JAL-1919 code improvement to make PDB sequence fetcher file format configurable....

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 09451dc..f1c5097 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -143,6 +143,7 @@ public class ChimeraViewFrame extends StructureViewerBase
             });
     viewMenu.add(seqColourBy);
     viewMenu.add(fitToWindow);
+    viewMenu.add(highlightSelection);
 
     final ItemListener handler;
     JMenu alpanels = new ViewSelectionMenu(
@@ -270,6 +271,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
         closeViewer(false);
@@ -460,6 +462,7 @@ public class ChimeraViewFrame extends StructureViewerBase
             MessageManager.getString("label.all"));
     menuItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         allChainsSelected = true;
@@ -482,6 +485,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       menuItem = new JCheckBoxMenuItem(chainName, true);
       menuItem.addItemListener(new ItemListener()
       {
+        @Override
         public void itemStateChanged(ItemEvent evt)
         {
           if (!allChainsSelected)
@@ -523,6 +527,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param closeChimera
    *          if true, close any linked Chimera process; if false, prompt first
    */
+  @Override
   public void closeViewer(boolean closeChimera)
   {
     if (jmb != null && jmb.isChimeraRunning())
@@ -553,6 +558,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * Open any newly added PDB structures in Chimera, having first fetched data
    * from PDB (if not already saved).
    */
+  @Override
   public void run()
   {
     _started = true;
@@ -699,6 +705,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       {
         new Thread(new Runnable()
         {
+          @Override
           public void run()
           {
             alignStructs_withAllAlignPanels();
@@ -1091,6 +1098,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     }
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI ucs)
   {
     jmb.setJalviewColourScheme(ucs);
@@ -1198,6 +1206,12 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   @Override
+  protected void highlightSelection_actionPerformed()
+  {
+    jmb.highlightSelection(getAlignmentPanel());
+  }
+
+  @Override
   public ViewerType getViewerType()
   {
     return ViewerType.CHIMERA;