JAL-2360 structure viewers now using ColourMenuHelper, obsolete methods

[jalview.git] / src / jalview / gui / JalviewChimeraBindingModel.java

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index 4637f07..a797872 100644 (file)
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,9 +21,11 @@
 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
@@ -32,11 +34,12 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 
   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;
   }
 
@@ -72,6 +75,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   {
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         cvf.updateTitleAndMenus();
@@ -80,6 +84,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -90,7 +95,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+      colourBySequence(ap);
     }
   }
 
@@ -113,6 +118,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
    * 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)
   {
@@ -135,4 +141,10 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     thread.start();
 
   }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return cvf;
+  }
 }