X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=5a9e382369288c89e3bb84a89a615deb9a139162;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=d1bccd8643f5219bfb7378e7652fb6639db0a082;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index d1bccd8..5a9e382 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.structure;
 
@@ -28,37 +29,47 @@ import jalview.datamodel.*;
 
 public class StructureSelectionManager
 {
-  static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
+  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);
-      }
-    }
-  }
+  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(StructureSelectionManagerProvider context)
+  public static StructureSelectionManager getStructureSelectionManager(
+          StructureSelectionManagerProvider context)
   {
+    if (context==null)
+    {
+      throw new Error("Implementation error. Structure selection manager's context is 'null'", new NullPointerException("SSM context is null"));
+    }
     if (instances == null)
     {
-      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
     }
-    StructureSelectionManager instance=instances.get(context);
-    if (instance==null)
+    StructureSelectionManager instance = instances.get(context);
+    if (instance == null)
     {
-      instances.put(context, instance=new StructureSelectionManager());
+      instances.put(context, instance = new StructureSelectionManager());
     }
     return instance;
   }
@@ -96,6 +107,7 @@ public class StructureSelectionManager
 
   /**
    * register a listener for alignment sequence mouseover events
+   * 
    * @param svl
    */
   public void addStructureViewerListener(Object svl)
@@ -156,12 +168,28 @@ public class StructureSelectionManager
     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 +201,12 @@ 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],
@@ -236,7 +262,8 @@ public class StructureSelectionManager
 
       // 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[][] mapping = new int[sequence[s].findPosition(sequence[s]
+              .getLength()) + 2][2];
       int resNum = -10000;
       int index = 0;
 
@@ -282,15 +309,16 @@ public class StructureSelectionManager
     listeners.removeElement(svl);
     if (svl instanceof SequenceListener)
     {
-      for (int i=0;i<listeners.size();i++)
+      for (int i = 0; i < listeners.size(); i++)
       {
         if (listeners.elementAt(i) instanceof StructureListener)
         {
-          ((StructureListener)listeners.elementAt(i)).releaseReferences(svl);
+          ((StructureListener) listeners.elementAt(i))
+                  .releaseReferences(svl);
         }
       }
     }
-      
+
     if (pdbfiles == null)
     {
       return;
@@ -336,6 +364,11 @@ 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;
@@ -380,7 +413,7 @@ public class StructureSelectionManager
         }
       }
     }
-    if (results!=null)
+    if (results != null)
     {
       for (int i = 0; i < listeners.size(); i++)
       {
@@ -415,9 +448,14 @@ 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 +478,7 @@ public class StructureSelectionManager
       else
       {
         if (relaySeqMappings && hasSequenceListeners
-                && listeners.elementAt(i) instanceof SequenceListener)
+                && listener instanceof SequenceListener)
         {
           // DEBUG
           // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
@@ -475,12 +513,10 @@ public class StructureSelectionManager
           }
           if (hasSequenceListeners)
           {
-            ((SequenceListener) listeners.elementAt(i))
-                    .highlightSequence(results);
+            ((SequenceListener) listener).highlightSequence(results);
           }
         }
-        else if (listeners.elementAt(i) instanceof VamsasListener
-                && !handlingVamsasMo)
+        else if (listener instanceof VamsasListener && !handlingVamsasMo)
         {
           // DEBUG
           // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
@@ -488,8 +524,12 @@ public class StructureSelectionManager
           // index);
           // pass the mouse over and absolute position onto the
           // VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
-                  indexpos, source);
+          ((VamsasListener) listener).mouseOver(seq, indexpos, source);
+        }
+        else if (listener instanceof SecondaryStructureListener)
+        {
+          ((SecondaryStructureListener) listener).mouseOverSequence(seq,
+                  indexpos);
         }
       }
     }
@@ -718,19 +758,21 @@ 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)
+
+  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();
+      Enumeration<AlignmentViewPanelListener> listeners = view_listeners
+              .elements();
       while (listeners.hasMoreElements())
       {
-        AlignmentViewPanelListener slis = listeners
-                .nextElement();
+        AlignmentViewPanelListener slis = listeners.nextElement();
         if (slis != source)
         {
           slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
@@ -739,45 +781,58 @@ public class StructureSelectionManager
       }
     }
   }
-  
 
-  public void finalize() throws Throwable {
-    if (listeners!=null) {
+  public void finalize() throws Throwable
+  {
+    if (listeners != null)
+    {
       listeners.clear();
-      listeners=null;
+      listeners = null;
     }
-    if (mappingData!=null)
+    if (mappingData != null)
     {
       mappingData.clear();
-      mappingData=null;
+      mappingData = null;
     }
-    if (sel_listeners!=null)
+    if (sel_listeners != null)
     {
       sel_listeners.clear();
-      sel_listeners=null;
+      sel_listeners = null;
     }
-    if (view_listeners!=null)
+    if (view_listeners != null)
     {
       view_listeners.clear();
-      view_listeners=null;
+      view_listeners = null;
     }
-    mappings=null;
-    seqmappingrefs=null;
+    mappings = null;
+    seqmappingrefs = null;
   }
 
   /**
    * release all references associated with this manager provider
+   * 
    * @param jalviewLite
    */
   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)
+        {
+        }
+        ;
+      }
     }
   }