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     @Override
 239     public void actionPerformed( final ActionEvent e ) {
 240         if ( e.getSource() == _select_input_msa_btn ) {
 241             readInputFile();
 242         }
 243         else if ( e.getSource() == _select_input_seqs_btn ) {
 244             readInputSeqsFile();
 245         }
 246         else if ( e.getSource() == _launch_btn ) {
 247             launch();
 248         }
 249         else if ( e.getSource() == _cancel_btn ) {
 250             cancel();
 251         }
 252     }
 253
 254     public void activate() {
 255         setVisible( true );
 256     }
 257
 258     private MainFrameApplication getParentFrame() {
 259         return _parent_frame;
 260     }
 261
 262     public PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
 263         return _opts;
 264     }
 265
 266     public int getValue() {
 267         return _value;
 268     }
 269
 270     private void initializeValues( final boolean from_unaligned_seqs ) {
 271         _value = JOptionPane.CANCEL_OPTION;
 272         if ( from_unaligned_seqs ) {
 273             updateSeqsItems();
 274             _input_seqs_msa_program_name_tf.setText( getPhylogeneticInferenceOptions().getMsaPrg() );
 275             _input_seqs_msa_paramenters_tf.setText( getPhylogeneticInferenceOptions().getMsaPrgParameters() );
 276         }
 277         else {
 278             updateMsaItems();
 279         }
 280         updateMsaProcessingItem();
 281         updateDistanceCalcMethod();
 282         _bootstrap_tf.setText( getPhylogeneticInferenceOptions().getBootstrapSamples() + "" );
 283         _random_seed_tf.setText( getPhylogeneticInferenceOptions().getRandomNumberGeneratorSeed() + "" );
 284     }
 285
 286     private void launch() {
 287         processPerformBootstrapResampling();
 288         if ( _bootstrap_cb.isSelected() ) {
 289             processBootstrapSamplesNumber();
 290             processRandomNumberGeneratorSeed();
 291         }
 292         if ( true ) {
 293             //TODO
 294             processMsaProcessing();
 295         }
 296         processDistanceCalcMethod();
 297         processMsaPrgParameters();
 298         setVisible( false );
 299         _value = JOptionPane.OK_OPTION;
 300     }
 301
 302     private void cancel() {
 303         setVisible( false );
 304         _value = JOptionPane.CANCEL_OPTION;
 305     }
 306
 307     private void processBootstrapSamplesNumber() {
 308         int bootstrap_samples = 0;
 309         try {
 310             bootstrap_samples = Integer.parseInt( _bootstrap_tf.getText().trim() );
 311         }
 312         catch ( final NumberFormatException e ) {
 313             // JOptionPane.showMessageDialog( this, "Could not parse number of bootstrap resamplings from: " +  _bootstrap_tf.getText().trim(), "User Error", JOptionPane.ERROR_MESSAGE );
 314             return;
 315         }
 316         if ( bootstrap_samples >= 0 ) {
 317             getPhylogeneticInferenceOptions().setBootstrapSamples( bootstrap_samples );
 318         }
 319     }
 320
 321     private void processRandomNumberGeneratorSeed() {
 322         long seed = PhylogeneticInferenceOptions.RANDOM_NUMBER_SEED_DEFAULT;
 323         try {
 324             seed = Long.parseLong( _random_seed_tf.getText().trim() );
 325         }
 326         catch ( final NumberFormatException e ) {
 327             return;
 328         }
 329         getPhylogeneticInferenceOptions().setRandomNumberGeneratorSeed( seed );
 330     }
 331
 332     private void processMsaProcessing() {
 333         getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
 334         getPhylogeneticInferenceOptions()
 335                 .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
 336         int min_length = -1;
 337         try {
 338             min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() );
 339         }
 340         catch ( final NumberFormatException e ) {
 341             min_length = -1;
 342         }
 343         if ( min_length > 0 ) {
 344             getPhylogeneticInferenceOptions().setMsaProcessingMinAllowedLength( min_length );
 345         }
 346         double msa_processing_max_allowed_gap_ratio = -1.0;
 347         try {
 348             msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf
 349                     .getText().trim() );
 350         }
 351         catch ( final NumberFormatException e ) {
 352             msa_processing_max_allowed_gap_ratio = -1.0;
 353         }
 354         if ( ( msa_processing_max_allowed_gap_ratio >= 0.0 ) && ( msa_processing_max_allowed_gap_ratio <= 1.0 ) ) {
 355             getPhylogeneticInferenceOptions().setMsaProcessingMaxAllowedGapRatio( msa_processing_max_allowed_gap_ratio );
 356         }
 357     }
 358
 359     private void processDistanceCalcMethod() {
 360         if ( ( _distance_calc_kimura_rb != null ) && _distance_calc_kimura_rb.isSelected() ) {
 361             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.KIMURA_DISTANCE );
 362         }
 363         else if ( ( _distance_calc_poisson_rb != null ) && _distance_calc_poisson_rb.isSelected() ) {
 364             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.POISSON_DISTANCE );
 365         }
 366         else if ( ( _distance_calc_fract_dissimilarity_rb != null )
 367                 && _distance_calc_fract_dissimilarity_rb.isSelected() ) {
 368             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.FRACTIONAL_DISSIMILARITY );
 369         }
 370     }
 371
 372     private void processPerformBootstrapResampling() {
 373         getPhylogeneticInferenceOptions().setPerformBootstrapResampling( _bootstrap_cb.isSelected() );
 374     }
 375
 376     private void processMsaPrgParameters() {
 377         if ( _input_seqs_msa_paramenters_tf != null ) {
 378             getPhylogeneticInferenceOptions().setMsaPrgParameters( _input_seqs_msa_paramenters_tf.getText() );
 379         }
 380     }
 381
 382     private void readInputFile() {
 383         getParentFrame().readMsaFromFile();
 384         updateMsaItems();
 385     }
 386
 387     private void readInputSeqsFile() {
 388         getParentFrame().readSeqsFromFile();
 389         updateSeqsItems();
 390     }
 391
 392     private void updateDistanceCalcMethod() {
 393         switch ( getPhylogeneticInferenceOptions().getPwdDistanceMethod() ) {
 394             case KIMURA_DISTANCE:
 395                 _distance_calc_kimura_rb.setSelected( true );
 396                 break;
 397             case POISSON_DISTANCE:
 398                 _distance_calc_poisson_rb.setSelected( true );
 399                 break;
 400             case FRACTIONAL_DISSIMILARITY:
 401                 _distance_calc_fract_dissimilarity_rb.setSelected( true );
 402                 break;
 403             default:
 404                 throw new RuntimeException( "invalid distance calc method" );
 405         }
 406     }
 407
 408     private void updateMsaProcessingItem() {
 409         _execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
 410         _msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
 411                 .isMsaProcessingRemoveAllGapColumns() );
 412         if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
 413             _msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
 414         }
 415         if ( _opts.getMsaProcessingMinAllowedLength() > 0 ) {
 416             _msa_processing_min_allowed_length_tf.setText( _opts.getMsaProcessingMinAllowedLength() + "" );
 417         }
 418     }
 419
 420     private void updateMsaItems() {
 421         if ( getParentFrame().getMsa() != null ) {
 422             _input_msa_file_tf.setText( getParentFrame().getMsaFile().toString() );
 423             _msa_length_tf.setText( getParentFrame().getMsa().getLength() + "" );
 424             _msa_size_tf.setText( getParentFrame().getMsa().getNumberOfSequences() + "" );
 425             _msa_type_tf.setText( getParentFrame().getMsa().getType() + "" );
 426             _input_msa_file_tf.setEnabled( true );
 427             _msa_length_tf.setEnabled( true );
 428             _msa_size_tf.setEnabled( true );
 429             _msa_type_tf.setEnabled( true );
 430             _launch_btn.setEnabled( true );
 431         }
 432         else {
 433             _input_msa_file_tf.setText( "" );
 434             _msa_length_tf.setText( "" );
 435             _msa_size_tf.setText( "" );
 436             _msa_type_tf.setText( "" );
 437             _input_msa_file_tf.setEnabled( false );
 438             _msa_length_tf.setEnabled( false );
 439             _msa_size_tf.setEnabled( false );
 440             _msa_type_tf.setEnabled( false );
 441             _launch_btn.setEnabled( false );
 442         }
 443     }
 444
 445     private void updateSeqsItems() {
 446         if ( getParentFrame().getSeqs() != null ) {
 447             final DescriptiveStatistics stats = calcSequenceStats( getParentFrame().getSeqs() );
 448             _input_seqs_tf.setText( getParentFrame().getSeqsFile().toString() );
 449             _input_seqs_median_length_tf.setText( ( int ) stats.median() + "" );
 450             _input_seqs_min_length_tf.setText( ( int ) stats.getMin() + "" );
 451             _input_seqs_max_length_tf.setText( ( int ) stats.getMax() + "" );
 452             _input_seqs_number_tf.setText( getParentFrame().getSeqs().size() + "" );
 453             _input_seqs_type_tf.setText( getParentFrame().getSeqs().get( 0 ).getType() + "" );
 454             _input_seqs_tf.setEnabled( true );
 455             _input_seqs_median_length_tf.setEnabled( true );
 456             _input_seqs_min_length_tf.setEnabled( true );
 457             _input_seqs_max_length_tf.setEnabled( true );
 458             _input_seqs_number_tf.setEnabled( true );
 459             _input_seqs_type_tf.setEnabled( true );
 460             _launch_btn.setEnabled( true );
 461         }
 462         else {
 463             _input_seqs_tf.setText( "" );
 464             _input_seqs_median_length_tf.setText( "" );
 465             _input_seqs_min_length_tf.setText( "" );
 466             _input_seqs_max_length_tf.setText( "" );
 467             _input_seqs_number_tf.setText( "" );
 468             _input_seqs_type_tf.setText( "" );
 469             _input_seqs_tf.setEnabled( false );
 470             _input_seqs_median_length_tf.setEnabled( false );
 471             _input_seqs_min_length_tf.setEnabled( false );
 472             _input_seqs_max_length_tf.setEnabled( false );
 473             _input_seqs_number_tf.setEnabled( false );
 474             _input_seqs_type_tf.setEnabled( false );
 475             _launch_btn.setEnabled( false );
 476         }
 477     }
 478
 479     DescriptiveStatistics calcSequenceStats( final List<Sequence> seqs ) {
 480         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 481         for( final Sequence s : seqs ) {
 482             stats.addValue( s.getLength() );
 483         }
 484         return stats;
 485     }
 486 }