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.Frame;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ActionListener;
  33 import java.util.List;
  34
  35 import javax.swing.BoxLayout;
  36 import javax.swing.ButtonGroup;
  37 import javax.swing.JButton;
  38 import javax.swing.JCheckBox;
  39 import javax.swing.JDialog;
  40 import javax.swing.JFormattedTextField;
  41 import javax.swing.JLabel;
  42 import javax.swing.JOptionPane;
  43 import javax.swing.JPanel;
  44 import javax.swing.JRadioButton;
  45 import javax.swing.JTextField;
  46 import javax.swing.border.Border;
  47 import javax.swing.border.LineBorder;
  48
  49 import org.forester.archaeopteryx.AptxUtil;
  50 import org.forester.archaeopteryx.MainFrameApplication;
  51 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
  52 import org.forester.sequence.MolecularSequence;
  53 import org.forester.util.BasicDescriptiveStatistics;
  54 import org.forester.util.DescriptiveStatistics;
  55
  56 public class PhyloInferenceDialog extends JDialog implements ActionListener {
  57
  58     private static final long                  serialVersionUID = 8337543508238133614L;
  59     private final JPanel                       _pnl;
  60     private final JButton                      _launch_btn;
  61     private final JButton                      _cancel_btn;
  62     private final JFormattedTextField          _bootstrap_tf;
  63     private final JCheckBox                    _bootstrap_cb;
  64     private final PhylogeneticInferenceOptions _opts;
  65     private JTextField                         _input_msa_file_tf;
  66     private JButton                            _select_input_msa_btn;
  67     private final MainFrameApplication         _parent_frame;
  68     private JTextField                         _msa_length_tf;
  69     private JTextField                         _msa_size_tf;
  70     private JTextField                         _msa_type_tf;
  71     private final JRadioButton                 _distance_calc_kimura_rb;
  72     private final JRadioButton                 _distance_calc_poisson_rb;
  73     private final JRadioButton                 _distance_calc_fract_dissimilarity_rb;
  74     private int                                _value           = JOptionPane.CANCEL_OPTION;
  75     private JTextField                         _input_seqs_tf;
  76     private JButton                            _select_input_seqs_btn;
  77     private JTextField                         _input_seqs_number_tf;
  78     private JTextField                         _input_seqs_median_length_tf;
  79     private JTextField                         _input_seqs_min_length_tf;
  80     private JTextField                         _input_seqs_max_length_tf;
  81     private JTextField                         _input_seqs_type_tf;
  82     private JTextField                         _mafft_paramenters_tf;
  83     private JTextField                         _msa_processing_max_allowed_gap_ratio_tf;
  84     private JTextField                         _msa_processing_min_allowed_length_tf;
  85     private JTextField                         _random_seed_tf;
  86     private JCheckBox                          _execute_msa_processing_cb;
  87     private JCheckBox                          _msa_processing_remove_all_gap_columns_cb;
  88     private JCheckBox                          _mafft_cb;
  89     private JCheckBox                          _save_pwd_file_cb;
  90     private JCheckBox                          _save_processed_msa_cb;
  91     private JCheckBox                          _save_original_msa_cb;
  92     private JTextField                         _pwd_outfile_tf;
  93     private JTextField                         _processed_msa_outfile_tf;
  94     private JTextField                         _original_msa_outfile_tf;
  95
  96     public PhyloInferenceDialog( final MainFrameApplication frame,
  97                                  final PhylogeneticInferenceOptions options,
  98                                  final boolean from_unaligned_seqs ) {
  99         super( (Frame) null, true );
 100         setVisible( false );
 101         _parent_frame = frame;
 102         _opts = options;
 103         _pnl = new JPanel();
 104         getContentPane().add( _pnl );
 105         final BoxLayout box_layout = new BoxLayout( _pnl, BoxLayout.PAGE_AXIS );
 106         _pnl.setLayout( box_layout );
 107         if ( from_unaligned_seqs ) {
 108             setTitle( "Phylogenetic Inference (including multiple sequence alignment)" );
 109             final JPanel inputfile_pnl_1 = new JPanel();
 110             final JPanel inputfile_pnl_2 = new JPanel();
 111             final JPanel inputfile_pnl_3 = new JPanel();
 112             final JPanel inputfile_pnl_4 = new JPanel();
 113             inputfile_pnl_1.setLayout( new FlowLayout() );
 114             inputfile_pnl_2.setLayout( new FlowLayout() );
 115             inputfile_pnl_3.setLayout( new FlowLayout() );
 116             inputfile_pnl_4.setLayout( new FlowLayout() );
 117             inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
 118             inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
 119             inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
 120             inputfile_pnl_2.add( new JLabel( "Sequences: " ) );
 121             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 122             inputfile_pnl_2.add( _input_seqs_number_tf = new JTextField() );
 123             inputfile_pnl_2.add( new JLabel( "Length: median:" ) );
 124             inputfile_pnl_2.add( _input_seqs_median_length_tf = new JTextField() );
 125             inputfile_pnl_2.add( new JLabel( "min:" ) );
 126             inputfile_pnl_2.add( _input_seqs_min_length_tf = new JTextField() );
 127             inputfile_pnl_2.add( new JLabel( "max:" ) );
 128             inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
 129             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 130             inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
 131             inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT" ) );
 132             inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
 133             inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
 134             _input_seqs_median_length_tf.setColumns( 4 );
 135             _input_seqs_min_length_tf.setColumns( 4 );
 136             _input_seqs_max_length_tf.setColumns( 4 );
 137             _input_seqs_number_tf.setColumns( 4 );
 138             _input_seqs_type_tf.setColumns( 2 );
 139             _input_seqs_tf.setColumns( 20 );
 140             _input_seqs_tf.setEditable( false );
 141             _input_seqs_median_length_tf.setEditable( false );
 142             _input_seqs_min_length_tf.setEditable( false );
 143             _input_seqs_max_length_tf.setEditable( false );
 144             _input_seqs_number_tf.setEditable( false );
 145             _input_seqs_type_tf.setEditable( false );
 146             _mafft_paramenters_tf.setColumns( 26 );
 147             _mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
 148             _select_input_seqs_btn.addActionListener( this );
 149             _pnl.add( inputfile_pnl_1 );
 150             _pnl.add( inputfile_pnl_2 );
 151             _pnl.add( inputfile_pnl_3 );
 152             _pnl.add( inputfile_pnl_4 );
 153         }
 154         else {
 155             setTitle( "Phylogenetic Inference (from already aligned sequences) " );
 156             // Inputfile (MSA):
 157             final JPanel inputfile_pnl_1 = new JPanel();
 158             final JPanel inputfile_pnl_2 = new JPanel();
 159             inputfile_pnl_1.setLayout( new FlowLayout() );
 160             inputfile_pnl_2.setLayout( new FlowLayout() );
 161             inputfile_pnl_1.add( new JLabel( "Input MSA File:" ) );
 162             inputfile_pnl_1.add( _input_msa_file_tf = new JTextField() );
 163             inputfile_pnl_1.add( _select_input_msa_btn = new JButton( "Select Input File" ) );
 164             inputfile_pnl_2.add( new JLabel( "MSA: " ) );
 165             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 166             inputfile_pnl_2.add( _msa_size_tf = new JTextField() );
 167             inputfile_pnl_2.add( new JLabel( "Length:" ) );
 168             inputfile_pnl_2.add( _msa_length_tf = new JTextField() );
 169             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 170             inputfile_pnl_2.add( _msa_type_tf = new JTextField() );
 171             _msa_length_tf.setColumns( 4 );
 172             _msa_size_tf.setColumns( 4 );
 173             _msa_type_tf.setColumns( 2 );
 174             _input_msa_file_tf.setColumns( 20 );
 175             _input_msa_file_tf.setEditable( false );
 176             _msa_length_tf.setEditable( false );
 177             _msa_size_tf.setEditable( false );
 178             _msa_type_tf.setEditable( false );
 179             _select_input_msa_btn.addActionListener( this );
 180             _pnl.add( inputfile_pnl_1 );
 181             _pnl.add( inputfile_pnl_2 );
 182         }
 183         //
 184         final JPanel inputfile_pnl_4 = new JPanel();
 185         inputfile_pnl_4.setLayout( new FlowLayout() );
 186         inputfile_pnl_4.add( new JLabel( "MSA Processing: " ) );
 187         inputfile_pnl_4.add( _execute_msa_processing_cb = new JCheckBox( "Process MSA" ) );
 188         inputfile_pnl_4.add( _msa_processing_remove_all_gap_columns_cb = new JCheckBox( "Remove all gap columns" ) );
 189         inputfile_pnl_4.add( new JLabel( "Max allowed gap ratio: " ) );
 190         inputfile_pnl_4.add( _msa_processing_max_allowed_gap_ratio_tf = new JTextField() );
 191         inputfile_pnl_4.add( new JLabel( "Min allowed non-gap sequence length: " ) );
 192         inputfile_pnl_4.add( _msa_processing_min_allowed_length_tf = new JTextField() );
 193         _msa_processing_max_allowed_gap_ratio_tf.setColumns( 4 );
 194         _msa_processing_min_allowed_length_tf.setColumns( 4 );
 195         final Border b = new LineBorder( Color.DARK_GRAY );
 196         inputfile_pnl_4.setBorder( b );
 197         _pnl.add( inputfile_pnl_4 );
 198         //
 199         // Distance calculation:
 200         // TODO if type==AA...
 201         final JPanel distance_calc_pnl_1 = new JPanel();
 202         distance_calc_pnl_1.setLayout( new FlowLayout() );
 203         distance_calc_pnl_1.add( new JLabel( "Distance calculation:" ) );
 204         distance_calc_pnl_1.add( _distance_calc_kimura_rb = new JRadioButton( "Kimura correction" ) );
 205         distance_calc_pnl_1.add( _distance_calc_poisson_rb = new JRadioButton( "Poisson" ) );
 206         distance_calc_pnl_1
 207         .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) );
 208         final ButtonGroup distance_calc_group_1 = new ButtonGroup();
 209         distance_calc_group_1.add( _distance_calc_kimura_rb );
 210         distance_calc_group_1.add( _distance_calc_poisson_rb );
 211         distance_calc_group_1.add( _distance_calc_fract_dissimilarity_rb );
 212         _pnl.add( distance_calc_pnl_1 );
 213         // Bootstrap resampling:
 214         final JPanel bootstrap_pnl = new JPanel();
 215         bootstrap_pnl.setLayout( new FlowLayout() );
 216         bootstrap_pnl.add( _bootstrap_cb = new JCheckBox( "Perform Bootstrap Resampling" ) );
 217         bootstrap_pnl.add( new JLabel( "Number of Bootstrap Samples:" ) );
 218         bootstrap_pnl.add( _bootstrap_tf = new JFormattedTextField( AptxUtil.createMaskFormatter( "###" ) ) );
 219         _bootstrap_tf.setColumns( 4 );
 220         // TODO see
 221         // http://download.oracle.com/javase/tutorial/uiswing/components/formattedtextfield.html
 222         // _bootstrap_tf.setColumns( 4 );
 223         bootstrap_pnl.add( new JLabel( "Random Seed:" ) );
 224         bootstrap_pnl.add( _random_seed_tf = new JTextField() );
 225         _random_seed_tf.setColumns( 4 );
 226         _pnl.add( bootstrap_pnl );
 227         final JPanel launch_pnl = new JPanel();
 228         launch_pnl.setLayout( new FlowLayout() );
 229         _launch_btn = new JButton( "Go!" );
 230         _launch_btn.addActionListener( this );
 231         launch_pnl.add( _launch_btn );
 232         _cancel_btn = new JButton( "Cancel" );
 233         _cancel_btn.addActionListener( this );
 234         launch_pnl.add( _cancel_btn );
 235         _pnl.add( launch_pnl );
 236         initializeValues( from_unaligned_seqs );
 237         pack();
 238         setLocationRelativeTo( getParentFrame().getThisFrame() );
 239         setResizable( false );
 240     }
 241
 242
 243
 244     @Override
 245     public void actionPerformed( final ActionEvent e ) {
 246         if ( e.getSource() == _select_input_msa_btn ) {
 247             readInputFile();
 248         }
 249         else if ( e.getSource() == _select_input_seqs_btn ) {
 250             readInputSeqsFile();
 251         }
 252         else if ( e.getSource() == _launch_btn ) {
 253             launch();
 254         }
 255         else if ( e.getSource() == _cancel_btn ) {
 256             cancel();
 257         }
 258     }
 259
 260     public void activate() {
 261         setVisible( true );
 262     }
 263
 264     private MainFrameApplication getParentFrame() {
 265         return _parent_frame;
 266     }
 267
 268     public PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
 269         return _opts;
 270     }
 271
 272     public int getValue() {
 273         return _value;
 274     }
 275
 276     private void initializeValues( final boolean from_unaligned_seqs ) {
 277         _value = JOptionPane.CANCEL_OPTION;
 278         if ( from_unaligned_seqs ) {
 279             updateSeqsItems();
 280         }
 281         else {
 282             updateMsaItems();
 283         }
 284         updateMsaProcessingItem();
 285         updateDistanceCalcMethod();
 286         _bootstrap_tf.setText( getPhylogeneticInferenceOptions().getBootstrapSamples() + "" );
 287         _random_seed_tf.setText( getPhylogeneticInferenceOptions().getRandomNumberGeneratorSeed() + "" );
 288     }
 289
 290     private void launch() {
 291         processPerformBootstrapResampling();
 292         if ( _bootstrap_cb.isSelected() ) {
 293             processBootstrapSamplesNumber();
 294             processRandomNumberGeneratorSeed();
 295         }
 296         if ( true ) {
 297             //TODO
 298             processMsaProcessing();
 299         }
 300         processDistanceCalcMethod();
 301         processMsaPrgParameters();
 302         setVisible( false );
 303         _value = JOptionPane.OK_OPTION;
 304     }
 305
 306     private void cancel() {
 307         setVisible( false );
 308         _value = JOptionPane.CANCEL_OPTION;
 309     }
 310
 311     private void processBootstrapSamplesNumber() {
 312         int bootstrap_samples = 0;
 313         try {
 314             bootstrap_samples = Integer.parseInt( _bootstrap_tf.getText().trim() );
 315         }
 316         catch ( final NumberFormatException e ) {
 317             // JOptionPane.showMessageDialog( this, "Could not parse number of bootstrap resamplings from: " +  _bootstrap_tf.getText().trim(), "User Error", JOptionPane.ERROR_MESSAGE );
 318             return;
 319         }
 320         if ( bootstrap_samples >= 0 ) {
 321             getPhylogeneticInferenceOptions().setBootstrapSamples( bootstrap_samples );
 322         }
 323     }
 324
 325     private void processRandomNumberGeneratorSeed() {
 326         long seed = PhylogeneticInferenceOptions.RANDOM_NUMBER_SEED_DEFAULT;
 327         try {
 328             seed = Long.parseLong( _random_seed_tf.getText().trim() );
 329         }
 330         catch ( final NumberFormatException e ) {
 331             return;
 332         }
 333         getPhylogeneticInferenceOptions().setRandomNumberGeneratorSeed( seed );
 334     }
 335
 336     private void processMsaProcessing() {
 337         getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
 338         getPhylogeneticInferenceOptions()
 339         .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
 340         int min_length = -1;
 341         try {
 342             min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() );
 343         }
 344         catch ( final NumberFormatException e ) {
 345             min_length = -1;
 346         }
 347         if ( min_length > 0 ) {
 348             getPhylogeneticInferenceOptions().setMsaProcessingMinAllowedLength( min_length );
 349         }
 350         double msa_processing_max_allowed_gap_ratio = -1.0;
 351         try {
 352             msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf
 353                                                                        .getText().trim() );
 354         }
 355         catch ( final NumberFormatException e ) {
 356             msa_processing_max_allowed_gap_ratio = -1.0;
 357         }
 358         if ( ( msa_processing_max_allowed_gap_ratio >= 0.0 ) && ( msa_processing_max_allowed_gap_ratio <= 1.0 ) ) {
 359             getPhylogeneticInferenceOptions().setMsaProcessingMaxAllowedGapRatio( msa_processing_max_allowed_gap_ratio );
 360         }
 361     }
 362
 363     private void processDistanceCalcMethod() {
 364         if ( ( _distance_calc_kimura_rb != null ) && _distance_calc_kimura_rb.isSelected() ) {
 365             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.KIMURA_DISTANCE );
 366         }
 367         else if ( ( _distance_calc_poisson_rb != null ) && _distance_calc_poisson_rb.isSelected() ) {
 368             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.POISSON_DISTANCE );
 369         }
 370         else if ( ( _distance_calc_fract_dissimilarity_rb != null )
 371                 && _distance_calc_fract_dissimilarity_rb.isSelected() ) {
 372             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.FRACTIONAL_DISSIMILARITY );
 373         }
 374     }
 375
 376     private void processPerformBootstrapResampling() {
 377         getPhylogeneticInferenceOptions().setPerformBootstrapResampling( _bootstrap_cb.isSelected() );
 378     }
 379
 380     private void processMsaPrgParameters() {
 381         if ( _mafft_paramenters_tf != null ) {
 382             getPhylogeneticInferenceOptions().setMsaPrgParameters( _mafft_paramenters_tf.getText() );
 383         }
 384     }
 385
 386     private void readInputFile() {
 387         getParentFrame().readMsaFromFile();
 388         updateMsaItems();
 389     }
 390
 391     private void readInputSeqsFile() {
 392         getParentFrame().readSeqsFromFileforPI();
 393         updateSeqsItems();
 394     }
 395
 396     private void updateDistanceCalcMethod() {
 397         switch ( getPhylogeneticInferenceOptions().getPwdDistanceMethod() ) {
 398             case KIMURA_DISTANCE:
 399                 _distance_calc_kimura_rb.setSelected( true );
 400                 break;
 401             case POISSON_DISTANCE:
 402                 _distance_calc_poisson_rb.setSelected( true );
 403                 break;
 404             case FRACTIONAL_DISSIMILARITY:
 405                 _distance_calc_fract_dissimilarity_rb.setSelected( true );
 406                 break;
 407             default:
 408                 throw new RuntimeException( "invalid distance calc method" );
 409         }
 410     }
 411
 412     private void updateMsaProcessingItem() {
 413         _execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
 414         _msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
 415                                                                .isMsaProcessingRemoveAllGapColumns() );
 416         if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
 417             _msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
 418         }
 419         if ( _opts.getMsaProcessingMinAllowedLength() > 0 ) {
 420             _msa_processing_min_allowed_length_tf.setText( _opts.getMsaProcessingMinAllowedLength() + "" );
 421         }
 422     }
 423
 424     private void updateMsaItems() {
 425         if ( getParentFrame().getMsa() != null ) {
 426             _input_msa_file_tf.setText( getParentFrame().getMsaFile().toString() );
 427             _msa_length_tf.setText( getParentFrame().getMsa().getLength() + "" );
 428             _msa_size_tf.setText( getParentFrame().getMsa().getNumberOfSequences() + "" );
 429             _msa_type_tf.setText( getParentFrame().getMsa().getType() + "" );
 430             _input_msa_file_tf.setEnabled( true );
 431             _msa_length_tf.setEnabled( true );
 432             _msa_size_tf.setEnabled( true );
 433             _msa_type_tf.setEnabled( true );
 434             _launch_btn.setEnabled( true );
 435         }
 436         else {
 437             _input_msa_file_tf.setText( "" );
 438             _msa_length_tf.setText( "" );
 439             _msa_size_tf.setText( "" );
 440             _msa_type_tf.setText( "" );
 441             _input_msa_file_tf.setEnabled( false );
 442             _msa_length_tf.setEnabled( false );
 443             _msa_size_tf.setEnabled( false );
 444             _msa_type_tf.setEnabled( false );
 445             _launch_btn.setEnabled( false );
 446         }
 447     }
 448
 449     private void updateSeqsItems() {
 450         if ( getParentFrame().getSeqs() != null ) {
 451             final DescriptiveStatistics stats = calcSequenceStats( getParentFrame().getSeqs() );
 452             _input_seqs_tf.setText( getParentFrame().getSeqsFile().toString() );
 453             _input_seqs_median_length_tf.setText( ( int ) stats.median() + "" );
 454             _input_seqs_min_length_tf.setText( ( int ) stats.getMin() + "" );
 455             _input_seqs_max_length_tf.setText( ( int ) stats.getMax() + "" );
 456             _input_seqs_number_tf.setText( getParentFrame().getSeqs().size() + "" );
 457             _input_seqs_type_tf.setText( getParentFrame().getSeqs().get( 0 ).getType() + "" );
 458             _input_seqs_tf.setEnabled( true );
 459             _input_seqs_median_length_tf.setEnabled( true );
 460             _input_seqs_min_length_tf.setEnabled( true );
 461             _input_seqs_max_length_tf.setEnabled( true );
 462             _input_seqs_number_tf.setEnabled( true );
 463             _input_seqs_type_tf.setEnabled( true );
 464             _launch_btn.setEnabled( true );
 465         }
 466         else {
 467             _input_seqs_tf.setText( "" );
 468             _input_seqs_median_length_tf.setText( "" );
 469             _input_seqs_min_length_tf.setText( "" );
 470             _input_seqs_max_length_tf.setText( "" );
 471             _input_seqs_number_tf.setText( "" );
 472             _input_seqs_type_tf.setText( "" );
 473             _input_seqs_tf.setEnabled( false );
 474             _input_seqs_median_length_tf.setEnabled( false );
 475             _input_seqs_min_length_tf.setEnabled( false );
 476             _input_seqs_max_length_tf.setEnabled( false );
 477             _input_seqs_number_tf.setEnabled( false );
 478             _input_seqs_type_tf.setEnabled( false );
 479             _launch_btn.setEnabled( false );
 480         }
 481     }
 482
 483     DescriptiveStatistics calcSequenceStats( final List<MolecularSequence> seqs ) {
 484         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 485         for( final MolecularSequence s : seqs ) {
 486             stats.addValue( s.getLength() );
 487         }
 488         return stats;
 489     }
 490 }