X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=f9e8fdba4db2f673da6c0c458a6c8a912d758d55;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=c4566d8b45f017780a93b91e40e646c2834304b9;hpb=caf13e6a9dc82023cd8648420201e5ad60ce0393;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index c4566d8..f9e8fdb 100644
--- 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, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -22,23 +22,44 @@ import java.util.*;
 
 import MCview.*;
 import jalview.analysis.*;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.*;
 
 public class StructureSelectionManager
 {
-  static StructureSelectionManager instance;
+  static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
 
   StructureMapping[] mappings;
 
+  /**
+   * debug function - write all mappings to stdout
+   */
+  public void reportMapping() {
+    if (mappings==null)
+    {
+      System.err.println("reportMapping: No PDB/Sequence mappings.");
+    }else{
+      System.err.println("reportMapping: There are "+mappings.length+" mappings.");
+      for (int m=0;m<mappings.length;m++)
+      {
+        System.err.println("mapping "+m+" : "+mappings[m].pdbfile);
+      }
+    }
+  }
   Hashtable mappingData = new Hashtable();
 
-  public static StructureSelectionManager getStructureSelectionManager()
+  public static StructureSelectionManager getStructureSelectionManager(StructureSelectionManagerProvider context)
   {
-    if (instance == null)
+    if (instances == null)
     {
-      instance = new StructureSelectionManager();
+      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+    }
+    StructureSelectionManager instance=instances.get(context);
+    if (instance==null)
+    {
+      instances.put(context, instance=new StructureSelectionManager());
     }
-
     return instance;
   }
 
@@ -131,16 +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 = "";
@@ -152,14 +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],
@@ -213,7 +247,9 @@ 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[sequence[s].findPosition(sequence[s].getLength()) + 2][2];
       int resNum = -10000;
       int index = 0;
 
@@ -257,6 +293,17 @@ public class StructureSelectionManager
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
     listeners.removeElement(svl);
+    if (svl instanceof SequenceListener)
+    {
+      for (int i=0;i<listeners.size();i++)
+      {
+        if (listeners.elementAt(i) instanceof StructureListener)
+        {
+          ((StructureListener)listeners.elementAt(i)).releaseReferences(svl);
+        }
+      }
+    }
+      
     if (pdbfiles == null)
     {
       return;
@@ -302,8 +349,15 @@ 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;
+    int lastipos = -1, indexpos;
     for (int i = 0; i < listeners.size(); i++)
     {
       if (listeners.elementAt(i) instanceof SequenceListener)
@@ -312,7 +366,6 @@ public class StructureSelectionManager
         {
           results = new SearchResults();
         }
-        int indexpos;
         if (mappings != null)
         {
           for (int j = 0; j < mappings.length; j++)
@@ -321,25 +374,31 @@ public class StructureSelectionManager
                     && mappings[j].pdbchain.equals(chain))
             {
               indexpos = mappings[j].getSeqPos(pdbResNum);
-              results.addResult(mappings[j].sequence, indexpos, indexpos);
-              // construct highlighted sequence list
-              if (seqmappings != null)
+              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);
+                  }
                 }
               }
+
             }
           }
         }
       }
     }
-    if (results.getSize() > 0)
+    if (results!=null)
     {
       for (int i = 0; i < listeners.size(); i++)
       {
@@ -363,7 +422,8 @@ 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, VamsasSource source)
+  public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+          VamsasSource source)
   {
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
@@ -446,8 +506,8 @@ public class StructureSelectionManager
           // index);
           // pass the mouse over and absolute position onto the
           // VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i))
-                  .mouseOver(seq, indexpos, source);
+          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
+                  indexpos, source);
         }
       }
     }
@@ -468,7 +528,8 @@ public class StructureSelectionManager
    * @param position
    *          in an alignment sequence
    */
-  public void mouseOverVamsasSequence(SequenceI sequenceI, int position, VamsasSource source)
+  public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
+          VamsasSource source)
   {
     handlingVamsasMo = true;
     long msg = sequenceI.hashCode() * (1 + position);
@@ -638,7 +699,7 @@ public class StructureSelectionManager
     modifySeqMappingList(true, codonFrames);
   }
 
-  Vector sel_listeners = new Vector();
+  Vector<SelectionListener> sel_listeners = new Vector<SelectionListener>();
 
   public void addSelectionListener(SelectionListener selecter)
   {
@@ -675,4 +736,78 @@ public class StructureSelectionManager
       }
     }
   }
+  
+  Vector<AlignmentViewPanelListener> view_listeners=new Vector<AlignmentViewPanelListener>();
+  public synchronized void sendViewPosition(jalview.api.AlignmentViewPanel source, int startRes,
+          int endRes, int startSeq, int endSeq)
+  {
+
+    if (view_listeners != null && view_listeners.size() > 0)
+    {
+      Enumeration<AlignmentViewPanelListener> listeners = view_listeners.elements();
+      while (listeners.hasMoreElements())
+      {
+        AlignmentViewPanelListener slis = listeners
+                .nextElement();
+        if (slis != source)
+        {
+          slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
+        }
+        ;
+      }
+    }
+  }
+  
+
+  public void finalize() throws Throwable {
+    if (listeners!=null) {
+      listeners.clear();
+      listeners=null;
+    }
+    if (mappingData!=null)
+    {
+      mappingData.clear();
+      mappingData=null;
+    }
+    if (sel_listeners!=null)
+    {
+      sel_listeners.clear();
+      sel_listeners=null;
+    }
+    if (view_listeners!=null)
+    {
+      view_listeners.clear();
+      view_listeners=null;
+    }
+    mappings=null;
+    seqmappingrefs=null;
+  }
+
+  /**
+   * release all references associated with this manager provider
+   * @param jalviewLite
+   */
+  public static void release(StructureSelectionManagerProvider jalviewLite)
+  {
+//    synchronized (instances)
+    {
+      if (instances == null)
+      {
+        return;
+      }
+      StructureSelectionManager mnger = (instances.get(jalviewLite));
+      if (mnger != null)
+      {
+        instances.remove(jalviewLite);
+        try
+        {
+          mnger.finalize();
+        } catch (Throwable x)
+        {
+        }
+        ;
+      }
+    }
+  }
+
 }