forester/java/src/org/forester/archaeopteryx/PhyloInferenceDialog.java

   1 // $Id:
   2 // forester -- software libraries and applications
   3 // for genomics and evolutionary biology research.
   4 //
   5 // Copyright (C) 2010 Christian M Zmasek
   6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.archaeopteryx;
  27
  28 import java.awt.Color;
  29 import java.awt.FlowLayout;
  30 import java.awt.event.ActionEvent;
  31 import java.awt.event.ActionListener;
  32 import java.util.List;
  33
  34 import javax.swing.BoxLayout;
  35 import javax.swing.ButtonGroup;
  36 import javax.swing.JButton;
  37 import javax.swing.JCheckBox;
  38 import javax.swing.JDialog;
  39 import javax.swing.JFormattedTextField;
  40 import javax.swing.JLabel;
  41 import javax.swing.JOptionPane;
  42 import javax.swing.JPanel;
  43 import javax.swing.JRadioButton;
  44 import javax.swing.JTextField;
  45 import javax.swing.border.Border;
  46 import javax.swing.border.LineBorder;
  47
  48 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
  49 import org.forester.sequence.Sequence;
  50 import org.forester.util.BasicDescriptiveStatistics;
  51 import org.forester.util.DescriptiveStatistics;
  52
  53 public class PhyloInferenceDialog extends JDialog implements ActionListener {
  54
  55     private static final long                  serialVersionUID = 8337543508238133614L;
  56     private final JPanel                       _pnl;
  57     private final JButton                      _launch_btn;
  58     private final JButton                      _cancel_btn;
  59     private final JFormattedTextField          _bootstrap_tf;
  60     private final JCheckBox                    _bootstrap_cb;
  61     private final PhylogeneticInferenceOptions _opts;
  62     private JTextField                         _input_msa_file_tf;
  63     private JButton                            _select_input_msa_btn;
  64     private final MainFrameApplication         _parent_frame;
  65     private JTextField                         _msa_length_tf;
  66     private JTextField                         _msa_size_tf;
  67     private JTextField                         _msa_type_tf;
  68     private final JRadioButton                 _distance_calc_kimura_rb;
  69     private final JRadioButton                 _distance_calc_poisson_rb;
  70     private final JRadioButton                 _distance_calc_fract_dissimilarity_rb;
  71     private int                                _value           = JOptionPane.CANCEL_OPTION;
  72     private JTextField                         _input_seqs_tf;
  73     private JButton                            _select_input_seqs_btn;
  74     private JTextField                         _input_seqs_number_tf;
  75     private JTextField                         _input_seqs_median_length_tf;
  76     private JTextField                         _input_seqs_min_length_tf;
  77     private JTextField                         _input_seqs_max_length_tf;
  78     private JTextField                         _input_seqs_type_tf;
  79     private JTextField                         _input_seqs_msa_program_name_tf;
  80     private JTextField                         _input_seqs_msa_paramenters_tf;
  81     private JTextField                         _msa_processing_max_allowed_gap_ratio_tf;
  82     private JTextField                         _msa_processing_min_allowed_length_tf;
  83     private JTextField                         _random_seed_tf;
  84     private JCheckBox                          _execute_msa_processing_cb;
  85     private JCheckBox                          _msa_processing_remove_all_gap_columns_cb;
  86     private JCheckBox                          _save_pwd_file_cb;
  87     private JCheckBox                          _save_processed_msa_cb;
  88     private JCheckBox                          _save_original_msa_cb;
  89     private JTextField                         _pwd_outfile_tf;
  90     private JTextField                         _processed_msa_outfile_tf;
  91     private JTextField                         _original_msa_outfile_tf;
  92
  93     public PhyloInferenceDialog( final MainFrameApplication frame,
  94                                  final PhylogeneticInferenceOptions options,
  95                                  final boolean from_unaligned_seqs ) {
  96         super( frame, true );
  97         setVisible( false );
  98         _parent_frame = frame;
  99         _opts = options;
 100         _pnl = new JPanel();
 101         getContentPane().add( _pnl );
 102         final BoxLayout box_layout = new BoxLayout( _pnl, BoxLayout.PAGE_AXIS );
 103         _pnl.setLayout( box_layout );
 104         if ( from_unaligned_seqs ) {
 105             setTitle( "Phylogenetic Inference (including multiple sequence alignment)" );
 106             final JPanel inputfile_pnl_1 = new JPanel();
 107             final JPanel inputfile_pnl_2 = new JPanel();
 108             final JPanel inputfile_pnl_3 = new JPanel();
 109             inputfile_pnl_1.setLayout( new FlowLayout() );
 110             inputfile_pnl_2.setLayout( new FlowLayout() );
 111             inputfile_pnl_3.setLayout( new FlowLayout() );
 112             inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
 113             inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
 114             inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
 115             inputfile_pnl_2.add( new JLabel( "Sequences: " ) );
 116             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 117             inputfile_pnl_2.add( _input_seqs_number_tf = new JTextField() );
 118             inputfile_pnl_2.add( new JLabel( "Length: median:" ) );
 119             inputfile_pnl_2.add( _input_seqs_median_length_tf = new JTextField() );
 120             inputfile_pnl_2.add( new JLabel( "min:" ) );
 121             inputfile_pnl_2.add( _input_seqs_min_length_tf = new JTextField() );
 122             inputfile_pnl_2.add( new JLabel( "max:" ) );
 123             inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
 124             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 125             inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
 126             inputfile_pnl_3.add( new JLabel( "Mutiple Sequence Alignment: " ) );
 127             inputfile_pnl_3.add( new JLabel( "Program: " ) );
 128             inputfile_pnl_3.add( _input_seqs_msa_program_name_tf = new JTextField() );
 129             inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
 130             inputfile_pnl_3.add( _input_seqs_msa_paramenters_tf = new JTextField() );
 131             _input_seqs_median_length_tf.setColumns( 4 );
 132             _input_seqs_min_length_tf.setColumns( 4 );
 133             _input_seqs_max_length_tf.setColumns( 4 );
 134             _input_seqs_number_tf.setColumns( 4 );
 135             _input_seqs_type_tf.setColumns( 2 );
 136             _input_seqs_tf.setColumns( 20 );
 137             _input_seqs_tf.setEditable( false );
 138             _input_seqs_median_length_tf.setEditable( false );
 139             _input_seqs_min_length_tf.setEditable( false );
 140             _input_seqs_max_length_tf.setEditable( false );
 141             _input_seqs_number_tf.setEditable( false );
 142             _input_seqs_type_tf.setEditable( false );
 143             _input_seqs_msa_program_name_tf.setEditable( false );
 144             _input_seqs_msa_paramenters_tf.setColumns( 26 );
 145             _select_input_seqs_btn.addActionListener( this );
 146             _pnl.add( inputfile_pnl_1 );
 147             _pnl.add( inputfile_pnl_2 );
 148             _pnl.add( inputfile_pnl_3 );
 149         }
 150         else {
 151             setTitle( "Phylogenetic Inference (from already aligned sequences) " );
 152             // Inputfile (MSA):
 153             final JPanel inputfile_pnl_1 = new JPanel();
 154             final JPanel inputfile_pnl_2 = new JPanel();
 155             inputfile_pnl_1.setLayout( new FlowLayout() );
 156             inputfile_pnl_2.setLayout( new FlowLayout() );
 157             inputfile_pnl_1.add( new JLabel( "Input MSA File:" ) );
 158             inputfile_pnl_1.add( _input_msa_file_tf = new JTextField() );
 159             inputfile_pnl_1.add( _select_input_msa_btn = new JButton( "Select Input File" ) );
 160             inputfile_pnl_2.add( new JLabel( "MSA: " ) );
 161             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 162             inputfile_pnl_2.add( _msa_size_tf = new JTextField() );
 163             inputfile_pnl_2.add( new JLabel( "Length:" ) );
 164             inputfile_pnl_2.add( _msa_length_tf = new JTextField() );
 165             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 166             inputfile_pnl_2.add( _msa_type_tf = new JTextField() );
 167             _msa_length_tf.setColumns( 4 );
 168             _msa_size_tf.setColumns( 4 );
 169             _msa_type_tf.setColumns( 2 );
 170             _input_msa_file_tf.setColumns( 20 );
 171             _input_msa_file_tf.setEditable( false );
 172             _msa_length_tf.setEditable( false );
 173             _msa_size_tf.setEditable( false );
 174             _msa_type_tf.setEditable( false );
 175             _select_input_msa_btn.addActionListener( this );
 176             _pnl.add( inputfile_pnl_1 );
 177             _pnl.add( inputfile_pnl_2 );
 178         }
 179         //
 180         final JPanel inputfile_pnl_4 = new JPanel();
 181         inputfile_pnl_4.setLayout( new FlowLayout() );
 182         inputfile_pnl_4.add( new JLabel( "MSA Processing: " ) );
 183         inputfile_pnl_4.add( _execute_msa_processing_cb = new JCheckBox( "Process MSA" ) );
 184         inputfile_pnl_4.add( _msa_processing_remove_all_gap_columns_cb = new JCheckBox( "Remove all gap columns" ) );
 185         inputfile_pnl_4.add( new JLabel( "Max allowed gap ratio: " ) );
 186         inputfile_pnl_4.add( _msa_processing_max_allowed_gap_ratio_tf = new JTextField() );
 187         inputfile_pnl_4.add( new JLabel( "Min allowed non-gap sequence length: " ) );
 188         inputfile_pnl_4.add( _msa_processing_min_allowed_length_tf = new JTextField() );
 189         _msa_processing_max_allowed_gap_ratio_tf.setColumns( 4 );
 190         _msa_processing_min_allowed_length_tf.setColumns( 4 );
 191         final Border b = new LineBorder( Color.DARK_GRAY );
 192         inputfile_pnl_4.setBorder( b );
 193         _pnl.add( inputfile_pnl_4 );
 194         //
 195         // Distance calculation:
 196         // TODO if type==AA...
 197         final JPanel distance_calc_pnl_1 = new JPanel();
 198         distance_calc_pnl_1.setLayout( new FlowLayout() );
 199         distance_calc_pnl_1.add( new JLabel( "Distance calculation:" ) );
 200         distance_calc_pnl_1.add( _distance_calc_kimura_rb = new JRadioButton( "Kimura correction" ) );
 201         distance_calc_pnl_1.add( _distance_calc_poisson_rb = new JRadioButton( "Poisson" ) );
 202         distance_calc_pnl_1
 203                 .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) );
 204         final ButtonGroup distance_calc_group_1 = new ButtonGroup();
 205         distance_calc_group_1.add( _distance_calc_kimura_rb );
 206         distance_calc_group_1.add( _distance_calc_poisson_rb );
 207         distance_calc_group_1.add( _distance_calc_fract_dissimilarity_rb );
 208         _pnl.add( distance_calc_pnl_1 );
 209         // Bootstrap resampling:
 210         final JPanel bootstrap_pnl = new JPanel();
 211         bootstrap_pnl.setLayout( new FlowLayout() );
 212         bootstrap_pnl.add( _bootstrap_cb = new JCheckBox( "Perform Bootstrap Resampling" ) );
 213         bootstrap_pnl.add( new JLabel( "Number of Bootstrap Samples:" ) );
 214         bootstrap_pnl.add( _bootstrap_tf = new JFormattedTextField( Util.createMaskFormatter( "###" ) ) );
 215         _bootstrap_tf.setColumns( 4 );
 216         // TODO see
 217         // http://download.oracle.com/javase/tutorial/uiswing/components/formattedtextfield.html
 218         // _bootstrap_tf.setColumns( 4 );
 219         bootstrap_pnl.add( new JLabel( "Random Seed:" ) );
 220         bootstrap_pnl.add( _random_seed_tf = new JTextField() );
 221         _random_seed_tf.setColumns( 4 );
 222         _pnl.add( bootstrap_pnl );
 223         final JPanel launch_pnl = new JPanel();
 224         launch_pnl.setLayout( new FlowLayout() );
 225         _launch_btn = new JButton( "Go!" );
 226         _launch_btn.addActionListener( this );
 227         launch_pnl.add( _launch_btn );
 228         _cancel_btn = new JButton( "Cancel" );
 229         _cancel_btn.addActionListener( this );
 230         launch_pnl.add( _cancel_btn );
 231         _pnl.add( launch_pnl );
 232         initializeValues( from_unaligned_seqs );
 233         pack();
 234         setLocationRelativeTo( getParentFrame() );
 235         setResizable( false );
 236     }
 237
 238     public void actionPerformed( final ActionEvent e ) {
 239         if ( e.getSource() == _select_input_msa_btn ) {
 240             readInputFile();
 241         }
 242         else if ( e.getSource() == _select_input_seqs_btn ) {
 243             readInputSeqsFile();
 244         }
 245         else if ( e.getSource() == _launch_btn ) {
 246             launch();
 247         }
 248         else if ( e.getSource() == _cancel_btn ) {
 249             cancel();
 250         }
 251     }
 252
 253     public void activate() {
 254         setVisible( true );
 255     }
 256
 257     private MainFrameApplication getParentFrame() {
 258         return _parent_frame;
 259     }
 260
 261     public PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
 262         return _opts;
 263     }
 264
 265     public int getValue() {
 266         return _value;
 267     }
 268
 269     private void initializeValues( final boolean from_unaligned_seqs ) {
 270         _value = JOptionPane.CANCEL_OPTION;
 271         if ( from_unaligned_seqs ) {
 272             updateSeqsItems();
 273             _input_seqs_msa_program_name_tf.setText( getPhylogeneticInferenceOptions().getMsaPrg() );
 274             _input_seqs_msa_paramenters_tf.setText( getPhylogeneticInferenceOptions().getMsaPrgParameters() );
 275         }
 276         else {
 277             updateMsaItems();
 278         }
 279         updateMsaProcessingItem();
 280         updateDistanceCalcMethod();
 281         _bootstrap_tf.setText( getPhylogeneticInferenceOptions().getBootstrapSamples() + "" );
 282         _random_seed_tf.setText( getPhylogeneticInferenceOptions().getRandomNumberGeneratorSeed() + "" );
 283     }
 284
 285     private void launch() {
 286         processPerformBootstrapResampling();
 287         if ( _bootstrap_cb.isSelected() ) {
 288             processBootstrapSamplesNumber();
 289             processRandomNumberGeneratorSeed();
 290         }
 291         if ( true ) {
 292             //TODO
 293             processMsaProcessing();
 294         }
 295         processDistanceCalcMethod();
 296         processMsaPrgParameters();
 297         setVisible( false );
 298         _value = JOptionPane.OK_OPTION;
 299     }
 300
 301     private void cancel() {
 302         setVisible( false );
 303         _value = JOptionPane.CANCEL_OPTION;
 304     }
 305
 306     private void processBootstrapSamplesNumber() {
 307         int bootstrap_samples = 0;
 308         try {
 309             bootstrap_samples = Integer.parseInt( _bootstrap_tf.getText().trim() );
 310         }
 311         catch ( final NumberFormatException e ) {
 312             // JOptionPane.showMessageDialog( this, "Could not parse number of bootstrap resamplings from: " +  _bootstrap_tf.getText().trim(), "User Error", JOptionPane.ERROR_MESSAGE );
 313             return;
 314         }
 315         if ( bootstrap_samples >= 0 ) {
 316             getPhylogeneticInferenceOptions().setBootstrapSamples( bootstrap_samples );
 317         }
 318     }
 319
 320     private void processRandomNumberGeneratorSeed() {
 321         long seed = PhylogeneticInferenceOptions.RANDOM_NUMBER_SEED_DEFAULT;
 322         try {
 323             seed = Long.parseLong( _random_seed_tf.getText().trim() );
 324         }
 325         catch ( final NumberFormatException e ) {
 326             return;
 327         }
 328         getPhylogeneticInferenceOptions().setRandomNumberGeneratorSeed( seed );
 329     }
 330
 331     private void processMsaProcessing() {
 332         getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
 333         getPhylogeneticInferenceOptions()
 334                 .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
 335         int min_length = -1;
 336         try {
 337             min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() );
 338         }
 339         catch ( final NumberFormatException e ) {
 340             min_length = -1;
 341         }
 342         if ( min_length > 0 ) {
 343             getPhylogeneticInferenceOptions().setMsaProcessingMinAllowedLength( min_length );
 344         }
 345         double msa_processing_max_allowed_gap_ratio = -1.0;
 346         try {
 347             msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf
 348                     .getText().trim() );
 349         }
 350         catch ( final NumberFormatException e ) {
 351             msa_processing_max_allowed_gap_ratio = -1.0;
 352         }
 353         if ( ( msa_processing_max_allowed_gap_ratio >= 0.0 ) && ( msa_processing_max_allowed_gap_ratio <= 1.0 ) ) {
 354             getPhylogeneticInferenceOptions().setMsaProcessingMaxAllowedGapRatio( msa_processing_max_allowed_gap_ratio );
 355         }
 356     }
 357
 358     private void processDistanceCalcMethod() {
 359         if ( ( _distance_calc_kimura_rb != null ) && _distance_calc_kimura_rb.isSelected() ) {
 360             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.KIMURA_DISTANCE );
 361         }
 362         else if ( ( _distance_calc_poisson_rb != null ) && _distance_calc_poisson_rb.isSelected() ) {
 363             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.POISSON_DISTANCE );
 364         }
 365         else if ( ( _distance_calc_fract_dissimilarity_rb != null )
 366                 && _distance_calc_fract_dissimilarity_rb.isSelected() ) {
 367             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.FRACTIONAL_DISSIMILARITY );
 368         }
 369     }
 370
 371     private void processPerformBootstrapResampling() {
 372         getPhylogeneticInferenceOptions().setPerformBootstrapResampling( _bootstrap_cb.isSelected() );
 373     }
 374
 375     private void processMsaPrgParameters() {
 376         if ( _input_seqs_msa_paramenters_tf != null ) {
 377             getPhylogeneticInferenceOptions().setMsaPrgParameters( _input_seqs_msa_paramenters_tf.getText() );
 378         }
 379     }
 380
 381     private void readInputFile() {
 382         getParentFrame().readMsaFromFile();
 383         updateMsaItems();
 384     }
 385
 386     private void readInputSeqsFile() {
 387         getParentFrame().readSeqsFromFile();
 388         updateSeqsItems();
 389     }
 390
 391     private void updateDistanceCalcMethod() {
 392         switch ( getPhylogeneticInferenceOptions().getPwdDistanceMethod() ) {
 393             case KIMURA_DISTANCE:
 394                 _distance_calc_kimura_rb.setSelected( true );
 395                 break;
 396             case POISSON_DISTANCE:
 397                 _distance_calc_poisson_rb.setSelected( true );
 398                 break;
 399             case FRACTIONAL_DISSIMILARITY:
 400                 _distance_calc_fract_dissimilarity_rb.setSelected( true );
 401                 break;
 402             default:
 403                 throw new RuntimeException( "invalid distance calc method" );
 404         }
 405     }
 406
 407     private void updateMsaProcessingItem() {
 408         _execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
 409         _msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
 410                 .isMsaProcessingRemoveAllGapColumns() );
 411         if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
 412             _msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
 413         }
 414         if ( _opts.getMsaProcessingMinAllowedLength() > 0 ) {
 415             _msa_processing_min_allowed_length_tf.setText( _opts.getMsaProcessingMinAllowedLength() + "" );
 416         }
 417     }
 418
 419     private void updateMsaItems() {
 420         if ( getParentFrame().getMsa() != null ) {
 421             _input_msa_file_tf.setText( getParentFrame().getMsaFile().toString() );
 422             _msa_length_tf.setText( getParentFrame().getMsa().getLength() + "" );
 423             _msa_size_tf.setText( getParentFrame().getMsa().getNumberOfSequences() + "" );
 424             _msa_type_tf.setText( getParentFrame().getMsa().getType() + "" );
 425             _input_msa_file_tf.setEnabled( true );
 426             _msa_length_tf.setEnabled( true );
 427             _msa_size_tf.setEnabled( true );
 428             _msa_type_tf.setEnabled( true );
 429             _launch_btn.setEnabled( true );
 430         }
 431         else {
 432             _input_msa_file_tf.setText( "" );
 433             _msa_length_tf.setText( "" );
 434             _msa_size_tf.setText( "" );
 435             _msa_type_tf.setText( "" );
 436             _input_msa_file_tf.setEnabled( false );
 437             _msa_length_tf.setEnabled( false );
 438             _msa_size_tf.setEnabled( false );
 439             _msa_type_tf.setEnabled( false );
 440             _launch_btn.setEnabled( false );
 441         }
 442     }
 443
 444     private void updateSeqsItems() {
 445         if ( getParentFrame().getSeqs() != null ) {
 446             final DescriptiveStatistics stats = calcSequenceStats( getParentFrame().getSeqs() );
 447             _input_seqs_tf.setText( getParentFrame().getSeqsFile().toString() );
 448             _input_seqs_median_length_tf.setText( ( int ) stats.median() + "" );
 449             _input_seqs_min_length_tf.setText( ( int ) stats.getMin() + "" );
 450             _input_seqs_max_length_tf.setText( ( int ) stats.getMax() + "" );
 451             _input_seqs_number_tf.setText( getParentFrame().getSeqs().size() + "" );
 452             _input_seqs_type_tf.setText( getParentFrame().getSeqs().get( 0 ).getType() + "" );
 453             _input_seqs_tf.setEnabled( true );
 454             _input_seqs_median_length_tf.setEnabled( true );
 455             _input_seqs_min_length_tf.setEnabled( true );
 456             _input_seqs_max_length_tf.setEnabled( true );
 457             _input_seqs_number_tf.setEnabled( true );
 458             _input_seqs_type_tf.setEnabled( true );
 459             _launch_btn.setEnabled( true );
 460         }
 461         else {
 462             _input_seqs_tf.setText( "" );
 463             _input_seqs_median_length_tf.setText( "" );
 464             _input_seqs_min_length_tf.setText( "" );
 465             _input_seqs_max_length_tf.setText( "" );
 466             _input_seqs_number_tf.setText( "" );
 467             _input_seqs_type_tf.setText( "" );
 468             _input_seqs_tf.setEnabled( false );
 469             _input_seqs_median_length_tf.setEnabled( false );
 470             _input_seqs_min_length_tf.setEnabled( false );
 471             _input_seqs_max_length_tf.setEnabled( false );
 472             _input_seqs_number_tf.setEnabled( false );
 473             _input_seqs_type_tf.setEnabled( false );
 474             _launch_btn.setEnabled( false );
 475         }
 476     }
 477
 478     DescriptiveStatistics calcSequenceStats( final List<Sequence> seqs ) {
 479         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 480         for( final Sequence s : seqs ) {
 481             stats.addValue( s.getLength() );
 482         }
 483         return stats;
 484     }
 485 }