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: www.phylosoft.org/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.Sequence;
  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
  82     private JTextField                         _mafft_paramenters_tf;
  83     private JTextField                         _clustalo_paramenters_tf;
  84     private JTextField                         _msa_processing_max_allowed_gap_ratio_tf;
  85     private JTextField                         _msa_processing_min_allowed_length_tf;
  86     private JTextField                         _random_seed_tf;
  87     private JCheckBox                          _execute_msa_processing_cb;
  88     private JCheckBox                          _msa_processing_remove_all_gap_columns_cb;
  89     private JCheckBox                          _mafft_cb;
  90     private JCheckBox                          _clustalo_cb;
  91     private JCheckBox                          _save_pwd_file_cb;
  92     private JCheckBox                          _save_processed_msa_cb;
  93     private JCheckBox                          _save_original_msa_cb;
  94     private JTextField                         _pwd_outfile_tf;
  95     private JTextField                         _processed_msa_outfile_tf;
  96     private JTextField                         _original_msa_outfile_tf;
  97
  98     public PhyloInferenceDialog( final MainFrameApplication frame,
  99                                  final PhylogeneticInferenceOptions options,
 100                                  final boolean from_unaligned_seqs ) {
 101         super( frame, true );
 102         setVisible( false );
 103         _parent_frame = frame;
 104         _opts = options;
 105         _pnl = new JPanel();
 106         getContentPane().add( _pnl );
 107         final BoxLayout box_layout = new BoxLayout( _pnl, BoxLayout.PAGE_AXIS );
 108         _pnl.setLayout( box_layout );
 109         if ( from_unaligned_seqs ) {
 110             setTitle( "Phylogenetic Inference (including multiple sequence alignment)" );
 111             final JPanel inputfile_pnl_1 = new JPanel();
 112             final JPanel inputfile_pnl_2 = new JPanel();
 113             final JPanel inputfile_pnl_3 = new JPanel();
 114             final JPanel inputfile_pnl_4 = new JPanel();
 115             inputfile_pnl_1.setLayout( new FlowLayout() );
 116             inputfile_pnl_2.setLayout( new FlowLayout() );
 117             inputfile_pnl_3.setLayout( new FlowLayout() );
 118             inputfile_pnl_4.setLayout( new FlowLayout() );
 119             inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
 120             inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
 121             inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
 122             inputfile_pnl_2.add( new JLabel( "Sequences: " ) );
 123             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 124             inputfile_pnl_2.add( _input_seqs_number_tf = new JTextField() );
 125             inputfile_pnl_2.add( new JLabel( "Length: median:" ) );
 126             inputfile_pnl_2.add( _input_seqs_median_length_tf = new JTextField() );
 127             inputfile_pnl_2.add( new JLabel( "min:" ) );
 128             inputfile_pnl_2.add( _input_seqs_min_length_tf = new JTextField() );
 129             inputfile_pnl_2.add( new JLabel( "max:" ) );
 130             inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
 131             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 132             inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
 133
 134
 135             inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT") );
 136             inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
 137             inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
 138
 139             inputfile_pnl_4.add( _clustalo_cb = new  JCheckBox( "ClustalO") );
 140             inputfile_pnl_4.add( new JLabel( "Parameters: " ) );
 141             inputfile_pnl_4.add( _clustalo_paramenters_tf = new JTextField() );
 142             _input_seqs_median_length_tf.setColumns( 4 );
 143             _input_seqs_min_length_tf.setColumns( 4 );
 144             _input_seqs_max_length_tf.setColumns( 4 );
 145             _input_seqs_number_tf.setColumns( 4 );
 146             _input_seqs_type_tf.setColumns( 2 );
 147             _input_seqs_tf.setColumns( 20 );
 148             _input_seqs_tf.setEditable( false );
 149             _input_seqs_median_length_tf.setEditable( false );
 150             _input_seqs_min_length_tf.setEditable( false );
 151             _input_seqs_max_length_tf.setEditable( false );
 152             _input_seqs_number_tf.setEditable( false );
 153             _input_seqs_type_tf.setEditable( false );
 154
 155             _mafft_paramenters_tf.setColumns( 26 );
 156             _mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
 157             _clustalo_paramenters_tf.setColumns( 26 );
 158             _clustalo_paramenters_tf.setText( "clustalo options" );
 159             _select_input_seqs_btn.addActionListener( this );
 160             _pnl.add( inputfile_pnl_1 );
 161             _pnl.add( inputfile_pnl_2 );
 162             _pnl.add( inputfile_pnl_3 );
 163             _pnl.add( inputfile_pnl_4 );
 164         }
 165         else {
 166             setTitle( "Phylogenetic Inference (from already aligned sequences) " );
 167             // Inputfile (MSA):
 168             final JPanel inputfile_pnl_1 = new JPanel();
 169             final JPanel inputfile_pnl_2 = new JPanel();
 170             inputfile_pnl_1.setLayout( new FlowLayout() );
 171             inputfile_pnl_2.setLayout( new FlowLayout() );
 172             inputfile_pnl_1.add( new JLabel( "Input MSA File:" ) );
 173             inputfile_pnl_1.add( _input_msa_file_tf = new JTextField() );
 174             inputfile_pnl_1.add( _select_input_msa_btn = new JButton( "Select Input File" ) );
 175             inputfile_pnl_2.add( new JLabel( "MSA: " ) );
 176             inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
 177             inputfile_pnl_2.add( _msa_size_tf = new JTextField() );
 178             inputfile_pnl_2.add( new JLabel( "Length:" ) );
 179             inputfile_pnl_2.add( _msa_length_tf = new JTextField() );
 180             inputfile_pnl_2.add( new JLabel( "Type:" ) );
 181             inputfile_pnl_2.add( _msa_type_tf = new JTextField() );
 182             _msa_length_tf.setColumns( 4 );
 183             _msa_size_tf.setColumns( 4 );
 184             _msa_type_tf.setColumns( 2 );
 185             _input_msa_file_tf.setColumns( 20 );
 186             _input_msa_file_tf.setEditable( false );
 187             _msa_length_tf.setEditable( false );
 188             _msa_size_tf.setEditable( false );
 189             _msa_type_tf.setEditable( false );
 190             _select_input_msa_btn.addActionListener( this );
 191             _pnl.add( inputfile_pnl_1 );
 192             _pnl.add( inputfile_pnl_2 );
 193         }
 194         //
 195         final JPanel inputfile_pnl_4 = new JPanel();
 196         inputfile_pnl_4.setLayout( new FlowLayout() );
 197         inputfile_pnl_4.add( new JLabel( "MSA Processing: " ) );
 198         inputfile_pnl_4.add( _execute_msa_processing_cb = new JCheckBox( "Process MSA" ) );
 199         inputfile_pnl_4.add( _msa_processing_remove_all_gap_columns_cb = new JCheckBox( "Remove all gap columns" ) );
 200         inputfile_pnl_4.add( new JLabel( "Max allowed gap ratio: " ) );
 201         inputfile_pnl_4.add( _msa_processing_max_allowed_gap_ratio_tf = new JTextField() );
 202         inputfile_pnl_4.add( new JLabel( "Min allowed non-gap sequence length: " ) );
 203         inputfile_pnl_4.add( _msa_processing_min_allowed_length_tf = new JTextField() );
 204         _msa_processing_max_allowed_gap_ratio_tf.setColumns( 4 );
 205         _msa_processing_min_allowed_length_tf.setColumns( 4 );
 206         final Border b = new LineBorder( Color.DARK_GRAY );
 207         inputfile_pnl_4.setBorder( b );
 208         _pnl.add( inputfile_pnl_4 );
 209         //
 210         // Distance calculation:
 211         // TODO if type==AA...
 212         final JPanel distance_calc_pnl_1 = new JPanel();
 213         distance_calc_pnl_1.setLayout( new FlowLayout() );
 214         distance_calc_pnl_1.add( new JLabel( "Distance calculation:" ) );
 215         distance_calc_pnl_1.add( _distance_calc_kimura_rb = new JRadioButton( "Kimura correction" ) );
 216         distance_calc_pnl_1.add( _distance_calc_poisson_rb = new JRadioButton( "Poisson" ) );
 217         distance_calc_pnl_1
 218                 .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) );
 219         final ButtonGroup distance_calc_group_1 = new ButtonGroup();
 220         distance_calc_group_1.add( _distance_calc_kimura_rb );
 221         distance_calc_group_1.add( _distance_calc_poisson_rb );
 222         distance_calc_group_1.add( _distance_calc_fract_dissimilarity_rb );
 223         _pnl.add( distance_calc_pnl_1 );
 224         // Bootstrap resampling:
 225         final JPanel bootstrap_pnl = new JPanel();
 226         bootstrap_pnl.setLayout( new FlowLayout() );
 227         bootstrap_pnl.add( _bootstrap_cb = new JCheckBox( "Perform Bootstrap Resampling" ) );
 228         bootstrap_pnl.add( new JLabel( "Number of Bootstrap Samples:" ) );
 229         bootstrap_pnl.add( _bootstrap_tf = new JFormattedTextField( AptxUtil.createMaskFormatter( "###" ) ) );
 230         _bootstrap_tf.setColumns( 4 );
 231         // TODO see
 232         // http://download.oracle.com/javase/tutorial/uiswing/components/formattedtextfield.html
 233         // _bootstrap_tf.setColumns( 4 );
 234         bootstrap_pnl.add( new JLabel( "Random Seed:" ) );
 235         bootstrap_pnl.add( _random_seed_tf = new JTextField() );
 236         _random_seed_tf.setColumns( 4 );
 237         _pnl.add( bootstrap_pnl );
 238         final JPanel launch_pnl = new JPanel();
 239         launch_pnl.setLayout( new FlowLayout() );
 240         _launch_btn = new JButton( "Go!" );
 241         _launch_btn.addActionListener( this );
 242         launch_pnl.add( _launch_btn );
 243         _cancel_btn = new JButton( "Cancel" );
 244         _cancel_btn.addActionListener( this );
 245         launch_pnl.add( _cancel_btn );
 246         _pnl.add( launch_pnl );
 247         initializeValues( from_unaligned_seqs );
 248         pack();
 249         setLocationRelativeTo( getParentFrame() );
 250         setResizable( false );
 251     }
 252
 253     @Override
 254     public void actionPerformed( final ActionEvent e ) {
 255         if ( e.getSource() == _select_input_msa_btn ) {
 256             readInputFile();
 257         }
 258         else if ( e.getSource() == _select_input_seqs_btn ) {
 259             readInputSeqsFile();
 260         }
 261         else if ( e.getSource() == _launch_btn ) {
 262             launch();
 263         }
 264         else if ( e.getSource() == _cancel_btn ) {
 265             cancel();
 266         }
 267     }
 268
 269     public void activate() {
 270         setVisible( true );
 271     }
 272
 273     private MainFrameApplication getParentFrame() {
 274         return _parent_frame;
 275     }
 276
 277     public PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
 278         return _opts;
 279     }
 280
 281     public int getValue() {
 282         return _value;
 283     }
 284
 285     private void initializeValues( final boolean from_unaligned_seqs ) {
 286         _value = JOptionPane.CANCEL_OPTION;
 287         if ( from_unaligned_seqs ) {
 288             updateSeqsItems();
 289               }
 290         else {
 291             updateMsaItems();
 292         }
 293         updateMsaProcessingItem();
 294         updateDistanceCalcMethod();
 295         _bootstrap_tf.setText( getPhylogeneticInferenceOptions().getBootstrapSamples() + "" );
 296         _random_seed_tf.setText( getPhylogeneticInferenceOptions().getRandomNumberGeneratorSeed() + "" );
 297     }
 298
 299     private void launch() {
 300         processPerformBootstrapResampling();
 301         if ( _bootstrap_cb.isSelected() ) {
 302             processBootstrapSamplesNumber();
 303             processRandomNumberGeneratorSeed();
 304         }
 305         if ( true ) {
 306             //TODO
 307             processMsaProcessing();
 308         }
 309         processDistanceCalcMethod();
 310         processMsaPrgParameters();
 311         setVisible( false );
 312         _value = JOptionPane.OK_OPTION;
 313     }
 314
 315     private void cancel() {
 316         setVisible( false );
 317         _value = JOptionPane.CANCEL_OPTION;
 318     }
 319
 320     private void processBootstrapSamplesNumber() {
 321         int bootstrap_samples = 0;
 322         try {
 323             bootstrap_samples = Integer.parseInt( _bootstrap_tf.getText().trim() );
 324         }
 325         catch ( final NumberFormatException e ) {
 326             // JOptionPane.showMessageDialog( this, "Could not parse number of bootstrap resamplings from: " +  _bootstrap_tf.getText().trim(), "User Error", JOptionPane.ERROR_MESSAGE );
 327             return;
 328         }
 329         if ( bootstrap_samples >= 0 ) {
 330             getPhylogeneticInferenceOptions().setBootstrapSamples( bootstrap_samples );
 331         }
 332     }
 333
 334     private void processRandomNumberGeneratorSeed() {
 335         long seed = PhylogeneticInferenceOptions.RANDOM_NUMBER_SEED_DEFAULT;
 336         try {
 337             seed = Long.parseLong( _random_seed_tf.getText().trim() );
 338         }
 339         catch ( final NumberFormatException e ) {
 340             return;
 341         }
 342         getPhylogeneticInferenceOptions().setRandomNumberGeneratorSeed( seed );
 343     }
 344
 345     private void processMsaProcessing() {
 346         getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
 347         getPhylogeneticInferenceOptions()
 348                 .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
 349         int min_length = -1;
 350         try {
 351             min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() );
 352         }
 353         catch ( final NumberFormatException e ) {
 354             min_length = -1;
 355         }
 356         if ( min_length > 0 ) {
 357             getPhylogeneticInferenceOptions().setMsaProcessingMinAllowedLength( min_length );
 358         }
 359         double msa_processing_max_allowed_gap_ratio = -1.0;
 360         try {
 361             msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf
 362                     .getText().trim() );
 363         }
 364         catch ( final NumberFormatException e ) {
 365             msa_processing_max_allowed_gap_ratio = -1.0;
 366         }
 367         if ( ( msa_processing_max_allowed_gap_ratio >= 0.0 ) && ( msa_processing_max_allowed_gap_ratio <= 1.0 ) ) {
 368             getPhylogeneticInferenceOptions().setMsaProcessingMaxAllowedGapRatio( msa_processing_max_allowed_gap_ratio );
 369         }
 370     }
 371
 372     private void processDistanceCalcMethod() {
 373         if ( ( _distance_calc_kimura_rb != null ) && _distance_calc_kimura_rb.isSelected() ) {
 374             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.KIMURA_DISTANCE );
 375         }
 376         else if ( ( _distance_calc_poisson_rb != null ) && _distance_calc_poisson_rb.isSelected() ) {
 377             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.POISSON_DISTANCE );
 378         }
 379         else if ( ( _distance_calc_fract_dissimilarity_rb != null )
 380                 && _distance_calc_fract_dissimilarity_rb.isSelected() ) {
 381             getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.FRACTIONAL_DISSIMILARITY );
 382         }
 383     }
 384
 385     private void processPerformBootstrapResampling() {
 386         getPhylogeneticInferenceOptions().setPerformBootstrapResampling( _bootstrap_cb.isSelected() );
 387     }
 388
 389     private void processMsaPrgParameters() {
 390         if ( _mafft_paramenters_tf != null ) {
 391             getPhylogeneticInferenceOptions().setMsaPrgParameters( _mafft_paramenters_tf.getText() );
 392         }
 393     }
 394
 395     private void readInputFile() {
 396         getParentFrame().readMsaFromFile();
 397         updateMsaItems();
 398     }
 399
 400     private void readInputSeqsFile() {
 401         getParentFrame().readSeqsFromFile();
 402         updateSeqsItems();
 403     }
 404
 405     private void updateDistanceCalcMethod() {
 406         switch ( getPhylogeneticInferenceOptions().getPwdDistanceMethod() ) {
 407             case KIMURA_DISTANCE:
 408                 _distance_calc_kimura_rb.setSelected( true );
 409                 break;
 410             case POISSON_DISTANCE:
 411                 _distance_calc_poisson_rb.setSelected( true );
 412                 break;
 413             case FRACTIONAL_DISSIMILARITY:
 414                 _distance_calc_fract_dissimilarity_rb.setSelected( true );
 415                 break;
 416             default:
 417                 throw new RuntimeException( "invalid distance calc method" );
 418         }
 419     }
 420
 421     private void updateMsaProcessingItem() {
 422         _execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
 423         _msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
 424                 .isMsaProcessingRemoveAllGapColumns() );
 425         if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
 426             _msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
 427         }
 428         if ( _opts.getMsaProcessingMinAllowedLength() > 0 ) {
 429             _msa_processing_min_allowed_length_tf.setText( _opts.getMsaProcessingMinAllowedLength() + "" );
 430         }
 431     }
 432
 433     private void updateMsaItems() {
 434         if ( getParentFrame().getMsa() != null ) {
 435             _input_msa_file_tf.setText( getParentFrame().getMsaFile().toString() );
 436             _msa_length_tf.setText( getParentFrame().getMsa().getLength() + "" );
 437             _msa_size_tf.setText( getParentFrame().getMsa().getNumberOfSequences() + "" );
 438             _msa_type_tf.setText( getParentFrame().getMsa().getType() + "" );
 439             _input_msa_file_tf.setEnabled( true );
 440             _msa_length_tf.setEnabled( true );
 441             _msa_size_tf.setEnabled( true );
 442             _msa_type_tf.setEnabled( true );
 443             _launch_btn.setEnabled( true );
 444         }
 445         else {
 446             _input_msa_file_tf.setText( "" );
 447             _msa_length_tf.setText( "" );
 448             _msa_size_tf.setText( "" );
 449             _msa_type_tf.setText( "" );
 450             _input_msa_file_tf.setEnabled( false );
 451             _msa_length_tf.setEnabled( false );
 452             _msa_size_tf.setEnabled( false );
 453             _msa_type_tf.setEnabled( false );
 454             _launch_btn.setEnabled( false );
 455         }
 456     }
 457
 458     private void updateSeqsItems() {
 459         if ( getParentFrame().getSeqs() != null ) {
 460             final DescriptiveStatistics stats = calcSequenceStats( getParentFrame().getSeqs() );
 461             _input_seqs_tf.setText( getParentFrame().getSeqsFile().toString() );
 462             _input_seqs_median_length_tf.setText( ( int ) stats.median() + "" );
 463             _input_seqs_min_length_tf.setText( ( int ) stats.getMin() + "" );
 464             _input_seqs_max_length_tf.setText( ( int ) stats.getMax() + "" );
 465             _input_seqs_number_tf.setText( getParentFrame().getSeqs().size() + "" );
 466             _input_seqs_type_tf.setText( getParentFrame().getSeqs().get( 0 ).getType() + "" );
 467             _input_seqs_tf.setEnabled( true );
 468             _input_seqs_median_length_tf.setEnabled( true );
 469             _input_seqs_min_length_tf.setEnabled( true );
 470             _input_seqs_max_length_tf.setEnabled( true );
 471             _input_seqs_number_tf.setEnabled( true );
 472             _input_seqs_type_tf.setEnabled( true );
 473             _launch_btn.setEnabled( true );
 474         }
 475         else {
 476             _input_seqs_tf.setText( "" );
 477             _input_seqs_median_length_tf.setText( "" );
 478             _input_seqs_min_length_tf.setText( "" );
 479             _input_seqs_max_length_tf.setText( "" );
 480             _input_seqs_number_tf.setText( "" );
 481             _input_seqs_type_tf.setText( "" );
 482             _input_seqs_tf.setEnabled( false );
 483             _input_seqs_median_length_tf.setEnabled( false );
 484             _input_seqs_min_length_tf.setEnabled( false );
 485             _input_seqs_max_length_tf.setEnabled( false );
 486             _input_seqs_number_tf.setEnabled( false );
 487             _input_seqs_type_tf.setEnabled( false );
 488             _launch_btn.setEnabled( false );
 489         }
 490     }
 491
 492     DescriptiveStatistics calcSequenceStats( final List<Sequence> seqs ) {
 493         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 494         for( final Sequence s : seqs ) {
 495             stats.addValue( s.getLength() );
 496         }
 497         return stats;
 498     }
 499 }