debian/0000755000000000000000000000000012235721554007174 5ustar debian/source/0000755000000000000000000000000012235721554010474 5ustar debian/source/format0000644000000000000000000000001412235720352011675 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000012235721554010623 5ustar debian/patches/mutilate-build-system.diff0000644000000000000000000000250112235720352015711 0ustar Index: jalview-2.7.dfsg~almost/build.xml =================================================================== --- jalview-2.7.dfsg~almost.orig/build.xml 2011-09-27 16:50:20.000000000 +0200 +++ jalview-2.7.dfsg~almost/build.xml 2011-10-16 00:25:56.823058139 +0200 @@ -18,13 +18,6 @@ --> - - - - - - - @@ -114,10 +107,6 @@ - - - - @@ -407,7 +396,7 @@ - + debian/patches/series0000644000000000000000000000010512235720352012027 0ustar mutilate-build-system.diff newer-jmol-api.diff newer-mime4j-api.diff debian/patches/newer-mime4j-api.diff0000644000000000000000000000124112235720352014520 0ustar Description: Patch to use the latest version of Apache Mime4J Author: Emmanuel Bourg Forwarded: no --- a/src/jalview/ws/io/mime/JalviewMimeContentHandler.java +++ b/src/jalview/ws/io/mime/JalviewMimeContentHandler.java @@ -26,9 +26,9 @@ import java.util.List; import org.apache.james.mime4j.MimeException; -import org.apache.james.mime4j.descriptor.BodyDescriptor; +import org.apache.james.mime4j.stream.BodyDescriptor; import org.apache.james.mime4j.parser.ContentHandler; -import org.apache.james.mime4j.parser.Field; +import org.apache.james.mime4j.stream.Field; /** * ContentHandler for parsing mime encoded messages into Jalview objects. debian/patches/newer-jmol-api.diff0000644000000000000000000002376112235720352014307 0ustar Author: Java upstream developers Description: fix build with newer Jmol API Patch from 12808bb..a60375a of http://source.jalview.org/git/jalview.git Index: jalview-2.7.dfsg/build.xml =================================================================== --- jalview-2.7.dfsg.orig/build.xml 2011-11-07 20:46:31.000000000 +0100 +++ jalview-2.7.dfsg/build.xml 2011-11-07 20:46:54.096166723 +0100 @@ -92,7 +92,7 @@ - + Index: jalview-2.7.dfsg/nbproject/project.properties =================================================================== --- jalview-2.7.dfsg.orig/nbproject/project.properties 2011-09-27 16:50:21.000000000 +0200 +++ jalview-2.7.dfsg/nbproject/project.properties 2011-11-07 20:46:54.096166723 +0100 @@ -59,8 +59,8 @@ file.reference.jaxrpc.jar=lib/jaxrpc.jar file.reference.JGoogleAnalytics_0.3.jar=lib/JGoogleAnalytics_0.3.jar file.reference.jhall.jar=lib/jhall.jar -file.reference.Jmol-12.1.13.jar=lib/Jmol-12.1.13.jar -file.reference.JmolApplet-12.1.13.jar=appletlib/JmolApplet-12.1.13.jar +file.reference.Jmol-12.2.4.jar=lib/Jmol-12.2.4.jar +file.reference.JmolApplet-12.2.4.jar=appletlib/JmolApplet-12.2.4.jar file.reference.log4j-1.2.8.jar=lib/log4j-1.2.8.jar file.reference.mail.jar=lib/mail.jar file.reference.min-jaba-client.jar=lib/min-jaba-client.jar @@ -91,7 +91,7 @@ ${file.reference.jaxrpc.jar}:\ ${file.reference.JGoogleAnalytics_0.3.jar}:\ ${file.reference.jhall.jar}:\ - ${file.reference.Jmol-12.1.13.jar}:\ + ${file.reference.Jmol-12.2.4.jar}:\ ${file.reference.miglayout-4.0-swing.jar}:\ ${file.reference.log4j-1.2.8.jar}:\ ${file.reference.mail.jar}:\ @@ -100,7 +100,7 @@ ${file.reference.xml-apis.jar}:\ ${file.reference.xercesImpl.jar}:\ ${file.reference.wsdl4j.jar}:\ - ${file.reference.JmolApplet-12.1.13.jar} + ${file.reference.JmolApplet-12.2.4.jar} # Space-separated list of extra javac options javac.compilerargs= javac.deprecation=false Index: jalview-2.7.dfsg/src/jalview/appletgui/AppletJmolBinding.java =================================================================== --- jalview-2.7.dfsg.orig/src/jalview/appletgui/AppletJmolBinding.java 2011-09-27 16:50:21.000000000 +0200 +++ jalview-2.7.dfsg/src/jalview/appletgui/AppletJmolBinding.java 2011-11-07 20:46:54.096166723 +0100 @@ -17,18 +17,16 @@ */ package jalview.appletgui; -import java.awt.Container; -import java.util.BitSet; - import jalview.api.AlignmentViewPanel; -import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.structure.StructureSelectionManager; +import java.awt.Container; +import java.util.BitSet; + import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolViewer; -import org.jmol.applet.AppletConsole; import org.jmol.popup.JmolPopup; class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding @@ -119,7 +117,8 @@ boolean asPopup) { - jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName, + jmolpopup = new JmolPopup(); + jmolpopup.initialize(viewer, translateLocale, menuName, asPopup); } @@ -150,7 +149,9 @@ protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2, Container consolePanel, String buttonsToShow) { - return new AppletConsole(viewer2, consolePanel); + //return new org.jmol.console.AppletConsole(viewer2, consolePanel); + JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole().getAppConsole(viewer2); + return appc; } @Override @@ -177,5 +178,10 @@ public void releaseReferences(Object svl) { } - + @Override + public void resizeInnerPanel(String data) + { + // TODO Auto-generated method stub + + } } Index: jalview-2.7.dfsg/src/jalview/ext/jmol/JalviewJmolBinding.java =================================================================== --- jalview-2.7.dfsg.orig/src/jalview/ext/jmol/JalviewJmolBinding.java 2011-09-27 16:50:21.000000000 +0200 +++ jalview-2.7.dfsg/src/jalview/ext/jmol/JalviewJmolBinding.java 2011-11-07 20:46:54.096166723 +0100 @@ -17,32 +17,40 @@ */ package jalview.ext.jmol; -import java.io.File; -import java.net.URL; -import java.util.*; -import java.applet.Applet; -import java.awt.*; -import java.awt.event.*; - -import javax.swing.JPanel; - import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.SequenceStructureBinding; import jalview.api.StructureSelectionManagerProvider; -import jalview.datamodel.*; -import jalview.structure.*; -import jalview.io.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; + +import java.awt.Color; +import java.awt.Container; +import java.awt.event.ComponentEvent; +import java.awt.event.ComponentListener; +import java.io.File; +import java.net.URL; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Map; +import java.util.Vector; -import org.jmol.api.*; import org.jmol.adapter.smarter.SmarterJmolAdapter; - -import org.jmol.popup.*; -import org.jmol.viewer.JmolConstants; -import org.jmol.viewer.Viewer; - -import jalview.schemes.*; +import org.jmol.api.JmolAppConsoleInterface; +import org.jmol.api.JmolSelectionListener; +import org.jmol.api.JmolStatusListener; +import org.jmol.api.JmolViewer; +import org.jmol.constant.EnumCallback; +import org.jmol.popup.JmolPopup; public abstract class JalviewJmolBinding implements StructureListener, JmolStatusListener, SequenceStructureBinding, @@ -940,47 +948,48 @@ } - public void notifyCallback(int type, Object[] data) + @Override + public void notifyCallback(EnumCallback type, Object[] data) { try { switch (type) { - case JmolConstants.CALLBACK_LOADSTRUCT: + case LOADSTRUCT: notifyFileLoaded((String) data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer) data[5]).intValue()); break; - case JmolConstants.CALLBACK_PICK: + case PICK: notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); // also highlight in alignment - case JmolConstants.CALLBACK_HOVER: + case HOVER: notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); break; - case JmolConstants.CALLBACK_SCRIPT: + case SCRIPT: notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue()); break; - case JmolConstants.CALLBACK_ECHO: + case ECHO: sendConsoleEcho((String) data[1]); break; - case JmolConstants.CALLBACK_MESSAGE: + case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) : (String) data[1]); break; - case JmolConstants.CALLBACK_ERROR: + case ERROR: // System.err.println("Ignoring error callback."); break; - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_RESIZE: + case SYNC: + case RESIZE: refreshGUI(); break; - case JmolConstants.CALLBACK_MEASURE: + case MEASURE: - case JmolConstants.CALLBACK_CLICK: + case CLICK: default: System.err.println("Unhandled callback " + type + " " + data[1].toString()); @@ -993,24 +1002,25 @@ } } - public boolean notifyEnabled(int callbackPick) + @Override + public boolean notifyEnabled(EnumCallback callbackPick) { switch (callbackPick) { - case JmolConstants.CALLBACK_ECHO: - case JmolConstants.CALLBACK_LOADSTRUCT: - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_MESSAGE: - case JmolConstants.CALLBACK_PICK: - case JmolConstants.CALLBACK_SCRIPT: - case JmolConstants.CALLBACK_HOVER: - case JmolConstants.CALLBACK_ERROR: + case ECHO: + case LOADSTRUCT: + case MEASURE: + case MESSAGE: + case PICK: + case SCRIPT: + case HOVER: + case ERROR: return true; - case JmolConstants.CALLBACK_RESIZE: - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_CLICK: - case JmolConstants.CALLBACK_ANIMFRAME: - case JmolConstants.CALLBACK_MINIMIZATION: + case RESIZE: + case SYNC: + case CLICK: + case ANIMFRAME: + case MINIMIZATION: } return false; } @@ -1542,5 +1552,10 @@ { return ssm.printMapping(pdbfile); } - + @Override + public void resizeInnerPanel(String data) + { + // Jalview doesn't honour resize panel requests + + } } Index: jalview-2.7.dfsg/src/jalview/gui/AppJmolBinding.java =================================================================== --- jalview-2.7.dfsg.orig/src/jalview/gui/AppJmolBinding.java 2011-09-27 16:50:21.000000000 +0200 +++ jalview-2.7.dfsg/src/jalview/gui/AppJmolBinding.java 2011-11-07 20:46:54.096166723 +0100 @@ -152,7 +152,8 @@ boolean asPopup) { - jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName, + jmolpopup = new JmolPopup(); + jmolpopup.initialize(viewer, translateLocale, menuName, asPopup); } debian/wrappers/0000755000000000000000000000000012235721554011037 5ustar debian/wrappers/jalview0000644000000000000000000000032412235720352012415 0ustar #!/bin/sh # Include the wrappers utility script . /usr/lib/java-wrappers/java-wrappers.sh # We need openjdk or sun6 find_java_runtime openjdk sun6 find_jar_classpath jalview run_java jalview.bin.Jalview "$@" debian/manpages/0000755000000000000000000000000012235721554010767 5ustar debian/manpages/jalview.10000644000000000000000000000164012235720352012506 0ustar .\" Hey, EMACS: -*- nroff -*- .\" First parameter, NAME, should be all caps .\" Copyright 2011 by Vincent Fourmond .\" Can be modified and distributed under the terms of the GNU General .\" public license, version 3 or any later version at your option. .TH JALVIEW 1 "26-01-2009" .SH NAME jalview \- Sequence alignement viewer .SH SYNOPSIS .B jalview .SH DESCRIPTION .B jalview provides facilities for viewing/editing and otherwise manipulating sequence alignments (DNA, amino acids). .SH JAVA-WRAPPERS NOTE This program is a shell script wrapper based on .BR java-wrappers (7). You therefore benefit from several features; please see the .BR java-wrappers (7) manual page for more information about them. .SH SEE ALSO .B http://www.jalview.org .SH AUTHOR This manual page was written by Vincent Fourmond from the Debian project, but may be used by others. debian/jalview.menu0000644000000000000000000000016312235720352011516 0ustar ?package(jalview):needs="X11" section="Applications/Science/Biology"\ title="Jalview" command="/usr/bin/jalview" debian/docs0000644000000000000000000000000712235720352010037 0ustar README debian/watch0000644000000000000000000000025112235720352010216 0ustar version=3 opts="dversionmangle=s/\.dfsg//,uversionmangle=s/_/./g;s/\.0(\d)/.0.$1/g" \ http://www.jalview.org/source jalview_([\d_]+)\.tar\.gz debian debian/new-upstream debian/control0000644000000000000000000000303112235721035010566 0ustar Source: jalview Section: science Priority: optional Maintainer: Debian Java Maintainers Uploaders: Vincent Fourmond Build-Depends: cdbs, debhelper (>= 7), default-jdk, ant, ant-optional, libxerces2-java, libxalan2-java, libaxis-java, libwsdl4j-java, libgnujaf-java, libgnumail-java, liblog4j1.2-java, javahelp2, libcommons-discovery-java, libcommons-logging-java, libjmol-java (>= 12.1.42), jmol-applet (>= 12.1.42), libcastor-xml-java, libjaba-client-java, javahelper, libjswingreader-java, libmiglayout-java, icedtea-netx-common, libhttpmime-java, libhttpcore-java, libapache-mime4j-java (>= 0.7.2), libhttpclient-java, libvamsas-client-java Standards-Version: 3.9.4 Homepage: http://www.jalview.org Vcs-Svn: svn://anonscm.debian.org/pkg-java/trunk/jalview Vcs-Browser: http://svn.debian.org/viewsvn/pkg-java/trunk/jalview Package: jalview Architecture: all Depends: ${misc:Depends}, default-jre | java6-runtime, java-wrappers (>= 0.1.22), libjmol-java (>= 12.1.42), ${java:Depends} Suggests: kalign, t-coffee, clustalw Description: multiple alignment editor JalView is a Java alignment editor that can work with sequence alignment produced by programs implementing alignment algorithms such as clustalw, kalign and t-coffee. . It has lots of features, is actively developed, and will compare advantageously to BioEdit, while being free as in free speech ! debian/jalview.manpages0000644000000000000000000000003112235720352012337 0ustar debian/manpages/jalview.1debian/dirs0000644000000000000000000000002612235720352010051 0ustar usr/share/java usr/bindebian/new-upstream0000755000000000000000000000214512235720352011546 0ustar #!/bin/sh # # new-upstream: copyright 2008, 2009 by Vincent Fourmond. # See debian/copyright file for details. # # Called by uscan; from uscan(1): # # Finally, if a third parameter (an action) is given in the watchfile # line, this is taken as the name of a command, and the command # command --upstream-version version filename # # is executed, using either the original file or the symlink name. # # Thanks to Sam Morris for giving me the idea # version=$2 filename=$3 dir=`mktemp -d` # We repackage the upstream source zip file: tar xvz -C $dir -f "$filename" origname=jalview_$version.dfsg.orig.tar.bz2 # We repackage excluding the lib/ subdir cd $dir # Removing the utils/ directory, not needed for build ? rm -rf jalview*/utils # Removing all binary jars... find -name '*.jar' | xargs rm # Removing examples/ subdirectory, whose copyright status is unclear # to me for the time being rm -rf jalview*/examples echo "Creating archive" tar cvj -f $origname jalview* cd - # We remove any file already existing there: it might be a symlink. rm -f $orginame mv $dir/$origname .. # rm -rf $dirdebian/jalview.jlibs0000644000000000000000000000002112235720352011646 0ustar dist/jalview.jar debian/rules0000755000000000000000000000213112235720352010244 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 VERSION = $(shell dpkg-parsechangelog | egrep '^Version' | \ sed -r 's/Version:\s*//' | sed -r 's/^[0-9]+://' | \ sed -r 's/(\.dfsg)?-[0-9.]+//') include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/javahelper.mk include /usr/share/cdbs/1/class/ant.mk JAVA_HOME_DIRS := /usr/lib/jvm/default-java ANT_HOME := /usr/share/ant DEB_ANT_COMPILER := modern DEB_BUILDDIR := . DEB_ANT_CLEAN_TARGET := clean DEB_ANT_BUILD_TARGET := makedist DEB_JARS := castor-xml commons-logging log4j-1.2 \ castor-core Jmol min-jaba-client axis-jaxrpc commons-discovery \ axis jh vamsas-client /usr/share/jmol-applet/JmolApplet.jar \ jswingreader miglayout /usr/share/icedtea-web/plugin.jar \ httpmime httpcore apache-mime4j-core httpclient jsearch-indexer ANT_OPTS := -Dbuild.sysclasspath=last \ -DJALVIEW_VERSION=$(VERSION) JH_CLASSPATH_ARGS := -c"$(shell echo $(DEB_CLASSPATH) | sed 's/:/ /g')" debian/jalview/usr/share/java/jalview.jar clean:: rm -Rf dist debian/compat0000644000000000000000000000000212235720352010365 0ustar 7 debian/changelog0000644000000000000000000000310212235721462011040 0ustar jalview (2.7.dfsg-3) unstable; urgency=low * Team upload. [Emmanuel Bourg] * Added a patch to compile with Apache Mime4J 0.7.2 * debian/control: - Updated Standards-Version to 3.9.4 (no changes) - Runtime dependency on default-jre | java6-runtime (Closes: #727791) - Removed the duplicate build dependencies on javahelp2 and libaxis-java - Fixed a typo in the package description (Closes: #676623) * debian/copyright: Updated the Format URI * Updated debian/watch to catch the new releases * debian/rules: - Added a clean target to allow rebuilds - Added jsearch-indexer.jar to the classpath to fix the buildindices target [Niels Thykier] * Move package under under the Debian Java team with permission from Vincent. -- Emmanuel Bourg Mon, 04 Nov 2013 14:37:52 +0100 jalview (2.7.dfsg-2) unstable; urgency=low * Upload to unstable now that jmol is there too * Pull patches/newer-jmol-api.diff from upstream's git repository to make jalview work with jmol currently in unstable. -- Vincent Fourmond Mon, 07 Nov 2011 20:47:14 +0100 jalview (2.7.dfsg-1) experimental; urgency=low * Initial release (Closes: #507436) * Adding a debian/new-upstream script to repackage the original tarball, getting rid of the bundled precompiled JAR files (I love JAR files) * Using dh 7 and javahelper * Using jh_build for building * Uploading to experimental as it works only with the version of jmol in experimental -- Vincent Fourmond Wed, 19 Oct 2011 20:19:46 +0200 debian/copyright0000644000000000000000000000646312235720352011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: jalview Upstream-Contact: jalview-discuss@jalview.org Source: The original tarball was made downloading the jalview-*.tar.gz tarball on http://www.jalview.org/versions.html, and stripping all binary jars. . For more details, see the debian/new-upstream script that takes care of the repackaging. Files: * Copyright: Copyright 2007-2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle License: GPL-3+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'. Files: src/org/biojava/dasobert/* Copyright: 2004-2007 Andreas Prlic License: LGPL-2.1 This code may be freely distributed and modified under the terms of the GNU Lesser General Public Licence. This should be distributed with the code. . On Debian systems, the complete text of the GNU Lesser Public License can be found in `/usr/share/common-licenses/LGPL-2.1'. Files: src/org/jibble/* Copyright: 2001-2004 Paul James Mutton License: GPL-2 This software is dual-licensed, allowing you to choose between the GNU General Public License (GPL) and the www.jibble.org Commercial License. Since the GPL may be too restrictive for use in a proprietary application, a commercial license is also provided. Full license information can be found at http://www.jibble.org/licenses/. . On Debian systems, the complete text of the GNU General Public License (version 2) can be found in `/usr/share/common-licenses/GPL-2'. Files: debian/* Copyright: Copyright (C) 2009-2011 Vincent Fourmond License: GPL-3+ (see above) Files: src/com/stevesoft/pat/* Copyright: Copyright 2001, Steven R. Brandt License: LGPL3+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU Lesser Public License version 3 can be found in `/usr/share/common-licenses/LGPL-3'. debian/jalview.install0000644000000000000000000000003712235720352012220 0ustar debian/wrappers/jalview usr/bin