2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.archaeopteryx;
29 import java.awt.BorderLayout;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.ComponentAdapter;
33 import java.awt.event.ComponentEvent;
34 import java.awt.event.WindowAdapter;
35 import java.awt.event.WindowEvent;
37 import java.io.FileInputStream;
38 import java.io.IOException;
39 import java.io.InputStream;
40 import java.net.MalformedURLException;
42 import java.util.ArrayList;
43 import java.util.HashSet;
44 import java.util.List;
47 import javax.swing.ButtonGroup;
48 import javax.swing.JCheckBoxMenuItem;
49 import javax.swing.JFileChooser;
50 import javax.swing.JMenu;
51 import javax.swing.JMenuBar;
52 import javax.swing.JMenuItem;
53 import javax.swing.JOptionPane;
54 import javax.swing.JRadioButtonMenuItem;
55 import javax.swing.UIManager;
56 import javax.swing.UnsupportedLookAndFeelException;
57 import javax.swing.WindowConstants;
58 import javax.swing.event.ChangeEvent;
59 import javax.swing.event.ChangeListener;
60 import javax.swing.filechooser.FileFilter;
61 import javax.swing.plaf.synth.SynthLookAndFeel;
63 import org.forester.analysis.TaxonomyDataManager;
64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
69 import org.forester.archaeopteryx.tools.GoAnnotation;
70 import org.forester.archaeopteryx.tools.InferenceManager;
71 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
72 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
73 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
74 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
75 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
76 import org.forester.archaeopteryx.webservices.WebservicesManager;
77 import org.forester.io.parsers.FastaParser;
78 import org.forester.io.parsers.GeneralMsaParser;
79 import org.forester.io.parsers.PhylogenyParser;
80 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
81 import org.forester.io.parsers.nhx.NHXParser;
82 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
83 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
84 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
85 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
86 import org.forester.io.parsers.tol.TolParser;
87 import org.forester.io.parsers.util.ParserUtils;
88 import org.forester.io.writers.PhylogenyWriter;
89 import org.forester.io.writers.SequenceWriter;
90 import org.forester.msa.Msa;
91 import org.forester.msa.MsaFormatException;
92 import org.forester.phylogeny.Phylogeny;
93 import org.forester.phylogeny.PhylogenyMethods;
94 import org.forester.phylogeny.PhylogenyNode;
95 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
96 import org.forester.phylogeny.data.Confidence;
97 import org.forester.phylogeny.data.Taxonomy;
98 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
99 import org.forester.phylogeny.factories.PhylogenyFactory;
100 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
101 import org.forester.sdi.GSDI;
102 import org.forester.sdi.GSDIR;
103 import org.forester.sdi.SDIException;
104 import org.forester.sdi.SDIR;
105 import org.forester.sequence.Sequence;
106 import org.forester.util.BasicDescriptiveStatistics;
107 import org.forester.util.BasicTable;
108 import org.forester.util.BasicTableParser;
109 import org.forester.util.DescriptiveStatistics;
110 import org.forester.util.ForesterUtil;
111 import org.forester.util.WindowsUtils;
113 public final class MainFrameApplication extends MainFrame {
115 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
116 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
117 private final static int FRAME_X_SIZE = 800;
118 private final static int FRAME_Y_SIZE = 800;
119 // Filters for the file-open dialog (classes defined in this file)
120 private final static NHFilter nhfilter = new NHFilter();
121 private final static NHXFilter nhxfilter = new NHXFilter();
122 private final static XMLFilter xmlfilter = new XMLFilter();
123 private final static TolFilter tolfilter = new TolFilter();
124 private final static NexusFilter nexusfilter = new NexusFilter();
125 private final static PdfFilter pdffilter = new PdfFilter();
126 private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
127 private final static MsaFileFilter msafilter = new MsaFileFilter();
128 private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
129 private final static DefaultFilter defaultfilter = new DefaultFilter();
130 private static final long serialVersionUID = -799735726778865234L;
131 private final JFileChooser _values_filechooser;
132 private final JFileChooser _open_filechooser;
133 private final JFileChooser _msa_filechooser;
134 private final JFileChooser _seqs_filechooser;
135 private final JFileChooser _open_filechooser_for_species_tree;
136 private final JFileChooser _save_filechooser;
137 private final JFileChooser _writetopdf_filechooser;
138 private final JFileChooser _writetographics_filechooser;
140 private JMenu _analysis_menu;
141 private JMenuItem _load_species_tree_item;
142 private JMenuItem _gsdi_item;
143 private JMenuItem _gsdir_item;
144 private JMenuItem _root_min_dups_item;
145 private JMenuItem _root_min_cost_l_item;
146 private JMenuItem _lineage_inference;
147 private JMenuItem _function_analysis;
148 // Application-only print menu items
149 private JMenuItem _print_item;
150 private JMenuItem _write_to_pdf_item;
151 private JMenuItem _write_to_jpg_item;
152 private JMenuItem _write_to_gif_item;
153 private JMenuItem _write_to_tif_item;
154 private JMenuItem _write_to_png_item;
155 private JMenuItem _write_to_bmp_item;
156 private Phylogeny _species_tree;
157 private File _current_dir;
158 private ButtonGroup _radio_group_1;
159 private ButtonGroup _radio_group_2;
161 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
162 // Phylogeny Inference menu
163 private JMenu _inference_menu;
164 private JMenuItem _inference_from_msa_item;
165 private JMenuItem _inference_from_seqs_item;
166 // Phylogeny Inference
167 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
168 private Msa _msa = null;
169 private File _msa_file = null;
170 private List<Sequence> _seqs = null;
171 private File _seqs_file = null;
172 // expression values menu:
173 JMenuItem _read_values_jmi;
175 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
176 _configuration = config;
177 if ( _configuration == null ) {
178 throw new IllegalArgumentException( "configuration is null" );
181 setOptions( Options.createInstance( _configuration ) );
182 _mainpanel = new MainPanel( _configuration, this );
183 _open_filechooser = null;
184 _open_filechooser_for_species_tree = null;
185 _save_filechooser = null;
186 _writetopdf_filechooser = null;
187 _writetographics_filechooser = null;
188 _msa_filechooser = null;
189 _seqs_filechooser = null;
190 _values_filechooser = null;
191 _jmenubar = new JMenuBar();
194 _contentpane = getContentPane();
195 _contentpane.setLayout( new BorderLayout() );
196 _contentpane.add( _mainpanel, BorderLayout.CENTER );
198 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
199 // The window listener
200 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
201 addWindowListener( new WindowAdapter() {
204 public void windowClosing( final WindowEvent e ) {
208 // setVisible( true );
209 if ( ( phys != null ) && ( phys.length > 0 ) ) {
210 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
212 getMainPanel().getControlPanel().showWholeAll();
213 getMainPanel().getControlPanel().showWhole();
215 //activateSaveAllIfNeeded();
216 // ...and its children
217 _contentpane.repaint();
220 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
221 this( phys, config, title, null );
224 private MainFrameApplication( final Phylogeny[] phys,
225 final Configuration config,
227 final File current_dir ) {
229 _configuration = config;
230 if ( _configuration == null ) {
231 throw new IllegalArgumentException( "configuration is null" );
234 boolean synth_exception = false;
235 if ( Constants.__SYNTH_LF ) {
237 final SynthLookAndFeel synth = new SynthLookAndFeel();
238 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
239 MainFrameApplication.class );
240 UIManager.setLookAndFeel( synth );
242 catch ( final Exception ex ) {
243 synth_exception = true;
244 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
245 "could not create synth look and feel: "
246 + ex.getLocalizedMessage() );
249 if ( !Constants.__SYNTH_LF || synth_exception ) {
250 if ( _configuration.isUseNativeUI() ) {
251 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
254 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
257 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
259 catch ( final UnsupportedLookAndFeelException e ) {
260 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
262 catch ( final ClassNotFoundException e ) {
263 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
265 catch ( final InstantiationException e ) {
266 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
268 catch ( final IllegalAccessException e ) {
269 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
271 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
272 setCurrentDir( current_dir );
274 // hide until everything is ready
276 setOptions( Options.createInstance( _configuration ) );
277 setInferenceManager( InferenceManager.createInstance( _configuration ) );
278 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
279 // _textframe = null; #~~~~
280 _species_tree = null;
282 setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
283 _mainpanel = new MainPanel( _configuration, this );
285 _open_filechooser = new JFileChooser();
286 _open_filechooser.setCurrentDirectory( new File( "." ) );
287 _open_filechooser.setMultiSelectionEnabled( false );
288 _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
289 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
290 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
291 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
292 _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
293 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
294 _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
295 _open_filechooser_for_species_tree = new JFileChooser();
296 _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
297 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
298 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
299 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
300 _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
301 _save_filechooser = new JFileChooser();
302 _save_filechooser.setCurrentDirectory( new File( "." ) );
303 _save_filechooser.setMultiSelectionEnabled( false );
304 _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
305 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
306 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
307 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
308 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
309 _writetopdf_filechooser = new JFileChooser();
310 _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
311 _writetographics_filechooser = new JFileChooser();
312 _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
314 _msa_filechooser = new JFileChooser();
315 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
316 _msa_filechooser.setCurrentDirectory( new File( "." ) );
317 _msa_filechooser.setMultiSelectionEnabled( false );
318 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
319 _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
321 _seqs_filechooser = new JFileChooser();
322 _seqs_filechooser.setName( "Read Sequences File" );
323 _seqs_filechooser.setCurrentDirectory( new File( "." ) );
324 _seqs_filechooser.setMultiSelectionEnabled( false );
325 _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() );
326 _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
328 _values_filechooser = new JFileChooser();
329 _values_filechooser.setCurrentDirectory( new File( "." ) );
330 _values_filechooser.setMultiSelectionEnabled( false );
331 // build the menu bar
332 _jmenubar = new JMenuBar();
333 if ( !_configuration.isUseNativeUI() ) {
334 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
337 if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
338 buildPhylogeneticInferenceMenu();
347 setJMenuBar( _jmenubar );
348 _jmenubar.add( _help_jmenu );
349 _contentpane = getContentPane();
350 _contentpane.setLayout( new BorderLayout() );
351 _contentpane.add( _mainpanel, BorderLayout.CENTER );
353 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
354 // addWindowFocusListener( new WindowAdapter() {
357 // public void windowGainedFocus( WindowEvent e ) {
358 // requestFocusInWindow();
361 // The window listener
362 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
363 addWindowListener( new WindowAdapter() {
366 public void windowClosing( final WindowEvent e ) {
367 if ( isUnsavedDataPresent() ) {
368 final int r = JOptionPane.showConfirmDialog( null,
369 "Exit despite potentially unsaved changes?",
371 JOptionPane.YES_NO_OPTION );
372 if ( r != JOptionPane.YES_OPTION ) {
377 final int r = JOptionPane.showConfirmDialog( null,
378 "Exit Archaeopteryx?",
380 JOptionPane.YES_NO_OPTION );
381 if ( r != JOptionPane.YES_OPTION ) {
388 // The component listener
389 addComponentListener( new ComponentAdapter() {
392 public void componentResized( final ComponentEvent e ) {
393 if ( _mainpanel.getCurrentTreePanel() != null ) {
394 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
396 _mainpanel.getCurrentTreePanel()
402 requestFocusInWindow();
403 // addKeyListener( this );
405 if ( ( phys != null ) && ( phys.length > 0 ) ) {
406 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
408 getMainPanel().getControlPanel().showWholeAll();
409 getMainPanel().getControlPanel().showWhole();
411 activateSaveAllIfNeeded();
412 // ...and its children
413 _contentpane.repaint();
417 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
418 // Reads the config file (false, false => not url, not applet):
419 this( phys, new Configuration( config_file, false, false, true ), title );
423 public void actionPerformed( final ActionEvent e ) {
425 super.actionPerformed( e );
426 final Object o = e.getSource();
427 // Handle app-specific actions here:
428 if ( o == _open_item ) {
429 readPhylogeniesFromFile();
431 else if ( o == _save_item ) {
432 writeToFile( _mainpanel.getCurrentPhylogeny() );
433 // If subtree currently displayed, save it, instead of complete
436 else if ( o == _new_item ) {
439 else if ( o == _save_all_item ) {
442 else if ( o == _close_item ) {
445 else if ( o == _write_to_pdf_item ) {
446 writeToPdf( _mainpanel.getCurrentPhylogeny() );
448 else if ( o == _write_to_jpg_item ) {
449 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
451 else if ( o == _write_to_png_item ) {
452 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
454 else if ( o == _write_to_gif_item ) {
455 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
457 else if ( o == _write_to_tif_item ) {
458 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
460 else if ( o == _write_to_bmp_item ) {
461 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
463 else if ( o == _print_item ) {
466 else if ( o == _load_species_tree_item ) {
467 readSpeciesTreeFromFile();
469 else if ( o == _lineage_inference ) {
470 if ( isSubtreeDisplayed() ) {
471 JOptionPane.showMessageDialog( this,
473 "Cannot infer ancestral taxonomies",
474 JOptionPane.ERROR_MESSAGE );
477 executeLineageInference();
479 else if ( o == _function_analysis ) {
480 executeFunctionAnalysis();
482 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
483 if ( isSubtreeDisplayed() ) {
486 obtainDetailedTaxonomicInformation();
488 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
489 if ( isSubtreeDisplayed() ) {
492 obtainDetailedTaxonomicInformationDelete();
494 else if ( o == _obtain_seq_information_jmi ) {
495 obtainSequenceInformation();
497 else if ( o == _read_values_jmi ) {
498 if ( isSubtreeDisplayed() ) {
501 addExpressionValuesFromFile();
503 else if ( o == _move_node_names_to_tax_sn_jmi ) {
504 moveNodeNamesToTaxSn();
506 else if ( o == _move_node_names_to_seq_names_jmi ) {
507 moveNodeNamesToSeqNames();
509 else if ( o == _extract_tax_code_from_node_names_jmi ) {
510 extractTaxDataFromNodeNames();
512 else if ( o == _gsdi_item ) {
513 if ( isSubtreeDisplayed() ) {
518 else if ( o == _gsdir_item ) {
519 if ( isSubtreeDisplayed() ) {
524 else if ( o == _root_min_dups_item ) {
525 if ( isSubtreeDisplayed() ) {
528 executeSDIR( false );
530 else if ( o == _root_min_cost_l_item ) {
531 if ( isSubtreeDisplayed() ) {
536 else if ( o == _graphics_export_visible_only_cbmi ) {
537 updateOptions( getOptions() );
539 else if ( o == _antialias_print_cbmi ) {
540 updateOptions( getOptions() );
542 else if ( o == _print_black_and_white_cbmi ) {
543 updateOptions( getOptions() );
545 else if ( o == _print_using_actual_size_cbmi ) {
546 updateOptions( getOptions() );
548 else if ( o == _graphics_export_using_actual_size_cbmi ) {
549 updateOptions( getOptions() );
551 else if ( o == _print_size_mi ) {
554 else if ( o == _choose_pdf_width_mi ) {
557 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
558 updateOptions( getOptions() );
560 else if ( o == _replace_underscores_cbmi ) {
561 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
562 _extract_taxonomy_no_rbmi.setSelected( true );
564 updateOptions( getOptions() );
566 else if ( o == _collapse_below_threshold ) {
567 if ( isSubtreeDisplayed() ) {
570 collapseBelowThreshold();
572 else if ( ( o == _extract_taxonomy_pfam_rbmi ) || ( o == _extract_taxonomy_yes_rbmi ) ) {
573 if ( _replace_underscores_cbmi != null ) {
574 _replace_underscores_cbmi.setSelected( false );
576 updateOptions( getOptions() );
578 else if ( o == _inference_from_msa_item ) {
579 executePhyleneticInference( false );
581 else if ( o == _inference_from_seqs_item ) {
582 executePhyleneticInference( true );
584 _contentpane.repaint();
586 catch ( final Exception ex ) {
587 AptxUtil.unexpectedException( ex );
589 catch ( final Error err ) {
590 AptxUtil.unexpectedError( err );
595 _mainpanel.terminate();
596 _contentpane.removeAll();
602 public MainPanel getMainPanel() {
606 public Msa getMsa() {
610 public File getMsaFile() {
614 public List<Sequence> getSeqs() {
618 public File getSeqsFile() {
622 public void readMsaFromFile() {
623 // Set an initial directory if none set yet
624 final File my_dir = getCurrentDir();
625 _msa_filechooser.setMultiSelectionEnabled( false );
626 // Open file-open dialog and set current directory
627 if ( my_dir != null ) {
628 _msa_filechooser.setCurrentDirectory( my_dir );
630 final int result = _msa_filechooser.showOpenDialog( _contentpane );
631 // All done: get the msa
632 final File file = _msa_filechooser.getSelectedFile();
633 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
634 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
639 final InputStream is = new FileInputStream( file );
640 if ( FastaParser.isLikelyFasta( file ) ) {
641 msa = FastaParser.parseMsa( is );
644 msa = GeneralMsaParser.parse( is );
647 catch ( final MsaFormatException e ) {
649 _mainpanel.getCurrentTreePanel().setArrowCursor();
651 catch ( final Exception ex ) {
654 JOptionPane.showMessageDialog( this,
655 e.getLocalizedMessage(),
656 "Multiple sequence alignment format error",
657 JOptionPane.ERROR_MESSAGE );
660 catch ( final IOException e ) {
662 _mainpanel.getCurrentTreePanel().setArrowCursor();
664 catch ( final Exception ex ) {
667 JOptionPane.showMessageDialog( this,
668 e.getLocalizedMessage(),
669 "Failed to read multiple sequence alignment",
670 JOptionPane.ERROR_MESSAGE );
673 catch ( final IllegalArgumentException e ) {
675 _mainpanel.getCurrentTreePanel().setArrowCursor();
677 catch ( final Exception ex ) {
680 JOptionPane.showMessageDialog( this,
681 e.getLocalizedMessage(),
682 "Unexpected error during reading of multiple sequence alignment",
683 JOptionPane.ERROR_MESSAGE );
686 catch ( final Exception e ) {
688 _mainpanel.getCurrentTreePanel().setArrowCursor();
690 catch ( final Exception ex ) {
694 JOptionPane.showMessageDialog( this,
695 e.getLocalizedMessage(),
696 "Unexpected error during reading of multiple sequence alignment",
697 JOptionPane.ERROR_MESSAGE );
700 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
701 JOptionPane.showMessageDialog( this,
702 "Multiple sequence alignment is empty",
703 "Illegal Multiple Sequence Alignment",
704 JOptionPane.ERROR_MESSAGE );
707 if ( msa.getNumberOfSequences() < 4 ) {
708 JOptionPane.showMessageDialog( this,
709 "Multiple sequence alignment needs to contain at least 3 sequences",
710 "Illegal multiple sequence alignment",
711 JOptionPane.ERROR_MESSAGE );
714 if ( msa.getLength() < 2 ) {
715 JOptionPane.showMessageDialog( this,
716 "Multiple sequence alignment needs to contain at least 2 residues",
717 "Illegal multiple sequence alignment",
718 JOptionPane.ERROR_MESSAGE );
722 setMsaFile( _msa_filechooser.getSelectedFile() );
727 public void readSeqsFromFile() {
728 // Set an initial directory if none set yet
729 final File my_dir = getCurrentDir();
730 _seqs_filechooser.setMultiSelectionEnabled( false );
731 // Open file-open dialog and set current directory
732 if ( my_dir != null ) {
733 _seqs_filechooser.setCurrentDirectory( my_dir );
735 final int result = _seqs_filechooser.showOpenDialog( _contentpane );
736 // All done: get the seqs
737 final File file = _seqs_filechooser.getSelectedFile();
738 setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
739 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
742 List<Sequence> seqs = null;
744 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
745 seqs = FastaParser.parse( new FileInputStream( file ) );
746 for( final Sequence seq : seqs ) {
747 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
754 catch ( final MsaFormatException e ) {
756 _mainpanel.getCurrentTreePanel().setArrowCursor();
758 catch ( final Exception ex ) {
761 JOptionPane.showMessageDialog( this,
762 e.getLocalizedMessage(),
763 "Multiple sequence file format error",
764 JOptionPane.ERROR_MESSAGE );
767 catch ( final IOException e ) {
769 _mainpanel.getCurrentTreePanel().setArrowCursor();
771 catch ( final Exception ex ) {
774 JOptionPane.showMessageDialog( this,
775 e.getLocalizedMessage(),
776 "Failed to read multiple sequence file",
777 JOptionPane.ERROR_MESSAGE );
780 catch ( final IllegalArgumentException e ) {
782 _mainpanel.getCurrentTreePanel().setArrowCursor();
784 catch ( final Exception ex ) {
787 JOptionPane.showMessageDialog( this,
788 e.getLocalizedMessage(),
789 "Unexpected error during reading of multiple sequence file",
790 JOptionPane.ERROR_MESSAGE );
793 catch ( final Exception e ) {
795 _mainpanel.getCurrentTreePanel().setArrowCursor();
797 catch ( final Exception ex ) {
801 JOptionPane.showMessageDialog( this,
802 e.getLocalizedMessage(),
803 "Unexpected error during reading of multiple sequence file",
804 JOptionPane.ERROR_MESSAGE );
807 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
808 JOptionPane.showMessageDialog( this,
809 "Multiple sequence file is empty",
810 "Illegal multiple sequence file",
811 JOptionPane.ERROR_MESSAGE );
814 if ( seqs.size() < 4 ) {
815 JOptionPane.showMessageDialog( this,
816 "Multiple sequence file needs to contain at least 3 sequences",
817 "Illegal multiple sequence file",
818 JOptionPane.ERROR_MESSAGE );
821 // if ( msa.getLength() < 2 ) {
822 // JOptionPane.showMessageDialog( this,
823 // "Multiple sequence alignment needs to contain at least 2 residues",
824 // "Illegal multiple sequence file",
825 // JOptionPane.ERROR_MESSAGE );
829 setSeqsFile( _seqs_filechooser.getSelectedFile() );
834 void buildAnalysisMenu() {
835 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
836 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
837 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
838 _analysis_menu.addSeparator();
839 _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
840 _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
841 _analysis_menu.addSeparator();
842 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
843 customizeJMenuItem( _gsdi_item );
844 customizeJMenuItem( _gsdir_item );
845 customizeJMenuItem( _root_min_dups_item );
846 customizeJMenuItem( _root_min_cost_l_item );
847 customizeJMenuItem( _load_species_tree_item );
848 _analysis_menu.addSeparator();
849 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
850 customizeJMenuItem( _lineage_inference );
851 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
852 _jmenubar.add( _analysis_menu );
856 void buildFileMenu() {
857 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
858 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
859 _file_jmenu.addSeparator();
860 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
861 _file_jmenu.addSeparator();
862 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
863 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
864 .getAvailablePhylogeniesWebserviceClients().size() ];
865 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
866 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
867 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
868 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
870 if ( getConfiguration().isEditable() ) {
871 _file_jmenu.addSeparator();
872 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
873 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
875 _file_jmenu.addSeparator();
876 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
877 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
878 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
879 _save_all_item.setEnabled( false );
880 _file_jmenu.addSeparator();
881 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
882 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
883 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
885 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
886 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
887 if ( AptxUtil.canWriteFormat( "gif" ) ) {
888 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
890 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
891 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
893 _file_jmenu.addSeparator();
894 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
895 _file_jmenu.addSeparator();
896 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
897 _close_item.setToolTipText( "To close the current pane." );
898 _close_item.setEnabled( true );
899 _file_jmenu.addSeparator();
900 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
901 // For print in color option item
902 customizeJMenuItem( _open_item );
904 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
905 customizeJMenuItem( _open_url_item );
906 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
907 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
909 customizeJMenuItem( _save_item );
910 if ( getConfiguration().isEditable() ) {
911 customizeJMenuItem( _new_item );
913 customizeJMenuItem( _close_item );
914 customizeJMenuItem( _save_all_item );
915 customizeJMenuItem( _write_to_pdf_item );
916 customizeJMenuItem( _write_to_png_item );
917 customizeJMenuItem( _write_to_jpg_item );
918 customizeJMenuItem( _write_to_gif_item );
919 customizeJMenuItem( _write_to_tif_item );
920 customizeJMenuItem( _write_to_bmp_item );
921 customizeJMenuItem( _print_item );
922 customizeJMenuItem( _exit_item );
923 _jmenubar.add( _file_jmenu );
926 void buildOptionsMenu() {
927 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
928 _options_jmenu.addChangeListener( new ChangeListener() {
931 public void stateChanged( final ChangeEvent e ) {
932 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
933 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
935 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
936 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
937 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
938 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
939 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
940 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
942 _show_branch_length_values_cbmi,
943 _non_lined_up_cladograms_rbmi,
944 _uniform_cladograms_rbmi,
945 _ext_node_dependent_cladogram_rbmi,
946 _label_direction_cbmi );
947 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
948 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
949 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
952 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
954 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
955 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
956 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
957 _radio_group_1 = new ButtonGroup();
958 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
959 _radio_group_1.add( _uniform_cladograms_rbmi );
960 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
961 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
962 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
964 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
965 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
966 _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
968 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
969 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
970 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
971 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
972 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
973 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
974 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
975 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
976 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
977 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
978 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
979 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
980 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
982 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
983 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
984 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
985 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
986 _options_jmenu.addSeparator();
987 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
988 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
989 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
990 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
991 _options_jmenu.addSeparator();
992 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
993 getConfiguration() ) );
994 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
995 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
997 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
999 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
1001 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
1002 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
1003 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
1004 _options_jmenu.addSeparator();
1005 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
1007 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
1008 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
1010 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
1012 .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
1013 _extract_taxonomy_pfam_rbmi
1014 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
1016 .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
1017 _extract_taxonomy_yes_rbmi
1018 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
1019 _radio_group_2 = new ButtonGroup();
1020 _radio_group_2.add( _extract_taxonomy_no_rbmi );
1021 _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
1022 _radio_group_2.add( _extract_taxonomy_yes_rbmi );
1024 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
1026 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
1027 _use_brackets_for_conf_in_nh_export_cbmi
1028 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
1030 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
1031 customizeJMenuItem( _choose_font_mi );
1032 customizeJMenuItem( _choose_minimal_confidence_mi );
1033 customizeJMenuItem( _switch_colors_mi );
1034 customizeJMenuItem( _print_size_mi );
1035 customizeJMenuItem( _choose_pdf_width_mi );
1036 customizeJMenuItem( _overview_placment_mi );
1037 customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
1038 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
1039 customizeJMenuItem( _cycle_node_shape_mi );
1040 customizeJMenuItem( _cycle_node_fill_mi );
1041 customizeJMenuItem( _choose_node_size_mi );
1042 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
1043 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
1044 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
1045 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
1046 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
1047 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
1048 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
1049 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
1050 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
1051 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
1052 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1053 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
1054 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1055 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
1056 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1057 customizeCheckBoxMenuItem( _label_direction_cbmi,
1058 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1059 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1060 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1061 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1062 .isInternalNumberAreConfidenceForNhParsing() );
1063 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1064 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1065 customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
1066 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
1067 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
1068 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1069 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1070 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1071 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1072 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1073 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1074 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1075 .isGraphicsExportUsingActualSize() );
1076 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1077 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1078 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1079 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1080 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1081 _jmenubar.add( _options_jmenu );
1084 void buildPhylogeneticInferenceMenu() {
1085 final InferenceManager im = getInferenceManager();
1086 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1087 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1088 customizeJMenuItem( _inference_from_msa_item );
1089 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1090 if ( im.canDoMsa() ) {
1091 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1092 customizeJMenuItem( _inference_from_seqs_item );
1093 _inference_from_seqs_item
1094 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1098 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1099 customizeJMenuItem( _inference_from_seqs_item );
1100 _inference_from_seqs_item.setEnabled( false );
1102 _jmenubar.add( _inference_menu );
1105 void buildToolsMenu() {
1106 _tools_menu = createMenu( "Tools", getConfiguration() );
1107 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1108 customizeJMenuItem( _confcolor_item );
1109 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1110 customizeJMenuItem( _color_rank_jmi );
1111 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1112 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1113 customizeJMenuItem( _taxcolor_item );
1114 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1115 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1116 customizeJMenuItem( _remove_branch_color_item );
1117 _tools_menu.addSeparator();
1118 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1119 customizeJMenuItem( _annotate_item );
1120 _tools_menu.addSeparator();
1121 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1122 customizeJMenuItem( _midpoint_root_item );
1123 _tools_menu.addSeparator();
1124 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1125 customizeJMenuItem( _collapse_species_specific_subtrees );
1127 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1128 customizeJMenuItem( _collapse_below_threshold );
1129 _collapse_below_threshold
1130 .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
1131 _tools_menu.addSeparator();
1133 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
1134 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1135 _extract_tax_code_from_node_names_jmi
1136 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
1138 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1139 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1140 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1141 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1142 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1143 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1144 _tools_menu.addSeparator();
1146 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1147 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1148 _obtain_detailed_taxonomic_information_jmi
1149 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1151 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1152 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1153 _obtain_detailed_taxonomic_information_deleting_jmi
1154 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1155 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1156 customizeJMenuItem( _obtain_seq_information_jmi );
1157 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1158 _tools_menu.addSeparator();
1159 if ( !Constants.__RELEASE ) {
1160 _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
1161 customizeJMenuItem( _function_analysis );
1163 .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
1164 _tools_menu.addSeparator();
1166 _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
1167 customizeJMenuItem( _read_values_jmi );
1168 _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
1169 _jmenubar.add( _tools_menu );
1174 if ( isUnsavedDataPresent() ) {
1175 final int r = JOptionPane.showConfirmDialog( this,
1176 "Exit despite potentially unsaved changes?",
1178 JOptionPane.YES_NO_OPTION );
1179 if ( r != JOptionPane.YES_OPTION ) {
1186 void executeFunctionAnalysis() {
1187 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1190 final GoAnnotation a = new GoAnnotation( this,
1191 _mainpanel.getCurrentTreePanel(),
1192 _mainpanel.getCurrentPhylogeny() );
1193 new Thread( a ).start();
1196 void executeGSDI() {
1197 if ( !isOKforSDI( false, true ) ) {
1200 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1201 JOptionPane.showMessageDialog( this,
1202 "Gene tree is not rooted.",
1203 "Cannot execute GSDI",
1204 JOptionPane.ERROR_MESSAGE );
1207 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1208 gene_tree.setAllNodesToNotCollapse();
1209 gene_tree.recalculateNumberOfExternalDescendants( false );
1211 final Phylogeny species_tree = _species_tree.copy();
1213 gsdi = new GSDI( gene_tree, species_tree, false, true, true );
1215 catch ( final SDIException e ) {
1216 JOptionPane.showMessageDialog( this,
1217 e.getLocalizedMessage(),
1218 "Error during GSDI",
1219 JOptionPane.ERROR_MESSAGE );
1222 catch ( final Exception e ) {
1223 AptxUtil.unexpectedException( e );
1226 gene_tree.setRerootable( false );
1227 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1228 _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
1229 _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
1230 _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1231 _mainpanel.getCurrentTreePanel().setEdited( true );
1232 getControlPanel().setShowEvents( true );
1234 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1235 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1237 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1239 _mainpanel.getCurrentTreePanel().setEdited( true );
1240 JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1241 + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
1242 + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
1245 void executeGSDIR() {
1246 if ( !isOKforSDI( false, true ) ) {
1249 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1250 gene_tree.setAllNodesToNotCollapse();
1251 gene_tree.recalculateNumberOfExternalDescendants( false );
1253 final Phylogeny species_tree = _species_tree.copy();
1255 gsdir = new GSDIR( gene_tree, species_tree, true, true );
1257 catch ( final SDIException e ) {
1258 JOptionPane.showMessageDialog( this,
1259 e.getLocalizedMessage(),
1260 "Error during GSDIR",
1261 JOptionPane.ERROR_MESSAGE );
1264 catch ( final Exception e ) {
1265 AptxUtil.unexpectedException( e );
1268 final List<Phylogeny> assigned_trees = gsdir.getMinDuplicationsSumGeneTrees();
1269 final List<Integer> shortests = GSDIR.getIndexesOfShortestTree( assigned_trees );
1270 final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) );
1271 result_gene_tree.setRerootable( false );
1272 result_gene_tree.clearHashIdToNodeMap();
1273 result_gene_tree.recalculateNumberOfExternalDescendants( true );
1274 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1275 getControlPanel().setShowEvents( true );
1277 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1278 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1280 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1282 _mainpanel.getCurrentTreePanel().setEdited( true );
1283 JOptionPane.showMessageDialog( this,
1284 "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
1285 + gsdir.getSpeciationsSum() + "\n"
1286 + "Number of root positions minimizing duplications sum: "
1287 + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n"
1288 + "Number of shortest trees: " + shortests.size(),
1289 "GSDIR successfully completed",
1290 JOptionPane.INFORMATION_MESSAGE );
1293 void executeLineageInference() {
1294 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1297 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1298 JOptionPane.showMessageDialog( this,
1299 "Phylogeny is not rooted.",
1300 "Cannot infer ancestral taxonomies",
1301 JOptionPane.ERROR_MESSAGE );
1304 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1305 _mainpanel.getCurrentTreePanel(),
1306 _mainpanel.getCurrentPhylogeny()
1308 new Thread( inferrer ).start();
1311 void executeSDIR( final boolean minimize_cost ) {
1312 if ( !isOKforSDI( true, true ) ) {
1315 Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1316 final SDIR sdiunrooted = new SDIR();
1317 gene_tree.setAllNodesToNotCollapse();
1318 gene_tree.recalculateNumberOfExternalDescendants( false );
1320 gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1321 !minimize_cost, // minimize sum of dups
1322 true, // minimize height
1323 true, // return tree(s)
1324 1 )[ 0 ]; // # of trees to return
1326 catch ( final Exception e ) {
1327 JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1330 final int duplications = sdiunrooted.getMinimalDuplications();
1331 gene_tree.setRerootable( false );
1332 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1333 getControlPanel().setShowEvents( true );
1335 _mainpanel.getCurrentTreePanel().setEdited( true );
1336 JOptionPane.showMessageDialog( this,
1337 "Number of duplications: " + duplications,
1338 "SDIR successfully completed",
1339 JOptionPane.INFORMATION_MESSAGE );
1343 removeAllTextFrames();
1344 _mainpanel.terminate();
1345 _contentpane.removeAll();
1346 setVisible( false );
1351 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1352 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1355 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1356 JOptionPane.showMessageDialog( this,
1357 "No species tree loaded",
1358 "Cannot execute SDI",
1359 JOptionPane.ERROR_MESSAGE );
1362 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1363 JOptionPane.showMessageDialog( this,
1364 "Species tree is not completely binary",
1365 "Cannot execute SDI",
1366 JOptionPane.ERROR_MESSAGE );
1369 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1370 JOptionPane.showMessageDialog( this,
1371 "Gene tree is not completely binary",
1372 "Cannot execute SDI",
1373 JOptionPane.ERROR_MESSAGE );
1382 void readPhylogeniesFromURL() {
1384 Phylogeny[] phys = null;
1385 final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1386 final String url_string = JOptionPane.showInputDialog( this,
1388 "Use URL/webservice to obtain a phylogeny",
1389 JOptionPane.QUESTION_MESSAGE );
1390 boolean nhx_or_nexus = false;
1391 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1393 url = new URL( url_string );
1394 PhylogenyParser parser = null;
1395 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1396 parser = new TolParser();
1399 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1400 .isValidatePhyloXmlAgainstSchema() );
1402 if ( parser instanceof NexusPhylogeniesParser ) {
1403 nhx_or_nexus = true;
1405 else if ( parser instanceof NHXParser ) {
1406 nhx_or_nexus = true;
1408 if ( _mainpanel.getCurrentTreePanel() != null ) {
1409 _mainpanel.getCurrentTreePanel().setWaitCursor();
1412 _mainpanel.setWaitCursor();
1414 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1415 phys = factory.create( url.openStream(), parser );
1417 catch ( final MalformedURLException e ) {
1418 JOptionPane.showMessageDialog( this,
1419 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1421 JOptionPane.ERROR_MESSAGE );
1423 catch ( final IOException e ) {
1424 JOptionPane.showMessageDialog( this,
1425 "Could not read from " + url + "\n"
1426 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1427 "Failed to read URL",
1428 JOptionPane.ERROR_MESSAGE );
1430 catch ( final Exception e ) {
1431 JOptionPane.showMessageDialog( this,
1432 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1433 "Unexpected Exception",
1434 JOptionPane.ERROR_MESSAGE );
1437 if ( _mainpanel.getCurrentTreePanel() != null ) {
1438 _mainpanel.getCurrentTreePanel().setArrowCursor();
1441 _mainpanel.setArrowCursor();
1444 if ( ( phys != null ) && ( phys.length > 0 ) ) {
1445 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1446 for( final Phylogeny phy : phys ) {
1447 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1450 AptxUtil.addPhylogeniesToTabs( phys,
1451 new File( url.getFile() ).getName(),
1452 new File( url.getFile() ).toString(),
1455 _mainpanel.getControlPanel().showWhole();
1458 activateSaveAllIfNeeded();
1462 void setMsa( final Msa msa ) {
1466 void setMsaFile( final File msa_file ) {
1467 _msa_file = msa_file;
1470 void setSeqs( final List<Sequence> seqs ) {
1474 void setSeqsFile( final File seqs_file ) {
1475 _seqs_file = seqs_file;
1478 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1479 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1480 _mainpanel.getCurrentTreePanel().getHeight(),
1482 String file_written_to = "";
1483 boolean error = false;
1485 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1486 _mainpanel.getCurrentTreePanel().getWidth(),
1487 _mainpanel.getCurrentTreePanel().getHeight(),
1488 _mainpanel.getCurrentTreePanel(),
1489 _mainpanel.getControlPanel(),
1493 catch ( final IOException e ) {
1495 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1498 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1499 JOptionPane.showMessageDialog( this,
1500 "Wrote image to: " + file_written_to,
1502 JOptionPane.INFORMATION_MESSAGE );
1505 JOptionPane.showMessageDialog( this,
1506 "There was an unknown problem when attempting to write to an image file: \""
1509 JOptionPane.ERROR_MESSAGE );
1512 _contentpane.repaint();
1515 private void addExpressionValuesFromFile() {
1516 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1517 JOptionPane.showMessageDialog( this,
1518 "Need to load evolutionary tree first",
1519 "Can Not Read Expression Values",
1520 JOptionPane.WARNING_MESSAGE );
1523 final File my_dir = getCurrentDir();
1524 if ( my_dir != null ) {
1525 _values_filechooser.setCurrentDirectory( my_dir );
1527 final int result = _values_filechooser.showOpenDialog( _contentpane );
1528 final File file = _values_filechooser.getSelectedFile();
1529 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1530 BasicTable<String> t = null;
1532 t = BasicTableParser.parse( file, "\t" );
1533 if ( t.getNumberOfColumns() < 2 ) {
1534 t = BasicTableParser.parse( file, "," );
1536 if ( t.getNumberOfColumns() < 2 ) {
1537 t = BasicTableParser.parse( file, " " );
1540 catch ( final IOException e ) {
1541 JOptionPane.showMessageDialog( this,
1543 "Could Not Read Expression Value Table",
1544 JOptionPane.ERROR_MESSAGE );
1547 if ( t.getNumberOfColumns() < 2 ) {
1548 JOptionPane.showMessageDialog( this,
1549 "Table contains " + t.getNumberOfColumns() + " column(s)",
1550 "Problem with Expression Value Table",
1551 JOptionPane.ERROR_MESSAGE );
1554 if ( t.getNumberOfRows() < 1 ) {
1555 JOptionPane.showMessageDialog( this,
1556 "Table contains zero rows",
1557 "Problem with Expression Value Table",
1558 JOptionPane.ERROR_MESSAGE );
1561 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1562 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1563 JOptionPane.showMessageDialog( this,
1564 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1565 + phy.getNumberOfExternalNodes() + " external nodes",
1567 JOptionPane.WARNING_MESSAGE );
1569 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1571 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1572 final PhylogenyNode node = iter.next();
1573 final String node_name = node.getName();
1574 if ( !ForesterUtil.isEmpty( node_name ) ) {
1577 row = t.findRow( node_name );
1579 catch ( final IllegalArgumentException e ) {
1581 .showMessageDialog( this,
1583 "Error Mapping Node Identifiers to Expression Value Identifiers",
1584 JOptionPane.ERROR_MESSAGE );
1588 if ( node.isExternal() ) {
1593 final List<Double> l = new ArrayList<Double>();
1594 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1597 d = Double.parseDouble( t.getValueAsString( col, row ) );
1599 catch ( final NumberFormatException e ) {
1600 JOptionPane.showMessageDialog( this,
1601 "Could not parse \"" + t.getValueAsString( col, row )
1602 + "\" into a decimal value",
1603 "Issue with Expression Value Table",
1604 JOptionPane.ERROR_MESSAGE );
1607 stats.addValue( d );
1610 if ( !l.isEmpty() ) {
1611 if ( node.getNodeData().getProperties() != null ) {
1612 node.getNodeData().getProperties()
1613 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1615 node.getNodeData().setVector( l );
1619 if ( not_found > 0 ) {
1620 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1621 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1623 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1627 private void choosePdfWidth() {
1628 final String s = ( String ) JOptionPane.showInputDialog( this,
1629 "Please enter the default line width for PDF export.\n"
1630 + "[current value: "
1631 + getOptions().getPrintLineWidth() + "]\n",
1632 "Line Width for PDF Export",
1633 JOptionPane.QUESTION_MESSAGE,
1636 getOptions().getPrintLineWidth() );
1637 if ( !ForesterUtil.isEmpty( s ) ) {
1638 boolean success = true;
1640 final String m_str = s.trim();
1641 if ( !ForesterUtil.isEmpty( m_str ) ) {
1643 f = Float.parseFloat( m_str );
1645 catch ( final Exception ex ) {
1652 if ( success && ( f > 0.0 ) ) {
1653 getOptions().setPrintLineWidth( f );
1658 private void choosePrintSize() {
1659 final String s = ( String ) JOptionPane.showInputDialog( this,
1660 "Please enter values for width and height,\nseparated by a comma.\n"
1661 + "[current values: "
1662 + getOptions().getPrintSizeX() + ", "
1663 + getOptions().getPrintSizeY() + "]\n"
1664 + "[A4: " + Constants.A4_SIZE_X + ", "
1665 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1666 + Constants.US_LETTER_SIZE_X + ", "
1667 + Constants.US_LETTER_SIZE_Y + "]",
1668 "Default Size for Graphics Export",
1669 JOptionPane.QUESTION_MESSAGE,
1672 getOptions().getPrintSizeX() + ", "
1673 + getOptions().getPrintSizeY() );
1674 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1675 boolean success = true;
1678 final String[] str_ary = s.split( "," );
1679 if ( str_ary.length == 2 ) {
1680 final String x_str = str_ary[ 0 ].trim();
1681 final String y_str = str_ary[ 1 ].trim();
1682 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1684 x = Integer.parseInt( x_str );
1685 y = Integer.parseInt( y_str );
1687 catch ( final Exception ex ) {
1698 if ( success && ( x > 1 ) && ( y > 1 ) ) {
1699 getOptions().setPrintSizeX( x );
1700 getOptions().setPrintSizeY( y );
1705 private void closeCurrentPane() {
1706 if ( getMainPanel().getCurrentTreePanel() != null ) {
1707 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1708 final int r = JOptionPane.showConfirmDialog( this,
1709 "Close tab despite potentially unsaved changes?",
1711 JOptionPane.YES_NO_OPTION );
1712 if ( r != JOptionPane.YES_OPTION ) {
1716 getMainPanel().closeCurrentPane();
1717 activateSaveAllIfNeeded();
1721 private void collapse( final Phylogeny phy, final double m ) {
1722 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1723 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1724 double min_support = Double.MAX_VALUE;
1725 boolean conf_present = false;
1726 while ( it.hasNext() ) {
1727 final PhylogenyNode n = it.next();
1728 if ( !n.isExternal() && !n.isRoot() ) {
1729 final List<Confidence> c = n.getBranchData().getConfidences();
1730 if ( ( c != null ) && ( c.size() > 0 ) ) {
1731 conf_present = true;
1733 for( final Confidence confidence : c ) {
1734 if ( confidence.getValue() > max ) {
1735 max = confidence.getValue();
1738 if ( max < getMinNotCollapseConfidenceValue() ) {
1739 to_be_removed.add( n );
1741 if ( max < min_support ) {
1747 if ( conf_present ) {
1748 for( final PhylogenyNode node : to_be_removed ) {
1749 PhylogenyMethods.removeNode( node, phy );
1751 if ( to_be_removed.size() > 0 ) {
1752 phy.externalNodesHaveChanged();
1753 phy.clearHashIdToNodeMap();
1754 phy.recalculateNumberOfExternalDescendants( true );
1755 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1756 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1757 getCurrentTreePanel().calculateLongestExtNodeInfo();
1758 getCurrentTreePanel().setNodeInPreorderToNull();
1759 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1760 getCurrentTreePanel().resetPreferredSize();
1761 getCurrentTreePanel().setEdited( true );
1762 getCurrentTreePanel().repaint();
1765 if ( to_be_removed.size() > 0 ) {
1766 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1767 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1768 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1771 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1772 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1776 JOptionPane.showMessageDialog( this,
1777 "No branch collapsed because no confidence values present",
1778 "No confidence values present",
1779 JOptionPane.INFORMATION_MESSAGE );
1783 private void collapseBelowThreshold() {
1784 if ( getCurrentTreePanel() != null ) {
1785 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1786 if ( ( phy != null ) && !phy.isEmpty() ) {
1787 final String s = ( String ) JOptionPane.showInputDialog( this,
1788 "Please enter the minimum confidence value\n",
1789 "Minimal Confidence Value",
1790 JOptionPane.QUESTION_MESSAGE,
1793 getMinNotCollapseConfidenceValue() );
1794 if ( !ForesterUtil.isEmpty( s ) ) {
1795 boolean success = true;
1797 final String m_str = s.trim();
1798 if ( !ForesterUtil.isEmpty( m_str ) ) {
1800 m = Double.parseDouble( m_str );
1802 catch ( final Exception ex ) {
1809 if ( success && ( m >= 0.0 ) ) {
1810 setMinNotCollapseConfidenceValue( m );
1818 private PhyloXmlParser createPhyloXmlParser() {
1819 PhyloXmlParser xml_parser = null;
1820 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1822 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1824 catch ( final Exception e ) {
1825 JOptionPane.showMessageDialog( this,
1826 e.getLocalizedMessage(),
1827 "failed to create validating XML parser",
1828 JOptionPane.WARNING_MESSAGE );
1831 if ( xml_parser == null ) {
1832 xml_parser = new PhyloXmlParser();
1837 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1838 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1839 getPhylogeneticInferenceOptions(),
1840 from_unaligned_seqs );
1842 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1843 if ( !from_unaligned_seqs ) {
1844 if ( getMsa() != null ) {
1845 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1846 getPhylogeneticInferenceOptions()
1848 new Thread( inferrer ).start();
1851 JOptionPane.showMessageDialog( this,
1852 "No multiple sequence alignment selected",
1853 "Phylogenetic Inference Not Launched",
1854 JOptionPane.WARNING_MESSAGE );
1858 if ( getSeqs() != null ) {
1859 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1860 getPhylogeneticInferenceOptions()
1862 new Thread( inferrer ).start();
1865 JOptionPane.showMessageDialog( this,
1866 "No input sequences selected",
1867 "Phylogenetic Inference Not Launched",
1868 JOptionPane.WARNING_MESSAGE );
1874 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1875 final StringBuilder sb = new StringBuilder();
1876 final StringBuilder sb_failed = new StringBuilder();
1878 int counter_failed = 0;
1879 if ( getCurrentTreePanel() != null ) {
1880 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1881 if ( ( phy != null ) && !phy.isEmpty() ) {
1882 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1883 while ( it.hasNext() ) {
1884 final PhylogenyNode n = it.next();
1885 final String name = n.getName().trim();
1886 if ( !ForesterUtil.isEmpty( name ) ) {
1887 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES );
1888 if ( !ForesterUtil.isEmpty( nt ) ) {
1889 if ( counter < 15 ) {
1890 sb.append( name + ": " + nt + "\n" );
1892 else if ( counter == 15 ) {
1893 sb.append( "...\n" );
1898 if ( counter_failed < 15 ) {
1899 sb_failed.append( name + "\n" );
1901 else if ( counter_failed == 15 ) {
1902 sb_failed.append( "...\n" );
1908 if ( counter > 0 ) {
1910 String all = "all ";
1911 if ( counter_failed > 0 ) {
1913 failed = "\nCould not extract taxonomic data for " + counter_failed
1914 + " named external nodes:\n" + sb_failed;
1916 JOptionPane.showMessageDialog( this,
1917 "Extracted taxonomic data from " + all + counter
1918 + " named external nodes:\n" + sb.toString() + failed,
1919 "Taxonomic Data Extraction Completed",
1920 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1921 : JOptionPane.INFORMATION_MESSAGE );
1925 .showMessageDialog( this,
1926 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1927 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1928 + "or nodes already have taxonomic data?\n",
1929 "No Taxonomic Data Extracted",
1930 JOptionPane.ERROR_MESSAGE );
1936 private ControlPanel getControlPanel() {
1937 return getMainPanel().getControlPanel();
1940 private File getCurrentDir() {
1941 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1942 if ( ForesterUtil.isWindowns() ) {
1944 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1946 catch ( final Exception e ) {
1947 _current_dir = null;
1951 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1952 if ( System.getProperty( "user.home" ) != null ) {
1953 _current_dir = new File( System.getProperty( "user.home" ) );
1955 else if ( System.getProperty( "user.dir" ) != null ) {
1956 _current_dir = new File( System.getProperty( "user.dir" ) );
1959 return _current_dir;
1962 private double getMinNotCollapseConfidenceValue() {
1963 return _min_not_collapse;
1966 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1967 if ( _phylogenetic_inference_options == null ) {
1968 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1970 return _phylogenetic_inference_options;
1973 private boolean isUnsavedDataPresent() {
1974 final List<TreePanel> tps = getMainPanel().getTreePanels();
1975 for( final TreePanel tp : tps ) {
1976 if ( tp.isEdited() ) {
1983 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1984 if ( getCurrentTreePanel() != null ) {
1985 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1986 if ( ( phy != null ) && !phy.isEmpty() ) {
1988 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1993 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1994 if ( getCurrentTreePanel() != null ) {
1995 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1996 if ( ( phy != null ) && !phy.isEmpty() ) {
1997 PhylogenyMethods.transferNodeNameToField( phy,
1998 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
2004 private void newTree() {
2005 final Phylogeny[] phys = new Phylogeny[ 1 ];
2006 final Phylogeny phy = new Phylogeny();
2007 final PhylogenyNode node = new PhylogenyNode();
2008 phy.setRoot( node );
2009 phy.setRooted( true );
2011 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
2012 _mainpanel.getControlPanel().showWhole();
2013 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2014 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2015 if ( getMainPanel().getMainFrame() == null ) {
2016 // Must be "E" applet version.
2017 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
2018 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2021 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2023 activateSaveAllIfNeeded();
2027 private void obtainDetailedTaxonomicInformation() {
2028 if ( getCurrentTreePanel() != null ) {
2029 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2030 if ( ( phy != null ) && !phy.isEmpty() ) {
2031 final TaxonomyDataManager t = new TaxonomyDataManager( this,
2032 _mainpanel.getCurrentTreePanel(),
2036 new Thread( t ).start();
2041 private void obtainDetailedTaxonomicInformationDelete() {
2042 if ( getCurrentTreePanel() != null ) {
2043 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2044 if ( ( phy != null ) && !phy.isEmpty() ) {
2045 final TaxonomyDataManager t = new TaxonomyDataManager( this,
2046 _mainpanel.getCurrentTreePanel(),
2050 new Thread( t ).start();
2055 private void obtainSequenceInformation() {
2056 if ( getCurrentTreePanel() != null ) {
2057 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2058 if ( ( phy != null ) && !phy.isEmpty() ) {
2059 final SequenceDataRetriver u = new SequenceDataRetriver( this,
2060 _mainpanel.getCurrentTreePanel(),
2062 new Thread( u ).start();
2067 private void print() {
2068 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2069 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2072 if ( !getOptions().isPrintUsingActualSize() ) {
2073 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
2074 getOptions().getPrintSizeY() - 140,
2076 getCurrentTreePanel().resetPreferredSize();
2077 getCurrentTreePanel().repaint();
2079 final String job_name = Constants.PRG_NAME;
2080 boolean error = false;
2081 String printer_name = null;
2083 printer_name = Printer.print( getCurrentTreePanel(), job_name );
2085 catch ( final Exception e ) {
2087 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2089 if ( !error && ( printer_name != null ) ) {
2090 String msg = "Printing data sent to printer";
2091 if ( printer_name.length() > 1 ) {
2092 msg += " [" + printer_name + "]";
2094 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2096 if ( !getOptions().isPrintUsingActualSize() ) {
2097 getControlPanel().showWhole();
2101 private void printPhylogenyToPdf( final String file_name ) {
2102 if ( !getOptions().isPrintUsingActualSize() ) {
2103 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
2104 getOptions().getPrintSizeY(),
2106 getCurrentTreePanel().resetPreferredSize();
2107 getCurrentTreePanel().repaint();
2109 String pdf_written_to = "";
2110 boolean error = false;
2112 if ( getOptions().isPrintUsingActualSize() ) {
2113 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2114 getCurrentTreePanel(),
2115 getCurrentTreePanel().getWidth(),
2116 getCurrentTreePanel().getHeight() );
2119 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2120 .getPrintSizeX(), getOptions().getPrintSizeY() );
2123 catch ( final IOException e ) {
2125 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2128 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2129 JOptionPane.showMessageDialog( this,
2130 "Wrote PDF to: " + pdf_written_to,
2132 JOptionPane.INFORMATION_MESSAGE );
2135 JOptionPane.showMessageDialog( this,
2136 "There was an unknown problem when attempting to write to PDF file: \""
2139 JOptionPane.ERROR_MESSAGE );
2142 if ( !getOptions().isPrintUsingActualSize() ) {
2143 getControlPanel().showWhole();
2147 private void readPhylogeniesFromFile() {
2148 boolean exception = false;
2149 Phylogeny[] phys = null;
2150 // Set an initial directory if none set yet
2151 final File my_dir = getCurrentDir();
2152 _open_filechooser.setMultiSelectionEnabled( true );
2153 // Open file-open dialog and set current directory
2154 if ( my_dir != null ) {
2155 _open_filechooser.setCurrentDirectory( my_dir );
2157 final int result = _open_filechooser.showOpenDialog( _contentpane );
2158 // All done: get the file
2159 final File[] files = _open_filechooser.getSelectedFiles();
2160 setCurrentDir( _open_filechooser.getCurrentDirectory() );
2161 boolean nhx_or_nexus = false;
2162 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2163 for( final File file : files ) {
2164 if ( ( file != null ) && !file.isDirectory() ) {
2165 if ( _mainpanel.getCurrentTreePanel() != null ) {
2166 _mainpanel.getCurrentTreePanel().setWaitCursor();
2169 _mainpanel.setWaitCursor();
2171 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2172 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2174 final NHXParser nhx = new NHXParser();
2175 setSpecialOptionsForNhxParser( nhx );
2176 phys = PhylogenyMethods.readPhylogenies( nhx, file );
2177 nhx_or_nexus = true;
2179 catch ( final Exception e ) {
2181 exceptionOccuredDuringOpenFile( e );
2184 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2185 warnIfNotPhyloXmlValidation( getConfiguration() );
2187 final PhyloXmlParser xml_parser = createPhyloXmlParser();
2188 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2190 catch ( final Exception e ) {
2192 exceptionOccuredDuringOpenFile( e );
2195 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2197 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2199 catch ( final Exception e ) {
2201 exceptionOccuredDuringOpenFile( e );
2204 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2206 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2207 setSpecialOptionsForNexParser( nex );
2208 phys = PhylogenyMethods.readPhylogenies( nex, file );
2209 nhx_or_nexus = true;
2211 catch ( final Exception e ) {
2213 exceptionOccuredDuringOpenFile( e );
2219 final PhylogenyParser parser = ParserUtils
2220 .createParserDependingOnFileType( file, getConfiguration()
2221 .isValidatePhyloXmlAgainstSchema() );
2222 if ( parser instanceof NexusPhylogeniesParser ) {
2223 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2224 setSpecialOptionsForNexParser( nex );
2225 nhx_or_nexus = true;
2227 else if ( parser instanceof NHXParser ) {
2228 final NHXParser nhx = ( NHXParser ) parser;
2229 setSpecialOptionsForNhxParser( nhx );
2230 nhx_or_nexus = true;
2232 else if ( parser instanceof PhyloXmlParser ) {
2233 warnIfNotPhyloXmlValidation( getConfiguration() );
2235 phys = PhylogenyMethods.readPhylogenies( parser, file );
2237 catch ( final Exception e ) {
2239 exceptionOccuredDuringOpenFile( e );
2242 if ( _mainpanel.getCurrentTreePanel() != null ) {
2243 _mainpanel.getCurrentTreePanel().setArrowCursor();
2246 _mainpanel.setArrowCursor();
2248 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2249 boolean one_desc = false;
2250 if ( nhx_or_nexus ) {
2251 for( final Phylogeny phy : phys ) {
2252 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2253 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2255 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2261 AptxUtil.addPhylogeniesToTabs( phys,
2263 file.getAbsolutePath(),
2266 _mainpanel.getControlPanel().showWhole();
2267 if ( nhx_or_nexus && one_desc ) {
2269 .showMessageDialog( this,
2270 "One or more trees contain (a) node(s) with one descendant, "
2271 + ForesterUtil.LINE_SEPARATOR
2272 + "possibly indicating illegal parentheses within node names.",
2273 "Warning: Possible Error in New Hampshire Formatted Data",
2274 JOptionPane.WARNING_MESSAGE );
2280 activateSaveAllIfNeeded();
2284 private void readSpeciesTreeFromFile() {
2286 boolean exception = false;
2287 final File my_dir = getCurrentDir();
2288 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2289 if ( my_dir != null ) {
2290 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2292 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2293 final File file = _open_filechooser_for_species_tree.getSelectedFile();
2294 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2295 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2297 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2300 catch ( final Exception e ) {
2302 exceptionOccuredDuringOpenFile( e );
2305 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2307 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2310 catch ( final Exception e ) {
2312 exceptionOccuredDuringOpenFile( e );
2318 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2321 catch ( final Exception e ) {
2323 exceptionOccuredDuringOpenFile( e );
2326 if ( !exception && ( t != null ) && !t.isRooted() ) {
2329 JOptionPane.showMessageDialog( this,
2330 "Species tree is not rooted",
2331 "Species tree not loaded",
2332 JOptionPane.ERROR_MESSAGE );
2334 if ( !exception && ( t != null ) ) {
2335 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2336 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2337 final PhylogenyNode node = it.next();
2338 if ( !node.getNodeData().isHasTaxonomy() ) {
2342 .showMessageDialog( this,
2343 "Species tree contains external node(s) without taxonomy information",
2344 "Species tree not loaded",
2345 JOptionPane.ERROR_MESSAGE );
2349 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2352 JOptionPane.showMessageDialog( this,
2354 + node.getNodeData().getTaxonomy().asSimpleText()
2355 + "] is not unique in species tree",
2356 "Species tree not loaded",
2357 JOptionPane.ERROR_MESSAGE );
2361 tax_set.add( node.getNodeData().getTaxonomy() );
2366 if ( !exception && ( t != null ) ) {
2368 JOptionPane.showMessageDialog( this,
2369 "Species tree successfully loaded",
2370 "Species tree loaded",
2371 JOptionPane.INFORMATION_MESSAGE );
2373 _contentpane.repaint();
2378 private void setCurrentDir( final File current_dir ) {
2379 _current_dir = current_dir;
2382 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2383 _min_not_collapse = min_not_collapse;
2386 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2387 _phylogenetic_inference_options = phylogenetic_inference_options;
2390 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2391 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2392 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2395 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2396 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2397 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2400 private void writeAllToFile() {
2401 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2404 final File my_dir = getCurrentDir();
2405 if ( my_dir != null ) {
2406 _save_filechooser.setCurrentDirectory( my_dir );
2408 _save_filechooser.setSelectedFile( new File( "" ) );
2409 final int result = _save_filechooser.showSaveDialog( _contentpane );
2410 final File file = _save_filechooser.getSelectedFile();
2411 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2412 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2413 if ( file.exists() ) {
2414 final int i = JOptionPane.showConfirmDialog( this,
2415 file + " already exists. Overwrite?",
2417 JOptionPane.OK_CANCEL_OPTION,
2418 JOptionPane.WARNING_MESSAGE );
2419 if ( i != JOptionPane.OK_OPTION ) {
2426 catch ( final Exception e ) {
2427 JOptionPane.showMessageDialog( this,
2428 "Failed to delete: " + file,
2430 JOptionPane.WARNING_MESSAGE );
2434 final int count = getMainPanel().getTabbedPane().getTabCount();
2435 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2436 for( int i = 0; i < count; ++i ) {
2437 trees.add( getMainPanel().getPhylogeny( i ) );
2438 getMainPanel().getTreePanels().get( i ).setEdited( false );
2440 final PhylogenyWriter writer = new PhylogenyWriter();
2442 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2444 catch ( final IOException e ) {
2445 JOptionPane.showMessageDialog( this,
2446 "Failed to write to: " + file,
2448 JOptionPane.WARNING_MESSAGE );
2453 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2455 final PhylogenyWriter writer = new PhylogenyWriter();
2456 writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2458 catch ( final Exception e ) {
2460 exceptionOccuredDuringSaveAs( e );
2465 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2467 final PhylogenyWriter writer = new PhylogenyWriter();
2468 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2470 catch ( final Exception e ) {
2472 exceptionOccuredDuringSaveAs( e );
2477 private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
2479 final PhylogenyWriter writer = new PhylogenyWriter();
2480 writer.toNewHampshireX( t, file );
2482 catch ( final Exception e ) {
2484 exceptionOccuredDuringSaveAs( e );
2489 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2491 final PhylogenyWriter writer = new PhylogenyWriter();
2492 writer.toPhyloXML( file, t, 0 );
2494 catch ( final Exception e ) {
2496 exceptionOccuredDuringSaveAs( e );
2501 private void writeToFile( final Phylogeny t ) {
2505 String initial_filename = null;
2506 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2508 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2510 catch ( final IOException e ) {
2511 initial_filename = null;
2514 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2515 _save_filechooser.setSelectedFile( new File( initial_filename ) );
2518 _save_filechooser.setSelectedFile( new File( "" ) );
2520 final File my_dir = getCurrentDir();
2521 if ( my_dir != null ) {
2522 _save_filechooser.setCurrentDirectory( my_dir );
2524 final int result = _save_filechooser.showSaveDialog( _contentpane );
2525 final File file = _save_filechooser.getSelectedFile();
2526 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2527 boolean exception = false;
2528 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2529 if ( file.exists() ) {
2530 final int i = JOptionPane.showConfirmDialog( this,
2531 file + " already exists.\nOverwrite?",
2533 JOptionPane.OK_CANCEL_OPTION,
2534 JOptionPane.QUESTION_MESSAGE );
2535 if ( i != JOptionPane.OK_OPTION ) {
2539 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2541 ForesterUtil.copyFile( file, to );
2543 catch ( final Exception e ) {
2544 JOptionPane.showMessageDialog( this,
2545 "Failed to create backup copy " + to,
2546 "Failed to Create Backup Copy",
2547 JOptionPane.WARNING_MESSAGE );
2552 catch ( final Exception e ) {
2553 JOptionPane.showMessageDialog( this,
2554 "Failed to delete: " + file,
2556 JOptionPane.WARNING_MESSAGE );
2560 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2561 exception = writeAsNewHampshire( t, exception, file );
2563 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
2564 exception = writeAsNHX( t, exception, file );
2566 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2567 exception = writeAsPhyloXml( t, exception, file );
2569 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2570 exception = writeAsNexus( t, exception, file );
2574 final String file_name = file.getName().trim().toLowerCase();
2575 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2576 || file_name.endsWith( ".tree" ) ) {
2577 exception = writeAsNewHampshire( t, exception, file );
2579 else if ( file_name.endsWith( ".nhx" ) ) {
2580 exception = writeAsNHX( t, exception, file );
2582 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2583 exception = writeAsNexus( t, exception, file );
2587 exception = writeAsPhyloXml( t, exception, file );
2591 getMainPanel().setTitleOfSelectedTab( file.getName() );
2592 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2593 getMainPanel().getCurrentTreePanel().setEdited( false );
2598 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2599 if ( ( t == null ) || t.isEmpty() ) {
2602 String initial_filename = "";
2603 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2604 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2606 if ( initial_filename.indexOf( '.' ) > 0 ) {
2607 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2609 initial_filename = initial_filename + "." + type;
2610 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2611 final File my_dir = getCurrentDir();
2612 if ( my_dir != null ) {
2613 _writetographics_filechooser.setCurrentDirectory( my_dir );
2615 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2616 File file = _writetographics_filechooser.getSelectedFile();
2617 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2618 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2619 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2620 file = new File( file.toString() + "." + type );
2622 if ( file.exists() ) {
2623 final int i = JOptionPane.showConfirmDialog( this,
2624 file + " already exists. Overwrite?",
2626 JOptionPane.OK_CANCEL_OPTION,
2627 JOptionPane.WARNING_MESSAGE );
2628 if ( i != JOptionPane.OK_OPTION ) {
2635 catch ( final Exception e ) {
2636 JOptionPane.showMessageDialog( this,
2637 "Failed to delete: " + file,
2639 JOptionPane.WARNING_MESSAGE );
2643 writePhylogenyToGraphicsFile( file.toString(), type );
2647 private void writeToPdf( final Phylogeny t ) {
2648 if ( ( t == null ) || t.isEmpty() ) {
2651 String initial_filename = "";
2652 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2653 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2655 if ( initial_filename.indexOf( '.' ) > 0 ) {
2656 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2658 initial_filename = initial_filename + ".pdf";
2659 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2660 final File my_dir = getCurrentDir();
2661 if ( my_dir != null ) {
2662 _writetopdf_filechooser.setCurrentDirectory( my_dir );
2664 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2665 File file = _writetopdf_filechooser.getSelectedFile();
2666 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2667 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2668 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2669 file = new File( file.toString() + ".pdf" );
2671 if ( file.exists() ) {
2672 final int i = JOptionPane.showConfirmDialog( this,
2673 file + " already exists. Overwrite?",
2675 JOptionPane.OK_CANCEL_OPTION,
2676 JOptionPane.WARNING_MESSAGE );
2677 if ( i != JOptionPane.OK_OPTION ) {
2681 printPhylogenyToPdf( file.toString() );
2685 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2686 return new MainFrameApplication( phys, config );
2689 public static MainFrame createInstance( final Phylogeny[] phys,
2690 final Configuration config,
2692 final File current_dir ) {
2693 return new MainFrameApplication( phys, config, title, current_dir );
2696 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2697 return new MainFrameApplication( phys, config, title );
2700 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2701 return new MainFrameApplication( phys, config_file_name, title );
2704 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2705 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2706 + o.getPrintSizeY() + ")" );
2709 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2710 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2713 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2714 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2716 .showMessageDialog( null,
2718 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2721 JOptionPane.WARNING_MESSAGE );
2724 } // MainFrameApplication.
2726 class DefaultFilter extends FileFilter {
2729 public boolean accept( final File f ) {
2730 final String file_name = f.getName().trim().toLowerCase();
2731 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2732 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2733 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2734 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2735 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2736 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2737 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2738 || file_name.endsWith( ".con" ) || f.isDirectory();
2742 public String getDescription() {
2743 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2747 class GraphicsFileFilter extends FileFilter {
2750 public boolean accept( final File f ) {
2751 final String file_name = f.getName().trim().toLowerCase();
2752 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2753 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2757 public String getDescription() {
2758 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2762 class MsaFileFilter extends FileFilter {
2765 public boolean accept( final File f ) {
2766 final String file_name = f.getName().trim().toLowerCase();
2767 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2768 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2772 public String getDescription() {
2773 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2777 class NexusFilter extends FileFilter {
2780 public boolean accept( final File f ) {
2781 final String file_name = f.getName().trim().toLowerCase();
2782 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2783 || file_name.endsWith( ".tre" ) || f.isDirectory();
2787 public String getDescription() {
2788 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2792 class NHFilter extends FileFilter {
2795 public boolean accept( final File f ) {
2796 final String file_name = f.getName().trim().toLowerCase();
2797 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2798 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2799 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2804 public String getDescription() {
2805 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2809 class NHXFilter extends FileFilter {
2812 public boolean accept( final File f ) {
2813 final String file_name = f.getName().trim().toLowerCase();
2814 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2818 public String getDescription() {
2819 return "NHX files (*.nhx)";
2823 class PdfFilter extends FileFilter {
2826 public boolean accept( final File f ) {
2827 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2831 public String getDescription() {
2832 return "PDF files (*.pdf)";
2836 class SequencesFileFilter extends FileFilter {
2839 public boolean accept( final File f ) {
2840 final String file_name = f.getName().trim().toLowerCase();
2841 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2842 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2846 public String getDescription() {
2847 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2851 class TolFilter extends FileFilter {
2854 public boolean accept( final File f ) {
2855 final String file_name = f.getName().trim().toLowerCase();
2856 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2857 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2861 public String getDescription() {
2862 return "Tree of Life files (*.tol, *.tolxml)";
2866 class XMLFilter extends FileFilter {
2869 public boolean accept( final File f ) {
2870 final String file_name = f.getName().trim().toLowerCase();
2871 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2872 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2876 public String getDescription() {
2877 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";