no more group editing mode. clustal implemented

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index be879ee..6c216ec 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -24,7 +24,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu calculateMenu = new JMenu();\r
   protected JMenu alignMenu = new JMenu();\r
   protected JMenuItem groupsMenuItem = new JMenuItem();\r
-  protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();\r
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
@@ -66,7 +65,6 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
-  protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
   JMenuItem htmlMenuItem = new JMenuItem();\r
@@ -82,8 +80,7 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
   JMenuItem findMenuItem = new JMenuItem();\r
   JMenu searchMenu = new JMenu();\r
-  protected JCheckBoxMenuItem modifyAlignmentMenuItem = new JCheckBoxMenuItem();\r
-  JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
   public GAlignFrame()\r
   {\r
     try\r
@@ -165,14 +162,6 @@ public class GAlignFrame extends JInternalFrame
         groupsMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    groupEditingMenuItem.setText("Group editing mode");\r
-    groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        groupEditingMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     selectAllSequenceMenuItem.setText("Select all sequences");\r
     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -374,7 +363,6 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setText("Status bar");\r
     outputTextboxMenu.setMnemonic('T');\r
     outputTextboxMenu.setText("Output alignment via textbox");\r
-    clustalColour.setEnabled(false);\r
     clustalColour.setSelected(false);\r
     clustalColour.setText("Clustalx colours");\r
     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
@@ -448,7 +436,7 @@ public class GAlignFrame extends JInternalFrame
         userDefinedColour_actionPerformed(e);\r
       }\r
     });\r
-    PIDColour.setText("By PID");\r
+    PIDColour.setText("Percentage Identity");\r
     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -456,7 +444,7 @@ public class GAlignFrame extends JInternalFrame
         PIDColour_actionPerformed(e);\r
       }\r
     });\r
-    BLOSUM62Colour.setText("By BLOSUM62 score");\r
+    BLOSUM62Colour.setText("BLOSUM62 score");\r
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -480,15 +468,6 @@ public class GAlignFrame extends JInternalFrame
         njTreeBlosumMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    conservationColourIncMenuItem.setEnabled(false);\r
-    conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
-    conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        conservationColourIncMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     consensusGraphMenuItem.setActionCommand("");\r
     consensusGraphMenuItem.setText("Consensus graph");\r
     consensusGraphMenuItem.setState(true);\r
@@ -611,16 +590,13 @@ public class GAlignFrame extends JInternalFrame
       }\r
     });\r
     searchMenu.setText("Search");\r
-    modifyAlignmentMenuItem.setText("Modify alignment");\r
-    modifyAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        modifyAlignmentMenuItem_actionPerformed(e);\r
+\r
+    abovePIDThreshold.setText("Above PID threshold");\r
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
+      public void actionPerformed(ActionEvent e) {\r
+        abovePIDThreshold_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
@@ -638,9 +614,7 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(undoMenuItem);\r
     editMenu.add(redoMenuItem);\r
     editMenu.addSeparator();\r
-    editMenu.add(modifyAlignmentMenuItem);\r
     editMenu.add(groupsMenuItem);\r
-    editMenu.add(groupEditingMenuItem);\r
     editMenu.addSeparator();\r
     editMenu.add(selectAllSequenceMenuItem);\r
     editMenu.add(deselectAllSequenceMenuItem);\r
@@ -674,15 +648,12 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(turnColour);\r
     colourMenu.add(buriedColour);\r
     colourMenu.add(userDefinedColour);\r
-     colourMenu.add(abovePIDThreshold);\r
-     colourMenu.addSeparator();\r
-    colourMenu.add(conservationMenuItem);\r
-    colourMenu.add(conservationColourIncMenuItem);\r
-    colourMenu.addSeparator();\r
-\r
     colourMenu.add(PIDColour);\r
     colourMenu.add(BLOSUM62Colour);\r
     colourMenu.addSeparator();\r
+    colourMenu.add(abovePIDThreshold);\r
+    colourMenu.add(conservationMenuItem);\r
+    colourMenu.addSeparator();\r
     colourMenu.add(schemeKeyMenuItem);\r
     calculateMenu.add(sortPairwiseMenuItem);\r
     calculateMenu.add(sortIDMenuItem);\r
@@ -742,10 +713,6 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -951,13 +918,6 @@ public class GAlignFrame extends JInternalFrame
   }\r
 \r
 \r
-  protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
 \r
   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
   {\r
@@ -1009,8 +969,8 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
+\r
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
 \r
   }\r
 \r