X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=0e4ec2fa50fb609a8e07a0d4d5edb9ea6c98d4f9;hb=2f3b33ed7140d07e2bb31960ce5aedfed134dfeb;hp=936f13916d3680f77617e23b9ce8bde3b31620ef;hpb=a90e0eeb2b61e962b86e9dcef586f9e4224405b0;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 936f139..0e4ec2f 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -73,6 +73,10 @@ public class StructureSelectionManager
 
   Vector listeners = new Vector();
 
+  /**
+   * register a listener for alignment sequence mouseover events
+   * @param svl
+   */
   public void addStructureViewerListener(Object svl)
   {
     if (!listeners.contains(svl))
@@ -97,12 +101,18 @@ public class StructureSelectionManager
   }
 
   /**
-   * create sequence structure mappings between each sequence and the given pdbFile (retrieved via the given protocol).
+   * create sequence structure mappings between each sequence and the given
+   * pdbFile (retrieved via the given protocol).
    * 
-   * @param sequence  - one or more sequences to be mapped to pdbFile
-   * @param targetChains - optional chain specification for mapping each sequence to pdb (may be nill, individual elements may be nill)  
-   * @param pdbFile - structure data resource
-   * @param protocol - how to resolve data from resource
+   * @param sequence
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChains
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill)
+   * @param pdbFile
+   *          - structure data resource
+   * @param protocol
+   *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
@@ -139,35 +149,37 @@ public class StructureSelectionManager
       AlignSeq maxAlignseq = null;
       String maxChainId = " ";
       PDBChain maxChain = null;
-      boolean first=true;
+      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 
+        // 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))
         {
           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], ((PDBChain) pdb.chains
-                .elementAt(i)).sequence, ((PDBChain) pdb.chains
-                .elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+        AlignSeq as = new AlignSeq(sequence[s],
+                ((PDBChain) pdb.chains.elementAt(i)).sequence,
+                ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                        : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
 
         if (first || as.maxscore > max
                 || (as.maxscore == max && chain.id.equals(targetChain)))
         {
-          first=false;
+          first = false;
           maxChain = chain;
           max = as.maxscore;
           maxAlignseq = as;
           maxChainId = chain.id;
         }
       }
-      if (maxChain==null)
+      if (maxChain == null)
       {
         continue;
       }
@@ -201,7 +213,9 @@ public class StructureSelectionManager
 
       maxChain.transferRESNUMFeatures(sequence[s], null);
 
-      int[][] mapping = new int[sequence[s].getEnd() + 2][2];
+      // allocate enough slots to store the mapping from positions in
+      // sequence[s] to the associated chain
+      int[][] mapping = new int[maxChain.sequence.getEnd() + 2][2];
       int resNum = -10000;
       int index = 0;
 
@@ -233,8 +247,8 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
 
       mappings[mappings.length - 1] = new StructureMapping(sequence[s],
-              pdbFile, pdb.id, maxChainId, mapping, mappingDetails
-                      .toString());
+              pdbFile, pdb.id, maxChainId, mapping,
+              mappingDetails.toString());
       maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
     }
     // ///////
@@ -245,7 +259,7 @@ public class StructureSelectionManager
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
     listeners.removeElement(svl);
-    if (pdbfiles==null)
+    if (pdbfiles == null)
     {
       return;
     }
@@ -271,8 +285,8 @@ public class StructureSelectionManager
 
       }
     }
-    
-    if (pdbs.size()>0  && mappings != null)
+
+    if (pdbs.size() > 0 && mappings != null)
     {
       Vector tmp = new Vector();
       for (int i = 0; i < mappings.length; i++)
@@ -292,6 +306,8 @@ public class StructureSelectionManager
   {
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
+    SequenceI lastseq = null;
+    int lastipos = -1, indexpos;
     for (int i = 0; i < listeners.size(); i++)
     {
       if (listeners.elementAt(i) instanceof SequenceListener)
@@ -300,25 +316,33 @@ public class StructureSelectionManager
         {
           results = new SearchResults();
         }
-        int indexpos;
-        for (int j = 0; j < mappings.length; j++)
+        if (mappings != null)
         {
-          if (mappings[j].pdbfile.equals(pdbfile)
-                  && mappings[j].pdbchain.equals(chain))
+          for (int j = 0; j < mappings.length; j++)
           {
-            indexpos = mappings[j].getSeqPos(pdbResNum);
-            results.addResult(mappings[j].sequence, indexpos, indexpos);
-            // construct highlighted sequence list
-            if (seqmappings != null)
+            if (mappings[j].pdbfile.equals(pdbfile)
+                    && mappings[j].pdbchain.equals(chain))
             {
+              indexpos = mappings[j].getSeqPos(pdbResNum);
+              if (lastipos != indexpos && lastseq != mappings[j].sequence)
+              {
+                results.addResult(mappings[j].sequence, indexpos, indexpos);
+                lastipos = indexpos;
+                lastseq = mappings[j].sequence;
+                // construct highlighted sequence list
+                if (seqmappings != null)
+                {
 
-              Enumeration e = seqmappings.elements();
-              while (e.hasMoreElements())
+                  Enumeration e = seqmappings.elements();
+                  while (e.hasMoreElements())
 
-              {
-                ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
-                        mappings[j].sequence, indexpos, results);
+                  {
+                    ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+                            mappings[j].sequence, indexpos, results);
+                  }
+                }
               }
+
             }
           }
         }
@@ -348,7 +372,8 @@ public class StructureSelectionManager
    *          the sequence position (if -1, seq.findPosition is called to
    *          resolve the residue number)
    */
-  public void mouseOverSequence(SequenceI seq, int indexpos, int index)
+  public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+          VamsasSource source)
   {
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
@@ -361,7 +386,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        if (mappings==null)
+        if (mappings == null)
         {
           continue;
         }
@@ -431,8 +456,8 @@ public class StructureSelectionManager
           // index);
           // pass the mouse over and absolute position onto the
           // VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i))
-                  .mouseOver(seq, indexpos);
+          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
+                  indexpos, source);
         }
       }
     }
@@ -453,14 +478,15 @@ public class StructureSelectionManager
    * @param position
    *          in an alignment sequence
    */
-  public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
+  public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
+          VamsasSource source)
   {
     handlingVamsasMo = true;
     long msg = sequenceI.hashCode() * (1 + position);
     if (lastmsg != msg)
     {
       lastmsg = msg;
-      mouseOverSequence(sequenceI, position, -1);
+      mouseOverSequence(sequenceI, position, -1, source);
     }
     handlingVamsasMo = false;
   }
@@ -524,14 +550,16 @@ public class StructureSelectionManager
   public StructureMapping[] getMapping(String pdbfile)
   {
     Vector tmp = new Vector();
-    for (int i = 0; i < mappings.length; i++)
+    if (mappings != null)
     {
-      if (mappings[i].pdbfile.equals(pdbfile))
+      for (int i = 0; i < mappings.length; i++)
       {
-        tmp.addElement(mappings[i]);
+        if (mappings[i].pdbfile.equals(pdbfile))
+        {
+          tmp.addElement(mappings[i]);
+        }
       }
     }
-
     StructureMapping[] ret = new StructureMapping[tmp.size()];
     for (int i = 0; i < tmp.size(); i++)
     {