[jalview] 03/03: v2.9, refresh patches, add testng
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 8 08:36:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository jalview.
commit b42f7b51dac884f1fdcb06fe07679bd4e430e863
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sun Feb 7 12:26:39 2016 -0800
v2.9, refresh patches, add testng
---
debian/changelog | 7 +-
debian/control | 4 +-
debian/patches/drop-lib | 100 ++++++++++
debian/patches/encoding-fix | 11 ++
debian/patches/mutilate-build-system.diff | 58 +++---
debian/patches/newer-jmol-api.diff | 304 +++---------------------------
debian/patches/newer-mime4j-api.diff | 8 +-
debian/patches/series | 4 +-
debian/patches/testng | 11 ++
9 files changed, 183 insertions(+), 324 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 4181047..80917a2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,14 @@
-jalview (2.7.dfsg-5) UNRELEASED; urgency=low
+jalview (2.9+dfsg-1) UNRELEASED; urgency=low
[ Steffen Moeller and Hervé Ménager ]
* Updated Standards-Version to 3.6
* Introduced EDAM annotation to
debian/upstream/edam
- -- Steffen Moeller <moeller at debian.org> Fri, 05 Feb 2016 13:47:26 +0100
+ [ Michael R. Crusoe ]
+ * Update to version 2.9
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Sun, 07 Feb 2016 12:26:10 -0800
jalview (2.7.dfsg-4) unstable; urgency=low
diff --git a/debian/control b/debian/control
index 8e70e37..066cc27 100644
--- a/debian/control
+++ b/debian/control
@@ -26,7 +26,9 @@ Build-Depends: ant,
liblog4j1.2-java,
libmiglayout-java,
libvamsas-client-java,
- libwsdl4j-java
+ libwsdl4j-java,
+ testng,
+ varna
Standards-Version: 3.9.6
Vcs-Git: git://anonscm.debian.org/git/pkg-java/jalview.git
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-java/jalview.git
diff --git a/debian/patches/drop-lib b/debian/patches/drop-lib
new file mode 100644
index 0000000..f7f3b28
--- /dev/null
+++ b/debian/patches/drop-lib
@@ -0,0 +1,100 @@
+--- jalview.orig/build.xml
++++ jalview/build.xml
+@@ -102,7 +102,7 @@
+ <property name="applet.caller-codebase" value="${applet.codebase}" />
+
+ <!-- build directory configuration -->
+- <property name="libDir" value="lib" />
++ <property name="libDir" value="/usr/share/java" />
+ <property name="resourceDir" value="resources" />
+ <property name="helpDir" value="help" />
+ <property name="docDir" value="doc" />
+@@ -143,7 +143,7 @@
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+- <fileset dir="appletlib">
++ <fileset dir="/usr/share/java">
+ <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
+ -->
+ <include name="${jmolJar}" />
+@@ -168,7 +168,7 @@
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+- <pathelement location="appletlib/${jmolJar}" />
++ <pathelement location="/usr/share/java/${jmolJar}" />
+ <pathelement location="lib/${varnaJar}" />
+ <pathelement location="lib/${jsoup}" />
+ <pathelement location="lib/${jsonSimple}" />
+@@ -246,6 +246,7 @@
+ <target name="build" depends="prepare">
+ <!-- not efficient yet. -->
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
++ <compilerarg line="-encoding utf-8"/>
+ <exclude name="jalview/*applet*" />
+ <exclude name="jalview/appletgui/**" />
+ <exclude name="com/stevesoft/**" />
+@@ -273,10 +274,12 @@
+
+ <target name="buildTests" depends="prepareTests">
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
+- debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
++ debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
++ <compilerarg line="-encoding utf-8"/>
+ </javac>
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
+ debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
++ <compilerarg line="-encoding utf-8"/>
+ </javac>
+ </target>
+
+@@ -554,6 +557,7 @@
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
+ classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
+ excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
++ <compilerarg line="-encoding utf-8"/>
+ </target>
+
+ <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+@@ -591,9 +595,9 @@
+
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}" />
+- <pathelement location="appletlib/${jmolJar}" />
+- <pathelement location="appletlib/${jsonSimple}" />
+- <pathelement location="appletlib/${javaJson}" />
++ <pathelement location="/usr/share/java/${jmolJar}" />
++ <pathelement location="/usr/share/java/${jsonSimple}" />
++ <pathelement location="/usr/share/java/${javaJson}" />
+ </path>
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+@@ -665,7 +669,7 @@
+ <include name="${libDir}/**/*" />
+ <include name="${resourceDir}/**/*" />
+ <include name="${helpDir}/**/*" />
+- <include name="appletlib/${jmolJar}" />
++ <include name="/usr/share/java/${jmolJar}" />
+ <exclude name="**/*locales" />
+ <exclude name="*locales/**" />
+ <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+@@ -690,9 +694,6 @@
+ <fileset dir=".">
+ <include name="${jalviewLiteJar}" />
+ </fileset>
+- <fileset dir="appletlib">
+- <include name="**/*"/>
+- </fileset>
+ </copy>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
+@@ -833,7 +834,7 @@
+ </fileset>
+ </signjar>
+ <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+- <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
++ <copy file="/usr/share/java/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <!-- finally, replace any launchApp servlet tags with a version specification -->
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
+ <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
diff --git a/debian/patches/encoding-fix b/debian/patches/encoding-fix
new file mode 100644
index 0000000..6bfdb7e
--- /dev/null
+++ b/debian/patches/encoding-fix
@@ -0,0 +1,11 @@
+--- jalview.orig/src/jalview/json/binding/biojson/v1/SequencePojo.java
++++ jalview/src/jalview/json/binding/biojson/v1/SequencePojo.java
+@@ -28,7 +28,7 @@
+ required = true,
+ minLength = 3,
+ maxLength = 2147483647,
+- description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.�?, “-�? or “ �?")
++ description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.”, “-” or “ ”")
+ private String seq;
+
+ @Attributes(required = true, description = "Sequence name")
diff --git a/debian/patches/mutilate-build-system.diff b/debian/patches/mutilate-build-system.diff
index 742adc5..0e54c8c 100644
--- a/debian/patches/mutilate-build-system.diff
+++ b/debian/patches/mutilate-build-system.diff
@@ -1,38 +1,22 @@
-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 @@
- -->
- <project name="jalviewX" default="usage" basedir=".">
- <!-- we use jalopy to format our sources -->
-- <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
-- <classpath>
-- <fileset dir="utils/jalopy/lib">
-- <include name="*.jar" />
-- </fileset>
-- </classpath>
-- </taskdef>
+--- jalview.orig/build.xml
++++ jalview/build.xml
+@@ -136,10 +136,6 @@
+ <property name="wsdl.ClientNS" value="ext.vamsas" />
+ <!-- the class path for building the application -->
+ <path id="build.classpath">
+- <fileset dir="utils">
+- <include name="*.jar" />
+- <include name="**/*.jar" />
+- </fileset>
+ <fileset dir="${libDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+@@ -503,7 +499,7 @@
+ </axis-wsdl2java>
+ </target>
- <target name="help" depends="usage" />
- <target name="usage">
-@@ -114,10 +107,6 @@
- <property name="wsdl.ClientNS" value="ext.vamsas" />
- <!-- the class path for building the application -->
- <path id="build.classpath">
-- <fileset dir="utils">
-- <include name="*.jar" />
-- <include name="**/*.jar" />
-- </fileset>
- <fileset dir="${libDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
-@@ -407,7 +396,7 @@
- </axis-wsdl2java>
- </target>
-
-- <target name="makedist" depends="build, buildPropertiesFile, buildindices">
-+ <target name="makedist" depends="build, buildindices">
- <!-- make the package jar if not already existing -->
- <mkdir dir="${packageDir}" />
- <!-- clean dir if it already existed -->
+-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
++<target name="makedist" depends="build, buildindices">
+ <!-- make the package jar if not already existing -->
+ <mkdir dir="${packageDir}" />
+ <!-- clean dir if it already existed -->
diff --git a/debian/patches/newer-jmol-api.diff b/debian/patches/newer-jmol-api.diff
index b96436a..8a26183 100644
--- a/debian/patches/newer-jmol-api.diff
+++ b/debian/patches/newer-jmol-api.diff
@@ -3,299 +3,45 @@ 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 @@
- <property name="packageDir" value="dist" />
- <property name="outputJar" value="jalview.jar" />
- <!-- Jalview Applet JMol Jar Dependency -->
-- <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
-+ <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
- <property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <!-- switch to indicate if we should obfuscate jalviewLite -->
- <!--<property name="donotobfuscate" value="true"/> -->
-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
+--- jalview.orig/build.xml
++++ jalview/build.xml
+@@ -112,7 +112,7 @@
+ <property name="packageDir" value="dist" />
+ <property name="outputJar" value="jalview.jar" />
+ <!-- Jalview Applet JMol Jar Dependency -->
+- <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
++ <property name="jmolJar" value="JmolApplet.jar" />
+ <property name="varnaJar" value="VARNAv3-93.jar" />
+ <property name="jsoup" value="jsoup-1.8.1.jar" />
+ <property name="jsonSimple" value="json_simple-1.1.jar" />
+--- jalview.orig/nbproject/project.properties
++++ jalview/nbproject/project.properties
@@ -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.Jmol-14.2.14_2015.06.11.jar=lib/Jmol-14.2.14_2015.06.11.jar
+-file.reference.JmolApplet-14.2.14_2015.06.11.jar=appletlib/JmolApplet-14.2.14_2015.06.11.jar
++file.reference.Jmol-12.2.32.jar=lib/Jmol-12.2.32.jar
++file.reference.JmolApplet-12.2.32.jar=appletlib/JmolApplet-12.2.32jar
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.min-jaba-client.jar=lib/min-jaba-client-2.0.jar
+@@ -92,7 +92,7 @@
${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.Jmol-14.2.14_2015.06.11.jar}:\
++ ${file.reference.Jmol-12.2.32.jar}:\
${file.reference.miglayout-4.0-swing.jar}:\
${file.reference.log4j-1.2.8.jar}:\
${file.reference.mail.jar}:\
-@@ -100,7 +100,7 @@
+@@ -101,7 +101,7 @@
${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}
+- ${file.reference.JmolApplet-14.2.14_2015.06.11.jar} \
++ ${file.reference.JmolApplet-12.2.32.jar} \
+ ${file.reference.varna-3.9-dev.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);
- }
-
diff --git a/debian/patches/newer-mime4j-api.diff b/debian/patches/newer-mime4j-api.diff
index 9dee41d..3f02e6c 100644
--- a/debian/patches/newer-mime4j-api.diff
+++ b/debian/patches/newer-mime4j-api.diff
@@ -1,9 +1,9 @@
Description: Patch to use the latest version of Apache Mime4J
Author: Emmanuel Bourg <ebourg at apache.org>
Forwarded: no
---- a/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
-+++ b/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
-@@ -26,9 +26,9 @@
+--- jalview.orig/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
++++ jalview/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
+@@ -29,9 +29,9 @@
import java.util.List;
import org.apache.james.mime4j.MimeException;
@@ -14,4 +14,4 @@ Forwarded: no
+import org.apache.james.mime4j.stream.Field;
/**
- * ContentHandler for parsing mime encoded messages into Jalview objects.
+ * ContentHandler for parsing mime encoded messages into Jalview objects. TODO:
diff --git a/debian/patches/series b/debian/patches/series
index e7ff9d4..4deee53 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,6 @@
+encoding-fix
mutilate-build-system.diff
newer-jmol-api.diff
newer-mime4j-api.diff
-java8-compatibility.patch
+testng
+drop-lib
diff --git a/debian/patches/testng b/debian/patches/testng
new file mode 100644
index 0000000..f7161fe
--- /dev/null
+++ b/debian/patches/testng
@@ -0,0 +1,11 @@
+--- jalview.orig/build.xml
++++ jalview/build.xml
+@@ -281,7 +281,7 @@
+ </target>
+
+ <taskdef name="testng" classname="org.testng.TestNGAntTask" >
+- <classpath location="utils/testnglibs/testng.jar" />
++ <classpath location="/usr/share/java/testng.jar" />
+ </taskdef>
+
+ <target name="testng" depends="buildTests">
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-java/jalview.git
More information about the pkg-java-commits
mailing list