patched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)

diff --git a/.classpath b/.classpath
index 82fde23..ccbed55 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -18,8 +18,7 @@
        <classpathentry kind="lib" path="lib/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
        <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/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
        <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"/>
-       <classpathentry kind="lib" path="lib/Jmol-12.1.5.jar" sourcepath="D:/InstallsDir/Sources for Development/jmol-12.1.5"/>
-       <classpathentry kind="lib" path="appletlib/JmolApplet-12.1.5.jar" sourcepath="D:/InstallsDir/Sources for Development/jmol-12.1.5"/>
+       <classpathentry kind="lib" path="lib/min-jaba-client.jar" sourcepath="/clustengine/webservices"/>
+       <classpathentry kind="lib" path="lib/Jmol-12.1.11_dev_patched.jar"/>

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

diff --git a/appletlib/JmolApplet-12.1.11_dev_patched.jar b/appletlib/JmolApplet-12.1.11_dev_patched.jar
new file mode 100644 (file)
index 0000000..5a7c6f2
Binary files /dev/null and b/appletlib/JmolApplet-12.1.11_dev_patched.jar differ

diff --git a/appletlib/JmolApplet-12.1.5.jar b/appletlib/JmolApplet-12.1.5.jar
deleted file mode 100644 (file)
index 42db0d3..0000000
Binary files a/appletlib/JmolApplet-12.1.5.jar and /dev/null differ

diff --git a/lib/Jmol-12.1.5.jar b/lib/Jmol-12.1.11_dev_patched.jar
similarity index 69%
rename from lib/Jmol-12.1.5.jar
rename to lib/Jmol-12.1.11_dev_patched.jar
index 9f36d65..d4f255a 100644 (file)
Binary files a/lib/Jmol-12.1.5.jar and b/lib/Jmol-12.1.11_dev_patched.jar differ

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 3afa805..3a2abcf 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -113,4 +113,10 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     
   }
 
     
   }
 

+  @Override
+  public void showConsole(boolean show)
+  {
+    appletJmolBinding.showConsole(show);
+  }
+

 }
\ 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 53c2f1c..b7fb311 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -121,4 +121,11 @@ public class ExtJmol extends JalviewJmolBinding
       pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
     }
   }
       pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
     }
   }

+
+  @Override
+  public void showConsole(boolean show)
+  {
+    // This never gets called because we haven't overriden the associated Jmol's console
+    System.err.println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="+show);
+  }

 }
 }

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2c34762..c852a1a 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -24,6 +24,8 @@ import java.applet.Applet;
 import java.awt.*;
 import java.awt.event.*;
 
 import java.awt.*;
 import java.awt.event.*;
 

+import javax.swing.JPanel;
+

 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.SequenceStructureBinding;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.SequenceStructureBinding;

@@ -36,6 +38,8 @@ import org.jmol.adapter.smarter.SmarterJmolAdapter;
 
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
 
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;

+import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.jmolpanel.AppConsole;

 
 import jalview.schemes.*;
 
 
 import jalview.schemes.*;
 

@@ -982,7 +986,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
       case JmolConstants.CALLBACK_MEASURE:
 
       case JmolConstants.CALLBACK_CLICK:
       case JmolConstants.CALLBACK_MEASURE:
 
       case JmolConstants.CALLBACK_CLICK:

-

       default:
         System.err.println("Unhandled callback " + type + " "
                 + data[1].toString());
       default:
         System.err.println("Unhandled callback " + type + " "
                 + data[1].toString());

@@ -1289,6 +1292,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public abstract void refreshGUI();
 
   /**
   public abstract void refreshGUI();
 
   /**

+   * called to show or hide the associated console window container.
+   * @param show
+   */
+  public abstract void showConsole(boolean show);
+  /**

    * @param renderPanel
    * @param jmolfileio
    *          - when true will initialise jmol's file IO system (should be false
    * @param renderPanel
    * @param jmolfileio
    *          - when true will initialise jmol's file IO system (should be false

@@ -1302,11 +1310,95 @@ public abstract class JalviewJmolBinding implements StructureListener,
           String htmlName, URL documentBase, URL codeBase,
           String commandOptions)
   {
           String htmlName, URL documentBase, URL codeBase,
           String commandOptions)
   {

-    viewer = JmolViewer.allocateViewer(renderPanel,
+    allocateViewer(renderPanel, jmolfileio, htmlName, documentBase, codeBase, commandOptions, null,null);
+  }
+  /**
+   * 
+   * @param renderPanel
+   * @param jmolfileio
+   *          - when true will initialise jmol's file IO system (should be false
+   *          in applet context)
+   * @param htmlName
+   * @param documentBase
+   * @param codeBase
+   * @param commandOptions
+   * @param consolePanel - panel to contain Jmol console
+   * @param buttonsToShow - buttons to show on the console, in ordr
+   */
+    public void allocateViewer(Component renderPanel, boolean jmolfileio,
+            String htmlName, URL documentBase, URL codeBase,
+            String commandOptions, final Container consolePanel, String buttonsToShow)
+    {
+      viewer = JmolViewer.allocateViewer(renderPanel,

             (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
                     + ((Object) this).toString(), documentBase, codeBase,
             commandOptions, this);
             (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
                     + ((Object) this).toString(), documentBase, codeBase,
             commandOptions, this);

+      console = new AppConsole(viewer, null, consolePanel,
+              buttonsToShow);
+      viewer.setConsole(new JmolAppConsoleInterface() {
+
+        @Override
+        public JmolScriptEditorInterface getScriptEditor()
+        {
+          return console.getScriptEditor();
+        }
+
+        @Override
+        public JmolAppConsoleInterface getAppConsole(Viewer viewer,
+                Component display)
+        {
+          return console;
+        }
+
+        public String getText()
+        {
+          return console.getText();
+        }
+
+        @Override
+        public Object getMyMenuBar()
+        {
+          return console.getMyMenuBar();
+        }
+
+        @Override
+        public void setVisible(boolean b)
+        {
+          showConsole(b);
+        }
+
+        @Override
+        public void sendConsoleEcho(String strEcho)
+        {
+          console.sendConsoleEcho(strEcho);
+          
+        }
+
+        @Override
+        public void sendConsoleMessage(String strInfo)
+        {
+          console.sendConsoleMessage(strInfo);
+        }
+
+        @Override
+        public void zap()
+        {
+          console.zap();
+        }
+
+        @Override
+        public void dispose()
+        {
+          console.dispose();
+        }
+        
+        
+      });
+      
+      

   }
   }

+    
+  protected org.jmol.api.JmolAppConsoleInterface console = null;

 
   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 74a9c22..0cc04f7 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -40,6 +40,7 @@ import org.jmol.api.*;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;

+import org.openscience.jmol.app.jmolpanel.AppConsole;

 
 public class AppJmol extends GStructureViewer implements Runnable,
         SequenceStructureBinding
 
 public class AppJmol extends GStructureViewer implements Runnable,
         SequenceStructureBinding

@@ -47,8 +48,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
 {
   AppJmolBinding jmb;
 
 {
   AppJmolBinding jmb;
 

-  ScriptWindow scriptWindow;
-
+  JPanel scriptWindow;
+  

   JSplitPane splitPane;
 
   RenderPanel renderPanel;
   JSplitPane splitPane;
 
   RenderPanel renderPanel;

@@ -332,7 +333,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
     jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
             getBounds().width, getBounds().height);
     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
     jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
             getBounds().width, getBounds().height);

-    jmb.allocateViewer(renderPanel, true, "", null, null, "");
+    if (scriptWindow == null)
+    {
+      BorderLayout bl = new BorderLayout();
+      bl.setHgap(0);
+      bl.setVgap(0);
+      scriptWindow = new JPanel(bl);
+    };
+    
+    jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null);

     jmb.newJmolPopup(true, "Jmol", true);
     jmb.evalStateCommand(command);
     jmb.setFinishedInit(true);
     jmb.newJmolPopup(true, "Jmol", true);
     jmb.evalStateCommand(command);
     jmb.setFinishedInit(true);

@@ -777,11 +786,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
     {
     }
   }
     {
     }
   }

-

   public void showConsole(boolean showConsole)
   {
   public void showConsole(boolean showConsole)
   {

-    if (scriptWindow == null)
-      scriptWindow = new ScriptWindow(this);

 
     if (showConsole)
     {
 
     if (showConsole)
     {

@@ -791,15 +797,19 @@ public class AppJmol extends GStructureViewer implements Runnable,
         splitPane.setTopComponent(renderPanel);
         splitPane.setBottomComponent(scriptWindow);
         this.getContentPane().add(splitPane, BorderLayout.CENTER);
         splitPane.setTopComponent(renderPanel);
         splitPane.setBottomComponent(scriptWindow);
         this.getContentPane().add(splitPane, BorderLayout.CENTER);

+        splitPane.setDividerLocation(getHeight() - 200);
+        scriptWindow.setVisible(true);
+        scriptWindow.validate();
+        splitPane.validate();

       }
 
       }
 

-      splitPane.setDividerLocation(getHeight() - 200);
-      splitPane.validate();

     }
     else
     {
       if (splitPane != null)
     }
     else
     {
       if (splitPane != null)

-        splitPane.setVisible(false);
+        {
+          splitPane.setVisible(false);
+        }

 
       splitPane = null;
 
 
       splitPane = null;
 

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 5727386..2a0e2a7 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -5,11 +5,14 @@ package jalview.gui;
 
 import java.util.BitSet;
 
 
 import java.util.BitSet;
 

+import javax.swing.JPanel;
+

 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
 import org.jmol.popup.JmolPopup;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
 import org.jmol.popup.JmolPopup;

+import org.openscience.jmol.app.jmolpanel.AppConsole;

 
 public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 {
 
 public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 {

@@ -53,19 +56,19 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   public void sendConsoleEcho(String strEcho)
   {
 
   public void sendConsoleEcho(String strEcho)
   {

-    if (appJmolWindow.scriptWindow != null)
+    if (console != null)

     {
     {

-      appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+      console.sendConsoleEcho(strEcho);

     }
   }
 
   public void sendConsoleMessage(String strStatus)
   {
     }
   }
 
   public void sendConsoleMessage(String strStatus)
   {

-    if (appJmolWindow.scriptWindow != null && strStatus != null)
+    if (console != null && strStatus != null)

     // && !strStatus.equals("Script completed"))
     // should we squash the script completed string ?
     {
     // && !strStatus.equals("Script completed"))
     // should we squash the script completed string ?
     {

-      appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+      console.sendConsoleMessage(strStatus);

     }
   }
 
     }
   }
 

@@ -104,9 +107,10 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {

-    if (appJmolWindow.scriptWindow != null)
-      appJmolWindow.scriptWindow.notifyScriptTermination(strStatus,
-              msWalltime);
+    // todo - script termination doesn't happen ?
+    //if (console != null)
+      //console.notifyScriptTermination(strStatus,
+      //        msWalltime);

   }
 
   public void showUrl(String url)
   }
 
   public void showUrl(String url)

@@ -134,6 +138,9 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
 
   }
 

+  public void showConsole(boolean b) {
+    appJmolWindow.showConsole(b);
+  }

 
   /**
    * add the given sequences to the mapping scope for the given pdb file handle
 
   /**
    * add the given sequences to the mapping scope for the given pdb file handle

@@ -153,5 +160,4 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
       }
     }
   }
       }
     }
   }

-

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