X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=e6634fc786a3cd2b8dc95552984e0b3d13b76a01;hb=cfbf1b2d6661bb62b2b8748b4c29c12690c7b0b4;hp=502c68e35b1cb0e8e9f1ed2e6e3076a006b7128f;hpb=245a1b805629bedf7a0d66aecb26de6bc220b991;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 502c68e..e6634fc 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -22,11 +22,13 @@ 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;
 
@@ -47,13 +49,17 @@ public class StructureSelectionManager
   }
   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;
   }
 
@@ -146,16 +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 = "";
@@ -167,14 +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],
@@ -330,6 +349,11 @@ 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;
@@ -374,7 +398,7 @@ public class StructureSelectionManager
         }
       }
     }
-    if (results.getSize() > 0)
+    if (results!=null)
     {
       for (int i = 0; i < listeners.size(); i++)
       {
@@ -675,7 +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)
   {
@@ -712,4 +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)
+        {
+        }
+        ;
+      }
+    }
+  }
+
 }