no more group editor

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1324173..7b67e81 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -40,18 +40,19 @@ public class AlignFrame extends GAlignFrame
     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
 \r
-\r
-    alignPanel = new AlignmentPanel(this, viewport);\r
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
-\r
     // add conservation graph to alignment\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
 \r
+\r
+    alignPanel = new AlignmentPanel(this, viewport);\r
+\r
     alignPanel.annotationPanel.adjustPanelHeight();\r
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
 \r
+    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+\r
 \r
     addInternalFrameListener(new InternalFrameAdapter()\r
    {\r
@@ -84,12 +85,6 @@ public class AlignFrame extends GAlignFrame
     else if(e.getActionCommand().equals("PFAM"))\r
       suffix = new String[]{"pfam"};\r
 \r
-    if(e.getActionCommand().equals("XML DUMP"))\r
-    {\r
-      XMLStore store = new XMLStore();\r
-      store.store(viewport);\r
-      return;\r
-    }\r
 \r
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
         , suffix, e.getActionCommand()+" file");\r
@@ -425,15 +420,6 @@ public class AlignFrame extends GAlignFrame
   }\r
 \r
 \r
-  public void groupsMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-    GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
-    JInternalFrame frame = new JInternalFrame();\r
-    frame.setContentPane(geditor);\r
-    Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
-    frame.setResizable(false);\r
-  }\r
-\r
   protected void deleteGroups_actionPerformed(ActionEvent e)\r
   {\r
     viewport.alignment.deleteAllGroups();\r

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8b68899..dfc664d 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -22,7 +22,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu colourMenu = new JMenu();
   protected JMenu calculateMenu = new JMenu();
   protected JMenu alignMenu = new JMenu();
-  protected JMenuItem groupsMenuItem = new JMenuItem();
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
@@ -166,15 +165,6 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
     alignMenu.setText("Web Service");
-    groupsMenuItem.setVisible(false);
-    groupsMenuItem.setText("Groups");
-    groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupsMenuItem_actionPerformed(e);
-      }
-    });
     selectAllSequenceMenuItem.setText("Select all");
     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -727,7 +717,6 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(selectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
     editMenu.add(deleteGroups);
-    editMenu.add(groupsMenuItem);
     editMenu.addSeparator();
     editMenu.add(deselectAllColumnsMenuItem);
     editMenu.add(remove2LeftMenuItem);
@@ -819,10 +808,6 @@ public class GAlignFrame extends JInternalFrame
   }
 
 
-  protected void groupsMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
 
 
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)