X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=7ba9186012e12510f70e0a174322a5a7a3114023;hb=62cdf4a06bef088c02f81c66ab2fe0bc3264e321;hp=1ce0d2b05934599faa99ca8a0b201cda7de5ef19;hpb=f3b39605256b4803fef19117e7e8bd682bb51758;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 1ce0d2b..7ba9186 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -101,17 +101,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private String lastCommand;
 
-  private boolean loadedInline;
-
-  /**
-   * current set of model filenames loaded
-   */
-  String[] modelFileNames = null;
-
   String lastHighlightCommand;
 
-  private List<String> lastReply;
-
   /*
    * incremented every time a load notification is successfully handled -
    * lightweight mechanism for other threads to detect when they can start
@@ -617,7 +608,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     if (lastCommand == null || !lastCommand.equals(command))
     {
       // trim command or it may never find a match in the replyLog!!
-      lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
+      List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+              logResponse);
       if (logResponse && debug)
       {
         log("Response from command ('" + command + "') was:\n" + lastReply);
@@ -715,17 +707,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // End StructureListener
   // //////////////////////////
 
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (getModelNum(pdbfile) < 0)
-    {
-      return null;
-    }
-    log("get model / residue colour attribute unimplemented");
-    return null;
-  }
-
   /**
    * returns the current featureRenderer that should be used to colour the
    * structures
@@ -795,15 +776,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * map from string to applet
-   */
-  public Map getRegistryInfo()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /**
    * returns the current sequenceRenderer that should be used to colour the
    * structures
    * 
@@ -815,20 +787,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           AlignmentViewPanel alignment);
 
   /**
-   * Construct and send a command to highlight zero, one or more atoms.
-   * 
-   * <pre>
-   * Done by generating a command like (to 'highlight' positions 44 and 46)
-   *   show #0:44,46.C
-   * </pre>
+   * Construct and send a command to highlight zero, one or more atoms. We do
+   * this by sending an "rlabel" command to show the residue label at that
+   * position.
    */
   @Override
   public void highlightAtoms(List<AtomSpec> atoms)
   {
-    if (atoms == null)
+    if (atoms == null || atoms.size() == 0)
     {
       return;
     }
+
     StringBuilder cmd = new StringBuilder(128);
     boolean first = true;
     boolean found = false;
@@ -843,7 +813,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       {
         if (first)
         {
-          cmd.append("show #").append(cms.get(0).getModelNumber())
+          cmd.append("rlabel #").append(cms.get(0).getModelNumber())
                   .append(":");
         }
         else
@@ -851,7 +821,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           cmd.append(",");
         }
         first = false;
-        cmd.append(cms.get(0).getModelNumber()).append(":");
         cmd.append(pdbResNum);
         if (!chain.equals(" "))
         {
@@ -863,19 +832,24 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     String command = cmd.toString();
 
     /*
-     * Avoid repeated commands for the same residue
+     * avoid repeated commands for the same residue
      */
     if (command.equals(lastHighlightCommand))
     {
       return;
     }
 
-    viewerCommandHistory(false);
+    /*
+     * unshow the label for the previous residue
+     */
+    if (lastHighlightCommand != null)
+    {
+      viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+    }
     if (found)
     {
-      viewer.sendChimeraCommand(command.toString(), false);
+      viewer.sendChimeraCommand(command, false);
     }
-    viewerCommandHistory(true);
     this.lastHighlightCommand = command;
   }