group autoannotation and consensus display settings

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 020e617..a89228e 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -284,9 +284,13 @@ public class GAlignFrame extends JInternalFrame
   private JMenuItem justifyLeftMenuItem=new JMenuItem();
 
   private JMenuItem justifyRightMenuItem=new JMenuItem();
-  
+
+  JMenu autoAnnMenu = new JMenu();
   protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem showConsensusProfile=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
 
   private JMenuItem grpsFromSelection = new JMenuItem();
   public GAlignFrame()
@@ -1025,6 +1029,38 @@ public class GAlignFrame extends JInternalFrame
       }
       
     });
+    showConsensusHistogram.setText("Show Consensus Histogram");
+    showConsensusHistogram.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showConsensusHistogram_actionPerformed(e);
+      }
+      
+    });
+    showConsensusProfile.setText("Show Consensus Logo");
+    showConsensusProfile.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showConsensusProfile_actionPerformed(e);
+      }
+      
+    });
+    applyAutoAnnotationSettings.setText("Apply to all groups");
+    applyAutoAnnotationSettings.setState(false);
+    applyAutoAnnotationSettings.setVisible(true);
+    applyAutoAnnotationSettings.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        applyAutoAnnotationSettings_actionPerformed(e);
+      }
+      
+    });
 
     nucleotideColour.setText("Nucleotide");
     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
@@ -1560,6 +1596,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     tooltipSettingsMenu.setText("Sequence ID Tooltip");
+    autoAnnMenu.setText("Autocalculated Annotation");
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
@@ -1613,8 +1650,13 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.addSeparator();
     viewMenu.add(followHighlightMenuItem);
     viewMenu.add(annotationPanelMenuItem);
-    viewMenu.add(showGroupConservation);
-    viewMenu.add(showGroupConsensus);
+    autoAnnMenu.add(applyAutoAnnotationSettings);
+    autoAnnMenu.add(showConsensusHistogram);
+    autoAnnMenu.add(showConsensusProfile);
+    autoAnnMenu.addSeparator();
+    autoAnnMenu.add(showGroupConservation);
+    autoAnnMenu.add(showGroupConsensus);
+    viewMenu.add(autoAnnMenu);
     viewMenu.addSeparator();
     viewMenu.add(showSeqFeatures);
     //viewMenu.add(showSeqFeaturesHeight);
@@ -1711,6 +1753,24 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(grpsFromSelection);
   }
 
+  protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void showConsensusProfile_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub