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 == _collapse_below_threshold ) {
535 if ( isSubtreeDisplayed() ) {
538 collapseBelowThreshold();
540 else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
541 || ( o == _extract_taxonomy_agressive_rbmi ) ) {
542 if ( _replace_underscores_cbmi != null ) {
543 _replace_underscores_cbmi.setSelected( false );
545 updateOptions( getOptions() );
547 else if ( o == _extract_taxonomy_no_rbmi ) {
548 updateOptions( getOptions() );
550 else if ( o == _inference_from_msa_item ) {
551 executePhyleneticInference( false );
553 else if ( o == _inference_from_seqs_item ) {
554 executePhyleneticInference( true );
556 _contentpane.repaint();
558 catch ( final Exception ex ) {
559 AptxUtil.unexpectedException( ex );
561 catch ( final Error err ) {
562 AptxUtil.unexpectedError( err );
567 _mainpanel.terminate();
568 _contentpane.removeAll();
574 public MainPanel getMainPanel() {
578 public Msa getMsa() {
582 public File getMsaFile() {
586 public List<Sequence> getSeqs() {
590 public File getSeqsFile() {
594 public void readMsaFromFile() {
595 // Set an initial directory if none set yet
596 final File my_dir = getCurrentDir();
597 _msa_filechooser.setMultiSelectionEnabled( false );
598 // Open file-open dialog and set current directory
599 if ( my_dir != null ) {
600 _msa_filechooser.setCurrentDirectory( my_dir );
602 final int result = _msa_filechooser.showOpenDialog( _contentpane );
603 // All done: get the msa
604 final File file = _msa_filechooser.getSelectedFile();
605 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
606 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
611 final InputStream is = new FileInputStream( file );
612 if ( FastaParser.isLikelyFasta( file ) ) {
613 msa = FastaParser.parseMsa( is );
616 msa = GeneralMsaParser.parse( is );
619 catch ( final MsaFormatException e ) {
621 JOptionPane.showMessageDialog( this,
622 e.getLocalizedMessage(),
623 "Multiple sequence alignment format error",
624 JOptionPane.ERROR_MESSAGE );
627 catch ( final IOException e ) {
629 JOptionPane.showMessageDialog( this,
630 e.getLocalizedMessage(),
631 "Failed to read multiple sequence alignment",
632 JOptionPane.ERROR_MESSAGE );
635 catch ( final IllegalArgumentException e ) {
637 JOptionPane.showMessageDialog( this,
638 e.getLocalizedMessage(),
639 "Unexpected error during reading of multiple sequence alignment",
640 JOptionPane.ERROR_MESSAGE );
643 catch ( final Exception e ) {
646 JOptionPane.showMessageDialog( this,
647 e.getLocalizedMessage(),
648 "Unexpected error during reading of multiple sequence alignment",
649 JOptionPane.ERROR_MESSAGE );
652 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
653 JOptionPane.showMessageDialog( this,
654 "Multiple sequence alignment is empty",
655 "Illegal Multiple Sequence Alignment",
656 JOptionPane.ERROR_MESSAGE );
659 if ( msa.getNumberOfSequences() < 4 ) {
660 JOptionPane.showMessageDialog( this,
661 "Multiple sequence alignment needs to contain at least 3 sequences",
662 "Illegal multiple sequence alignment",
663 JOptionPane.ERROR_MESSAGE );
666 if ( msa.getLength() < 2 ) {
667 JOptionPane.showMessageDialog( this,
668 "Multiple sequence alignment needs to contain at least 2 residues",
669 "Illegal multiple sequence alignment",
670 JOptionPane.ERROR_MESSAGE );
674 setMsaFile( _msa_filechooser.getSelectedFile() );
679 public void readSeqsFromFileforPI() {
680 // Set an initial directory if none set yet
681 final File my_dir = getCurrentDir();
682 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
683 // Open file-open dialog and set current directory
684 if ( my_dir != null ) {
685 _seqs_pi_filechooser.setCurrentDirectory( my_dir );
687 final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
688 // All done: get the seqs
689 final File file = _seqs_pi_filechooser.getSelectedFile();
690 setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
691 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
694 List<Sequence> seqs = null;
696 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
697 seqs = FastaParser.parse( new FileInputStream( file ) );
698 for( final Sequence seq : seqs ) {
699 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
706 catch ( final MsaFormatException e ) {
708 JOptionPane.showMessageDialog( this,
709 e.getLocalizedMessage(),
710 "Multiple sequence file format error",
711 JOptionPane.ERROR_MESSAGE );
714 catch ( final IOException e ) {
716 JOptionPane.showMessageDialog( this,
717 e.getLocalizedMessage(),
718 "Failed to read multiple sequence file",
719 JOptionPane.ERROR_MESSAGE );
722 catch ( final IllegalArgumentException e ) {
724 JOptionPane.showMessageDialog( this,
725 e.getLocalizedMessage(),
726 "Unexpected error during reading of multiple sequence file",
727 JOptionPane.ERROR_MESSAGE );
730 catch ( final Exception e ) {
733 JOptionPane.showMessageDialog( this,
734 e.getLocalizedMessage(),
735 "Unexpected error during reading of multiple sequence file",
736 JOptionPane.ERROR_MESSAGE );
739 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
740 JOptionPane.showMessageDialog( this,
741 "Multiple sequence file is empty",
742 "Illegal multiple sequence file",
743 JOptionPane.ERROR_MESSAGE );
746 if ( seqs.size() < 4 ) {
747 JOptionPane.showMessageDialog( this,
748 "Multiple sequence file needs to contain at least 3 sequences",
749 "Illegal multiple sequence file",
750 JOptionPane.ERROR_MESSAGE );
753 // if ( msa.getLength() < 2 ) {
754 // JOptionPane.showMessageDialog( this,
755 // "Multiple sequence alignment needs to contain at least 2 residues",
756 // "Illegal multiple sequence file",
757 // JOptionPane.ERROR_MESSAGE );
761 setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
766 void buildAnalysisMenu() {
767 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
768 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
769 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
770 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
771 customizeJMenuItem( _gsdi_item );
772 customizeJMenuItem( _gsdir_item );
773 customizeJMenuItem( _load_species_tree_item );
774 _analysis_menu.addSeparator();
775 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
776 customizeJMenuItem( _lineage_inference );
777 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
778 _jmenubar.add( _analysis_menu );
782 void buildFileMenu() {
783 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
784 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
785 _file_jmenu.addSeparator();
786 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
787 _file_jmenu.addSeparator();
788 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
789 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
790 .getAvailablePhylogeniesWebserviceClients().size() ];
791 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
792 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
793 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
794 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
796 if ( getConfiguration().isEditable() ) {
797 _file_jmenu.addSeparator();
798 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
799 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
801 _file_jmenu.addSeparator();
802 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
803 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
804 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
805 _save_all_item.setEnabled( false );
806 _file_jmenu.addSeparator();
807 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
808 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
809 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
811 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
812 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
813 if ( AptxUtil.canWriteFormat( "gif" ) ) {
814 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
816 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
817 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
819 _file_jmenu.addSeparator();
820 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
821 _file_jmenu.addSeparator();
822 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
823 _close_item.setToolTipText( "To close the current pane." );
824 _close_item.setEnabled( true );
825 _file_jmenu.addSeparator();
826 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
827 // For print in color option item
828 customizeJMenuItem( _open_item );
830 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
831 customizeJMenuItem( _open_url_item );
832 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
833 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
835 customizeJMenuItem( _save_item );
836 if ( getConfiguration().isEditable() ) {
837 customizeJMenuItem( _new_item );
839 customizeJMenuItem( _close_item );
840 customizeJMenuItem( _save_all_item );
841 customizeJMenuItem( _write_to_pdf_item );
842 customizeJMenuItem( _write_to_png_item );
843 customizeJMenuItem( _write_to_jpg_item );
844 customizeJMenuItem( _write_to_gif_item );
845 customizeJMenuItem( _write_to_tif_item );
846 customizeJMenuItem( _write_to_bmp_item );
847 customizeJMenuItem( _print_item );
848 customizeJMenuItem( _exit_item );
849 _jmenubar.add( _file_jmenu );
852 void buildOptionsMenu() {
853 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
854 _options_jmenu.addChangeListener( new ChangeListener() {
857 public void stateChanged( final ChangeEvent e ) {
858 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
859 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
861 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
862 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
863 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
864 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
865 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
866 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
868 _show_branch_length_values_cbmi,
869 _non_lined_up_cladograms_rbmi,
870 _uniform_cladograms_rbmi,
871 _ext_node_dependent_cladogram_rbmi,
872 _label_direction_cbmi );
873 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
874 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
875 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
878 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
880 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
881 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
882 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
883 _radio_group_1 = new ButtonGroup();
884 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
885 _radio_group_1.add( _uniform_cladograms_rbmi );
886 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
887 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
888 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
890 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
892 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
894 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
895 _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
897 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
898 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
899 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
900 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
901 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
902 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
903 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
904 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
905 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
906 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
907 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
908 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
909 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
910 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
912 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
913 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
914 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
915 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
916 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
917 _options_jmenu.addSeparator();
918 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
919 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
920 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
921 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
922 _options_jmenu.addSeparator();
923 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
924 getConfiguration() ) );
925 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
926 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
928 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
930 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
932 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
933 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
934 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
935 _options_jmenu.addSeparator();
936 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
938 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
939 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
941 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
943 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
945 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
947 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
948 _extract_taxonomy_pfam_strict_rbmi
949 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
950 _extract_taxonomy_pfam_relaxed_rbmi
951 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
952 _extract_taxonomy_agressive_rbmi
953 .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\"" );
954 _radio_group_2 = new ButtonGroup();
955 _radio_group_2.add( _extract_taxonomy_no_rbmi );
956 _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
957 _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
958 _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
960 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
962 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
963 _use_brackets_for_conf_in_nh_export_cbmi
964 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
966 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
967 customizeJMenuItem( _choose_font_mi );
968 customizeJMenuItem( _choose_minimal_confidence_mi );
969 customizeJMenuItem( _switch_colors_mi );
970 customizeJMenuItem( _print_size_mi );
971 customizeJMenuItem( _choose_pdf_width_mi );
972 customizeJMenuItem( _overview_placment_mi );
973 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
974 .isShowDefaultNodeShapesExternal() );
975 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
976 .isShowDefaultNodeShapesInternal() );
977 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
978 customizeJMenuItem( _cycle_node_shape_mi );
979 customizeJMenuItem( _cycle_node_fill_mi );
980 customizeJMenuItem( _choose_node_size_mi );
981 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
982 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
983 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
984 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
985 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
986 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
987 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
988 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
989 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
990 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
991 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
992 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
993 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
994 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
995 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
996 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
997 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
998 customizeCheckBoxMenuItem( _label_direction_cbmi,
999 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1000 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1001 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1002 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1003 .isInternalNumberAreConfidenceForNhParsing() );
1004 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1005 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1006 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
1007 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1008 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
1009 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1010 customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
1011 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
1012 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1013 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1014 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1015 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1016 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1017 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1018 .isGraphicsExportUsingActualSize() );
1019 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1020 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1021 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1022 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1023 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1024 _jmenubar.add( _options_jmenu );
1027 void buildPhylogeneticInferenceMenu() {
1028 final InferenceManager im = getInferenceManager();
1029 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1030 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1031 customizeJMenuItem( _inference_from_msa_item );
1032 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1033 if ( im.canDoMsa() ) {
1034 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1035 customizeJMenuItem( _inference_from_seqs_item );
1036 _inference_from_seqs_item
1037 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1041 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1042 customizeJMenuItem( _inference_from_seqs_item );
1043 _inference_from_seqs_item.setEnabled( false );
1045 _jmenubar.add( _inference_menu );
1048 void buildToolsMenu() {
1049 _tools_menu = createMenu( "Tools", getConfiguration() );
1050 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1051 customizeJMenuItem( _confcolor_item );
1052 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1053 customizeJMenuItem( _color_rank_jmi );
1054 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1055 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1056 customizeJMenuItem( _taxcolor_item );
1057 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1058 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1059 customizeJMenuItem( _remove_branch_color_item );
1060 _tools_menu.addSeparator();
1061 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1062 customizeJMenuItem( _annotate_item );
1063 _tools_menu.addSeparator();
1064 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1065 customizeJMenuItem( _midpoint_root_item );
1066 _tools_menu.addSeparator();
1067 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1068 customizeJMenuItem( _collapse_species_specific_subtrees );
1070 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1071 customizeJMenuItem( _collapse_below_threshold );
1072 _collapse_below_threshold
1073 .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)" );
1074 _tools_menu.addSeparator();
1076 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
1077 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1078 _extract_tax_code_from_node_names_jmi
1079 .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'" );
1081 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1082 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1083 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1084 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1085 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1086 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1087 _tools_menu.addSeparator();
1088 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1089 customizeJMenuItem( _obtain_seq_information_jmi );
1090 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1092 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1093 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1094 _obtain_detailed_taxonomic_information_jmi
1095 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1097 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1098 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1099 _obtain_detailed_taxonomic_information_deleting_jmi
1100 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1101 _tools_menu.addSeparator();
1102 _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
1103 customizeJMenuItem( _read_values_jmi );
1104 _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
1105 _jmenubar.add( _tools_menu );
1106 _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
1107 customizeJMenuItem( _read_seqs_jmi );
1109 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
1110 _jmenubar.add( _tools_menu );
1115 if ( isUnsavedDataPresent() ) {
1116 final int r = JOptionPane.showConfirmDialog( this,
1117 "Exit despite potentially unsaved changes?",
1119 JOptionPane.YES_NO_OPTION );
1120 if ( r != JOptionPane.YES_OPTION ) {
1127 void executeLineageInference() {
1128 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1131 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1132 JOptionPane.showMessageDialog( this,
1133 "Phylogeny is not rooted.",
1134 "Cannot infer ancestral taxonomies",
1135 JOptionPane.ERROR_MESSAGE );
1138 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1139 _mainpanel.getCurrentTreePanel(),
1140 _mainpanel.getCurrentPhylogeny()
1142 new Thread( inferrer ).start();
1146 removeAllTextFrames();
1147 _mainpanel.terminate();
1148 _contentpane.removeAll();
1149 setVisible( false );
1155 void readPhylogeniesFromURL() {
1157 Phylogeny[] phys = null;
1158 final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1159 final String url_string = JOptionPane.showInputDialog( this,
1161 "Use URL/webservice to obtain a phylogeny",
1162 JOptionPane.QUESTION_MESSAGE );
1163 boolean nhx_or_nexus = false;
1164 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1166 url = new URL( url_string );
1167 PhylogenyParser parser = null;
1168 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1169 parser = new TolParser();
1172 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1173 .isValidatePhyloXmlAgainstSchema() );
1175 if ( parser instanceof NexusPhylogeniesParser ) {
1176 nhx_or_nexus = true;
1178 else if ( parser instanceof NHXParser ) {
1179 nhx_or_nexus = true;
1181 if ( _mainpanel.getCurrentTreePanel() != null ) {
1182 _mainpanel.getCurrentTreePanel().setWaitCursor();
1185 _mainpanel.setWaitCursor();
1187 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1188 phys = factory.create( url.openStream(), parser );
1190 catch ( final MalformedURLException e ) {
1191 JOptionPane.showMessageDialog( this,
1192 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1194 JOptionPane.ERROR_MESSAGE );
1196 catch ( final IOException e ) {
1197 JOptionPane.showMessageDialog( this,
1198 "Could not read from " + url + "\n"
1199 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1200 "Failed to read URL",
1201 JOptionPane.ERROR_MESSAGE );
1203 catch ( final Exception e ) {
1204 JOptionPane.showMessageDialog( this,
1205 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1206 "Unexpected Exception",
1207 JOptionPane.ERROR_MESSAGE );
1210 if ( _mainpanel.getCurrentTreePanel() != null ) {
1211 _mainpanel.getCurrentTreePanel().setArrowCursor();
1214 _mainpanel.setArrowCursor();
1217 if ( ( phys != null ) && ( phys.length > 0 ) ) {
1218 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1219 for( final Phylogeny phy : phys ) {
1220 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1223 AptxUtil.addPhylogeniesToTabs( phys,
1224 new File( url.getFile() ).getName(),
1225 new File( url.getFile() ).toString(),
1228 _mainpanel.getControlPanel().showWhole();
1231 activateSaveAllIfNeeded();
1235 void setMsa( final Msa msa ) {
1239 void setMsaFile( final File msa_file ) {
1240 _msa_file = msa_file;
1243 void setSeqs( final List<Sequence> seqs ) {
1247 void setSeqsFile( final File seqs_file ) {
1248 _seqs_file = seqs_file;
1251 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1252 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1253 _mainpanel.getCurrentTreePanel().getHeight(),
1255 String file_written_to = "";
1256 boolean error = false;
1258 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1259 _mainpanel.getCurrentTreePanel().getWidth(),
1260 _mainpanel.getCurrentTreePanel().getHeight(),
1261 _mainpanel.getCurrentTreePanel(),
1262 _mainpanel.getControlPanel(),
1266 catch ( final IOException e ) {
1268 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1271 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1272 JOptionPane.showMessageDialog( this,
1273 "Wrote image to: " + file_written_to,
1275 JOptionPane.INFORMATION_MESSAGE );
1278 JOptionPane.showMessageDialog( this,
1279 "There was an unknown problem when attempting to write to an image file: \""
1282 JOptionPane.ERROR_MESSAGE );
1285 _contentpane.repaint();
1288 private void addExpressionValuesFromFile() {
1289 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1290 JOptionPane.showMessageDialog( this,
1291 "Need to load evolutionary tree first",
1292 "Can Not Read Expression Values",
1293 JOptionPane.WARNING_MESSAGE );
1296 final File my_dir = getCurrentDir();
1297 if ( my_dir != null ) {
1298 _values_filechooser.setCurrentDirectory( my_dir );
1300 final int result = _values_filechooser.showOpenDialog( _contentpane );
1301 final File file = _values_filechooser.getSelectedFile();
1302 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1303 BasicTable<String> t = null;
1305 t = BasicTableParser.parse( file, '\t' );
1306 if ( t.getNumberOfColumns() < 2 ) {
1307 t = BasicTableParser.parse( file, ',' );
1309 if ( t.getNumberOfColumns() < 2 ) {
1310 t = BasicTableParser.parse( file, ' ' );
1313 catch ( final IOException e ) {
1314 JOptionPane.showMessageDialog( this,
1316 "Could Not Read Expression Value Table",
1317 JOptionPane.ERROR_MESSAGE );
1320 if ( t.getNumberOfColumns() < 2 ) {
1321 JOptionPane.showMessageDialog( this,
1322 "Table contains " + t.getNumberOfColumns() + " column(s)",
1323 "Problem with Expression Value Table",
1324 JOptionPane.ERROR_MESSAGE );
1327 if ( t.getNumberOfRows() < 1 ) {
1328 JOptionPane.showMessageDialog( this,
1329 "Table contains zero rows",
1330 "Problem with Expression Value Table",
1331 JOptionPane.ERROR_MESSAGE );
1334 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1335 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1336 JOptionPane.showMessageDialog( this,
1337 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1338 + phy.getNumberOfExternalNodes() + " external nodes",
1340 JOptionPane.WARNING_MESSAGE );
1342 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1344 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1345 final PhylogenyNode node = iter.next();
1346 final String node_name = node.getName();
1347 if ( !ForesterUtil.isEmpty( node_name ) ) {
1350 row = t.findRow( node_name );
1352 catch ( final IllegalArgumentException e ) {
1354 .showMessageDialog( this,
1356 "Error Mapping Node Identifiers to Expression Value Identifiers",
1357 JOptionPane.ERROR_MESSAGE );
1361 if ( node.isExternal() ) {
1366 final List<Double> l = new ArrayList<Double>();
1367 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1370 d = Double.parseDouble( t.getValueAsString( col, row ) );
1372 catch ( final NumberFormatException e ) {
1373 JOptionPane.showMessageDialog( this,
1374 "Could not parse \"" + t.getValueAsString( col, row )
1375 + "\" into a decimal value",
1376 "Issue with Expression Value Table",
1377 JOptionPane.ERROR_MESSAGE );
1380 stats.addValue( d );
1383 if ( !l.isEmpty() ) {
1384 if ( node.getNodeData().getProperties() != null ) {
1385 node.getNodeData().getProperties()
1386 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1388 node.getNodeData().setVector( l );
1392 if ( not_found > 0 ) {
1393 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1394 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1396 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1400 private void addSequencesFromFile() {
1401 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1402 JOptionPane.showMessageDialog( this,
1403 "Need to load evolutionary tree first",
1404 "Can Not Read Sequences",
1405 JOptionPane.WARNING_MESSAGE );
1408 final File my_dir = getCurrentDir();
1409 if ( my_dir != null ) {
1410 _sequences_filechooser.setCurrentDirectory( my_dir );
1412 final int result = _sequences_filechooser.showOpenDialog( _contentpane );
1413 final File file = _sequences_filechooser.getSelectedFile();
1414 List<Sequence> seqs = null;
1415 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1417 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1418 seqs = FastaParser.parse( new FileInputStream( file ) );
1421 JOptionPane.showMessageDialog( this,
1422 "Format does not appear to be Fasta",
1423 "Multiple sequence file format error",
1424 JOptionPane.ERROR_MESSAGE );
1428 catch ( final MsaFormatException e ) {
1430 JOptionPane.showMessageDialog( this,
1431 e.getLocalizedMessage(),
1432 "Multiple sequence file format error",
1433 JOptionPane.ERROR_MESSAGE );
1436 catch ( final IOException e ) {
1438 JOptionPane.showMessageDialog( this,
1439 e.getLocalizedMessage(),
1440 "Failed to read multiple sequence file",
1441 JOptionPane.ERROR_MESSAGE );
1444 catch ( final Exception e ) {
1446 e.printStackTrace();
1447 JOptionPane.showMessageDialog( this,
1448 e.getLocalizedMessage(),
1449 "Unexpected error during reading of multiple sequence file",
1450 JOptionPane.ERROR_MESSAGE );
1453 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1454 JOptionPane.showMessageDialog( this,
1455 "Multiple sequence file is empty",
1456 "Empty multiple sequence file",
1457 JOptionPane.ERROR_MESSAGE );
1462 if ( seqs != null ) {
1463 for( final Sequence seq : seqs ) {
1464 System.out.println( seq.getIdentifier() );
1466 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1467 int total_counter = 0;
1468 int attached_counter = 0;
1469 for( final Sequence seq : seqs ) {
1471 final String seq_name = seq.getIdentifier();
1472 if ( !ForesterUtil.isEmpty( seq_name ) ) {
1473 List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
1474 if ( nodes.isEmpty() ) {
1475 nodes = phy.getNodesViaSequenceSymbol( seq_name );
1477 if ( nodes.isEmpty() ) {
1478 nodes = phy.getNodesViaGeneName( seq_name );
1480 if ( nodes.isEmpty() ) {
1481 nodes = phy.getNodes( seq_name );
1483 if ( nodes.size() > 1 ) {
1484 JOptionPane.showMessageDialog( this,
1485 "Sequence name \"" + seq_name + "\" is not unique",
1486 "Sequence name not unique",
1487 JOptionPane.ERROR_MESSAGE );
1491 final String[] a = seq_name.split( "\\s" );
1492 if ( nodes.isEmpty() && ( a.length > 1 ) ) {
1493 final String seq_name_split = a[ 0 ];
1494 nodes = phy.getNodesViaSequenceName( seq_name_split );
1495 if ( nodes.isEmpty() ) {
1496 nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
1498 if ( nodes.isEmpty() ) {
1499 nodes = phy.getNodes( seq_name_split );
1501 if ( nodes.size() > 1 ) {
1502 JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
1503 + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
1508 if ( nodes.size() == 1 ) {
1510 final PhylogenyNode n = nodes.get( 0 );
1511 if ( !n.getNodeData().isHasSequence() ) {
1512 n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
1514 n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
1515 if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
1516 n.getNodeData().getSequence().setName( seq_name );
1521 if ( attached_counter > 0 ) {
1523 int ext_nodes_with_seq = 0;
1524 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
1526 final PhylogenyNode n = iter.next();
1527 if ( n.getNodeData().isHasSequence()
1528 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
1529 ++ext_nodes_with_seq;
1533 if ( ext_nodes == ext_nodes_with_seq ) {
1534 s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
1537 s = ext_nodes_with_seq + " out of " + ext_nodes
1538 + " external nodes now have a molecular sequence attached to them.";
1540 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
1541 JOptionPane.showMessageDialog( this,
1542 "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
1543 "All sequences attached",
1544 JOptionPane.INFORMATION_MESSAGE );
1547 JOptionPane.showMessageDialog( this, "Attached " + attached_counter
1548 + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
1549 + " sequences attached", JOptionPane.WARNING_MESSAGE );
1553 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
1554 + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
1559 private void choosePdfWidth() {
1560 final String s = ( String ) JOptionPane.showInputDialog( this,
1561 "Please enter the default line width for PDF export.\n"
1562 + "[current value: "
1563 + getOptions().getPrintLineWidth() + "]\n",
1564 "Line Width for PDF Export",
1565 JOptionPane.QUESTION_MESSAGE,
1568 getOptions().getPrintLineWidth() );
1569 if ( !ForesterUtil.isEmpty( s ) ) {
1570 boolean success = true;
1572 final String m_str = s.trim();
1573 if ( !ForesterUtil.isEmpty( m_str ) ) {
1575 f = Float.parseFloat( m_str );
1577 catch ( final Exception ex ) {
1584 if ( success && ( f > 0.0 ) ) {
1585 getOptions().setPrintLineWidth( f );
1590 private void choosePrintSize() {
1591 final String s = ( String ) JOptionPane.showInputDialog( this,
1592 "Please enter values for width and height,\nseparated by a comma.\n"
1593 + "[current values: "
1594 + getOptions().getPrintSizeX() + ", "
1595 + getOptions().getPrintSizeY() + "]\n"
1596 + "[A4: " + Constants.A4_SIZE_X + ", "
1597 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1598 + Constants.US_LETTER_SIZE_X + ", "
1599 + Constants.US_LETTER_SIZE_Y + "]",
1600 "Default Size for Graphics Export",
1601 JOptionPane.QUESTION_MESSAGE,
1604 getOptions().getPrintSizeX() + ", "
1605 + getOptions().getPrintSizeY() );
1606 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1607 boolean success = true;
1610 final String[] str_ary = s.split( "," );
1611 if ( str_ary.length == 2 ) {
1612 final String x_str = str_ary[ 0 ].trim();
1613 final String y_str = str_ary[ 1 ].trim();
1614 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1616 x = Integer.parseInt( x_str );
1617 y = Integer.parseInt( y_str );
1619 catch ( final Exception ex ) {
1630 if ( success && ( x > 1 ) && ( y > 1 ) ) {
1631 getOptions().setPrintSizeX( x );
1632 getOptions().setPrintSizeY( y );
1637 private void closeCurrentPane() {
1638 if ( getMainPanel().getCurrentTreePanel() != null ) {
1639 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1640 final int r = JOptionPane.showConfirmDialog( this,
1641 "Close tab despite potentially unsaved changes?",
1643 JOptionPane.YES_NO_OPTION );
1644 if ( r != JOptionPane.YES_OPTION ) {
1648 getMainPanel().closeCurrentPane();
1649 activateSaveAllIfNeeded();
1653 private void collapse( final Phylogeny phy, final double m ) {
1654 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1655 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1656 double min_support = Double.MAX_VALUE;
1657 boolean conf_present = false;
1658 while ( it.hasNext() ) {
1659 final PhylogenyNode n = it.next();
1660 if ( !n.isExternal() && !n.isRoot() ) {
1661 final List<Confidence> c = n.getBranchData().getConfidences();
1662 if ( ( c != null ) && ( c.size() > 0 ) ) {
1663 conf_present = true;
1665 for( final Confidence confidence : c ) {
1666 if ( confidence.getValue() > max ) {
1667 max = confidence.getValue();
1670 if ( max < getMinNotCollapseConfidenceValue() ) {
1671 to_be_removed.add( n );
1673 if ( max < min_support ) {
1679 if ( conf_present ) {
1680 for( final PhylogenyNode node : to_be_removed ) {
1681 PhylogenyMethods.removeNode( node, phy );
1683 if ( to_be_removed.size() > 0 ) {
1684 phy.externalNodesHaveChanged();
1685 phy.clearHashIdToNodeMap();
1686 phy.recalculateNumberOfExternalDescendants( true );
1687 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1688 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1689 getCurrentTreePanel().calculateLongestExtNodeInfo();
1690 getCurrentTreePanel().setNodeInPreorderToNull();
1691 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1692 getCurrentTreePanel().resetPreferredSize();
1693 getCurrentTreePanel().setEdited( true );
1694 getCurrentTreePanel().repaint();
1697 if ( to_be_removed.size() > 0 ) {
1698 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1699 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1700 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1703 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1704 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1708 JOptionPane.showMessageDialog( this,
1709 "No branch collapsed because no confidence values present",
1710 "No confidence values present",
1711 JOptionPane.INFORMATION_MESSAGE );
1715 private void collapseBelowThreshold() {
1716 if ( getCurrentTreePanel() != null ) {
1717 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1718 if ( ( phy != null ) && !phy.isEmpty() ) {
1719 final String s = ( String ) JOptionPane.showInputDialog( this,
1720 "Please enter the minimum confidence value\n",
1721 "Minimal Confidence Value",
1722 JOptionPane.QUESTION_MESSAGE,
1725 getMinNotCollapseConfidenceValue() );
1726 if ( !ForesterUtil.isEmpty( s ) ) {
1727 boolean success = true;
1729 final String m_str = s.trim();
1730 if ( !ForesterUtil.isEmpty( m_str ) ) {
1732 m = Double.parseDouble( m_str );
1734 catch ( final Exception ex ) {
1741 if ( success && ( m >= 0.0 ) ) {
1742 setMinNotCollapseConfidenceValue( m );
1750 private PhyloXmlParser createPhyloXmlParser() {
1751 PhyloXmlParser xml_parser = null;
1752 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1754 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1756 catch ( final Exception e ) {
1757 JOptionPane.showMessageDialog( this,
1758 e.getLocalizedMessage(),
1759 "failed to create validating XML parser",
1760 JOptionPane.WARNING_MESSAGE );
1763 if ( xml_parser == null ) {
1764 xml_parser = PhyloXmlParser.createPhyloXmlParser();
1769 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1770 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1771 getPhylogeneticInferenceOptions(),
1772 from_unaligned_seqs );
1774 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1775 if ( !from_unaligned_seqs ) {
1776 if ( getMsa() != null ) {
1777 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1778 getPhylogeneticInferenceOptions()
1780 new Thread( inferrer ).start();
1783 JOptionPane.showMessageDialog( this,
1784 "No multiple sequence alignment selected",
1785 "Phylogenetic Inference Not Launched",
1786 JOptionPane.WARNING_MESSAGE );
1790 if ( getSeqs() != null ) {
1791 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1792 getPhylogeneticInferenceOptions()
1794 new Thread( inferrer ).start();
1797 JOptionPane.showMessageDialog( this,
1798 "No input sequences selected",
1799 "Phylogenetic Inference Not Launched",
1800 JOptionPane.WARNING_MESSAGE );
1806 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1807 final StringBuilder sb = new StringBuilder();
1808 final StringBuilder sb_failed = new StringBuilder();
1810 int counter_failed = 0;
1811 if ( getCurrentTreePanel() != null ) {
1812 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1813 if ( ( phy != null ) && !phy.isEmpty() ) {
1814 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1815 while ( it.hasNext() ) {
1816 final PhylogenyNode n = it.next();
1817 final String name = n.getName().trim();
1818 if ( !ForesterUtil.isEmpty( name ) ) {
1819 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
1820 TAXONOMY_EXTRACTION.AGGRESSIVE );
1821 if ( !ForesterUtil.isEmpty( nt ) ) {
1822 if ( counter < 15 ) {
1823 sb.append( name + ": " + nt + "\n" );
1825 else if ( counter == 15 ) {
1826 sb.append( "...\n" );
1831 if ( counter_failed < 15 ) {
1832 sb_failed.append( name + "\n" );
1834 else if ( counter_failed == 15 ) {
1835 sb_failed.append( "...\n" );
1841 if ( counter > 0 ) {
1843 String all = "all ";
1844 if ( counter_failed > 0 ) {
1846 failed = "\nCould not extract taxonomic data for " + counter_failed
1847 + " named external nodes:\n" + sb_failed;
1849 JOptionPane.showMessageDialog( this,
1850 "Extracted taxonomic data from " + all + counter
1851 + " named external nodes:\n" + sb.toString() + failed,
1852 "Taxonomic Data Extraction Completed",
1853 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1854 : JOptionPane.INFORMATION_MESSAGE );
1858 .showMessageDialog( this,
1859 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1860 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1861 + "or nodes already have taxonomic data?\n",
1862 "No Taxonomic Data Extracted",
1863 JOptionPane.ERROR_MESSAGE );
1869 private ControlPanel getControlPanel() {
1870 return getMainPanel().getControlPanel();
1873 private File getCurrentDir() {
1874 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1875 if ( ForesterUtil.isWindows() ) {
1877 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1879 catch ( final Exception e ) {
1880 _current_dir = null;
1884 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1885 if ( System.getProperty( "user.home" ) != null ) {
1886 _current_dir = new File( System.getProperty( "user.home" ) );
1888 else if ( System.getProperty( "user.dir" ) != null ) {
1889 _current_dir = new File( System.getProperty( "user.dir" ) );
1892 return _current_dir;
1895 private double getMinNotCollapseConfidenceValue() {
1896 return _min_not_collapse;
1899 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1900 if ( _phylogenetic_inference_options == null ) {
1901 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1903 return _phylogenetic_inference_options;
1906 private boolean isUnsavedDataPresent() {
1907 final List<TreePanel> tps = getMainPanel().getTreePanels();
1908 for( final TreePanel tp : tps ) {
1909 if ( tp.isEdited() ) {
1916 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1917 if ( getCurrentTreePanel() != null ) {
1918 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1919 if ( ( phy != null ) && !phy.isEmpty() ) {
1921 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1926 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1927 if ( getCurrentTreePanel() != null ) {
1928 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1929 if ( ( phy != null ) && !phy.isEmpty() ) {
1930 PhylogenyMethods.transferNodeNameToField( phy,
1931 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1937 private void newTree() {
1938 final Phylogeny[] phys = new Phylogeny[ 1 ];
1939 final Phylogeny phy = new Phylogeny();
1940 final PhylogenyNode node = new PhylogenyNode();
1941 phy.setRoot( node );
1942 phy.setRooted( true );
1944 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1945 _mainpanel.getControlPanel().showWhole();
1946 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1947 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1948 if ( getMainPanel().getMainFrame() == null ) {
1949 // Must be "E" applet version.
1950 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1951 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1954 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1956 activateSaveAllIfNeeded();
1960 private void obtainDetailedTaxonomicInformation() {
1961 if ( getCurrentTreePanel() != null ) {
1962 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1963 if ( ( phy != null ) && !phy.isEmpty() ) {
1964 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1965 _mainpanel.getCurrentTreePanel(),
1969 new Thread( t ).start();
1974 private void obtainDetailedTaxonomicInformationDelete() {
1975 if ( getCurrentTreePanel() != null ) {
1976 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1977 if ( ( phy != null ) && !phy.isEmpty() ) {
1978 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1979 _mainpanel.getCurrentTreePanel(),
1983 new Thread( t ).start();
1988 private void obtainSequenceInformation() {
1989 if ( getCurrentTreePanel() != null ) {
1990 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1991 if ( ( phy != null ) && !phy.isEmpty() ) {
1992 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1993 _mainpanel.getCurrentTreePanel(),
1995 new Thread( u ).start();
2000 private void print() {
2001 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2002 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2005 if ( !getOptions().isPrintUsingActualSize() ) {
2006 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
2007 getOptions().getPrintSizeY() - 140,
2009 getCurrentTreePanel().resetPreferredSize();
2010 getCurrentTreePanel().repaint();
2012 final String job_name = Constants.PRG_NAME;
2013 boolean error = false;
2014 String printer_name = null;
2016 printer_name = Printer.print( getCurrentTreePanel(), job_name );
2018 catch ( final Exception e ) {
2020 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2022 if ( !error && ( printer_name != null ) ) {
2023 String msg = "Printing data sent to printer";
2024 if ( printer_name.length() > 1 ) {
2025 msg += " [" + printer_name + "]";
2027 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2029 if ( !getOptions().isPrintUsingActualSize() ) {
2030 getControlPanel().showWhole();
2034 private void printPhylogenyToPdf( final String file_name ) {
2035 if ( !getOptions().isPrintUsingActualSize() ) {
2036 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
2037 getOptions().getPrintSizeY(),
2039 getCurrentTreePanel().resetPreferredSize();
2040 getCurrentTreePanel().repaint();
2042 String pdf_written_to = "";
2043 boolean error = false;
2045 if ( getOptions().isPrintUsingActualSize() ) {
2046 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2047 getCurrentTreePanel(),
2048 getCurrentTreePanel().getWidth(),
2049 getCurrentTreePanel().getHeight() );
2052 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2053 .getPrintSizeX(), getOptions().getPrintSizeY() );
2056 catch ( final IOException e ) {
2058 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2061 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2062 JOptionPane.showMessageDialog( this,
2063 "Wrote PDF to: " + pdf_written_to,
2065 JOptionPane.INFORMATION_MESSAGE );
2068 JOptionPane.showMessageDialog( this,
2069 "There was an unknown problem when attempting to write to PDF file: \""
2072 JOptionPane.ERROR_MESSAGE );
2075 if ( !getOptions().isPrintUsingActualSize() ) {
2076 getControlPanel().showWhole();
2080 private void readPhylogeniesFromFile() {
2081 boolean exception = false;
2082 Phylogeny[] phys = null;
2083 // Set an initial directory if none set yet
2084 final File my_dir = getCurrentDir();
2085 _open_filechooser.setMultiSelectionEnabled( true );
2086 // Open file-open dialog and set current directory
2087 if ( my_dir != null ) {
2088 _open_filechooser.setCurrentDirectory( my_dir );
2090 final int result = _open_filechooser.showOpenDialog( _contentpane );
2091 // All done: get the file
2092 final File[] files = _open_filechooser.getSelectedFiles();
2093 setCurrentDir( _open_filechooser.getCurrentDirectory() );
2094 boolean nhx_or_nexus = false;
2095 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2096 for( final File file : files ) {
2097 if ( ( file != null ) && !file.isDirectory() ) {
2098 if ( _mainpanel.getCurrentTreePanel() != null ) {
2099 _mainpanel.getCurrentTreePanel().setWaitCursor();
2102 _mainpanel.setWaitCursor();
2104 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2105 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2107 final NHXParser nhx = new NHXParser();
2108 setSpecialOptionsForNhxParser( nhx );
2109 phys = PhylogenyMethods.readPhylogenies( nhx, file );
2110 nhx_or_nexus = true;
2112 catch ( final Exception e ) {
2114 exceptionOccuredDuringOpenFile( e );
2117 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2118 warnIfNotPhyloXmlValidation( getConfiguration() );
2120 final PhyloXmlParser xml_parser = createPhyloXmlParser();
2121 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2123 catch ( final Exception e ) {
2125 exceptionOccuredDuringOpenFile( e );
2128 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2130 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2132 catch ( final Exception e ) {
2134 exceptionOccuredDuringOpenFile( e );
2137 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2139 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2140 setSpecialOptionsForNexParser( nex );
2141 phys = PhylogenyMethods.readPhylogenies( nex, file );
2142 nhx_or_nexus = true;
2144 catch ( final Exception e ) {
2146 exceptionOccuredDuringOpenFile( e );
2152 final PhylogenyParser parser = ParserUtils
2153 .createParserDependingOnFileType( file, getConfiguration()
2154 .isValidatePhyloXmlAgainstSchema() );
2155 if ( parser instanceof NexusPhylogeniesParser ) {
2156 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2157 setSpecialOptionsForNexParser( nex );
2158 nhx_or_nexus = true;
2160 else if ( parser instanceof NHXParser ) {
2161 final NHXParser nhx = ( NHXParser ) parser;
2162 setSpecialOptionsForNhxParser( nhx );
2163 nhx_or_nexus = true;
2165 else if ( parser instanceof PhyloXmlParser ) {
2166 warnIfNotPhyloXmlValidation( getConfiguration() );
2168 phys = PhylogenyMethods.readPhylogenies( parser, file );
2170 catch ( final Exception e ) {
2172 exceptionOccuredDuringOpenFile( e );
2175 if ( _mainpanel.getCurrentTreePanel() != null ) {
2176 _mainpanel.getCurrentTreePanel().setArrowCursor();
2179 _mainpanel.setArrowCursor();
2181 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2182 boolean one_desc = false;
2183 if ( nhx_or_nexus ) {
2184 for( final Phylogeny phy : phys ) {
2185 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2186 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2188 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2194 AptxUtil.addPhylogeniesToTabs( phys,
2196 file.getAbsolutePath(),
2199 _mainpanel.getControlPanel().showWhole();
2200 if ( nhx_or_nexus && one_desc ) {
2202 .showMessageDialog( this,
2203 "One or more trees contain (a) node(s) with one descendant, "
2204 + ForesterUtil.LINE_SEPARATOR
2205 + "possibly indicating illegal parentheses within node names.",
2206 "Warning: Possible Error in New Hampshire Formatted Data",
2207 JOptionPane.WARNING_MESSAGE );
2213 activateSaveAllIfNeeded();
2217 private void readSpeciesTreeFromFile() {
2219 boolean exception = false;
2220 final File my_dir = getCurrentDir();
2221 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2222 if ( my_dir != null ) {
2223 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2225 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2226 final File file = _open_filechooser_for_species_tree.getSelectedFile();
2227 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2228 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2230 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
2231 .createPhyloXmlParserXsdValidating(), file );
2234 catch ( final Exception e ) {
2236 exceptionOccuredDuringOpenFile( e );
2239 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2241 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2244 catch ( final Exception e ) {
2246 exceptionOccuredDuringOpenFile( e );
2252 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
2253 .createPhyloXmlParserXsdValidating(), file );
2256 catch ( final Exception e ) {
2258 exceptionOccuredDuringOpenFile( e );
2261 if ( !exception && ( t != null ) && !t.isRooted() ) {
2264 JOptionPane.showMessageDialog( this,
2265 "Species tree is not rooted",
2266 "Species tree not loaded",
2267 JOptionPane.ERROR_MESSAGE );
2269 if ( !exception && ( t != null ) ) {
2270 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2271 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2272 final PhylogenyNode node = it.next();
2273 if ( !node.getNodeData().isHasTaxonomy() ) {
2277 .showMessageDialog( this,
2278 "Species tree contains external node(s) without taxonomy information",
2279 "Species tree not loaded",
2280 JOptionPane.ERROR_MESSAGE );
2284 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2287 JOptionPane.showMessageDialog( this,
2289 + node.getNodeData().getTaxonomy().asSimpleText()
2290 + "] is not unique in species tree",
2291 "Species tree not loaded",
2292 JOptionPane.ERROR_MESSAGE );
2296 tax_set.add( node.getNodeData().getTaxonomy() );
2301 if ( !exception && ( t != null ) ) {
2302 setSpeciesTree( t );
2303 JOptionPane.showMessageDialog( this,
2304 "Species tree successfully loaded",
2305 "Species tree loaded",
2306 JOptionPane.INFORMATION_MESSAGE );
2308 _contentpane.repaint();
2313 private void setArrowCursor() {
2315 _mainpanel.getCurrentTreePanel().setArrowCursor();
2317 catch ( final Exception ex ) {
2322 private void setCurrentDir( final File current_dir ) {
2323 _current_dir = current_dir;
2326 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2327 _min_not_collapse = min_not_collapse;
2330 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2331 _phylogenetic_inference_options = phylogenetic_inference_options;
2334 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2335 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2336 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2339 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2340 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2341 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2344 private void writeAllToFile() {
2345 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2348 final File my_dir = getCurrentDir();
2349 if ( my_dir != null ) {
2350 _save_filechooser.setCurrentDirectory( my_dir );
2352 _save_filechooser.setSelectedFile( new File( "" ) );
2353 final int result = _save_filechooser.showSaveDialog( _contentpane );
2354 final File file = _save_filechooser.getSelectedFile();
2355 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2356 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2357 if ( file.exists() ) {
2358 final int i = JOptionPane.showConfirmDialog( this,
2359 file + " already exists. Overwrite?",
2361 JOptionPane.OK_CANCEL_OPTION,
2362 JOptionPane.WARNING_MESSAGE );
2363 if ( i != JOptionPane.OK_OPTION ) {
2370 catch ( final Exception e ) {
2371 JOptionPane.showMessageDialog( this,
2372 "Failed to delete: " + file,
2374 JOptionPane.WARNING_MESSAGE );
2378 final int count = getMainPanel().getTabbedPane().getTabCount();
2379 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2380 for( int i = 0; i < count; ++i ) {
2381 final Phylogeny phy = getMainPanel().getPhylogeny( i );
2382 if ( ForesterUtil.isEmpty( phy.getName() )
2383 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
2384 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
2387 getMainPanel().getTreePanels().get( i ).setEdited( false );
2389 final PhylogenyWriter writer = new PhylogenyWriter();
2391 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2393 catch ( final IOException e ) {
2394 JOptionPane.showMessageDialog( this,
2395 "Failed to write to: " + file,
2397 JOptionPane.WARNING_MESSAGE );
2402 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2404 final PhylogenyWriter writer = new PhylogenyWriter();
2405 writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2407 catch ( final Exception e ) {
2409 exceptionOccuredDuringSaveAs( e );
2414 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2416 final PhylogenyWriter writer = new PhylogenyWriter();
2417 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2419 catch ( final Exception e ) {
2421 exceptionOccuredDuringSaveAs( e );
2426 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2428 final PhylogenyWriter writer = new PhylogenyWriter();
2429 writer.toPhyloXML( file, t, 0 );
2431 catch ( final Exception e ) {
2433 exceptionOccuredDuringSaveAs( e );
2438 private void writeToFile( final Phylogeny t ) {
2442 String initial_filename = null;
2443 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2445 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2447 catch ( final IOException e ) {
2448 initial_filename = null;
2451 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2452 _save_filechooser.setSelectedFile( new File( initial_filename ) );
2455 _save_filechooser.setSelectedFile( new File( "" ) );
2457 final File my_dir = getCurrentDir();
2458 if ( my_dir != null ) {
2459 _save_filechooser.setCurrentDirectory( my_dir );
2461 final int result = _save_filechooser.showSaveDialog( _contentpane );
2462 final File file = _save_filechooser.getSelectedFile();
2463 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2464 boolean exception = false;
2465 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2466 if ( file.exists() ) {
2467 final int i = JOptionPane.showConfirmDialog( this,
2468 file + " already exists.\nOverwrite?",
2470 JOptionPane.OK_CANCEL_OPTION,
2471 JOptionPane.QUESTION_MESSAGE );
2472 if ( i != JOptionPane.OK_OPTION ) {
2476 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2478 ForesterUtil.copyFile( file, to );
2480 catch ( final Exception e ) {
2481 JOptionPane.showMessageDialog( this,
2482 "Failed to create backup copy " + to,
2483 "Failed to Create Backup Copy",
2484 JOptionPane.WARNING_MESSAGE );
2489 catch ( final Exception e ) {
2490 JOptionPane.showMessageDialog( this,
2491 "Failed to delete: " + file,
2493 JOptionPane.WARNING_MESSAGE );
2497 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2498 exception = writeAsNewHampshire( t, exception, file );
2500 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2501 exception = writeAsPhyloXml( t, exception, file );
2503 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2504 exception = writeAsNexus( t, exception, file );
2508 final String file_name = file.getName().trim().toLowerCase();
2509 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2510 || file_name.endsWith( ".tree" ) ) {
2511 exception = writeAsNewHampshire( t, exception, file );
2513 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2514 exception = writeAsNexus( t, exception, file );
2518 exception = writeAsPhyloXml( t, exception, file );
2522 getMainPanel().setTitleOfSelectedTab( file.getName() );
2523 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2524 getMainPanel().getCurrentTreePanel().setEdited( false );
2529 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2530 if ( ( t == null ) || t.isEmpty() ) {
2533 String initial_filename = "";
2534 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2535 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2537 if ( initial_filename.indexOf( '.' ) > 0 ) {
2538 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2540 initial_filename = initial_filename + "." + type;
2541 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2542 final File my_dir = getCurrentDir();
2543 if ( my_dir != null ) {
2544 _writetographics_filechooser.setCurrentDirectory( my_dir );
2546 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2547 File file = _writetographics_filechooser.getSelectedFile();
2548 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2549 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2550 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2551 file = new File( file.toString() + "." + type );
2553 if ( file.exists() ) {
2554 final int i = JOptionPane.showConfirmDialog( this,
2555 file + " already exists. Overwrite?",
2557 JOptionPane.OK_CANCEL_OPTION,
2558 JOptionPane.WARNING_MESSAGE );
2559 if ( i != JOptionPane.OK_OPTION ) {
2566 catch ( final Exception e ) {
2567 JOptionPane.showMessageDialog( this,
2568 "Failed to delete: " + file,
2570 JOptionPane.WARNING_MESSAGE );
2574 writePhylogenyToGraphicsFile( file.toString(), type );
2578 private void writeToPdf( final Phylogeny t ) {
2579 if ( ( t == null ) || t.isEmpty() ) {
2582 String initial_filename = "";
2583 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2584 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2586 if ( initial_filename.indexOf( '.' ) > 0 ) {
2587 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2589 initial_filename = initial_filename + ".pdf";
2590 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2591 final File my_dir = getCurrentDir();
2592 if ( my_dir != null ) {
2593 _writetopdf_filechooser.setCurrentDirectory( my_dir );
2595 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2596 File file = _writetopdf_filechooser.getSelectedFile();
2597 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2598 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2599 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2600 file = new File( file.toString() + ".pdf" );
2602 if ( file.exists() ) {
2603 final int i = JOptionPane.showConfirmDialog( this,
2604 file + " already exists. Overwrite?",
2606 JOptionPane.OK_CANCEL_OPTION,
2607 JOptionPane.WARNING_MESSAGE );
2608 if ( i != JOptionPane.OK_OPTION ) {
2612 printPhylogenyToPdf( file.toString() );
2616 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2617 return new MainFrameApplication( phys, config );
2620 public static MainFrame createInstance( final Phylogeny[] phys,
2621 final Configuration config,
2623 final File current_dir ) {
2624 return new MainFrameApplication( phys, config, title, current_dir );
2627 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2628 return new MainFrameApplication( phys, config, title );
2631 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2632 return new MainFrameApplication( phys, config_file_name, title );
2635 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2636 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2637 + o.getPrintSizeY() + ")" );
2640 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2641 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2644 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2645 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2647 .showMessageDialog( null,
2649 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2652 JOptionPane.WARNING_MESSAGE );
2655 } // MainFrameApplication.
2657 class DefaultFilter extends FileFilter {
2660 public boolean accept( final File f ) {
2661 final String file_name = f.getName().trim().toLowerCase();
2662 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2663 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2664 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2665 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2666 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2667 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2668 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2669 || file_name.endsWith( ".con" ) || f.isDirectory();
2673 public String getDescription() {
2674 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2678 class GraphicsFileFilter extends FileFilter {
2681 public boolean accept( final File f ) {
2682 final String file_name = f.getName().trim().toLowerCase();
2683 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2684 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2688 public String getDescription() {
2689 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2693 class MsaFileFilter extends FileFilter {
2696 public boolean accept( final File f ) {
2697 final String file_name = f.getName().trim().toLowerCase();
2698 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2699 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2703 public String getDescription() {
2704 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2708 class NexusFilter extends FileFilter {
2711 public boolean accept( final File f ) {
2712 final String file_name = f.getName().trim().toLowerCase();
2713 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2714 || file_name.endsWith( ".tre" ) || f.isDirectory();
2718 public String getDescription() {
2719 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2723 class NHFilter extends FileFilter {
2726 public boolean accept( final File f ) {
2727 final String file_name = f.getName().trim().toLowerCase();
2728 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2729 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2730 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2735 public String getDescription() {
2736 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2740 class NHXFilter extends FileFilter {
2743 public boolean accept( final File f ) {
2744 final String file_name = f.getName().trim().toLowerCase();
2745 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2749 public String getDescription() {
2750 return "NHX files (*.nhx) [deprecated]";
2754 class PdfFilter extends FileFilter {
2757 public boolean accept( final File f ) {
2758 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2762 public String getDescription() {
2763 return "PDF files (*.pdf)";
2767 class SequencesFileFilter extends FileFilter {
2770 public boolean accept( final File f ) {
2771 final String file_name = f.getName().trim().toLowerCase();
2772 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2773 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2777 public String getDescription() {
2778 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2782 class TolFilter extends FileFilter {
2785 public boolean accept( final File f ) {
2786 final String file_name = f.getName().trim().toLowerCase();
2787 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2788 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2792 public String getDescription() {
2793 return "Tree of Life files (*.tol, *.tolxml)";
2797 class XMLFilter extends FileFilter {
2800 public boolean accept( final File f ) {
2801 final String file_name = f.getName().trim().toLowerCase();
2802 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2803 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2807 public String getDescription() {
2808 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";