X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=58034d964ab064234ec9a4a95e52a24cf76182bf;hb=342037486db348e0d40faf044b8111ddb06c222e;hp=b759d64026a27efcd0fc99be86fd0d019665475e;hpb=d4a9ea73ba6f86fdcb69e08529f38600db3a99fc;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b759d64..58034d9 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -129,7 +129,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sort = new JMenu();
 
-  protected JMenu calculateTree = new JMenu();
+  protected JMenuItem calculateTree = new JMenuItem();
 
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 
@@ -523,36 +523,6 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    JMenuItem PCAMenuItem = new JMenuItem(
-            MessageManager.getString("label.principal_component_analysis"));
-    PCAMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        PCAMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_identity"));
-    averageDistanceTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem neighbourTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_joining_identity"));
-    neighbourTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
 
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -563,27 +533,6 @@ public class GAlignFrame extends JInternalFrame
     outputTextboxMenu.setText(MessageManager
             .getString("label.out_to_textbox"));
 
-
-    JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_blosum62"));
-    avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        avTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem njTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_blosum62"));
-    njTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText(MessageManager
             .getString("label.show_annotations"));
@@ -1203,7 +1152,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeMenu();
+        buildTreeSortMenu();
       }
 
       @Override
@@ -1240,8 +1189,8 @@ public class GAlignFrame extends JInternalFrame
     });
     sortByAnnotScore.setVisible(false);
 
-    calculateTree
-            .setText(MessageManager.getString("action.calculate_tree"));
+    calculateTree.setText(MessageManager
+            .getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem.setState(jalview.bin.Cache
@@ -1843,7 +1792,6 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(showReverse);
@@ -2330,26 +2278,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
@@ -2634,7 +2566,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
 
   }