From 6f9e452300ac8853e5c10ec29828f420f3909341 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 6 May 2015 12:50:25 +0100
Subject: [PATCH] JAL-1725 parse atomSpec with submodel; debug output removed

---
 src/jalview/ext/rbvi/chimera/ChimeraListener.java  |    2 +-
 .../ext/rbvi/chimera/JalviewChimeraBinding.java    |   83 ++++++++++----------
 2 files changed, 41 insertions(+), 44 deletions(-)

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraListener.java b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
index 2479a1b..c9ec136 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraListener.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
@@ -122,7 +122,7 @@ public class ChimeraListener extends AbstractRequestHandler implements
    */
   protected void processModelChanged(String message)
   {
-    System.out.println(message + " (not implemented in Jalview)");
+    // System.out.println(message + " (not implemented in Jalview)");
   }
 
   /**
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 1434c76..3c751e7 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -23,7 +23,6 @@ package jalview.ext.rbvi.chimera;
 import java.awt.Color;
 import java.net.BindException;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -931,58 +930,43 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void highlightChimeraSelection()
   {
+    /*
+     * Ask Chimera for its current selection
+     */
     List<String> selection = viewer.getSelectedResidueSpecs();
-    // System.out.println("Chimera selection: " + selection.toString());
 
-    // TODO handle more than one!!
-    if (selection.size() > 0)
-    {
-      highlightChimeraSelection(selection);
-    }
-  }
-
-  private void log(String message)
-  {
-    System.err.println("## Chimera log: " + message);
-  }
-
-  private void viewerCommandHistory(boolean enable)
-  {
-    // log("(Not yet implemented) History "
-    // + ((debug || enable) ? "on" : "off"));
-  }
-
-  /**
-   * Propagate atom selections from Chimera
-   * 
-   * @param atoms
-   *          for example "#0:70.A" (model/residue/chain)
-   */
-  public void highlightChimeraSelection(List<String> atoms)
-  {
+    /*
+     * Parse model number, residue and chain for each selected position,
+     * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
+     */
     List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
-    for (String atomSpec : atoms)
+    for (String atomSpec : selection)
     {
-      int hashPos = atomSpec.indexOf("#");
       int colonPos = atomSpec.indexOf(":");
-      int dotPos = atomSpec.indexOf(".");
-
       if (colonPos == -1)
       {
         continue; // malformed
       }
-      int pdbResNum = Integer.parseInt(dotPos == -1 ? atomSpec
-              .substring(colonPos) : atomSpec.substring(colonPos + 1,
-              dotPos));
-
-      String chainId = dotPos == -1 ? "" : atomSpec.substring(dotPos + 1);
+    
+      int hashPos = atomSpec.indexOf("#");
+      String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
+      int dotPos = modelSubmodel.indexOf(".");
       int modelId = 0;
       try {
-        modelId = Integer.valueOf(atomSpec.substring(hashPos + 1, colonPos));
+        modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
+                : modelSubmodel.substring(0, dotPos));
       } catch (NumberFormatException e) {
         // ignore, default to model 0
       }
-
+    
+      String residueChain = atomSpec.substring(colonPos + 1);
+      dotPos = residueChain.indexOf(".");
+      int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
+              : residueChain.substring(0, dotPos));
+    
+      String chainId = dotPos == -1 ? "" : residueChain
+              .substring(dotPos + 1);
+    
       /*
        * Work out the pdbfilename from the model number
        */
@@ -1000,10 +984,23 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       }
       atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
     }
-    if (!atomSpecs.isEmpty())
-    {
-      getSsm().mouseOverStructure(atomSpecs);
-    }
+
+    /*
+     * Broadcast the selection (which may be empty, if the user just cleared all
+     * selections)
+     */
+    getSsm().mouseOverStructure(atomSpecs);
+  }
+
+  private void log(String message)
+  {
+    System.err.println("## Chimera log: " + message);
+  }
+
+  private void viewerCommandHistory(boolean enable)
+  {
+    // log("(Not yet implemented) History "
+    // + ((debug || enable) ? "on" : "off"));
   }
 
   public long getLoadNotifiesHandled()
-- 
1.7.10.2