[pkg-java] r16038 - in tags/jalview: . 2.7.dfsg-2/debian 2.7.dfsg-2/debian/patches
Vincent Fourmond
fourmond at alioth.debian.org
Thu May 3 18:16:16 UTC 2012
Author: fourmond
Date: 2012-05-03 18:16:15 +0000 (Thu, 03 May 2012)
New Revision: 16038
Added:
tags/jalview/2.7.dfsg-2/
tags/jalview/2.7.dfsg-2/debian/changelog
tags/jalview/2.7.dfsg-2/debian/patches/newer-jmol-api.diff
tags/jalview/2.7.dfsg-2/debian/patches/series
Removed:
tags/jalview/2.7.dfsg-2/debian/changelog
tags/jalview/2.7.dfsg-2/debian/patches/series
Log:
[svn-buildpackage] Tagging jalview 2.7.dfsg-2
Deleted: tags/jalview/2.7.dfsg-2/debian/changelog
===================================================================
--- trunk/jalview/debian/changelog 2012-01-24 23:09:55 UTC (rev 15740)
+++ tags/jalview/2.7.dfsg-2/debian/changelog 2012-05-03 18:16:15 UTC (rev 16038)
@@ -1,11 +0,0 @@
-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 <fourmond at debian.org> Wed, 19 Oct 2011 20:19:46 +0200
Copied: tags/jalview/2.7.dfsg-2/debian/changelog (from rev 16037, trunk/jalview/debian/changelog)
===================================================================
--- tags/jalview/2.7.dfsg-2/debian/changelog (rev 0)
+++ tags/jalview/2.7.dfsg-2/debian/changelog 2012-05-03 18:16:15 UTC (rev 16038)
@@ -0,0 +1,19 @@
+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 <fourmond at debian.org> 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 <fourmond at debian.org> Wed, 19 Oct 2011 20:19:46 +0200
Copied: tags/jalview/2.7.dfsg-2/debian/patches/newer-jmol-api.diff (from rev 16037, trunk/jalview/debian/patches/newer-jmol-api.diff)
===================================================================
--- tags/jalview/2.7.dfsg-2/debian/patches/newer-jmol-api.diff (rev 0)
+++ tags/jalview/2.7.dfsg-2/debian/patches/newer-jmol-api.diff 2012-05-03 18:16:15 UTC (rev 16038)
@@ -0,0 +1,301 @@
+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 @@
+ <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
+@@ -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);
+ }
+
Deleted: tags/jalview/2.7.dfsg-2/debian/patches/series
===================================================================
--- trunk/jalview/debian/patches/series 2012-01-24 23:09:55 UTC (rev 15740)
+++ tags/jalview/2.7.dfsg-2/debian/patches/series 2012-05-03 18:16:15 UTC (rev 16038)
@@ -1 +0,0 @@
-mutilate-build-system.diff
Copied: tags/jalview/2.7.dfsg-2/debian/patches/series (from rev 16037, trunk/jalview/debian/patches/series)
===================================================================
--- tags/jalview/2.7.dfsg-2/debian/patches/series (rev 0)
+++ tags/jalview/2.7.dfsg-2/debian/patches/series 2012-05-03 18:16:15 UTC (rev 16038)
@@ -0,0 +1,2 @@
+mutilate-build-system.diff
+newer-jmol-api.diff
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