From 113a10be0f01e898644fba0e6a6ba854c9d8e671 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 25 Aug 2010 14:12:10 +0000
Subject: [PATCH] excluded methods related to broken Jmol applet binding
 mechanism (JAL-621) and implemented default 'search all
 alignment' mode when opening a new PDB structure view

---
 src/jalview/appletgui/AlignFrame.java |   42 ++++++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 8 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 388d20f..adb0da5 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -3195,21 +3195,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * create a new binding between structures in an existing jmol viewer instance
    * and an alignpanel with sequences that have existing PDBFile entries. Note,
    * this does not open a new Jmol window, or modify the display of the
-   * structures in the original jmol window.
+   * structures in the original jmol window. Note
    * 
    * @param viewer JmolViewer instance
    * @param sequenceIds
    *          - sequence Ids to search for associations
-   */
+   * This method doesn't work. See http://issues.jalview.org/browse/JAL-621
+   * 
   public SequenceStructureBinding addStructureViewInstance(Object jmolviewer, String[] sequenceIds)
   {
-    org.jmol.api.JmolViewer viewer;
-    if (jmolviewer instanceof JmolViewer)
-    {
+    org.jmol.api.JmolViewer viewer=null;
+    try {
+      viewer = (org.jmol.api.JmolViewer) jmolviewer;
+    } 
+    catch (ClassCastException ex) {
       System.err.println("Unsupported viewer object :"+jmolviewer.getClass());
+    }
+    if (viewer==null)
+    {
+      System.err.println("Can't use this object as a structure viewer:"+jmolviewer.getClass());
       return null;
-    } else {
-      viewer = (JmolViewer) jmolviewer;
     }
     SequenceI[] seqs=null;
     if (sequenceIds==null || sequenceIds.length==0)
@@ -3230,6 +3235,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           seqs[sid] = (SequenceI) sqi.elementAt(sid);
         }
+      } else {
+        return null;
       }
     }
     ExtJmol jmv=null;
@@ -3241,7 +3248,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return jmv;
     
   }
-
+  **/
   public boolean addPdbFile(String sequenceId, String pdbEntryString,
           String pdbFile)
   {
@@ -3293,6 +3300,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void newStructureView(JalviewLite applet, PDBEntry pdb, SequenceI[] seqs,
           String[] chains, String protocol)
   {
+    if (seqs!=null)
+    {
+      Vector sequences=new Vector();
+     for (int i=0;i<seqs.length;i++) {
+       if (seqs[i]!=null)
+       {
+         sequences.addElement(seqs[i]);
+       }
+     }
+     seqs = new SequenceI[sequences.size()];
+     for (int i=0,isize=sequences.size(); i<isize; i++)
+     {
+       seqs[i] = (SequenceI) sequences.elementAt(i);
+     }
+    }
+    if (seqs==null || seqs.length==0)
+    {
+      System.err.println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+    }
     if (protocol==null || protocol.trim().length()==0 || protocol.equals("null"))
     {
       protocol = (String) pdb.getProperty().get("protocol");
-- 
1.7.10.2