X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalviewChimeraBindingModel.java;h=a5af244af4b7bdc4e4cd2956d588fd8fa8075a6f;hb=24b1a26ec167233d202778338f62471edcc0bacd;hp=ece88567231e3104ae41023bcd09c78f87f61b1a;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index ece8856..a5af244 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -10,6 +10,8 @@ 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)
@@ -18,13 +20,11 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     cvf = chimeraViewFrame;
   }
 
-  FeatureRenderer fr = null;
-
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(
+  public FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? cvf.ap
+    AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
             : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
@@ -47,10 +47,10 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
+
   @Override
   public void refreshGUI()
   {
-    // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
       public void run()
@@ -63,7 +63,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source, topap;
+    AlignmentPanel ap = (AlignmentPanel) source;
     // ignore events from panels not used to colour this view
     if (!cvf.isUsedforcolourby(ap))
     {
@@ -74,24 +74,46 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
       colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
   }
+
   @Override
   public void releaseReferences(Object svl)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   protected void releaseUIResources()
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void refreshPdbEntries()
   {
-    // TODO Auto-generated method stub
+  }
+
+  /**
+   * Send an asynchronous command to Chimera, in a new thread, optionally with
+   * an 'in progress' message in a progress bar somewhere
+   */
+  protected void sendAsynchronousCommand(final String command,
+          final String progressMsg)
+  {
+    Thread thread = new Thread(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+    long stm = cvf.startProgressBar(progressMsg);
+    try
+    {
+      sendChimeraCommand(command, false);
+    } finally
+    {
+      cvf.stopProgressBar(null, stm);
+    }
+      }
+    });
+  thread.start();
 
   }
 }