X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=8eaeed2f659f8d9a75691f86b34feae3567eef32;hb=e8dba2ced1a06b2b4e8bd90d5d79817668e3f46b;hp=47bc8236b2dc433dcfab31ebd0b6ce6833dde9ba;hpb=9811278f9e18ee6cb88470dbae98da046734a0af;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 47bc823..8eaeed2 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -711,18 +711,36 @@ public abstract class StructureViewerBase extends GStructureViewer
             });
     viewMenu.add(seqColourBy);
 
-    showAlignmentOnly = new JCheckBoxMenuItem("Visible alignment only");
+    showAlignmentOnly = new JCheckBoxMenuItem(
+            MessageManager.getString("label.show_alignment_only"));
     showAlignmentOnly.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
+        hideHiddenRegions.setEnabled(showAlignmentOnly.isSelected());
         getBinding().setShowAlignmentOnly(showAlignmentOnly.isSelected());
-        getBinding().showStructures(getAlignmentPanel().getAlignViewport());
+        getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+                true);
       }
     });
     viewMenu.add(showAlignmentOnly);
 
+    hideHiddenRegions = new JCheckBoxMenuItem(
+            MessageManager.getString("label.hide_hidden_regions"));
+    hideHiddenRegions.setEnabled(false);
+    hideHiddenRegions.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        getBinding().setHideHiddenRegions(hideHiddenRegions.isSelected());
+        getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+                false);
+      }
+    });
+    viewMenu.add(hideHiddenRegions);
+
     final ItemListener handler = new ItemListener()
     {
       @Override
@@ -761,12 +779,6 @@ public abstract class StructureViewerBase extends GStructureViewer
     buildColourMenu();
   }
 
-  @Override
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    getBinding().setJalviewColourScheme(cs);
-  }
-
   /**
    * Sends commands to the structure viewer to superimpose structures based on
    * currently associated alignments. May optionally return an error message for