[med-svn] r19925 - in trunk/packages/figtree/tags: . 1.4.2-1/debian 1.4.2-1/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Wed Aug 12 09:14:03 UTC 2015
Author: osallou
Date: 2015-08-12 09:14:03 +0000 (Wed, 12 Aug 2015)
New Revision: 19925
Added:
trunk/packages/figtree/tags/1.4.2-1/
trunk/packages/figtree/tags/1.4.2-1/debian/changelog
trunk/packages/figtree/tags/1.4.2-1/debian/control
trunk/packages/figtree/tags/1.4.2-1/debian/figtree.manifest
trunk/packages/figtree/tags/1.4.2-1/debian/patches/build_figtree_gui_only.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_classpath_in_build_xml.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_jebl.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/ignore_quaqua.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/java7-compat.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/series
Removed:
trunk/packages/figtree/tags/1.4.2-1/debian/changelog
trunk/packages/figtree/tags/1.4.2-1/debian/control
trunk/packages/figtree/tags/1.4.2-1/debian/figtree.manifest
trunk/packages/figtree/tags/1.4.2-1/debian/patches/build_figtree_gui_only.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_classpath_in_build_xml.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/ignore_quaqua.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/java7-compat.patch
trunk/packages/figtree/tags/1.4.2-1/debian/patches/series
Log:
[svn-buildpackage] Tagging figtree 1.4.2-1
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/changelog
===================================================================
--- trunk/packages/figtree/trunk/debian/changelog 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/changelog 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,45 +0,0 @@
-figtree (1.4-2) unstable; urgency=low
-
- * Force set of JAVA_HOME in debian/rules (Closes: #715225).
-
- -- Olivier Sallou <osallou at debian.org> Tue, 09 Jul 2013 14:42:53 +0200
-
-figtree (1.4-1) unstable; urgency=low
-
- [ Andreas Tille ]
- * New upstream version (adapted quilt patches)
- * debian/control:
- - Standards-Version: 3.9.4 (no changes needed)
- - Versioned Build-Depends: libjam-java (>= 0.0.r304)
- - cme fix dpkg-control
- - Use anonscm in Vcs fields
- * debian/get-orig-source: Use xz compression for source tarball
-
- [ Olivier Sallou ]
- * debian/patches/fix_itext_api_change.patch: Add patch to manage iText
- API change
- Closes: #713143
- * Patch build.xml to load JVM Hotspot library
-
- -- Andreas Tille <tille at debian.org> Mon, 17 Dec 2012 13:32:34 +0100
-
-figtree (1.3.1-2) unstable; urgency=low
-
- * Apply patch provided by James Page <james.page at ubuntu.com> to build
- with openjdk-7 (thanks to James)
- Closes: #683532
- * debian/control:
- - Switch Build-Depends to default-jdk (also thanks to James)
- - Fixed Vcs fields
- - Standards-Version: 3.9.3 (no changes needed)
- * debhelper 9 (control+compat)
- * debian/copyright: Fixed some DEP5 issues
-
- -- Andreas Tille <tille at debian.org> Thu, 02 Aug 2012 09:43:00 +0200
-
-figtree (1.3.1-1) unstable; urgency=low
-
- * Initial release (Closes: #614278)
- Fixed copyright regarding some LGPLed files
-
- -- Andreas Tille <tille at debian.org> Mon, 21 Feb 2011 08:17:38 +0100
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/changelog (from rev 19924, trunk/packages/figtree/trunk/debian/changelog)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/changelog (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/changelog 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,52 @@
+figtree (1.4.2-1) unstable; urgency=medium
+
+ * New upstream release
+ * d/control: use standards 3.9.6
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 12 Aug 2015 09:35:33 +0200
+
+figtree (1.4-2) unstable; urgency=low
+
+ * Force set of JAVA_HOME in debian/rules (Closes: #715225).
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 09 Jul 2013 14:42:53 +0200
+
+figtree (1.4-1) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * New upstream version (adapted quilt patches)
+ * debian/control:
+ - Standards-Version: 3.9.4 (no changes needed)
+ - Versioned Build-Depends: libjam-java (>= 0.0.r304)
+ - cme fix dpkg-control
+ - Use anonscm in Vcs fields
+ * debian/get-orig-source: Use xz compression for source tarball
+
+ [ Olivier Sallou ]
+ * debian/patches/fix_itext_api_change.patch: Add patch to manage iText
+ API change
+ Closes: #713143
+ * Patch build.xml to load JVM Hotspot library
+
+ -- Andreas Tille <tille at debian.org> Mon, 17 Dec 2012 13:32:34 +0100
+
+figtree (1.3.1-2) unstable; urgency=low
+
+ * Apply patch provided by James Page <james.page at ubuntu.com> to build
+ with openjdk-7 (thanks to James)
+ Closes: #683532
+ * debian/control:
+ - Switch Build-Depends to default-jdk (also thanks to James)
+ - Fixed Vcs fields
+ - Standards-Version: 3.9.3 (no changes needed)
+ * debhelper 9 (control+compat)
+ * debian/copyright: Fixed some DEP5 issues
+
+ -- Andreas Tille <tille at debian.org> Thu, 02 Aug 2012 09:43:00 +0200
+
+figtree (1.3.1-1) unstable; urgency=low
+
+ * Initial release (Closes: #614278)
+ Fixed copyright regarding some LGPLed files
+
+ -- Andreas Tille <tille at debian.org> Mon, 21 Feb 2011 08:17:38 +0100
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/control
===================================================================
--- trunk/packages/figtree/trunk/debian/control 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/control 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,35 +0,0 @@
-Source: figtree
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Olivier Sallou <osallou at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9),
- javahelper (>=0.25),
- default-jdk,
- ant,
- libjebl2-java,
- libjam-java (>= 0.0.r304),
- libtrove-java,
- libfreehep-graphics2d-java,
- libfreehep-graphicsio-java,
- libfreehep-graphicsio-pdf-java,
- libfreehep-graphicsio-ps-java,
- libfreehep-graphicsio-swf-java,
- libfreehep-graphicsio-svg-java,
- libfreehep-graphicsio-emf-java,
- libitext5-java
-Standards-Version: 3.9.4
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/figtree/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/figtree/trunk
-Homepage: http://tree.bio.ed.ac.uk/software/figtree/
-
-Package: figtree
-Architecture: all
-Depends: ${misc:Depends},
- ${java:Depends}
-Description: graphical phylogenetic tree viewer
- FigTree is designed as a graphical viewer of phylogenetic trees and as
- a program for producing publication-ready figures. In particular it is
- designed to display summarized and annotated trees produced by BEAST.
-
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/control (from rev 19920, trunk/packages/figtree/trunk/debian/control)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/control (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/control 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,36 @@
+Source: figtree
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Olivier Sallou <osallou at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ javahelper (>=0.25),
+ default-jdk,
+ ant,
+ libbatik-java,
+ libjebl2-java,
+ libjam-java (>= 0.0.r304),
+ libtrove-java,
+ libfreehep-graphics2d-java,
+ libfreehep-graphicsio-java,
+ libfreehep-graphicsio-pdf-java,
+ libfreehep-graphicsio-ps-java,
+ libfreehep-graphicsio-swf-java,
+ libfreehep-graphicsio-svg-java,
+ libfreehep-graphicsio-emf-java,
+ libitext5-java
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/figtree/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/figtree/trunk
+Homepage: http://tree.bio.ed.ac.uk/software/figtree/
+
+Package: figtree
+Architecture: all
+Depends: ${misc:Depends},
+ ${java:Depends}
+Description: graphical phylogenetic tree viewer
+ FigTree is designed as a graphical viewer of phylogenetic trees and as
+ a program for producing publication-ready figures. In particular it is
+ designed to display summarized and annotated trees produced by BEAST.
+
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/figtree.manifest
===================================================================
--- trunk/packages/figtree/trunk/debian/figtree.manifest 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/figtree.manifest 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,3 +0,0 @@
-usr/share/java/figtree.jar:
- Class-Path: /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/freehep-graphics2d.jar /usr/share/java/freehep-graphicsio.jar /usr/share/java/freehep-graphicsio-pdf.jar /usr/share/java/freehep-graphicsio-ps.jar /usr/share/java/freehep-graphicsio-emf.jar /usr/share/java/freehep-graphicsio-swf.jar /usr/share/java/freehep-graphicsio-svg.jar /usr/share/java/freehep-export.jar /usr/share/java/itext5.jar
- Main-Class: figtree/application/FigTreeApplication
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/figtree.manifest (from rev 19920, trunk/packages/figtree/trunk/debian/figtree.manifest)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/figtree.manifest (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/figtree.manifest 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,3 @@
+usr/share/java/figtree.jar:
+ Class-Path: /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/freehep-graphics2d.jar /usr/share/java/freehep-graphicsio.jar /usr/share/java/freehep-graphicsio-pdf.jar /usr/share/java/freehep-graphicsio-ps.jar /usr/share/java/freehep-graphicsio-emf.jar /usr/share/java/freehep-graphicsio-swf.jar /usr/share/java/freehep-graphicsio-svg.jar /usr/share/java/freehep-export.jar /usr/share/java/itext5.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-awt-util.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-util.jar /usr/share/java/batik-xml.jar
+ Main-Class: figtree/application/FigTreeApplication
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/patches/build_figtree_gui_only.patch
===================================================================
--- trunk/packages/figtree/trunk/debian/patches/build_figtree_gui_only.patch 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/build_figtree_gui_only.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,43 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Mon, 07 Feb 2011 12:02:43 +0100
-Description: Do not build targets figtree-pdf.jar and figtree.war
-
---- a/build.xml
-+++ b/build.xml
-@@ -59,36 +59,6 @@
- </manifest>
- </jar>
-
-- <jar jarfile="${dist}/figtree-pdf.jar">
-- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
-- <zipgroupfileset dir="${lib}" includes="iText.jar"/>
-- <fileset dir="${build}" includes="**/*.class,**/*.properties,**/*.png,**/*.gif"/>
-- <manifest>
-- <attribute name="Built-By" value="${user.name}"/>
-- <attribute name="Main-Class" value="figtree.application.FigTreePDF"/>
-- </manifest>
-- </jar>
--
-- <war destfile="${dist}/figtree.war"
-- webxml="WebRoot/WEB-INF/web.xml">
-- <fileset dir="WebRoot"/>
-- <lib dir="${lib}/jwt">
-- <include name="commons-fileupload-1.2.1.jar" />
-- <include name="commons-io-1.4.jar" />
-- <include name="jwt-3.1.6.jar" />
-- </lib>
-- <lib dir="${lib}">
-- <include name="freehep.jar" />
-- <include name="iText.jar" />
-- <include name="jam.jar" />
-- <include name="jdom.jar" />
-- <include name="jebl.jar" />
-- </lib>
-- <classes dir="${build}"/>
-- </war>
--
--
- </target>
-
- <property name="version" value="1.4.1" />
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/patches/build_figtree_gui_only.patch (from rev 19922, trunk/packages/figtree/trunk/debian/patches/build_figtree_gui_only.patch)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/patches/build_figtree_gui_only.patch (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/build_figtree_gui_only.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,41 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Mon, 07 Feb 2011 12:02:43 +0100
+Description: Do not build targets figtree-pdf.jar and figtree.war
+--- a/build.xml
++++ b/build.xml
+@@ -60,35 +60,6 @@
+ </manifest>
+ </jar>
+
+- <jar jarfile="${dist}/figtree-pdf.jar">
+- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
+- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
+- <zipgroupfileset dir="${lib}" includes="iText.jar"/>
+- <fileset dir="${build}" includes="**/*.class,**/*.properties,**/*.png,**/*.gif"/>
+- <manifest>
+- <attribute name="Built-By" value="${user.name}"/>
+- <attribute name="Main-Class" value="figtree.application.FigTreePDF"/>
+- </manifest>
+- </jar>
+-
+- <war destfile="${dist}/figtree.war"
+- webxml="WebRoot/WEB-INF/web.xml">
+- <fileset dir="WebRoot"/>
+- <lib dir="${lib}/jwt">
+- <include name="commons-fileupload-1.2.1.jar" />
+- <include name="commons-io-1.4.jar" />
+- <include name="jwt-3.1.6.jar" />
+- </lib>
+- <lib dir="${lib}">
+- <include name="iText.jar" />
+- <include name="jam.jar" />
+- <include name="jdom.jar" />
+- <include name="jebl.jar" />
+- </lib>
+- <classes dir="${build}"/>
+- </war>
+-
+-
+ </target>
+
+ <property name="version" value="1.4.3" />
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_classpath_in_build_xml.patch
===================================================================
--- trunk/packages/figtree/trunk/debian/patches/fix_classpath_in_build_xml.patch 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_classpath_in_build_xml.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,24 +0,0 @@
-Description: Fix Classpath to use Debian packaged classes
-Author: Andreas Tille <tille at debian.org>
-Last-Updated: 2013-06-28
-Forwarded: no
-Subject: adapt build file to match debian env
---- a/build.xml
-+++ b/build.xml
-@@ -11,6 +11,7 @@
- <property name="build" location="build"/>
-
- <property name="lib" location="lib"/>
-+ <property name="deblib" location="/usr/share/java"/>
- <property name="dist" location="dist"/>
-
- <property environment="env"/>
-@@ -35,7 +36,7 @@
- <target name="compile" depends="init">
- <!-- Compile the java code from ${src} into ${build} -->
- <javac source="1.5" target="1.5" srcdir="${src}" destdir="${build}"
-- classpath="${lib}/jebl.jar:${lib}/jam.jar:${lib}/freehep.jar:${lib}/iText.jar:${lib}/quaqua.jar:${lib}/jwt/servlet-api-2.5-6.0.2.jar:${lib}/jwt/jwt-3.1.7pre1.jar">
-+ classpath="${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/freehep-graphics2d.jar:${deblib}/freehep-graphicsio.jar:${deblib}/freehep-graphicsio-pdf.jar:${deblib}/freehep-graphicsio-ps.jar:${deblib}/freehep-graphicsio-emf.jar:${deblib}/freehep-graphicsio-swf.jar:${deblib}/freehep-graphicsio-svg.jar:${deblib}/freehep-export.jar:${deblib}/itext5.jar:${env.JAVA_HOME}/lib/sa-jdi.jar">
- <include name="figtree/**"/>
- </javac>
- <copy todir="${build}" verbose="true">
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_classpath_in_build_xml.patch (from rev 19920, trunk/packages/figtree/trunk/debian/patches/fix_classpath_in_build_xml.patch)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_classpath_in_build_xml.patch (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_classpath_in_build_xml.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,38 @@
+Description: Fix Classpath to use Debian packaged classes
+Author: Andreas Tille <tille at debian.org>
+Last-Updated: 2013-06-28
+Forwarded: no
+Subject: adapt build file to match debian env
+--- a/build.xml
++++ b/build.xml
+@@ -11,6 +11,7 @@
+ <property name="build" location="build"/>
+
+ <property name="lib" location="lib"/>
++ <property name="deblib" location="/usr/share/java"/>
+ <property name="dist" location="dist"/>
+
+ <property environment="env"/>
+@@ -35,7 +36,7 @@
+ <target name="compile" depends="init">
+ <!-- Compile the java code from ${src} into ${build} -->
+ <javac source="1.6" target="1.6" srcdir="${src}" destdir="${build}"
+- classpath="${lib}/jebl.jar:${lib}/jam.jar:${lib}/batik-awt-util.jar:${lib}/batik-dom.jar:${lib}/batik-ext.jar:${lib}/batik-svggen.jar:${lib}/batik-util.jar:${lib}/batik-xml.jar:${lib}/xml-apis.jar:${lib}/iText.jar:${lib}/quaqua.jar:${lib}/jwt/servlet-api-2.5-6.0.2.jar:${lib}/jwt/jwt-3.1.7pre1.jar">
++ classpath="${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/batik-awt-util.jar:${deblib}/batik-dom.jar:${deblib}/batik-ext.jar:${deblib}/batik-svggen.jar:${deblib}/batik-util.jar:${deblib}/batik-xml.jar:${deblib}/freehep-graphics2d.jar:${deblib}/freehep-graphicsio.jar:${deblib}/freehep-graphicsio-pdf.jar:${deblib}/freehep-graphicsio-ps.jar:${deblib}/freehep-graphicsio-emf.jar:${deblib}/freehep-graphicsio-swf.jar:${deblib}/freehep-graphicsio-svg.jar:${deblib}/freehep-export.jar:${deblib}/itext5.jar:${env.JAVA_HOME}/lib/sa-jdi.jar">
+ <include name="figtree/**"/>
+ </javac>
+ <copy todir="${build}" verbose="true">
+@@ -48,11 +49,13 @@
+ <mkdir dir="${dist}"/>
+
+ <jar jarfile="${dist}/figtree.jar">
++ <!--
+ <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
+ <zipgroupfileset dir="${lib}" includes="jam.jar"/>
+ <zipgroupfileset dir="${lib}" includes="batik*.jar"/>
+ <zipgroupfileset dir="${lib}" includes="xml-apis.jar"/>
+ <zipgroupfileset dir="${lib}" includes="iText.jar"/>
++ -->
+ <fileset dir="${build}" includes="**/*.class,**/*.properties,**/*.png,**/*.gif"/>
+ <manifest>
+ <attribute name="Built-By" value="${user.name}"/>
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_jebl.patch (from rev 19922, trunk/packages/figtree/trunk/debian/patches/fix_jebl.patch)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_jebl.patch (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/fix_jebl.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,15 @@
+Author: Olivier Sallou <osallou at debian.org>
+Subject: update code to match jebl version
+Description: jebl in Debian has different API, modify code to match it.
+Last-Updated: 2015-08-12
+--- a/src/figtree/application/FigTreeFrame.java
++++ b/src/figtree/application/FigTreeFrame.java
+@@ -930,7 +930,7 @@
+
+ FileWriter writer = new FileWriter(file);
+ FigTreeNexusExporter exporter = new FigTreeNexusExporter(writer, true);
+- exporter.exportTrees(treeViewer.getTrees(), true);
++ exporter.exportTrees(treeViewer.getTrees());
+ exporter.writeFigTreeBlock(settings);
+
+ writer.close();
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/patches/ignore_quaqua.patch
===================================================================
--- trunk/packages/figtree/trunk/debian/patches/ignore_quaqua.patch 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/ignore_quaqua.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,147 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Mon, 07 Feb 2011 12:02:43 +0100
-Description: Quaqua (http://www.randelshofer.ch/quaqua/)
- is a Java class which provides OSX look and feel but only
- works on Mac. So this is simply not used on Linux and I
- simply deleted all lines containing the string [qQ]aqua
- which seems to lead to a usable application.
-
---- a/src/figtree/application/FigTreeApplication.java
-+++ b/src/figtree/application/FigTreeApplication.java
-@@ -55,8 +55,6 @@
-
- import javax.swing.*;
-
--import ch.randelshofer.quaqua.QuaquaManager;
--
- public class FigTreeApplication extends MultiDocApplication {
-
- public static final String VERSION = "1.4.1";
-@@ -321,41 +319,6 @@
- System.setProperty("apple.awt.showGrowBox","true");
- System.setProperty("apple.awt.graphics.UseQuartz","true");
-
-- try {
-- // set the Quaqua Look and Feel in the UIManager
-- javax.swing.SwingUtilities.invokeAndWait(new Runnable() {
-- public void run() {
-- try {
-- // Only override the UI's necessary for ColorChooser and
-- // FileChooser:
-- Set includes = new HashSet();
-- includes.add("ColorChooser");
-- includes.add("FileChooser");
-- includes.add("Component");
-- includes.add("Browser");
-- includes.add("Tree");
-- includes.add("SplitPane");
-- includes.add("TitledBorder");
--
-- try {
-- QuaquaManager.setIncludedUIs(includes);
-- } catch (java.lang.NoClassDefFoundError ncdfe) {
-- // this is to protect against the figtree.jar being
-- // run on Mac OS without Quaqua on the classpath
-- }
--
-- UIManager.setLookAndFeel(
-- "ch.randelshofer.quaqua.QuaquaLookAndFeel"
-- );
--
-- lafLoaded = true;
-- } catch (Exception e) {
-- }
-- }
-- });
-- } catch (Exception e) {
-- }
--
- UIManager.put("SystemFont", new Font("Lucida Grande", Font.PLAIN, 13));
- UIManager.put("SmallSystemFont", new Font("Lucida Grande", Font.PLAIN, 11));
- }
-@@ -423,4 +386,4 @@
- }
- }
-
--}
-\ No newline at end of file
-+}
---- a/src/figtree/treeviewer/TreeViewerController.java
-+++ b/src/figtree/treeviewer/TreeViewerController.java
-@@ -86,13 +86,10 @@
- rectangularTreeToggle.setFocusable(false);
- polarTreeToggle.setFocusable(false);
- radialTreeToggle.setFocusable(false);
-- rectangularTreeToggle.putClientProperty("Quaqua.Button.style", "toggleWest");
- rectangularTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured");
- rectangularTreeToggle.putClientProperty("JButton.segmentPosition", "first");
-- polarTreeToggle.putClientProperty("Quaqua.Button.style", "toggleCenter");
- polarTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured");
- polarTreeToggle.putClientProperty("JButton.segmentPosition", "middle");
-- radialTreeToggle.putClientProperty("Quaqua.Button.style", "toggleEast");
- radialTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured");
- radialTreeToggle.putClientProperty("JButton.segmentPosition", "last");
- ButtonGroup buttonGroup = new ButtonGroup();
---- a/src/figtree/application/FigTreeFrame.java
-+++ b/src/figtree/application/FigTreeFrame.java
-@@ -206,7 +206,6 @@
- // treeViewer.showStatistics();
- // }
- // });
--// settingsToolButton.putClientProperty("Quaqua.Button.style", "toolBarRollover");
- // toolBar.addComponent(settingsToolButton);
- // settingsToolButton.setEnabled(false);
-
-@@ -217,19 +216,16 @@
- toggle1.setFocusable(false);
- toggle1.putClientProperty("JButton.buttonType", "segmentedTextured");
- toggle1.putClientProperty("JButton.segmentPosition", "first");
-- toggle1.putClientProperty( "Quaqua.Button.style", "toggleWest");
-
- final JToggleButton toggle2 = new JToggleButton("Clade");
- toggle2.setFocusable(false);
- toggle2.putClientProperty("JButton.buttonType", "segmentedTextured");
- toggle2.putClientProperty("JButton.segmentPosition", "middle");
-- toggle2.putClientProperty( "Quaqua.Button.style", "toggleCenter");
-
- final JToggleButton toggle3 = new JToggleButton("Taxa");
- toggle3.setFocusable(false);
- toggle3.putClientProperty("JButton.buttonType", "segmentedTextured");
- toggle3.putClientProperty("JButton.segmentPosition", "last");
-- toggle3.putClientProperty( "Quaqua.Button.style", "toggleEast");
-
- ButtonGroup buttonGroup = new ButtonGroup();
- buttonGroup.add(toggle1);
-@@ -283,7 +279,6 @@
- prevTreeToolButton.setFocusable(false);
- prevTreeToolButton.putClientProperty("JButton.buttonType", "segmentedTextured");
- prevTreeToolButton.putClientProperty("JButton.segmentPosition", "first");
-- prevTreeToolButton.putClientProperty( "Quaqua.Button.style", "toggleWest");
-
- final ToolbarAction nextTreeToolbarAction =
- new ToolbarAction(null, "Next Tree...", nextIcon) {
-@@ -303,7 +298,6 @@
- nextTreeToolButton.setFocusable(false);
- nextTreeToolButton.putClientProperty("JButton.buttonType", "segmentedTextured");
- nextTreeToolButton.putClientProperty("JButton.segmentPosition", "last");
-- nextTreeToolButton.putClientProperty( "Quaqua.Button.style", "toggleEast");
-
- nextTreeToolbarAction.setEnabled(treeViewer.getCurrentTreeIndex() < treeViewer.getTreeCount() - 1);
- prevTreeToolbarAction.setEnabled(treeViewer.getCurrentTreeIndex() > 0);
-@@ -1718,4 +1712,4 @@
- private AnnotationDialog annotationDialog = null;
- private AnnotationDialog copyAnnotationDialog = null;
- private SelectAnnotationDialog selectAnnotationDialog = null;
--}
-\ No newline at end of file
-+}
---- a/src/figtree/treeviewer/ControllerOptionsPanel.java
-+++ b/src/figtree/treeviewer/ControllerOptionsPanel.java
-@@ -25,7 +25,6 @@
- }
-
- public static void setComponentLook(JComponent comp) {
-- comp.putClientProperty("Quaqua.Component.visualMargin", new Insets(0,0,0,0));
- Font font = UIManager.getFont("SmallSystemFont");
- if (font != null) {
- comp.setFont(font);
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/patches/ignore_quaqua.patch (from rev 19920, trunk/packages/figtree/trunk/debian/patches/ignore_quaqua.patch)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/patches/ignore_quaqua.patch (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/ignore_quaqua.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,145 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Mon, 07 Feb 2011 12:02:43 +0100
+Description: Quaqua (http://www.randelshofer.ch/quaqua/)
+ is a Java class which provides OSX look and feel but only
+ works on Mac. So this is simply not used on Linux and I
+ simply deleted all lines containing the string [qQ]aqua
+ which seems to lead to a usable application.
+
+--- a/src/figtree/application/FigTreeApplication.java
++++ b/src/figtree/application/FigTreeApplication.java
+@@ -51,7 +51,6 @@
+ import javax.imageio.ImageIO;
+ import javax.swing.*;
+
+-import ch.randelshofer.quaqua.QuaquaManager;
+
+ /**
+ * Application class for FigTree including main() method for invoking it.
+@@ -336,40 +335,6 @@
+ System.setProperty("apple.awt.showGrowBox","true");
+ System.setProperty("apple.awt.graphics.UseQuartz","true");
+
+- try {
+- // set the Quaqua Look and Feel in the UIManager
+- javax.swing.SwingUtilities.invokeAndWait(new Runnable() {
+- public void run() {
+- try {
+- // Only override the UI's necessary for ColorChooser and
+- // FileChooser:
+- Set includes = new HashSet();
+- includes.add("ColorChooser");
+- includes.add("FileChooser");
+- includes.add("Component");
+- includes.add("Browser");
+- includes.add("Tree");
+- includes.add("SplitPane");
+- includes.add("TitledBorder");
+-
+- try {
+- QuaquaManager.setIncludedUIs(includes);
+- } catch (java.lang.NoClassDefFoundError ncdfe) {
+- // this is to protect against the figtree.jar being
+- // run on Mac OS without Quaqua on the classpath
+- }
+-
+- UIManager.setLookAndFeel(
+- "ch.randelshofer.quaqua.QuaquaLookAndFeel"
+- );
+-
+- lafLoaded = true;
+- } catch (Exception e) {
+- }
+- }
+- });
+- } catch (Exception e) {
+- }
+
+ UIManager.put("SystemFont", new Font("Lucida Grande", Font.PLAIN, 13));
+ UIManager.put("SmallSystemFont", new Font("Lucida Grande", Font.PLAIN, 11));
+@@ -465,4 +430,4 @@
+ }
+ }
+
+-}
+\ No newline at end of file
++}
+--- a/src/figtree/treeviewer/TreeViewerController.java
++++ b/src/figtree/treeviewer/TreeViewerController.java
+@@ -112,13 +112,10 @@
+ rectangularTreeToggle.setFocusable(false);
+ polarTreeToggle.setFocusable(false);
+ radialTreeToggle.setFocusable(false);
+- rectangularTreeToggle.putClientProperty("Quaqua.Button.style", "toggleWest");
+ rectangularTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured");
+ rectangularTreeToggle.putClientProperty("JButton.segmentPosition", "first");
+- polarTreeToggle.putClientProperty("Quaqua.Button.style", "toggleCenter");
+ polarTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured");
+ polarTreeToggle.putClientProperty("JButton.segmentPosition", "middle");
+- radialTreeToggle.putClientProperty("Quaqua.Button.style", "toggleEast");
+ radialTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured");
+ radialTreeToggle.putClientProperty("JButton.segmentPosition", "last");
+ ButtonGroup buttonGroup = new ButtonGroup();
+--- a/src/figtree/application/FigTreeFrame.java
++++ b/src/figtree/application/FigTreeFrame.java
+@@ -224,7 +224,6 @@
+ // treeViewer.showStatistics();
+ // }
+ // });
+-// settingsToolButton.putClientProperty("Quaqua.Button.style", "toolBarRollover");
+ // toolBar.addComponent(settingsToolButton);
+ // settingsToolButton.setEnabled(false);
+
+@@ -235,19 +234,16 @@
+ toggle1.setFocusable(false);
+ toggle1.putClientProperty("JButton.buttonType", "segmentedTextured");
+ toggle1.putClientProperty("JButton.segmentPosition", "first");
+- toggle1.putClientProperty( "Quaqua.Button.style", "toggleWest");
+
+ final JToggleButton toggle2 = new JToggleButton("Clade");
+ toggle2.setFocusable(false);
+ toggle2.putClientProperty("JButton.buttonType", "segmentedTextured");
+ toggle2.putClientProperty("JButton.segmentPosition", "middle");
+- toggle2.putClientProperty( "Quaqua.Button.style", "toggleCenter");
+
+ final JToggleButton toggle3 = new JToggleButton("Taxa");
+ toggle3.setFocusable(false);
+ toggle3.putClientProperty("JButton.buttonType", "segmentedTextured");
+ toggle3.putClientProperty("JButton.segmentPosition", "last");
+- toggle3.putClientProperty( "Quaqua.Button.style", "toggleEast");
+
+ ButtonGroup buttonGroup = new ButtonGroup();
+ buttonGroup.add(toggle1);
+@@ -301,7 +297,6 @@
+ prevTreeToolButton.setFocusable(false);
+ prevTreeToolButton.putClientProperty("JButton.buttonType", "segmentedTextured");
+ prevTreeToolButton.putClientProperty("JButton.segmentPosition", "first");
+- prevTreeToolButton.putClientProperty( "Quaqua.Button.style", "toggleWest");
+
+ final ToolbarAction nextTreeToolbarAction =
+ new ToolbarAction(null, "Next Tree...", nextIcon) {
+@@ -321,7 +316,6 @@
+ nextTreeToolButton.setFocusable(false);
+ nextTreeToolButton.putClientProperty("JButton.buttonType", "segmentedTextured");
+ nextTreeToolButton.putClientProperty("JButton.segmentPosition", "last");
+- nextTreeToolButton.putClientProperty( "Quaqua.Button.style", "toggleEast");
+
+ nextTreeToolbarAction.setEnabled(treeViewer.getCurrentTreeIndex() < treeViewer.getTreeCount() - 1);
+ prevTreeToolbarAction.setEnabled(treeViewer.getCurrentTreeIndex() > 0);
+@@ -1852,4 +1846,4 @@
+ private AnnotationDialog annotationDialog = null;
+ private AnnotationDialog copyAnnotationDialog = null;
+ private SelectAnnotationDialog selectAnnotationDialog = null;
+-}
+\ No newline at end of file
++}
+--- a/src/figtree/treeviewer/ControllerOptionsPanel.java
++++ b/src/figtree/treeviewer/ControllerOptionsPanel.java
+@@ -51,7 +51,6 @@
+ }
+
+ public static void setComponentLook(JComponent comp) {
+- comp.putClientProperty("Quaqua.Component.visualMargin", new Insets(0,0,0,0));
+ Font font = UIManager.getFont("SmallSystemFont");
+ if (font != null) {
+ comp.setFont(font);
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/patches/java7-compat.patch
===================================================================
--- trunk/packages/figtree/trunk/debian/patches/java7-compat.patch 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/java7-compat.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,22 +0,0 @@
-Author: James Page <james.page at ubuntu.com>
-Date: Wed, 01 Aug 2012 14:58:30 +0100
-Bugs-Debian: http://bugs.debian.org/683532
-Description: Fix up Painter symbol resolution issue in TreeView class.
-
---- a/src/figtree/treeviewer/TreePane.java
-+++ b/src/figtree/treeviewer/TreePane.java
-@@ -8,6 +8,7 @@
- import figtree.treeviewer.decorators.*;
- import figtree.treeviewer.painters.*;
- import figtree.treeviewer.treelayouts.*;
-+import figtree.treeviewer.painters.Painter;
-
- import javax.swing.*;
- import java.awt.*;
-@@ -2231,4 +2232,4 @@
-
- private Map<Node, Shape> calloutPaths = new HashMap<Node, Shape>();
-
--}
-\ No newline at end of file
-+}
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/patches/java7-compat.patch (from rev 19920, trunk/packages/figtree/trunk/debian/patches/java7-compat.patch)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/patches/java7-compat.patch (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/java7-compat.patch 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,22 @@
+Author: James Page <james.page at ubuntu.com>
+Date: Wed, 01 Aug 2012 14:58:30 +0100
+Bugs-Debian: http://bugs.debian.org/683532
+Description: Fix up Painter symbol resolution issue in TreeView class.
+
+--- a/src/figtree/treeviewer/TreePane.java
++++ b/src/figtree/treeviewer/TreePane.java
+@@ -28,6 +28,7 @@
+ import figtree.treeviewer.decorators.*;
+ import figtree.treeviewer.painters.*;
+ import figtree.treeviewer.treelayouts.*;
++import figtree.treeviewer.painters.Painter;
+
+ import javax.swing.*;
+ import java.awt.*;
+@@ -2349,4 +2350,4 @@
+
+ private Map<Node, Shape> calloutPaths = new HashMap<Node, Shape>();
+
+-}
+\ No newline at end of file
++}
Deleted: trunk/packages/figtree/tags/1.4.2-1/debian/patches/series
===================================================================
--- trunk/packages/figtree/trunk/debian/patches/series 2015-08-12 08:05:22 UTC (rev 19919)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/series 2015-08-12 09:14:03 UTC (rev 19925)
@@ -1,6 +0,0 @@
-build_figtree_gui_only.patch
-ignore_quaqua.patch
-remove_webui.patch
-fix_classpath_in_build_xml.patch
-java7-compat.patch
-fix_itext_api_change.patch
Copied: trunk/packages/figtree/tags/1.4.2-1/debian/patches/series (from rev 19920, trunk/packages/figtree/trunk/debian/patches/series)
===================================================================
--- trunk/packages/figtree/tags/1.4.2-1/debian/patches/series (rev 0)
+++ trunk/packages/figtree/tags/1.4.2-1/debian/patches/series 2015-08-12 09:14:03 UTC (rev 19925)
@@ -0,0 +1,10 @@
+#build_figtree_gui_only.patch
+#ignore_quaqua.patch
+remove_webui.patch
+#fix_classpath_in_build_xml.patch
+java7-compat.patch
+build_figtree_gui_only.patch
+ignore_quaqua.patch
+fix_classpath_in_build_xml.patch
+fix_itext_api_change.patch
+fix_jebl.patch
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