forester/java/src/org/forester/archaeopteryx/tools/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: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.archaeopteryx.tools;
  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.archaeopteryx.AptxUtil;
  49 import org.forester.archaeopteryx.MainFrameApplication;
  50 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
  51 import org.forester.sequence.MolecularSequence;
  52 import org.forester.util.BasicDescriptiveStatistics;
  53 import org.forester.util.DescriptiveStatistics;
  54
  55 public class PhyloInferenceDialog extends JDialog implements ActionListener {
  56
  57     private static final long                  serialVersionUID = 8337543508238133614L;
  58     private final JPanel                       _pnl;
  59     private final JButton                      _launch_btn;
  60     private final JButton                      _cancel_btn;
  61     private final JFormattedTextField          _bootstrap_tf;
  62     private final JCheckBox                    _bootstrap_cb;
  63     private final PhylogeneticInferenceOptions _opts;
  64     private JTextField                         _input_msa_file_tf;
  65     private JButton                            _select_input_msa_btn;
  66     private final MainFrameApplication         _parent_frame;
  67     private JTextField                         _msa_length_tf;
  68     private JTextField                         _msa_size_tf;
  69     private JTextField                         _msa_type_tf;
  70     private final JRadioButton                 _distance_calc_kimura_rb;
  71     private final JRadioButton                 _distance_calc_poisson_rb;
  72     private final JRadioButton                 _distance_calc_fract_dissimilarity_rb;
  73     private int                                _value           = JOptionPane.CANCEL_OPTION;
  74     private JTextField                         _input_seqs_tf;
  75     private JButton                            _select_input_seqs_btn;
  76     private JTextField                         _input_seqs_number_tf;
  77     private JTextField                         _input_seqs_median_length_tf;
  78     private JTextField                         _input_seqs_min_length_tf;
  79     private JTextField                         _input_seqs_max_length_tf;
  80     private JTextField                         _input_seqs_type_tf;
  81     private JTextField                         _mafft_paramenters_tf;
  82     private JTextField                         _msa_processing_max_allowed_gap_ratio_tf;
  83     private JTextField                         _msa_processing_min_allowed_length_tf;
  84     private JTextField                         _random_seed_tf;
  85     private JCheckBox                          _execute_msa_processing_cb;
  86     private JCheckBox                          _msa_processing_remove_all_gap_columns_cb;
  87     private JCheckBox                          _mafft_cb;
  88     private JCheckBox                          _save_pwd_file_cb;
  89     private JCheckBox                          _save_processed_msa_cb;
  90     private JCheckBox                          _save_original_msa_cb;
  91     private JTextField                         _pwd_outfile_tf;
  92     private JTextField                         _processed_msa_outfile_tf;
  93     private JTextField                         _original_msa_outfile_tf;
  94
  95     public PhyloInferenceDialog( final MainFrameApplication frame,
  96                                  final PhylogeneticInferenceOptions options,
  97                                  final boolean from_unaligned_seqs ) {
  98         super( frame, true );
  99         setVisible( false );
 100         _parent_frame = frame;
 101         _opts = options;
 102         _pnl = new JPanel();
 103         getContentPane().add( _pnl );
 104         final BoxLayout box_layout = new BoxLayout( _pnl, BoxLayout.PAGE_AXIS );
 105         _pnl.setLayout( box_layout );
 106         if ( from_unaligned_seqs ) {
 107             setTitle( "Phylogenetic Inference (including multiple sequence alignment)" );
 108             final JPanel inputfile_pnl_1 = new JPanel();
 109             final JPanel inputfile_pnl_2 = new JPanel();
 110             final JPanel inputfile_pnl_3 = new JPanel();
 111             final JPanel inputfile_pnl_4 = new JPanel();
 112             inputfile_pnl_1.setLayout( new FlowLayout() );
 113             inputfile_pnl_2.setLayout( new FlowLayout() );
 114             inputfile_pnl_3.setLayout( new FlowLayout() );
 115             inputfile_pnl_4.setLayout( new FlowLayout() );
 116             inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
 117             inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
 118             inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
 119             inputfile_pnl_2.add( new JLabel( "Sequences: " ) );
 120             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 121             inputfile_pnl_2.add( _input_seqs_number_tf = new JTextField() );
 122             inputfile_pnl_2.add( new JLabel( "Length: median:" ) );
 123             inputfile_pnl_2.add( _input_seqs_median_length_tf = new JTextField() );
 124             inputfile_pnl_2.add( new JLabel( "min:" ) );
 125             inputfile_pnl_2.add( _input_seqs_min_length_tf = new JTextField() );
 126             inputfile_pnl_2.add( new JLabel( "max:" ) );
 127             inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
 128             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 129             inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
 130             inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT" ) );
 131             inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
 132             inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
 133             _input_seqs_median_length_tf.setColumns( 4 );
 134             _input_seqs_min_length_tf.setColumns( 4 );
 135             _input_seqs_max_length_tf.setColumns( 4 );
 136             _input_seqs_number_tf.setColumns( 4 );
 137             _input_seqs_type_tf.setColumns( 2 );
 138             _input_seqs_tf.setColumns( 20 );
 139             _input_seqs_tf.setEditable( false );
 140             _input_seqs_median_length_tf.setEditable( false );
 141             _input_seqs_min_length_tf.setEditable( false );
 142             _input_seqs_max_length_tf.setEditable( false );
 143             _input_seqs_number_tf.setEditable( false );
 144             _input_seqs_type_tf.setEditable( false );
 145             _mafft_paramenters_tf.setColumns( 26 );
 146             _mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
 147             _select_input_seqs_btn.addActionListener( this );
 148             _pnl.add( inputfile_pnl_1 );
 149             _pnl.add( inputfile_pnl_2 );
 150             _pnl.add( inputfile_pnl_3 );
 151             _pnl.add( inputfile_pnl_4 );
 152         }
 153         else {
 154             setTitle( "Phylogenetic Inference (from already aligned sequences) " );
 155             // Inputfile (MSA):
 156             final JPanel inputfile_pnl_1 = new JPanel();
 157             final JPanel inputfile_pnl_2 = new JPanel();
 158             inputfile_pnl_1.setLayout( new FlowLayout() );
 159             inputfile_pnl_2.setLayout( new FlowLayout() );
 160             inputfile_pnl_1.add( new JLabel( "Input MSA File:" ) );
 161             inputfile_pnl_1.add( _input_msa_file_tf = new JTextField() );
 162             inputfile_pnl_1.add( _select_input_msa_btn = new JButton( "Select Input File" ) );
 163             inputfile_pnl_2.add( new JLabel( "MSA: " ) );
 164             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 165             inputfile_pnl_2.add( _msa_size_tf = new JTextField() );
 166             inputfile_pnl_2.add( new JLabel( "Length:" ) );
 167             inputfile_pnl_2.add( _msa_length_tf = new JTextField() );
 168             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 169             inputfile_pnl_2.add( _msa_type_tf = new JTextField() );
 170             _msa_length_tf.setColumns( 4 );
 171             _msa_size_tf.setColumns( 4 );
 172             _msa_type_tf.setColumns( 2 );
 173             _input_msa_file_tf.setColumns( 20 );
 174             _input_msa_file_tf.setEditable( false );
 175             _msa_length_tf.setEditable( false );
 176             _msa_size_tf.setEditable( false );
 177             _msa_type_tf.setEditable( false );
 178             _select_input_msa_btn.addActionListener( this );
 179             _pnl.add( inputfile_pnl_1 );
 180             _pnl.add( inputfile_pnl_2 );
 181         }
 182         //
 183         final JPanel inputfile_pnl_4 = new JPanel();
 184         inputfile_pnl_4.setLayout( new FlowLayout() );
 185         inputfile_pnl_4.add( new JLabel( "MSA Processing: " ) );
 186         inputfile_pnl_4.add( _execute_msa_processing_cb = new JCheckBox( "Process MSA" ) );
 187         inputfile_pnl_4.add( _msa_processing_remove_all_gap_columns_cb = new JCheckBox( "Remove all gap columns" ) );
 188         inputfile_pnl_4.add( new JLabel( "Max allowed gap ratio: " ) );
 189         inputfile_pnl_4.add( _msa_processing_max_allowed_gap_ratio_tf = new JTextField() );
 190         inputfile_pnl_4.add( new JLabel( "Min allowed non-gap sequence length: " ) );
 191         inputfile_pnl_4.add( _msa_processing_min_allowed_length_tf = new JTextField() );
 192         _msa_processing_max_allowed_gap_ratio_tf.setColumns( 4 );
 193         _msa_processing_min_allowed_length_tf.setColumns( 4 );
 194         final Border b = new LineBorder( Color.DARK_GRAY );
 195         inputfile_pnl_4.setBorder( b );
 196         _pnl.add( inputfile_pnl_4 );
 197         //
 198         // Distance calculation:
 199         // TODO if type==AA...
 200         final JPanel distance_calc_pnl_1 = new JPanel();
 201         distance_calc_pnl_1.setLayout( new FlowLayout() );
 202         distance_calc_pnl_1.add( new JLabel( "Distance calculation:" ) );
 203         distance_calc_pnl_1.add( _distance_calc_kimura_rb = new JRadioButton( "Kimura correction" ) );
 204         distance_calc_pnl_1.add( _distance_calc_poisson_rb = new JRadioButton( "Poisson" ) );
 205         distance_calc_pnl_1
 206         .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) );
 207         final ButtonGroup distance_calc_group_1 = new ButtonGroup();
 208         distance_calc_group_1.add( _distance_calc_kimura_rb );
 209         distance_calc_group_1.add( _distance_calc_poisson_rb );
 210         distance_calc_group_1.add( _distance_calc_fract_dissimilarity_rb );
 211         _pnl.add( distance_calc_pnl_1 );
 212         // Bootstrap resampling:
 213         final JPanel bootstrap_pnl = new JPanel();
 214         bootstrap_pnl.setLayout( new FlowLayout() );
 215         bootstrap_pnl.add( _bootstrap_cb = new JCheckBox( "Perform Bootstrap Resampling" ) );
 216         bootstrap_pnl.add( new JLabel( "Number of Bootstrap Samples:" ) );
 217         bootstrap_pnl.add( _bootstrap_tf = new JFormattedTextField( AptxUtil.createMaskFormatter( "###" ) ) );
 218         _bootstrap_tf.setColumns( 4 );
 219         // TODO see
 220         // http://download.oracle.com/javase/tutorial/uiswing/components/formattedtextfield.html
 221         // _bootstrap_tf.setColumns( 4 );
 222         bootstrap_pnl.add( new JLabel( "Random Seed:" ) );
 223         bootstrap_pnl.add( _random_seed_tf = new JTextField() );
 224         _random_seed_tf.setColumns( 4 );
 225         _pnl.add( bootstrap_pnl );
 226         final JPanel launch_pnl = new JPanel();
 227         launch_pnl.setLayout( new FlowLayout() );
 228         _launch_btn = new JButton( "Go!" );
 229         _launch_btn.addActionListener( this );
 230         launch_pnl.add( _launch_btn );
 231         _cancel_btn = new JButton( "Cancel" );
 232         _cancel_btn.addActionListener( this );
 233         launch_pnl.add( _cancel_btn );
 234         _pnl.add( launch_pnl );
 235         initializeValues( from_unaligned_seqs );
 236         pack();
 237         setLocationRelativeTo( getParentFrame() );
 238         setResizable( false );
 239     }
 240
 241     @Override
 242     public void actionPerformed( final ActionEvent e ) {
 243         if ( e.getSource() == _select_input_msa_btn ) {
 244             readInputFile();
 245         }
 246         else if ( e.getSource() == _select_input_seqs_btn ) {
 247             readInputSeqsFile();
 248         }
 249         else if ( e.getSource() == _launch_btn ) {
 250             launch();
 251         }
 252         else if ( e.getSource() == _cancel_btn ) {
 253             cancel();
 254         }
 255     }
 256
 257     public void activate() {
 258         setVisible( true );
 259     }
 260
 261     private MainFrameApplication getParentFrame() {
 262         return _parent_frame;
 263     }
 264
 265     public PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
 266         return _opts;
 267     }
 268
 269     public int getValue() {
 270         return _value;
 271     }
 272
 273     private void initializeValues( final boolean from_unaligned_seqs ) {
 274         _value = JOptionPane.CANCEL_OPTION;
 275         if ( from_unaligned_seqs ) {
 276             updateSeqsItems();
 277         }
 278         else {
 279             updateMsaItems();
 280         }
 281         updateMsaProcessingItem();
 282         updateDistanceCalcMethod();
 283         _bootstrap_tf.setText( getPhylogeneticInferenceOptions().getBootstrapSamples() + "" );
 284         _random_seed_tf.setText( getPhylogeneticInferenceOptions().getRandomNumberGeneratorSeed() + "" );
 285     }
 286
 287     private void launch() {
 288         processPerformBootstrapResampling();
 289         if ( _bootstrap_cb.isSelected() ) {
 290             processBootstrapSamplesNumber();
 291             processRandomNumberGeneratorSeed();
 292         }
 293         if ( true ) {
 294             //TODO
 295             processMsaProcessing();
 296         }
 297         processDistanceCalcMethod();
 298         processMsaPrgParameters();
 299         setVisible( false );
 300         _value = JOptionPane.OK_OPTION;
 301     }
 302
 303     private void cancel() {
 304         setVisible( false );
 305         _value = JOptionPane.CANCEL_OPTION;
 306     }
 307
 308     private void processBootstrapSamplesNumber() {
 309         int bootstrap_samples = 0;
 310         try {
 311             bootstrap_samples = Integer.parseInt( _bootstrap_tf.getText().trim() );
 312         }
 313         catch ( final NumberFormatException e ) {
 314             // JOptionPane.showMessageDialog( this, "Could not parse number of bootstrap resamplings from: " +  _bootstrap_tf.getText().trim(), "User Error", JOptionPane.ERROR_MESSAGE );
 315             return;
 316         }
 317         if ( bootstrap_samples >= 0 ) {
 318             getPhylogeneticInferenceOptions().setBootstrapSamples( bootstrap_samples );
 319         }
 320     }
 321
 322     private void processRandomNumberGeneratorSeed() {
 323         long seed = PhylogeneticInferenceOptions.RANDOM_NUMBER_SEED_DEFAULT;
 324         try {
 325             seed = Long.parseLong( _random_seed_tf.getText().trim() );
 326         }
 327         catch ( final NumberFormatException e ) {
 328             return;
 329         }
 330         getPhylogeneticInferenceOptions().setRandomNumberGeneratorSeed( seed );
 331     }
 332
 333     private void processMsaProcessing() {
 334         getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
 335         getPhylogeneticInferenceOptions()
 336         .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
 337         int min_length = -1;
 338         try {
 339             min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() );
 340         }
 341         catch ( final NumberFormatException e ) {
 342             min_length = -1;
 343         }
 344         if ( min_length > 0 ) {
 345             getPhylogeneticInferenceOptions().setMsaProcessingMinAllowedLength( min_length );
 346         }
 347         double msa_processing_max_allowed_gap_ratio = -1.0;
 348         try {
 349             msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf
 350                                                                        .getText().trim() );
 351         }
 352         catch ( final NumberFormatException e ) {
 353             msa_processing_max_allowed_gap_ratio = -1.0;
 354         }
 355         if ( ( msa_processing_max_allowed_gap_ratio >= 0.0 ) && ( msa_processing_max_allowed_gap_ratio <= 1.0 ) ) {
 356             getPhylogeneticInferenceOptions().setMsaProcessingMaxAllowedGapRatio( msa_processing_max_allowed_gap_ratio );
 357         }
 358     }
 359
 360     private void processDistanceCalcMethod() {
 361         if ( ( _distance_calc_kimura_rb != null ) && _distance_calc_kimura_rb.isSelected() ) {
 362             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.KIMURA_DISTANCE );
 363         }
 364         else if ( ( _distance_calc_poisson_rb != null ) && _distance_calc_poisson_rb.isSelected() ) {
 365             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.POISSON_DISTANCE );
 366         }
 367         else if ( ( _distance_calc_fract_dissimilarity_rb != null )
 368                 && _distance_calc_fract_dissimilarity_rb.isSelected() ) {
 369             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.FRACTIONAL_DISSIMILARITY );
 370         }
 371     }
 372
 373     private void processPerformBootstrapResampling() {
 374         getPhylogeneticInferenceOptions().setPerformBootstrapResampling( _bootstrap_cb.isSelected() );
 375     }
 376
 377     private void processMsaPrgParameters() {
 378         if ( _mafft_paramenters_tf != null ) {
 379             getPhylogeneticInferenceOptions().setMsaPrgParameters( _mafft_paramenters_tf.getText() );
 380         }
 381     }
 382
 383     private void readInputFile() {
 384         getParentFrame().readMsaFromFile();
 385         updateMsaItems();
 386     }
 387
 388     private void readInputSeqsFile() {
 389         getParentFrame().readSeqsFromFileforPI();
 390         updateSeqsItems();
 391     }
 392
 393     private void updateDistanceCalcMethod() {
 394         switch ( getPhylogeneticInferenceOptions().getPwdDistanceMethod() ) {
 395             case KIMURA_DISTANCE:
 396                 _distance_calc_kimura_rb.setSelected( true );
 397                 break;
 398             case POISSON_DISTANCE:
 399                 _distance_calc_poisson_rb.setSelected( true );
 400                 break;
 401             case FRACTIONAL_DISSIMILARITY:
 402                 _distance_calc_fract_dissimilarity_rb.setSelected( true );
 403                 break;
 404             default:
 405                 throw new RuntimeException( "invalid distance calc method" );
 406         }
 407     }
 408
 409     private void updateMsaProcessingItem() {
 410         _execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
 411         _msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
 412                                                                .isMsaProcessingRemoveAllGapColumns() );
 413         if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
 414             _msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
 415         }
 416         if ( _opts.getMsaProcessingMinAllowedLength() > 0 ) {
 417             _msa_processing_min_allowed_length_tf.setText( _opts.getMsaProcessingMinAllowedLength() + "" );
 418         }
 419     }
 420
 421     private void updateMsaItems() {
 422         if ( getParentFrame().getMsa() != null ) {
 423             _input_msa_file_tf.setText( getParentFrame().getMsaFile().toString() );
 424             _msa_length_tf.setText( getParentFrame().getMsa().getLength() + "" );
 425             _msa_size_tf.setText( getParentFrame().getMsa().getNumberOfSequences() + "" );
 426             _msa_type_tf.setText( getParentFrame().getMsa().getType() + "" );
 427             _input_msa_file_tf.setEnabled( true );
 428             _msa_length_tf.setEnabled( true );
 429             _msa_size_tf.setEnabled( true );
 430             _msa_type_tf.setEnabled( true );
 431             _launch_btn.setEnabled( true );
 432         }
 433         else {
 434             _input_msa_file_tf.setText( "" );
 435             _msa_length_tf.setText( "" );
 436             _msa_size_tf.setText( "" );
 437             _msa_type_tf.setText( "" );
 438             _input_msa_file_tf.setEnabled( false );
 439             _msa_length_tf.setEnabled( false );
 440             _msa_size_tf.setEnabled( false );
 441             _msa_type_tf.setEnabled( false );
 442             _launch_btn.setEnabled( false );
 443         }
 444     }
 445
 446     private void updateSeqsItems() {
 447         if ( getParentFrame().getSeqs() != null ) {
 448             final DescriptiveStatistics stats = calcSequenceStats( getParentFrame().getSeqs() );
 449             _input_seqs_tf.setText( getParentFrame().getSeqsFile().toString() );
 450             _input_seqs_median_length_tf.setText( ( int ) stats.median() + "" );
 451             _input_seqs_min_length_tf.setText( ( int ) stats.getMin() + "" );
 452             _input_seqs_max_length_tf.setText( ( int ) stats.getMax() + "" );
 453             _input_seqs_number_tf.setText( getParentFrame().getSeqs().size() + "" );
 454             _input_seqs_type_tf.setText( getParentFrame().getSeqs().get( 0 ).getType() + "" );
 455             _input_seqs_tf.setEnabled( true );
 456             _input_seqs_median_length_tf.setEnabled( true );
 457             _input_seqs_min_length_tf.setEnabled( true );
 458             _input_seqs_max_length_tf.setEnabled( true );
 459             _input_seqs_number_tf.setEnabled( true );
 460             _input_seqs_type_tf.setEnabled( true );
 461             _launch_btn.setEnabled( true );
 462         }
 463         else {
 464             _input_seqs_tf.setText( "" );
 465             _input_seqs_median_length_tf.setText( "" );
 466             _input_seqs_min_length_tf.setText( "" );
 467             _input_seqs_max_length_tf.setText( "" );
 468             _input_seqs_number_tf.setText( "" );
 469             _input_seqs_type_tf.setText( "" );
 470             _input_seqs_tf.setEnabled( false );
 471             _input_seqs_median_length_tf.setEnabled( false );
 472             _input_seqs_min_length_tf.setEnabled( false );
 473             _input_seqs_max_length_tf.setEnabled( false );
 474             _input_seqs_number_tf.setEnabled( false );
 475             _input_seqs_type_tf.setEnabled( false );
 476             _launch_btn.setEnabled( false );
 477         }
 478     }
 479
 480     DescriptiveStatistics calcSequenceStats( final List<MolecularSequence> seqs ) {
 481         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 482         for( final MolecularSequence s : seqs ) {
 483             stats.addValue( s.getLength() );
 484         }
 485         return stats;
 486     }
 487 }