2 // forester -- software libraries and applications
3 // for genomics and evolutionary biology research.
5 // Copyright (C) 2010 Christian M Zmasek
6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
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.
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.
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
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.archaeopteryx;
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;
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;
48 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
49 import org.forester.sequence.Sequence;
50 import org.forester.util.BasicDescriptiveStatistics;
51 import org.forester.util.DescriptiveStatistics;
53 public class PhyloInferenceDialog extends JDialog implements ActionListener {
55 private static final long serialVersionUID = 8337543508238133614L;
56 private final JPanel _pnl;
57 private final JButton _launch_btn;
58 private final JButton _cancel_btn;
59 private final JFormattedTextField _bootstrap_tf;
60 private final JCheckBox _bootstrap_cb;
61 private final PhylogeneticInferenceOptions _opts;
62 private JTextField _input_msa_file_tf;
63 private JButton _select_input_msa_btn;
64 private final MainFrameApplication _parent_frame;
65 private JTextField _msa_length_tf;
66 private JTextField _msa_size_tf;
67 private JTextField _msa_type_tf;
68 private final JRadioButton _distance_calc_kimura_rb;
69 private final JRadioButton _distance_calc_poisson_rb;
70 private final JRadioButton _distance_calc_fract_dissimilarity_rb;
71 private int _value = JOptionPane.CANCEL_OPTION;
72 private JTextField _input_seqs_tf;
73 private JButton _select_input_seqs_btn;
74 private JTextField _input_seqs_number_tf;
75 private JTextField _input_seqs_median_length_tf;
76 private JTextField _input_seqs_min_length_tf;
77 private JTextField _input_seqs_max_length_tf;
78 private JTextField _input_seqs_type_tf;
79 private JTextField _input_seqs_msa_program_name_tf;
80 private JTextField _input_seqs_msa_paramenters_tf;
81 private JTextField _msa_processing_max_allowed_gap_ratio_tf;
82 private JTextField _msa_processing_min_allowed_length_tf;
83 private JTextField _random_seed_tf;
84 private JCheckBox _execute_msa_processing_cb;
85 private JCheckBox _msa_processing_remove_all_gap_columns_cb;
86 private JCheckBox _save_pwd_file_cb;
87 private JCheckBox _save_processed_msa_cb;
88 private JCheckBox _save_original_msa_cb;
89 private JTextField _pwd_outfile_tf;
90 private JTextField _processed_msa_outfile_tf;
91 private JTextField _original_msa_outfile_tf;
93 public PhyloInferenceDialog( final MainFrameApplication frame,
94 final PhylogeneticInferenceOptions options,
95 final boolean from_unaligned_seqs ) {
98 _parent_frame = frame;
101 getContentPane().add( _pnl );
102 final BoxLayout box_layout = new BoxLayout( _pnl, BoxLayout.PAGE_AXIS );
103 _pnl.setLayout( box_layout );
104 if ( from_unaligned_seqs ) {
105 setTitle( "Phylogenetic Inference (including multiple sequence alignment)" );
106 final JPanel inputfile_pnl_1 = new JPanel();
107 final JPanel inputfile_pnl_2 = new JPanel();
108 final JPanel inputfile_pnl_3 = new JPanel();
109 inputfile_pnl_1.setLayout( new FlowLayout() );
110 inputfile_pnl_2.setLayout( new FlowLayout() );
111 inputfile_pnl_3.setLayout( new FlowLayout() );
112 inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
113 inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
114 inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
115 inputfile_pnl_2.add( new JLabel( "Sequences: " ) );
116 inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
117 inputfile_pnl_2.add( _input_seqs_number_tf = new JTextField() );
118 inputfile_pnl_2.add( new JLabel( "Length: median:" ) );
119 inputfile_pnl_2.add( _input_seqs_median_length_tf = new JTextField() );
120 inputfile_pnl_2.add( new JLabel( "min:" ) );
121 inputfile_pnl_2.add( _input_seqs_min_length_tf = new JTextField() );
122 inputfile_pnl_2.add( new JLabel( "max:" ) );
123 inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
124 inputfile_pnl_2.add( new JLabel( "Type:" ) );
125 inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
126 inputfile_pnl_3.add( new JLabel( "Mutiple Sequence Alignment: " ) );
127 inputfile_pnl_3.add( new JLabel( "Program: " ) );
128 inputfile_pnl_3.add( _input_seqs_msa_program_name_tf = new JTextField() );
129 inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
130 inputfile_pnl_3.add( _input_seqs_msa_paramenters_tf = new JTextField() );
131 _input_seqs_median_length_tf.setColumns( 4 );
132 _input_seqs_min_length_tf.setColumns( 4 );
133 _input_seqs_max_length_tf.setColumns( 4 );
134 _input_seqs_number_tf.setColumns( 4 );
135 _input_seqs_type_tf.setColumns( 2 );
136 _input_seqs_tf.setColumns( 20 );
137 _input_seqs_tf.setEditable( false );
138 _input_seqs_median_length_tf.setEditable( false );
139 _input_seqs_min_length_tf.setEditable( false );
140 _input_seqs_max_length_tf.setEditable( false );
141 _input_seqs_number_tf.setEditable( false );
142 _input_seqs_type_tf.setEditable( false );
143 _input_seqs_msa_program_name_tf.setEditable( false );
144 _input_seqs_msa_paramenters_tf.setColumns( 26 );
145 _select_input_seqs_btn.addActionListener( this );
146 _pnl.add( inputfile_pnl_1 );
147 _pnl.add( inputfile_pnl_2 );
148 _pnl.add( inputfile_pnl_3 );
151 setTitle( "Phylogenetic Inference (from already aligned sequences) " );
153 final JPanel inputfile_pnl_1 = new JPanel();
154 final JPanel inputfile_pnl_2 = new JPanel();
155 inputfile_pnl_1.setLayout( new FlowLayout() );
156 inputfile_pnl_2.setLayout( new FlowLayout() );
157 inputfile_pnl_1.add( new JLabel( "Input MSA File:" ) );
158 inputfile_pnl_1.add( _input_msa_file_tf = new JTextField() );
159 inputfile_pnl_1.add( _select_input_msa_btn = new JButton( "Select Input File" ) );
160 inputfile_pnl_2.add( new JLabel( "MSA: " ) );
161 inputfile_pnl_2.add( new JLabel( "Number of Sequences:" ) );
162 inputfile_pnl_2.add( _msa_size_tf = new JTextField() );
163 inputfile_pnl_2.add( new JLabel( "Length:" ) );
164 inputfile_pnl_2.add( _msa_length_tf = new JTextField() );
165 inputfile_pnl_2.add( new JLabel( "Type:" ) );
166 inputfile_pnl_2.add( _msa_type_tf = new JTextField() );
167 _msa_length_tf.setColumns( 4 );
168 _msa_size_tf.setColumns( 4 );
169 _msa_type_tf.setColumns( 2 );
170 _input_msa_file_tf.setColumns( 20 );
171 _input_msa_file_tf.setEditable( false );
172 _msa_length_tf.setEditable( false );
173 _msa_size_tf.setEditable( false );
174 _msa_type_tf.setEditable( false );
175 _select_input_msa_btn.addActionListener( this );
176 _pnl.add( inputfile_pnl_1 );
177 _pnl.add( inputfile_pnl_2 );
180 final JPanel inputfile_pnl_4 = new JPanel();
181 inputfile_pnl_4.setLayout( new FlowLayout() );
182 inputfile_pnl_4.add( new JLabel( "MSA Processing: " ) );
183 inputfile_pnl_4.add( _execute_msa_processing_cb = new JCheckBox( "Process MSA" ) );
184 inputfile_pnl_4.add( _msa_processing_remove_all_gap_columns_cb = new JCheckBox( "Remove all gap columns" ) );
185 inputfile_pnl_4.add( new JLabel( "Max allowed gap ratio: " ) );
186 inputfile_pnl_4.add( _msa_processing_max_allowed_gap_ratio_tf = new JTextField() );
187 inputfile_pnl_4.add( new JLabel( "Min allowed non-gap sequence length: " ) );
188 inputfile_pnl_4.add( _msa_processing_min_allowed_length_tf = new JTextField() );
189 _msa_processing_max_allowed_gap_ratio_tf.setColumns( 4 );
190 _msa_processing_min_allowed_length_tf.setColumns( 4 );
191 final Border b = new LineBorder( Color.DARK_GRAY );
192 inputfile_pnl_4.setBorder( b );
193 _pnl.add( inputfile_pnl_4 );
195 // Distance calculation:
196 // TODO if type==AA...
197 final JPanel distance_calc_pnl_1 = new JPanel();
198 distance_calc_pnl_1.setLayout( new FlowLayout() );
199 distance_calc_pnl_1.add( new JLabel( "Distance calculation:" ) );
200 distance_calc_pnl_1.add( _distance_calc_kimura_rb = new JRadioButton( "Kimura correction" ) );
201 distance_calc_pnl_1.add( _distance_calc_poisson_rb = new JRadioButton( "Poisson" ) );
203 .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) );
204 final ButtonGroup distance_calc_group_1 = new ButtonGroup();
205 distance_calc_group_1.add( _distance_calc_kimura_rb );
206 distance_calc_group_1.add( _distance_calc_poisson_rb );
207 distance_calc_group_1.add( _distance_calc_fract_dissimilarity_rb );
208 _pnl.add( distance_calc_pnl_1 );
209 // Bootstrap resampling:
210 final JPanel bootstrap_pnl = new JPanel();
211 bootstrap_pnl.setLayout( new FlowLayout() );
212 bootstrap_pnl.add( _bootstrap_cb = new JCheckBox( "Perform Bootstrap Resampling" ) );
213 bootstrap_pnl.add( new JLabel( "Number of Bootstrap Samples:" ) );
214 bootstrap_pnl.add( _bootstrap_tf = new JFormattedTextField( Util.createMaskFormatter( "###" ) ) );
215 _bootstrap_tf.setColumns( 4 );
217 // http://download.oracle.com/javase/tutorial/uiswing/components/formattedtextfield.html
218 // _bootstrap_tf.setColumns( 4 );
219 bootstrap_pnl.add( new JLabel( "Random Seed:" ) );
220 bootstrap_pnl.add( _random_seed_tf = new JTextField() );
221 _random_seed_tf.setColumns( 4 );
222 _pnl.add( bootstrap_pnl );
223 final JPanel launch_pnl = new JPanel();
224 launch_pnl.setLayout( new FlowLayout() );
225 _launch_btn = new JButton( "Go!" );
226 _launch_btn.addActionListener( this );
227 launch_pnl.add( _launch_btn );
228 _cancel_btn = new JButton( "Cancel" );
229 _cancel_btn.addActionListener( this );
230 launch_pnl.add( _cancel_btn );
231 _pnl.add( launch_pnl );
232 initializeValues( from_unaligned_seqs );
234 setLocationRelativeTo( getParentFrame() );
235 setResizable( false );
238 public void actionPerformed( final ActionEvent e ) {
239 if ( e.getSource() == _select_input_msa_btn ) {
242 else if ( e.getSource() == _select_input_seqs_btn ) {
245 else if ( e.getSource() == _launch_btn ) {
248 else if ( e.getSource() == _cancel_btn ) {
253 public void activate() {
257 private MainFrameApplication getParentFrame() {
258 return _parent_frame;
261 public PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
265 public int getValue() {
269 private void initializeValues( final boolean from_unaligned_seqs ) {
270 _value = JOptionPane.CANCEL_OPTION;
271 if ( from_unaligned_seqs ) {
273 _input_seqs_msa_program_name_tf.setText( getPhylogeneticInferenceOptions().getMsaPrg() );
274 _input_seqs_msa_paramenters_tf.setText( getPhylogeneticInferenceOptions().getMsaPrgParameters() );
279 updateMsaProcessingItem();
280 updateDistanceCalcMethod();
281 _bootstrap_tf.setText( getPhylogeneticInferenceOptions().getBootstrapSamples() + "" );
282 _random_seed_tf.setText( getPhylogeneticInferenceOptions().getRandomNumberGeneratorSeed() + "" );
285 private void launch() {
286 processPerformBootstrapResampling();
287 if ( _bootstrap_cb.isSelected() ) {
288 processBootstrapSamplesNumber();
289 processRandomNumberGeneratorSeed();
293 processMsaProcessing();
295 processDistanceCalcMethod();
296 processMsaPrgParameters();
298 _value = JOptionPane.OK_OPTION;
301 private void cancel() {
303 _value = JOptionPane.CANCEL_OPTION;
306 private void processBootstrapSamplesNumber() {
307 int bootstrap_samples = 0;
309 bootstrap_samples = Integer.parseInt( _bootstrap_tf.getText().trim() );
311 catch ( final NumberFormatException e ) {
312 // JOptionPane.showMessageDialog( this, "Could not parse number of bootstrap resamplings from: " + _bootstrap_tf.getText().trim(), "User Error", JOptionPane.ERROR_MESSAGE );
315 if ( bootstrap_samples >= 0 ) {
316 getPhylogeneticInferenceOptions().setBootstrapSamples( bootstrap_samples );
320 private void processRandomNumberGeneratorSeed() {
321 long seed = PhylogeneticInferenceOptions.RANDOM_NUMBER_SEED_DEFAULT;
323 seed = Long.parseLong( _random_seed_tf.getText().trim() );
325 catch ( final NumberFormatException e ) {
328 getPhylogeneticInferenceOptions().setRandomNumberGeneratorSeed( seed );
331 private void processMsaProcessing() {
332 getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
333 getPhylogeneticInferenceOptions()
334 .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
337 min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() );
339 catch ( final NumberFormatException e ) {
342 if ( min_length > 0 ) {
343 getPhylogeneticInferenceOptions().setMsaProcessingMinAllowedLength( min_length );
345 double msa_processing_max_allowed_gap_ratio = -1.0;
347 msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf
350 catch ( final NumberFormatException e ) {
351 msa_processing_max_allowed_gap_ratio = -1.0;
353 if ( ( msa_processing_max_allowed_gap_ratio >= 0.0 ) && ( msa_processing_max_allowed_gap_ratio <= 1.0 ) ) {
354 getPhylogeneticInferenceOptions().setMsaProcessingMaxAllowedGapRatio( msa_processing_max_allowed_gap_ratio );
358 private void processDistanceCalcMethod() {
359 if ( ( _distance_calc_kimura_rb != null ) && _distance_calc_kimura_rb.isSelected() ) {
360 getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.KIMURA_DISTANCE );
362 else if ( ( _distance_calc_poisson_rb != null ) && _distance_calc_poisson_rb.isSelected() ) {
363 getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.POISSON_DISTANCE );
365 else if ( ( _distance_calc_fract_dissimilarity_rb != null )
366 && _distance_calc_fract_dissimilarity_rb.isSelected() ) {
367 getPhylogeneticInferenceOptions().setPwdDistanceMethod( PWD_DISTANCE_METHOD.FRACTIONAL_DISSIMILARITY );
371 private void processPerformBootstrapResampling() {
372 getPhylogeneticInferenceOptions().setPerformBootstrapResampling( _bootstrap_cb.isSelected() );
375 private void processMsaPrgParameters() {
376 if ( _input_seqs_msa_paramenters_tf != null ) {
377 getPhylogeneticInferenceOptions().setMsaPrgParameters( _input_seqs_msa_paramenters_tf.getText() );
381 private void readInputFile() {
382 getParentFrame().readMsaFromFile();
386 private void readInputSeqsFile() {
387 getParentFrame().readSeqsFromFile();
391 private void updateDistanceCalcMethod() {
392 switch ( getPhylogeneticInferenceOptions().getPwdDistanceMethod() ) {
393 case KIMURA_DISTANCE:
394 _distance_calc_kimura_rb.setSelected( true );
396 case POISSON_DISTANCE:
397 _distance_calc_poisson_rb.setSelected( true );
399 case FRACTIONAL_DISSIMILARITY:
400 _distance_calc_fract_dissimilarity_rb.setSelected( true );
403 throw new RuntimeException( "invalid distance calc method" );
407 private void updateMsaProcessingItem() {
408 _execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
409 _msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
410 .isMsaProcessingRemoveAllGapColumns() );
411 if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
412 _msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
414 if ( _opts.getMsaProcessingMinAllowedLength() > 0 ) {
415 _msa_processing_min_allowed_length_tf.setText( _opts.getMsaProcessingMinAllowedLength() + "" );
419 private void updateMsaItems() {
420 if ( getParentFrame().getMsa() != null ) {
421 _input_msa_file_tf.setText( getParentFrame().getMsaFile().toString() );
422 _msa_length_tf.setText( getParentFrame().getMsa().getLength() + "" );
423 _msa_size_tf.setText( getParentFrame().getMsa().getNumberOfSequences() + "" );
424 _msa_type_tf.setText( getParentFrame().getMsa().getType() + "" );
425 _input_msa_file_tf.setEnabled( true );
426 _msa_length_tf.setEnabled( true );
427 _msa_size_tf.setEnabled( true );
428 _msa_type_tf.setEnabled( true );
429 _launch_btn.setEnabled( true );
432 _input_msa_file_tf.setText( "" );
433 _msa_length_tf.setText( "" );
434 _msa_size_tf.setText( "" );
435 _msa_type_tf.setText( "" );
436 _input_msa_file_tf.setEnabled( false );
437 _msa_length_tf.setEnabled( false );
438 _msa_size_tf.setEnabled( false );
439 _msa_type_tf.setEnabled( false );
440 _launch_btn.setEnabled( false );
444 private void updateSeqsItems() {
445 if ( getParentFrame().getSeqs() != null ) {
446 final DescriptiveStatistics stats = calcSequenceStats( getParentFrame().getSeqs() );
447 _input_seqs_tf.setText( getParentFrame().getSeqsFile().toString() );
448 _input_seqs_median_length_tf.setText( ( int ) stats.median() + "" );
449 _input_seqs_min_length_tf.setText( ( int ) stats.getMin() + "" );
450 _input_seqs_max_length_tf.setText( ( int ) stats.getMax() + "" );
451 _input_seqs_number_tf.setText( getParentFrame().getSeqs().size() + "" );
452 _input_seqs_type_tf.setText( getParentFrame().getSeqs().get( 0 ).getType() + "" );
453 _input_seqs_tf.setEnabled( true );
454 _input_seqs_median_length_tf.setEnabled( true );
455 _input_seqs_min_length_tf.setEnabled( true );
456 _input_seqs_max_length_tf.setEnabled( true );
457 _input_seqs_number_tf.setEnabled( true );
458 _input_seqs_type_tf.setEnabled( true );
459 _launch_btn.setEnabled( true );
462 _input_seqs_tf.setText( "" );
463 _input_seqs_median_length_tf.setText( "" );
464 _input_seqs_min_length_tf.setText( "" );
465 _input_seqs_max_length_tf.setText( "" );
466 _input_seqs_number_tf.setText( "" );
467 _input_seqs_type_tf.setText( "" );
468 _input_seqs_tf.setEnabled( false );
469 _input_seqs_median_length_tf.setEnabled( false );
470 _input_seqs_min_length_tf.setEnabled( false );
471 _input_seqs_max_length_tf.setEnabled( false );
472 _input_seqs_number_tf.setEnabled( false );
473 _input_seqs_type_tf.setEnabled( false );
474 _launch_btn.setEnabled( false );
478 DescriptiveStatistics calcSequenceStats( final List<Sequence> seqs ) {
479 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
480 for( final Sequence s : seqs ) {
481 stats.addValue( s.getLength() );