JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index cc431ac..2ffcee1 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -711,12 +711,14 @@ 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(),
                 true);
@@ -724,6 +726,21 @@ public abstract class StructureViewerBase extends GStructureViewer
     });
     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
@@ -762,12 +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
@@ -885,7 +896,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       // Set the colour using the current view for the associated alignframe
       for (AlignmentViewPanel avp : _colourwith)
       {
-        binding.colourBySequence(avp);
+        binding.updateStructureColours(avp);
       }
       seqColoursApplied = true;
     }