X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=58034d964ab064234ec9a4a95e52a24cf76182bf;hb=e0aacff0a162fdf1beb71cd5965b6ff4f8c9de0d;hp=c8aa94f9be11ef2c85df359786b02521dadbd0d8;hpb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c8aa94f..58034d9 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -113,7 +113,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu colourMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
+  protected JMenuItem textColour;
 
   protected JCheckBoxMenuItem conservationMenuItem;
 
@@ -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"));
@@ -752,17 +701,6 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 
-    conservationMenuItem.setText(MessageManager
-            .getString("action.by_conservation"));
-    conservationMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed();
-      }
-    });
-
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -815,17 +753,6 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 
-    abovePIDThreshold.setText(MessageManager
-            .getString("label.above_identity_threshold"));
-    abovePIDThreshold.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDThreshold_actionPerformed();
-      }
-    });
-
     showSeqFeatures.setText(MessageManager
             .getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
@@ -997,7 +924,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem createGroup = new JMenuItem(
-            MessageManager.getString("action.create_groups"));
+            MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1217,27 +1144,6 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    modifyPID = new JMenuItem(
-            MessageManager.getString("label.modify_identity_threshold"));
-    modifyPID.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyPID_actionPerformed();
-      }
-    });
-    modifyConservation.setText(MessageManager
-            .getString("label.modify_conservation_threshold"));
-    modifyConservation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyConservation_actionPerformed();
-      }
-    });
-
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1246,7 +1152,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeMenu();
+        buildTreeSortMenu();
       }
 
       @Override
@@ -1283,8 +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
@@ -1696,6 +1602,7 @@ public class GAlignFrame extends JInternalFrame
 
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
     idRightAlign.setText(MessageManager
             .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
@@ -1885,7 +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);
@@ -1947,6 +1853,12 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void configureSelectMenu()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
@@ -1960,12 +1872,12 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        applyToAllGroups_actionPerformed();
+        applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
       }
     });
 
-    textColour = new JRadioButtonMenuItem(
-            MessageManager.getString("action.set_text_colour"));
+    textColour = new JMenuItem(
+            MessageManager.getString("label.text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -1982,7 +1894,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
       }
     });
 
@@ -1993,7 +1906,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed();
+        abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
       }
     });
     modifyPID = new JMenuItem(
@@ -2365,27 +2278,11 @@ 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()
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
 
@@ -2401,7 +2298,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed()
+  protected void abovePIDThreshold_actionPerformed(boolean selected)
   {
   }
 
@@ -2441,7 +2338,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void applyToAllGroups_actionPerformed()
+  protected void applyToAllGroups_actionPerformed(boolean selected)
   {
   }
 
@@ -2669,7 +2566,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
 
   }