Merge branch 'Release_2_7_Branch' into develop

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 4f60de3..7ea492f 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -216,13 +216,13 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu showProducts = new JMenu();
 
-  public JMenuItem featureSettings = new JMenuItem();
+  public JMenuItem openFeatureSettings = new JMenuItem();
 
   JMenuItem fetchSequence = new JMenuItem();
 
   JMenuItem annotationColour = new JMenuItem();
 
-  JMenuItem rnahelicesColour = new JMenuItem();
+  protected JMenuItem rnahelicesColour = new JMenuItem();
 
   JMenuItem associatedData = new JMenuItem();
 
@@ -314,6 +314,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 
+  protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
   private JMenuItem grpsFromSelection = new JMenuItem();
@@ -1113,6 +1115,16 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
+    normaliseSequenceLogo.setText("Normalise Consensus Logo");
+    normaliseSequenceLogo.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        normaliseSequenceLogo_actionPerformed(e);
+      }
+
+    });
     applyAutoAnnotationSettings.setText("Apply to all groups");
     applyAutoAnnotationSettings.setState(false);
     applyAutoAnnotationSettings.setVisible(true);
@@ -1408,8 +1420,8 @@ public class GAlignFrame extends JInternalFrame
      * public void actionPerformed(ActionEvent e) {
      * showProducts_actionPerformed(e); } });
      */
-    featureSettings.setText("Feature Settings...");
-    featureSettings.addActionListener(new ActionListener()
+    openFeatureSettings.setText("Feature Settings...");
+    openFeatureSettings.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -1783,6 +1795,7 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(applyAutoAnnotationSettings);
     autoAnnMenu.add(showConsensusHistogram);
     autoAnnMenu.add(showSequenceLogo);
+    autoAnnMenu.add(normaliseSequenceLogo);
     autoAnnMenu.addSeparator();
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
@@ -1791,7 +1804,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(showSeqFeatures);
     // viewMenu.add(showSeqFeaturesHeight);
 
-    viewMenu.add(featureSettings);
+    viewMenu.add(openFeatureSettings);
     tooltipSettingsMenu.add(showDbRefsMenuitem);
     tooltipSettingsMenu.add(showNpFeatsMenuitem);
     viewMenu.add(tooltipSettingsMenu);
@@ -1894,6 +1907,12 @@ public class GAlignFrame extends JInternalFrame
     //selectMenu.add(listenToViewSelections);
   }
 
+  protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void listenToViewSelections_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub