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);
   }