Jalview 2.6 source licence

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 31f91ee..c6871a9 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.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.
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.

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

 
 {
   /**
 
 {
   /**

@@ -80,6 +81,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   public Vector chainNames;
 
 
   public Vector chainNames;
 

+  Hashtable chainFile;
+

   /**
    * array of target chains for seuqences - tied to pdbentry and sequence[]
    */
   /**
    * array of target chains for seuqences - tied to pdbentry and sequence[]
    */

@@ -210,8 +213,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
         p = mlength;
         mlength = lbl.indexOf(":", p);
       } while (p < mlength && mlength < (lbl.length() - 2));
         p = mlength;
         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) + " /"
       cmd.append(":" + lbl.substring(mlength + 1) + " /"

-              + getModelNum(lbl.substring(0, mlength)) + " or ");
+              + (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);

@@ -229,8 +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;

@@ -543,7 +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)
+              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() : "")

@@ -1051,6 +1062,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
     chainNames = new Vector();
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
     chainNames = new Vector();

+    chainFile = new Hashtable();

     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
     ssm = StructureSelectionManager.getStructureSelectionManager();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
     ssm = StructureSelectionManager.getStructureSelectionManager();

@@ -1160,8 +1172,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
             // add an entry for every chain in the model
             for (int i = 0; i < pdb.chains.size(); i++)
             {
             // add an entry for every chain in the model
             for (int i = 0; i < pdb.chains.size(); i++)
             {

-              chainNames.addElement(new String(pdb.id + ":"
-                      + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
+              String chid = new String(pdb.id + ":"
+                      + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
+              chainFile.put(chid, pdbentry[pe].getFile());
+              chainNames.addElement(chid);

             }
             notifyLoaded = true;
           }
             }
             notifyLoaded = true;
           }

@@ -1314,7 +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)
   {

@@ -1337,7 +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)

@@ -1348,75 +1362,42 @@ public abstract class JalviewJmolBinding implements StructureListener,
             commandOptions, this);
 
     console = createJmolConsole(viewer, consolePanel, buttonsToShow);
             commandOptions, this);
 
     console = createJmolConsole(viewer, consolePanel, buttonsToShow);

-    if (console != null)
+    if (consolePanel != null)

     {
     {

-      viewer.setConsole(new JmolAppConsoleInterface()
-      {
-
-        @Override
-        public JmolScriptEditorInterface getScriptEditor()
-        {
-          return console.getScriptEditor();
-        }
-
-        @Override
-        public JmolAppConsoleInterface getAppConsole(Viewer viewer,
-                Component display)
-        {
-          return console;
-        }
+      consolePanel.addComponentListener(this);

 
 

-        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);
+  }

 
 

-        }
+  protected abstract JmolAppConsoleInterface createJmolConsole(
+          JmolViewer viewer2, Container consolePanel, String buttonsToShow);

 
 

-        @Override
-        public void sendConsoleMessage(String strInfo)
-        {
-          console.sendConsoleMessage(strInfo);
-        }
+  protected org.jmol.api.JmolAppConsoleInterface console = null;

 
 

-        @Override
-        public void zap()
-        {
-          console.zap();
-        }
+  @Override
+  public void componentResized(ComponentEvent e)
+  {

 
 

-        @Override
-        public void dispose()
-        {
-          console.dispose();
-        }
+  }

 
 

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

 
   }
 
 
   }
 

-  protected abstract JmolAppConsoleInterface createJmolConsole(
-          JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+  @Override
+  public void componentShown(ComponentEvent e)
+  {
+    showConsole(true);
+  }

 
 

-  protected org.jmol.api.JmolAppConsoleInterface console = null;
+  @Override
+  public void componentHidden(ComponentEvent e)
+  {
+    showConsole(false);
+  }

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