pickmanager on sequence and alignment position, vamsas pick broadcast and refactor...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index b07b7a4..d36d009 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -293,10 +293,12 @@ public class StructureSelectionManager
 
   // pairs
 
-  public void mouseOverSequence(SequenceI seq, int index)
+  public void mouseOverSequence(SequenceI seq, int indexpos, int index)
   {
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
+    if (index==-1)
+      index=seq.findPosition(indexpos);
     StructureListener sl;
     int atomNo = 0;
     for (int i = 0; i < listeners.size(); i++)
@@ -307,7 +309,7 @@ public class StructureSelectionManager
 
         for (int j = 0; j < mappings.length; j++)
         {
-          if (mappings[j].sequence == seq)
+          if (mappings[j].sequence == seq || mappings[j].sequence==seq.getDatasetSequence())
           {
             atomNo = mappings[j].getAtomNum(index);
 
@@ -348,6 +350,7 @@ public class StructureSelectionManager
               // hasSequenceListeners = results.getSize() > 0;
               if (handlingVamsasMo)
               {
+                // maybe have to resolve seq to a dataset seqeunce...
                 // add in additional direct sequence and/or dataset sequence
                 // highlighting
                 results.addResult(seq, index, index);
@@ -366,8 +369,8 @@ public class StructureSelectionManager
           // DEBUG 
           //System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " " +
           // index);
-          // pass the mouse over onto the VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, index);
+          // pass the mouse over and absolute position onto the VamsasListener(s)
+          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, indexpos);
         }
       }
     }
@@ -378,18 +381,23 @@ public class StructureSelectionManager
    * handled
    */
   boolean handlingVamsasMo = false;
-
+  long lastmsg=0;
   /**
    * as mouseOverSequence but only route event to SequenceListeners
    * 
    * @param sequenceI
-   * @param position
+   * @param position in an alignment sequence
    */
   public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
   {
     handlingVamsasMo = true;
-    mouseOverSequence(sequenceI, position);
-    handlingVamsasMo = false;
+    long msg = sequenceI.hashCode()*(1+position);
+    if (lastmsg!=msg)
+    {
+      lastmsg = msg;
+      mouseOverSequence(sequenceI, position, -1);
+    }
+      handlingVamsasMo = false;
   }
 
   public Annotation[] colourSequenceFromStructure(SequenceI seq,