X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=88322785ee9fbce68679087362a8bbfcaa40fe6c;hb=9d6a8dc7426c9a27fd9cd702805c1797e7f78c3f;hp=bbb75cfae492b512118388df13c24de5a6f7795b;hpb=0defe3aeb990d75fd672e882edbe9e8156b34414;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index bbb75cf..8832278 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -52,8 +52,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javax.swing.SwingUtilities;
-
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -480,6 +478,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastCommand = command;
   }
 
+  Thread colourby = null;
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -489,7 +488,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   protected void colourBySequence(
           final StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    SwingUtilities.invokeLater(new Runnable()
+    if (colourby != null)
+    {
+      colourby.interrupt();
+      colourby = null;
+    }
+    colourby = new Thread(new Runnable()
     {
       @Override
       public void run()
@@ -503,6 +507,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         }
       }
     });
+    colourby.start();
   }
 
   /**
@@ -871,19 +876,30 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       try
       {
         // recover PDB filename for the model hovered over.
-        int _mp = _modelFileNameMap.length - 1,
-                mnumber = new Integer(mdlId).intValue() - 1;
-        while (mnumber < _modelFileNameMap[_mp])
+        int mnumber = new Integer(mdlId).intValue() - 1;
+        if (_modelFileNameMap != null)
         {
-          _mp--;
+          int _mp = _modelFileNameMap.length - 1;
+
+          while (mnumber < _modelFileNameMap[_mp])
+          {
+            _mp--;
+          }
+          pdbfilename = modelFileNames[_mp];
         }
-        pdbfilename = modelFileNames[_mp];
-        if (pdbfilename == null)
+        else
         {
-          pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
-                  .getAbsolutePath();
-        }
+          if (mnumber >= 0 && mnumber < modelFileNames.length)
+          {
+            pdbfilename = modelFileNames[mnumber];
+          }
 
+          if (pdbfilename == null)
+          {
+            pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
+                    .getAbsolutePath();
+          }
+        }
       } catch (Exception e)
       {
       }