JAL-777/JAL-641 debugging

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index ed56ebb..c8d9ae3 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -26,7 +26,9 @@ 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;
 
@@ -53,26 +55,27 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   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((AlignmentPanel)alignment);
       }
 
-      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-              .getFeatureRenderer());
+      fr.transferSettings(((AlignmentPanel)alignment).
+              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)
@@ -122,11 +125,13 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+    AlignmentPanel ap = (AlignmentPanel) source,topap;
+    // ignore events from unrelated or non-user interactive frames
+    if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || 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)
@@ -212,4 +217,13 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     }
 
   }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    if (svl instanceof SeqPanel) {
+      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+      
+    };
+  }
 }