patch for JAL-655

[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 09303c7..67b688c 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.
@@ -43,7 +43,8 @@ import org.jmol.viewer.Viewer;
 import jalview.schemes.*;
 
 public abstract class JalviewJmolBinding implements StructureListener,
-        JmolStatusListener, SequenceStructureBinding, JmolSelectionListener, ComponentListener
+        JmolStatusListener, SequenceStructureBinding,
+        JmolSelectionListener, ComponentListener
 
 {
   /**
@@ -80,6 +81,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   public Vector chainNames;
 
+  Hashtable chainFile;
+
   /**
    * array of target chains for seuqences - tied to pdbentry and sequence[]
    */
@@ -113,7 +116,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public PDBEntry[] pdbentry;
 
   /**
-   * datasource protocol for access to PDBEntry
+   * datasource protocol for access to PDBEntrylatest
    */
   String protocol = null;
 
@@ -210,8 +213,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
         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) + " /"
-              + getModelNum(lbl.substring(0, mlength)) + " or ");
+              + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
     }
     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;
+    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;
@@ -306,6 +317,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String isel[] = new String[files.length];
     // reference structure - all others are superposed in it
     String[] targetC = new String[files.length];
+    String[] chainNames = new String[files.length];
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -368,6 +380,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
             {
               targetC[pdbfnum] = ":" + mapping[m].getChain();
             }
+            chainNames[pdbfnum] = mapping[m].getPdbId()+targetC[pdbfnum];
             // move on to next pdb file
             s = sequence[pdbfnum].length;
             break;
@@ -450,7 +463,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
       {
         continue;
       }
-      command.append("compare ");
+      command.append("echo ");
+      command.append("\"Superposing (");
+      command.append(chainNames[pdbfnum]);
+      command.append(") against reference (");
+      command.append(chainNames[refStructure]);
+      command.append(")\";\ncompare ");
       command.append("{");
       command.append(1 + pdbfnum);
       command.append(".1} {");
@@ -543,7 +561,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
               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() : "")
@@ -1051,6 +1069,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
     chainNames = new Vector();
+    chainFile = new Hashtable();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
     ssm = StructureSelectionManager.getStructureSelectionManager();
@@ -1160,8 +1179,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
             // add an entry for every chain in the model
             for (int i = 0; i < pdb.chains.size(); i++)
             {
-              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;
           }
@@ -1314,7 +1335,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * @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)
   {
@@ -1337,7 +1358,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * @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)
@@ -1351,9 +1372,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     if (consolePanel != null)
     {
       consolePanel.addComponentListener(this);
-      
-    }
 
+    }
 
   }
 
@@ -1362,30 +1382,25 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
-@Override
-public void componentResized(ComponentEvent e)
-{
-  
-}
+  public void componentResized(ComponentEvent e)
+  {
 
-@Override
-public void componentMoved(ComponentEvent e)
-{
-  
-}
+  }
 
-@Override
-public void componentShown(ComponentEvent e)
-{
-  showConsole(true);
-}
+  public void componentMoved(ComponentEvent e)
+  {
 
-@Override
-public void componentHidden(ComponentEvent e)
-{
-  showConsole(false);
-}
+  }
 
+  public void componentShown(ComponentEvent e)
+  {
+    showConsole(true);
+  }
+
+  public void componentHidden(ComponentEvent e)
+  {
+    showConsole(false);
+  }
 
   public void setLoadingFromArchive(boolean loadingFromArchive)
   {