X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=a5b1110b4bf6bd236fc31486b377e6e1c7865f8e;hb=aab74f8748bf49bf6b17ba82f0bc5644d4dc2853;hp=50aba6248234771f97320a85a15ecb05f0b3d498;hpb=b08367336ea5d5c095b5d570e81c8f8a44fc73e2;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 50aba62..a5b1110 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
@@ -72,7 +73,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private boolean associateNewStructs = false;
 
-  Vector<String> atomsPicked = new Vector<String>();
+  Vector<String> atomsPicked = new Vector<>();
 
   private List<String> chainNames;
 
@@ -477,6 +478,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastCommand = command;
   }
 
+  Thread colourby = null;
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -484,15 +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();
   }
 
   /**
@@ -610,7 +625,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     if (modelFileNames == null)
     {
-      List<String> mset = new ArrayList<String>();
+      List<String> mset = new ArrayList<>();
       _modelFileNameMap = new int[viewer.ms.mc];
       String m = viewer.ms.getModelFileName(0);
       if (m != null)
@@ -670,7 +685,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public synchronized String[] getStructureFiles()
   {
-    List<String> mset = new ArrayList<String>();
+    List<String> mset = new ArrayList<>();
     if (viewer == null)
     {
       return new String[0];
@@ -861,19 +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)
       {
       }
@@ -1060,8 +1086,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new ArrayList<String>();
-    chainFile = new Hashtable<String, String>();
+    chainNames = new ArrayList<>();
+    chainFile = new Hashtable<>();
     boolean notifyLoaded = false;
     String[] modelfilenames = getStructureFiles();
     // first check if we've lost any structures
@@ -1127,7 +1153,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           // see JAL-623 - need method of matching pasted data up
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    pdbfile, DataSourceType.PASTE);
+                    pdbfile, DataSourceType.PASTE,
+                    getIProgressIndicator());
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
@@ -1159,7 +1186,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             }
             // Explicitly map to the filename used by Jmol ;
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    fileName, protocol);
+                    fileName, protocol, getIProgressIndicator());
             // pdbentry[pe].getFile(), protocol);
 
           }
@@ -1227,6 +1254,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return chainNames;
   }
 
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return null;
+  }
+
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {
     notifyAtomPicked(iatom, strMeasure, null);