From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 16 Nov 2004 15:25:14 +0000 (+0000)
Subject: ConservationColour added
X-Git-Tag: Release_2_0~924
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=be81a18dc614d4d778017060945a10a85d5b5c24;p=jalview.git

ConservationColour added
---

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8588524..4410880 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -11,8 +11,6 @@ package jalview.jbgui;
 import javax.swing.*;
 import java.awt.event.*;
 import java.awt.*;
-import javax.swing.event.*;
-
 
 public class GAlignFrame extends JInternalFrame
 {
@@ -67,19 +65,23 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem conservationColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-  JMenuItem conservationColourIncMenuItem = new JMenuItem();
+  protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
   JMenuItem htmlMenuItem = new JMenuItem();
   JMenuItem schemeKeyMenuItem = new JMenuItem();
   JMenuItem overviewMenuItem = new JMenuItem();
+  protected JMenuItem undoMenuItem = new JMenuItem();
+  protected JMenuItem redoMenuItem = new JMenuItem();
+  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  JMenuItem noColourmenuItem = new JMenuItem();
+  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
     try
@@ -127,7 +129,6 @@ public class GAlignFrame extends JInternalFrame
     colours.add(strandColour);
     colours.add(turnColour);
     colours.add(buriedColour);
-    colours.add(conservationColour);
     colours.add(abovePIDColour);
     colours.add(userDefinedColour);
     colours.add(PIDColour);
@@ -163,7 +164,6 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
     alignMenu.setText("Web Service");
-    groupsMenuItem.setEnabled(false);
     groupsMenuItem.setText("Groups");
     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -172,7 +172,6 @@ public class GAlignFrame extends JInternalFrame
         groupsMenuItem_actionPerformed(e);
       }
     });
-    groupEditingMenuItem.setEnabled(false);
     groupEditingMenuItem.setText("Group editing mode");
     groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -406,6 +405,7 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setText("Status bar");
     outputTextboxMenu.setMnemonic('T');
     outputTextboxMenu.setText("Output alignment via textbox");
+    clustalColour.setEnabled(false);
     clustalColour.setSelected(false);
     clustalColour.setText("Clustalx colours");
     clustalColour.addActionListener(new java.awt.event.ActionListener()
@@ -472,15 +472,6 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);
       }
     });
-    conservationColour.setEnabled(false);
-    conservationColour.setText("By conservation");
-    conservationColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationColour_actionPerformed(e);
-      }
-    });
     abovePIDColour.setEnabled(false);
     abovePIDColour.setText("Above PID threshold only");
     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
@@ -582,6 +573,51 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);
       }
     });
+    undoMenuItem.setEnabled(false);
+    undoMenuItem.setMnemonic('Z');
+    undoMenuItem.setText("Undo");
+    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        undoMenuItem_actionPerformed(e);
+      }
+    });
+    redoMenuItem.setEnabled(false);
+    redoMenuItem.setMnemonic('0');
+    redoMenuItem.setText("Redo");
+    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        redoMenuItem_actionPerformed(e);
+      }
+    });
+    conservationMenuItem.setText("By conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(e);
+      }
+    });
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed(e);
+      }
+    });
+    wrapMenuItem.setEnabled(false);
+    wrapMenuItem.setText("Wrap alignment");
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        wrapMenuItem_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(fontMenu);
@@ -595,6 +631,9 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(htmlMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
+    editMenu.add(undoMenuItem);
+    editMenu.add(redoMenuItem);
+    editMenu.addSeparator();
     editMenu.add(groupsMenuItem);
     editMenu.add(groupEditingMenuItem);
     editMenu.addSeparator();
@@ -618,10 +657,12 @@ public class GAlignFrame extends JInternalFrame
     fontMenu.add(fontStyleMenuItem);
     fontMenu.addSeparator();
     fontMenu.add(colourTextMenuItem);
+    viewMenu.add(wrapMenuItem);
     viewMenu.add(viewBoxesMenuItem);
     viewMenu.add(viewTextMenuItem);
     viewMenu.add(consensusGraphMenuItem);
     viewMenu.add(overviewMenuItem);
+    colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(zappoColour);
     colourMenu.add(taylorColour);
@@ -632,7 +673,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(buriedColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
-    colourMenu.add(conservationColour);
+    colourMenu.add(conservationMenuItem);
     colourMenu.add(conservationColourIncMenuItem);
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
@@ -685,6 +726,17 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
   protected void groupsMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -771,6 +823,12 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -906,10 +964,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void conservationColour_actionPerformed(ActionEvent e)
-  {
-
-  }
 
   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
  {
@@ -943,4 +997,14 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
 }