Merge develop to Release_2_8_3_Branch

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index f24a976..9d1ed43 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -39,7 +39,6 @@ import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -87,8 +86,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private Map<String, String> chainFile;
 
-  private StringBuffer eval = new StringBuffer();
-
   public String fileLoadingError;
 
   /*
@@ -109,6 +106,15 @@ 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
@@ -173,16 +179,6 @@ 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
@@ -693,7 +689,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     AlignmentI alignment = alignmentv.getAlignment();
 
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+            files, sr, fr, alignment))
     {
       for (String command : cpdbbyseq.commands)
       {
@@ -713,10 +710,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    return ChimeraCommands
-            .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
-                    fr,
-                    alignment);
+    return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
+            getSequence(), sr, fr, alignment);
   }
 
   /**
@@ -740,7 +735,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
   }
 
-  
+
 
   // End StructureListener
   // //////////////////////////
@@ -843,44 +838,44 @@ 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("~show " + lastMousedOverAtomSpec + ";");
       }
-      // complete select string
-
-      eval.append(":" + pdbResNum);
-      resetLastRes.append(":" + pdbResNum);
-      if (!chain.equals(" "))
+      viewerCommandHistory(false);
+      command.append("show ").append(atomSpec);
+      String cmd = command.toString();
+      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;
     }
   }
 
@@ -1140,20 +1135,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       return;
     }
 
-    String res;
     int index;
     Color col;
     // Chimera expects RBG values in the range 0-1
     final double normalise = 255D;
     viewerCommandHistory(false);
     // TODO: Switch between nucleotide or aa selection expressions
-    Enumeration en = ResidueProperties.aa3Hash.keys();
     StringBuilder command = new StringBuilder(128);
     command.append("color white;");
-    while (en.hasMoreElements())
+    for (String res : ResidueProperties.aa3Hash.keySet())
     {
-      res = en.nextElement().toString();
-      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
+      index = ResidueProperties.aa3Hash.get(res).intValue();
       if (index > 20)
       {
         continue;