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