From cd8f0eb5083ecbb73bde4b87c45e0d4286998ab9 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 10 Nov 2016 11:03:14 +0000
Subject: [PATCH] JAL-2320 added getViewer() method to return Chimera or Jmol
 panel

---
 src/jalview/gui/AppJmolBinding.java                        |   10 ++++++++++
 src/jalview/gui/JalviewChimeraBindingModel.java            |   11 +++++++++++
 src/jalview/structures/models/AAStructureBindingModel.java |   11 +++++++++++
 3 files changed, 32 insertions(+)

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 1c54a5e..ffa34f83 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -113,6 +114,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         appJmolWindow.updateTitleAndMenus();
@@ -121,6 +123,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -144,6 +147,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // msWalltime);
   }
 
+  @Override
   public void showUrl(String url)
   {
     showUrl(url, "jmol");
@@ -205,4 +209,10 @@ public class AppJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return appJmolWindow;
+  }
 }
diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index 7a54732..4bb7180 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -21,6 +21,7 @@
 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;
@@ -72,6 +73,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   {
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         cvf.updateTitleAndMenus();
@@ -80,6 +82,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -113,6 +116,7 @@ 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 +139,11 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     thread.start();
 
   }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return cvf;
+  }
+
 }
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index b00f1bc..b618bc0 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -21,6 +21,7 @@
 package jalview.structures.models;
 
 import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -674,4 +675,14 @@ public abstract class AAStructureBindingModel extends
   {
     this.finishedInit = fi;
   }
+
+  /**
+   * Returns the Jalview panel hosting the structure viewer (if any)
+   * 
+   * @return
+   */
+  public JalviewStructureDisplayI getViewer()
+  {
+    return null;
+  }
 }
-- 
1.7.10.2