EditMenu.java

/* EditMenu.java
 *
 * created: Thu Dec  3 1998
 *
 * This file is part of Artemis
 *
 * Copyright (C) 1998,1999,2000,2001,2002  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EditMenu.java,v 1.44 2008-01-17 10:15:56 tjc Exp $
 **/

package uk.ac.sanger.artemis.components;

import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.components.genebuilder.GeneBuilderFrame;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.components.genebuilder.GeneViewerPanel;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.Location;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.io.InvalidRelationException;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.OutOfDateException;
import uk.ac.sanger.artemis.io.GFFStreamFeature;

import java.awt.*;
import java.awt.event.*;
import java.io.IOException;

import javax.swing.*;

import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.Vector;

/**
 *  A menu with editing commands.
 *
 *  @author Kim Rutherford
 *  @version $Id: EditMenu.java,v 1.44 2008-01-17 10:15:56 tjc Exp $
 **/

public class EditMenu extends SelectionMenu
    implements EntryGroupChangeListener, EntryChangeListener 
{

  /**
   * 
   */
  private static final long serialVersionUID = 1L;

  /**
   *  The GotoEventSource object that was passed to the constructor.
   **/
  private GotoEventSource goto_event_source = null;

  /**
   *  The EntryGroup object that was passed to the constructor.
   **/
  private EntryGroup entry_group = null;

  /**
   *  The BasePlotGroup object that was passed to the constructor.
   **/
  private BasePlotGroup base_plot_group = null;

  /** FeatureDisplay */
  private DisplayComponent owner;


  public static org.apache.log4j.Logger logger4j = 
    org.apache.log4j.Logger.getLogger(EditMenu.class);
  /**
   *  Create a new EditMenu object.
   *  @param frame The JFrame that owns this JMenu.
   *  @param selection The Selection that the commands in the menu will
   *    operate on.
   *  @param goto_event_source The object the we will call makeBaseVisible()
   *    on.
   *  @param entry_group The EntryGroup object where new features/entries will
   *    be added.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   *  @param menu_name The name of the new menu.
   **/
  public EditMenu(final JFrame frame,
                  final Selection selection,
                  final GotoEventSource goto_event_source,
                  final EntryGroup entry_group,
                  final BasePlotGroup base_plot_group,
                  final String menu_name,
                  final DisplayComponent owner)
  {
    super(frame, menu_name, selection);

    this.entry_group = entry_group;
    this.goto_event_source = goto_event_source;
    this.base_plot_group = base_plot_group;
    this.owner = owner;

    getEntryGroup().addEntryGroupChangeListener(this);
    getEntryGroup().addEntryChangeListener(this);
    refreshMenu();
  }

  /**
   *  Create a new EditMenu object and use "Edit" as the menu name.
   *  @param frame The JFrame that owns this JMenu.
   *  @param selection The Selection that the commands in the menu will
   *    operate on.
   *  @param goto_event_source The object the we will call makeBaseVisible()
   *    on.
   *  @param entry_group The EntryGroup object where new features/entries will
   *    be added.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  public EditMenu(final JFrame frame,
                  final Selection selection,
                  final GotoEventSource goto_event_source,
                  final EntryGroup entry_group,
                  final BasePlotGroup base_plot_group,
                  final DisplayComponent owner) 
  {
    this(frame, selection, goto_event_source, entry_group,
         base_plot_group, "Edit", owner);
  }

  /**
   *  The shortcut for Edit Selected Features.
   **/
  final static KeyStroke EDIT_FEATURES_KEY =
    KeyStroke.getKeyStroke(KeyEvent.VK_E, 
                           Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);
  final static public int EDIT_FEATURES_KEY_CODE = KeyEvent.VK_E;

  /**
   *  The shortcut for Merge Selected Features.
   **/
  final static KeyStroke MERGE_FEATURES_KEY =
    KeyStroke.getKeyStroke(KeyEvent.VK_M,
                           Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); // InputEvent.CTRL_MASK);
  final static public int MERGE_FEATURES_KEY_CODE = KeyEvent.VK_M;

  /**
   *  The shortcut for Duplicate Selected Features.
   **/
  final static KeyStroke DUPLICATE_KEY =
    KeyStroke.getKeyStroke(KeyEvent.VK_D,
                           Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); // InputEvent.CTRL_MASK);
  final static public int DUPLICATE_KEY_CODE = KeyEvent.VK_D;

  /**
   *  The shortcut for Delete Selected Features.
   **/
  final static KeyStroke DELETE_FEATURES_KEY =
    KeyStroke.getKeyStroke(KeyEvent.VK_DELETE,
                           Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); // InputEvent.CTRL_MASK);
  final static public int DELETE_FEATURES_KEY_CODE = KeyEvent.VK_DELETE;

  /**
   *  The shortcut for Trim Selected Features.
   **/
  final static KeyStroke TRIM_FEATURES_KEY =
    KeyStroke.getKeyStroke(KeyEvent.VK_T,
                           Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); // InputEvent.CTRL_MASK);
  final static public int TRIM_FEATURES_KEY_CODE = KeyEvent.VK_T;

  /**
   *  The shortcut for Trim Selected Features To Next Any.
   **/
  final static KeyStroke TRIM_FEATURES_TO_NEXT_ANY_KEY =
    KeyStroke.getKeyStroke(KeyEvent.VK_Y,
                           Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); // InputEvent.CTRL_MASK);
  final static public int TRIM_FEATURES_TO_NEXT_ANY_KEY_CODE = KeyEvent.VK_Y;

  /**
   *  The shortcut for Extend to Previous Stop Codon.
   **/
  final static public int EXTEND_TO_PREVIOUS_STOP_CODON_KEY_CODE =
    KeyEvent.VK_Q;
  final static KeyStroke EXTEND_TO_PREVIOUS_STOP_CODON_KEY =
    makeMenuKeyStroke(EXTEND_TO_PREVIOUS_STOP_CODON_KEY_CODE);

  /**
   *  The shortcut for Undo.
   **/
  final static public int UNDO_KEY_CODE = KeyEvent.VK_U;
  final static KeyStroke UNDO_KEY =
    KeyStroke.getKeyStroke(UNDO_KEY_CODE,
                           Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); // InputEvent.CTRL_MASK);

  /**
   *  Implementation of the EntryGroupChangeListener interface.  We listen to
   *  EntryGroupChange events so that we can update the display if entries
   *  are added or deleted.
   **/
  public void entryGroupChanged(final EntryGroupChangeEvent event) 
  {
    switch(event.getType()) 
    {
      case EntryGroupChangeEvent.ENTRY_ADDED:
      case EntryGroupChangeEvent.ENTRY_DELETED:
      case EntryGroupChangeEvent.ENTRY_INACTIVE:
      case EntryGroupChangeEvent.ENTRY_ACTIVE:
      case EntryGroupChangeEvent.NEW_DEFAULT_ENTRY:
        refreshMenu();
        break;
    }
  }

  /**
   *  Implementation of the EntryChangeListener interface.
   **/
  public void entryChanged(final EntryChangeEvent event) 
  {
    if(event.getType() == EntryChangeEvent.NAME_CHANGED) 
      refreshMenu();
  }

  /**
   *  Update the menus to the reflect the current contents of the EntryGroup.
   **/
  private void refreshMenu() 
  {
    removeAll();

    final JMenuItem undo_item = new JMenuItem("Undo");
    undo_item.setAccelerator(UNDO_KEY);
    undo_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        undo(getParentFrame(), getSelection(), getEntryGroup());
      }
    });

    final JMenuItem contig_reordering = new JMenuItem("Contig Reordering");
    contig_reordering.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event)
      {
        FeatureDisplay display = (FeatureDisplay)owner;
        FeatureVector contig_features = display.getContigs();
         
        final JFrame frame = new JFrame("Contig Tool");

        JScrollPane jsp = new JScrollPane();
        final ContigTool ct = new ContigTool(contig_features, 
                                 (FeatureDisplay)owner, jsp,
                                 getSelection());
        jsp.setViewportView(ct);

        jsp.getViewport().setBackground(Color.white);
        jsp.setPreferredSize(new Dimension(display.getWidth(),
                 ct.getPreferredSize().height+
                 jsp.getVerticalScrollBar().getPreferredSize().height));
        frame.getContentPane().add(jsp, BorderLayout.CENTER);
        frame.getContentPane().add(ct.getStatusBar(), 
                                 BorderLayout.SOUTH);

        frame.pack();
        frame.addWindowListener(new WindowAdapter()
        {
          public void windowClosing(WindowEvent event)
          {
            getSelection().removeSelectionChangeListener(ct);
            frame.dispose();
          }
        });

        Utilities.centreJustifyFrame(frame,0);
        frame.setVisible(true);
      }
    });

    final JMenuItem edit_feature_item = new JMenuItem("Edit Selected Features");
    edit_feature_item.setAccelerator(EDIT_FEATURES_KEY);
    edit_feature_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        editSelectedFeatures(getParentFrame(), getEntryGroup(),
                             getSelection(), goto_event_source);
      }
    });

    final JMenuItem edit_subsequence_item = new JMenuItem("Edit Subsequence (and Features)");
    edit_subsequence_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        editSubSequence();
      }
    });

    final JMenu qualifier_menu = new JMenu("Qualifier of Selected Feature(s)");
    final JMenuItem add_qualifiers_item = new JMenuItem("Change ...");
    add_qualifiers_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        addQualifiers(getParentFrame(), getSelection());
      }
    });

    final JMenuItem remove_qualifier_item = new JMenuItem("Remove ...");
    remove_qualifier_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        removeQualifier(getParentFrame(), getSelection());
      }
    });

    final JMenuItem convert_qualifier_item = new JMenuItem("Convert ...");
    convert_qualifier_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        convertQualifier(getParentFrame(), getSelection());
      }
    });

    final JMenu feature_menu = new JMenu("Selected Feature(s)");
    final JMenuItem merge_features_item = new JMenuItem("Merge");
    merge_features_item.setAccelerator(MERGE_FEATURES_KEY);
    merge_features_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        mergeFeatures(getParentFrame(), getSelection(), getEntryGroup());
      }
    });

    final JMenuItem unmerge_feature_item = new JMenuItem("Unmerge");
      
    unmerge_feature_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        unmergeFeature(getParentFrame(), getSelection(), getEntryGroup());
      }
    });

    final JMenuItem unmerge_all_feature_item = new JMenuItem("Unmerge All Segments");
    if(GeneUtils.isDatabaseEntry(entry_group))
      unmerge_all_feature_item.setEnabled(false);
    
    unmerge_all_feature_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event)
      {
        unmergeAllFeature(getParentFrame(), getSelection(), getEntryGroup());
      }
    });

    final JMenuItem duplicate_item  = new JMenuItem("Duplicate");
    duplicate_item.setAccelerator(DUPLICATE_KEY);
    duplicate_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        duplicateFeatures(getParentFrame(), getSelection(),
                          getEntryGroup());
      }
    });
   
    
    final JMenuItem delete_features_item = new JMenuItem("Delete");
    delete_features_item.setAccelerator(DELETE_FEATURES_KEY);
    delete_features_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        deleteSelectedFeatures(getParentFrame(), getSelection(),
                               getEntryGroup());
      }
    });

    final JMenuItem delete_segments_item = new JMenuItem("Delete Exons");
    delete_segments_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        deleteSelectedSegments();
      }
    });

    final JMenuItem delete_introns_item =
      new JMenuItem("Remove Introns");
    delete_introns_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        removeIntrons();
      }
    });

    final JMenuItem edit_header_item = new JMenuItem("Edit Header Of Default Entry");
    edit_header_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event)
      {
        editHeader();
      }
    });

    final JMenu move_features_menu = new JMenu("Move Selected Features To");
    final JMenu copy_features_menu = new JMenu("Copy Selected Features To");

    if(entry_group == null || getEntryGroup().size() == 0) 
    {
      move_features_menu.add(new JMenuItem("(No Entries Currently)"));
      copy_features_menu.add(new JMenuItem("(No Entries Currently)"));
    }
    else
    {
      for(int i = 0 ; i < getEntryGroup().size() ; ++i) 
      {
        final Entry this_entry = getEntryGroup().elementAt(i);

        String entry_name = this_entry.getName();
        if(entry_name == null)
          entry_name = "no name";

        final JMenuItem move_to_item = new JMenuItem(entry_name);
        move_to_item.addActionListener(new ActionListener() 
        {
          public void actionPerformed(ActionEvent event) 
          {
            // unselect, move, then reselect (for speed)
            final FeatureVector selected_features =
              getSelection().getAllFeatures();
            getSelection().clear();
            moveFeatures(selected_features, this_entry);
            getSelection().set(selected_features);
          }
        });
        move_features_menu.add(move_to_item);

        final JMenuItem copy_to_item = new JMenuItem(entry_name);

        copy_to_item.addActionListener(new ActionListener() 
        {
          public void actionPerformed(ActionEvent event) 
          {
            copyFeatures(getSelection().getAllFeatures(), this_entry);
          }
        });
        copy_features_menu.add(copy_to_item);
      }
    }

    final JMenu trim_menu = new JMenu("Trim Selected Features");
    final JMenuItem trim_to_any_item = new JMenuItem("To Any");
    trim_to_any_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) {
        EditMenu.trimSelected(getParentFrame(), getSelection(),
                              getEntryGroup(), true, false);
      }
    });

    final JMenuItem trim_item = new JMenuItem("To Met");
    trim_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        EditMenu.trimSelected(getParentFrame(), getSelection(),
                              getEntryGroup(), false, false);
      }
    });

    final JMenuItem trim_to_next_any_item =
      new JMenuItem("To Next Any");
    trim_to_next_any_item.setAccelerator(TRIM_FEATURES_TO_NEXT_ANY_KEY);
    trim_to_next_any_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        EditMenu.trimSelected(getParentFrame(), getSelection(),
                              getEntryGroup(), true, true);
      }
    });

    final JMenuItem trim_to_next_item = new JMenuItem("To Next Met");
    trim_to_next_item.setAccelerator(TRIM_FEATURES_KEY);
    trim_to_next_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        EditMenu.trimSelected(getParentFrame(), getSelection(),
                              getEntryGroup(), false, true);
      }
    });

    final JMenu extend_menu = new JMenu("Extend Selected Features");
    final JMenuItem extend_to_prev_stop_item =
      new JMenuItem("To Previous Stop Codon");
    extend_to_prev_stop_item.setAccelerator(EXTEND_TO_PREVIOUS_STOP_CODON_KEY);
    extend_to_prev_stop_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        extendToORF(getParentFrame(), getSelection(),
                    getEntryGroup(), false);
      }
    });

    final JMenuItem extend_to_next_stop_item = new JMenuItem("To Next Stop Codon");
    extend_to_next_stop_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        extendToORF(getParentFrame(), getSelection(),
                    getEntryGroup(), true);
      }
    });

    final JMenuItem fix_stop_codons_item = new JMenuItem("Fix Stop Codons");
    fix_stop_codons_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        fixStopCodons();
      }
    });

    final JMenuItem extend_to_next_stop_and_fix_item = new JMenuItem("To Next Stop Codon and Fix");
    extend_to_next_stop_and_fix_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        extendToORF(getParentFrame(), getSelection(),
                    getEntryGroup(), true);
        fixStopCodons();
      }
    });
    
    final JMenuItem auto_gene_name_item = new JMenuItem("Automatically Create Gene Names");
    auto_gene_name_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        autoGeneName();
      }
    });

    final JMenuItem fix_gene_names_item = new JMenuItem("Fix Gene Names");
    fix_gene_names_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        fixGeneNames(getParentFrame(), getEntryGroup(),
                     getSelection());
      }
    });

    final JMenuItem reverse_complement_item = new JMenuItem("Reverse And Complement");
    reverse_complement_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        reverseAndComplement();
      }
    });

    final JMenuItem reverse_complement_range_item = new JMenuItem("Reverse And Complement Selected Contig");
    reverse_complement_range_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event)
      {
        if(getEntryGroup().isReadOnly()) 
        {
          final String message =
            "one or more of the entries or features are read only - " +
            "cannot continue";
          new MessageDialog(getParentFrame(), message);
          return;
        }

        final FeatureVector selected_features = getSelection().getAllFeatures();

        if(selected_features.size() == 1)
        {
          final Feature selection_feature = selected_features.elementAt(0);

          final YesNoDialog dialog =
                new YesNoDialog (getParentFrame (),
                                 "Are you sure you want to reverse complement this " +
                                 "region "+ selection_feature.getFirstBase()+".."+
                                            selection_feature.getLastBase()+"?");
         if(!dialog.getResult())
           return;

          try 
          {
            getEntryGroup().getBases().reverseComplement(selection_feature);
          }
          catch(ReadOnlyException roe)
          {
            final String message =
              "one or more of the features is read-only or is in a " +
              "read-only entry - cannot continue";
            new MessageDialog(null, message);
            return;
          }
        }
        else
        {
          final String message =
              "Select a single contig to reverse and complement";
          new MessageDialog(null, message);
          return;   
        }
      }
    });

    final JMenu bases_item = new JMenu("Bases");
    
    final JMenuItem delete_bases_item = new JMenuItem("Delete Selected Bases");
    delete_bases_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event)
      {
        deleteSelectedBases("Are you sure you want to delete the " +
                            "selected bases?");
      }
    });

    final JMenuItem add_bases_item = new JMenuItem("Add Bases At Selection");
    add_bases_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        addBases();
      }
    });
    
    
    final JMenuItem replace_bases_item = new JMenuItem("Replace Bases At Selection");
    replace_bases_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        MarkerRange marker_range = getSelection ().getMarkerRange ();
        int start = getSelection().getHighestBaseOfSelection().getPosition();
        boolean hasDeleted = deleteSelectedBases(
            "Are you sure you want to replace the " +
            "selected bases?");
        
        if(!hasDeleted)
          return;
        
        if(!marker_range.isForwardMarker())
        {
          try
          {
            marker_range = new MarkerRange(
                getEntryGroup().getBases().getReverseStrand(),
                start,start+1);
          }
          catch(OutOfRangeException e)
          {
            e.printStackTrace();
            return;
          }
        }
        getSelection ().setMarkerRange (marker_range);
        addBases();
        getSelection ().setMarkerRange (null);
      }
    });

    if(Options.getOptions().getPropertyTruthValue("val_mode")) 
    {
      add(edit_feature_item);
      add(edit_subsequence_item);
      addSeparator();
      add(edit_header_item);
      addSeparator();
    }

    if(Options.getOptions().getUndoLevels() > 0) 
    {
      add(undo_item);
      addSeparator();
    }

    if(!Options.getOptions().getPropertyTruthValue("val_mode")) 
    {
      add(edit_feature_item);
      add(edit_subsequence_item);
      addSeparator();
      add(edit_header_item);
      addSeparator();
    }

    add(qualifier_menu);
    qualifier_menu.add(add_qualifiers_item);
    qualifier_menu.add(remove_qualifier_item);
    qualifier_menu.add(convert_qualifier_item);
    add(feature_menu);
    feature_menu.add(duplicate_item);
    feature_menu.add(merge_features_item);
    feature_menu.add(unmerge_feature_item);
    feature_menu.add(unmerge_all_feature_item);
    feature_menu.add(delete_features_item);
    feature_menu.add(delete_segments_item);
    feature_menu.add(delete_introns_item);
    addSeparator();
    add(move_features_menu);
    add(copy_features_menu);
    addSeparator();
    add(trim_menu);
    trim_menu.add(trim_item);
    trim_menu.add(trim_to_any_item);
    trim_menu.add(trim_to_next_item);
    trim_menu.add(trim_to_next_any_item);
    add(extend_menu);
    extend_menu.add(extend_to_prev_stop_item);
    extend_menu.add(extend_to_next_stop_item);
    add(fix_stop_codons_item);
    extend_menu.add(extend_to_next_stop_and_fix_item);
    addSeparator();
    add(auto_gene_name_item);
    add(fix_gene_names_item);
    add(bases_item);
    bases_item.add(reverse_complement_item); 
    bases_item.add(reverse_complement_range_item);
    bases_item.add(delete_bases_item);
    bases_item.add(add_bases_item);

    if(Options.readWritePossible()) 
    {
      // only the standalone version can save or read
      final JMenuItem add_bases_from_file_item = new JMenuItem("Add Bases From File ...");
      add_bases_from_file_item.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent event)
        {
          addBasesFromFile();
        }
      });

      bases_item.add(add_bases_from_file_item);
    }

    bases_item.add(replace_bases_item);
    
    if(owner instanceof FeatureDisplay)
    {
      addSeparator();
      add(contig_reordering);
    }
  }

  /**
   *  Undo the last change by calling ActionController.undo().
   *  @param frame The Frame to use for MessageDialog components.
   *  @param selection The current Selection - needs to be cleared before undo
   *  @param entry_group Used to get the ActionController for calling
   *    ActionController.undo().
   **/
  private static void undo(final JFrame frame,
                          final Selection selection,
                          final EntryGroup entry_group) 
  {
    // undo disabled
    if(Options.getOptions().getUndoLevels() == 0)
      return;

    // clear the selection because something in the selection might
    // disappear after the undo() eg. create a feature, select it then undo
    if(entry_group.getActionController().canUndo())
      selection.clear();

    if(!entry_group.getActionController().undo()) 
      new MessageDialog(frame, "sorry - no further undo information");
  }

  /**
   *  Open an edit window (FeatureEdit) for each of the selected features.
   *  The edit component will listen for feature change events and update
   *  itself.
   *  @param frame The JFrame to use for MessageDialog components.
   *  @param selection The selected features to edit.
   *  @param entry_group Used to get the ActionController for calling
   *    startAction() and endAction().
   **/
  protected static void editSelectedFeatures(final JFrame frame,
                                   final EntryGroup entry_group,
                                   final Selection selection,
                                   final GotoEventSource goto_event_source) 
  {
    frame.setCursor(new Cursor(Cursor.WAIT_CURSOR));
    final int MAX_SELECTED_FEATURES = 25;
    final FeatureVector features_to_edit = selection.getAllFeatures();
    boolean featureEdit = true;
    
    if(features_to_edit.size() > MAX_SELECTED_FEATURES)
      new MessageDialog(frame, "warning: only editing the first " +
                        MAX_SELECTED_FEATURES + " selected features");

    for(int i = 0; i < features_to_edit.size() && i < MAX_SELECTED_FEATURES;
        ++i)
    {
      final Feature selection_feature = features_to_edit.elementAt(i);

      featureEdit = editSelectedFeatures(entry_group, selection, goto_event_source,
          selection_feature, null, null);
    }

    if(featureEdit)
      selection.set(features_to_edit);
    frame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
  }

  public static boolean editSelectedFeatures(
      final EntryGroup entry_group,
      final Selection selection,
      final GotoEventSource goto_event_source,
      final Feature selection_feature,
      final ActionListener cancel_listener,
      final ActionListener apply_listener) 
  {
    if(selection_feature.getEmblFeature() instanceof GFFStreamFeature &&
        ((GFFStreamFeature)selection_feature.getEmblFeature()).getChadoGene() != null)
    {
      new GeneBuilderFrame(selection_feature, entry_group,
                           selection, goto_event_source);
      return false;
    }
    else
    {
      final JFrame edit_frame = new JFrame("Artemis Feature Edit: " + 
           selection_feature.getIDString() +
           (selection_feature.isReadOnly() ?
               "  -  (read only)" :
               ""));
       
       final FeatureEdit fe = new FeatureEdit(selection_feature, entry_group,
                                   selection, goto_event_source, edit_frame);
       
       edit_frame.addWindowListener(new WindowAdapter() 
       {
         public void windowClosing(WindowEvent event) 
         {
           fe.stopListening();
           edit_frame.dispose();
         }
       });
       
       if(cancel_listener != null)
         fe.addCancelActionListener(cancel_listener);
       if(apply_listener != null)
         fe.addApplyActionListener(apply_listener);
       edit_frame.getContentPane().add(fe);
       edit_frame.pack();

       Utilities.centreFrame(edit_frame);
       edit_frame.setVisible(true);
       return true;
     } 
  }
  
  /**
   *  Create a new EntryEdit component that contains only the selected
   *  sequence and the features in the selected range.
   **/
  private void editSubSequence() 
  {
    if(getSelection().isEmpty()) 
      new MessageDialog(getParentFrame(), "nothing selected");

    final Range range = getSelection().getSelectionRange();
    final EntryGroup new_entry_group = getEntryGroup().truncate(range);
    new EntryEdit(new_entry_group).setVisible(true);
  }

  /**
   *  Open a EntryHeaderEdit window for the default entry.
   **/
  private void editHeader()
  {
    final Entry default_entry = getEntryGroup().getDefaultEntry();

    if(default_entry == null)
    {
      final String message = "there is no default entry";
      new MessageDialog(getParentFrame(), message);
    }
    else 
    {
      if(default_entry.isReadOnly()) 
      {
        new MessageDialog(getParentFrame(),
                          "the default entry is read-only " +
                          "- cannot continue");
        return;
      }

      new EntryHeaderEdit(entry_group, default_entry);
    }
  }

  /**
   *  Merge the selected features into one Feature.  If there are selected
   *  segments then the owning Feature of each segment will be the Feature
   *  that is merged.  This method will create a new Feature.
   *  @param frame The JFrame to use for MessageDialog components.
   *  @param selection The Selection containing the features to merge.
   *  @param entry_group Used to get the ActionController for calling
   *    startAction() and endAction().
   **/
  protected static void mergeFeatures(final JFrame frame,
                            final Selection selection,
                            final EntryGroup entry_group) 
  {
    try 
    {
      entry_group.getActionController().startAction();

      if(!checkForSelectionFeatures(frame, selection, 10,
                 "really merge all (>10) " + "selected features?"))
        return;

      final FeatureVector features_to_merge = selection.getAllFeatures();

      if(features_to_merge.size() < 2) 
      {
        new MessageDialog(frame,
                          "nothing to merge - select more than one feature");
        return;
      }

      final Feature merge_feature = features_to_merge.elementAt(0);

      // make sure all the features are on the same strand
      for(int i = 1; i < features_to_merge.size(); ++i) 
      {
        final Feature this_feature = features_to_merge.elementAt(i);

        if(this_feature.isForwardFeature() !=
           merge_feature.isForwardFeature()) 
        {
          new MessageDialog(frame,
                            "all the features in a merge must be on the " +
                            "same strand");
          return;
        }

        if(!this_feature.getKey().equals(merge_feature.getKey())) 
        {
          new MessageDialog(frame,
                            "all the features in a merge must have the " +
                            "same key");
          return;
        }
      }

      if(Options.getOptions().isNoddyMode()) 
      {
        final YesNoDialog dialog =
          new YesNoDialog(frame, "Are you sure you want to merge the selected " +
                                 "features?");
        if(!dialog.getResult())
          return;
      }

      final Feature new_feature;
      //
      //  GFF merge
      if(merge_feature.getEmblFeature() instanceof GFFStreamFeature)
      {
        if(!merge_feature.getKey().equals(DatabaseDocument.EXONMODEL) &&
           !merge_feature.getKey().equals("pseudogenic_exon")) 
        {