first hack to get true DNA and Sequence highlighting from Structure mouseovers

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index d33c380..e12e3ab 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -259,6 +259,7 @@ public class StructureSelectionManager
 
   public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
   {
+    boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
     for (int i = 0; i < listeners.size(); i++)
     {
@@ -267,41 +268,62 @@ public class StructureSelectionManager
         if (results == null)
         {
           results = new SearchResults();
-
-          for (int j = 0; j < mappings.length; j++)
+        }
+        int indexpos;
+        for (int j = 0; j < mappings.length; j++)
+        {
+          if (mappings[j].pdbfile.equals(pdbfile)
+                  && mappings[j].pdbchain.equals(chain))
           {
-            if (mappings[j].pdbfile.equals(pdbfile)
-                    && mappings[j].pdbchain.equals(chain))
+            indexpos = mappings[j].getSeqPos(pdbResNum);
+            results.addResult(mappings[j].sequence, indexpos, indexpos);
+            // construct highlighted sequence list
+            if (seqmappings!=null)
             {
-              results.addResult(mappings[j].sequence, mappings[j]
-                      .getSeqPos(pdbResNum), mappings[j]
-                      .getSeqPos(pdbResNum));
+              
+              Enumeration e = seqmappings.elements();
+              while (e.hasMoreElements())
+
+              {
+                ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+                        mappings[j].sequence, indexpos, results);
+              }
             }
           }
         }
-        if (results.getSize() > 0)
-        {
-          ((SequenceListener) listeners.elementAt(i))
-                  .highlightSequence(results);
-        }
-
+      }
+    }
+    if (results.getSize() > 0)
+    {
+      for (int i = 0; i < listeners.size(); i++)
+      {
+        Object li = listeners.elementAt(i);
+        if (li instanceof SequenceListener)
+          ((SequenceListener) li).highlightSequence(results);
       }
     }
   }
 
   Vector seqmappings = null; // should be a simpler list of mapped seuqence
+
   /**
    * highlight regions associated with a position (indexpos) in seq
-   * @param seq the sequeence that the mouse over occured on
-   * @param indexpos the absolute position being mouseovered in seq (0 to seq.length())
-   * @param index the sequence position (if -1, seq.findPosition is called to resolve the residue number)
+   * 
+   * @param seq
+   *                the sequeence that the mouse over occured on
+   * @param indexpos
+   *                the absolute position being mouseovered in seq (0 to
+   *                seq.length())
+   * @param index
+   *                the sequence position (if -1, seq.findPosition is called to
+   *                resolve the residue number)
    */
   public void mouseOverSequence(SequenceI seq, int indexpos, int index)
   {
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
-    if (index==-1)
-      index=seq.findPosition(indexpos);
+    if (index == -1)
+      index = seq.findPosition(indexpos);
     StructureListener sl;
     int atomNo = 0;
     for (int i = 0; i < listeners.size(); i++)
@@ -312,7 +334,8 @@ public class StructureSelectionManager
 
         for (int j = 0; j < mappings.length; j++)
         {
-          if (mappings[j].sequence == seq || mappings[j].sequence==seq.getDatasetSequence())
+          if (mappings[j].sequence == seq
+                  || mappings[j].sequence == seq.getDatasetSequence())
           {
             atomNo = mappings[j].getAtomNum(index);
 
@@ -329,9 +352,9 @@ public class StructureSelectionManager
         if (relaySeqMappings && hasSequenceListeners
                 && listeners.elementAt(i) instanceof SequenceListener)
         {
-          // DEBUG 
-          //System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
-          //  index);
+          // DEBUG
+          // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
+          // index);
 
           if (results == null)
           {
@@ -340,7 +363,7 @@ public class StructureSelectionManager
             {
               // construct highlighted sequence list
 
-              if (seqmappings!=null)
+              if (seqmappings != null)
               {
                 Enumeration e = seqmappings.elements();
                 while (e.hasMoreElements())
@@ -369,11 +392,14 @@ public class StructureSelectionManager
         else if (listeners.elementAt(i) instanceof VamsasListener
                 && !handlingVamsasMo)
         {
-          // DEBUG 
-          //System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " " +
+          // DEBUG
+          // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
+          // " +
           // index);
-          // pass the mouse over and absolute position onto the VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, indexpos);
+          // pass the mouse over and absolute position onto the
+          // VamsasListener(s)
+          ((VamsasListener) listeners.elementAt(i))
+                  .mouseOver(seq, indexpos);
         }
       }
     }
@@ -384,23 +410,26 @@ public class StructureSelectionManager
    * handled
    */
   boolean handlingVamsasMo = false;
-  long lastmsg=0;
+
+  long lastmsg = 0;
+
   /**
    * as mouseOverSequence but only route event to SequenceListeners
    * 
    * @param sequenceI
-   * @param position in an alignment sequence
+   * @param position
+   *                in an alignment sequence
    */
   public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
   {
     handlingVamsasMo = true;
-    long msg = sequenceI.hashCode()*(1+position);
-    if (lastmsg!=msg)
+    long msg = sequenceI.hashCode() * (1 + position);
+    if (lastmsg != msg)
     {
       lastmsg = msg;
       mouseOverSequence(sequenceI, position, -1);
     }
-      handlingVamsasMo = false;
+    handlingVamsasMo = false;
   }
 
   public Annotation[] colourSequenceFromStructure(SequenceI seq,