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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 33d3565..6a91cc4 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 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -122,6 +122,8 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 
+  public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem htmlMenuItem = new JMenuItem();
 
   JMenuItem overviewMenuItem = new JMenuItem();
@@ -282,7 +284,15 @@ 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 showSequenceLogo=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
+
+  private JMenuItem grpsFromSelection = new JMenuItem();
   public GAlignFrame()
   {
     try
@@ -538,6 +548,15 @@ public class GAlignFrame extends JInternalFrame
                 invertSequenceMenuItem_actionPerformed(e);
               }
             });
+    grpsFromSelection.setText("Make Groups for selection");
+    grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        makeGrpsFromSelection_actionPerformed(e);
+      }      
+    });
+
     remove2LeftMenuItem.setText("Remove Left");
     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
@@ -621,6 +640,15 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
+    showUnconservedMenuItem.setText("Show Unconserved");
+    showUnconservedMenuItem.setState(false);
+    showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showUnconservedMenuItem_actionPerformed(e);
+      }
+    });
     sortPairwiseMenuItem.setText("by Pairwise Identity");
     sortPairwiseMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -951,14 +979,15 @@ public class GAlignFrame extends JInternalFrame
         showSeqFeatures_actionPerformed(actionEvent);
       }
     });
-    showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+/*
+ *     showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
     showSeqFeaturesHeight.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
         showSeqFeaturesHeight_actionPerformed(actionEvent);
       }
-    });
+    }); */
     showDbRefsMenuitem.setText("Show Database Refs");
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
@@ -979,6 +1008,60 @@ public class GAlignFrame extends JInternalFrame
       }
       
     });
+    showGroupConservation.setText("Group Conservation");
+    showGroupConservation.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showGroupConservation_actionPerformed(e);
+      }
+      
+    });
+
+    showGroupConsensus.setText("Group Consensus");
+    showGroupConsensus.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showGroupConsensus_actionPerformed(e);
+      }
+      
+    });
+    showConsensusHistogram.setText("Show Consensus Histogram");
+    showConsensusHistogram.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showConsensusHistogram_actionPerformed(e);
+      }
+      
+    });
+    showSequenceLogo.setText("Show Consensus Logo");
+    showSequenceLogo.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showSequenceLogo_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()
     {
@@ -1513,6 +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);
@@ -1552,6 +1636,7 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
+    // dont add these yet in the CVS build - they cannot be undone!
     editMenu.add(justifyLeftMenuItem);
     editMenu.add(justifyRightMenuItem);
     editMenu.addSeparator();
@@ -1565,9 +1650,16 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.addSeparator();
     viewMenu.add(followHighlightMenuItem);
     viewMenu.add(annotationPanelMenuItem);
+    autoAnnMenu.add(applyAutoAnnotationSettings);
+    autoAnnMenu.add(showConsensusHistogram);
+    autoAnnMenu.add(showSequenceLogo);
+    autoAnnMenu.addSeparator();
+    autoAnnMenu.add(showGroupConservation);
+    autoAnnMenu.add(showGroupConsensus);
+    viewMenu.add(autoAnnMenu);
     viewMenu.addSeparator();
     viewMenu.add(showSeqFeatures);
-    viewMenu.add(showSeqFeaturesHeight);
+    //viewMenu.add(showSeqFeaturesHeight);
    
     viewMenu.add(featureSettings);
     tooltipSettingsMenu.add(showDbRefsMenuitem);
@@ -1650,6 +1742,7 @@ public class GAlignFrame extends JInternalFrame
     formatMenu.add(colourTextMenuItem);
     formatMenu.add(renderGapsMenuItem);
     formatMenu.add(centreColumnLabelsMenuItem);
+    formatMenu.add(showUnconservedMenuItem);
     selectMenu.add(findMenuItem);
     selectMenu.addSeparator();
     selectMenu.add(selectAllSequenceMenuItem);
@@ -1657,6 +1750,49 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(invertSequenceMenuItem);
     selectMenu.add(invertColSel);
     selectMenu.add(deleteGroups);
+    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 showSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void showGroupConsensus_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void showGroupConservation_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
   }
 
   protected void showSeqFeaturesHeight_actionPerformed(