From c7f05058ff22c137f7f2f62e8c0d64c41d38c871 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 20 Aug 2010 11:58:12 +0000
Subject: [PATCH] refactored external structure viewer binding API calls so
 they do not reference Jmol classes (re-instate's Jmol free
 launch of JalviewLite).

---
 src/jalview/appletgui/AlignFrame.java |  120 +++++++++++++++++++++++++++++++--
 src/jalview/bin/JalviewLite.java      |   43 +++---------
 2 files changed, 123 insertions(+), 40 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 14606b7..388d20f 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -21,6 +21,7 @@ import java.io.*;
 import java.net.*;
 import java.util.*;
 
+import java.applet.Applet;
 import java.awt.*;
 import java.awt.event.*;
 
@@ -3190,21 +3191,126 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
   }
 
-  public SequenceStructureBinding addJmolInstance(JmolViewer viewer, String[] sequenceIds)
+  /**
+   * 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.
+   * 
+   * @param viewer JmolViewer instance
+   * @param sequenceIds
+   *          - sequence Ids to search for associations
+   */
+  public SequenceStructureBinding addStructureViewInstance(Object jmolviewer, String[] sequenceIds)
   {
+    org.jmol.api.JmolViewer viewer;
+    if (jmolviewer instanceof JmolViewer)
+    {
+      System.err.println("Unsupported viewer object :"+jmolviewer.getClass());
+      return null;
+    } else {
+      viewer = (JmolViewer) jmolviewer;
+    }
     SequenceI[] seqs=null;
     if (sequenceIds==null || sequenceIds.length==0)
     {
       seqs = viewport.getAlignment().getSequencesArray();
     } else {
-      // resolve seqs for sequenceIds.
+      Vector sqi=new Vector();
+      AlignmentI al = viewport.getAlignment();
+      for (int sid=0;sid<sequenceIds.length;sid++) {
+        SequenceI sq = al.findName(sequenceIds[sid]);
+        if (sq!=null) {
+          sqi.addElement(sq);
+        }
+      }
+      if (sqi.size()>0) {
+        seqs = new SequenceI[sqi.size()];
+        for (int sid=0,sSize=sqi.size();sid<sSize;sid++)
+        {
+          seqs[sid] = (SequenceI) sqi.elementAt(sid);
+        }
+      }
     }
-    if (// viewer is not mapped)
-            true){
-      AppletJmol jmv = new AppletJmol(viewer, alignPanel, seqs);
-      return jmv;
+    ExtJmol jmv=null;
+    // TODO: search for a jmv that involves viewer
+    if (jmv==null){
+      // create a new viewer/jalview binding.
+      jmv = new ExtJmol(viewer, alignPanel, seqs);
     }
-    return null;
+    return jmv;
     
   }
+
+  public boolean addPdbFile(String sequenceId, String pdbEntryString,
+          String pdbFile)
+  {
+    SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+    boolean needtoadd=false;
+    if (toaddpdb!=null)
+    {
+      Vector pdbe = toaddpdb.getPDBId();
+      PDBEntry pdbentry = null;
+      if (pdbe!=null && pdbe.size()>0)
+      {
+        for (int pe=0,peSize=pdbe.size(); pe<peSize; pe++)
+        {
+          pdbentry = (PDBEntry) pdbe.elementAt(pe);
+          if (!pdbentry.getId().equals(pdbEntryString) && !pdbentry.getFile().equals(pdbFile))
+          {
+            pdbentry = null;
+          }
+          else
+          {
+              continue;
+          }
+        }
+      }
+      if (pdbentry==null)
+      {
+        pdbentry = new PDBEntry();
+        pdbentry.setId(pdbEntryString);
+        pdbentry.setFile(pdbFile);
+        needtoadd=true; // add this new entry to sequence.
+      }
+      // resolve data source
+      // TODO: this code should be a refactored to an io package
+      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+      if (protocol == null)
+      {
+        return false;
+      }
+      if (needtoadd)
+      {
+        // make a note of the access mode and add
+        pdbentry.getProperty().put("protocol", protocol);
+        toaddpdb.addPDBId(pdbentry);
+      }
+    }
+    return true;
+  }
+
+  public void newStructureView(JalviewLite applet, PDBEntry pdb, SequenceI[] seqs,
+          String[] chains, String protocol)
+  {
+    if (protocol==null || protocol.trim().length()==0 || protocol.equals("null"))
+    {
+      protocol = (String) pdb.getProperty().get("protocol");
+      if (protocol==null)
+      {
+        System.err.println("Couldn't work out protocol to open structure: "+pdb.getId());
+        return;
+      }
+    }
+    if (applet.jmolAvailable)
+    {
+      new jalview.appletgui.AppletJmol(pdb, seqs, chains,
+              alignPanel, protocol);
+      applet.lastFrameX += 40;
+      applet.lastFrameY += 40;
+    }
+    else
+      new MCview.AppletPDBViewer(pdb, seqs, chains,
+              alignPanel, protocol);
+  }
 }
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 338b319..90092b6 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -281,9 +281,9 @@ public class JalviewLite extends Applet
   // //////////////////////////////////////////////
   // //////////////////////////////////////////////
 
-  static int lastFrameX = 200;
+  public static int lastFrameX = 200;
 
-  static int lastFrameY = 200;
+  public static int lastFrameY = 200;
 
   boolean fileFound = true;
 
@@ -982,16 +982,8 @@ public class JalviewLite extends Applet
                 }
               }
 
-              if (jmolAvailable)
-              {
-                new jalview.appletgui.AppletJmol(pdb, seqs, chains,
-                        newAlignFrame.alignPanel, protocol);
-                lastFrameX += 40;
-                lastFrameY += 40;
-              }
-              else
-                new MCview.AppletPDBViewer(pdb, seqs, chains,
-                        newAlignFrame.alignPanel, protocol);
+              newAlignFrame.newStructureView(applet, pdb, seqs, chains, protocol);
+              
             }
           }
 
@@ -1303,40 +1295,25 @@ public class JalviewLite extends Applet
    */
   public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile)
   {
-    System.err.println("addPdbFile not yet implemented.");
-      return true;
-  }
-  /**
-   * bind the viewer instance to the pdbFile associated with sequences in the given alFrame.
-   * @param alFrame
-   * @param pdbFile - pdbFile URI as given via applet's parameters or by addPdb 
-   * @param viewer
-   * @return binding for viewer 
-   * TODO: consider making an exception structure for indicating when binding fails
-   */
-  public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, String pdbFile, org.jmol.api.JmolViewer viewer) 
-  {
-    System.err.println("addJmolInstance not yet implemented.");
-    /**
-     */
-    return null;
+    return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
   }
   /**
-   * bind structures in a viewer to any matching sequences in an alignFrame (use seuqenceIds to limit scope of search to specific sequences)
+   * bind structures in a viewer to any matching sequences in an alignFrame (use sequenceIds to limit scope of search to specific sequences)
    * @param alFrame
    * @param viewer
    * @param sequenceIds
    * @return
+   * TODO: consider making an exception structure for indicating when binding fails
    */
-  public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, org.jmol.api.JmolViewer viewer, String sequenceIds) 
+  public SequenceStructureBinding addStructureViewInstance(AlignFrame alFrame, Object viewer, String sequenceIds) 
   {
     if (viewer!=null)
     {
       if (sequenceIds!=null && sequenceIds.length()>0)
       {
-        return alFrame.addJmolInstance(viewer, separatorListToArray(sequenceIds));
+        return alFrame.addStructureViewInstance(viewer, separatorListToArray(sequenceIds));
       } else {
-        return alFrame.addJmolInstance(viewer, null);
+        return alFrame.addStructureViewInstance(viewer, null);
       }
     }
     return null;
-- 
1.7.10.2