From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 24 Mar 2016 11:12:27 +0000 (+0000)
Subject: merge
X-Git-Tag: Release_2_10_0~285
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=15a5ef9f79696762a81ed5a77930fc1936959f5a;hp=94a0ba746b70ae1e6396d18a55992dedf86de5dc;p=jalview.git

merge
---

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index f1c5097..f2244d5 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -143,7 +143,6 @@ public class ChimeraViewFrame extends StructureViewerBase
             });
     viewMenu.add(seqColourBy);
     viewMenu.add(fitToWindow);
-    viewMenu.add(highlightSelection);
 
     final ItemListener handler;
     JMenu alpanels = new ViewSelectionMenu(
@@ -1206,12 +1205,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   @Override
-  protected void highlightSelection_actionPerformed()
-  {
-    jmb.highlightSelection(getAlignmentPanel());
-  }
-
-  @Override
   public ViewerType getViewerType()
   {
     return ViewerType.CHIMERA;
diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 179607f..bd0f1de 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -53,8 +53,6 @@ public abstract class GStructureViewer extends JInternalFrame implements
 
   protected JMenuItem fitToWindow = new JMenuItem();
 
-  protected JMenuItem highlightSelection = new JMenuItem();
-
   protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
@@ -169,17 +167,6 @@ public abstract class GStructureViewer extends JInternalFrame implements
       }
     });
 
-    highlightSelection.setText(MessageManager
-            .getString("label.highlight_selection"));
-    highlightSelection.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        highlightSelection_actionPerformed();
-      }
-    });
-
     JMenu colourMenu = new JMenu();
     colourMenu.setText(MessageManager.getString("label.colours"));
 
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 6bb04ab..28fc3d1 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -880,7 +880,10 @@ public class StructureSelectionManager
     List<AtomSpec> atoms = new ArrayList<AtomSpec>();
     for (StructureMapping sm : mappings)
     {
-      if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
+      if (sm.sequence == seq
+              || sm.sequence == seq.getDatasetSequence()
+              || (sm.sequence.getDatasetSequence() != null && sm.sequence
+                      .getDatasetSequence() == seq.getDatasetSequence()))
       {
         for (int index : positions)
         {
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 2ed59ae..42fbfa9 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -633,7 +633,10 @@ public abstract class AAStructureBindingModel extends
         {
           for (SequenceI s : seqs)
           {
-            if (s == seq)
+            if (s == seq
+                    || (s.getDatasetSequence() != null && s
+                            .getDatasetSequence() == seq
+                            .getDatasetSequence()))
             {
               return true;
             }