Author: fourmond Date: 2012-05-03 18:11:21 +0000 (Thu, 03 May 2012) New Revision: 16037
Added: trunk/jalview/debian/patches/newer-jmol-api.diff Modified: trunk/jalview/debian/changelog trunk/jalview/debian/patches/series Log: [jalview] long forgotten commit to SVN... Modified: trunk/jalview/debian/changelog =================================================================== --- trunk/jalview/debian/changelog 2012-05-02 22:28:55 UTC (rev 16036) +++ trunk/jalview/debian/changelog 2012-05-03 18:11:21 UTC (rev 16037) @@ -1,3 +1,11 @@ +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 <[email protected]> Mon, 07 Nov 2011 20:47:14 +0100 + jalview (2.7.dfsg-1) experimental; urgency=low * Initial release (Closes: #507436) Added: trunk/jalview/debian/patches/newer-jmol-api.diff =================================================================== --- trunk/jalview/debian/patches/newer-jmol-api.diff (rev 0) +++ trunk/jalview/debian/patches/newer-jmol-api.diff 2012-05-03 18:11:21 UTC (rev 16037) @@ -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); + } + Modified: trunk/jalview/debian/patches/series =================================================================== --- trunk/jalview/debian/patches/series 2012-05-02 22:28:55 UTC (rev 16036) +++ trunk/jalview/debian/patches/series 2012-05-03 18:11:21 UTC (rev 16037) @@ -1 +1,2 @@ mutilate-build-system.diff +newer-jmol-api.diff _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
