From 5a30658d78a2ced8b01abacae8ff68a774b0ef81 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 20 Feb 2015 17:19:21 +0000
Subject: [PATCH] JAL-1675 correct highlighting in Chimera for mouseover of
 sequence

---
 .../ext/rbvi/chimera/JalviewChimeraBinding.java    |   71 ++++++++++----------
 1 file changed, 34 insertions(+), 37 deletions(-)

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index f511a65..754bc7f 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -66,8 +66,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private Map<String, String> chainFile;
 
-  private StringBuffer eval = new StringBuffer();
-
   public String fileLoadingError;
 
   /*
@@ -88,6 +86,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   private boolean loadedInline;
 
   /**
+   * current set of model filenames loaded
+   */
+  String[] modelFileNames = null;
+
+  String lastMousedOverAtomSpec;
+
+  private List<String> lastReply;
+
+  /**
    * Open a PDB structure file in Chimera and set up mappings from Jalview.
    * 
    * We check if the PDB model id is already loaded in Chimera, if so don't
@@ -152,16 +159,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * current set of model filenames loaded
-   */
-  String[] modelFileNames = null;
-
-
-  StringBuffer resetLastRes = new StringBuffer();
-
-  private List<String> lastReply;
-
-  /**
    * Constructor
    * 
    * @param ssm
@@ -821,44 +818,44 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   public abstract SequenceRenderer getSequenceRenderer(
           AlignmentViewPanel alignment);
 
-  // jmol/ssm only
+  /**
+   * Construct and send a command to highlight an atom.
+   * 
+   * <pre>
+   * Done by generating a command like (to 'highlight' position 44)
+   *   ~select #0:43.C;select #0:44.C
+   * Note this removes the selection from the previous position.
+   * </pre>
+   */
   public void highlightAtom(int atomIndex, int pdbResNum, String chain,
           String pdbfile)
   {
     List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
     if (cms != null)
     {
-      int mdlNum = cms.get(0).getModelNumber();
-
-      viewerCommandHistory(false);
-      // viewer.stopListening();
-      if (resetLastRes.length() > 0)
+      StringBuilder sb = new StringBuilder();
+      sb.append(" #" + cms.get(0).getModelNumber());
+      sb.append(":" + pdbResNum);
+      if (!chain.equals(" "))
       {
-        eval.setLength(0);
-        eval.append(resetLastRes.toString() + ";");
+        sb.append("." + chain);
       }
+      String atomSpec = sb.toString();
 
-      eval.append("display "); // +modelNum
-
-      resetLastRes.setLength(0);
-      resetLastRes.append("~display ");
+      StringBuilder command = new StringBuilder(32);
+      if (lastMousedOverAtomSpec != null)
       {
-        eval.append(" #" + (mdlNum));
-        resetLastRes.append(" #" + (mdlNum));
+        command.append("~select " + lastMousedOverAtomSpec + ";");
       }
-      // complete select string
-
-      eval.append(":" + pdbResNum);
-      resetLastRes.append(":" + pdbResNum);
-      if (!chain.equals(" "))
+      viewerCommandHistory(false);
+      String cmd = command.toString();
+      cmd = "select " + atomSpec;
+      if (cmd.length() > 0)
       {
-        eval.append("." + chain);
-        resetLastRes.append("." + chain);
+        viewer.sendChimeraCommand(cmd, false);
       }
-
-      viewer.sendChimeraCommand(eval.toString(), false);
       viewerCommandHistory(true);
-      // viewer.startListening();
+      this.lastMousedOverAtomSpec = atomSpec;
     }
   }
 
@@ -1262,4 +1259,4 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     return chainNames;
   }
 
-}
\ No newline at end of file
+}
-- 
1.7.10.2