X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=22776f2717fc56dbdb66b89cd3f9855965adbfc8;hb=691798cf6a90094f4c83e79fd5c703457b1135b0;hp=38c9e704720b144c2e45c8547d82d5631a967c85;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 38c9e70..22776f2 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -26,16 +26,19 @@ import java.util.BitSet;
 
 import javax.swing.JPanel;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
 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
 {
 
   /**
@@ -43,36 +46,37 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppJmol appJmolWindow;
 
-  public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
+  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
           SequenceI[][] sequenceIs, String[][] chains, String protocol)
   {
-    super(pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, chains, protocol);
     appJmolWindow = appJmol;
   }
 
   FeatureRenderer fr = null;
 
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    if (appJmolWindow.ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
+    if (ap.av.showSequenceFeatures)
     {
       if (fr == null)
       {
-        fr = new FeatureRenderer(appJmolWindow.ap);
+        fr = new FeatureRenderer(ap);
       }
 
-      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-              .getFeatureRenderer());
+      fr.transferSettings(ap.
+              seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     return fr;
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer()
+  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(appJmolWindow.ap.av);
+    return new SequenceRenderer(((AlignmentPanel)alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -110,28 +114,33 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void refreshGUI()
   {
     // appJmolWindow.repaint();
-    javax.swing.SwingUtilities.invokeLater(new Runnable() {
-      public void run() {
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
         appJmolWindow.updateTitleAndMenus();
         appJmolWindow.revalidate();
-      }});
+      }
+    });
   }
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+    AlignmentPanel ap = (AlignmentPanel) source,topap;
+    // ignore events from panels not used to colour this view
+    if (!appJmolWindow.isUsedforcolourby(ap))
       return;
-
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    if (!isLoadingFromArchive()) {
+      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    }
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // todo - script termination doesn't happen ?
-    //if (console != null)
-      //console.notifyScriptTermination(strStatus,
-      //        msWalltime);
+    // if (console != null)
+    // console.notifyScriptTermination(strStatus,
+    // msWalltime);
   }
 
   public void showUrl(String url)
@@ -159,7 +168,8 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
-  public void showConsole(boolean b) {
+  public void showConsole(boolean b)
+  {
     appJmolWindow.showConsole(b);
   }
 
@@ -193,12 +203,28 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   protected void releaseUIResources()
   {
     appJmolWindow = null;
-    if (console!=null) {
-      try {
+    if (console != null)
+    {
+      try
+      {
         console.setVisible(false);
-      } catch (Error e) {} catch (Exception x) {};
-      console=null;
+      } catch (Error e)
+      {
+      } catch (Exception x)
+      {
+      }
+      ;
+      console = null;
     }
-    
+
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    if (svl instanceof SeqPanel) {
+      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+      
+    };
   }
 }