jmol update

diff --git a/.classpath b/.classpath
index 6815d73..a20ed44 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -19,7 +19,7 @@
        <classpathentry kind="lib" path="lib/JGoogleAnalytics-0.2.1-SNAPSHOT.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
        <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
        <classpathentry kind="lib" path="lib/min-jaba-client.jar" sourcepath="/clustengine/webservices"/>
        <classpathentry kind="lib" path="lib/JGoogleAnalytics-0.2.1-SNAPSHOT.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
        <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
        <classpathentry kind="lib" path="lib/min-jaba-client.jar" sourcepath="/clustengine/webservices"/>

-       <classpathentry kind="lib" path="lib/Jmol-12.1.11_dev.jar"/>
-       <classpathentry kind="lib" path="appletlib/JmolApplet-12.1.11_dev.jar"/>
+       <classpathentry kind="lib" path="lib/Jmol-12.1.13.jar" sourcepath="/Jmol/src"/>
+       <classpathentry kind="lib" path="appletlib/JmolApplet-12.1.13.jar"/>

        <classpathentry kind="output" path="classes"/>
 </classpath>
        <classpathentry kind="output" path="classes"/>
 </classpath>

diff --git a/appletlib/JmolApplet-12.1.11_dev.jar b/appletlib/JmolApplet-12.1.13.jar
similarity index 65%
rename from appletlib/JmolApplet-12.1.11_dev.jar
rename to appletlib/JmolApplet-12.1.13.jar
index f1a51a2..27c7bd6 100644 (file)
Binary files a/appletlib/JmolApplet-12.1.11_dev.jar and b/appletlib/JmolApplet-12.1.13.jar differ

diff --git a/build.xml b/build.xml
index 818415d..fdefa36 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -99,7 +99,7 @@
                <property name="packageDir" value="dist" />
                <property name="outputJar" value="jalview.jar" />
                <!-- Jalview Applet JMol Jar Dependency -->
                <property name="packageDir" value="dist" />
                <property name="outputJar" value="jalview.jar" />
                <!-- Jalview Applet JMol Jar Dependency -->

-               <property name="jmolJar" value="JmolApplet-12.1.11_dev.jar" />
+               <property name="jmolJar" value="JmolApplet-12.1.13.jar" />

                <property name="jalviewLiteJar" value="jalviewApplet.jar" />
                <!-- switch to indicate if we should obfuscate jalviewLite -->
                <!--<property name="donotobfuscate" value="true"/> -->
                <property name="jalviewLiteJar" value="jalviewApplet.jar" />
                <!-- switch to indicate if we should obfuscate jalviewLite -->
                <!--<property name="donotobfuscate" value="true"/> -->

diff --git a/lib/Jmol-12.1.11_dev.jar b/lib/Jmol-12.1.13.jar
similarity index 82%
rename from lib/Jmol-12.1.11_dev.jar
rename to lib/Jmol-12.1.13.jar
index 3aac3ca..a017034 100644 (file)
Binary files a/lib/Jmol-12.1.11_dev.jar and b/lib/Jmol-12.1.13.jar differ

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 12a09d5..472ac75 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -129,5 +129,17 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
     return new AppletConsole(viewer2, consolePanel);
   }
   {
     return new AppletConsole(viewer2, consolePanel);
   }

+  @Override
+  protected void releaseUIResources()
+  {
+    appletJmolBinding = null;
+    if (console!=null) {
+      try {
+        console.setVisible(false);
+      } catch (Error e) {} catch (Exception x) {};
+      console=null;
+    }
+    
+  }

 
 }
\ No newline at end of file
 
 }
\ No newline at end of file

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 63c1ca7..4bee84c 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -138,4 +138,17 @@ public class ExtJmol extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
     // TODO Auto-generated method stub
     return null;
   }

+  @Override
+  protected void releaseUIResources()
+  {
+    ap = null;
+    if (console!=null) {
+      try {
+        console.setVisible(false);
+      } catch (Error e) {} catch (Exception x) {};
+      console=null;
+    }
+    
+  }
+

 }
 }

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 916579f..3bac3bc 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -43,7 +43,8 @@ import org.jmol.viewer.Viewer;
 import jalview.schemes.*;
 
 public abstract class JalviewJmolBinding implements StructureListener,
 import jalview.schemes.*;
 
 public abstract class JalviewJmolBinding implements StructureListener,

-        JmolStatusListener, SequenceStructureBinding, JmolSelectionListener, ComponentListener
+        JmolStatusListener, SequenceStructureBinding,
+        JmolSelectionListener, ComponentListener

 
 {
   /**
 
 {
   /**

@@ -79,6 +80,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   Vector atomsPicked = new Vector();
 
   public Vector chainNames;
   Vector atomsPicked = new Vector();
 
   public Vector chainNames;

+

   Hashtable chainFile;
 
   /**
   Hashtable chainFile;
 
   /**

@@ -212,8 +214,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
         mlength = lbl.indexOf(":", p);
       } while (p < mlength && mlength < (lbl.length() - 2));
       // TODO: lookup each pdb id and recover proper model number for it.
         mlength = lbl.indexOf(":", p);
       } while (p < mlength && mlength < (lbl.length() - 2));
       // TODO: lookup each pdb id and recover proper model number for it.

-      cmd.append(":" +  lbl.substring(mlength + 1) + " /"
-              + (1+getModelNum((String)chainFile.get(lbl))) + " or ");
+      cmd.append(":" + lbl.substring(mlength + 1) + " /"
+              + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");

     }
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
     }
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);

@@ -231,8 +233,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
     viewer.setJmolStatusListener(null);
     lastCommand = null;
     viewer = null;
     viewer.setJmolStatusListener(null);
     lastCommand = null;
     viewer = null;

+    releaseUIResources();

   }
 
   }
 

+  /**
+   * called by JalviewJmolbinding after closeViewer is called - release any
+   * resources and references so they can be garbage collected.
+   */
+  protected abstract void releaseUIResources();
+

   public void colourByChain()
   {
     colourBySequence = false;
   public void colourByChain()
   {
     colourBySequence = false;

@@ -545,7 +554,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 
 
               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 

-              if (showFeatures && fr!=null)
+              if (showFeatures && fr != null)

                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")

@@ -1319,7 +1328,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * @param codeBase
    * @param commandOptions
    */
    * @param codeBase
    * @param commandOptions
    */

-  public void allocateViewer(Component renderPanel, boolean jmolfileio,
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,

           String htmlName, URL documentBase, URL codeBase,
           String commandOptions)
   {
           String htmlName, URL documentBase, URL codeBase,
           String commandOptions)
   {

@@ -1342,7 +1351,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * @param buttonsToShow
    *          - buttons to show on the console, in ordr
    */
    * @param buttonsToShow
    *          - buttons to show on the console, in ordr
    */

-  public void allocateViewer(Component renderPanel, boolean jmolfileio,
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,

           String htmlName, URL documentBase, URL codeBase,
           String commandOptions, final Container consolePanel,
           String buttonsToShow)
           String htmlName, URL documentBase, URL codeBase,
           String commandOptions, final Container consolePanel,
           String buttonsToShow)

@@ -1356,9 +1365,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     if (consolePanel != null)
     {
       consolePanel.addComponentListener(this);
     if (consolePanel != null)
     {
       consolePanel.addComponentListener(this);

-      
-    }

 
 

+    }

 
   }
 
 
   }
 

@@ -1367,30 +1375,29 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 

-@Override
-public void componentResized(ComponentEvent e)
-{
-  
-}
+  @Override
+  public void componentResized(ComponentEvent e)
+  {

 
 

-@Override
-public void componentMoved(ComponentEvent e)
-{
-  
-}
+  }

 
 

-@Override
-public void componentShown(ComponentEvent e)
-{
-  showConsole(true);
-}
+  @Override
+  public void componentMoved(ComponentEvent e)
+  {

 
 

-@Override
-public void componentHidden(ComponentEvent e)
-{
-  showConsole(false);
-}
+  }

 
 

+  @Override
+  public void componentShown(ComponentEvent e)
+  {
+    showConsole(true);
+  }
+
+  @Override
+  public void componentHidden(ComponentEvent e)
+  {
+    showConsole(false);
+  }

 
   public void setLoadingFromArchive(boolean loadingFromArchive)
   {
 
   public void setLoadingFromArchive(boolean loadingFromArchive)
   {

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 1b0a5cb..7af2cfb 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -414,6 +414,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
   void closeViewer()
   {
     jmb.closeViewer();
   void closeViewer()
   {
     jmb.closeViewer();

+    

     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     jmb = null;
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     jmb = null;

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 5280900..f051838 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -174,4 +174,17 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
     return new AppConsole(viewer, consolePanel, buttonsToShow);
   }
   {
     return new AppConsole(viewer, consolePanel, buttonsToShow);
   }

+
+  @Override
+  protected void releaseUIResources()
+  {
+    appJmolWindow = null;
+    if (console!=null) {
+      try {
+        console.setVisible(false);
+      } catch (Error e) {} catch (Exception x) {};
+      console=null;
+    }
+    
+  }

 }
\ No newline at end of file
 }
\ No newline at end of file

diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index 88416aa..8563793 100755 (executable)
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -964,7 +964,7 @@ and any path to a file to save to the file]]></string>
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">

-                                                               <string><![CDATA[Jmol-12.1.11_dev.jar]]></string>
+                                                               <string><![CDATA[Jmol-12.1.13.jar]]></string>

                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>

@@ -982,7 +982,7 @@ and any path to a file to save to the file]]></string>
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">

-                                                               <string><![CDATA[Jmol-12.1.5.jar]]></string>
+                                                               <string><![CDATA[Jmol-12.1.13.jar]]></string>

                                                        </property>
                                                        <property name="fileSize">
                                                                <long>5898736</long>
                                                        </property>
                                                        <property name="fileSize">
                                                                <long>5898736</long>