JAL-968 incremental - PNG/EPS output has annotation overlapping alignment when annota...

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 32241a5..35e0ea5 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -349,6 +349,11 @@ public class StructureSelectionManager
 
   public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
   {
+    if (listeners==null)
+    {
+      // old or prematurely sent event
+      return;
+    }
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
     SequenceI lastseq = null;
@@ -428,9 +433,14 @@ public class StructureSelectionManager
     int atomNo = 0;
     for (int i = 0; i < listeners.size(); i++)
     {
-      if (listeners.elementAt(i) instanceof StructureListener)
+      Object listener=listeners.elementAt(i);
+      if (listener==source)
       {
-        sl = (StructureListener) listeners.elementAt(i);
+        continue;
+      }
+      if (listener instanceof StructureListener)
+      {
+        sl = (StructureListener) listener;
         if (mappings == null)
         {
           continue;
@@ -453,7 +463,7 @@ public class StructureSelectionManager
       else
       {
         if (relaySeqMappings && hasSequenceListeners
-                && listeners.elementAt(i) instanceof SequenceListener)
+                && listener instanceof SequenceListener)
         {
           // DEBUG
           // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
@@ -488,11 +498,11 @@ public class StructureSelectionManager
           }
           if (hasSequenceListeners)
           {
-            ((SequenceListener) listeners.elementAt(i))
+            ((SequenceListener) listener)
                     .highlightSequence(results);
           }
         }
-        else if (listeners.elementAt(i) instanceof VamsasListener
+        else if (listener instanceof VamsasListener
                 && !handlingVamsasMo)
         {
           // DEBUG
@@ -501,9 +511,12 @@ public class StructureSelectionManager
           // index);
           // pass the mouse over and absolute position onto the
           // VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
+          ((VamsasListener) listener).mouseOver(seq,
                   indexpos, source);
         }
+        else if(listener instanceof SecondaryStructureListener){
+               ((SecondaryStructureListener) listener).mouseOverSequence(seq,indexpos);
+        }
       }
     }
   }
@@ -784,13 +797,24 @@ public class StructureSelectionManager
    */
   public static void release(StructureSelectionManagerProvider jalviewLite)
   {
-    StructureSelectionManager mnger=(instances.get(jalviewLite));
-    if (mnger!=null)
+//    synchronized (instances)
     {
-      instances.remove(jalviewLite);
-      try {
-        mnger.finalize();
-      } catch (Throwable x){};
+      if (instances == null)
+      {
+        return;
+      }
+      StructureSelectionManager mnger = (instances.get(jalviewLite));
+      if (mnger != null)
+      {
+        instances.remove(jalviewLite);
+        try
+        {
+          mnger.finalize();
+        } catch (Throwable x)
+        {
+        }
+        ;
+      }
     }
   }