X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalviewChimeraBindingModel.java;h=a797872f2129bad214193648d4ff8b4dcde67749;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=c582c5d08627a3cddb8d44a63fab92f52d69779e;hpb=f11efa71475b7bf825090716543a36b012db224a;p=jalview.git

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index c582c5d..a797872 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -1,36 +1,58 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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;
 
 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;
   }
 
-  FeatureRenderer fr = null;
-
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? cvf.ap
+    AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
             : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
-        fr = ap.cloneFeatureRenderer();
+        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
       }
       else
       {
@@ -47,12 +69,13 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
+
   @Override
   public void refreshGUI()
   {
-    // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         cvf.updateTitleAndMenus();
@@ -61,9 +84,10 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     });
   }
 
+  @Override
   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))
     {
@@ -71,34 +95,56 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+      colourBySequence(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
+   */
   @Override
-  public void showUrl(String url, String target)
+  protected void sendAsynchronousCommand(final String command,
+          final String progressMsg)
   {
-    // TODO Auto-generated method stub
+    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();
+
+  }
 
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return cvf;
   }
 }