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 ) );
891 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
893 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
895 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
897 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
898 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
899 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
900 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
901 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
902 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
903 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
904 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
905 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
906 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
907 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
908 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
909 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
911 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
912 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
913 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
914 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
915 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
916 _options_jmenu.addSeparator();
917 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
918 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
919 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
920 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
921 _options_jmenu.addSeparator();
922 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
923 getConfiguration() ) );
924 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
925 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
927 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
929 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
931 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
932 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
933 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
934 _options_jmenu.addSeparator();
935 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
937 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
938 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
940 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
942 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
944 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
946 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
947 _extract_taxonomy_pfam_strict_rbmi
948 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
949 _extract_taxonomy_pfam_relaxed_rbmi
950 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
951 _extract_taxonomy_agressive_rbmi
952 .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\"" );
953 _radio_group_2 = new ButtonGroup();
954 _radio_group_2.add( _extract_taxonomy_no_rbmi );
955 _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
956 _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
957 _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
959 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
961 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
962 _use_brackets_for_conf_in_nh_export_cbmi
963 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
965 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
966 customizeJMenuItem( _choose_font_mi );
967 customizeJMenuItem( _choose_minimal_confidence_mi );
968 customizeJMenuItem( _switch_colors_mi );
969 customizeJMenuItem( _print_size_mi );
970 customizeJMenuItem( _choose_pdf_width_mi );
971 customizeJMenuItem( _overview_placment_mi );
972 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
973 .isShowDefaultNodeShapesExternal() );
974 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
975 .isShowDefaultNodeShapesInternal() );
976 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
977 customizeJMenuItem( _cycle_node_shape_mi );
978 customizeJMenuItem( _cycle_node_fill_mi );
979 customizeJMenuItem( _choose_node_size_mi );
980 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
981 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
982 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
983 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
984 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
985 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
986 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
987 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
988 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
989 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
990 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
991 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
992 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
993 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
994 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
995 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
996 customizeCheckBoxMenuItem( _label_direction_cbmi,
997 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
998 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
999 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1000 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1001 .isInternalNumberAreConfidenceForNhParsing() );
1002 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1003 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1004 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
1005 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1006 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
1007 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1008 customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
1009 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
1010 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1011 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1012 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1013 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1014 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1015 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1016 .isGraphicsExportUsingActualSize() );
1017 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1018 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1019 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1020 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1021 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1022 _jmenubar.add( _options_jmenu );
1025 void buildPhylogeneticInferenceMenu() {
1026 final InferenceManager im = getInferenceManager();
1027 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1028 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1029 customizeJMenuItem( _inference_from_msa_item );
1030 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1031 if ( im.canDoMsa() ) {
1032 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1033 customizeJMenuItem( _inference_from_seqs_item );
1034 _inference_from_seqs_item
1035 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1039 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1040 customizeJMenuItem( _inference_from_seqs_item );
1041 _inference_from_seqs_item.setEnabled( false );
1043 _jmenubar.add( _inference_menu );
1046 void buildToolsMenu() {
1047 _tools_menu = createMenu( "Tools", getConfiguration() );
1048 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1049 customizeJMenuItem( _confcolor_item );
1050 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1051 customizeJMenuItem( _color_rank_jmi );
1052 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1053 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1054 customizeJMenuItem( _taxcolor_item );
1055 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1056 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1057 customizeJMenuItem( _remove_branch_color_item );
1058 _tools_menu.addSeparator();
1059 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1060 customizeJMenuItem( _annotate_item );
1061 _tools_menu.addSeparator();
1062 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1063 customizeJMenuItem( _midpoint_root_item );
1064 _tools_menu.addSeparator();
1065 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1066 customizeJMenuItem( _collapse_species_specific_subtrees );
1068 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1069 customizeJMenuItem( _collapse_below_threshold );
1070 _collapse_below_threshold
1071 .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)" );
1072 _tools_menu.addSeparator();
1074 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
1075 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1076 _extract_tax_code_from_node_names_jmi
1077 .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'" );
1079 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1080 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1081 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1082 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1083 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1084 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1085 _tools_menu.addSeparator();
1086 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1087 customizeJMenuItem( _obtain_seq_information_jmi );
1088 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1090 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1091 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1092 _obtain_detailed_taxonomic_information_jmi
1093 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1095 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1096 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1097 _obtain_detailed_taxonomic_information_deleting_jmi
1098 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1099 _tools_menu.addSeparator();
1100 _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
1101 customizeJMenuItem( _read_values_jmi );
1102 _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
1103 _jmenubar.add( _tools_menu );
1104 _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
1105 customizeJMenuItem( _read_seqs_jmi );
1107 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
1108 _jmenubar.add( _tools_menu );
1113 if ( isUnsavedDataPresent() ) {
1114 final int r = JOptionPane.showConfirmDialog( this,
1115 "Exit despite potentially unsaved changes?",
1117 JOptionPane.YES_NO_OPTION );
1118 if ( r != JOptionPane.YES_OPTION ) {
1125 void executeLineageInference() {
1126 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1129 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1130 JOptionPane.showMessageDialog( this,
1131 "Phylogeny is not rooted.",
1132 "Cannot infer ancestral taxonomies",
1133 JOptionPane.ERROR_MESSAGE );
1136 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1137 _mainpanel.getCurrentTreePanel(),
1138 _mainpanel.getCurrentPhylogeny()
1140 new Thread( inferrer ).start();
1144 removeAllTextFrames();
1145 _mainpanel.terminate();
1146 _contentpane.removeAll();
1147 setVisible( false );
1153 void readPhylogeniesFromURL() {
1155 Phylogeny[] phys = null;
1156 final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1157 final String url_string = JOptionPane.showInputDialog( this,
1159 "Use URL/webservice to obtain a phylogeny",
1160 JOptionPane.QUESTION_MESSAGE );
1161 boolean nhx_or_nexus = false;
1162 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1164 url = new URL( url_string );
1165 PhylogenyParser parser = null;
1166 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1167 parser = new TolParser();
1170 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1171 .isValidatePhyloXmlAgainstSchema() );
1173 if ( parser instanceof NexusPhylogeniesParser ) {
1174 nhx_or_nexus = true;
1176 else if ( parser instanceof NHXParser ) {
1177 nhx_or_nexus = true;
1179 if ( _mainpanel.getCurrentTreePanel() != null ) {
1180 _mainpanel.getCurrentTreePanel().setWaitCursor();
1183 _mainpanel.setWaitCursor();
1185 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1186 phys = factory.create( url.openStream(), parser );
1188 catch ( final MalformedURLException e ) {
1189 JOptionPane.showMessageDialog( this,
1190 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1192 JOptionPane.ERROR_MESSAGE );
1194 catch ( final IOException e ) {
1195 JOptionPane.showMessageDialog( this,
1196 "Could not read from " + url + "\n"
1197 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1198 "Failed to read URL",
1199 JOptionPane.ERROR_MESSAGE );
1201 catch ( final Exception e ) {
1202 JOptionPane.showMessageDialog( this,
1203 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1204 "Unexpected Exception",
1205 JOptionPane.ERROR_MESSAGE );
1208 if ( _mainpanel.getCurrentTreePanel() != null ) {
1209 _mainpanel.getCurrentTreePanel().setArrowCursor();
1212 _mainpanel.setArrowCursor();
1215 if ( ( phys != null ) && ( phys.length > 0 ) ) {
1216 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1217 for( final Phylogeny phy : phys ) {
1218 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1221 AptxUtil.addPhylogeniesToTabs( phys,
1222 new File( url.getFile() ).getName(),
1223 new File( url.getFile() ).toString(),
1226 _mainpanel.getControlPanel().showWhole();
1229 activateSaveAllIfNeeded();
1233 void setMsa( final Msa msa ) {
1237 void setMsaFile( final File msa_file ) {
1238 _msa_file = msa_file;
1241 void setSeqs( final List<Sequence> seqs ) {
1245 void setSeqsFile( final File seqs_file ) {
1246 _seqs_file = seqs_file;
1249 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1250 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1251 _mainpanel.getCurrentTreePanel().getHeight(),
1253 String file_written_to = "";
1254 boolean error = false;
1256 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1257 _mainpanel.getCurrentTreePanel().getWidth(),
1258 _mainpanel.getCurrentTreePanel().getHeight(),
1259 _mainpanel.getCurrentTreePanel(),
1260 _mainpanel.getControlPanel(),
1264 catch ( final IOException e ) {
1266 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1269 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1270 JOptionPane.showMessageDialog( this,
1271 "Wrote image to: " + file_written_to,
1273 JOptionPane.INFORMATION_MESSAGE );
1276 JOptionPane.showMessageDialog( this,
1277 "There was an unknown problem when attempting to write to an image file: \""
1280 JOptionPane.ERROR_MESSAGE );
1283 _contentpane.repaint();
1286 private void addExpressionValuesFromFile() {
1287 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1288 JOptionPane.showMessageDialog( this,
1289 "Need to load evolutionary tree first",
1290 "Can Not Read Expression Values",
1291 JOptionPane.WARNING_MESSAGE );
1294 final File my_dir = getCurrentDir();
1295 if ( my_dir != null ) {
1296 _values_filechooser.setCurrentDirectory( my_dir );
1298 final int result = _values_filechooser.showOpenDialog( _contentpane );
1299 final File file = _values_filechooser.getSelectedFile();
1300 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1301 BasicTable<String> t = null;
1303 t = BasicTableParser.parse( file, '\t' );
1304 if ( t.getNumberOfColumns() < 2 ) {
1305 t = BasicTableParser.parse( file, ',' );
1307 if ( t.getNumberOfColumns() < 2 ) {
1308 t = BasicTableParser.parse( file, ' ' );
1311 catch ( final IOException e ) {
1312 JOptionPane.showMessageDialog( this,
1314 "Could Not Read Expression Value Table",
1315 JOptionPane.ERROR_MESSAGE );
1318 if ( t.getNumberOfColumns() < 2 ) {
1319 JOptionPane.showMessageDialog( this,
1320 "Table contains " + t.getNumberOfColumns() + " column(s)",
1321 "Problem with Expression Value Table",
1322 JOptionPane.ERROR_MESSAGE );
1325 if ( t.getNumberOfRows() < 1 ) {
1326 JOptionPane.showMessageDialog( this,
1327 "Table contains zero rows",
1328 "Problem with Expression Value Table",
1329 JOptionPane.ERROR_MESSAGE );
1332 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1333 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1334 JOptionPane.showMessageDialog( this,
1335 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1336 + phy.getNumberOfExternalNodes() + " external nodes",
1338 JOptionPane.WARNING_MESSAGE );
1340 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1342 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1343 final PhylogenyNode node = iter.next();
1344 final String node_name = node.getName();
1345 if ( !ForesterUtil.isEmpty( node_name ) ) {
1348 row = t.findRow( node_name );
1350 catch ( final IllegalArgumentException e ) {
1352 .showMessageDialog( this,
1354 "Error Mapping Node Identifiers to Expression Value Identifiers",
1355 JOptionPane.ERROR_MESSAGE );
1359 if ( node.isExternal() ) {
1364 final List<Double> l = new ArrayList<Double>();
1365 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1368 d = Double.parseDouble( t.getValueAsString( col, row ) );
1370 catch ( final NumberFormatException e ) {
1371 JOptionPane.showMessageDialog( this,
1372 "Could not parse \"" + t.getValueAsString( col, row )
1373 + "\" into a decimal value",
1374 "Issue with Expression Value Table",
1375 JOptionPane.ERROR_MESSAGE );
1378 stats.addValue( d );
1381 if ( !l.isEmpty() ) {
1382 if ( node.getNodeData().getProperties() != null ) {
1383 node.getNodeData().getProperties()
1384 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1386 node.getNodeData().setVector( l );
1390 if ( not_found > 0 ) {
1391 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1392 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1394 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1398 private void addSequencesFromFile() {
1399 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1400 JOptionPane.showMessageDialog( this,
1401 "Need to load evolutionary tree first",
1402 "Can Not Read Sequences",
1403 JOptionPane.WARNING_MESSAGE );
1406 final File my_dir = getCurrentDir();
1407 if ( my_dir != null ) {
1408 _sequences_filechooser.setCurrentDirectory( my_dir );
1410 final int result = _sequences_filechooser.showOpenDialog( _contentpane );
1411 final File file = _sequences_filechooser.getSelectedFile();
1412 List<Sequence> seqs = null;
1413 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1415 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1416 seqs = FastaParser.parse( new FileInputStream( file ) );
1419 JOptionPane.showMessageDialog( this,
1420 "Format does not appear to be Fasta",
1421 "Multiple sequence file format error",
1422 JOptionPane.ERROR_MESSAGE );
1426 catch ( final MsaFormatException e ) {
1428 JOptionPane.showMessageDialog( this,
1429 e.getLocalizedMessage(),
1430 "Multiple sequence file format error",
1431 JOptionPane.ERROR_MESSAGE );
1434 catch ( final IOException e ) {
1436 JOptionPane.showMessageDialog( this,
1437 e.getLocalizedMessage(),
1438 "Failed to read multiple sequence file",
1439 JOptionPane.ERROR_MESSAGE );
1442 catch ( final Exception e ) {
1444 e.printStackTrace();
1445 JOptionPane.showMessageDialog( this,
1446 e.getLocalizedMessage(),
1447 "Unexpected error during reading of multiple sequence file",
1448 JOptionPane.ERROR_MESSAGE );
1451 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1452 JOptionPane.showMessageDialog( this,
1453 "Multiple sequence file is empty",
1454 "Empty multiple sequence file",
1455 JOptionPane.ERROR_MESSAGE );
1460 if ( seqs != null ) {
1461 for( final Sequence seq : seqs ) {
1462 System.out.println( seq.getIdentifier() );
1464 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1465 int total_counter = 0;
1466 int attached_counter = 0;
1467 for( final Sequence seq : seqs ) {
1469 final String seq_name = seq.getIdentifier();
1470 if ( !ForesterUtil.isEmpty( seq_name ) ) {
1471 List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
1472 if ( nodes.isEmpty() ) {
1473 nodes = phy.getNodesViaSequenceSymbol( seq_name );
1475 if ( nodes.isEmpty() ) {
1476 nodes = phy.getNodesViaGeneName( seq_name );
1478 if ( nodes.isEmpty() ) {
1479 nodes = phy.getNodes( seq_name );
1481 if ( nodes.size() > 1 ) {
1482 JOptionPane.showMessageDialog( this,
1483 "Sequence name \"" + seq_name + "\" is not unique",
1484 "Sequence name not unique",
1485 JOptionPane.ERROR_MESSAGE );
1489 final String[] a = seq_name.split( "\\s" );
1490 if ( nodes.isEmpty() && ( a.length > 1 ) ) {
1491 final String seq_name_split = a[ 0 ];
1492 nodes = phy.getNodesViaSequenceName( seq_name_split );
1493 if ( nodes.isEmpty() ) {
1494 nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
1496 if ( nodes.isEmpty() ) {
1497 nodes = phy.getNodes( seq_name_split );
1499 if ( nodes.size() > 1 ) {
1500 JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
1501 + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
1506 if ( nodes.size() == 1 ) {
1508 final PhylogenyNode n = nodes.get( 0 );
1509 if ( !n.getNodeData().isHasSequence() ) {
1510 n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
1512 n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
1513 if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
1514 n.getNodeData().getSequence().setName( seq_name );
1519 if ( attached_counter > 0 ) {
1521 int ext_nodes_with_seq = 0;
1522 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
1524 final PhylogenyNode n = iter.next();
1525 if ( n.getNodeData().isHasSequence()
1526 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
1527 ++ext_nodes_with_seq;
1531 if ( ext_nodes == ext_nodes_with_seq ) {
1532 s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
1535 s = ext_nodes_with_seq + " out of " + ext_nodes
1536 + " external nodes now have a molecular sequence attached to them.";
1538 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
1539 JOptionPane.showMessageDialog( this,
1540 "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
1541 "All sequences attached",
1542 JOptionPane.INFORMATION_MESSAGE );
1545 JOptionPane.showMessageDialog( this, "Attached " + attached_counter
1546 + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
1547 + " sequences attached", JOptionPane.WARNING_MESSAGE );
1551 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
1552 + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
1557 private void choosePdfWidth() {
1558 final String s = ( String ) JOptionPane.showInputDialog( this,
1559 "Please enter the default line width for PDF export.\n"
1560 + "[current value: "
1561 + getOptions().getPrintLineWidth() + "]\n",
1562 "Line Width for PDF Export",
1563 JOptionPane.QUESTION_MESSAGE,
1566 getOptions().getPrintLineWidth() );
1567 if ( !ForesterUtil.isEmpty( s ) ) {
1568 boolean success = true;
1570 final String m_str = s.trim();
1571 if ( !ForesterUtil.isEmpty( m_str ) ) {
1573 f = Float.parseFloat( m_str );
1575 catch ( final Exception ex ) {
1582 if ( success && ( f > 0.0 ) ) {
1583 getOptions().setPrintLineWidth( f );
1588 private void choosePrintSize() {
1589 final String s = ( String ) JOptionPane.showInputDialog( this,
1590 "Please enter values for width and height,\nseparated by a comma.\n"
1591 + "[current values: "
1592 + getOptions().getPrintSizeX() + ", "
1593 + getOptions().getPrintSizeY() + "]\n"
1594 + "[A4: " + Constants.A4_SIZE_X + ", "
1595 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1596 + Constants.US_LETTER_SIZE_X + ", "
1597 + Constants.US_LETTER_SIZE_Y + "]",
1598 "Default Size for Graphics Export",
1599 JOptionPane.QUESTION_MESSAGE,
1602 getOptions().getPrintSizeX() + ", "
1603 + getOptions().getPrintSizeY() );
1604 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1605 boolean success = true;
1608 final String[] str_ary = s.split( "," );
1609 if ( str_ary.length == 2 ) {
1610 final String x_str = str_ary[ 0 ].trim();
1611 final String y_str = str_ary[ 1 ].trim();
1612 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1614 x = Integer.parseInt( x_str );
1615 y = Integer.parseInt( y_str );
1617 catch ( final Exception ex ) {
1628 if ( success && ( x > 1 ) && ( y > 1 ) ) {
1629 getOptions().setPrintSizeX( x );
1630 getOptions().setPrintSizeY( y );
1635 private void closeCurrentPane() {
1636 if ( getMainPanel().getCurrentTreePanel() != null ) {
1637 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1638 final int r = JOptionPane.showConfirmDialog( this,
1639 "Close tab despite potentially unsaved changes?",
1641 JOptionPane.YES_NO_OPTION );
1642 if ( r != JOptionPane.YES_OPTION ) {
1646 getMainPanel().closeCurrentPane();
1647 activateSaveAllIfNeeded();
1651 private void collapse( final Phylogeny phy, final double m ) {
1652 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1653 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1654 double min_support = Double.MAX_VALUE;
1655 boolean conf_present = false;
1656 while ( it.hasNext() ) {
1657 final PhylogenyNode n = it.next();
1658 if ( !n.isExternal() && !n.isRoot() ) {
1659 final List<Confidence> c = n.getBranchData().getConfidences();
1660 if ( ( c != null ) && ( c.size() > 0 ) ) {
1661 conf_present = true;
1663 for( final Confidence confidence : c ) {
1664 if ( confidence.getValue() > max ) {
1665 max = confidence.getValue();
1668 if ( max < getMinNotCollapseConfidenceValue() ) {
1669 to_be_removed.add( n );
1671 if ( max < min_support ) {
1677 if ( conf_present ) {
1678 for( final PhylogenyNode node : to_be_removed ) {
1679 PhylogenyMethods.removeNode( node, phy );
1681 if ( to_be_removed.size() > 0 ) {
1682 phy.externalNodesHaveChanged();
1683 phy.clearHashIdToNodeMap();
1684 phy.recalculateNumberOfExternalDescendants( true );
1685 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1686 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1687 getCurrentTreePanel().calculateLongestExtNodeInfo();
1688 getCurrentTreePanel().setNodeInPreorderToNull();
1689 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1690 getCurrentTreePanel().resetPreferredSize();
1691 getCurrentTreePanel().setEdited( true );
1692 getCurrentTreePanel().repaint();
1695 if ( to_be_removed.size() > 0 ) {
1696 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1697 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1698 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1701 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1702 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1706 JOptionPane.showMessageDialog( this,
1707 "No branch collapsed because no confidence values present",
1708 "No confidence values present",
1709 JOptionPane.INFORMATION_MESSAGE );
1713 private void collapseBelowThreshold() {
1714 if ( getCurrentTreePanel() != null ) {
1715 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1716 if ( ( phy != null ) && !phy.isEmpty() ) {
1717 final String s = ( String ) JOptionPane.showInputDialog( this,
1718 "Please enter the minimum confidence value\n",
1719 "Minimal Confidence Value",
1720 JOptionPane.QUESTION_MESSAGE,
1723 getMinNotCollapseConfidenceValue() );
1724 if ( !ForesterUtil.isEmpty( s ) ) {
1725 boolean success = true;
1727 final String m_str = s.trim();
1728 if ( !ForesterUtil.isEmpty( m_str ) ) {
1730 m = Double.parseDouble( m_str );
1732 catch ( final Exception ex ) {
1739 if ( success && ( m >= 0.0 ) ) {
1740 setMinNotCollapseConfidenceValue( m );
1748 private PhyloXmlParser createPhyloXmlParser() {
1749 PhyloXmlParser xml_parser = null;
1750 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1752 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1754 catch ( final Exception e ) {
1755 JOptionPane.showMessageDialog( this,
1756 e.getLocalizedMessage(),
1757 "failed to create validating XML parser",
1758 JOptionPane.WARNING_MESSAGE );
1761 if ( xml_parser == null ) {
1762 xml_parser = new PhyloXmlParser();
1767 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1768 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1769 getPhylogeneticInferenceOptions(),
1770 from_unaligned_seqs );
1772 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1773 if ( !from_unaligned_seqs ) {
1774 if ( getMsa() != null ) {
1775 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1776 getPhylogeneticInferenceOptions()
1778 new Thread( inferrer ).start();
1781 JOptionPane.showMessageDialog( this,
1782 "No multiple sequence alignment selected",
1783 "Phylogenetic Inference Not Launched",
1784 JOptionPane.WARNING_MESSAGE );
1788 if ( getSeqs() != null ) {
1789 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1790 getPhylogeneticInferenceOptions()
1792 new Thread( inferrer ).start();
1795 JOptionPane.showMessageDialog( this,
1796 "No input sequences selected",
1797 "Phylogenetic Inference Not Launched",
1798 JOptionPane.WARNING_MESSAGE );
1804 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1805 final StringBuilder sb = new StringBuilder();
1806 final StringBuilder sb_failed = new StringBuilder();
1808 int counter_failed = 0;
1809 if ( getCurrentTreePanel() != null ) {
1810 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1811 if ( ( phy != null ) && !phy.isEmpty() ) {
1812 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1813 while ( it.hasNext() ) {
1814 final PhylogenyNode n = it.next();
1815 final String name = n.getName().trim();
1816 if ( !ForesterUtil.isEmpty( name ) ) {
1817 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
1818 TAXONOMY_EXTRACTION.AGGRESSIVE );
1819 if ( !ForesterUtil.isEmpty( nt ) ) {
1820 if ( counter < 15 ) {
1821 sb.append( name + ": " + nt + "\n" );
1823 else if ( counter == 15 ) {
1824 sb.append( "...\n" );
1829 if ( counter_failed < 15 ) {
1830 sb_failed.append( name + "\n" );
1832 else if ( counter_failed == 15 ) {
1833 sb_failed.append( "...\n" );
1839 if ( counter > 0 ) {
1841 String all = "all ";
1842 if ( counter_failed > 0 ) {
1844 failed = "\nCould not extract taxonomic data for " + counter_failed
1845 + " named external nodes:\n" + sb_failed;
1847 JOptionPane.showMessageDialog( this,
1848 "Extracted taxonomic data from " + all + counter
1849 + " named external nodes:\n" + sb.toString() + failed,
1850 "Taxonomic Data Extraction Completed",
1851 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1852 : JOptionPane.INFORMATION_MESSAGE );
1856 .showMessageDialog( this,
1857 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1858 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1859 + "or nodes already have taxonomic data?\n",
1860 "No Taxonomic Data Extracted",
1861 JOptionPane.ERROR_MESSAGE );
1867 private ControlPanel getControlPanel() {
1868 return getMainPanel().getControlPanel();
1871 private File getCurrentDir() {
1872 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1873 if ( ForesterUtil.isWindows() ) {
1875 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1877 catch ( final Exception e ) {
1878 _current_dir = null;
1882 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1883 if ( System.getProperty( "user.home" ) != null ) {
1884 _current_dir = new File( System.getProperty( "user.home" ) );
1886 else if ( System.getProperty( "user.dir" ) != null ) {
1887 _current_dir = new File( System.getProperty( "user.dir" ) );
1890 return _current_dir;
1893 private double getMinNotCollapseConfidenceValue() {
1894 return _min_not_collapse;
1897 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1898 if ( _phylogenetic_inference_options == null ) {
1899 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1901 return _phylogenetic_inference_options;
1904 private boolean isUnsavedDataPresent() {
1905 final List<TreePanel> tps = getMainPanel().getTreePanels();
1906 for( final TreePanel tp : tps ) {
1907 if ( tp.isEdited() ) {
1914 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1915 if ( getCurrentTreePanel() != null ) {
1916 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1917 if ( ( phy != null ) && !phy.isEmpty() ) {
1919 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1924 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1925 if ( getCurrentTreePanel() != null ) {
1926 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1927 if ( ( phy != null ) && !phy.isEmpty() ) {
1928 PhylogenyMethods.transferNodeNameToField( phy,
1929 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1935 private void newTree() {
1936 final Phylogeny[] phys = new Phylogeny[ 1 ];
1937 final Phylogeny phy = new Phylogeny();
1938 final PhylogenyNode node = new PhylogenyNode();
1939 phy.setRoot( node );
1940 phy.setRooted( true );
1942 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1943 _mainpanel.getControlPanel().showWhole();
1944 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1945 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1946 if ( getMainPanel().getMainFrame() == null ) {
1947 // Must be "E" applet version.
1948 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1949 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1952 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1954 activateSaveAllIfNeeded();
1958 private void obtainDetailedTaxonomicInformation() {
1959 if ( getCurrentTreePanel() != null ) {
1960 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1961 if ( ( phy != null ) && !phy.isEmpty() ) {
1962 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1963 _mainpanel.getCurrentTreePanel(),
1967 new Thread( t ).start();
1972 private void obtainDetailedTaxonomicInformationDelete() {
1973 if ( getCurrentTreePanel() != null ) {
1974 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1975 if ( ( phy != null ) && !phy.isEmpty() ) {
1976 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1977 _mainpanel.getCurrentTreePanel(),
1981 new Thread( t ).start();
1986 private void obtainSequenceInformation() {
1987 if ( getCurrentTreePanel() != null ) {
1988 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1989 if ( ( phy != null ) && !phy.isEmpty() ) {
1990 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1991 _mainpanel.getCurrentTreePanel(),
1993 new Thread( u ).start();
1998 private void print() {
1999 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2000 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2003 if ( !getOptions().isPrintUsingActualSize() ) {
2004 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
2005 getOptions().getPrintSizeY() - 140,
2007 getCurrentTreePanel().resetPreferredSize();
2008 getCurrentTreePanel().repaint();
2010 final String job_name = Constants.PRG_NAME;
2011 boolean error = false;
2012 String printer_name = null;
2014 printer_name = Printer.print( getCurrentTreePanel(), job_name );
2016 catch ( final Exception e ) {
2018 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2020 if ( !error && ( printer_name != null ) ) {
2021 String msg = "Printing data sent to printer";
2022 if ( printer_name.length() > 1 ) {
2023 msg += " [" + printer_name + "]";
2025 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2027 if ( !getOptions().isPrintUsingActualSize() ) {
2028 getControlPanel().showWhole();
2032 private void printPhylogenyToPdf( final String file_name ) {
2033 if ( !getOptions().isPrintUsingActualSize() ) {
2034 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
2035 getOptions().getPrintSizeY(),
2037 getCurrentTreePanel().resetPreferredSize();
2038 getCurrentTreePanel().repaint();
2040 String pdf_written_to = "";
2041 boolean error = false;
2043 if ( getOptions().isPrintUsingActualSize() ) {
2044 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2045 getCurrentTreePanel(),
2046 getCurrentTreePanel().getWidth(),
2047 getCurrentTreePanel().getHeight() );
2050 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2051 .getPrintSizeX(), getOptions().getPrintSizeY() );
2054 catch ( final IOException e ) {
2056 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2059 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2060 JOptionPane.showMessageDialog( this,
2061 "Wrote PDF to: " + pdf_written_to,
2063 JOptionPane.INFORMATION_MESSAGE );
2066 JOptionPane.showMessageDialog( this,
2067 "There was an unknown problem when attempting to write to PDF file: \""
2070 JOptionPane.ERROR_MESSAGE );
2073 if ( !getOptions().isPrintUsingActualSize() ) {
2074 getControlPanel().showWhole();
2078 private void readPhylogeniesFromFile() {
2079 boolean exception = false;
2080 Phylogeny[] phys = null;
2081 // Set an initial directory if none set yet
2082 final File my_dir = getCurrentDir();
2083 _open_filechooser.setMultiSelectionEnabled( true );
2084 // Open file-open dialog and set current directory
2085 if ( my_dir != null ) {
2086 _open_filechooser.setCurrentDirectory( my_dir );
2088 final int result = _open_filechooser.showOpenDialog( _contentpane );
2089 // All done: get the file
2090 final File[] files = _open_filechooser.getSelectedFiles();
2091 setCurrentDir( _open_filechooser.getCurrentDirectory() );
2092 boolean nhx_or_nexus = false;
2093 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2094 for( final File file : files ) {
2095 if ( ( file != null ) && !file.isDirectory() ) {
2096 if ( _mainpanel.getCurrentTreePanel() != null ) {
2097 _mainpanel.getCurrentTreePanel().setWaitCursor();
2100 _mainpanel.setWaitCursor();
2102 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2103 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2105 final NHXParser nhx = new NHXParser();
2106 setSpecialOptionsForNhxParser( nhx );
2107 phys = PhylogenyMethods.readPhylogenies( nhx, file );
2108 nhx_or_nexus = true;
2110 catch ( final Exception e ) {
2112 exceptionOccuredDuringOpenFile( e );
2115 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2116 warnIfNotPhyloXmlValidation( getConfiguration() );
2118 final PhyloXmlParser xml_parser = createPhyloXmlParser();
2119 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2121 catch ( final Exception e ) {
2123 exceptionOccuredDuringOpenFile( e );
2126 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2128 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2130 catch ( final Exception e ) {
2132 exceptionOccuredDuringOpenFile( e );
2135 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2137 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2138 setSpecialOptionsForNexParser( nex );
2139 phys = PhylogenyMethods.readPhylogenies( nex, file );
2140 nhx_or_nexus = true;
2142 catch ( final Exception e ) {
2144 exceptionOccuredDuringOpenFile( e );
2150 final PhylogenyParser parser = ParserUtils
2151 .createParserDependingOnFileType( file, getConfiguration()
2152 .isValidatePhyloXmlAgainstSchema() );
2153 if ( parser instanceof NexusPhylogeniesParser ) {
2154 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2155 setSpecialOptionsForNexParser( nex );
2156 nhx_or_nexus = true;
2158 else if ( parser instanceof NHXParser ) {
2159 final NHXParser nhx = ( NHXParser ) parser;
2160 setSpecialOptionsForNhxParser( nhx );
2161 nhx_or_nexus = true;
2163 else if ( parser instanceof PhyloXmlParser ) {
2164 warnIfNotPhyloXmlValidation( getConfiguration() );
2166 phys = PhylogenyMethods.readPhylogenies( parser, file );
2168 catch ( final Exception e ) {
2170 exceptionOccuredDuringOpenFile( e );
2173 if ( _mainpanel.getCurrentTreePanel() != null ) {
2174 _mainpanel.getCurrentTreePanel().setArrowCursor();
2177 _mainpanel.setArrowCursor();
2179 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2180 boolean one_desc = false;
2181 if ( nhx_or_nexus ) {
2182 for( final Phylogeny phy : phys ) {
2183 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2184 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2186 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2192 AptxUtil.addPhylogeniesToTabs( phys,
2194 file.getAbsolutePath(),
2197 _mainpanel.getControlPanel().showWhole();
2198 if ( nhx_or_nexus && one_desc ) {
2200 .showMessageDialog( this,
2201 "One or more trees contain (a) node(s) with one descendant, "
2202 + ForesterUtil.LINE_SEPARATOR
2203 + "possibly indicating illegal parentheses within node names.",
2204 "Warning: Possible Error in New Hampshire Formatted Data",
2205 JOptionPane.WARNING_MESSAGE );
2211 activateSaveAllIfNeeded();
2215 private void readSpeciesTreeFromFile() {
2217 boolean exception = false;
2218 final File my_dir = getCurrentDir();
2219 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2220 if ( my_dir != null ) {
2221 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2223 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2224 final File file = _open_filechooser_for_species_tree.getSelectedFile();
2225 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2226 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2228 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2231 catch ( final Exception e ) {
2233 exceptionOccuredDuringOpenFile( e );
2236 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2238 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2241 catch ( final Exception e ) {
2243 exceptionOccuredDuringOpenFile( e );
2249 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2252 catch ( final Exception e ) {
2254 exceptionOccuredDuringOpenFile( e );
2257 if ( !exception && ( t != null ) && !t.isRooted() ) {
2260 JOptionPane.showMessageDialog( this,
2261 "Species tree is not rooted",
2262 "Species tree not loaded",
2263 JOptionPane.ERROR_MESSAGE );
2265 if ( !exception && ( t != null ) ) {
2266 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2267 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2268 final PhylogenyNode node = it.next();
2269 if ( !node.getNodeData().isHasTaxonomy() ) {
2273 .showMessageDialog( this,
2274 "Species tree contains external node(s) without taxonomy information",
2275 "Species tree not loaded",
2276 JOptionPane.ERROR_MESSAGE );
2280 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2283 JOptionPane.showMessageDialog( this,
2285 + node.getNodeData().getTaxonomy().asSimpleText()
2286 + "] is not unique in species tree",
2287 "Species tree not loaded",
2288 JOptionPane.ERROR_MESSAGE );
2292 tax_set.add( node.getNodeData().getTaxonomy() );
2297 if ( !exception && ( t != null ) ) {
2298 setSpeciesTree( t );
2299 JOptionPane.showMessageDialog( this,
2300 "Species tree successfully loaded",
2301 "Species tree loaded",
2302 JOptionPane.INFORMATION_MESSAGE );
2304 _contentpane.repaint();
2309 private void setArrowCursor() {
2311 _mainpanel.getCurrentTreePanel().setArrowCursor();
2313 catch ( final Exception ex ) {
2318 private void setCurrentDir( final File current_dir ) {
2319 _current_dir = current_dir;
2322 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2323 _min_not_collapse = min_not_collapse;
2326 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2327 _phylogenetic_inference_options = phylogenetic_inference_options;
2330 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2331 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2332 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2335 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2336 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2337 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2340 private void writeAllToFile() {
2341 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2344 final File my_dir = getCurrentDir();
2345 if ( my_dir != null ) {
2346 _save_filechooser.setCurrentDirectory( my_dir );
2348 _save_filechooser.setSelectedFile( new File( "" ) );
2349 final int result = _save_filechooser.showSaveDialog( _contentpane );
2350 final File file = _save_filechooser.getSelectedFile();
2351 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2352 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2353 if ( file.exists() ) {
2354 final int i = JOptionPane.showConfirmDialog( this,
2355 file + " already exists. Overwrite?",
2357 JOptionPane.OK_CANCEL_OPTION,
2358 JOptionPane.WARNING_MESSAGE );
2359 if ( i != JOptionPane.OK_OPTION ) {
2366 catch ( final Exception e ) {
2367 JOptionPane.showMessageDialog( this,
2368 "Failed to delete: " + file,
2370 JOptionPane.WARNING_MESSAGE );
2374 final int count = getMainPanel().getTabbedPane().getTabCount();
2375 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2376 for( int i = 0; i < count; ++i ) {
2377 final Phylogeny phy = getMainPanel().getPhylogeny( i );
2378 if ( ForesterUtil.isEmpty( phy.getName() )
2379 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
2380 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
2383 getMainPanel().getTreePanels().get( i ).setEdited( false );
2385 final PhylogenyWriter writer = new PhylogenyWriter();
2387 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2389 catch ( final IOException e ) {
2390 JOptionPane.showMessageDialog( this,
2391 "Failed to write to: " + file,
2393 JOptionPane.WARNING_MESSAGE );
2398 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2400 final PhylogenyWriter writer = new PhylogenyWriter();
2401 writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2403 catch ( final Exception e ) {
2405 exceptionOccuredDuringSaveAs( e );
2410 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2412 final PhylogenyWriter writer = new PhylogenyWriter();
2413 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2415 catch ( final Exception e ) {
2417 exceptionOccuredDuringSaveAs( e );
2422 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2424 final PhylogenyWriter writer = new PhylogenyWriter();
2425 writer.toPhyloXML( file, t, 0 );
2427 catch ( final Exception e ) {
2429 exceptionOccuredDuringSaveAs( e );
2434 private void writeToFile( final Phylogeny t ) {
2438 String initial_filename = null;
2439 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2441 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2443 catch ( final IOException e ) {
2444 initial_filename = null;
2447 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2448 _save_filechooser.setSelectedFile( new File( initial_filename ) );
2451 _save_filechooser.setSelectedFile( new File( "" ) );
2453 final File my_dir = getCurrentDir();
2454 if ( my_dir != null ) {
2455 _save_filechooser.setCurrentDirectory( my_dir );
2457 final int result = _save_filechooser.showSaveDialog( _contentpane );
2458 final File file = _save_filechooser.getSelectedFile();
2459 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2460 boolean exception = false;
2461 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2462 if ( file.exists() ) {
2463 final int i = JOptionPane.showConfirmDialog( this,
2464 file + " already exists.\nOverwrite?",
2466 JOptionPane.OK_CANCEL_OPTION,
2467 JOptionPane.QUESTION_MESSAGE );
2468 if ( i != JOptionPane.OK_OPTION ) {
2472 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2474 ForesterUtil.copyFile( file, to );
2476 catch ( final Exception e ) {
2477 JOptionPane.showMessageDialog( this,
2478 "Failed to create backup copy " + to,
2479 "Failed to Create Backup Copy",
2480 JOptionPane.WARNING_MESSAGE );
2485 catch ( final Exception e ) {
2486 JOptionPane.showMessageDialog( this,
2487 "Failed to delete: " + file,
2489 JOptionPane.WARNING_MESSAGE );
2493 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2494 exception = writeAsNewHampshire( t, exception, file );
2496 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2497 exception = writeAsPhyloXml( t, exception, file );
2499 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2500 exception = writeAsNexus( t, exception, file );
2504 final String file_name = file.getName().trim().toLowerCase();
2505 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2506 || file_name.endsWith( ".tree" ) ) {
2507 exception = writeAsNewHampshire( t, exception, file );
2509 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2510 exception = writeAsNexus( t, exception, file );
2514 exception = writeAsPhyloXml( t, exception, file );
2518 getMainPanel().setTitleOfSelectedTab( file.getName() );
2519 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2520 getMainPanel().getCurrentTreePanel().setEdited( false );
2525 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2526 if ( ( t == null ) || t.isEmpty() ) {
2529 String initial_filename = "";
2530 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2531 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2533 if ( initial_filename.indexOf( '.' ) > 0 ) {
2534 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2536 initial_filename = initial_filename + "." + type;
2537 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2538 final File my_dir = getCurrentDir();
2539 if ( my_dir != null ) {
2540 _writetographics_filechooser.setCurrentDirectory( my_dir );
2542 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2543 File file = _writetographics_filechooser.getSelectedFile();
2544 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2545 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2546 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2547 file = new File( file.toString() + "." + type );
2549 if ( file.exists() ) {
2550 final int i = JOptionPane.showConfirmDialog( this,
2551 file + " already exists. Overwrite?",
2553 JOptionPane.OK_CANCEL_OPTION,
2554 JOptionPane.WARNING_MESSAGE );
2555 if ( i != JOptionPane.OK_OPTION ) {
2562 catch ( final Exception e ) {
2563 JOptionPane.showMessageDialog( this,
2564 "Failed to delete: " + file,
2566 JOptionPane.WARNING_MESSAGE );
2570 writePhylogenyToGraphicsFile( file.toString(), type );
2574 private void writeToPdf( final Phylogeny t ) {
2575 if ( ( t == null ) || t.isEmpty() ) {
2578 String initial_filename = "";
2579 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2580 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2582 if ( initial_filename.indexOf( '.' ) > 0 ) {
2583 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2585 initial_filename = initial_filename + ".pdf";
2586 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2587 final File my_dir = getCurrentDir();
2588 if ( my_dir != null ) {
2589 _writetopdf_filechooser.setCurrentDirectory( my_dir );
2591 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2592 File file = _writetopdf_filechooser.getSelectedFile();
2593 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2594 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2595 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2596 file = new File( file.toString() + ".pdf" );
2598 if ( file.exists() ) {
2599 final int i = JOptionPane.showConfirmDialog( this,
2600 file + " already exists. Overwrite?",
2602 JOptionPane.OK_CANCEL_OPTION,
2603 JOptionPane.WARNING_MESSAGE );
2604 if ( i != JOptionPane.OK_OPTION ) {
2608 printPhylogenyToPdf( file.toString() );
2612 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2613 return new MainFrameApplication( phys, config );
2616 public static MainFrame createInstance( final Phylogeny[] phys,
2617 final Configuration config,
2619 final File current_dir ) {
2620 return new MainFrameApplication( phys, config, title, current_dir );
2623 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2624 return new MainFrameApplication( phys, config, title );
2627 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2628 return new MainFrameApplication( phys, config_file_name, title );
2631 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2632 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2633 + o.getPrintSizeY() + ")" );
2636 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2637 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2640 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2641 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2643 .showMessageDialog( null,
2645 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2648 JOptionPane.WARNING_MESSAGE );
2651 } // MainFrameApplication.
2653 class DefaultFilter extends FileFilter {
2656 public boolean accept( final File f ) {
2657 final String file_name = f.getName().trim().toLowerCase();
2658 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2659 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2660 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2661 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2662 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2663 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2664 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2665 || file_name.endsWith( ".con" ) || f.isDirectory();
2669 public String getDescription() {
2670 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2674 class GraphicsFileFilter extends FileFilter {
2677 public boolean accept( final File f ) {
2678 final String file_name = f.getName().trim().toLowerCase();
2679 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2680 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2684 public String getDescription() {
2685 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2689 class MsaFileFilter extends FileFilter {
2692 public boolean accept( final File f ) {
2693 final String file_name = f.getName().trim().toLowerCase();
2694 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2695 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2699 public String getDescription() {
2700 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2704 class NexusFilter extends FileFilter {
2707 public boolean accept( final File f ) {
2708 final String file_name = f.getName().trim().toLowerCase();
2709 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2710 || file_name.endsWith( ".tre" ) || f.isDirectory();
2714 public String getDescription() {
2715 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2719 class NHFilter extends FileFilter {
2722 public boolean accept( final File f ) {
2723 final String file_name = f.getName().trim().toLowerCase();
2724 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2725 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2726 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2731 public String getDescription() {
2732 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2736 class NHXFilter extends FileFilter {
2739 public boolean accept( final File f ) {
2740 final String file_name = f.getName().trim().toLowerCase();
2741 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2745 public String getDescription() {
2746 return "NHX files (*.nhx) [deprecated]";
2750 class PdfFilter extends FileFilter {
2753 public boolean accept( final File f ) {
2754 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2758 public String getDescription() {
2759 return "PDF files (*.pdf)";
2763 class SequencesFileFilter extends FileFilter {
2766 public boolean accept( final File f ) {
2767 final String file_name = f.getName().trim().toLowerCase();
2768 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2769 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2773 public String getDescription() {
2774 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2778 class TolFilter extends FileFilter {
2781 public boolean accept( final File f ) {
2782 final String file_name = f.getName().trim().toLowerCase();
2783 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2784 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2788 public String getDescription() {
2789 return "Tree of Life files (*.tol, *.tolxml)";
2793 class XMLFilter extends FileFilter {
2796 public boolean accept( final File f ) {
2797 final String file_name = f.getName().trim().toLowerCase();
2798 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2799 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2803 public String getDescription() {
2804 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";