call to release any explicit event handler references

[jalview.git] / src / jalview / appletgui / AppletJmol.java

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 42e6f56..619d522 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -83,6 +83,7 @@ public class AppletJmol extends EmbmenuFrame implements
   RenderPanel renderPanel;
 
   AlignmentPanel ap;
+  ArrayList _aps = new ArrayList();
 
   String fileLoadingError;
 
@@ -489,7 +490,7 @@ public class AppletJmol extends EmbmenuFrame implements
     if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -517,7 +518,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
   public void updateTitleAndMenus()
@@ -528,7 +529,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -632,4 +633,16 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     jmb.setJalviewColourScheme(ucs);
   }
+
+  public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+  {
+    for (int i=0;i<_aps.size();i++)
+    {
+      if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment)
+      {
+        return ((AlignmentPanel)_aps.get(i));
+      }
+    }
+    return ap;
+  }
 }