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    /* WriteMenu.java
     *
     * created: Mon Jan 11 1999
     *
     * This file is part of Artemis
     *
     * Copyright (C) 1998,1999,2000  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/WriteMenu.java,v 1.1 2004-06-09 09:48:00 tjc Exp $
     **/
    
    package uk.ac.sanger.artemis.components;
    
    import uk.ac.sanger.artemis.*;
    import uk.ac.sanger.artemis.sequence.*;
    
    import uk.ac.sanger.artemis.io.Sequence;
    import uk.ac.sanger.artemis.io.StreamSequence;
    import uk.ac.sanger.artemis.io.FastaStreamSequence;
    import uk.ac.sanger.artemis.io.RawStreamSequence;
    import uk.ac.sanger.artemis.io.EmblStreamSequence;
    import uk.ac.sanger.artemis.io.GenbankStreamSequence;
    import uk.ac.sanger.artemis.io.StreamSequenceFactory;
    
    import java.awt.*;
    import java.awt.event.*;
    import java.io.*;
    
    import javax.swing.*;
    
    /**
     *  A menu of commands for writing out protein and bases.
     *
     *  @author Kim Rutherford
     *  @version $Id: WriteMenu.java,v 1.1 2004-06-09 09:48:00 tjc Exp $
     **/
    
    public class WriteMenu extends SelectionMenu {
      /**
       *  Create a new WriteMenu component.
       *  @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 to use when writing a sequence.
       *  @param menu_name The name of the new menu.
       **/
      public WriteMenu (final JFrame frame,
                        final Selection selection,
                        final EntryGroup entry_group,
                        final String menu_name) {
        super (frame, menu_name, selection);
    
        this.entry_group = entry_group;
    
        final JMenuItem aa_item = new JMenuItem ("Amino Acids Of Selected Features");
        aa_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeAminoAcids ();
          }
        });
    
        add (aa_item);
    
        final JMenuItem pir_item =
          new JMenuItem ("PIR Database Of Selected Features");
        pir_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writePIRDataBase ();
          }
        });
    
        add (pir_item);
    
        addSeparator ();
    
        final JMenu bases_menu = new JMenu ("Bases Of Selection");
    
        final JMenuItem raw_bases_item = new JMenuItem ("Raw Format");
        raw_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeBasesOfSelection (StreamSequenceFactory.RAW_FORMAT);
          }
        });
    
        bases_menu.add (raw_bases_item);
    
        final JMenuItem fasta_bases_item = new JMenuItem ("FASTA Format");
        fasta_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeBasesOfSelection (StreamSequenceFactory.FASTA_FORMAT);
          }
        });
    
        bases_menu.add (fasta_bases_item);
    
        final JMenuItem embl_bases_item = new JMenuItem ("EMBL Format");
        embl_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeBasesOfSelection (StreamSequenceFactory.EMBL_FORMAT);
          }
        });
    
        bases_menu.add (embl_bases_item);
    
        final JMenuItem genbank_bases_item = new JMenuItem ("Genbank Format");
        genbank_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeBasesOfSelection (StreamSequenceFactory.GENBANK_FORMAT);
          }
        });
    
        bases_menu.add (genbank_bases_item);
    
        add (bases_menu);
    
        final JMenu upstream_bases_menu =
          new JMenu ("Upstream Bases Of Selected Features");
    
        final JMenuItem raw_upstream_bases_item = new JMenuItem ("Raw Format");
        raw_upstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeUpstreamBases (StreamSequenceFactory.RAW_FORMAT);
          }
        });
    
        upstream_bases_menu.add (raw_upstream_bases_item);
    
        final JMenuItem fasta_upstream_bases_item = new JMenuItem ("FASTA Format");
        fasta_upstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeUpstreamBases (StreamSequenceFactory.FASTA_FORMAT);
          }
        });
    
        upstream_bases_menu.add (fasta_upstream_bases_item);
    
        final JMenuItem embl_upstream_bases_item = new JMenuItem ("EMBL Format");
        embl_upstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeUpstreamBases (StreamSequenceFactory.EMBL_FORMAT);
          }
        });
    
        upstream_bases_menu.add (embl_upstream_bases_item);
    
        final JMenuItem genbank_upstream_bases_item = new JMenuItem ("Genbank Format");
        genbank_upstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeUpstreamBases (StreamSequenceFactory.GENBANK_FORMAT);
          }
        });
    
        upstream_bases_menu.add (genbank_upstream_bases_item);
    
        add (upstream_bases_menu);
    
        final JMenu downstream_bases_menu =
          new JMenu ("Downstream Bases Of Selected Features");
    
        final JMenuItem raw_downstream_bases_item = new JMenuItem ("Raw Format");
        raw_downstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeDownstreamBases (StreamSequenceFactory.RAW_FORMAT);
          }
        });
    
        downstream_bases_menu.add (raw_downstream_bases_item);
    
        final JMenuItem fasta_downstream_bases_item = new JMenuItem ("FASTA Format");
        fasta_downstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeDownstreamBases (StreamSequenceFactory.FASTA_FORMAT);
          }
        });
    
        downstream_bases_menu.add (fasta_downstream_bases_item);
    
        final JMenuItem embl_downstream_bases_item = new JMenuItem ("EMBL Format");
        embl_downstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeDownstreamBases (StreamSequenceFactory.EMBL_FORMAT);
          }
        });
    
        downstream_bases_menu.add (embl_downstream_bases_item);
    
        final JMenuItem genbank_downstream_bases_item =
          new JMenuItem ("Genbank Format");
        genbank_downstream_bases_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeDownstreamBases (StreamSequenceFactory.GENBANK_FORMAT);
          }
        });
    
        downstream_bases_menu.add (genbank_downstream_bases_item);
    
        add (downstream_bases_menu);
    
        addSeparator ();
    
        final JMenu write_all_bases_menu = new JMenu ("Write All Bases");
    
        final JMenuItem write_raw_item = new JMenuItem ("Raw Format");
        write_raw_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeAllSequence (StreamSequenceFactory.RAW_FORMAT);
          }
        });
    
        write_all_bases_menu.add (write_raw_item);
    
        final JMenuItem write_fasta_item = new JMenuItem ("FASTA Format");
        write_fasta_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeAllSequence (StreamSequenceFactory.FASTA_FORMAT);
          }
        });
    
        write_all_bases_menu.add (write_fasta_item);
    
        final JMenuItem write_embl_item = new JMenuItem ("EMBL Format");
        write_embl_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeAllSequence (StreamSequenceFactory.EMBL_FORMAT);
          }
        });
    
        write_all_bases_menu.add (write_embl_item);
    
        final JMenuItem write_genbank_item = new JMenuItem ("Genbank Format");
        write_genbank_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeAllSequence (StreamSequenceFactory.GENBANK_FORMAT);
          }
        });
    
        write_all_bases_menu.add (write_genbank_item);
    
        add (write_all_bases_menu);
    
        addSeparator ();
    
        final JMenuItem codon_usage_item =
          new JMenuItem ("Write Codon Usage of Selected Features");
        codon_usage_item.addActionListener (new ActionListener () {
          public void actionPerformed (ActionEvent event) {
            writeCodonUsage ();
          }
        });
    
        add (codon_usage_item);
      }
    
      /**
       *  Create a new WriteMenu component.
       *  @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 to use when writing a sequence.
       **/
      public WriteMenu (final JFrame frame,
                        final Selection selection,
                        final EntryGroup entry_group) {
        this (frame, selection, entry_group, "Write");
      }
      
      /**
       *  Write a PIR database of the selected features to a file choosen by the
       *  user.
       **/
      private void writePIRDataBase () {
        if (! checkForSelectionFeatures ()) {
          return;
        }
    
        final File write_file =
          getWriteFile ("Select a PIR output file name ...", "cosmid.pir");
    
        if (write_file == null) {
          return;
        }
    
        try {
          final FileWriter writer = new FileWriter (write_file);
    
          final FeatureVector features_to_write =
            getSelection ().getAllFeatures ();
    
          for (int i = 0 ; i < features_to_write.size () ; ++i) {
            final Feature selection_feature = features_to_write.elementAt (i);
    
            selection_feature.writePIROfFeature (writer);
          }
    
          writer.close ();
        } catch (IOException e) {
          new MessageDialog (getParentFrame (),
                             "error while writing: " + e.getMessage ());
        }
      }
    
      /**
       *  Write the amino acid symbols of the selected features to a file choosen
       *  by the user.
       **/
      private void writeAminoAcids () {
        if (! checkForSelectionFeatures ()) {
          return;
        }
    
        final File write_file =
          getWriteFile ("Select an output file name..", "amino_acids");
    
        if (write_file == null) {
          return;
        }
    
        try {
          final FileWriter writer = new FileWriter (write_file);
    
          final FeatureVector features_to_write =
            getSelection ().getAllFeatures ();
    
          for (int i = 0 ; i < features_to_write.size () ; ++i) {
            final Feature selection_feature = features_to_write.elementAt (i);
    
            selection_feature.writeAminoAcidsOfFeature (writer);
          }
    
          writer.close ();
        } catch (IOException e) {
          new MessageDialog (getParentFrame (),
                             "error while writing: " + e.getMessage ());
        }
      }
    
      /**
       *  Write the bases of the selection to a file choosen by the user.
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private void writeBasesOfSelection (final int output_type) {
        final MarkerRange marker_range = getSelection ().getMarkerRange ();
    
        if (marker_range == null) {
          writeFeatureBases (output_type);
        } else {
          final String selection_bases = Strand.markerRangeBases (marker_range);
    
          writeBases (selection_bases,
                      "selected bases",
                      getSequenceFileName (output_type),
                      output_type);
        }
      }
    
      /**
       *  Write the bases of the selected features to a file choosen by the user
       *  or show a message and return immediately if there are no selected
       *  features.
       *  @param sequence The sequence to be written.
       *  @param header The header line that will be used on those output formats
       *    that need it.
       *  @param default_output_filename The filename that is passed to
       *    getWriteFile ()
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private void writeBases (final String sequence,
                               final String header,
                               final String default_output_filename,
                               final int output_type) {
        final File write_file =
          getWriteFile ("Select an output file name ...", default_output_filename);
    
        if (write_file == null) {
          return;
        }
    
        try {
          final FileWriter writer = new FileWriter (write_file);
    
          final StreamSequence stream_sequence;
    
          switch (output_type) {
          case StreamSequenceFactory.FASTA_FORMAT:
            stream_sequence =
              new FastaStreamSequence (sequence, header);
            break;
    
          case StreamSequenceFactory.EMBL_FORMAT:
            stream_sequence =
              new EmblStreamSequence (sequence);
            break;
    
          case StreamSequenceFactory.GENBANK_FORMAT:
            stream_sequence =
              new GenbankStreamSequence (sequence);
            break;
    
          case StreamSequenceFactory.RAW_FORMAT:
          default:
            stream_sequence =
              new RawStreamSequence (sequence);
            break;
          }
    
          stream_sequence.writeToStream (writer);
    
          writer.close ();
        } catch (IOException e) {
          new MessageDialog (getParentFrame (),
                             "error while writing: " + e.getMessage ());
        }
      }
    
      /**
       *  Write the bases of the selected features to a file choosen by the user
       *  or show a message and return immediately if there are no selected
       *  features.
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private void writeFeatureBases (final int output_type) {
        if (! checkForSelectionFeatures ()) {
          return;
        }
    
        final File write_file =
          getWriteFile ("Select an output file name ...", "bases");
    
        if (write_file == null) {
          return;
        }
    
        try {
          final FileWriter writer = new FileWriter (write_file);
    
          final FeatureVector features_to_write =
            getSelection ().getAllFeatures ();
    
          for (int i = 0 ; i < features_to_write.size () ; ++i) {
            final Feature selection_feature = features_to_write.elementAt (i);
    
            final StringBuffer header_buffer = new StringBuffer ();
    
            header_buffer.append (selection_feature.getSystematicName ());
            header_buffer.append (" ");
            header_buffer.append (selection_feature.getIDString ());
            header_buffer.append (" ");
    
            final String product = selection_feature.getProductString ();
    
            if (product == null) {
              header_buffer.append ("undefined product");
            } else {
              header_buffer.append (product);
            }
            
            header_buffer.append (" ").append (selection_feature.getWriteRange ());
    
            final StreamSequence stream_sequence =
              getStreamSequence (selection_feature.getBases (),
                                 header_buffer.toString (),
                                 output_type);
    
            stream_sequence.writeToStream (writer);
          }
    
          writer.close ();
        } catch (IOException e) {
          new MessageDialog (getParentFrame (),
                             "error while writing: " + e.getMessage ());
        }
      }
    
      /**
       *  Return a StreamSequence object for the given sequence string and the
       *  given type.
       *  @param sequence A String containing the sequence.
       *  @param header The header line that will be used on those output formats
       *    that need it.
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private StreamSequence getStreamSequence (final String sequence,
                                                final String header,
                                                final int output_type) {
    
        switch (output_type) {
        case StreamSequenceFactory.FASTA_FORMAT:
          return new FastaStreamSequence (sequence, header);
    
        case StreamSequenceFactory.EMBL_FORMAT:
          return new EmblStreamSequence (sequence);
    
        case StreamSequenceFactory.GENBANK_FORMAT:
          return new GenbankStreamSequence (sequence);
    
        case StreamSequenceFactory.RAW_FORMAT:
        default:
          return new RawStreamSequence (sequence);
        }
      }
    
      /**
       *  Write the upstream bases of the selected features to a file choosen by
       *  the user.  The user can also choose the number of upstream base to
       *  write.
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private void writeUpstreamBases (final int output_type) {
        if (! checkForSelectionFeatures ()) {
          return;
        }
    
        final TextRequester text_requester =
          new TextRequester ("write how many bases upstream of each feature?",
                             18, "");
    
        text_requester.addTextRequesterListener (new TextRequesterListener () {
          public void actionPerformed (final TextRequesterEvent event) {
            if (event.getType () == TextRequesterEvent.CANCEL) {
              return;
            }
    
            final String base_count_string = event.getRequesterText ().trim ();
    
            if (base_count_string.length () == 0) {
              new MessageDialog (getParentFrame (), "no bases written");
              return;
            }
    
            try {
              final int base_count =
                Integer.valueOf (base_count_string).intValue ();
    
    
              final File write_file =
                getWriteFile ("Select an output file name ...",
                              "upstream_" + getSequenceFileName (output_type));
    
              if (write_file == null) {
                return;
              }
    
              try {
                final FileWriter writer = new FileWriter (write_file);
    
                final FeatureVector features_to_write =
                  getSelection ().getAllFeatures ();
    
                for (int i = 0 ; i < features_to_write.size () ; ++i) {
                  final Feature selection_feature =
                    features_to_write.elementAt (i);
    
                  final String sequence_string =
                    selection_feature.getUpstreamBases (base_count);
    
    
                  final String header_line =
                    selection_feature.getIDString () + " - " +
                    sequence_string.length () + " bases upstream";
    
                  final StreamSequence stream_sequence =
                    getStreamSequence (sequence_string,
                                       header_line,
                                       output_type);
                  
                  stream_sequence.writeToStream (writer);
                }
    
                writer.close ();
              } catch (IOException e) {
                new MessageDialog (getParentFrame (),
                                   "error while writing: " + e.getMessage ());
              }
            } catch (NumberFormatException e) {
              new MessageDialog (getParentFrame (),
                                 "this is not a number: " + base_count_string);
            }
          }
        });
    
        text_requester.show ();
      }
    
      /**
       *  Write the downstream bases of the selected features to a file choosen by
       *  the user.  The user can also choose the number of downstream base to
       *  write.
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private void writeDownstreamBases (final int output_type) {
        if (! checkForSelectionFeatures ()) {
          return;
        }
    
        final TextRequester text_requester =
          new TextRequester ("write how many bases downstream of each feature?",
                             18, "");
    
        text_requester.addTextRequesterListener (new TextRequesterListener () {
          public void actionPerformed (final TextRequesterEvent event) {
            if (event.getType () == TextRequesterEvent.CANCEL) {
              return;
            }
    
            final String base_count_string = event.getRequesterText ().trim ();
    
            if (base_count_string.length () == 0) {
              new MessageDialog (getParentFrame (), "no bases written");
              return;
            }
    
            try {
              final int base_count =
                Integer.valueOf (base_count_string).intValue ();
    
              final File write_file =
                getWriteFile ("Select an output file name ...",
                              "downstream_" + getSequenceFileName (output_type));
    
              if (write_file == null) {
                return;
              }
    
              try {
                final FileWriter writer = new FileWriter (write_file);
    
                final FeatureVector features_to_write =
                  getSelection ().getAllFeatures ();
    
                for (int i = 0 ; i < features_to_write.size () ; ++i) {
                  final Feature selection_feature =
                    features_to_write.elementAt (i);
    
                  final String sequence_string =
                    selection_feature.getDownstreamBases (base_count);
    
    
                  final String header_line =
                    selection_feature.getIDString () + " - " +
                    sequence_string.length () + " bases downstream ";
    
                  final StreamSequence stream_sequence =
                    getStreamSequence (sequence_string,
                                       header_line,
                                       output_type);
                  
                  stream_sequence.writeToStream (writer);
                }
    
                writer.close ();
              } catch (IOException e) {
                new MessageDialog (getParentFrame (),
                                   "error while writing: " + e.getMessage ());
              }
            } catch (NumberFormatException e) {
              new MessageDialog (getParentFrame (),
                                 "this is not a number: " + base_count_string);
            }
          }
        });
    
        text_requester.show ();
      }
    
      /**
       *  Helper method for writeFeatureBases (), writeUpstreamBases () and
       *  writeDownstreamBases (). 
       *  @return A string of the form "100:200 reverse" or "1:2222 forward".
       **/
      private static String getWriteRange (final Feature feature) {
        return (feature.isForwardFeature () ?
                feature.getFirstCodingBaseMarker ().getRawPosition () + ":" +
                feature.getLastBaseMarker ().getRawPosition () +
                " forward" :
                feature.getLastBaseMarker ().getRawPosition () + ":" +
                feature.getFirstCodingBaseMarker ().getRawPosition () +
                " reverse");
      }
    
      
      /**
       *  Return a sensible file name to write sequence of the given type to.
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private String getSequenceFileName (final int output_type) {
        switch (output_type) {
          case StreamSequenceFactory.FASTA_FORMAT:
            return "sequence.dna";
    
          case StreamSequenceFactory.EMBL_FORMAT:
            return "sequence.embl";
    
          case StreamSequenceFactory.GENBANK_FORMAT:
            return "sequence.genbank";
    
          case StreamSequenceFactory.RAW_FORMAT:
          default:
            return "sequence.seq";
        }
      }
      
      /**
       *  Write the bases from entry_group as raw sequence.
       *  @param output_type One of EMBL_FORMAT, RAW_FORMAT etc.
       **/
      private void writeAllSequence (final int output_type) {
        final String file_name = getSequenceFileName (output_type);
    
        writeBases (entry_group.getBases ().toString (),
                    "all_bases", file_name, output_type);
      }
    
      /**
       *  Popup a requester and ask for a file name to write to.  If the file
       *  exists ask the user whether to overwrite.
       *  @param title The title of the new FileDialog JFrame.
       *  @param default_name The name to put in the FileDialog as a default.
       **/
      private File getWriteFile (final String title, final String default_name) {
        final JFileChooser dialog = new StickyFileChooser ();
    
        dialog.setDialogTitle (title);
    
        dialog.setFileSelectionMode (JFileChooser.FILES_ONLY);
    
        dialog.setSelectedFile (new File (default_name));
        dialog.setDialogType (JFileChooser.SAVE_DIALOG);
        final int status = dialog.showSaveDialog (getParentFrame ());
    
        if (status != JFileChooser.APPROVE_OPTION) {
          return null;
        }
    
        if (dialog.getSelectedFile () == null) {
          return null;
        } else {
          final File write_file = dialog.getSelectedFile ();
    
          if (write_file.exists ()) {
            final YesNoDialog yes_no_dialog =
              new YesNoDialog (getParentFrame (),
                               "this file exists: " + write_file +
                               " overwrite it?");
            
            if (yes_no_dialog.getResult ()) {
              // yes - continue
            } else {
              // no
              return null;
            }
          }
    
          return write_file;
        }
      }
    
      /**
       *  Write a table of codon usage for the selected features to a file choosen
       *  by the user.
       **/
      private void writeCodonUsage () {
        if (! checkForSelectionFeatures ()) {
          return;
        }
    
        final File write_file =
          getWriteFile ("Select a codon usage output file ...", "usage");
    
        if (write_file == null) {
          return;
        }
    
        try {
          final PrintWriter writer = new PrintWriter (new FileWriter (write_file));
    
          final int [] [] [] codon_counts = new int [4][4][4];
    
          final FeatureVector features_to_write =
            getSelection ().getAllFeatures ();
    
          int codon_total = 0;
    
          for (int i = 0 ; i < features_to_write.size () ; ++i) {
            final Feature selection_feature = features_to_write.elementAt (i);
    
            for (int base1 = 0 ; base1 < 4 ; ++base1) {
              for (int base2 = 0 ; base2 < 4 ; ++base2) {
                for (int base3 = 0 ; base3 < 4 ; ++base3) {
                  codon_counts[base1][base2][base3] +=
                    selection_feature.getCodonCount (base1, base2, base3);
                }
              }
            }
    
            codon_total += selection_feature.getTranslationBasesLength () / 3;
          }
    
          for (int base1 = 0 ; base1 < 4 ; ++base1) {
            for (int base3 = 0 ; base3 < 4 ; ++base3) {
              final StringBuffer buffer = new StringBuffer ();
    
              for (int base2 = 0 ; base2 < 4 ; ++base2) {
                buffer.append (Bases.letter_index[base1]);
                buffer.append (Bases.letter_index[base2]);
                buffer.append (Bases.letter_index[base3]);
                buffer.append (' ');
    
                final float per_thousand;
    
                if (codon_total > 0) {
                  per_thousand =
                    10000 * codon_counts[base1][base2][base3] / codon_total *
                    1.0F / 10;
                } else {
                  per_thousand = 0.0F;
                }
    
                buffer.append (per_thousand);
                buffer.append ("( ").append (codon_counts[base1][base2][base3]);
                buffer.append (")  ");
              }
    
              writer.println (buffer.toString ());
            }
          }
    
          writer.close ();
        } catch (IOException e) {
          new MessageDialog (getParentFrame (),
                             "error while writing: " + e.getMessage ());
        }
      }
    
      /**
       *  The EntryGroup object that was passed to the constructor.
       **/
      private EntryGroup entry_group;
    }