sortByTreeMenu added

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a1e8c3d..3630528 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -36,7 +36,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
   protected JMenuItem sortIDMenuItem = new JMenuItem();
   protected JMenuItem sortGroupMenuItem = new JMenuItem();
-  protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
   protected JMenuItem PCAMenuItem = new JMenuItem();
@@ -93,6 +92,9 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  JMenuItem modifyPID = new JMenuItem();
+  JMenuItem modifyConservation = new JMenuItem();
+  protected JMenu sortByTreeMenu = new JMenu();
   public GAlignFrame()
   {
 
@@ -282,14 +284,6 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-    sortTreeOrderMenuItem.setText("Sort by tree order");
-    sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortTreeOrderMenuItem_actionPerformed(e);
-      }
-    });
     removeRedundancyMenuItem.setText("Remove redundancy");
     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -720,6 +714,23 @@ public class GAlignFrame extends JInternalFrame
         scaleRight_actionPerformed(e);
       }
     });
+    modifyPID.setText("Modify PID Threshold");
+    modifyPID.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed(e);
+      }
+    });
+    modifyConservation.setText("Modify Conservation Threshold");
+    modifyConservation.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed(e);
+      }
+    });
+    sortByTreeMenu.setText("Sort by tree order");
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -788,12 +799,14 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(PIDColour);
     colourMenu.add(BLOSUM62Colour);
     colourMenu.addSeparator();
-    colourMenu.add(abovePIDThreshold);
     colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(modifyPID);
     calculateMenu.add(sortPairwiseMenuItem);
     calculateMenu.add(sortIDMenuItem);
     calculateMenu.add(sortGroupMenuItem);
-    calculateMenu.add(sortTreeOrderMenuItem);
+    calculateMenu.add(sortByTreeMenu);
     calculateMenu.add(removeRedundancyMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
@@ -946,10 +959,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
 
   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1177,6 +1186,17 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
 
 
 }