From 794501173d6cea5fc3a965cee3792ae78304abe9 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 20 Aug 2010 11:54:04 +0000
Subject: [PATCH] extend jmol binding handles selection events and add in a
 'refreshPdbEntries' step so the list of PDB entries jalview
 knows about can be updated before a Jmol notifyUpdate event
 is handled

---
 src/jalview/appletgui/AppletJmolBinding.java |   16 ++-
 src/jalview/ext/jmol/JalviewJmolBinding.java |  173 +++++++++++++++-----------
 src/jalview/gui/AppJmolBinding.java          |   13 ++
 3 files changed, 129 insertions(+), 73 deletions(-)

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 4c29e05..89d053b 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -3,6 +3,8 @@
  */
 package jalview.appletgui;
 
+import java.util.BitSet;
+
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
@@ -12,7 +14,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 {
 
   /**
-   * 
+   * Window that contains the bound Jmol instance
    */
   private AppletJmol appletJmolBinding;
 
@@ -99,4 +101,16 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     // do nothing.
   }
 
+  public void selectionChanged(BitSet arg0)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  public void refreshPdbEntries()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
 }
\ No newline at end of file
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index af83e48..929411f 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -39,7 +39,7 @@ import org.jmol.viewer.JmolConstants;
 import jalview.schemes.*;
 
 public abstract class JalviewJmolBinding implements StructureListener,
-        JmolStatusListener, SequenceStructureBinding
+        JmolStatusListener, SequenceStructureBinding, JmolSelectionListener
 
 {
   /**
@@ -48,11 +48,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * time.
    */
   private boolean loadingFromArchive = false;
+
   /**
    * state flag used to check if the Jmol viewer's paint method can be called
    */
-  private boolean finishedInit=false;
-  
+  private boolean finishedInit = false;
+
   public boolean isFinishedInit()
   {
     return finishedInit;
@@ -134,14 +135,25 @@ public abstract class JalviewJmolBinding implements StructureListener,
      */
   }
 
+  public JalviewJmolBinding(JmolViewer viewer2)
+  {
+    viewer = viewer2;
+    viewer.setJmolStatusListener(this);
+    viewer.addSelectionListener(this);
+  }
+
   /**
-   * construct a title string for the viewer window based on the data jalview knows about
-   * @return 
+   * construct a title string for the viewer window based on the data jalview
+   * knows about
+   * 
+   * @return
    */
-  public String getViewerTitle() {
-    if (sequence==null || pdbentry==null || sequence.length<1 || pdbentry.length<1)
+  public String getViewerTitle()
+  {
+    if (sequence == null || pdbentry == null || sequence.length < 1
+            || pdbentry.length < 1)
     {
-      return("Jalview Jmol Window");
+      return ("Jalview Jmol Window");
     }
     StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
             + pdbentry[0].getId());
@@ -188,8 +200,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     }
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
-    evalStateCommand("select *;restrict " + cmd + ";cartoon;center "
-                    + cmd);
+    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
   }
 
   public void closeViewer()
@@ -201,7 +212,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     // and shut down jmol
     viewer.evalStringQuiet("zap");
     viewer.setJmolStatusListener(null);
-    lastCommand=null;
+    lastCommand = null;
     viewer = null;
   }
 
@@ -294,15 +305,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
     evalStateCommand(command.toString());
   }
 
-  public void evalStateCommand(String command) {
+  public void evalStateCommand(String command)
+  {
     jmolHistory(false);
     if (lastCommand == null || !lastCommand.equals(command))
     {
-      viewer.evalStringQuiet(command+"\n");
+      viewer.evalStringQuiet(command + "\n");
     }
     jmolHistory(true);
     lastCommand = command;
   }
+
   /**
    * colour any structures associated with sequences in the given alignment
    * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
@@ -312,7 +325,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     if (!colourBySequence)
       return;
-    if (ssm==null)
+    if (ssm == null)
     {
       return;
     }
@@ -404,8 +417,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
   StringBuffer condenseCommand(String command, int pos)
   {
 
-    StringBuffer sb = new StringBuffer(command.substring(0, command
-            .lastIndexOf("select") + 7));
+    StringBuffer sb = new StringBuffer(command.substring(0,
+            command.lastIndexOf("select") + 7));
 
     command = command.substring(sb.length());
 
@@ -475,6 +488,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   public abstract FeatureRenderer getFeatureRenderer();
 
+  /**
+   * instruct the Jalview binding to update the pdbentries vector if necessary
+   * prior to matching the jmol view's contents to the list of structure files
+   * Jalview knows about.
+   */
+  public abstract void refreshPdbEntries();
+
   private int getModelNum(String modelFileName)
   {
     String[] mfn = getPdbFile();
@@ -623,8 +643,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String chainId;
 
     if (strInfo.indexOf(":") > -1)
-      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
-              .indexOf("."));
+      chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+              strInfo.indexOf("."));
     else
     {
       chainId = " ";
@@ -660,7 +680,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     if (data != null)
     {
-      System.err.println("Ignoring additional hover info: " + data+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+      System.err.println("Ignoring additional hover info: " + data
+              + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
     }
     mouseOverStructure(atomIndex, strInfo);
   }
@@ -713,12 +734,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
     jmolHistory(true);
     // TODO: in application this happens
     //
-//if (scriptWindow != null)
-//    {
-//      scriptWindow.sendConsoleMessage(strInfo);
-//      scriptWindow.sendConsoleMessage("\n");
-//    }
-
+    // if (scriptWindow != null)
+    // {
+    // scriptWindow.sendConsoleMessage(strInfo);
+    // scriptWindow.sendConsoleMessage("\n");
+    // }
 
   }
 
@@ -730,8 +750,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
       {
       case JmolConstants.CALLBACK_LOADSTRUCT:
         notifyFileLoaded((String) data[1], (String) data[2],
-                (String) data[3], (String) data[4], ((Integer) data[5])
-                        .intValue());
+                (String) data[3], (String) data[4],
+                ((Integer) data[5]).intValue());
 
         break;
       case JmolConstants.CALLBACK_PICK:
@@ -743,8 +763,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
                 (String) data[0]);
         break;
       case JmolConstants.CALLBACK_SCRIPT:
-        notifyScriptTermination((String) data[2], ((Integer) data[3])
-                .intValue());
+        notifyScriptTermination((String) data[2],
+                ((Integer) data[3]).intValue());
         break;
       case JmolConstants.CALLBACK_ECHO:
         sendConsoleEcho((String) data[1]);
@@ -761,11 +781,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
         updateUI();
         break;
       case JmolConstants.CALLBACK_MEASURE:
-        
+
       case JmolConstants.CALLBACK_CLICK:
-        
+
       default:
-        System.err.println("Unhandled callback " + type + " " + data[1].toString());
+        System.err.println("Unhandled callback " + type + " "
+                + data[1].toString());
         break;
       }
     } catch (Exception e)
@@ -806,6 +827,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
       updateUI();
       return;
     }
+    // the rest of this routine ignores the arguments, and simply interrogates
+    // the Jmol view to find out what structures it contains, and adds them to
+    // the structure selection manager.
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
@@ -814,49 +838,51 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String[] modelfilenames = getPdbFile();
     ssm = StructureSelectionManager.getStructureSelectionManager();
     // first check if we've lost any structures
-    if (oldmodels!=null && oldmodels.length>0)
+    if (oldmodels != null && oldmodels.length > 0)
     {
-      int oldm=0;
-      for (int i=0;i<oldmodels.length;i++)
+      int oldm = 0;
+      for (int i = 0; i < oldmodels.length; i++)
       {
-        for (int n=0;n<modelfilenames.length; n++)
+        for (int n = 0; n < modelfilenames.length; n++)
         {
-          if (modelfilenames[n]==oldmodels[i])
+          if (modelfilenames[n] == oldmodels[i])
           {
-            oldmodels[i]=null;
+            oldmodels[i] = null;
             break;
           }
         }
-        if (oldmodels[i]!=null)
+        if (oldmodels[i] != null)
         {
           oldm++;
         }
       }
-      if (oldm>0)
+      if (oldm > 0)
       {
         String[] oldmfn = new String[oldm];
-        oldm=0;
-        for (int i=0;i<oldmodels.length; i++)
+        oldm = 0;
+        for (int i = 0; i < oldmodels.length; i++)
         {
-          if (oldmodels[i]!=null) {
+          if (oldmodels[i] != null)
+          {
             oldmfn[oldm++] = oldmodels[i];
           }
         }
-        // deregister the Jmol instance for these structures - we'll add 
-        // ourselves again at the end for the current structure set. 
+        // deregister the Jmol instance for these structures - we'll add
+        // ourselves again at the end for the current structure set.
         ssm.removeStructureViewerListener(this, oldmfn);
       }
     }
+    refreshPdbEntries();
     for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
     {
       String fileName = modelfilenames[modelnum];
       if (fileName != null)
       {
+        boolean foundEntry = false;
         // search pdbentries and sequences to find correct pdbentry and
         // sequence[] pair for this filename
         if (pdbentry != null)
         {
-          boolean foundEntry = false;
           for (int pe = 0; pe < pdbentry.length; pe++)
           {
             if (pdbentry[pe].getFile().equals(fileName))
@@ -866,8 +892,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
               if (loadedInline)
               {
                 // TODO: replace with getData ?
-                pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
-                        .getFile(), AppletFormatAdapter.PASTE);
+                pdb = ssm.setMapping(sequence, chains,
+                        pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
                 pdbentry[pe].setFile("INLINE" + pdb.id);
               }
               else
@@ -891,8 +917,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
                 {
                 }
                 ;
-                pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
-                        .getFile(), protocol);
+                pdb = ssm.setMapping(sequence, chains,
+                        pdbentry[pe].getFile(), protocol);
 
               }
 
@@ -906,32 +932,32 @@ public abstract class JalviewJmolBinding implements StructureListener,
               notifyLoaded = true;
             }
           }
-          if (!foundEntry && associateNewStructs)
-          {
-            // this is a foreign pdb file that jalview doesn't know about - add
-            // it
-            // to the dataset
-            // and try to find a home - either on a matching sequence or as a
-            // new
-            // sequence.
-            String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
-                    "PDB");
-            // parse pdb file into a chain, etc.
-            // locate best match for pdb in associated views and add mapping to
-            // ssm
-            // if properly registered then
-            notifyLoaded = true;
-          }
+        }
+        if (!foundEntry && associateNewStructs)
+        {
+          // this is a foreign pdb file that jalview doesn't know about - add
+          // it to the dataset and try to find a home - either on a matching
+          // sequence or as a new sequence.
+          String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+                  "PDB");
+          // parse pdb file into a chain, etc.
+          // locate best match for pdb in associated views and add mapping to
+          // ssm
+          // if properly registered then
+          notifyLoaded = true;
+
         }
       }
     }
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
-    jmolpopup.updateComputedMenus();
+    if (jmolpopup != null)
+    {
+      jmolpopup.updateComputedMenus();
+    }
     if (!isLoadingFromArchive())
     {
-      viewer
-              .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+      viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
     }
     setLoadingFromArchive(false);
     // register ourselves as a listener and notify the gui that it needs to
@@ -940,7 +966,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     if (notifyLoaded)
     {
       FeatureRenderer fr = getFeatureRenderer();
-      if (fr!=null)
+      if (fr != null)
       {
         fr.featuresAdded();
       }
@@ -953,7 +979,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     notifyAtomPicked(iatom, strMeasure, null);
   }
 
-  public abstract void notifyScriptTermination(String strStatus, int msWalltime);
+  public abstract void notifyScriptTermination(String strStatus,
+          int msWalltime);
 
   /**
    * display a message echoed from the jmol viewer
@@ -1039,7 +1066,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
           URL documentBase, URL codeBase, String commandOptions)
   {
     viewer = JmolViewer.allocateViewer(renderPanel,
-            new SmarterJmolAdapter(), htmlName+((Object) this).toString(), documentBase, codeBase,
+            new SmarterJmolAdapter(),
+            htmlName + ((Object) this).toString(), documentBase, codeBase,
             commandOptions, this);
   }
 
@@ -1052,6 +1080,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     return loadingFromArchive;
   }
+
   public void setBackgroundColour(java.awt.Color col)
   {
     jmolHistory(false);
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 831fd5a..9f7090a 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -3,6 +3,7 @@
  */
 package jalview.gui;
 
+import java.util.BitSet;
 import java.util.Vector;
 
 import jalview.bin.Cache;
@@ -127,4 +128,16 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     v.copyInto(tmp);
     sequence = tmp;
   }
+
+  public void selectionChanged(BitSet arg0)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  public void refreshPdbEntries()
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }
\ No newline at end of file
-- 
1.7.10.2