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 d1bccd8..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.
  * 
@@ -152,16 +152,32 @@ public class StructureSelectionManager
       ex.printStackTrace();
       return null;
     }
-
+    
     String targetChain;
     for (int s = 0; s < sequence.length; s++)
     {
+      boolean infChain = true;
       if (targetChains != null && targetChains[s] != null)
+      {
+        infChain = false;
         targetChain = targetChains[s];
+      }
       else if (sequence[s].getName().indexOf("|") > -1)
       {
         targetChain = sequence[s].getName().substring(
                 sequence[s].getName().lastIndexOf("|") + 1);
+        if (targetChain.length() > 1)
+        {
+          if (targetChain.trim().length() == 0)
+          {
+            targetChain = " ";
+          }
+          else
+          {
+            // not a valid chain identifier
+            targetChain = "";
+          }
+        }
       }
       else
         targetChain = "";
@@ -173,14 +189,11 @@ public class StructureSelectionManager
       boolean first = true;
       for (int i = 0; i < pdb.chains.size(); i++)
       {
-        // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may
-        // need to be revoked
         PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
-        if (targetChain.length() > 0 && !targetChain.equals(chain.id))
+        if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain)
         {
           continue; // don't try to map chains don't match.
         }
-        // end of patch for limiting computed mappings
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         AlignSeq as = new AlignSeq(sequence[s],
@@ -336,6 +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;
@@ -415,9 +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;
@@ -440,7 +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) + " " +
@@ -475,11 +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
@@ -488,9 +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);
+        }
       }
     }
   }
@@ -771,13 +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)
+        {
+        }
+        ;
+      }
     }
   }