Merge branch 'releases/Release_2_10_4_Branch' into develop

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 41bc116..8832278 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -478,6 +478,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastCommand = command;
   }
 
+  Thread colourby = null;
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -485,15 +486,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   @Override
   protected void colourBySequence(
-          StructureMappingcommandSet[] colourBySequenceCommands)
+          final StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+    if (colourby != null)
     {
-      for (String cbyseq : cpdbbyseq.commands)
+      colourby.interrupt();
+      colourby = null;
+    }
+    colourby = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
       {
-        executeWhenReady(cbyseq);
+        for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+        {
+          for (String cbyseq : cpdbbyseq.commands)
+          {
+            executeWhenReady(cbyseq);
+          }
+        }
       }
-    }
+    });
+    colourby.start();
   }
 
   /**
@@ -862,19 +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)
       {
       }