X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=19178f23b7d62ed8fd977c3ed19de3e023851dd4;hb=a35cbe12ed4e2e736bd73695ece71d59671cabb8;hp=74a9c221ee3787ea37eabf067cfea2a878cb4f15;hpb=3357d18e685c4fd5f089df73f0290eb1b72ce0ee;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 74a9c22..19178f2 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -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.openscience.jmol.app.jmolpanel.AppConsole;
 
 public class AppJmol extends GStructureViewer implements Runnable,
         SequenceStructureBinding
@@ -47,7 +48,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
 {
   AppJmolBinding jmb;
 
-  ScriptWindow scriptWindow;
+  JPanel scriptWindow;
 
   JSplitPane splitPane;
 
@@ -254,12 +255,13 @@ public class AppJmol extends GStructureViewer implements Runnable,
    * @param pdbentry
    * @param seq
    * @param chains
-   * @param alignFrame 
+   * @param alignFrame
    * @param align
    *          if true, new structure(s) will be align using associated alignment
    */
   private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
-          final String[] chains, final boolean b, final IProgressIndicator alignFrame)
+          final String[] chains, final boolean b,
+          final IProgressIndicator alignFrame)
   {
     if (pdbentry.getFile() == null)
     {
@@ -297,7 +299,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     addingStructures = true;
     _started = false;
     alignAddedStructures = b;
-    progressBar = alignFrame; // visual indication happens on caller frame. 
+    progressBar = alignFrame; // visual indication happens on caller frame.
     (worker = new Thread(this)).start();
     return;
   }
@@ -332,7 +334,17 @@ 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);
-    jmb.allocateViewer(renderPanel, true, "", null, null, "");
+    if (scriptWindow == null)
+    {
+      BorderLayout bl = new BorderLayout();
+      bl.setHgap(0);
+      bl.setVgap(0);
+      scriptWindow = new JPanel(bl);
+      scriptWindow.setVisible(false);
+    }
+    ;
+    jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+            null);
     jmb.newJmolPopup(true, "Jmol", true);
     jmb.evalStateCommand(command);
     jmb.setFinishedInit(true);
@@ -405,6 +417,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
   void closeViewer()
   {
     jmb.closeViewer();
+
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     jmb = null;
@@ -435,11 +448,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
           pdbid = jmb.pdbentry[pi].getId();
-          long hdl=pdbid.hashCode()-System.currentTimeMillis();
+          long hdl = pdbid.hashCode() - System.currentTimeMillis();
           if (progressBar != null)
           {
-            progressBar.setProgressBar("Fetching PDB " + pdbid,
-                    hdl);
+            progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
           }
           try
           {
@@ -534,6 +546,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
         cmd.append("\nloadingJalviewdata=null");
         final String command = cmd.toString();
         cmd = null;
+        long lastnotify = jmb.getLoadNotifiesHandled();
         try
         {
           jmb.evalStateCommand(command);
@@ -547,23 +560,23 @@ public class AppJmol extends GStructureViewer implements Runnable,
         {
           Cache.log.error("Couldn't add files to Jmol viewer!", ex);
         }
-          long lastnotify=jmb.getLoadNotifiesHandled();
-          // need to wait around until script has finished
-          while (lastnotify>=jmb.getLoadNotifiesHandled()); 
+        // need to wait around until script has finished
+        while (lastnotify >= jmb.getLoadNotifiesHandled())
+          ;
+        {
+          try
           {
-            try
-            {
-              Thread.sleep(35);
-            } catch (Exception e)
-            {
-            }
-          }
-          // refresh the sequence colours for the new structure(s)
-          jmb.updateColours(ap);
-          // do superposition if asked to
-          if (alignAddedStructures)
+            Thread.sleep(35);
+          } catch (Exception e)
           {
-            javax.swing.SwingUtilities.invokeLater(new Runnable()
+          }
+        }
+        // refresh the sequence colours for the new structure(s)
+        jmb.updateColours(ap);
+        // do superposition if asked to
+        if (alignAddedStructures)
+        {
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
             public void run()
             {
@@ -780,8 +793,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
   public void showConsole(boolean showConsole)
   {
-    if (scriptWindow == null)
-      scriptWindow = new ScriptWindow(this);
 
     if (showConsole)
     {
@@ -791,15 +802,19 @@ public class AppJmol extends GStructureViewer implements Runnable,
         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)
+      {
         splitPane.setVisible(false);
+      }
 
       splitPane = null;