From f2cc1f45f6d4bdc47a491b01aa7b0f2b2d9ed1bd Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 11 Nov 2015 14:21:20 +0000
Subject: [PATCH] JAL-1479 JAL-1957 Added code to enable simultaneous
 highlight of multiple atoms positions in all chains

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |   17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index b464c94..a1b6917 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -552,6 +552,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     System.out.println("JMOL CREATE IMAGE");
   }
 
+  @Override
   public String createImage(String fileName, String type,
           Object textOrBytes, int quality)
   {
@@ -559,6 +560,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
+  @Override
   public String eval(String strEval)
   {
     // System.out.println(strEval);
@@ -569,11 +571,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   // End StructureListener
   // //////////////////////////
 
+  @Override
   public float[][] functionXY(String functionName, int x, int y)
   {
     return null;
   }
 
+  @Override
   public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
   {
     // TODO Auto-generated method stub
@@ -737,6 +741,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
+      if (resetLastRes.length() > 0)
+      {
+        viewer.evalStringQuiet(resetLastRes.toString());
+        resetLastRes.setLength(0);
+      }
       for (AtomSpec atom : atoms)
       {
         highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
@@ -768,17 +777,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
 
     jmolHistory(false);
-    // if (!pdbfile.equals(pdbentry.getFile()))
-    // return;
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
 
     StringBuilder cmd = new StringBuilder(64);
     cmd.append("select " + pdbResNum); // +modelNum
 
-    resetLastRes.setLength(0);
     resetLastRes.append("select " + pdbResNum); // +modelNum
 
     cmd.append(":");
@@ -1264,6 +1266,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   public abstract void sendConsoleMessage(String strStatus);
 
+  @Override
   public void setCallbackFunction(String callbackType,
           String callbackFunction)
   {
-- 
1.7.10.2