ConservationColour added

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8588524..4410880 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -11,8 +11,6 @@ package jalview.jbgui;
 import javax.swing.*;\r
 import java.awt.event.*;\r
 import java.awt.*;\r
-import javax.swing.event.*;\r
-\r
 \r
 public class GAlignFrame extends JInternalFrame\r
 {\r
@@ -67,19 +65,23 @@ 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 conservationColour = 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
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
-  JMenuItem conservationColourIncMenuItem = 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
   JMenuItem schemeKeyMenuItem = new JMenuItem();\r
   JMenuItem overviewMenuItem = new JMenuItem();\r
+  protected JMenuItem undoMenuItem = new JMenuItem();\r
+  protected JMenuItem redoMenuItem = new JMenuItem();\r
+  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+  JMenuItem noColourmenuItem = new JMenuItem();\r
+  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
   public GAlignFrame()\r
   {\r
     try\r
@@ -127,7 +129,6 @@ public class GAlignFrame extends JInternalFrame
     colours.add(strandColour);\r
     colours.add(turnColour);\r
     colours.add(buriedColour);\r
-    colours.add(conservationColour);\r
     colours.add(abovePIDColour);\r
     colours.add(userDefinedColour);\r
     colours.add(PIDColour);\r
@@ -163,7 +164,6 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.setText("Colour");\r
     calculateMenu.setText("Calculate");\r
     alignMenu.setText("Web Service");\r
-    groupsMenuItem.setEnabled(false);\r
     groupsMenuItem.setText("Groups");\r
     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -172,7 +172,6 @@ public class GAlignFrame extends JInternalFrame
         groupsMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    groupEditingMenuItem.setEnabled(false);\r
     groupEditingMenuItem.setText("Group editing mode");\r
     groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -406,6 +405,7 @@ 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
@@ -472,15 +472,6 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);\r
       }\r
     });\r
-    conservationColour.setEnabled(false);\r
-    conservationColour.setText("By conservation");\r
-    conservationColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        conservationColour_actionPerformed(e);\r
-      }\r
-    });\r
     abovePIDColour.setEnabled(false);\r
     abovePIDColour.setText("Above PID threshold only");\r
     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
@@ -582,6 +573,51 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);\r
       }\r
     });\r
+    undoMenuItem.setEnabled(false);\r
+    undoMenuItem.setMnemonic('Z');\r
+    undoMenuItem.setText("Undo");\r
+    undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        undoMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    redoMenuItem.setEnabled(false);\r
+    redoMenuItem.setMnemonic('0');\r
+    redoMenuItem.setText("Redo");\r
+    redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        redoMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    conservationMenuItem.setText("By conservation");\r
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        conservationMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    noColourmenuItem.setText("None");\r
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        noColourmenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    wrapMenuItem.setEnabled(false);\r
+    wrapMenuItem.setText("Wrap alignment");\r
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        wrapMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(fontMenu);\r
@@ -595,6 +631,9 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(htmlMenuItem);\r
     fileMenu.addSeparator();\r
     fileMenu.add(closeMenuItem);\r
+    editMenu.add(undoMenuItem);\r
+    editMenu.add(redoMenuItem);\r
+    editMenu.addSeparator();\r
     editMenu.add(groupsMenuItem);\r
     editMenu.add(groupEditingMenuItem);\r
     editMenu.addSeparator();\r
@@ -618,10 +657,12 @@ public class GAlignFrame extends JInternalFrame
     fontMenu.add(fontStyleMenuItem);\r
     fontMenu.addSeparator();\r
     fontMenu.add(colourTextMenuItem);\r
+    viewMenu.add(wrapMenuItem);\r
     viewMenu.add(viewBoxesMenuItem);\r
     viewMenu.add(viewTextMenuItem);\r
     viewMenu.add(consensusGraphMenuItem);\r
     viewMenu.add(overviewMenuItem);\r
+    colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(zappoColour);\r
     colourMenu.add(taylorColour);\r
@@ -632,7 +673,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(buriedColour);\r
     colourMenu.add(userDefinedColour);\r
     colourMenu.addSeparator();\r
-    colourMenu.add(conservationColour);\r
+    colourMenu.add(conservationMenuItem);\r
     colourMenu.add(conservationColourIncMenuItem);\r
     colourMenu.addSeparator();\r
     colourMenu.add(abovePIDColour);\r
@@ -685,6 +726,17 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
+  protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+\r
   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
   {\r
 \r
@@ -771,6 +823,12 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+\r
   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
   {\r
 \r
@@ -906,10 +964,6 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  protected void conservationColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
  {\r
@@ -943,4 +997,14 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
 }\r