X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalviewChimeraBindingModel.java;h=689106af84e9e6ffeb5bd7fb8cf04659b5b27905;hb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;hp=ec30e7fbc02c0606602f4dc121722e5c84544e3a;hpb=e8276f5598621d3f7e19c6bdbc49276706322c43;p=jalview.git

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index ec30e7f..689106a 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -20,44 +20,25 @@
  */
 package jalview.gui;
 
+import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
+
 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;
 
 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);
-    cvf = chimeraViewFrame;
-  }
-
-  @Override
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
-  {
-    AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
-            : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      if (fr == null)
-      {
-        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
-    }
-
-    return fr;
+    super(ssm, pdbentry, sequenceIs, protocol);
+    setViewer(chimeraViewFrame);
   }
 
   @Override
@@ -70,79 +51,15 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   @Override
   public void refreshGUI()
   {
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    SwingUtilities.invokeLater(new Runnable()
     {
       @Override
       public void run()
       {
-        cvf.updateTitleAndMenus();
-        cvf.revalidate();
+        JalviewStructureDisplayI theViewer = getViewer();
+        theViewer.updateTitleAndMenus();
+        ((JComponent) theViewer).revalidate();
       }
     });
   }
-
-  @Override
-  public void updateColours(Object source)
-  {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    // ignore events from panels not used to colour this view
-    if (!cvf.isUsedforcolourby(ap))
-    {
-      return;
-    }
-    if (!isLoadingFromArchive())
-    {
-      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
-    }
-  }
-
-  @Override
-  public void releaseReferences(Object svl)
-  {
-  }
-
-  @Override
-  protected void releaseUIResources()
-  {
-  }
-
-  @Override
-  public void refreshPdbEntries()
-  {
-  }
-
-  /**
-   * Send an asynchronous command to Chimera, in a new thread, optionally with
-   * an 'in progress' message in a progress bar somewhere
-   */
-  @Override
-  protected void sendAsynchronousCommand(final String command,
-          final String progressMsg)
-  {
-    Thread thread = new Thread(new Runnable()
-    {
-
-      @Override
-      public void run()
-      {
-        long handle = 0;
-        if (progressMsg != null)
-        {
-          handle = cvf.startProgressBar(progressMsg);
-        }
-        try
-        {
-          sendChimeraCommand(command, false);
-        } finally
-        {
-          if (progressMsg != null)
-          {
-            cvf.stopProgressBar(null, handle);
-          }
-        }
-      }
-    });
-    thread.start();
-
-  }
 }