From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:23:28 +0000 (+0000)
Subject: no more group editing mode. clustal implemented
X-Git-Tag: Release_2_0~806
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2ad962de3c320cdde1a5004359c0ceffc79fa435;p=jalview.git

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
--- 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();
   protected JMenu alignMenu = new JMenu();
   protected JMenuItem groupsMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
@@ -66,7 +65,6 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-  protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
   JMenuItem htmlMenuItem = new JMenuItem();
@@ -82,8 +80,7 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
   JMenuItem findMenuItem = new JMenuItem();
   JMenu searchMenu = new JMenu();
-  protected JCheckBoxMenuItem modifyAlignmentMenuItem = new JCheckBoxMenuItem();
-  JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
     try
@@ -165,14 +162,6 @@ public class GAlignFrame extends JInternalFrame
         groupsMenuItem_actionPerformed(e);
       }
     });
-    groupEditingMenuItem.setText("Group editing mode");
-    groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupEditingMenuItem_actionPerformed(e);
-      }
-    });
     selectAllSequenceMenuItem.setText("Select all sequences");
     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -374,7 +363,6 @@ 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()
@@ -448,7 +436,7 @@ public class GAlignFrame extends JInternalFrame
         userDefinedColour_actionPerformed(e);
       }
     });
-    PIDColour.setText("By PID");
+    PIDColour.setText("Percentage Identity");
     PIDColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -456,7 +444,7 @@ public class GAlignFrame extends JInternalFrame
         PIDColour_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("By BLOSUM62 score");
+    BLOSUM62Colour.setText("BLOSUM62 score");
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -480,15 +468,6 @@ public class GAlignFrame extends JInternalFrame
         njTreeBlosumMenuItem_actionPerformed(e);
       }
     });
-    conservationColourIncMenuItem.setEnabled(false);
-    conservationColourIncMenuItem.setText("Conservation Colour Increment");
-    conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationColourIncMenuItem_actionPerformed(e);
-      }
-    });
     consensusGraphMenuItem.setActionCommand("");
     consensusGraphMenuItem.setText("Consensus graph");
     consensusGraphMenuItem.setState(true);
@@ -611,16 +590,13 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     searchMenu.setText("Search");
-    modifyAlignmentMenuItem.setText("Modify alignment");
-    modifyAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyAlignmentMenuItem_actionPerformed(e);
+
+    abovePIDThreshold.setText("Above PID threshold");
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
+      public void actionPerformed(ActionEvent e) {
+        abovePIDThreshold_actionPerformed(e);
       }
     });
-    abovePIDThreshold.setEnabled(false);
-    abovePIDThreshold.setText("Above PID threshold");
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -638,9 +614,7 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(undoMenuItem);
     editMenu.add(redoMenuItem);
     editMenu.addSeparator();
-    editMenu.add(modifyAlignmentMenuItem);
     editMenu.add(groupsMenuItem);
-    editMenu.add(groupEditingMenuItem);
     editMenu.addSeparator();
     editMenu.add(selectAllSequenceMenuItem);
     editMenu.add(deselectAllSequenceMenuItem);
@@ -674,15 +648,12 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(userDefinedColour);
-     colourMenu.add(abovePIDThreshold);
-     colourMenu.addSeparator();
-    colourMenu.add(conservationMenuItem);
-    colourMenu.add(conservationColourIncMenuItem);
-    colourMenu.addSeparator();
-
     colourMenu.add(PIDColour);
     colourMenu.add(BLOSUM62Colour);
     colourMenu.addSeparator();
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(conservationMenuItem);
+    colourMenu.addSeparator();
     colourMenu.add(schemeKeyMenuItem);
     calculateMenu.add(sortPairwiseMenuItem);
     calculateMenu.add(sortIDMenuItem);
@@ -742,10 +713,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
 
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -951,13 +918,6 @@ public class GAlignFrame extends JInternalFrame
   }
 
 
-  protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
-
-
 
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
@@ -1009,8 +969,8 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)
-  {
+
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
 
   }