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.InferenceManager;
70 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
71 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
72 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
73 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
74 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
75 import org.forester.archaeopteryx.webservices.WebservicesManager;
76 import org.forester.io.parsers.FastaParser;
77 import org.forester.io.parsers.GeneralMsaParser;
78 import org.forester.io.parsers.PhylogenyParser;
79 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
80 import org.forester.io.parsers.nhx.NHXParser;
81 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
82 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
83 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
84 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
85 import org.forester.io.parsers.tol.TolParser;
86 import org.forester.io.parsers.util.ParserUtils;
87 import org.forester.io.writers.PhylogenyWriter;
88 import org.forester.io.writers.SequenceWriter;
89 import org.forester.msa.Msa;
90 import org.forester.msa.MsaFormatException;
91 import org.forester.phylogeny.Phylogeny;
92 import org.forester.phylogeny.PhylogenyMethods;
93 import org.forester.phylogeny.PhylogenyNode;
94 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
95 import org.forester.phylogeny.data.Confidence;
96 import org.forester.phylogeny.data.Taxonomy;
97 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
98 import org.forester.phylogeny.factories.PhylogenyFactory;
99 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
100 import org.forester.sequence.Sequence;
101 import org.forester.util.BasicDescriptiveStatistics;
102 import org.forester.util.BasicTable;
103 import org.forester.util.BasicTableParser;
104 import org.forester.util.DescriptiveStatistics;
105 import org.forester.util.ForesterUtil;
106 import org.forester.util.WindowsUtils;
108 public final class MainFrameApplication extends MainFrame {
110 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
111 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
112 private final static int FRAME_X_SIZE = 800;
113 private final static int FRAME_Y_SIZE = 800;
114 // Filters for the file-open dialog (classes defined in this file)
115 private final static NHFilter nhfilter = new NHFilter();
116 private final static NHXFilter nhxfilter = new NHXFilter();
117 private final static XMLFilter xmlfilter = new XMLFilter();
118 private final static TolFilter tolfilter = new TolFilter();
119 private final static NexusFilter nexusfilter = new NexusFilter();
120 private final static PdfFilter pdffilter = new PdfFilter();
121 private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
122 private final static MsaFileFilter msafilter = new MsaFileFilter();
123 private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
124 private final static DefaultFilter defaultfilter = new DefaultFilter();
125 private static final long serialVersionUID = -799735726778865234L;
126 private final JFileChooser _values_filechooser;
127 private final JFileChooser _sequences_filechooser;
128 private final JFileChooser _open_filechooser;
129 private final JFileChooser _msa_filechooser;
130 private final JFileChooser _seqs_pi_filechooser;
131 private final JFileChooser _open_filechooser_for_species_tree;
132 private final JFileChooser _save_filechooser;
133 private final JFileChooser _writetopdf_filechooser;
134 private final JFileChooser _writetographics_filechooser;
135 // Application-only print menu items
136 private JMenuItem _print_item;
137 private JMenuItem _write_to_pdf_item;
138 private JMenuItem _write_to_jpg_item;
139 private JMenuItem _write_to_gif_item;
140 private JMenuItem _write_to_tif_item;
141 private JMenuItem _write_to_png_item;
142 private JMenuItem _write_to_bmp_item;
143 private File _current_dir;
144 private ButtonGroup _radio_group_1;
145 private ButtonGroup _radio_group_2;
147 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
148 // Phylogeny Inference menu
149 private JMenu _inference_menu;
150 private JMenuItem _inference_from_msa_item;
151 private JMenuItem _inference_from_seqs_item;
152 // Phylogeny Inference
153 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
154 private Msa _msa = null;
155 private File _msa_file = null;
156 private List<Sequence> _seqs = null;
157 private File _seqs_file = null;
158 JMenuItem _read_values_jmi;
159 JMenuItem _read_seqs_jmi;
161 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
162 _configuration = config;
163 if ( _configuration == null ) {
164 throw new IllegalArgumentException( "configuration is null" );
167 setOptions( Options.createInstance( _configuration ) );
168 _mainpanel = new MainPanel( _configuration, this );
169 _open_filechooser = null;
170 _open_filechooser_for_species_tree = null;
171 _save_filechooser = null;
172 _writetopdf_filechooser = null;
173 _writetographics_filechooser = null;
174 _msa_filechooser = null;
175 _seqs_pi_filechooser = null;
176 _values_filechooser = null;
177 _sequences_filechooser = null;
178 _jmenubar = new JMenuBar();
181 _contentpane = getContentPane();
182 _contentpane.setLayout( new BorderLayout() );
183 _contentpane.add( _mainpanel, BorderLayout.CENTER );
185 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
186 // The window listener
187 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
188 addWindowListener( new WindowAdapter() {
191 public void windowClosing( final WindowEvent e ) {
195 // setVisible( true );
196 if ( ( phys != null ) && ( phys.length > 0 ) ) {
197 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
199 getMainPanel().getControlPanel().showWholeAll();
200 getMainPanel().getControlPanel().showWhole();
202 //activateSaveAllIfNeeded();
203 // ...and its children
204 _contentpane.repaint();
207 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
208 this( phys, config, title, null );
211 private MainFrameApplication( final Phylogeny[] phys,
212 final Configuration config,
214 final File current_dir ) {
216 _configuration = config;
217 if ( _configuration == null ) {
218 throw new IllegalArgumentException( "configuration is null" );
221 boolean synth_exception = false;
222 if ( Constants.__SYNTH_LF ) {
224 final SynthLookAndFeel synth = new SynthLookAndFeel();
225 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
226 MainFrameApplication.class );
227 UIManager.setLookAndFeel( synth );
229 catch ( final Exception ex ) {
230 synth_exception = true;
231 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
232 "could not create synth look and feel: "
233 + ex.getLocalizedMessage() );
236 if ( !Constants.__SYNTH_LF || synth_exception ) {
237 if ( _configuration.isUseNativeUI() ) {
238 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
241 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
244 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
246 catch ( final UnsupportedLookAndFeelException e ) {
247 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
249 catch ( final ClassNotFoundException e ) {
250 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
252 catch ( final InstantiationException e ) {
253 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
255 catch ( final IllegalAccessException e ) {
256 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
258 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
259 setCurrentDir( current_dir );
261 // hide until everything is ready
263 setOptions( Options.createInstance( _configuration ) );
264 setInferenceManager( InferenceManager.createInstance( _configuration ) );
265 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
266 // _textframe = null; #~~~~
268 setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
269 _mainpanel = new MainPanel( _configuration, this );
271 _open_filechooser = new JFileChooser();
272 _open_filechooser.setCurrentDirectory( new File( "." ) );
273 _open_filechooser.setMultiSelectionEnabled( false );
274 _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
275 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
276 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
277 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
278 _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
279 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
280 _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
281 _open_filechooser_for_species_tree = new JFileChooser();
282 _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
283 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
284 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
285 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
286 _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
287 _save_filechooser = new JFileChooser();
288 _save_filechooser.setCurrentDirectory( new File( "." ) );
289 _save_filechooser.setMultiSelectionEnabled( false );
290 _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
291 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
292 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
293 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
294 _writetopdf_filechooser = new JFileChooser();
295 _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
296 _writetographics_filechooser = new JFileChooser();
297 _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
299 _msa_filechooser = new JFileChooser();
300 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
301 _msa_filechooser.setCurrentDirectory( new File( "." ) );
302 _msa_filechooser.setMultiSelectionEnabled( false );
303 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
304 _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
306 _seqs_pi_filechooser = new JFileChooser();
307 _seqs_pi_filechooser.setName( "Read Sequences File" );
308 _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
309 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
310 _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
311 _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
313 _values_filechooser = new JFileChooser();
314 _values_filechooser.setCurrentDirectory( new File( "." ) );
315 _values_filechooser.setMultiSelectionEnabled( false );
317 _sequences_filechooser = new JFileChooser();
318 _sequences_filechooser.setCurrentDirectory( new File( "." ) );
319 _sequences_filechooser.setMultiSelectionEnabled( false );
320 // build the menu bar
321 _jmenubar = new JMenuBar();
322 if ( !_configuration.isUseNativeUI() ) {
323 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
326 if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
327 buildPhylogeneticInferenceMenu();
336 setJMenuBar( _jmenubar );
337 _jmenubar.add( _help_jmenu );
338 _contentpane = getContentPane();
339 _contentpane.setLayout( new BorderLayout() );
340 _contentpane.add( _mainpanel, BorderLayout.CENTER );
342 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
343 // addWindowFocusListener( new WindowAdapter() {
346 // public void windowGainedFocus( WindowEvent e ) {
347 // requestFocusInWindow();
350 // The window listener
351 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
352 addWindowListener( new WindowAdapter() {
355 public void windowClosing( final WindowEvent e ) {
356 if ( isUnsavedDataPresent() ) {
357 final int r = JOptionPane.showConfirmDialog( null,
358 "Exit despite potentially unsaved changes?",
360 JOptionPane.YES_NO_OPTION );
361 if ( r != JOptionPane.YES_OPTION ) {
366 final int r = JOptionPane.showConfirmDialog( null,
367 "Exit Archaeopteryx?",
369 JOptionPane.YES_NO_OPTION );
370 if ( r != JOptionPane.YES_OPTION ) {
377 // The component listener
378 addComponentListener( new ComponentAdapter() {
381 public void componentResized( final ComponentEvent e ) {
382 if ( _mainpanel.getCurrentTreePanel() != null ) {
383 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
385 _mainpanel.getCurrentTreePanel()
387 getOptions().isAllowFontSizeChange() );
391 requestFocusInWindow();
392 // addKeyListener( this );
394 if ( ( phys != null ) && ( phys.length > 0 ) ) {
395 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
397 getMainPanel().getControlPanel().showWholeAll();
398 getMainPanel().getControlPanel().showWhole();
400 activateSaveAllIfNeeded();
401 // ...and its children
402 _contentpane.repaint();
406 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
407 // Reads the config file (false, false => not url, not applet):
408 this( phys, new Configuration( config_file, false, false, true ), title );
412 public void actionPerformed( final ActionEvent e ) {
414 super.actionPerformed( e );
415 final Object o = e.getSource();
416 // Handle app-specific actions here:
417 if ( o == _open_item ) {
418 readPhylogeniesFromFile();
420 else if ( o == _save_item ) {
421 writeToFile( _mainpanel.getCurrentPhylogeny() );
422 // If subtree currently displayed, save it, instead of complete
425 else if ( o == _new_item ) {
428 else if ( o == _save_all_item ) {
431 else if ( o == _close_item ) {
434 else if ( o == _write_to_pdf_item ) {
435 writeToPdf( _mainpanel.getCurrentPhylogeny() );
437 else if ( o == _write_to_jpg_item ) {
438 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
440 else if ( o == _write_to_png_item ) {
441 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
443 else if ( o == _write_to_gif_item ) {
444 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
446 else if ( o == _write_to_tif_item ) {
447 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
449 else if ( o == _write_to_bmp_item ) {
450 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
452 else if ( o == _print_item ) {
455 else if ( o == _load_species_tree_item ) {
456 readSpeciesTreeFromFile();
458 else if ( o == _lineage_inference ) {
459 if ( isSubtreeDisplayed() ) {
460 JOptionPane.showMessageDialog( this,
462 "Cannot infer ancestral taxonomies",
463 JOptionPane.ERROR_MESSAGE );
466 executeLineageInference();
468 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
469 if ( isSubtreeDisplayed() ) {
472 obtainDetailedTaxonomicInformation();
474 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
475 if ( isSubtreeDisplayed() ) {
478 obtainDetailedTaxonomicInformationDelete();
480 else if ( o == _obtain_seq_information_jmi ) {
481 obtainSequenceInformation();
483 else if ( o == _read_values_jmi ) {
484 if ( isSubtreeDisplayed() ) {
487 addExpressionValuesFromFile();
489 else if ( o == _read_seqs_jmi ) {
490 if ( isSubtreeDisplayed() ) {
493 addSequencesFromFile();
495 else if ( o == _move_node_names_to_tax_sn_jmi ) {
496 moveNodeNamesToTaxSn();
498 else if ( o == _move_node_names_to_seq_names_jmi ) {
499 moveNodeNamesToSeqNames();
501 else if ( o == _extract_tax_code_from_node_names_jmi ) {
502 extractTaxDataFromNodeNames();
504 else if ( o == _graphics_export_visible_only_cbmi ) {
505 updateOptions( getOptions() );
507 else if ( o == _antialias_print_cbmi ) {
508 updateOptions( getOptions() );
510 else if ( o == _print_black_and_white_cbmi ) {
511 updateOptions( getOptions() );
513 else if ( o == _print_using_actual_size_cbmi ) {
514 updateOptions( getOptions() );
516 else if ( o == _graphics_export_using_actual_size_cbmi ) {
517 updateOptions( getOptions() );
519 else if ( o == _print_size_mi ) {
522 else if ( o == _choose_pdf_width_mi ) {
525 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
526 updateOptions( getOptions() );
528 else if ( o == _replace_underscores_cbmi ) {
529 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
530 _extract_taxonomy_no_rbmi.setSelected( true );
532 updateOptions( getOptions() );
534 else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
535 updateOptions( getOptions() );
537 else if ( o == _collapse_below_threshold ) {
538 if ( isSubtreeDisplayed() ) {
541 collapseBelowThreshold();
543 else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
544 || ( o == _extract_taxonomy_agressive_rbmi ) ) {
545 if ( _replace_underscores_cbmi != null ) {
546 _replace_underscores_cbmi.setSelected( false );
548 updateOptions( getOptions() );
550 else if ( o == _extract_taxonomy_no_rbmi ) {
551 updateOptions( getOptions() );
553 else if ( o == _inference_from_msa_item ) {
554 executePhyleneticInference( false );
556 else if ( o == _inference_from_seqs_item ) {
557 executePhyleneticInference( true );
559 _contentpane.repaint();
561 catch ( final Exception ex ) {
562 AptxUtil.unexpectedException( ex );
564 catch ( final Error err ) {
565 AptxUtil.unexpectedError( err );
570 _mainpanel.terminate();
571 _contentpane.removeAll();
577 public MainPanel getMainPanel() {
581 public Msa getMsa() {
585 public File getMsaFile() {
589 public List<Sequence> getSeqs() {
593 public File getSeqsFile() {
597 public void readMsaFromFile() {
598 // Set an initial directory if none set yet
599 final File my_dir = getCurrentDir();
600 _msa_filechooser.setMultiSelectionEnabled( false );
601 // Open file-open dialog and set current directory
602 if ( my_dir != null ) {
603 _msa_filechooser.setCurrentDirectory( my_dir );
605 final int result = _msa_filechooser.showOpenDialog( _contentpane );
606 // All done: get the msa
607 final File file = _msa_filechooser.getSelectedFile();
608 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
609 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
614 final InputStream is = new FileInputStream( file );
615 if ( FastaParser.isLikelyFasta( file ) ) {
616 msa = FastaParser.parseMsa( is );
619 msa = GeneralMsaParser.parse( is );
622 catch ( final MsaFormatException e ) {
624 JOptionPane.showMessageDialog( this,
625 e.getLocalizedMessage(),
626 "Multiple sequence alignment format error",
627 JOptionPane.ERROR_MESSAGE );
630 catch ( final IOException e ) {
632 JOptionPane.showMessageDialog( this,
633 e.getLocalizedMessage(),
634 "Failed to read multiple sequence alignment",
635 JOptionPane.ERROR_MESSAGE );
638 catch ( final IllegalArgumentException e ) {
640 JOptionPane.showMessageDialog( this,
641 e.getLocalizedMessage(),
642 "Unexpected error during reading of multiple sequence alignment",
643 JOptionPane.ERROR_MESSAGE );
646 catch ( final Exception e ) {
649 JOptionPane.showMessageDialog( this,
650 e.getLocalizedMessage(),
651 "Unexpected error during reading of multiple sequence alignment",
652 JOptionPane.ERROR_MESSAGE );
655 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
656 JOptionPane.showMessageDialog( this,
657 "Multiple sequence alignment is empty",
658 "Illegal Multiple Sequence Alignment",
659 JOptionPane.ERROR_MESSAGE );
662 if ( msa.getNumberOfSequences() < 4 ) {
663 JOptionPane.showMessageDialog( this,
664 "Multiple sequence alignment needs to contain at least 3 sequences",
665 "Illegal multiple sequence alignment",
666 JOptionPane.ERROR_MESSAGE );
669 if ( msa.getLength() < 2 ) {
670 JOptionPane.showMessageDialog( this,
671 "Multiple sequence alignment needs to contain at least 2 residues",
672 "Illegal multiple sequence alignment",
673 JOptionPane.ERROR_MESSAGE );
677 setMsaFile( _msa_filechooser.getSelectedFile() );
682 public void readSeqsFromFileforPI() {
683 // Set an initial directory if none set yet
684 final File my_dir = getCurrentDir();
685 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
686 // Open file-open dialog and set current directory
687 if ( my_dir != null ) {
688 _seqs_pi_filechooser.setCurrentDirectory( my_dir );
690 final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
691 // All done: get the seqs
692 final File file = _seqs_pi_filechooser.getSelectedFile();
693 setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
694 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
697 List<Sequence> seqs = null;
699 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
700 seqs = FastaParser.parse( new FileInputStream( file ) );
701 for( final Sequence seq : seqs ) {
702 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
709 catch ( final MsaFormatException e ) {
711 JOptionPane.showMessageDialog( this,
712 e.getLocalizedMessage(),
713 "Multiple sequence file format error",
714 JOptionPane.ERROR_MESSAGE );
717 catch ( final IOException e ) {
719 JOptionPane.showMessageDialog( this,
720 e.getLocalizedMessage(),
721 "Failed to read multiple sequence file",
722 JOptionPane.ERROR_MESSAGE );
725 catch ( final IllegalArgumentException e ) {
727 JOptionPane.showMessageDialog( this,
728 e.getLocalizedMessage(),
729 "Unexpected error during reading of multiple sequence file",
730 JOptionPane.ERROR_MESSAGE );
733 catch ( final Exception e ) {
736 JOptionPane.showMessageDialog( this,
737 e.getLocalizedMessage(),
738 "Unexpected error during reading of multiple sequence file",
739 JOptionPane.ERROR_MESSAGE );
742 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
743 JOptionPane.showMessageDialog( this,
744 "Multiple sequence file is empty",
745 "Illegal multiple sequence file",
746 JOptionPane.ERROR_MESSAGE );
749 if ( seqs.size() < 4 ) {
750 JOptionPane.showMessageDialog( this,
751 "Multiple sequence file needs to contain at least 3 sequences",
752 "Illegal multiple sequence file",
753 JOptionPane.ERROR_MESSAGE );
756 // if ( msa.getLength() < 2 ) {
757 // JOptionPane.showMessageDialog( this,
758 // "Multiple sequence alignment needs to contain at least 2 residues",
759 // "Illegal multiple sequence file",
760 // JOptionPane.ERROR_MESSAGE );
764 setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
769 void buildAnalysisMenu() {
770 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
771 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
772 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
773 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
774 customizeJMenuItem( _gsdi_item );
775 customizeJMenuItem( _gsdir_item );
776 customizeJMenuItem( _load_species_tree_item );
777 _analysis_menu.addSeparator();
778 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
779 customizeJMenuItem( _lineage_inference );
780 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
781 _jmenubar.add( _analysis_menu );
785 void buildFileMenu() {
786 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
787 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
788 _file_jmenu.addSeparator();
789 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
790 _file_jmenu.addSeparator();
791 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
792 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
793 .getAvailablePhylogeniesWebserviceClients().size() ];
794 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
795 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
796 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
797 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
799 if ( getConfiguration().isEditable() ) {
800 _file_jmenu.addSeparator();
801 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
802 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
804 _file_jmenu.addSeparator();
805 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
806 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
807 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
808 _save_all_item.setEnabled( false );
809 _file_jmenu.addSeparator();
810 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
811 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
812 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
814 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
815 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
816 if ( AptxUtil.canWriteFormat( "gif" ) ) {
817 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
819 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
820 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
822 _file_jmenu.addSeparator();
823 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
824 _file_jmenu.addSeparator();
825 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
826 _close_item.setToolTipText( "To close the current pane." );
827 _close_item.setEnabled( true );
828 _file_jmenu.addSeparator();
829 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
830 // For print in color option item
831 customizeJMenuItem( _open_item );
833 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
834 customizeJMenuItem( _open_url_item );
835 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
836 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
838 customizeJMenuItem( _save_item );
839 if ( getConfiguration().isEditable() ) {
840 customizeJMenuItem( _new_item );
842 customizeJMenuItem( _close_item );
843 customizeJMenuItem( _save_all_item );
844 customizeJMenuItem( _write_to_pdf_item );
845 customizeJMenuItem( _write_to_png_item );
846 customizeJMenuItem( _write_to_jpg_item );
847 customizeJMenuItem( _write_to_gif_item );
848 customizeJMenuItem( _write_to_tif_item );
849 customizeJMenuItem( _write_to_bmp_item );
850 customizeJMenuItem( _print_item );
851 customizeJMenuItem( _exit_item );
852 _jmenubar.add( _file_jmenu );
855 void buildOptionsMenu() {
856 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
857 _options_jmenu.addChangeListener( new ChangeListener() {
860 public void stateChanged( final ChangeEvent e ) {
861 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
862 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
864 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
865 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
866 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
867 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
868 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
869 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
871 _show_branch_length_values_cbmi,
872 _non_lined_up_cladograms_rbmi,
873 _uniform_cladograms_rbmi,
874 _ext_node_dependent_cladogram_rbmi,
875 _label_direction_cbmi );
876 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
877 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
878 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
881 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
883 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
884 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
885 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
886 _radio_group_1 = new ButtonGroup();
887 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
888 _radio_group_1.add( _uniform_cladograms_rbmi );
889 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
891 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
892 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
894 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
896 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
898 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
899 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
900 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
902 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
903 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
904 _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
905 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
906 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
907 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
908 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
909 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
910 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
911 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
912 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
913 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
914 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
915 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
916 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
917 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
918 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
920 _options_jmenu.addSeparator();
921 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
922 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
923 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
924 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
925 _options_jmenu.addSeparator();
926 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
927 getConfiguration() ) );
928 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
929 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
931 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
933 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
935 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
936 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
937 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
938 _options_jmenu.addSeparator();
939 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
941 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
942 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
944 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
946 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
948 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
950 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
952 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
953 _extract_taxonomy_pfam_strict_rbmi
954 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
955 _extract_taxonomy_pfam_relaxed_rbmi
956 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
957 _extract_taxonomy_agressive_rbmi
958 .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
959 _radio_group_2 = new ButtonGroup();
960 _radio_group_2.add( _extract_taxonomy_no_rbmi );
961 _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
962 _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
963 _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
965 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
967 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
968 _use_brackets_for_conf_in_nh_export_cbmi
969 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
971 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
972 customizeJMenuItem( _choose_font_mi );
973 customizeJMenuItem( _choose_minimal_confidence_mi );
974 customizeJMenuItem( _switch_colors_mi );
975 customizeJMenuItem( _print_size_mi );
976 customizeJMenuItem( _choose_pdf_width_mi );
977 customizeJMenuItem( _overview_placment_mi );
978 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
979 .isShowDefaultNodeShapesExternal() );
980 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
981 .isShowDefaultNodeShapesInternal() );
982 customizeJMenuItem( _cycle_node_shape_mi );
983 customizeJMenuItem( _cycle_node_fill_mi );
984 customizeJMenuItem( _choose_node_size_mi );
985 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
986 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
987 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
988 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
989 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
990 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
991 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
992 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
993 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
994 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
995 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
996 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
997 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
998 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
999 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1000 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
1001 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1002 customizeCheckBoxMenuItem( _label_direction_cbmi,
1003 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1004 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1005 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1006 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1007 .isInternalNumberAreConfidenceForNhParsing() );
1008 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1009 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1010 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
1011 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1012 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
1013 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1014 customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
1015 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
1016 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1017 customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
1018 .isReplaceUnderscoresInNhParsing() );
1019 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1020 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1021 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1022 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1023 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1024 .isGraphicsExportUsingActualSize() );
1025 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1026 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1027 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1028 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1029 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1030 _jmenubar.add( _options_jmenu );
1033 void buildPhylogeneticInferenceMenu() {
1034 final InferenceManager im = getInferenceManager();
1035 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1036 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1037 customizeJMenuItem( _inference_from_msa_item );
1038 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1039 if ( im.canDoMsa() ) {
1040 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1041 customizeJMenuItem( _inference_from_seqs_item );
1042 _inference_from_seqs_item
1043 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1047 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1048 customizeJMenuItem( _inference_from_seqs_item );
1049 _inference_from_seqs_item.setEnabled( false );
1051 _jmenubar.add( _inference_menu );
1054 void buildToolsMenu() {
1055 _tools_menu = createMenu( "Tools", getConfiguration() );
1056 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1057 customizeJMenuItem( _confcolor_item );
1058 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1059 customizeJMenuItem( _color_rank_jmi );
1060 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1061 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1062 customizeJMenuItem( _taxcolor_item );
1063 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1064 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1065 customizeJMenuItem( _remove_branch_color_item );
1066 _tools_menu.addSeparator();
1067 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1068 customizeJMenuItem( _annotate_item );
1069 _tools_menu.addSeparator();
1070 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1071 customizeJMenuItem( _midpoint_root_item );
1072 _tools_menu.addSeparator();
1073 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1074 customizeJMenuItem( _collapse_species_specific_subtrees );
1076 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1077 customizeJMenuItem( _collapse_below_threshold );
1078 _collapse_below_threshold
1079 .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)" );
1080 _tools_menu.addSeparator();
1082 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
1083 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1084 _extract_tax_code_from_node_names_jmi
1085 .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'" );
1087 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1088 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1089 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1090 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1091 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1092 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1093 _tools_menu.addSeparator();
1094 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1095 customizeJMenuItem( _obtain_seq_information_jmi );
1096 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1098 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1099 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1100 _obtain_detailed_taxonomic_information_jmi
1101 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1103 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1104 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1105 _obtain_detailed_taxonomic_information_deleting_jmi
1106 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1107 _tools_menu.addSeparator();
1108 _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
1109 customizeJMenuItem( _read_values_jmi );
1110 _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
1111 _jmenubar.add( _tools_menu );
1112 _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
1113 customizeJMenuItem( _read_seqs_jmi );
1115 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
1116 _jmenubar.add( _tools_menu );
1121 if ( isUnsavedDataPresent() ) {
1122 final int r = JOptionPane.showConfirmDialog( this,
1123 "Exit despite potentially unsaved changes?",
1125 JOptionPane.YES_NO_OPTION );
1126 if ( r != JOptionPane.YES_OPTION ) {
1133 void executeLineageInference() {
1134 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1137 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1138 JOptionPane.showMessageDialog( this,
1139 "Phylogeny is not rooted.",
1140 "Cannot infer ancestral taxonomies",
1141 JOptionPane.ERROR_MESSAGE );
1144 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1145 _mainpanel.getCurrentTreePanel(),
1146 _mainpanel.getCurrentPhylogeny()
1148 new Thread( inferrer ).start();
1152 removeAllTextFrames();
1153 _mainpanel.terminate();
1154 _contentpane.removeAll();
1155 setVisible( false );
1161 void readPhylogeniesFromURL() {
1163 Phylogeny[] phys = null;
1164 final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1165 final String url_string = JOptionPane.showInputDialog( this,
1167 "Use URL/webservice to obtain a phylogeny",
1168 JOptionPane.QUESTION_MESSAGE );
1169 boolean nhx_or_nexus = false;
1170 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1172 url = new URL( url_string );
1173 PhylogenyParser parser = null;
1174 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1175 parser = new TolParser();
1178 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1179 .isValidatePhyloXmlAgainstSchema() );
1181 if ( parser instanceof NexusPhylogeniesParser ) {
1182 nhx_or_nexus = true;
1184 else if ( parser instanceof NHXParser ) {
1185 nhx_or_nexus = true;
1187 if ( _mainpanel.getCurrentTreePanel() != null ) {
1188 _mainpanel.getCurrentTreePanel().setWaitCursor();
1191 _mainpanel.setWaitCursor();
1193 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1194 phys = factory.create( url.openStream(), parser );
1196 catch ( final MalformedURLException e ) {
1197 JOptionPane.showMessageDialog( this,
1198 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1200 JOptionPane.ERROR_MESSAGE );
1202 catch ( final IOException e ) {
1203 JOptionPane.showMessageDialog( this,
1204 "Could not read from " + url + "\n"
1205 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1206 "Failed to read URL",
1207 JOptionPane.ERROR_MESSAGE );
1209 catch ( final Exception e ) {
1210 JOptionPane.showMessageDialog( this,
1211 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1212 "Unexpected Exception",
1213 JOptionPane.ERROR_MESSAGE );
1216 if ( _mainpanel.getCurrentTreePanel() != null ) {
1217 _mainpanel.getCurrentTreePanel().setArrowCursor();
1220 _mainpanel.setArrowCursor();
1223 if ( ( phys != null ) && ( phys.length > 0 ) ) {
1224 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1225 for( final Phylogeny phy : phys ) {
1226 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1229 AptxUtil.addPhylogeniesToTabs( phys,
1230 new File( url.getFile() ).getName(),
1231 new File( url.getFile() ).toString(),
1234 _mainpanel.getControlPanel().showWhole();
1237 activateSaveAllIfNeeded();
1241 void setMsa( final Msa msa ) {
1245 void setMsaFile( final File msa_file ) {
1246 _msa_file = msa_file;
1249 void setSeqs( final List<Sequence> seqs ) {
1253 void setSeqsFile( final File seqs_file ) {
1254 _seqs_file = seqs_file;
1257 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1258 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1259 _mainpanel.getCurrentTreePanel().getHeight(),
1261 String file_written_to = "";
1262 boolean error = false;
1264 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1265 _mainpanel.getCurrentTreePanel().getWidth(),
1266 _mainpanel.getCurrentTreePanel().getHeight(),
1267 _mainpanel.getCurrentTreePanel(),
1268 _mainpanel.getControlPanel(),
1272 catch ( final IOException e ) {
1274 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1277 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1278 JOptionPane.showMessageDialog( this,
1279 "Wrote image to: " + file_written_to,
1281 JOptionPane.INFORMATION_MESSAGE );
1284 JOptionPane.showMessageDialog( this,
1285 "There was an unknown problem when attempting to write to an image file: \""
1288 JOptionPane.ERROR_MESSAGE );
1291 _contentpane.repaint();
1294 private void addExpressionValuesFromFile() {
1295 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1296 JOptionPane.showMessageDialog( this,
1297 "Need to load evolutionary tree first",
1298 "Can Not Read Expression Values",
1299 JOptionPane.WARNING_MESSAGE );
1302 final File my_dir = getCurrentDir();
1303 if ( my_dir != null ) {
1304 _values_filechooser.setCurrentDirectory( my_dir );
1306 final int result = _values_filechooser.showOpenDialog( _contentpane );
1307 final File file = _values_filechooser.getSelectedFile();
1308 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1309 BasicTable<String> t = null;
1311 t = BasicTableParser.parse( file, '\t' );
1312 if ( t.getNumberOfColumns() < 2 ) {
1313 t = BasicTableParser.parse( file, ',' );
1315 if ( t.getNumberOfColumns() < 2 ) {
1316 t = BasicTableParser.parse( file, ' ' );
1319 catch ( final IOException e ) {
1320 JOptionPane.showMessageDialog( this,
1322 "Could Not Read Expression Value Table",
1323 JOptionPane.ERROR_MESSAGE );
1326 if ( t.getNumberOfColumns() < 2 ) {
1327 JOptionPane.showMessageDialog( this,
1328 "Table contains " + t.getNumberOfColumns() + " column(s)",
1329 "Problem with Expression Value Table",
1330 JOptionPane.ERROR_MESSAGE );
1333 if ( t.getNumberOfRows() < 1 ) {
1334 JOptionPane.showMessageDialog( this,
1335 "Table contains zero rows",
1336 "Problem with Expression Value Table",
1337 JOptionPane.ERROR_MESSAGE );
1340 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1341 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1342 JOptionPane.showMessageDialog( this,
1343 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1344 + phy.getNumberOfExternalNodes() + " external nodes",
1346 JOptionPane.WARNING_MESSAGE );
1348 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1350 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1351 final PhylogenyNode node = iter.next();
1352 final String node_name = node.getName();
1353 if ( !ForesterUtil.isEmpty( node_name ) ) {
1356 row = t.findRow( node_name );
1358 catch ( final IllegalArgumentException e ) {
1360 .showMessageDialog( this,
1362 "Error Mapping Node Identifiers to Expression Value Identifiers",
1363 JOptionPane.ERROR_MESSAGE );
1367 if ( node.isExternal() ) {
1372 final List<Double> l = new ArrayList<Double>();
1373 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1376 d = Double.parseDouble( t.getValueAsString( col, row ) );
1378 catch ( final NumberFormatException e ) {
1379 JOptionPane.showMessageDialog( this,
1380 "Could not parse \"" + t.getValueAsString( col, row )
1381 + "\" into a decimal value",
1382 "Issue with Expression Value Table",
1383 JOptionPane.ERROR_MESSAGE );
1386 stats.addValue( d );
1389 if ( !l.isEmpty() ) {
1390 if ( node.getNodeData().getProperties() != null ) {
1391 node.getNodeData().getProperties()
1392 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1394 node.getNodeData().setVector( l );
1398 if ( not_found > 0 ) {
1399 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1400 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1402 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1406 private void addSequencesFromFile() {
1407 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1408 JOptionPane.showMessageDialog( this,
1409 "Need to load evolutionary tree first",
1410 "Can Not Read Sequences",
1411 JOptionPane.WARNING_MESSAGE );
1414 final File my_dir = getCurrentDir();
1415 if ( my_dir != null ) {
1416 _sequences_filechooser.setCurrentDirectory( my_dir );
1418 final int result = _sequences_filechooser.showOpenDialog( _contentpane );
1419 final File file = _sequences_filechooser.getSelectedFile();
1420 List<Sequence> seqs = null;
1421 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1423 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1424 seqs = FastaParser.parse( new FileInputStream( file ) );
1427 JOptionPane.showMessageDialog( this,
1428 "Format does not appear to be Fasta",
1429 "Multiple sequence file format error",
1430 JOptionPane.ERROR_MESSAGE );
1434 catch ( final MsaFormatException e ) {
1436 JOptionPane.showMessageDialog( this,
1437 e.getLocalizedMessage(),
1438 "Multiple sequence file format error",
1439 JOptionPane.ERROR_MESSAGE );
1442 catch ( final IOException e ) {
1444 JOptionPane.showMessageDialog( this,
1445 e.getLocalizedMessage(),
1446 "Failed to read multiple sequence file",
1447 JOptionPane.ERROR_MESSAGE );
1450 catch ( final Exception e ) {
1452 e.printStackTrace();
1453 JOptionPane.showMessageDialog( this,
1454 e.getLocalizedMessage(),
1455 "Unexpected error during reading of multiple sequence file",
1456 JOptionPane.ERROR_MESSAGE );
1459 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1460 JOptionPane.showMessageDialog( this,
1461 "Multiple sequence file is empty",
1462 "Empty multiple sequence file",
1463 JOptionPane.ERROR_MESSAGE );
1468 if ( seqs != null ) {
1469 for( final Sequence seq : seqs ) {
1470 System.out.println( seq.getIdentifier() );
1472 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1473 int total_counter = 0;
1474 int attached_counter = 0;
1475 for( final Sequence seq : seqs ) {
1477 final String seq_name = seq.getIdentifier();
1478 if ( !ForesterUtil.isEmpty( seq_name ) ) {
1479 List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
1480 if ( nodes.isEmpty() ) {
1481 nodes = phy.getNodesViaSequenceSymbol( seq_name );
1483 if ( nodes.isEmpty() ) {
1484 nodes = phy.getNodesViaGeneName( seq_name );
1486 if ( nodes.isEmpty() ) {
1487 nodes = phy.getNodes( seq_name );
1489 if ( nodes.size() > 1 ) {
1490 JOptionPane.showMessageDialog( this,
1491 "Sequence name \"" + seq_name + "\" is not unique",
1492 "Sequence name not unique",
1493 JOptionPane.ERROR_MESSAGE );
1497 final String[] a = seq_name.split( "\\s" );
1498 if ( nodes.isEmpty() && ( a.length > 1 ) ) {
1499 final String seq_name_split = a[ 0 ];
1500 nodes = phy.getNodesViaSequenceName( seq_name_split );
1501 if ( nodes.isEmpty() ) {
1502 nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
1504 if ( nodes.isEmpty() ) {
1505 nodes = phy.getNodes( seq_name_split );
1507 if ( nodes.size() > 1 ) {
1508 JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
1509 + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
1514 if ( nodes.size() == 1 ) {
1516 final PhylogenyNode n = nodes.get( 0 );
1517 if ( !n.getNodeData().isHasSequence() ) {
1518 n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
1520 n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
1521 if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
1522 n.getNodeData().getSequence().setName( seq_name );
1527 if ( attached_counter > 0 ) {
1529 int ext_nodes_with_seq = 0;
1530 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
1532 final PhylogenyNode n = iter.next();
1533 if ( n.getNodeData().isHasSequence()
1534 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
1535 ++ext_nodes_with_seq;
1539 if ( ext_nodes == ext_nodes_with_seq ) {
1540 s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
1543 s = ext_nodes_with_seq + " out of " + ext_nodes
1544 + " external nodes now have a molecular sequence attached to them.";
1546 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
1547 JOptionPane.showMessageDialog( this,
1548 "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
1549 "All sequences attached",
1550 JOptionPane.INFORMATION_MESSAGE );
1553 JOptionPane.showMessageDialog( this, "Attached " + attached_counter
1554 + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
1555 + " sequences attached", JOptionPane.WARNING_MESSAGE );
1559 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
1560 + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
1565 private void choosePdfWidth() {
1566 final String s = ( String ) JOptionPane.showInputDialog( this,
1567 "Please enter the default line width for PDF export.\n"
1568 + "[current value: "
1569 + getOptions().getPrintLineWidth() + "]\n",
1570 "Line Width for PDF Export",
1571 JOptionPane.QUESTION_MESSAGE,
1574 getOptions().getPrintLineWidth() );
1575 if ( !ForesterUtil.isEmpty( s ) ) {
1576 boolean success = true;
1578 final String m_str = s.trim();
1579 if ( !ForesterUtil.isEmpty( m_str ) ) {
1581 f = Float.parseFloat( m_str );
1583 catch ( final Exception ex ) {
1590 if ( success && ( f > 0.0 ) ) {
1591 getOptions().setPrintLineWidth( f );
1596 private void choosePrintSize() {
1597 final String s = ( String ) JOptionPane.showInputDialog( this,
1598 "Please enter values for width and height,\nseparated by a comma.\n"
1599 + "[current values: "
1600 + getOptions().getPrintSizeX() + ", "
1601 + getOptions().getPrintSizeY() + "]\n"
1602 + "[A4: " + Constants.A4_SIZE_X + ", "
1603 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1604 + Constants.US_LETTER_SIZE_X + ", "
1605 + Constants.US_LETTER_SIZE_Y + "]",
1606 "Default Size for Graphics Export",
1607 JOptionPane.QUESTION_MESSAGE,
1610 getOptions().getPrintSizeX() + ", "
1611 + getOptions().getPrintSizeY() );
1612 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1613 boolean success = true;
1616 final String[] str_ary = s.split( "," );
1617 if ( str_ary.length == 2 ) {
1618 final String x_str = str_ary[ 0 ].trim();
1619 final String y_str = str_ary[ 1 ].trim();
1620 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1622 x = Integer.parseInt( x_str );
1623 y = Integer.parseInt( y_str );
1625 catch ( final Exception ex ) {
1636 if ( success && ( x > 1 ) && ( y > 1 ) ) {
1637 getOptions().setPrintSizeX( x );
1638 getOptions().setPrintSizeY( y );
1643 private void closeCurrentPane() {
1644 if ( getMainPanel().getCurrentTreePanel() != null ) {
1645 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1646 final int r = JOptionPane.showConfirmDialog( this,
1647 "Close tab despite potentially unsaved changes?",
1649 JOptionPane.YES_NO_OPTION );
1650 if ( r != JOptionPane.YES_OPTION ) {
1654 getMainPanel().closeCurrentPane();
1655 activateSaveAllIfNeeded();
1659 private void collapse( final Phylogeny phy, final double m ) {
1660 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1661 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1662 double min_support = Double.MAX_VALUE;
1663 boolean conf_present = false;
1664 while ( it.hasNext() ) {
1665 final PhylogenyNode n = it.next();
1666 if ( !n.isExternal() && !n.isRoot() ) {
1667 final List<Confidence> c = n.getBranchData().getConfidences();
1668 if ( ( c != null ) && ( c.size() > 0 ) ) {
1669 conf_present = true;
1671 for( final Confidence confidence : c ) {
1672 if ( confidence.getValue() > max ) {
1673 max = confidence.getValue();
1676 if ( max < getMinNotCollapseConfidenceValue() ) {
1677 to_be_removed.add( n );
1679 if ( max < min_support ) {
1685 if ( conf_present ) {
1686 for( final PhylogenyNode node : to_be_removed ) {
1687 PhylogenyMethods.removeNode( node, phy );
1689 if ( to_be_removed.size() > 0 ) {
1690 phy.externalNodesHaveChanged();
1691 phy.clearHashIdToNodeMap();
1692 phy.recalculateNumberOfExternalDescendants( true );
1693 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1694 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1695 getCurrentTreePanel().calculateLongestExtNodeInfo();
1696 getCurrentTreePanel().setNodeInPreorderToNull();
1697 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1698 getCurrentTreePanel().resetPreferredSize();
1699 getCurrentTreePanel().setEdited( true );
1700 getCurrentTreePanel().repaint();
1703 if ( to_be_removed.size() > 0 ) {
1704 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1705 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1706 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1709 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1710 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1714 JOptionPane.showMessageDialog( this,
1715 "No branch collapsed because no confidence values present",
1716 "No confidence values present",
1717 JOptionPane.INFORMATION_MESSAGE );
1721 private void collapseBelowThreshold() {
1722 if ( getCurrentTreePanel() != null ) {
1723 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1724 if ( ( phy != null ) && !phy.isEmpty() ) {
1725 final String s = ( String ) JOptionPane.showInputDialog( this,
1726 "Please enter the minimum confidence value\n",
1727 "Minimal Confidence Value",
1728 JOptionPane.QUESTION_MESSAGE,
1731 getMinNotCollapseConfidenceValue() );
1732 if ( !ForesterUtil.isEmpty( s ) ) {
1733 boolean success = true;
1735 final String m_str = s.trim();
1736 if ( !ForesterUtil.isEmpty( m_str ) ) {
1738 m = Double.parseDouble( m_str );
1740 catch ( final Exception ex ) {
1747 if ( success && ( m >= 0.0 ) ) {
1748 setMinNotCollapseConfidenceValue( m );
1756 private PhyloXmlParser createPhyloXmlParser() {
1757 PhyloXmlParser xml_parser = null;
1758 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1760 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1762 catch ( final Exception e ) {
1763 JOptionPane.showMessageDialog( this,
1764 e.getLocalizedMessage(),
1765 "failed to create validating XML parser",
1766 JOptionPane.WARNING_MESSAGE );
1769 if ( xml_parser == null ) {
1770 xml_parser = PhyloXmlParser.createPhyloXmlParser();
1775 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1776 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1777 getPhylogeneticInferenceOptions(),
1778 from_unaligned_seqs );
1780 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1781 if ( !from_unaligned_seqs ) {
1782 if ( getMsa() != null ) {
1783 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1784 getPhylogeneticInferenceOptions()
1786 new Thread( inferrer ).start();
1789 JOptionPane.showMessageDialog( this,
1790 "No multiple sequence alignment selected",
1791 "Phylogenetic Inference Not Launched",
1792 JOptionPane.WARNING_MESSAGE );
1796 if ( getSeqs() != null ) {
1797 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1798 getPhylogeneticInferenceOptions()
1800 new Thread( inferrer ).start();
1803 JOptionPane.showMessageDialog( this,
1804 "No input sequences selected",
1805 "Phylogenetic Inference Not Launched",
1806 JOptionPane.WARNING_MESSAGE );
1812 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1813 final StringBuilder sb = new StringBuilder();
1814 final StringBuilder sb_failed = new StringBuilder();
1816 int counter_failed = 0;
1817 if ( getCurrentTreePanel() != null ) {
1818 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1819 if ( ( phy != null ) && !phy.isEmpty() ) {
1820 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1821 while ( it.hasNext() ) {
1822 final PhylogenyNode n = it.next();
1823 final String name = n.getName().trim();
1824 if ( !ForesterUtil.isEmpty( name ) ) {
1825 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
1826 TAXONOMY_EXTRACTION.AGGRESSIVE );
1827 if ( !ForesterUtil.isEmpty( nt ) ) {
1828 if ( counter < 15 ) {
1829 sb.append( name + ": " + nt + "\n" );
1831 else if ( counter == 15 ) {
1832 sb.append( "...\n" );
1837 if ( counter_failed < 15 ) {
1838 sb_failed.append( name + "\n" );
1840 else if ( counter_failed == 15 ) {
1841 sb_failed.append( "...\n" );
1847 if ( counter > 0 ) {
1849 String all = "all ";
1850 if ( counter_failed > 0 ) {
1852 failed = "\nCould not extract taxonomic data for " + counter_failed
1853 + " named external nodes:\n" + sb_failed;
1855 JOptionPane.showMessageDialog( this,
1856 "Extracted taxonomic data from " + all + counter
1857 + " named external nodes:\n" + sb.toString() + failed,
1858 "Taxonomic Data Extraction Completed",
1859 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1860 : JOptionPane.INFORMATION_MESSAGE );
1864 .showMessageDialog( this,
1865 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1866 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1867 + "or nodes already have taxonomic data?\n",
1868 "No Taxonomic Data Extracted",
1869 JOptionPane.ERROR_MESSAGE );
1875 private ControlPanel getControlPanel() {
1876 return getMainPanel().getControlPanel();
1879 private File getCurrentDir() {
1880 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1881 if ( ForesterUtil.isWindows() ) {
1883 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1885 catch ( final Exception e ) {
1886 _current_dir = null;
1890 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1891 if ( System.getProperty( "user.home" ) != null ) {
1892 _current_dir = new File( System.getProperty( "user.home" ) );
1894 else if ( System.getProperty( "user.dir" ) != null ) {
1895 _current_dir = new File( System.getProperty( "user.dir" ) );
1898 return _current_dir;
1901 private double getMinNotCollapseConfidenceValue() {
1902 return _min_not_collapse;
1905 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1906 if ( _phylogenetic_inference_options == null ) {
1907 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1909 return _phylogenetic_inference_options;
1912 private boolean isUnsavedDataPresent() {
1913 final List<TreePanel> tps = getMainPanel().getTreePanels();
1914 for( final TreePanel tp : tps ) {
1915 if ( tp.isEdited() ) {
1922 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1923 if ( getCurrentTreePanel() != null ) {
1924 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1925 if ( ( phy != null ) && !phy.isEmpty() ) {
1927 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1932 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1933 if ( getCurrentTreePanel() != null ) {
1934 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1935 if ( ( phy != null ) && !phy.isEmpty() ) {
1936 PhylogenyMethods.transferNodeNameToField( phy,
1937 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1943 private void newTree() {
1944 final Phylogeny[] phys = new Phylogeny[ 1 ];
1945 final Phylogeny phy = new Phylogeny();
1946 final PhylogenyNode node = new PhylogenyNode();
1947 phy.setRoot( node );
1948 phy.setRooted( true );
1950 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1951 _mainpanel.getControlPanel().showWhole();
1952 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1953 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1954 if ( getMainPanel().getMainFrame() == null ) {
1955 // Must be "E" applet version.
1956 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1957 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1960 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1962 activateSaveAllIfNeeded();
1966 private void obtainDetailedTaxonomicInformation() {
1967 if ( getCurrentTreePanel() != null ) {
1968 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1969 if ( ( phy != null ) && !phy.isEmpty() ) {
1970 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1971 _mainpanel.getCurrentTreePanel(),
1975 new Thread( t ).start();
1980 private void obtainDetailedTaxonomicInformationDelete() {
1981 if ( getCurrentTreePanel() != null ) {
1982 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1983 if ( ( phy != null ) && !phy.isEmpty() ) {
1984 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1985 _mainpanel.getCurrentTreePanel(),
1989 new Thread( t ).start();
1994 private void obtainSequenceInformation() {
1995 if ( getCurrentTreePanel() != null ) {
1996 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1997 if ( ( phy != null ) && !phy.isEmpty() ) {
1998 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1999 _mainpanel.getCurrentTreePanel(),
2001 new Thread( u ).start();
2006 private void print() {
2007 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2008 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2011 if ( !getOptions().isPrintUsingActualSize() ) {
2012 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
2013 getOptions().getPrintSizeY() - 140,
2015 getCurrentTreePanel().resetPreferredSize();
2016 getCurrentTreePanel().repaint();
2018 final String job_name = Constants.PRG_NAME;
2019 boolean error = false;
2020 String printer_name = null;
2022 printer_name = Printer.print( getCurrentTreePanel(), job_name );
2024 catch ( final Exception e ) {
2026 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2028 if ( !error && ( printer_name != null ) ) {
2029 String msg = "Printing data sent to printer";
2030 if ( printer_name.length() > 1 ) {
2031 msg += " [" + printer_name + "]";
2033 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2035 if ( !getOptions().isPrintUsingActualSize() ) {
2036 getControlPanel().showWhole();
2040 private void printPhylogenyToPdf( final String file_name ) {
2041 if ( !getOptions().isPrintUsingActualSize() ) {
2042 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
2043 getOptions().getPrintSizeY(),
2045 getCurrentTreePanel().resetPreferredSize();
2046 getCurrentTreePanel().repaint();
2048 String pdf_written_to = "";
2049 boolean error = false;
2051 if ( getOptions().isPrintUsingActualSize() ) {
2052 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2053 getCurrentTreePanel(),
2054 getCurrentTreePanel().getWidth(),
2055 getCurrentTreePanel().getHeight() );
2058 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2059 .getPrintSizeX(), getOptions().getPrintSizeY() );
2062 catch ( final IOException e ) {
2064 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2067 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2068 JOptionPane.showMessageDialog( this,
2069 "Wrote PDF to: " + pdf_written_to,
2071 JOptionPane.INFORMATION_MESSAGE );
2074 JOptionPane.showMessageDialog( this,
2075 "There was an unknown problem when attempting to write to PDF file: \""
2078 JOptionPane.ERROR_MESSAGE );
2081 if ( !getOptions().isPrintUsingActualSize() ) {
2082 getControlPanel().showWhole();
2086 private void readPhylogeniesFromFile() {
2087 boolean exception = false;
2088 Phylogeny[] phys = null;
2089 // Set an initial directory if none set yet
2090 final File my_dir = getCurrentDir();
2091 _open_filechooser.setMultiSelectionEnabled( true );
2092 // Open file-open dialog and set current directory
2093 if ( my_dir != null ) {
2094 _open_filechooser.setCurrentDirectory( my_dir );
2096 final int result = _open_filechooser.showOpenDialog( _contentpane );
2097 // All done: get the file
2098 final File[] files = _open_filechooser.getSelectedFiles();
2099 setCurrentDir( _open_filechooser.getCurrentDirectory() );
2100 boolean nhx_or_nexus = false;
2101 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2102 for( final File file : files ) {
2103 if ( ( file != null ) && !file.isDirectory() ) {
2104 if ( _mainpanel.getCurrentTreePanel() != null ) {
2105 _mainpanel.getCurrentTreePanel().setWaitCursor();
2108 _mainpanel.setWaitCursor();
2110 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2111 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2113 final NHXParser nhx = new NHXParser();
2114 setSpecialOptionsForNhxParser( nhx );
2115 phys = PhylogenyMethods.readPhylogenies( nhx, file );
2116 nhx_or_nexus = true;
2118 catch ( final Exception e ) {
2120 exceptionOccuredDuringOpenFile( e );
2123 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2124 warnIfNotPhyloXmlValidation( getConfiguration() );
2126 final PhyloXmlParser xml_parser = createPhyloXmlParser();
2127 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2129 catch ( final Exception e ) {
2131 exceptionOccuredDuringOpenFile( e );
2134 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2136 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2138 catch ( final Exception e ) {
2140 exceptionOccuredDuringOpenFile( e );
2143 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2145 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2146 setSpecialOptionsForNexParser( nex );
2147 phys = PhylogenyMethods.readPhylogenies( nex, file );
2148 nhx_or_nexus = true;
2150 catch ( final Exception e ) {
2152 exceptionOccuredDuringOpenFile( e );
2158 final PhylogenyParser parser = ParserUtils
2159 .createParserDependingOnFileType( file, getConfiguration()
2160 .isValidatePhyloXmlAgainstSchema() );
2161 if ( parser instanceof NexusPhylogeniesParser ) {
2162 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2163 setSpecialOptionsForNexParser( nex );
2164 nhx_or_nexus = true;
2166 else if ( parser instanceof NHXParser ) {
2167 final NHXParser nhx = ( NHXParser ) parser;
2168 setSpecialOptionsForNhxParser( nhx );
2169 nhx_or_nexus = true;
2171 else if ( parser instanceof PhyloXmlParser ) {
2172 warnIfNotPhyloXmlValidation( getConfiguration() );
2174 phys = PhylogenyMethods.readPhylogenies( parser, file );
2176 catch ( final Exception e ) {
2178 exceptionOccuredDuringOpenFile( e );
2181 if ( _mainpanel.getCurrentTreePanel() != null ) {
2182 _mainpanel.getCurrentTreePanel().setArrowCursor();
2185 _mainpanel.setArrowCursor();
2187 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2188 boolean one_desc = false;
2189 if ( nhx_or_nexus ) {
2190 for( final Phylogeny phy : phys ) {
2191 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2192 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2194 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2200 AptxUtil.addPhylogeniesToTabs( phys,
2202 file.getAbsolutePath(),
2205 _mainpanel.getControlPanel().showWhole();
2206 if ( nhx_or_nexus && one_desc ) {
2208 .showMessageDialog( this,
2209 "One or more trees contain (a) node(s) with one descendant, "
2210 + ForesterUtil.LINE_SEPARATOR
2211 + "possibly indicating illegal parentheses within node names.",
2212 "Warning: Possible Error in New Hampshire Formatted Data",
2213 JOptionPane.WARNING_MESSAGE );
2219 activateSaveAllIfNeeded();
2223 private void readSpeciesTreeFromFile() {
2225 boolean exception = false;
2226 final File my_dir = getCurrentDir();
2227 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2228 if ( my_dir != null ) {
2229 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2231 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2232 final File file = _open_filechooser_for_species_tree.getSelectedFile();
2233 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2234 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2236 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
2237 .createPhyloXmlParserXsdValidating(), file );
2240 catch ( final Exception e ) {
2242 exceptionOccuredDuringOpenFile( e );
2245 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2247 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2250 catch ( final Exception e ) {
2252 exceptionOccuredDuringOpenFile( e );
2258 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
2259 .createPhyloXmlParserXsdValidating(), file );
2262 catch ( final Exception e ) {
2264 exceptionOccuredDuringOpenFile( e );
2267 if ( !exception && ( t != null ) && !t.isRooted() ) {
2270 JOptionPane.showMessageDialog( this,
2271 "Species tree is not rooted",
2272 "Species tree not loaded",
2273 JOptionPane.ERROR_MESSAGE );
2275 if ( !exception && ( t != null ) ) {
2276 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2277 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2278 final PhylogenyNode node = it.next();
2279 if ( !node.getNodeData().isHasTaxonomy() ) {
2283 .showMessageDialog( this,
2284 "Species tree contains external node(s) without taxonomy information",
2285 "Species tree not loaded",
2286 JOptionPane.ERROR_MESSAGE );
2290 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2293 JOptionPane.showMessageDialog( this,
2295 + node.getNodeData().getTaxonomy().asSimpleText()
2296 + "] is not unique in species tree",
2297 "Species tree not loaded",
2298 JOptionPane.ERROR_MESSAGE );
2302 tax_set.add( node.getNodeData().getTaxonomy() );
2307 if ( !exception && ( t != null ) ) {
2308 setSpeciesTree( t );
2309 JOptionPane.showMessageDialog( this,
2310 "Species tree successfully loaded",
2311 "Species tree loaded",
2312 JOptionPane.INFORMATION_MESSAGE );
2314 _contentpane.repaint();
2319 private void setArrowCursor() {
2321 _mainpanel.getCurrentTreePanel().setArrowCursor();
2323 catch ( final Exception ex ) {
2328 private void setCurrentDir( final File current_dir ) {
2329 _current_dir = current_dir;
2332 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2333 _min_not_collapse = min_not_collapse;
2336 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2337 _phylogenetic_inference_options = phylogenetic_inference_options;
2340 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2341 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2342 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2345 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2346 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2347 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2348 nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
2351 private void writeAllToFile() {
2352 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2355 final File my_dir = getCurrentDir();
2356 if ( my_dir != null ) {
2357 _save_filechooser.setCurrentDirectory( my_dir );
2359 _save_filechooser.setSelectedFile( new File( "" ) );
2360 final int result = _save_filechooser.showSaveDialog( _contentpane );
2361 final File file = _save_filechooser.getSelectedFile();
2362 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2363 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2364 if ( file.exists() ) {
2365 final int i = JOptionPane.showConfirmDialog( this,
2366 file + " already exists. Overwrite?",
2368 JOptionPane.OK_CANCEL_OPTION,
2369 JOptionPane.WARNING_MESSAGE );
2370 if ( i != JOptionPane.OK_OPTION ) {
2377 catch ( final Exception e ) {
2378 JOptionPane.showMessageDialog( this,
2379 "Failed to delete: " + file,
2381 JOptionPane.WARNING_MESSAGE );
2385 final int count = getMainPanel().getTabbedPane().getTabCount();
2386 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2387 for( int i = 0; i < count; ++i ) {
2388 final Phylogeny phy = getMainPanel().getPhylogeny( i );
2389 if ( ForesterUtil.isEmpty( phy.getName() )
2390 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
2391 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
2394 getMainPanel().getTreePanels().get( i ).setEdited( false );
2396 final PhylogenyWriter writer = new PhylogenyWriter();
2398 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2400 catch ( final IOException e ) {
2401 JOptionPane.showMessageDialog( this,
2402 "Failed to write to: " + file,
2404 JOptionPane.WARNING_MESSAGE );
2409 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2411 final PhylogenyWriter writer = new PhylogenyWriter();
2412 writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2414 catch ( final Exception e ) {
2416 exceptionOccuredDuringSaveAs( e );
2421 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2423 final PhylogenyWriter writer = new PhylogenyWriter();
2424 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2426 catch ( final Exception e ) {
2428 exceptionOccuredDuringSaveAs( e );
2433 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2435 final PhylogenyWriter writer = new PhylogenyWriter();
2436 writer.toPhyloXML( file, t, 0 );
2438 catch ( final Exception e ) {
2440 exceptionOccuredDuringSaveAs( e );
2445 private void writeToFile( final Phylogeny t ) {
2449 String initial_filename = null;
2450 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2452 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2454 catch ( final IOException e ) {
2455 initial_filename = null;
2458 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2459 _save_filechooser.setSelectedFile( new File( initial_filename ) );
2462 _save_filechooser.setSelectedFile( new File( "" ) );
2464 final File my_dir = getCurrentDir();
2465 if ( my_dir != null ) {
2466 _save_filechooser.setCurrentDirectory( my_dir );
2468 final int result = _save_filechooser.showSaveDialog( _contentpane );
2469 final File file = _save_filechooser.getSelectedFile();
2470 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2471 boolean exception = false;
2472 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2473 if ( file.exists() ) {
2474 final int i = JOptionPane.showConfirmDialog( this,
2475 file + " already exists.\nOverwrite?",
2477 JOptionPane.OK_CANCEL_OPTION,
2478 JOptionPane.QUESTION_MESSAGE );
2479 if ( i != JOptionPane.OK_OPTION ) {
2483 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2485 ForesterUtil.copyFile( file, to );
2487 catch ( final Exception e ) {
2488 JOptionPane.showMessageDialog( this,
2489 "Failed to create backup copy " + to,
2490 "Failed to Create Backup Copy",
2491 JOptionPane.WARNING_MESSAGE );
2496 catch ( final Exception e ) {
2497 JOptionPane.showMessageDialog( this,
2498 "Failed to delete: " + file,
2500 JOptionPane.WARNING_MESSAGE );
2504 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2505 exception = writeAsNewHampshire( t, exception, file );
2507 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2508 exception = writeAsPhyloXml( t, exception, file );
2510 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2511 exception = writeAsNexus( t, exception, file );
2515 final String file_name = file.getName().trim().toLowerCase();
2516 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2517 || file_name.endsWith( ".tree" ) ) {
2518 exception = writeAsNewHampshire( t, exception, file );
2520 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2521 exception = writeAsNexus( t, exception, file );
2525 exception = writeAsPhyloXml( t, exception, file );
2529 getMainPanel().setTitleOfSelectedTab( file.getName() );
2530 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2531 getMainPanel().getCurrentTreePanel().setEdited( false );
2536 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2537 if ( ( t == null ) || t.isEmpty() ) {
2540 String initial_filename = "";
2541 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2542 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2544 if ( initial_filename.indexOf( '.' ) > 0 ) {
2545 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2547 initial_filename = initial_filename + "." + type;
2548 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2549 final File my_dir = getCurrentDir();
2550 if ( my_dir != null ) {
2551 _writetographics_filechooser.setCurrentDirectory( my_dir );
2553 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2554 File file = _writetographics_filechooser.getSelectedFile();
2555 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2556 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2557 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2558 file = new File( file.toString() + "." + type );
2560 if ( file.exists() ) {
2561 final int i = JOptionPane.showConfirmDialog( this,
2562 file + " already exists. Overwrite?",
2564 JOptionPane.OK_CANCEL_OPTION,
2565 JOptionPane.WARNING_MESSAGE );
2566 if ( i != JOptionPane.OK_OPTION ) {
2573 catch ( final Exception e ) {
2574 JOptionPane.showMessageDialog( this,
2575 "Failed to delete: " + file,
2577 JOptionPane.WARNING_MESSAGE );
2581 writePhylogenyToGraphicsFile( file.toString(), type );
2585 private void writeToPdf( final Phylogeny t ) {
2586 if ( ( t == null ) || t.isEmpty() ) {
2589 String initial_filename = "";
2590 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2591 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2593 if ( initial_filename.indexOf( '.' ) > 0 ) {
2594 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2596 initial_filename = initial_filename + ".pdf";
2597 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2598 final File my_dir = getCurrentDir();
2599 if ( my_dir != null ) {
2600 _writetopdf_filechooser.setCurrentDirectory( my_dir );
2602 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2603 File file = _writetopdf_filechooser.getSelectedFile();
2604 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2605 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2606 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2607 file = new File( file.toString() + ".pdf" );
2609 if ( file.exists() ) {
2610 final int i = JOptionPane.showConfirmDialog( this,
2611 file + " already exists. Overwrite?",
2613 JOptionPane.OK_CANCEL_OPTION,
2614 JOptionPane.WARNING_MESSAGE );
2615 if ( i != JOptionPane.OK_OPTION ) {
2619 printPhylogenyToPdf( file.toString() );
2623 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2624 return new MainFrameApplication( phys, config );
2627 public static MainFrame createInstance( final Phylogeny[] phys,
2628 final Configuration config,
2630 final File current_dir ) {
2631 return new MainFrameApplication( phys, config, title, current_dir );
2634 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2635 return new MainFrameApplication( phys, config, title );
2638 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2639 return new MainFrameApplication( phys, config_file_name, title );
2642 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2643 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2644 + o.getPrintSizeY() + ")" );
2647 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2648 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2651 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2652 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2654 .showMessageDialog( null,
2656 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2659 JOptionPane.WARNING_MESSAGE );
2662 } // MainFrameApplication.
2664 class DefaultFilter extends FileFilter {
2667 public boolean accept( final File f ) {
2668 final String file_name = f.getName().trim().toLowerCase();
2669 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2670 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2671 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2672 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2673 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2674 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2675 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2676 || file_name.endsWith( ".con" ) || f.isDirectory();
2680 public String getDescription() {
2681 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2685 class GraphicsFileFilter extends FileFilter {
2688 public boolean accept( final File f ) {
2689 final String file_name = f.getName().trim().toLowerCase();
2690 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2691 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2695 public String getDescription() {
2696 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2700 class MsaFileFilter extends FileFilter {
2703 public boolean accept( final File f ) {
2704 final String file_name = f.getName().trim().toLowerCase();
2705 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2706 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2710 public String getDescription() {
2711 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2715 class NexusFilter extends FileFilter {
2718 public boolean accept( final File f ) {
2719 final String file_name = f.getName().trim().toLowerCase();
2720 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2721 || file_name.endsWith( ".tre" ) || f.isDirectory();
2725 public String getDescription() {
2726 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2730 class NHFilter extends FileFilter {
2733 public boolean accept( final File f ) {
2734 final String file_name = f.getName().trim().toLowerCase();
2735 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2736 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2737 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2742 public String getDescription() {
2743 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2747 class NHXFilter extends FileFilter {
2750 public boolean accept( final File f ) {
2751 final String file_name = f.getName().trim().toLowerCase();
2752 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2756 public String getDescription() {
2757 return "NHX files (*.nhx) [deprecated]";
2761 class PdfFilter extends FileFilter {
2764 public boolean accept( final File f ) {
2765 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2769 public String getDescription() {
2770 return "PDF files (*.pdf)";
2774 class SequencesFileFilter extends FileFilter {
2777 public boolean accept( final File f ) {
2778 final String file_name = f.getName().trim().toLowerCase();
2779 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2780 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2784 public String getDescription() {
2785 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2789 class TolFilter extends FileFilter {
2792 public boolean accept( final File f ) {
2793 final String file_name = f.getName().trim().toLowerCase();
2794 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2795 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2799 public String getDescription() {
2800 return "Tree of Life files (*.tol, *.tolxml)";
2804 class XMLFilter extends FileFilter {
2807 public boolean accept( final File f ) {
2808 final String file_name = f.getName().trim().toLowerCase();
2809 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2810 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2814 public String getDescription() {
2815 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";