X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalviewChimeraBindingModel.java;h=2f11c30d32ac16b928b84d794eaaaded51e3b20e;hb=b3ec8456ea631e97597568e9bc66ec546eb0417f;hp=ec30e7fbc02c0606602f4dc121722e5c84544e3a;hpb=e8276f5598621d3f7e19c6bdbc49276706322c43;p=jalview.git

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index ec30e7f..2f11c30 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -21,22 +21,24 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
+import javax.swing.SwingUtilities;
+
 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 {
   private ChimeraViewFrame cvf;
 
-  private FeatureRenderer fr = null;
-
   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
           StructureSelectionManager ssm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
+          SequenceI[][] sequenceIs, DataSourceType protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     cvf = chimeraViewFrame;
   }
 
@@ -47,17 +49,10 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
             : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
-      if (fr == null)
-      {
-        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
+      return ap.getSeqPanel().seqCanvas.fr;
     }
 
-    return fr;
+    return null;
   }
 
   @Override
@@ -92,7 +87,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+      colourBySequence(ap);
     }
   }
 
@@ -119,17 +114,13 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   protected void sendAsynchronousCommand(final String command,
           final String progressMsg)
   {
-    Thread thread = new Thread(new Runnable()
+    final long handle = progressMsg == null ? 0
+            : cvf.startProgressBar(progressMsg);
+    SwingUtilities.invokeLater(new Runnable()
     {
-
       @Override
       public void run()
       {
-        long handle = 0;
-        if (progressMsg != null)
-        {
-          handle = cvf.startProgressBar(progressMsg);
-        }
         try
         {
           sendChimeraCommand(command, false);
@@ -142,7 +133,11 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
         }
       }
     });
-    thread.start();
+  }
 
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return cvf;
   }
 }