Enable PID menuitem

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a4ec5cc..be879ee 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -61,7 +61,6 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
@@ -84,6 +83,7 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem findMenuItem = new JMenuItem();\r
   JMenu searchMenu = new JMenu();\r
   protected JCheckBoxMenuItem modifyAlignmentMenuItem = new JCheckBoxMenuItem();\r
+  JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
   public GAlignFrame()\r
   {\r
     try\r
@@ -132,7 +132,6 @@ public class GAlignFrame extends JInternalFrame
     colours.add(strandColour);\r
     colours.add(turnColour);\r
     colours.add(buriedColour);\r
-    colours.add(abovePIDColour);\r
     colours.add(userDefinedColour);\r
     colours.add(PIDColour);\r
     colours.add(BLOSUM62Colour);\r
@@ -441,15 +440,6 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);\r
       }\r
     });\r
-    abovePIDColour.setEnabled(false);\r
-    abovePIDColour.setText("Above PID threshold only");\r
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        abovePIDColour_actionPerformed(e);\r
-      }\r
-    });\r
     userDefinedColour.setText("User defined colours");\r
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -458,7 +448,6 @@ public class GAlignFrame extends JInternalFrame
         userDefinedColour_actionPerformed(e);\r
       }\r
     });\r
-    PIDColour.setEnabled(false);\r
     PIDColour.setText("By PID");\r
     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -630,6 +619,8 @@ public class GAlignFrame extends JInternalFrame
         modifyAlignmentMenuItem_actionPerformed(e);\r
       }\r
     });\r
+    abovePIDThreshold.setEnabled(false);\r
+    abovePIDThreshold.setText("Above PID threshold");\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -683,11 +674,12 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(turnColour);\r
     colourMenu.add(buriedColour);\r
     colourMenu.add(userDefinedColour);\r
-    colourMenu.addSeparator();\r
+     colourMenu.add(abovePIDThreshold);\r
+     colourMenu.addSeparator();\r
     colourMenu.add(conservationMenuItem);\r
     colourMenu.add(conservationColourIncMenuItem);\r
     colourMenu.addSeparator();\r
-    colourMenu.add(abovePIDColour);\r
+\r
     colourMenu.add(PIDColour);\r
     colourMenu.add(BLOSUM62Colour);\r
     colourMenu.addSeparator();\r
@@ -965,10 +957,6 @@ public class GAlignFrame extends JInternalFrame
  }\r
 \r
 \r
-  protected void abovePIDColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
 \r
   protected void userDefinedColour_actionPerformed(ActionEvent e)\r