ViewMenu.java

/* ViewMenu.java
 *
 * created: Tue Dec 29 1998
 *
 * This file is part of Artemis
 *
 * Copyright (C) 1998,1999,2000,2002  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/ViewMenu.java,v 1.15 2009-04-22 08:50:13 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.filetree.FileList;
import uk.ac.sanger.artemis.components.filetree.RemoteFileNode;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.InvalidRelationException;
import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.j2ssh.FTProgress;
import uk.ac.sanger.artemis.j2ssh.FileTransferProgressMonitor;

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

import javax.swing.*;

import com.sshtools.j2ssh.sftp.FileAttributes;

/**
 *  A popup menu with viewing commands.
 *
 *  @author Kim Rutherford
 *  @version $Id: ViewMenu.java,v 1.15 2009-04-22 08:50:13 tjc Exp $
 **/

public class ViewMenu extends SelectionMenu 
{
  /** */
  private static final long serialVersionUID = 1L;

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

  /**
   *  The Selection that was passed to the constructor.
   **/
  private Selection selection = null;

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

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

    this.entry_group = entry_group;
    this.selection = selection;

    this.base_plot_group = base_plot_group;

    final JMenuItem plot_features_item = new JMenuItem("Feature Plots");
    plot_features_item.setAccelerator(PLOT_FEATURES_KEY);
    plot_features_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        plotSelectedFeatures(getParentFrame(), getSelection());
      }
    });

    final JMenuItem view_feature_item = new JMenuItem("Selected Features");
    view_feature_item.setAccelerator(VIEW_FEATURES_KEY);
    view_feature_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        viewSelectedFeatures(getParentFrame(), getSelection());
      }
    });

    final JMenuItem view_selection_item = new JMenuItem("Selection");
    view_selection_item.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent event) {
        new SelectionViewer(getSelection(), entry_group);
      }
    });

    final JMenuItem feature_info_item = new JMenuItem("Feature Statistics");
    feature_info_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        viewSelectedFeatureInfo();
      }
    });

    final JMenuItem view_bases_item = new JMenuItem("Bases Of Selection");
    view_bases_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        viewSelectedBases(true);
      }
    });

    final JMenuItem view_bases_as_fasta_item =
      new JMenuItem("Bases Of Selection As FASTA");
    view_bases_as_fasta_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        viewSelectedBases(false);
      }
    });

    final JMenuItem view_aa_item = new JMenuItem("Amino Acids Of Selection");
    view_aa_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        viewSelectedAminoAcids(true);
      }
    });

    final JMenuItem view_aa_as_fasta_item =
      new JMenuItem("Amino Acids Of Selection As FASTA");
    view_aa_as_fasta_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        viewSelectedAminoAcids(false);
      }
    });

    final JMenuItem overview_item = new JMenuItem("Overview");
    overview_item.setAccelerator(OVERVIEW_KEY);
    overview_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        new EntryGroupInfoDisplay(getParentFrame(), entry_group);
      }
    });

    final JMenuItem forward_overview_item = new JMenuItem("Forward Strand Overview");
    forward_overview_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event)
      {
        new EntryGroupInfoDisplay(getParentFrame(), entry_group,
                                  Bases.FORWARD);
      }
    });

    final JMenuItem reverse_overview_item = new JMenuItem("Reverse Strand Overview");
    reverse_overview_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event)
      {
        new EntryGroupInfoDisplay(getParentFrame(), entry_group,
                                  Bases.REVERSE);
      }
    });

    final JMenuItem view_cds_item = new JMenuItem("CDS Genes And Products");
    if(GeneUtils.isDatabaseEntry(entry_group))
      view_cds_item.setEnabled(false);
    view_cds_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        final FeaturePredicate feature_predicate =
          new FeatureKeyPredicate(Key.CDS);

        final String filter_name =
          "CDS features (filtered from: " +
          getParentFrame().getTitle() + ")";

        final FilteredEntryGroup filtered_entry_group =
          new FilteredEntryGroup(entry_group, feature_predicate, filter_name);

        final FeatureListFrame feature_list_frame =
          new FeatureListFrame(filter_name,
                                selection, goto_event_source,
                                filtered_entry_group,
                                base_plot_group);

        feature_list_frame.getFeatureList().setShowGenes(true);
        feature_list_frame.getFeatureList().setShowProducts(true);

        feature_list_frame.setVisible(true);
      }
    });

    JMenu search_results_menu = null;

    search_results_menu = new JMenu("Search Results");

    final boolean sanger_options =
      Options.getOptions().getPropertyTruthValue("sanger_options");

    final ExternalProgramVector external_programs =
      Options.getOptions().getExternalPrograms();

    final StringVector external_program_names = new StringVector();

    for(int i = 0 ; i < external_programs.size() ; ++i) 
    {
      final ExternalProgram external_program =
        external_programs.elementAt(i);

      final String new_name = external_program.getName();

      if(!external_program_names.contains(new_name)) 
        external_program_names.add(new_name);
    }

    for(int i = 0 ; i < external_program_names.size() ; ++i) 
    {
      final String external_program_name =
        (String)external_program_names.elementAt(i);

      final JMenuItem new_menu =
        makeSearchResultsMenu(external_program_name, false, sanger_options);
      search_results_menu.add(new_menu);
    }

    if(sanger_options) 
    {
      search_results_menu.addSeparator();

      for(int i = 0 ; i < external_program_names.size() ; ++i)
      {
        final String external_program_name =
          (String)external_program_names.elementAt(i);

        final JMenuItem new_menu =
          makeSearchResultsMenu(external_program_name, true, sanger_options);
        search_results_menu.add(new_menu);
      }
    }

    final int MAX_FILTER_FEATURE_COUNT = 10000;

    final JMenu feature_filters_menu = new JMenu("Feature Filters");

    final JMenuItem bad_start_codons_item =
      new JMenuItem("Suspicious Start Codons ...");
    bad_start_codons_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
          showBadStartCodons(getParentFrame(), selection, 
                             entry_group, goto_event_source,
                             base_plot_group);
      }
    });

    final JMenuItem bad_stop_codons_item =
      new JMenuItem("Suspicious Stop Codons ...");
    bad_stop_codons_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT)) 
          showBadStopCodons(getParentFrame(), selection,
                            entry_group, goto_event_source,
                            base_plot_group);
      }
    });

    final JMenuItem stop_codons_in_translation =
      new JMenuItem("Stop Codons In Translation ...");
    stop_codons_in_translation.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT)) 
          showStopsInTranslation(getParentFrame(), selection,
                                 entry_group, goto_event_source,
                                 base_plot_group);
      }
    });

    final JMenuItem bad_feature_keys_item =
      new JMenuItem("Non EMBL Keys ...");
    bad_feature_keys_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
          showNonEMBLKeys(getParentFrame(), selection,
                          entry_group, goto_event_source,
                          base_plot_group);
      }
    });

    final JMenuItem duplicated_keys_item =
      new JMenuItem("Duplicated Features ...");
    duplicated_keys_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT)) 
          showDuplicatedFeatures(getParentFrame(), selection,
                                 entry_group, goto_event_source,
                                 base_plot_group);
      }
    });

    final JMenuItem overlapping_cds_features_item;
    
    if(GeneUtils.isDatabaseEntry(entry_group))
      overlapping_cds_features_item =
        new JMenuItem("Overlapping "+DatabaseDocument.EXONMODEL+" Features ...");
    else
      overlapping_cds_features_item =   
        new JMenuItem("Overlapping CDS Features ...");
    overlapping_cds_features_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT)) 
          showOverlappingCDSs(getParentFrame(), selection,
                              entry_group, goto_event_source,
                              base_plot_group);
      }
    });

    final JMenuItem same_stop_cds_features_item;
    if(GeneUtils.isDatabaseEntry(entry_group))
      same_stop_cds_features_item = new JMenuItem(
          DatabaseDocument.EXONMODEL+"s Sharing Stop Codons ...");
    else
      same_stop_cds_features_item = new JMenuItem("CDSs Sharing Stop Codons ...");
    same_stop_cds_features_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT)) 
          showFeaturesWithSameStopCodons(getParentFrame(), 
                                         selection, entry_group,
                                         goto_event_source,
                                         base_plot_group);
      }
    });

    final JMenuItem missing_qualifier_features_item =
      new JMenuItem("Features Missing Required Qualifiers ...");
    missing_qualifier_features_item.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT)) 
          showMissingQualifierFeatures(getParentFrame(), selection,
                                       entry_group, goto_event_source,
                                       base_plot_group);
      }
    });

    final JMenuItem filter_by_key_item =
      new JMenuItem("Filter By Key ...");
    filter_by_key_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT)) 
          showFilterByKey(getParentFrame(), selection,
                          entry_group, goto_event_source,
                          base_plot_group);
      }
    });


    final JMenuItem filter_by_multiple_sys_id =
      new JMenuItem("Duplicate Systematic Name Qualifier ...");
    filter_by_multiple_sys_id.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        showFilterByMultipleID(getParentFrame(), selection,
                               entry_group, goto_event_source,
                               base_plot_group);
      }
    });
    
    
    final JMenuItem filter_by_selection_item =
      new JMenuItem("Selected Features ...");
    filter_by_selection_item.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent event) 
      {
        showFilterBySelection(getParentFrame(),
                              selection, entry_group, goto_event_source,
                              base_plot_group);
      }
    });

    feature_filters_menu.add(bad_start_codons_item);
    feature_filters_menu.add(bad_stop_codons_item);
    feature_filters_menu.add(stop_codons_in_translation);
    feature_filters_menu.add(bad_feature_keys_item);
    feature_filters_menu.add(duplicated_keys_item);
    feature_filters_menu.add(overlapping_cds_features_item);
    feature_filters_menu.add(same_stop_cds_features_item);
    feature_filters_menu.add(missing_qualifier_features_item);
    feature_filters_menu.add(filter_by_multiple_sys_id);
    feature_filters_menu.addSeparator();
    feature_filters_menu.add(filter_by_key_item);
    feature_filters_menu.add(filter_by_selection_item);

    add(view_feature_item);
    add(view_selection_item);
    addSeparator();
    if(search_results_menu != null)
      add(search_results_menu);
    
    add(view_cds_item);
    add(feature_filters_menu);
    addSeparator();
    add(overview_item);
    add(forward_overview_item);
    add(reverse_overview_item);
    addSeparator();
    add(view_bases_item);
    add(view_bases_as_fasta_item);
    add(view_aa_item);
    add(view_aa_as_fasta_item);
    addSeparator();
    add(feature_info_item);
    add(plot_features_item);
  }

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

  /**
   *  The shortcut for Show Feature Plots.
   **/
  final static KeyStroke PLOT_FEATURES_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_W, 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int PLOT_FEATURES_KEY_CODE = KeyEvent.VK_W;

  /**
   *  The shortcut for View Selected Features.
   **/
  final static KeyStroke VIEW_FEATURES_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_V, 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int VIEW_FEATURES_KEY_CODE = KeyEvent.VK_V;

  /**
   *  The shortcut for Show Overview.
   **/
  final static KeyStroke OVERVIEW_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_O, 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int OVERVIEW_KEY_CODE = KeyEvent.VK_O;

  /**
   *  The shortcut for View FASTA in browser.
   **/
  final static KeyStroke FASTA_IN_BROWSER_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_F, 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int FASTA_IN_BROWSER_KEY_CODE = KeyEvent.VK_F;

  /**
   *  The shortcut for View FASTA.
   **/
  final static KeyStroke VIEW_FASTA_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_R, 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int VIEW_FASTA_KEY_CODE = KeyEvent.VK_R;

  /**
   *  The shortcut for View BLASTP in browser.
   **/
  final static KeyStroke BLASTP_IN_BROWSER_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_B, 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int BLASTP_IN_BROWSER_KEY_CODE = KeyEvent.VK_B;

  /**
   *  The shortcut for View BLASTP.
   **/
  final static KeyStroke VIEW_BLASTP_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_BACK_QUOTE , 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int VIEW_BLASTP_KEY_CODE = KeyEvent.VK_BACK_QUOTE;

  /**
   *  The shortcut for View HTH.
   **/
  final static KeyStroke VIEW_HTH_KEY =
    KeyStroke.getKeyStroke (KeyEvent.VK_H, 
                            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); //InputEvent.CTRL_MASK);

  final static public int VIEW_HTH_KEY_CODE = KeyEvent.VK_H;

  /**
   *  Make a JMenuItem for viewing the results of running the given program.
   *  @param send_to_browser if true the results should be sent straight to
   *    the web browser rather than using a SearchResultViewer object.
   *  @param sanger_options true if the sanger_options is set to true in the
   *    options file.
   **/
  private JMenuItem makeSearchResultsMenu(final String program_name,
                                          final boolean send_to_browser,
                                          final boolean sanger_options) 
  {
    final String suffix;
    if(send_to_browser)
      suffix = new String(" results (in browser)");
    else
      suffix = new String(" results");

    final JMenuItem new_menu = new JMenuItem(program_name + suffix);

    if ((sanger_options && send_to_browser || !sanger_options)
        && program_name.equals("fasta"))
      new_menu.setAccelerator (FASTA_IN_BROWSER_KEY);
    else 
    {
      if ((sanger_options && send_to_browser || !sanger_options)
          && program_name.equals("blastp")) 
        new_menu.setAccelerator (BLASTP_IN_BROWSER_KEY);
      else 
      {
        if(program_name.equals("fasta"))
          new_menu.setAccelerator (VIEW_FASTA_KEY);
        else if(program_name.equals("blastp")) 
          new_menu.setAccelerator (VIEW_BLASTP_KEY);
        else if(program_name.equals("hth")) 
          new_menu.setAccelerator (VIEW_HTH_KEY);
      }
    }

    new_menu.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event) 
      {
        viewExternalResults(getParentFrame(), getSelection(),
                            program_name, send_to_browser);
      }
    });

    return new_menu;
  }

  /**
   *  Popup a FeatureListFrame containing the non-pseudo CDS features that
   *  have invalid start codons.
   *  @param parent_frame The parent JFrame.
   *  @param selection The Selection to pass to the FeatureList.
   *  @param entry_group The EntryGroup to pass to the FilteredEntryGroup.
   *  @param goto_source The GotoEventSource to pass to the FeatureList.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  protected static void showBadStartCodons (final JFrame parent_frame,
                                         final Selection selection,
                                         final EntryGroup entry_group,
                                         final GotoEventSource goto_source,
                                         final BasePlotGroup base_plot_group) 
  {
    final FeaturePredicate cds_predicate;
    
    if(GeneUtils.isDatabaseEntry(entry_group))
      cds_predicate = new FeatureKeyPredicate(new Key(DatabaseDocument.EXONMODEL));
    else
      cds_predicate =
        new FeatureKeyQualifierPredicate (Key.CDS, "pseudo", false);

    final FeaturePredicate feature_predicate = new FeaturePredicate ()
    {
      public boolean testPredicate (final Feature feature) 
      {
        if(!cds_predicate.testPredicate (feature))
          return false;

        if(feature.hasValidStartCodon (true)) 
          return false;
        else 
          return true;
      }
    };

    final String filter_name;
    
    if(GeneUtils.isDatabaseEntry(entry_group))
      filter_name =
        DatabaseDocument.EXONMODEL+" features with suspicious start codons (filtered from: " +
        parent_frame.getTitle () + ")";
    else
      filter_name =
        "CDS features with suspicious start codons (filtered from: " +
        parent_frame.getTitle () + ")";

    final FilteredEntryGroup filtered_entry_group =
      new FilteredEntryGroup (entry_group, feature_predicate, filter_name);

    final FeatureListFrame feature_list_frame =
      new FeatureListFrame (filter_name,
                            selection, goto_source, filtered_entry_group,
                            base_plot_group);

    feature_list_frame.setVisible (true);
  }

  /**
   *  Popup a FeatureListFrame containing the non-pseudo CDS features that
   *  have invalid stop codons.
   *  @param parent_frame The parent JFrame.
   *  @param selection The Selection to pass to the FeatureList.
   *  @param entry_group The EntryGroup to pass to the FilteredEntryGroup.
   *  @param goto_source The GotoEventSource to pass to the FeatureList.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  protected static void showBadStopCodons (final JFrame parent_frame,
                                        final Selection selection,
                                        final EntryGroup entry_group,
                                        final GotoEventSource goto_source,
                                        final BasePlotGroup
                                          base_plot_group) 
  {
    final FeaturePredicate cds_predicate;

    if(GeneUtils.isDatabaseEntry(entry_group))
      cds_predicate = new FeatureKeyPredicate(new Key(DatabaseDocument.EXONMODEL));
    else
      cds_predicate =
        new FeatureKeyQualifierPredicate (Key.CDS, "pseudo", false);

    final FeaturePredicate feature_predicate =  new FeaturePredicate () 
    {
      public boolean testPredicate (final Feature feature) 
      {
        if(!cds_predicate.testPredicate (feature)) 
          return false;

        if(feature.hasValidStopCodon (true)) 
          return false;
        else 
          return true;
      }
    };

    final String filter_name;
    
    if(GeneUtils.isDatabaseEntry(entry_group))
      filter_name=
        DatabaseDocument.EXONMODEL+" features with suspicious stop codons (filtered from: " +
        parent_frame.getTitle () + ")";
    else
      filter_name =
        "CDS features with suspicious stop codons (filtered from: " +
        parent_frame.getTitle () + ")";

    final FilteredEntryGroup filtered_entry_group =
      new FilteredEntryGroup (entry_group, feature_predicate, filter_name);

    final FeatureListFrame feature_list_frame =
      new FeatureListFrame (filter_name,
                            selection, goto_source, filtered_entry_group,
                            base_plot_group);

    feature_list_frame.setVisible (true);
  }

  /**
   *  Popup a FeatureListFrame containing the non-pseudo CDS features that
   *  contain a stop codon in the translation.
   *  @param parent_frame The parent Frame.
   *  @param selection The Selection to pass to the FeatureList.
   *  @param entry_group The EntryGroup to pass to the FilteredEntryGroup.
   *  @param goto_source The GotoEventSource to pass to the FeatureList.
   *  @param base_plot_group The BasePlotGroup associated with this Menu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  private static void showStopsInTranslation(final Frame parent_frame,
                                             final Selection selection,
                                             final EntryGroup entry_group,
                                             final GotoEventSource goto_source,
                                             final BasePlotGroup
                                               base_plot_group) 
  {
    final FeaturePredicate cds_predicate;

    if(GeneUtils.isDatabaseEntry(entry_group))
      cds_predicate = new FeatureKeyPredicate(new Key(DatabaseDocument.EXONMODEL));
    else
      cds_predicate =
        new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false);

    final FeaturePredicate feature_predicate = new FeaturePredicate () 
    {
      public boolean testPredicate (final Feature feature) 
      {
        if(!cds_predicate.testPredicate (feature)) 
          return false;

        final AminoAcidSequence amino_acids = feature.getTranslation ();
        if(amino_acids.containsStopCodon ())
          return true;
        else
          return false;
      }
    };

    final String filter_name;
    if(GeneUtils.isDatabaseEntry(entry_group))
      filter_name =
        DatabaseDocument.EXONMODEL+" features with stop codon(s) in translation (filtered from: " +
        parent_frame.getTitle () + ")";
    else
      filter_name =
        "CDS features with stop codon(s) in translation (filtered from: " +
        parent_frame.getTitle () + ")";

    final FilteredEntryGroup filtered_entry_group =
      new FilteredEntryGroup (entry_group, feature_predicate, filter_name);

    final FeatureListFrame feature_list_frame =
      new FeatureListFrame (filter_name,
                            selection, goto_source, filtered_entry_group,
                            base_plot_group);

    feature_list_frame.setVisible (true);
  }

  /**
   *  Popup a FeatureListFrame containing the features that have non-EMBL keys.
   *  @param parent_frame The parent JFrame.
   *  @param selection The Selection to pass to the FeatureList.
   *  @param entry_group The EntryGroup to pass to the FilteredEntryGroup.
   *  @param goto_source The GotoEventSource to pass to the FeatureList.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  protected static void showNonEMBLKeys(final JFrame parent_frame,
                                        final Selection selection,
                                        final EntryGroup entry_group,
                                        final GotoEventSource goto_source,
                                        final BasePlotGroup
                                        base_plot_group) 
  {
    final FeaturePredicate feature_predicate =
      new FeaturePredicate () {
        public boolean testPredicate (final Feature feature) {
          if (feature.hasValidEMBLKey ()) {
            return false;
          } else {
            return true;
          }
        }
      };

    final String filter_name =
      "features with a non-EMBL key (filtered from: " +
      parent_frame.getTitle () + ")";

    final FilteredEntryGroup filtered_entry_group =
      new FilteredEntryGroup (entry_group, feature_predicate, filter_name);

    final FeatureListFrame feature_list_frame =
      new FeatureListFrame (filter_name,
                            selection, goto_source, filtered_entry_group,
                            base_plot_group);

    feature_list_frame.setVisible (true);
  }


  /**
   *  Popup a FeatureListFrame containing the features that have the same key
   *  and location as another features (ie. duplicates).
   *  @param parent_frame The parent JFrame.
   *  @param selection The Selection to pass to the FeatureList.
   *  @param entry_group The EntryGroup to pass to the FilteredEntryGroup.
   *  @param goto_source The GotoEventSource to pass to the FeatureList.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  protected static void showDuplicatedFeatures (final JFrame parent_frame,
                                             final Selection selection,
                                             final EntryGroup entry_group,
                                             final GotoEventSource goto_source,
                                             final BasePlotGroup
                                               base_plot_group)
  {
    final FeaturePredicate feature_predicate =
      new FeaturePredicate () {
        public boolean testPredicate (final Feature feature) {
          final Entry feature_entry = feature.getEntry ();

          final int feature_index = feature_entry.indexOf (feature);

          if (feature_index + 1 == feature_entry.getFeatureCount ()) {
            // last in the Entry
            return false;
          }

          final Feature next_feature =
            feature_entry.getFeature (feature_index + 1);

          if (feature.getKey ().equals (next_feature.getKey ()) &&
              feature.getLocation ().equals (next_feature.getLocation ())) {
            return true;
          } else {
            return false;
          }
        }
      };

    final String filter_name =
      "duplicated Features (filtered from: " +
      parent_frame.getTitle () + ")";

    final FilteredEntryGroup filtered_entry_group =
      new FilteredEntryGroup (entry_group, feature_predicate, filter_name);

    final FeatureListFrame feature_list_frame =
      new FeatureListFrame (filter_name,
                            selection, goto_source, filtered_entry_group,
                            base_plot_group);

    feature_list_frame.setVisible (true);
  }

  /**
   *  Popup a FeatureListFrame containing those CDS features that overlap with
   *  the next feature.
   *  @param parent_frame The parent JFrame.
   *  @param selection The Selection to pass to the FeatureList.
   *  @param entry_group The EntryGroup to pass to the FilteredEntryGroup.
   *  @param goto_source The GotoEventSource to pass to the FeatureList.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  protected static void showOverlappingCDSs(final JFrame parent_frame,
                                            final Selection selection,
                                            final EntryGroup entry_group,
                                            final GotoEventSource goto_source,
                                            final BasePlotGroup base_plot_group) 
  {
    final Key key;
    if(GeneUtils.isDatabaseEntry(entry_group))
      key = new Key(DatabaseDocument.EXONMODEL);
    else
      key = Key.CDS;
    
    final FeatureKeyPredicate cds_predicate = new FeatureKeyPredicate (key);

    final FeaturePredicate feature_predicate =
      new FeaturePredicate () {
        public boolean testPredicate (final Feature test_feature) {
          if (!cds_predicate.testPredicate (test_feature)) {
            return false;
          }

          final Range feature_range = test_feature.getMaxRawRange ();

          final FeatureVector overlapping_features;

          try {
            overlapping_features =
              entry_group.getFeaturesInRange (feature_range);
          } catch (OutOfRangeException e) {
            throw new Error ("internal error - unexpected exception: " + e);
          }

          for (int i = 0 ; i < overlapping_features.size () ; ++i) {
            final Feature current_feature = overlapping_features.elementAt (i);

            if (current_feature != test_feature &&
                cds_predicate.testPredicate (current_feature)) {
              return true;
            }
          }

          return false;
        }
      };

    final String filter_name =
      "overlapping "+key.getKeyString()+" features (filtered from: " +
      parent_frame.getTitle () + ")";

    final FilteredEntryGroup filtered_entry_group =
      new FilteredEntryGroup (entry_group, feature_predicate, filter_name);

    final FeatureListFrame feature_list_frame =
      new FeatureListFrame (filter_name,
                            selection, goto_source, filtered_entry_group,
                            base_plot_group);

    feature_list_frame.setVisible (true);
  }

  /**
   *  Popup a FeatureListFrame containing those CDS features that overlap with
   *  the next feature.
   *  @param parent_frame The parent JFrame.
   *  @param selection The Selection to pass to the FeatureList.
   *  @param entry_group The EntryGroup to pass to the FilteredEntryGroup.
   *  @param goto_source The GotoEventSource to pass to the FeatureList.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  private static void
    showFeaturesWithSameStopCodons(final JFrame parent_frame,
                                   final Selection selection,
                                   final EntryGroup entry_group,
                                   final GotoEventSource goto_source,
                                   final BasePlotGroup base_plot_group) 
  {
    final Key key;
    if(GeneUtils.isDatabaseEntry(entry_group))
      key = new Key(DatabaseDocument.EXONMODEL);
    else
      key = Key.CDS;
    final FeatureKeyPredicate cds_predicate = new FeatureKeyPredicate (key);