK - : potassium concentration entered by the userTris - : Tris buffer concentration entered by the user.dNTP - : dNTP concentration entered by the userpublic java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.ionCorrection.sodiumEquivalence |
| Class and Description |
|---|
| SodiumEquivalent
This class represents the methods to compute a sodium equivalence.
|
public abstract class SodiumEquivalent extends java.lang.Object implements SodiumEquivalentMethod
| Constructor and Description |
|---|
SodiumEquivalent() |
| Modifier and Type | Method and Description |
|---|---|
double |
getSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP,
double b)
This method is called to get a sodium equivalent concentration when other cations are present.
|
boolean |
isApplicable(java.util.HashMap<java.lang.String,java.lang.String> options)
Check if the model to compute an equivalent sodium cencentration is applicable with the options entered by the user.
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitcomputeSodiumEquivalentpublic boolean isApplicable(java.util.HashMap<java.lang.String,java.lang.String> options)
SodiumEquivalentMethodisApplicable in interface SodiumEquivalentMethodoptions - which contains the options. (default options and options entered by the user)public double getSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP,
double b)
Na - : sodium concentrationMg - : magnesium concentrationK - : potassium concentrationTris - : Tris buffer concentrationdNTP - : dNTP concentrationb - : a formula parameter depending on the model.| Package | Description |
|---|---|
| melting.ionCorrection.sodiumEquivalence |
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01_NaEquivalent
This class represents the model for a sodium equivalence ahs01.
|
class |
Mitsuhashi96NaEquivalent
This class represents the model for a sodium equivalence mit96.
|
class |
Peyret00_NaEquivalent
This class represents the model for a sodium equivalence pey00.
|
| Class | Description |
|---|---|
| Ahsen01_NaEquivalent |
This class represents the model for a sodium equivalence ahs01.
|
| Mitsuhashi96NaEquivalent |
This class represents the model for a sodium equivalence mit96.
|
| Peyret00_NaEquivalent |
This class represents the model for a sodium equivalence pey00.
|
| SodiumEquivalent |
This class represents the methods to compute a sodium equivalence.
|
public class Tan07MixedNaMgCorrection extends EntropyCorrection implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
protected static java.lang.String |
entropyCorrection
String entropyCorrection : formula for the entropy correction
|
protected static java.lang.String |
gFormula
String gFormula : function associated with the electrostatic folding free energy per base stack.
|
protected static java.lang.String |
x1Formula
String x1Formula : formula representing the fractional contribution of Na+ ions
|
protected static java.lang.String |
x2Formula
String x2Formula : formula representing the fractional contribution of Mg2+ ions
|
| Constructor and Description |
|---|
Tan07MixedNaMgCorrection() |
| Modifier and Type | Method and Description |
|---|---|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
correctMeltingResultsprotected static java.lang.String entropyCorrection
protected static java.lang.String x1Formula
protected static java.lang.String x2Formula
protected static java.lang.String gFormula
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodisApplicable in class EntropyCorrectionprotected double correctEntropy(Environment environment)
EntropyCorrectioncorrectEntropy in class EntropyCorrectionpublic java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| Owczarzy08MixedNaMgCorrection |
This class represents the mixed (Na,Mg) correction model owcmix08.
|
| Tan07MixedNaMgCorrection |
This class represents the mixed (Na,Mg) correction model tanmix07.
|
public class Owczarzy08MixedNaMgCorrection extends Owczarzy08MagnesiumCorrection implements NamedMethod
a, b, c, d, e, f, g, temperatureCorrection| Constructor and Description |
|---|
Owczarzy08MixedNaMgCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
protected void |
displayVariable()
logs the a, d and g variables.
|
java.lang.String |
getName()
Gets the full name of the method.
|
correctTemperature, isApplicablepublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodcorrectMeltingResults in class Owczarzy08MagnesiumCorrectionprotected void displayVariable()
Owczarzy08MagnesiumCorrectiondisplayVariable in class Owczarzy08MagnesiumCorrectionpublic java.lang.String getName()
getName in interface NamedMethodgetName in class Owczarzy08MagnesiumCorrectionpublic class Tan07SodiumCorrection extends EntropyCorrection implements NamedMethod
| Constructor and Description |
|---|
Tan07SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
static double |
calculateFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodisApplicable in class EntropyCorrectionpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodcorrectMeltingResults in class EntropyCorrectionprotected double correctEntropy(Environment environment)
EntropyCorrectioncorrectEntropy in class EntropyCorrectionpublic static double calculateFreeEnergyPerBaseStack(Environment environment)
environment - public java.lang.String getName()
getName in interface NamedMethodpublic class SchildkrautLifson65SodiumCorrection extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
SchildkrautLifson65SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Tan06SodiumCorrection extends EntropyCorrection implements NamedMethod
| Constructor and Description |
|---|
Tan06SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
static double |
calculateFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodisApplicable in class EntropyCorrectionpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodcorrectMeltingResults in class EntropyCorrectionprotected double correctEntropy(Environment environment)
EntropyCorrectioncorrectEntropy in class EntropyCorrectionpublic static double calculateFreeEnergyPerBaseStack(Environment environment)
environment - public java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia98_04SodiumCorrection extends EntropyCorrection implements NamedMethod
| Constructor and Description |
|---|
Santalucia98_04SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodisApplicable in class EntropyCorrectionpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodcorrectMeltingResults in class EntropyCorrectionprotected double correctEntropy(Environment environment)
EntropyCorrectioncorrectEntropy in class EntropyCorrectionpublic java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia96SodiumCorrection extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
Santalucia96SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class FrankKamenetskii71SodiumCorrection extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
FrankKamenetskii71SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| Ahsen01SodiumCorrection |
This class represents the sodium correction model ahs01.
|
| FrankKamenetskii71SodiumCorrection |
This class represents the sodium correction model kam71.
|
| MarmurSchildkrautDoty98_62SodiumCorrection |
This class represents the sodium correction model marschdot.
|
| Owczarzy04SodiumCorrection19 |
This class represents the sodium correction model owc1904.
|
| Owczarzy04SodiumCorrection20 |
This class represents the sodium correction model owc2004.
|
| Owczarzy04SodiumCorrection21 |
This class represents the sodium correction model owc2104.
|
| Owczarzy04SodiumCorrection22 |
This class represents the sodium correction model owc2204.
|
| Santalucia96SodiumCorrection |
This class represents the sodium correction model san96.
|
| Santalucia98_04SodiumCorrection |
This class represents the sodium correction model san04.
|
| SchildkrautLifson65SodiumCorrection |
This class represents the sodium correction model schlif.
|
| Tan06SodiumCorrection |
This class represents the sodium correction model tanna06.
|
| Tan07SodiumCorrection |
This class represents the sodium correction model tanna07.
|
| Wetmur91SodiumCorrection |
This class represents the sodium correction model wet91.
|
public class Owczarzy04SodiumCorrection20 extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
Owczarzy04SodiumCorrection20() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Owczarzy04SodiumCorrection22 extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
Owczarzy04SodiumCorrection22() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Owczarzy04SodiumCorrection21 extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
Owczarzy04SodiumCorrection21() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Owczarzy04SodiumCorrection19 extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
Owczarzy04SodiumCorrection19() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Wetmur91SodiumCorrection extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
Wetmur91SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class MarmurSchildkrautDoty98_62SodiumCorrection extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
MarmurSchildkrautDoty98_62SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public MarmurSchildkrautDoty98_62SodiumCorrection()
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Ahsen01SodiumCorrection extends EntropyCorrection implements NamedMethod
| Constructor and Description |
|---|
Ahsen01SodiumCorrection() |
| Modifier and Type | Method and Description |
|---|---|
protected double |
correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
correctMeltingResultspublic boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodisApplicable in class EntropyCorrectionprotected double correctEntropy(Environment environment)
EntropyCorrectioncorrectEntropy in class EntropyCorrectionpublic java.lang.String getName()
getName in interface NamedMethod| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| Thermodynamics
This class represents the thermodynamic energy.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Thermodynamics
This class represents the thermodynamic energy.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| DataCollect
This class is useful to extract the different thermodynamic parameters from the HashMap which contains them.
|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| DataCollect
This class is useful to extract the different thermodynamic parameters from the HashMap which contains them.
|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| Environment
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| ThermoResult
This class extends Thermodynamics.
|
| Class and Description |
|---|
| ThermoResult
This class extends Thermodynamics.
|
public class DataCollect
extends java.lang.Object
| Constructor and Description |
|---|
DataCollect() |
| Modifier and Type | Method and Description |
|---|---|
void |
addData(java.util.HashMap<java.lang.String,Thermodynamics> parameters)
add all of the mappings from the specified HashMap to the data of DataCollect.
|
Thermodynamics |
getAsymmetry()
to get the Thermodynamics object containing the parameters for the internal loop asymmetry.
|
Thermodynamics |
getAzobenzeneValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing an
azobenzene ("X_C" or "X_T").
|
Thermodynamics |
getBonus(java.lang.String base1,
java.lang.String lastBase,
java.lang.String seqLoop,
java.lang.String type)
to get the Thermodynamics object containing the parameters for a Hairpin loop 'seqLoop' preceded
by the base 'base1' and followed by the base 'lastBase'.
|
Thermodynamics |
getBulgeLoopvalue(java.lang.String size)
to get the Thermodynamics object containing the parameters for a bulge loop of size 'size'.
|
Thermodynamics |
getClosureValue(java.lang.String base1,
java.lang.String base2)
to get the Thermodynamics object containing the parameters for the base pair (base1, base2) next to the mismatching base pair.
|
Thermodynamics |
getCNGvalue(java.lang.String repeats,
java.lang.String seq1)
to get the Thermodynamics object containing the parameters for the CNG pattern 'seq1'.
|
Thermodynamics |
getDanglingValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2.
|
java.util.HashMap<java.lang.String,Thermodynamics> |
getData()
This method is called to get the data of DataCollect.
|
Thermodynamics |
getFirstMismatch(java.lang.String seq1,
java.lang.String seq2,
java.lang.String loop)
to get the Thermodynamics object containing the parameters for the first non canonical pair in the internal loop.
|
Thermodynamics |
getHairpinLoopvalue(java.lang.String size)
to get the Thermodynamics object containing the parameters for a Hairpin loop of size 'size'.
|
Thermodynamics |
getHydroxyadenosineValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
hydroxyadenine ("A*").
|
Thermodynamics |
getInitiation()
to get the Thermodynamics object containing the parameters for the hybridization initiation.
|
Thermodynamics |
getInitiation(java.lang.String type)
to get the Thermodynamics object containing the parameters for the initiation with the specified type of initiation.
|
Thermodynamics |
getInitiationBulgevalue(java.lang.String size)
to get the Thermodynamics object containing the parameters for the initiation of a bulge loop of size 'size'.
|
Thermodynamics |
getInitiationLoopValue()
to get the Thermodynamics object containing the parameters for the initiation of an internal loop.
|
Thermodynamics |
getInitiationLoopValue(java.lang.String size)
to get the Thermodynamics object containing the parameters for the initiation of an internal loop with a specified size.
|
Thermodynamics |
getInternalLoopValue(java.lang.String size)
to get the Thermodynamics object containing the parameters for an internal loop with a specified size.
|
Thermodynamics |
getLockedAcidValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
locked nucleic acid ("AL", "TL", "GL" or "CL").
|
Thermodynamics |
getMismatchParameterValue(java.lang.String base1,
java.lang.String base2)
to get the Thermodynamics object containing the parameters for the mismatching base pair (base1, base2).
|
Thermodynamics |
getMismatchValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the mismatch(es) present in the duplex
composed of seq1 and seq2.
|
Thermodynamics |
getMismatchValue(java.lang.String seq1,
java.lang.String seq2,
java.lang.String closing)
to get the Thermodynamics object containing the parameters for the the duplex composed of seq1 and seq2 with the
specified type of closing base pairs.
|
Thermodynamics |
getModifiedvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the crick's pair composed of the String seq1 and the String seq2 with
one of the sequences containing a specific nucleic acid.
|
Thermodynamics |
getModifiedvalue(java.lang.String seq1,
java.lang.String seq2,
java.lang.String sens)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a specific
nucleic acid and a dangling end.
|
Thermodynamics |
getNNvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics containing the parameters for the crick's pair composed of the String seq1 and the String seq2.
|
Thermodynamics |
getPenalty(java.lang.String type)
to get the Thermodynamics object containing the parameters for the penalty of type 'type'.
|
Thermodynamics |
getPenalty(java.lang.String type,
java.lang.String parameter)
to get the Thermodynamics object containing the parameters for a penalty of type 'type'
for the specified parameter.
|
Thermodynamics |
getSecondDanglingValue(java.lang.String seq1,
java.lang.String seq2,
java.lang.String sens)
to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2 with the specified sens.
|
Thermodynamics |
getSingleBulgeLoopvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the single bulge (seq1, seq2).
|
Thermodynamics |
getsymmetry()
to get the Thermodynamics object containing the parameters for the symmetry correction.
|
Thermodynamics |
getTerminal(java.lang.String type)
to get the Thermodynamics containing the parameters for the specified type of terminal base pair.
|
Thermodynamics |
getTerminalMismatchvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the terminal mismatching base pair (seq1, seq2)
of a hairpin loop.
|
public java.util.HashMap<java.lang.String,Thermodynamics> getData()
public void addData(java.util.HashMap<java.lang.String,Thermodynamics> parameters)
public Thermodynamics getTerminal(java.lang.String type)
type - : type of the terminal base pair.public Thermodynamics getNNvalue(java.lang.String seq1, java.lang.String seq2)
seq1 - : nucleic acids from the sequence (5'3') in the Crick's pair.seq2 - : nucleic acids from the complementary sequence (3'5') in the Crick's pair.public Thermodynamics getInitiation()
public Thermodynamics getInitiation(java.lang.String type)
type - : type of initiationpublic Thermodynamics getsymmetry()
public Thermodynamics getModifiedvalue(java.lang.String seq1, java.lang.String seq2)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').public Thermodynamics getModifiedvalue(java.lang.String seq1, java.lang.String seq2, java.lang.String sens)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').sens - : sens of the dangling endpublic Thermodynamics getAzobenzeneValue(java.lang.String seq1, java.lang.String seq2)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').public Thermodynamics getLockedAcidValue(java.lang.String seq1, java.lang.String seq2)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').public Thermodynamics getHydroxyadenosineValue(java.lang.String seq1, java.lang.String seq2)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').public Thermodynamics getSecondDanglingValue(java.lang.String seq1, java.lang.String seq2, java.lang.String sens)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').sens - : sens of the dangling endpublic Thermodynamics getDanglingValue(java.lang.String seq1, java.lang.String seq2)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').public Thermodynamics getMismatchValue(java.lang.String seq1, java.lang.String seq2)
seq1 - : sequence (5'3').seq2 - : complementary sequence (3'5').public Thermodynamics getInternalLoopValue(java.lang.String size)
size - : size of the internal loop.public Thermodynamics getInitiationLoopValue(java.lang.String size)
size - : size of the internal loop.public Thermodynamics getInitiationLoopValue()
public Thermodynamics getMismatchParameterValue(java.lang.String base1, java.lang.String base2)
base1 - : from the sequence (5'3')base2 - : from the complementary sequence (3'5')public Thermodynamics getClosureValue(java.lang.String base1, java.lang.String base2)
base1 - : from the sequence (5'3')base2 - : from the complementary sequence (3'5')public Thermodynamics getMismatchValue(java.lang.String seq1, java.lang.String seq2, java.lang.String closing)
seq1 - : from the sequence (5'3')seq2 - : from the complementary sequence (3'5')closing - : type of the base pair next to the mismatching base pair..public Thermodynamics getPenalty(java.lang.String type)
type - : type of the penaltypublic Thermodynamics getAsymmetry()
public Thermodynamics getFirstMismatch(java.lang.String seq1, java.lang.String seq2, java.lang.String loop)
seq1 - : from the sequence (5'3')seq2 - : from the complementary sequence (3'5')loop - : type of internal loop.public Thermodynamics getHairpinLoopvalue(java.lang.String size)
size - : size of the hairpin loop.public Thermodynamics getBonus(java.lang.String base1, java.lang.String lastBase, java.lang.String seqLoop, java.lang.String type)
base1 - : base preceding the hairpin loop. (from the sequence (5'3'))lastBase - : base following the hairpin loop. (from the sequence (5'3'))seqLoop - : hairpin loop sequence.type - : type of hairpin looppublic Thermodynamics getPenalty(java.lang.String type, java.lang.String parameter)
type - : type of penaltyparameter - public Thermodynamics getTerminalMismatchvalue(java.lang.String seq1, java.lang.String seq2)
seq1 - : (5'3') orientationseq2 - : (3'5') orientationpublic Thermodynamics getCNGvalue(java.lang.String repeats, java.lang.String seq1)
repeats - : number of CNG repeats in the sequence.seq1 - : CNG pattern (5'3')public Thermodynamics getSingleBulgeLoopvalue(java.lang.String seq1, java.lang.String seq2)
seq1 - : from the sequence (5'3')seq2 - : from the complementary sequence (3'5')public Thermodynamics getBulgeLoopvalue(java.lang.String size)
size - : size of the bulge looppublic Thermodynamics getInitiationBulgevalue(java.lang.String size)
size - : size of the bulge looppublic class Helper
extends java.lang.Object
| Constructor and Description |
|---|
Helper() |
| Modifier and Type | Method and Description |
|---|---|
static double |
computesNaEquivalent(Environment environment)
computes a sodium equivalent concentration from the different ion concentrations of the Environment object.
|
static java.lang.String |
extractsOptionFileName(java.lang.String methodName)
This method is called to extract the new file name to the method or model option entered by the user.
|
static java.lang.String |
extractsOptionMethodName(java.lang.String methodName)
This method is called to extract the method or model name to the method or model option entered by the user.
|
static boolean |
useOtherDataFile(java.lang.String methodName)
to check if the user wants to use another thermodynamic parameters file with the used model.
|
public static boolean useOtherDataFile(java.lang.String methodName)
methodName - : the method or model option entered by the user.public static java.lang.String extractsOptionFileName(java.lang.String methodName)
methodName - : the method or model option entered by the user.public static java.lang.String extractsOptionMethodName(java.lang.String methodName)
methodName - : the method or model option entered by the user.public static double computesNaEquivalent(Environment environment)
environment - public class Thermodynamics
extends java.lang.Object
| Modifier and Type | Field and Description |
|---|---|
protected double |
enthalpy
protected double enthalpy : the enthalpy value (delta H).
|
protected double |
entropy
protected double entropy : the entropy value (delta S).
|
| Constructor and Description |
|---|
Thermodynamics(double H,
double S) |
| Modifier and Type | Method and Description |
|---|---|
double |
getEnthalpy()
This method is called to get the enthalpy of Thermodynamics.
|
double |
getEntropy()
This method is called to get the entropy of Thermodynamics.
|
void |
setEnthalpy(double enthalpy)
This method is called to change the enthalpy of Thermodynamics.
|
void |
setEntropy(double entropy)
This method is called to change the entropy of Thermodynamics.
|
protected double enthalpy
protected double entropy
public double getEnthalpy()
public void setEnthalpy(double enthalpy)
enthalpy - : new enthalpy valuepublic double getEntropy()
public void setEntropy(double entropy)
entropy - : new entropy value| Modifier and Type | Method and Description |
|---|---|
static ThermoResult |
Main.getMeltingResults(String[] args,
OptionManagement optionManager)
Compute the entropy, enthalpy and melting temperature, and return
these results.
|
ThermoResult |
Environment.getResult()
This method is called to get the ThermoResult of Environment.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Environment.setResult(ThermoResult result)
changes the result ThermoResult of Environment.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Santalucia98.computesThermodynamics() |
ThermoResult |
WetmurDNARNA91.computesThermodynamics() |
ThermoResult |
ApproximativeMode.computesThermodynamics() |
ThermoResult |
Wetmur91.computesThermodynamics() |
ThermoResult |
MarmurChester62_93.computesThermodynamics() |
ThermoResult |
MarmurSchildkrautDoty.computesThermodynamics() |
ThermoResult |
Owen69.computesThermodynamics() |
ThermoResult |
WetmurDNA91.computesThermodynamics() |
ThermoResult |
Ahsen01.computesThermodynamics() |
ThermoResult |
WetmurRNA91.computesThermodynamics() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
RegisterMethods.computeOtherMeltingCorrections(Environment environment)
corrects the melting temperature if other agents are present in the solution (formamide, DMSO, ...)
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
DNADMSOCorrections.correctMeltingResult(Environment environment,
double parameter) |
ThermoResult |
EntropyCorrection.correctMeltingResults(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Owczarzy08MagnesiumCorrection.correctMeltingResults(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Owczarzy08MixedNaMgCorrection.correctMeltingResults(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Owczarzy04SodiumCorrection19.correctMeltingResults(Environment environment) |
ThermoResult |
Santalucia96SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
MarmurSchildkrautDoty98_62SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Tan07SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Tan06SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection22.correctMeltingResults(Environment environment) |
ThermoResult |
FrankKamenetskii71SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Wetmur91SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
SchildkrautLifson65SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection21.correctMeltingResults(Environment environment) |
ThermoResult |
Santalucia98_04SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection20.correctMeltingResults(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
MeltingComputationMethod.computesThermodynamics()
This method is called to compute the melting temperature.
|
ThermoResult |
PatternComputationMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
CorrectionMethod.correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
PatternComputationMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
NearestNeighborMode.computesThermodynamics() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Musielski81DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Escara80DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Cullen76DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Ahsen01DMSOCorrection.correctMeltingResults(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
FormamideLinearMethod.correctMeltingResults(Environment environment) |
ThermoResult |
Blake96FormamideCorrection.correctMeltingResults(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
abstract ThermoResult |
PatternComputation.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
abstract ThermoResult |
PatternComputation.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Broda05CNGRepeats.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Broda05CNGRepeats.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Znosko071x2Loop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Znosko071x2Loop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Turner99_06LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Turner99_06LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Sugimoto02RNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SugimotoLongDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto02DNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Sugimoto02RNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SugimotoLongDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto02DNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Serra05DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SecondDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Serra05DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SecondDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Tanaka04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99_06SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
GlobalSingleBulgeLoopMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra07SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Tanaka04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99_06SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
GlobalSingleBulgeLoopMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra07SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Bommarito00SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06_08SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SingleDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Bommarito00SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06_08SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SingleDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Znosko08mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
ZnoskoMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Watkins11mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Znosko08mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
ZnoskoMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Watkins11mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Sugimoto01Hydroxyadenine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Asanuma05Azobenzene.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
McTigue04LockedAcid.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Sugimoto01Hydroxyadenine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Asanuma05Azobenzene.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
McTigue04LockedAcid.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Turner99_06tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Turner99_06tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Santalucia05Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
InosineNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra12Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Turner99Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Serra12Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Santalucia05Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
InosineNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra12Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Turner99Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Serra12Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
MeltingCalculator.fetchMeltingResults()
Computes and returns the results from MELTING.
|
ThermoResult |
MeltingCalculator.getResults()
Returns the results from MELTING.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ResultsPanel.displayMeltingResults(ThermoResult results)
Displays the results from the MELTING program.
|
| Modifier and Type | Method and Description |
|---|---|
void |
MeltingFrame.displayMeltingResults(ThermoResult results)
Displays the MELTING results.
|
void |
OuterFrame.displayMeltingResults(ThermoResult results)
Displays MELTING results on the MELTING frame.
|
| Modifier and Type | Method and Description |
|---|---|
static double |
Helper.computesNaEquivalent(Environment environment)
computes a sodium equivalent concentration from the different ion concentrations of the Environment object.
|
| Modifier and Type | Field and Description |
|---|---|
protected Environment |
ApproximativeMode.environment
environment containing the sequences, ion and agent concentrations and the options (default options and
options entered by the user)
|
| Modifier and Type | Method and Description |
|---|---|
Environment |
OptionManagement.createEnvironment(String[] args)
collects the options entered by the user and creates an Environment from them.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
RegisterMethods.computeOtherMeltingCorrections(Environment environment)
corrects the melting temperature if other agents are present in the solution (formamide, DMSO, ...)
|
CorrectionMethod |
RegisterMethods.getIonCorrectionMethod(Environment environment)
This method is called to get the CorrectionMethod which represents the method or model
used for the ion correction in the environment 'environment'.
|
| Modifier and Type | Method and Description |
|---|---|
protected double |
EntropyCorrection.correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
ThermoResult |
DNADMSOCorrections.correctMeltingResult(Environment environment,
double parameter) |
ThermoResult |
EntropyCorrection.correctMeltingResults(Environment environment) |
boolean |
DNADMSOCorrections.isApplicable(Environment environment) |
boolean |
EntropyCorrection.isApplicable(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
static double |
Tan06MagnesiumCorrection.computeFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
static double |
Tan07MagnesiumCorrection.computeFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
Tan06MagnesiumCorrection.correctEntropy(Environment environment) |
protected double |
Tan07MagnesiumCorrection.correctEntropy(Environment environment) |
ThermoResult |
Owczarzy08MagnesiumCorrection.correctMeltingResults(Environment environment) |
protected double |
Owczarzy08MagnesiumCorrection.correctTemperature(Environment environment)
corrects the computed melting temperature depending on the environment.
|
boolean |
Tan06MagnesiumCorrection.isApplicable(Environment environment) |
boolean |
Tan07MagnesiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy08MagnesiumCorrection.isApplicable(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
protected double |
Tan07MixedNaMgCorrection.correctEntropy(Environment environment) |
ThermoResult |
Owczarzy08MixedNaMgCorrection.correctMeltingResults(Environment environment) |
boolean |
Tan07MixedNaMgCorrection.isApplicable(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
static double |
Tan07SodiumCorrection.calculateFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
static double |
Tan06SodiumCorrection.calculateFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
Tan07SodiumCorrection.correctEntropy(Environment environment) |
protected double |
Tan06SodiumCorrection.correctEntropy(Environment environment) |
protected double |
Santalucia98_04SodiumCorrection.correctEntropy(Environment environment) |
protected double |
Ahsen01SodiumCorrection.correctEntropy(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection19.correctMeltingResults(Environment environment) |
ThermoResult |
Santalucia96SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
MarmurSchildkrautDoty98_62SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Tan07SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Tan06SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection22.correctMeltingResults(Environment environment) |
ThermoResult |
FrankKamenetskii71SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Wetmur91SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
SchildkrautLifson65SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection21.correctMeltingResults(Environment environment) |
ThermoResult |
Santalucia98_04SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection20.correctMeltingResults(Environment environment) |
boolean |
Owczarzy04SodiumCorrection19.isApplicable(Environment environment) |
boolean |
Santalucia96SodiumCorrection.isApplicable(Environment environment) |
boolean |
MarmurSchildkrautDoty98_62SodiumCorrection.isApplicable(Environment environment) |
boolean |
Tan07SodiumCorrection.isApplicable(Environment environment) |
boolean |
Tan06SodiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy04SodiumCorrection22.isApplicable(Environment environment) |
boolean |
FrankKamenetskii71SodiumCorrection.isApplicable(Environment environment) |
boolean |
Wetmur91SodiumCorrection.isApplicable(Environment environment) |
boolean |
SchildkrautLifson65SodiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy04SodiumCorrection21.isApplicable(Environment environment) |
boolean |
Santalucia98_04SodiumCorrection.isApplicable(Environment environment) |
boolean |
Ahsen01SodiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy04SodiumCorrection20.isApplicable(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
CorrectionMethod.correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
boolean |
CorrectionMethod.isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
boolean |
PatternComputationMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
static double |
NearestNeighborMode.computesHairpinTemperature(Environment environment)
computes the melting temperature of a hairpin loop (when there is more than 4 CNG repeats in a sequence)
|
static double |
NearestNeighborMode.computesMeltingTemperature(Environment environment)
computes the melting temperature for for the Environment 'environment'.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Musielski81DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Escara80DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Cullen76DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Ahsen01DMSOCorrection.correctMeltingResults(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
FormamideLinearMethod.correctMeltingResults(Environment environment) |
ThermoResult |
Blake96FormamideCorrection.correctMeltingResults(Environment environment) |
boolean |
FormamideLinearMethod.isApplicable(Environment environment) |
boolean |
Blake96FormamideCorrection.isApplicable(Environment environment) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
PatternComputation.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Broda05CNGRepeats.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
Xia98.computesHybridizationInitiation(Environment environment) |
ThermoResult |
DecomposedInitiation.computesHybridizationInitiation(Environment environment) |
ThermoResult |
Turner06.computesHybridizationInitiation(Environment environment) |
ThermoResult |
CricksNNMethod.computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
ThermoResult |
GlobalInitiation.computesHybridizationInitiation(Environment environment) |
ThermoResult |
Santalucia04.computesHybridizationInitiation(Environment environment) |
ThermoResult |
Santalucia96.computesHybridizationInitiation(Environment environment) |
boolean |
Breslauer86.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Freier86.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Xia98.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Sugimoto96.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Sugimoto95.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner06.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia04.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Tanaka04.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
AllawiSantalucia97.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia96.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Znosko071x2Loop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner06InternalLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia04InternalLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Turner99_06LongBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia04LongBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Sugimoto02RNADanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
SugimotoLongDanglingEndMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Sugimoto02DNADanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
SecondDanglingEndMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Tanaka04SingleBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Serra07SingleBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Bommarito00SingleDanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Serra06_08SingleDanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
SingleDanglingEndMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Znosko08mm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
ZnoskoMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Watkins11mm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner06mm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99mm.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Sugimoto01Hydroxyadenine.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Asanuma05Azobenzene.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
McTigue04LockedAcid.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Turner99_06tanmm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99tanmm.isApplicable(Environment environment,
int pos1,
int pos2) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Santalucia05Inosine.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner99Wobble.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Znosko07Inosine.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Serra12Wobble.isApplicable(Environment environment,
int pos1,
int pos2) |
| Package | Description |
|---|---|
| melting.methodInterfaces | |
| melting.patternModels |
| Modifier and Type | Method and Description |
|---|---|
DataCollect |
PatternComputationMethod.getCollector()
This method is called to get the DataCollect of the implemented class.
|
| Modifier and Type | Method and Description |
|---|---|
void |
PatternComputationMethod.loadFile(String name,
DataCollect collector)
To load the thermodynamic parameters from the file "name" and stock them in the map of a DataCollect object.
|
| Modifier and Type | Field and Description |
|---|---|
protected DataCollect |
PatternComputation.collector
DataCollect collector : contains the data HasMap with the thermodynamic parameters for the pattern computation.
|
| Modifier and Type | Method and Description |
|---|---|
DataCollect |
PatternComputation.getCollector() |
| Modifier and Type | Method and Description |
|---|---|
void |
PatternComputation.loadFile(String name,
DataCollect collector) |
| Package | Description |
|---|---|
| melting | |
| melting.handlers |
| Modifier and Type | Class and Description |
|---|---|
class |
ThermoResult
This class extends Thermodynamics.
|
| Modifier and Type | Method and Description |
|---|---|
Thermodynamics |
DataCollect.getAsymmetry()
to get the Thermodynamics object containing the parameters for the internal loop asymmetry.
|
Thermodynamics |
DataCollect.getAzobenzeneValue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing an
azobenzene ("X_C" or "X_T").
|
Thermodynamics |
DataCollect.getBonus(String base1,
String lastBase,
String seqLoop,
String type)
to get the Thermodynamics object containing the parameters for a Hairpin loop 'seqLoop' preceded
by the base 'base1' and followed by the base 'lastBase'.
|
Thermodynamics |
DataCollect.getBulgeLoopvalue(String size)
to get the Thermodynamics object containing the parameters for a bulge loop of size 'size'.
|
Thermodynamics |
DataCollect.getClosureValue(String base1,
String base2)
to get the Thermodynamics object containing the parameters for the base pair (base1, base2) next to the mismatching base pair.
|
Thermodynamics |
DataCollect.getCNGvalue(String repeats,
String seq1)
to get the Thermodynamics object containing the parameters for the CNG pattern 'seq1'.
|
Thermodynamics |
DataCollect.getDanglingValue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2.
|
Thermodynamics |
DataCollect.getFirstMismatch(String seq1,
String seq2,
String loop)
to get the Thermodynamics object containing the parameters for the first non canonical pair in the internal loop.
|
Thermodynamics |
DataCollect.getHairpinLoopvalue(String size)
to get the Thermodynamics object containing the parameters for a Hairpin loop of size 'size'.
|
Thermodynamics |
DataCollect.getHydroxyadenosineValue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
hydroxyadenine ("A*").
|
Thermodynamics |
DataCollect.getInitiation()
to get the Thermodynamics object containing the parameters for the hybridization initiation.
|
Thermodynamics |
DataCollect.getInitiation(String type)
to get the Thermodynamics object containing the parameters for the initiation with the specified type of initiation.
|
Thermodynamics |
DataCollect.getInitiationBulgevalue(String size)
to get the Thermodynamics object containing the parameters for the initiation of a bulge loop of size 'size'.
|
Thermodynamics |
DataCollect.getInitiationLoopValue()
to get the Thermodynamics object containing the parameters for the initiation of an internal loop.
|
Thermodynamics |
DataCollect.getInitiationLoopValue(String size)
to get the Thermodynamics object containing the parameters for the initiation of an internal loop with a specified size.
|
Thermodynamics |
DataCollect.getInternalLoopValue(String size)
to get the Thermodynamics object containing the parameters for an internal loop with a specified size.
|
Thermodynamics |
DataCollect.getLockedAcidValue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
locked nucleic acid ("AL", "TL", "GL" or "CL").
|
Thermodynamics |
DataCollect.getMismatchParameterValue(String base1,
String base2)
to get the Thermodynamics object containing the parameters for the mismatching base pair (base1, base2).
|
Thermodynamics |
DataCollect.getMismatchValue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the mismatch(es) present in the duplex
composed of seq1 and seq2.
|
Thermodynamics |
DataCollect.getMismatchValue(String seq1,
String seq2,
String closing)
to get the Thermodynamics object containing the parameters for the the duplex composed of seq1 and seq2 with the
specified type of closing base pairs.
|
Thermodynamics |
DataCollect.getModifiedvalue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the crick's pair composed of the String seq1 and the String seq2 with
one of the sequences containing a specific nucleic acid.
|
Thermodynamics |
DataCollect.getModifiedvalue(String seq1,
String seq2,
String sens)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a specific
nucleic acid and a dangling end.
|
Thermodynamics |
DataCollect.getNNvalue(String seq1,
String seq2)
to get the Thermodynamics containing the parameters for the crick's pair composed of the String seq1 and the String seq2.
|
Thermodynamics |
DataCollect.getPenalty(String type)
to get the Thermodynamics object containing the parameters for the penalty of type 'type'.
|
Thermodynamics |
DataCollect.getPenalty(String type,
String parameter)
to get the Thermodynamics object containing the parameters for a penalty of type 'type'
for the specified parameter.
|
Thermodynamics |
DataCollect.getSecondDanglingValue(String seq1,
String seq2,
String sens)
to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2 with the specified sens.
|
Thermodynamics |
DataCollect.getSingleBulgeLoopvalue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the single bulge (seq1, seq2).
|
Thermodynamics |
DataCollect.getsymmetry()
to get the Thermodynamics object containing the parameters for the symmetry correction.
|
Thermodynamics |
DataCollect.getTerminal(String type)
to get the Thermodynamics containing the parameters for the specified type of terminal base pair.
|
Thermodynamics |
DataCollect.getTerminalMismatchvalue(String seq1,
String seq2)
to get the Thermodynamics object containing the parameters for the terminal mismatching base pair (seq1, seq2)
of a hairpin loop.
|
| Modifier and Type | Method and Description |
|---|---|
HashMap<String,Thermodynamics> |
DataCollect.getData()
This method is called to get the data of DataCollect.
|
static HashMap<String,HashMap<String,Thermodynamics>> |
FileReader.getLoadedData()
This method is called to get the loadedData of FileReader.
|
static HashMap<String,Thermodynamics> |
FileReader.readFile(File file)
stocks the thermodynamic parameters from the file in a HashMap.
|
| Modifier and Type | Method and Description |
|---|---|
void |
DataCollect.addData(HashMap<String,Thermodynamics> parameters)
add all of the mappings from the specified HashMap to the data of DataCollect.
|
| Modifier and Type | Method and Description |
|---|---|
Thermodynamics |
ThermoHandler.getThermo()
This method is called to get the Thermodynamics of the ThermoHandler object.
|
| Modifier and Type | Method and Description |
|---|---|
HashMap<String,Thermodynamics> |
DataHandler.getMap()
This method is called to get the map of DataHandler.
|
public class Blake96FormamideCorrection extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
Blake96FormamideCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| Blake96FormamideCorrection |
This class represents the formamide correction model bla96.
|
| FormamideLinearMethod |
This class represents the linear formamide correction model lincorr.
|
public class FormamideLinearMethod extends java.lang.Object implements CorrectionMethod, NamedMethod
| Constructor and Description |
|---|
FormamideLinearMethod() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
public boolean isApplicable(Environment environment)
CorrectionMethodisApplicable in interface CorrectionMethodpublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Musielski81DMSOCorrection extends DNADMSOCorrections implements NamedMethod
| Constructor and Description |
|---|
Musielski81DMSOCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
correctMeltingResult, isApplicablepublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Ahsen01DMSOCorrection extends DNADMSOCorrections implements NamedMethod
| Constructor and Description |
|---|
Ahsen01DMSOCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
correctMeltingResult, isApplicablepublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Escara80DMSOCorrection extends DNADMSOCorrections implements NamedMethod
| Constructor and Description |
|---|
Escara80DMSOCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
correctMeltingResult, isApplicablepublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethodpublic class Cullen76DMSOCorrection extends DNADMSOCorrections implements NamedMethod
| Constructor and Description |
|---|
Cullen76DMSOCorrection() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
correctMeltingResult, isApplicablepublic ThermoResult correctMeltingResults(Environment environment)
CorrectionMethodcorrectMeltingResults in interface CorrectionMethodpublic java.lang.String getName()
getName in interface NamedMethod| Class | Description |
|---|---|
| Ahsen01DMSOCorrection |
This class represents the DMSO correction model ahs01.
|
| Cullen76DMSOCorrection |
This class represents the DMSO correction model cul76.
|
| Escara80DMSOCorrection |
This class represents the DMSO correction model esc80.
|
| Musielski81DMSOCorrection |
This class represents the DMSO correction model mus81.
|
public class BatchMain
extends java.lang.Object
| Constructor and Description |
|---|
BatchMain() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
static void |
readFile(java.io.InputStream is,
java.io.OutputStream os,
java.lang.String[] defaultArgs) |
static void |
runMelting(java.io.OutputStream os,
java.lang.String[] args) |
public static void main(java.lang.String[] args)
public static void readFile(java.io.InputStream is,
java.io.OutputStream os,
java.lang.String[] defaultArgs)
throws java.io.IOException
java.io.IOExceptionpublic static void runMelting(java.io.OutputStream os,
java.lang.String[] args)
| Class | Description |
|---|---|
| BatchMain | |
| CompatibleMain | |
| DataCollect |
This class is useful to extract the different thermodynamic parameters from the HashMap which contains them.
|
| Environment |
This class represents the environment of the sequences for which we want to know the melting temperature.
|
| FileReader |
This class is useful to parse the xml files containing the thermodynamic parameters and load the data (stock them in a map).
|
| Helper |
This class contains useful public static methods.
|
| Main |
The Melting main class which contains the public static void main(String[] args) method.
|
| MeltingFormatter |
This class extends Formatter.
|
| Thermodynamics |
This class represents the thermodynamic energy.
|
| ThermoResult |
This class extends Thermodynamics.
|
public interface PatternComputationMethod
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
DataCollect |
getCollector()
This method is called to get the DataCollect of the implemented class.
|
java.lang.String |
getDataFileName(java.lang.String methodName) |
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
void |
loadFile(java.lang.String name,
DataCollect collector)
To load the thermodynamic parameters from the file "name" and stock them in the map of a DataCollect object.
|
boolean isApplicable(Environment environment, int pos1, int pos2)
environment - pos1. - Start position of the pattern in the sequence.pos2. - End position of the pattern in the sequence.ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
sequences - which contains the sequences entered by the user.pos1. - Start position of the pattern in the sequence.pos2. - End position of the pattern in the sequence.result - which contains the computed enthalpy, entropy and melting temperature.boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
sequences - which contains the sequences entered by the user.pos1. - Start position of the pattern in the sequence.pos2. - End position of the pattern in the sequence.DataCollect getCollector()
void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
options - which contains the current options. (default options and options entered by the user)void loadFile(java.lang.String name,
DataCollect collector)
name - : the file name where to find the thermodynamic parameterscollector - : The object which stocks the different thermodynamic parameters in a map.java.lang.String getDataFileName(java.lang.String methodName)
methodName - : method or model name entered by the user.void initialiseFileName(java.lang.String methodName)
methodName - : method or model name entered by the user.public interface MeltingComputationMethod
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
RegisterMethods |
getRegister()
This method is called to get the RegisterMethod of the implemented class.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
void |
setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
Creates the Environment object and set up the variables of the chosen model.
|
ThermoResult computesThermodynamics()
boolean isApplicable()
void setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
options - containing all the options (default options and options entered by the user)RegisterMethods getRegister()
public interface NamedMethod
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getName() |
public interface SodiumEquivalentMethod
| Modifier and Type | Method and Description |
|---|---|
double |
computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
This method is called to convert an initial sodium concentration in a new equivalent sodium concentration
which takes in account the other cation concentrations.
|
boolean |
isApplicable(java.util.HashMap<java.lang.String,java.lang.String> options)
Check if the model to compute an equivalent sodium cencentration is applicable with the options entered by the user.
|
double computeSodiumEquivalent(double Na,
double Mg,
double K,
double Tris,
double dNTP)
Na - : sodium concentration entered by the userMg - : magnesium concentration entered by the userK - : potassium concentration entered by the userTris - : Tris buffer concentration entered by the user.dNTP - : dNTP concentration entered by the userboolean isApplicable(java.util.HashMap<java.lang.String,java.lang.String> options)
options - which contains the options. (default options and options entered by the user)| Class and Description |
|---|
| MeltingComputationMethod
This interface is implemented by classes which contain methods to compute the melting temperature.
|
| Class and Description |
|---|
| MeltingComputationMethod
This interface is implemented by classes which contain methods to compute the melting temperature.
|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| Class and Description |
|---|
| CorrectionMethod
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| MeltingComputationMethod
This interface is implemented by classes which contain methods to compute the melting temperature.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| SodiumEquivalentMethod
This interface is implemented by classes which contain a method to compute an equivalent sodium concentration when
other ions are present.
|
| Class and Description |
|---|
| CorrectionMethod
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| Class and Description |
|---|
| CorrectionMethod
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| Class and Description |
|---|
| CorrectionMethod
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| Class and Description |
|---|
| CorrectionMethod
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| SodiumEquivalentMethod
This interface is implemented by classes which contain a method to compute an equivalent sodium concentration when
other ions are present.
|
| Class and Description |
|---|
| MeltingComputationMethod
This interface is implemented by classes which contain methods to compute the melting temperature.
|
| Class and Description |
|---|
| CorrectionMethod
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| Class and Description |
|---|
| CorrectionMethod
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| Class and Description |
|---|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Class and Description |
|---|
| NamedMethod
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| Modifier and Type | Method and Description |
|---|---|
PatternComputationMethod |
RegisterMethods.getPatternComputationMethod(String optionName,
String methodName)
This method is called to get the PatternComputationMethod which represents the method 'methodName'
entered with the option 'optionName'.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PatternComputation
This class represents the different pattern models.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Broda05CNGRepeats
This class represents the CNG repeats model bro05.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantalucia97
This class represents the nearest neighbor model all97.
|
class |
Breslauer86
This class represents the nearest neighbor model bre86.
|
class |
CricksNNMethod
This class represents the NN nearest neighbor model (adds the thermodynamic energy (enthalpy and entropy) for each Crick's pair composing the duplex).
|
class |
DecomposedInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
class |
Freier86
This class represents the nearest neighbor model fre86.
|
class |
GlobalInitiation
This class represents one model to compute the initiation enthalpy and entropy.
|
class |
Santalucia04
This class represents the nearest neighbor model san04.
|
class |
Santalucia96
This class represents the nearest neighbor model san96.
|
class |
Sugimoto95
This class represents the nearest neighbor model sug95.
|
class |
Sugimoto96
This class represents the nearest neighbor model sug96.
|
class |
Tanaka04
This class represents the nearest neighbor model tan04.
|
class |
Turner06
This class represents the nearest neighbor model tur06.
|
class |
Xia98
This class represents the nearest neighbor model xia98.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Santalucia04InternalLoop
This class represents the internal loop model san04.
|
class |
Turner06InternalLoop
This class represents the internal loop model tur06.
|
class |
Znosko071x2Loop
This class represents the 1x2 internal loop model zno07.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Santalucia04LongBulgeLoop
This class represents the long bulge loop model san04.
|
class |
Turner99_06LongBulgeLoop
This class represents the long bulge loop model tur06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Sugimoto02DNADanglingEnd
This class represents the long dangling end model sugdna02 (for long poly A only).
|
class |
Sugimoto02RNADanglingEnd
This class represents the long dangling end model sugrna02 (for long poly A only).
|
class |
SugimotoLongDanglingEndMethod
This class represents the long dangling end model (for long poly A only)from Sugimoto et al. 2002.
|
| Modifier and Type | Class and Description |
|---|---|
class |
SecondDanglingEndMethod
This class represents the second dangling end model.
|
class |
Serra05DoubleDanglingEnd
This class represents the second dangling end model ser05.
|
class |
Serra06DoubleDanglingEnd
This class represents the second dangling end model ser06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
GlobalSingleBulgeLoopMethod
This class represents one single bulge loop model.
|
class |
Santalucia04SingleBulgeLoop
This class represents the single bulge loop model san04.
|
class |
Serra07SingleBulgeLoop
This class represents the single bulge loop model ser07.
|
class |
Tanaka04SingleBulgeLoop
This class represents the single bulge loop model tan04.
|
class |
Turner99_06SingleBulgeLoop
This class represents the single bulge loop model tur06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Bommarito00SingleDanglingEnd
This class represents the single dangling end model bom00.
|
class |
Serra06_08SingleDanglingEnd
This class represents the single dangling end model ser08.
|
class |
SingleDanglingEndMethod
This class represents the single dangling end model.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantaluciaPeyret97_98_99mm
This class represents the single mismatch model allsanpey.
|
class |
Turner06mm
This class represents the single mismatch model tur06.
|
class |
Watkins11mm
This class represents the DNA/RNA single mismatch model wat11.
|
class |
Znosko07mm
This class represents the single mismatch model zno07.
|
class |
Znosko08mm
This class represents the single mismatch model zno08.
|
class |
ZnoskoMethod
This class represents the single mismatch model from Znosco et al, 2007, 2008.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Asanuma05Azobenzene
This class represents the azobenzene (X_C or X_T) model asa05.
|
class |
McTigue04LockedAcid
This class represents the locked nucleic acid (AL, GL, CL or TL) model mct04.
|
class |
Sugimoto01Hydroxyadenine
This class represents the hydroxyadenine (A*) model sug01.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AllawiSantaluciaPeyret97_98_99tanmm
This class represents the tandem mismatches model allsanpey.
|
class |
Turner99_06tanmm
This class represents the tandem mismatches model tur06.
|
| Modifier and Type | Class and Description |
|---|---|
class |
InosineNNMethod
This class represents the inosine model.
|
class |
Santalucia05Inosine
This class represents the inosine model san05.
|
class |
Serra12Wobble
This class represents the GU base pair model ser12.
|
class |
Turner99Wobble
This class represents the GU base pair model tur99.
|
class |
Znosko07Inosine
This class represents the inosine model zno07.
|
| Package | Description |
|---|---|
| melting | |
| melting.approximativeMethods | |
| melting.configuration | |
| melting.nearestNeighborModel |
| Modifier and Type | Method and Description |
|---|---|
MeltingComputationMethod |
ThermoResult.getCalculMethod()
Gets the calculation method of the
ThermoResult. |
| Modifier and Type | Method and Description |
|---|---|
void |
ThermoResult.setCalculMethod(MeltingComputationMethod calculMethod)
Changes the calculation method in the
ThermoResult. |
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01
This class represents the approxiamtive model ahs01.
|
class |
ApproximativeMode
This class represents the approximative model.
|
class |
MarmurChester62_93
This class represents the model che93.
|
class |
MarmurChester62_93_corr
This class represents the model che93corr.
|
class |
MarmurSchildkrautDoty
This class represents the model schdot.
|
class |
Owen69
This class represents the model owe69.
|
class |
Santalucia98
This class represents the model san98.
|
class |
Wetmur91
This class represents the model from Wetmur 1991.
|
class |
WetmurDNA91
This class represents the model wetdna91.
|
class |
WetmurDNARNA91
This class represents the model wetdnarna91.
|
class |
WetmurRNA91
This class represents the model wetrna91.
|
| Modifier and Type | Method and Description |
|---|---|
MeltingComputationMethod |
RegisterMethods.getMeltingComputationMethod(HashMap<String,String> optionSet)
This method is called to get the MeltingComputationMethod which represents the method or model
for the enthalpy, entropy and melting temperature computation in the HashMap 'optionSet'.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NearestNeighborMode
This class represents the nearest neighbor model.
|
| Package | Description |
|---|---|
| melting.configuration | |
| melting.ionCorrection.sodiumEquivalence |
| Modifier and Type | Method and Description |
|---|---|
SodiumEquivalentMethod |
RegisterMethods.getNaEqMethod(HashMap<String,String> optionSet)
This method is called to get the SodiumEquivalentMethod which represents the method or model
for the sodium equivalence in the HashMap 'optionSet'.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01_NaEquivalent
This class represents the model for a sodium equivalence ahs01.
|
class |
Mitsuhashi96NaEquivalent
This class represents the model for a sodium equivalence mit96.
|
class |
Peyret00_NaEquivalent
This class represents the model for a sodium equivalence pey00.
|
class |
SodiumEquivalent
This class represents the methods to compute a sodium equivalence.
|
| Modifier and Type | Method and Description |
|---|---|
CorrectionMethod |
RegisterMethods.getCorrectionMethod(String optionName,
String methodName)
This method is called to get the CorrectionMethod which represents the method 'methodName'
entered with the option 'optionName'.
|
CorrectionMethod |
RegisterMethods.getIonCorrectionMethod(Environment environment)
This method is called to get the CorrectionMethod which represents the method or model
used for the ion correction in the environment 'environment'.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DNADMSOCorrections
This class represents the DMSO correction.
|
class |
EntropyCorrection
This class represents a specific type of ion correction which corrects the entropy value.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Owczarzy08MagnesiumCorrection
This class represents the magnesium correction model owc08.
|
class |
Tan06MagnesiumCorrection
This class represents the magnesium correction model tanmg06.
|
class |
Tan07MagnesiumCorrection
This class represents the magnesium correction model tanmg07.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Owczarzy08MixedNaMgCorrection
This class represents the mixed (Na,Mg) correction model owcmix08.
|
class |
Tan07MixedNaMgCorrection
This class represents the mixed (Na,Mg) correction model tanmix07.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01SodiumCorrection
This class represents the sodium correction model ahs01.
|
class |
FrankKamenetskii71SodiumCorrection
This class represents the sodium correction model kam71.
|
class |
MarmurSchildkrautDoty98_62SodiumCorrection
This class represents the sodium correction model marschdot.
|
class |
Owczarzy04SodiumCorrection19
This class represents the sodium correction model owc1904.
|
class |
Owczarzy04SodiumCorrection20
This class represents the sodium correction model owc2004.
|
class |
Owczarzy04SodiumCorrection21
This class represents the sodium correction model owc2104.
|
class |
Owczarzy04SodiumCorrection22
This class represents the sodium correction model owc2204.
|
class |
Santalucia96SodiumCorrection
This class represents the sodium correction model san96.
|
class |
Santalucia98_04SodiumCorrection
This class represents the sodium correction model san04.
|
class |
SchildkrautLifson65SodiumCorrection
This class represents the sodium correction model schlif.
|
class |
Tan06SodiumCorrection
This class represents the sodium correction model tanna06.
|
class |
Tan07SodiumCorrection
This class represents the sodium correction model tanna07.
|
class |
Wetmur91SodiumCorrection
This class represents the sodium correction model wet91.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01DMSOCorrection
This class represents the DMSO correction model ahs01.
|
class |
Cullen76DMSOCorrection
This class represents the DMSO correction model cul76.
|
class |
Escara80DMSOCorrection
This class represents the DMSO correction model esc80.
|
class |
Musielski81DMSOCorrection
This class represents the DMSO correction model mus81.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Blake96FormamideCorrection
This class represents the formamide correction model bla96.
|
class |
FormamideLinearMethod
This class represents the linear formamide correction model lincorr.
|
public interface CorrectionMethod
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
boolean |
isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
boolean isApplicable(Environment environment)
environment - ThermoResult correctMeltingResults(Environment environment)
environment - | Interface | Description |
|---|---|
| CorrectionMethod |
This interface is implemented by classes which contain methods to correct the melting temperature.
|
| MeltingComputationMethod |
This interface is implemented by classes which contain methods to compute the melting temperature.
|
| NamedMethod |
An interface representing a method that can be used in the MELTING software.
|
| PatternComputationMethod |
This interface is implemented by classes which contain a method or model to compute the pattern enthalpy and entropy.
|
| SodiumEquivalentMethod |
This interface is implemented by classes which contain a method to compute an equivalent sodium concentration when
other ions are present.
|
public class Main
extends java.lang.Object
| Constructor and Description |
|---|
Main() |
| Modifier and Type | Method and Description |
|---|---|
static ThermoResult |
getMeltingResults(java.lang.String[] args,
OptionManagement optionManager)
Compute the entropy, enthalpy and melting temperature, and return
these results.
|
static void |
main(java.lang.String[] args) |
public static ThermoResult getMeltingResults(java.lang.String[] args, OptionManagement optionManager)
args - options (entered by the user) that determine the
sequence, hybridization type and other features of the
environment.optionManager - the OptionManagementpublic static void main(java.lang.String[] args)
args - : contains the options entered by the user.public abstract class Wetmur91 extends ApproximativeMode
environment, register| Constructor and Description |
|---|
Wetmur91() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
getRegister, isApplicable, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class ApproximativeModepublic class WetmurDNARNA91 extends Wetmur91 implements NamedMethod
environment, register| Constructor and Description |
|---|
WetmurDNARNA91() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
getRegister, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class Wetmur91public boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic java.lang.String getName()
getName in interface NamedMethodpublic class MarmurChester62_93_corr extends MarmurChester62_93
MarmurChester62_93.
von Ahsen et al. 2001, Marmur 1962, Chester et al. 1993.environment, register| Constructor and Description |
|---|
MarmurChester62_93_corr()
Sets up the private variables for the corrected method.
|
computesThermodynamics, getName, isApplicable, isNaEqPossible, setUpVariablesgetRegisterpublic class MarmurChester62_93 extends ApproximativeMode implements NamedMethod
environment, register| Constructor and Description |
|---|
MarmurChester62_93()
Sets up the private variables for the uncorrected version.
|
MarmurChester62_93(double parameter,
java.lang.String methodName)
Sets up the private variables:
parameter and
methodName. |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
protected boolean |
isNaEqPossible()
to check if a sodium equivalence is necessary.
|
void |
setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
Creates the Environment object and set up the variables of the chosen model.
|
getRegisterpublic MarmurChester62_93(double parameter,
java.lang.String methodName)
parameter and
methodName.parameter - 535 for the corrected version,
650 for the uncorrected version.methodName - The name of the method.public MarmurChester62_93()
public ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class ApproximativeModepublic boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic void setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
MeltingComputationMethodsetUpVariables in interface MeltingComputationMethodsetUpVariables in class ApproximativeModeoptions - containing all the options (default options and options entered by the user)public java.lang.String getName()
getName in interface NamedMethodprotected boolean isNaEqPossible()
ApproximativeModeisNaEqPossible in class ApproximativeModepublic class WetmurRNA91 extends Wetmur91 implements NamedMethod
environment, register| Constructor and Description |
|---|
WetmurRNA91() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
getRegister, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class Wetmur91public boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic java.lang.String getName()
getName in interface NamedMethod| Package | Description |
|---|---|
| melting.approximativeMethods |
| Class and Description |
|---|
| ApproximativeMode
This class represents the approximative model.
|
| MarmurChester62_93
This class represents the model che93.
|
| Wetmur91
This class represents the model from Wetmur 1991.
|
public class ApproximativeMode extends java.lang.Object implements MeltingComputationMethod
| Modifier and Type | Field and Description |
|---|---|
protected Environment |
environment
environment containing the sequences, ion and agent concentrations and the options (default options and
options entered by the user)
|
protected RegisterMethods |
register
RegisterMethods register : registers all the pattern computation methods implemented by Melting
|
| Constructor and Description |
|---|
ApproximativeMode() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
RegisterMethods |
getRegister()
This method is called to get the RegisterMethod of the implemented class.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
protected boolean |
isNaEqPossible()
to check if a sodium equivalence is necessary.
|
void |
setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
Creates the Environment object and set up the variables of the chosen model.
|
protected Environment environment
protected RegisterMethods register
public ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodpublic boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodpublic void setUpVariables(java.util.HashMap<java.lang.String,java.lang.String> options)
MeltingComputationMethodsetUpVariables in interface MeltingComputationMethodoptions - containing all the options (default options and options entered by the user)public RegisterMethods getRegister()
MeltingComputationMethodgetRegister in interface MeltingComputationMethodprotected boolean isNaEqPossible()
| Package | Description |
|---|---|
| melting.approximativeMethods |
| Modifier and Type | Class and Description |
|---|---|
class |
WetmurDNA91
This class represents the model wetdna91.
|
class |
WetmurDNARNA91
This class represents the model wetdnarna91.
|
class |
WetmurRNA91
This class represents the model wetrna91.
|
| Package | Description |
|---|---|
| melting.approximativeMethods |
| Modifier and Type | Class and Description |
|---|---|
class |
MarmurChester62_93_corr
This class represents the model che93corr.
|
| Package | Description |
|---|---|
| melting.approximativeMethods |
| Modifier and Type | Class and Description |
|---|---|
class |
Ahsen01
This class represents the approxiamtive model ahs01.
|
class |
MarmurChester62_93
This class represents the model che93.
|
class |
MarmurChester62_93_corr
This class represents the model che93corr.
|
class |
MarmurSchildkrautDoty
This class represents the model schdot.
|
class |
Owen69
This class represents the model owe69.
|
class |
Santalucia98
This class represents the model san98.
|
class |
Wetmur91
This class represents the model from Wetmur 1991.
|
class |
WetmurDNA91
This class represents the model wetdna91.
|
class |
WetmurDNARNA91
This class represents the model wetdnarna91.
|
class |
WetmurRNA91
This class represents the model wetrna91.
|
| Class | Description |
|---|---|
| Ahsen01 |
This class represents the approxiamtive model ahs01.
|
| ApproximativeMode |
This class represents the approximative model.
|
| MarmurChester62_93 |
This class represents the model che93.
|
| MarmurChester62_93_corr |
This class represents the model che93corr.
|
| MarmurSchildkrautDoty |
This class represents the model schdot.
|
| Owen69 |
This class represents the model owe69.
|
| Santalucia98 |
This class represents the model san98.
|
| Wetmur91 |
This class represents the model from Wetmur 1991.
|
| WetmurDNA91 |
This class represents the model wetdna91.
|
| WetmurDNARNA91 |
This class represents the model wetdnarna91.
|
| WetmurRNA91 |
This class represents the model wetrna91.
|
public class Owen69 extends ApproximativeMode implements NamedMethod
environment, register| Constructor and Description |
|---|
Owen69() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
getRegister, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class ApproximativeModepublic boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic java.lang.String getName()
getName in interface NamedMethodpublic class MarmurSchildkrautDoty extends ApproximativeMode implements NamedMethod
environment, register| Constructor and Description |
|---|
MarmurSchildkrautDoty() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
getRegister, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class ApproximativeModepublic boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic java.lang.String getName()
getName in interface NamedMethodpublic class WetmurDNA91 extends Wetmur91 implements NamedMethod
environment, register| Constructor and Description |
|---|
WetmurDNA91() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
getRegister, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class Wetmur91public boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic java.lang.String getName()
getName in interface NamedMethodpublic class Ahsen01 extends ApproximativeMode implements NamedMethod
environment, register| Constructor and Description |
|---|
Ahsen01() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
getRegister, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class ApproximativeModepublic boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic java.lang.String getName()
getName in interface NamedMethodpublic class Santalucia98 extends ApproximativeMode implements NamedMethod
environment, register| Constructor and Description |
|---|
Santalucia98() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computesThermodynamics()
This method is called to compute the melting temperature.
|
java.lang.String |
getName()
Gets the full name of the method.
|
boolean |
isApplicable()
This method is called to check that the options entered by the users are applicable with the used model (class).
|
getRegister, isNaEqPossible, setUpVariablespublic ThermoResult computesThermodynamics()
MeltingComputationMethodcomputesThermodynamics in interface MeltingComputationMethodcomputesThermodynamics in class ApproximativeModepublic boolean isApplicable()
MeltingComputationMethodisApplicable in interface MeltingComputationMethodisApplicable in class ApproximativeModepublic java.lang.String getName()
getName in interface NamedMethodpublic abstract class NodeHandler
extends org.xml.sax.helpers.DefaultHandler
| Modifier and Type | Field and Description |
|---|---|
protected NodeHandler |
subHandler
NodeHandler subHandler : the Handler for the subnode.
|
| Constructor and Description |
|---|
NodeHandler() |
| Modifier and Type | Method and Description |
|---|---|
protected void |
completedNode()
if the node is completed, the boolean completed becomes true.
|
boolean |
hasCompletedNode()
To check if a node is completed.
|
characters, endDocument, endElement, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startElement, startPrefixMapping, unparsedEntityDecl, warningprotected NodeHandler subHandler
| Package | Description |
|---|---|
| melting.handlers |
| Class and Description |
|---|
| NodeHandler
This class represents a Handler for any node of the data xml files.
|
| Package | Description |
|---|---|
| melting.handlers |
| Modifier and Type | Class and Description |
|---|---|
class |
DataHandler
This class represents a Handler to parse the Data nodes in the xml files.
|
class |
EnergyHandler
This class represents a Handler to parse the enthalpy or entropy nodes in the xml files.
|
class |
ThermoHandler
This class represents a Handler to parse the subnodes to the data nodes in the xml files.
|
| Modifier and Type | Field and Description |
|---|---|
protected NodeHandler |
NodeHandler.subHandler
NodeHandler subHandler : the Handler for the subnode.
|
public class DataHandler extends NodeHandler
subHandler| Constructor and Description |
|---|
DataHandler() |
| Modifier and Type | Method and Description |
|---|---|
void |
characters(char[] ch,
int start,
int length) |
void |
endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name) |
java.util.HashMap<java.lang.String,Thermodynamics> |
getMap()
This method is called to get the map of DataHandler.
|
java.lang.String |
getType()
This method is called to get the type String of DataHandler.
|
void |
startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name,
org.xml.sax.Attributes attributes) |
completedNode, hasCompletedNodepublic java.util.HashMap<java.lang.String,Thermodynamics> getMap()
public java.lang.String getType()
public void startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name,
org.xml.sax.Attributes attributes)
throws org.xml.sax.SAXException
startElement in interface org.xml.sax.ContentHandlerstartElement in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic void characters(char[] ch,
int start,
int length)
throws org.xml.sax.SAXException
characters in interface org.xml.sax.ContentHandlercharacters in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic void endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name)
throws org.xml.sax.SAXException
endElement in interface org.xml.sax.ContentHandlerendElement in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXException| Class | Description |
|---|---|
| DataHandler |
This class represents a Handler to parse the Data nodes in the xml files.
|
| EnergyHandler |
This class represents a Handler to parse the enthalpy or entropy nodes in the xml files.
|
| NodeHandler |
This class represents a Handler for any node of the data xml files.
|
| ThermoHandler |
This class represents a Handler to parse the subnodes to the data nodes in the xml files.
|
public class EnergyHandler extends NodeHandler
subHandler| Constructor and Description |
|---|
EnergyHandler() |
| Modifier and Type | Method and Description |
|---|---|
void |
characters(char[] ch,
int start,
int length) |
void |
endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name) |
double |
getEnergy()
This method is called to get the energy of EnergyHandler.
|
boolean |
getHasEnergy()
This method is called to get the hasEnergy of EnergyHandler.
|
void |
startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name,
org.xml.sax.Attributes attributes) |
completedNode, hasCompletedNodepublic double getEnergy()
public boolean getHasEnergy()
public void startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name,
org.xml.sax.Attributes attributes)
throws org.xml.sax.SAXException
startElement in interface org.xml.sax.ContentHandlerstartElement in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic void characters(char[] ch,
int start,
int length)
throws org.xml.sax.SAXException
characters in interface org.xml.sax.ContentHandlercharacters in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic void endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name)
throws org.xml.sax.SAXException
endElement in interface org.xml.sax.ContentHandlerendElement in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic class ThermoHandler extends NodeHandler
subHandler| Constructor and Description |
|---|
ThermoHandler(java.lang.String nodeName)
creates a ThermoHandler object and initialises the instance variables of this object.
|
| Modifier and Type | Method and Description |
|---|---|
void |
characters(char[] ch,
int start,
int length) |
void |
endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name) |
java.util.HashMap<java.lang.String,java.lang.String> |
getAttribut()
This method is called to get the attribut HashMap of the ThermoHandler object.
|
java.lang.Double |
getEnthalpy()
This method is called to get the enthalpy double value of the ThermoHandler object.
|
java.lang.Double |
getEntropy()
This method is called to get the entropy double value of the ThermoHandler object.
|
java.lang.String |
getName()
This method is called to get the name String of the ThermoHandler object.
|
Thermodynamics |
getThermo()
This method is called to get the Thermodynamics of the ThermoHandler object.
|
void |
initialiseAttributes()
initialises the attribut HashMap of the ThermoHandler object.
|
void |
startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name,
org.xml.sax.Attributes attributes) |
completedNode, hasCompletedNodepublic ThermoHandler(java.lang.String nodeName)
nodeName - : node namepublic java.lang.String getName()
public java.lang.Double getEnthalpy()
public java.lang.Double getEntropy()
public Thermodynamics getThermo()
public java.util.HashMap<java.lang.String,java.lang.String> getAttribut()
public void initialiseAttributes()
public void startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name,
org.xml.sax.Attributes attributes)
throws org.xml.sax.SAXException
startElement in interface org.xml.sax.ContentHandlerstartElement in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic void characters(char[] ch,
int start,
int length)
throws org.xml.sax.SAXException
characters in interface org.xml.sax.ContentHandlercharacters in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic void endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String name)
throws org.xml.sax.SAXException
endElement in interface org.xml.sax.ContentHandlerendElement in class org.xml.sax.helpers.DefaultHandlerorg.xml.sax.SAXExceptionpublic class CompatibleMain
extends java.lang.Object
| Constructor and Description |
|---|
CompatibleMain() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
| Method and Description |
|---|
| meltinggui.MeltingLayout.addLayoutComponent(String, Component)
Only here because the interface demands it. Replaced by
addLayoutComponent(Component, Object). |
OuterFrame outerFrame
java.lang.String commandLineText
java.lang.String mandatoryCommandLineText
java.lang.String generalCommandLineText
java.awt.Container parent
Container.int hgap
int vgap
boolean isValid
java.util.Map<K,V> componentGroupTypes
java.util.LinkedList<E> componentLines
java.lang.String commandLineTag
javax.swing.JLabel comboBoxLabel
MeltingComboBox comboBox
java.lang.String[] ionNames
java.lang.String[] comboBoxOptions
int currentIonIndex
meltinggui.dialogs.IonConcentrationDialog.IonDialogEditor editor
OutputField enthalpyOutputField
javax.swing.JLabel enthalpyUnitsLabel
OutputField entropyOutputField
javax.swing.JLabel entropyUnitsLabel
OutputField tmOutputField
javax.swing.JLabel tmUnitsLabel
javax.swing.Box centerBox
javax.swing.JLabel titleLabel
javax.swing.JTextArea exceptionLogTextArea
javax.swing.JScrollPane exceptionLogScrollPane
FrameScreenPosition outerFrameScreenPosition
FrameScreenPosition meltingFrameScreenPosition
FrameScreenPosition errorFrameScreenPosition
MeltingObservable observable
java.lang.String commandLineText
javax.swing.JPanel mainPanel
javax.swing.JPanel sequencesPanel
SequenceDialog sequenceDialog
javax.swing.JPanel hybridizationPanel
HybridizationDialog hybridizationDialog
javax.swing.JPanel oligomerConcentrationPanel
OligomerConcentrationDialog oligomerConcentrationDialog
javax.swing.JPanel ionConcentrationsPanel
IonConcentrationDialog ionConcentrationDialog
javax.swing.JPanel buttonsPanel
javax.swing.JButton getThermodynamicsButton
javax.swing.JToggleButton moreOptionsButton
javax.swing.JPanel commandLinePanel
javax.swing.JTextArea commandLineTextArea
javax.swing.JPanel resultsPanelPanel
ResultsPanel resultsPanel
javax.swing.JDesktopPane desktopPane
MeltingFrame meltingFrame
ErrorFrame errorFrame
java.lang.String screenPositionsPath
ComboBoxOption[] comboBoxOptions
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final java.lang.String |
approximativeMode |
"-am" |
public static final java.lang.String |
azobenzeneMethod |
"-azo" |
public static final java.lang.String |
CNGMethod |
"-CNG" |
public static final java.lang.String |
complementarySequence |
"-C" |
public static final java.lang.String |
dataPathway |
"-p" |
public static final java.lang.String |
DMSOCorrection |
"-DMSO" |
public static final java.lang.String |
doubleDanglingEndMethod |
"-secDE" |
public static final java.lang.String |
factor |
"-F" |
public static final java.lang.String |
formamideCorrection |
"-for" |
public static final java.lang.String |
globalMethod |
"-mode" |
public static final java.lang.String |
hybridization |
"-H" |
public static final java.lang.String |
hydroxyadenineMethod |
"-ha" |
public static final java.lang.String |
inosineMethod |
"-ino" |
public static final java.lang.String |
internalLoopMethod |
"-intLP" |
public static final java.lang.String |
ionCorrection |
"-ion" |
public static final java.lang.String |
legalInformation |
"-L" |
public static final java.lang.String |
lockedAcidMethod |
"-lck" |
public static final java.lang.String |
lockedAcidSingleMismatchMethod |
"-sinMMLck" |
public static final java.lang.String |
longBulgeLoopMethod |
"-lonBU" |
public static final java.lang.String |
longDanglingEndMethod |
"-lonDE" |
public static final java.lang.String |
meltingHelp |
"-h" |
public static final java.lang.String |
meltingHelpAlt |
"-?" |
public static final java.lang.String |
NaEquivalentMethod |
"-naeq" |
public static final java.lang.String |
NN_Path |
"-NNPath" |
public static final java.lang.String |
NNMethod |
"-nn" |
public static final java.lang.String |
nucleotides |
"-P" |
public static final java.lang.String |
outPutFile |
"-O" |
public static final java.lang.String |
selfComplementarity |
"-self" |
public static final java.lang.String |
sequence |
"-S" |
public static final java.lang.String |
singleBulgeLoopMethod |
"-sinBU" |
public static final java.lang.String |
singleDanglingEndMethod |
"-sinDE" |
public static final java.lang.String |
singleMismatchMethod |
"-sinMM" |
public static final java.lang.String |
solutioncomposition |
"-E" |
public static final java.lang.String |
tandemLockedAcidMethod |
"-tanLck" |
public static final java.lang.String |
tandemMismatchMethod |
"-tan" |
public static final java.lang.String |
threshold |
"-T" |
public static final java.lang.String |
verboseMode |
"-v" |
public static final java.lang.String |
versionNumber |
"-V" |
public static final java.lang.String |
wobbleBaseMethod |
"-GU" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final java.lang.String |
defaultFileName |
"Watkins2011mm.xml" |
MELTING5.2.0/javadoc/examples/ 0000755 0001750 0001750 00000000000 12371207646 015305 5 ustar marine marine MELTING5.2.0/javadoc/examples/MainTestAzobenzene.html 0000644 0001750 0001750 00000017556 12371207646 021756 0 ustar marine marine
public class MainTestAzobenzene
extends java.lang.Object
| Constructor and Description |
|---|
MainTestAzobenzene() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTest
extends java.lang.Object
| Constructor and Description |
|---|
MainTest() |
| Modifier and Type | Method and Description |
|---|---|
static void |
displayResults(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
displays the computed and experimental melting temperature for each method or model to test.
|
static void |
displayResultsDanglingEndMeltingC(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for single dangling ends.
|
static void |
displayResultsDNA_RNAMelting4_3(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for DNA/RNA duplexes.
|
static void |
displayResultsDNA_RNAMeltingC(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for DNA/RNA duplexes.
|
static void |
displayResultsInosineMelting4_3WithComplementarySequence(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
|
static void |
displayResultsLongDanglingEnd(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
displays the computed and experimental melting temperature for each dangling end method or model.
|
static void |
displayResultsMagnesium(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String nucleotides,
java.lang.String option)
displays the computed and experimental melting temperature for each method or model to test with different magnesium concentrations.
|
static void |
displayResultsMeltingC(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
|
static void |
displayResultsMeltingC4_3(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
|
static void |
displayResultsMeltingC4_3SelfComplementary(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
|
static void |
displayResultsMeltingCSelfComplementary(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
|
static void |
displayResultsMismatchMeltingCWithComplementarySequence(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
displays the computed and experimental melting temperature for single mismatches.
|
static void |
displayResultsNaEq(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String nucleotides,
java.lang.String option)
displays the computed and experimental melting temperature for each NaEq method or model to test with different magnesium concentrations.
|
static void |
displayResultsNaEq(java.util.Properties properties,
java.lang.String hybridization)
displays the computed and experimental melting temperature with MELTING 4.2 approximative formula and with different magnesium concentrations.
|
static void |
displayResultsSelf(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
displays the computed and experimental melting temperature for each method or model to test.
|
static void |
displayResultsSodium(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String nucleotides,
java.lang.String option)
displays the computed and experimental melting temperature for each method or model to test with different sodium concentrations.
|
static void |
displayResultsWithComplementarySequence(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
displays the computed and experimental melting temperature for each method or model to test.
|
static double |
getC4_3MeltingResult(java.lang.String args)
to run melting 4.3 and get the results
|
static double |
getCMeltingResult(java.lang.String args)
to run melting 4.2 and get the results
|
static double |
getMeltingTest(java.lang.String[] args)
computes the enthalpy, entropy and melting temperature with the options in String [] args.
|
static java.util.Properties |
loadSequencesTest(java.lang.String fileName)
loads the data from the file and stocks them in a Properties object.
|
public static java.util.Properties loadSequencesTest(java.lang.String fileName)
fileName - : name or pathway of the file containing the experimental data.public static double getMeltingTest(java.lang.String[] args)
args - : contains the test optionspublic static void displayResults(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationsolution - : contains the different ion and agent concentrationsnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsSodium(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String nucleotides,
java.lang.String option)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsMagnesium(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String nucleotides,
java.lang.String option)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsNaEq(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String nucleotides,
java.lang.String option)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsNaEq(java.util.Properties properties,
java.lang.String hybridization)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsLongDanglingEnd(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationsolution - : contains the different ion and agent concentrationsnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsWithComplementarySequence(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationsolution - : contains the different ion and agent concentrationsnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsInosineMelting4_3WithComplementarySequence(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationsolution - : contains the different ion and agent concentrationsnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsMismatchMeltingCWithComplementarySequence(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationion - : contains the different ion concentrationsnucleotides - : oligomer concentrationpublic static void displayResultsDanglingEndMeltingC(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationion - : contains the different ion concentrationsnucleotides - : oligomer concentrationpublic static void displayResultsSelf(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String solution,
java.lang.String nucleotides,
java.lang.String option)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationsolution - : contains the different ion and agent concentrationsnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static double getCMeltingResult(java.lang.String args)
args - : contains test optionspublic static double getC4_3MeltingResult(java.lang.String args)
args - : contains test optionspublic static void displayResultsMeltingC(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationion - : contains the different ion concentrationsnucleotides - : oligomer concentrationpublic static void displayResultsDNA_RNAMeltingC(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationion - : contains the different ion concentrationsnucleotides - : oligomer concentrationpublic static void displayResultsDNA_RNAMelting4_3(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationion - : contains the different ion concentrationsnucleotides - : oligomer concentrationpublic static void displayResultsMeltingC4_3(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationion - : contains the different ion concentrationsnucleotides - : oligomer concentrationpublic static void displayResultsMeltingCSelfComplementary(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationsolution - : contains the different ion and agent concentrationsnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public static void displayResultsMeltingC4_3SelfComplementary(java.util.Properties properties,
java.util.ArrayList<java.lang.String> methodNames,
java.lang.String hybridization,
java.lang.String ion,
java.lang.String nucleotides)
properties - : contains the experimental data.methodNames - : contains all the method or model to test with the experimental data.hybridization - : type of hybridizationsolution - : contains the different ion and agent concentrationsnucleotides - : oligomer concentrationoption - : option name for the pattern computation method.public class MainTestInosineMelting4_3
extends java.lang.Object
| Constructor and Description |
|---|
MainTestInosineMelting4_3() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestMeltingCPerfectMatching
extends java.lang.Object
| Constructor and Description |
|---|
MainTestMeltingCPerfectMatching() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestLockedAcidNucleic
extends java.lang.Object
| Constructor and Description |
|---|
MainTestLockedAcidNucleic() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestGUBasePairs
extends java.lang.Object
| Constructor and Description |
|---|
MainTestGUBasePairs() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestDNADanglingEndMeltingC
extends java.lang.Object
| Constructor and Description |
|---|
MainTestDNADanglingEndMeltingC() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestPerfectMatching
extends java.lang.Object
| Constructor and Description |
|---|
MainTestPerfectMatching() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestApproximativeMode
extends java.lang.Object
| Constructor and Description |
|---|
MainTestApproximativeMode() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestSecondDanglingEnd
extends java.lang.Object
| Constructor and Description |
|---|
MainTestSecondDanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestInosineBasePairs
extends java.lang.Object
| Constructor and Description |
|---|
MainTestInosineBasePairs() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestSingleDanglingEnd
extends java.lang.Object
| Constructor and Description |
|---|
MainTestSingleDanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestNaEqMethods
extends java.lang.Object
| Constructor and Description |
|---|
MainTestNaEqMethods() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestCNGSequences
extends java.lang.Object
| Constructor and Description |
|---|
MainTestCNGSequences() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestLongDanglingEnd
extends java.lang.Object
| Constructor and Description |
|---|
MainTestLongDanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestHydroxyadenine
extends java.lang.Object
| Constructor and Description |
|---|
MainTestHydroxyadenine() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestSingleMismatchLockedAcidNucleic
extends java.lang.Object
| Constructor and Description |
|---|
MainTestSingleMismatchLockedAcidNucleic() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
| Class | Description |
|---|---|
| MainTest |
This class contains the different method tests.
|
| MainTestApproximativeMode |
This class exists to test the different approximative methods.
|
| MainTestApproximativeModeMeltingC |
This class exists to test the formulas approximations of MELTING 4.2 with DNA sequences.
|
| MainTestAzobenzene |
This class exists to test the different azobenzene methods.
|
| MainTestCNGSequences |
This class exists to test the different CNG repeats methods.
|
| MainTestDNADanglingEndMeltingC | |
| MainTestDNAMagnesiumCorrections |
This class exists to test the different magnesium corrections with DNA sequences.
|
| MainTestDNAMismatchesMeltingC | |
| MainTestDNASodiumCorrections |
This class exists to test the different sodium corrections with DNA sequences.
|
| MainTestGUBasePairs |
This class exists to test the different GU base pair methods.
|
| MainTestHydroxyadenine |
This class exists to test the different hydroxyadenine methods.
|
| MainTestInosineBasePairs |
This class exists to test the different inosine methods.
|
| MainTestInosineMelting4_3 | |
| MainTestInternalLoop |
This class exists to test the different internal loop methods.
|
| MainTestLockedAcidNucleic |
This class exists to test the different locked nucleic acid methods.
|
| MainTestLongDanglingEnd |
This class exists to test the different long dangling end methods.
|
| MainTestMeltingC4_3PerfectMatching |
This class exists to test the different nearest neighbor parameters with Melting 4.3.
|
| MainTestMeltingCPerfectMatching |
This class exists to test the different nearest neighbor parameters with Melting 4.2.
|
| MainTestNaEqMethods |
This class exists to test the sodium equivalent formulas with DNA sequences.
|
| MainTestPerfectMatching |
This class exists to test the different nearest neighbor methods.
|
| MainTestSecondDanglingEnd |
This class exists to test the different second dangling end methods.
|
| MainTestSingleBulgeLoops |
This class exists to test the different single bulge loop methods.
|
| MainTestSingleDanglingEnd |
This class exists to test the different single dangling end methods.
|
| MainTestSingleMismatches |
This class exists to test the different single mismatch methods.
|
| MainTestSingleMismatchLockedAcidNucleic |
This class exists to test the different tandem locked nucleic acid methods.
|
| MainTestTandemLockedAcidNucleic |
This class exists to test the different tandem locked nucleic acid methods.
|
| MainTestTandemMismatches |
This class exists to test the different tandem mimsatches methods.
|
public class MainTestMeltingC4_3PerfectMatching
extends java.lang.Object
| Constructor and Description |
|---|
MainTestMeltingC4_3PerfectMatching() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestTandemMismatches
extends java.lang.Object
| Constructor and Description |
|---|
MainTestTandemMismatches() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestDNAMagnesiumCorrections
extends java.lang.Object
| Constructor and Description |
|---|
MainTestDNAMagnesiumCorrections() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestInternalLoop
extends java.lang.Object
| Constructor and Description |
|---|
MainTestInternalLoop() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestDNASodiumCorrections
extends java.lang.Object
| Constructor and Description |
|---|
MainTestDNASodiumCorrections() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestTandemLockedAcidNucleic
extends java.lang.Object
| Constructor and Description |
|---|
MainTestTandemLockedAcidNucleic() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestApproximativeModeMeltingC
extends java.lang.Object
| Constructor and Description |
|---|
MainTestApproximativeModeMeltingC() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestSingleMismatches
extends java.lang.Object
| Constructor and Description |
|---|
MainTestSingleMismatches() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestSingleBulgeLoops
extends java.lang.Object
| Constructor and Description |
|---|
MainTestSingleBulgeLoops() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
public class MainTestDNAMismatchesMeltingC
extends java.lang.Object
| Constructor and Description |
|---|
MainTestDNAMismatchesMeltingC() |
| Modifier and Type | Method and Description |
|---|---|
static void |
main(java.lang.String[] args) |
The Overview page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.
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