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: www.phylosoft.org/forester
27 package org.forester.archaeopteryx;
29 import java.awt.BorderLayout;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.ComponentAdapter;
33 import java.awt.event.ComponentEvent;
34 import java.awt.event.WindowAdapter;
35 import java.awt.event.WindowEvent;
37 import java.io.FileInputStream;
38 import java.io.IOException;
39 import java.io.InputStream;
40 import java.net.MalformedURLException;
42 import java.util.ArrayList;
43 import java.util.HashSet;
44 import java.util.List;
47 import javax.swing.ButtonGroup;
48 import javax.swing.JCheckBoxMenuItem;
49 import javax.swing.JFileChooser;
50 import javax.swing.JMenu;
51 import javax.swing.JMenuBar;
52 import javax.swing.JMenuItem;
53 import javax.swing.JOptionPane;
54 import javax.swing.JRadioButtonMenuItem;
55 import javax.swing.UIManager;
56 import javax.swing.UnsupportedLookAndFeelException;
57 import javax.swing.WindowConstants;
58 import javax.swing.event.ChangeEvent;
59 import javax.swing.event.ChangeListener;
60 import javax.swing.filechooser.FileFilter;
61 import javax.swing.plaf.synth.SynthLookAndFeel;
63 import org.forester.analysis.TaxonomyDataManager;
64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
69 import org.forester.archaeopteryx.tools.GoAnnotation;
70 import org.forester.archaeopteryx.tools.InferenceManager;
71 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
72 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
73 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
74 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
75 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
76 import org.forester.archaeopteryx.webservices.WebservicesManager;
77 import org.forester.io.parsers.FastaParser;
78 import org.forester.io.parsers.GeneralMsaParser;
79 import org.forester.io.parsers.PhylogenyParser;
80 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
81 import org.forester.io.parsers.nhx.NHXParser;
82 import org.forester.io.parsers.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.PhylogenyNodeI.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.sdi.GSDI;
101 import org.forester.sdi.SDIR;
102 import org.forester.sequence.Sequence;
103 import org.forester.util.BasicDescriptiveStatistics;
104 import org.forester.util.BasicTable;
105 import org.forester.util.BasicTableParser;
106 import org.forester.util.DescriptiveStatistics;
107 import org.forester.util.ForesterUtil;
108 import org.forester.util.WindowsUtils;
110 class DefaultFilter extends FileFilter {
113 public boolean accept( final File f ) {
114 final String file_name = f.getName().trim().toLowerCase();
115 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
116 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
117 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
118 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
119 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
120 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
121 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
122 || file_name.endsWith( ".con" ) || f.isDirectory();
126 public String getDescription() {
127 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
131 class GraphicsFileFilter extends FileFilter {
134 public boolean accept( final File f ) {
135 final String file_name = f.getName().trim().toLowerCase();
136 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
137 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
141 public String getDescription() {
142 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
146 class MsaFileFilter extends FileFilter {
149 public boolean accept( final File f ) {
150 final String file_name = f.getName().trim().toLowerCase();
151 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
152 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
156 public String getDescription() {
157 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
161 class SequencesFileFilter extends FileFilter {
164 public boolean accept( final File f ) {
165 final String file_name = f.getName().trim().toLowerCase();
166 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
167 || file_name.endsWith( ".seqs" ) || f.isDirectory();
171 public String getDescription() {
172 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
176 public final class MainFrameApplication extends MainFrame {
178 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
179 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
180 private final static int FRAME_X_SIZE = 800;
181 private final static int FRAME_Y_SIZE = 800;
182 // Filters for the file-open dialog (classes defined in this file)
183 private final static NHFilter nhfilter = new NHFilter();
184 private final static NHXFilter nhxfilter = new NHXFilter();
185 private final static XMLFilter xmlfilter = new XMLFilter();
186 private final static TolFilter tolfilter = new TolFilter();
187 private final static NexusFilter nexusfilter = new NexusFilter();
188 private final static PdfFilter pdffilter = new PdfFilter();
189 private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
190 private final static MsaFileFilter msafilter = new MsaFileFilter();
191 private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
192 private final static DefaultFilter defaultfilter = new DefaultFilter();
193 private static final long serialVersionUID = -799735726778865234L;
194 private final JFileChooser _values_filechooser;
195 private final JFileChooser _open_filechooser;
196 private final JFileChooser _msa_filechooser;
197 private final JFileChooser _seqs_filechooser;
198 private final JFileChooser _open_filechooser_for_species_tree;
199 private final JFileChooser _save_filechooser;
200 private final JFileChooser _writetopdf_filechooser;
201 private final JFileChooser _writetographics_filechooser;
203 private JMenu _analysis_menu;
204 private JMenuItem _load_species_tree_item;
205 private JMenuItem _gsdi_item;
206 private JMenuItem _root_min_dups_item;
207 private JMenuItem _root_min_cost_l_item;
208 private JMenuItem _lineage_inference;
209 private JMenuItem _function_analysis;
210 // Application-only print menu items
211 private JMenuItem _print_item;
212 private JMenuItem _write_to_pdf_item;
213 private JMenuItem _write_to_jpg_item;
214 private JMenuItem _write_to_gif_item;
215 private JMenuItem _write_to_tif_item;
216 private JMenuItem _write_to_png_item;
217 private JMenuItem _write_to_bmp_item;
218 private Phylogeny _species_tree;
219 private File _current_dir;
220 private ButtonGroup _radio_group_1;
222 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
223 // Phylogeny Inference menu
224 private JMenu _inference_menu;
225 private JMenuItem _inference_from_msa_item;
226 private JMenuItem _inference_from_seqs_item;
227 // Phylogeny Inference
228 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
229 private Msa _msa = null;
230 private File _msa_file = null;
231 private List<Sequence> _seqs = null;
232 private File _seqs_file = null;
233 // expression values menu:
234 JMenuItem _read_values_jmi;
236 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
237 this( phys, config, title, null );
240 private MainFrameApplication( final Phylogeny[] phys,
241 final Configuration config,
243 final File current_dir ) {
245 _configuration = config;
246 if ( _configuration == null ) {
247 throw new IllegalArgumentException( "configuration is null" );
250 boolean synth_exception = false;
251 if ( Constants.__SYNTH_LF ) {
253 final SynthLookAndFeel synth = new SynthLookAndFeel();
254 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
255 MainFrameApplication.class );
256 UIManager.setLookAndFeel( synth );
258 catch ( final Exception ex ) {
259 synth_exception = true;
260 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
261 "could not create synth look and feel: "
262 + ex.getLocalizedMessage() );
265 if ( !Constants.__SYNTH_LF || synth_exception ) {
266 if ( _configuration.isUseNativeUI() ) {
267 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
270 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
273 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
275 catch ( final UnsupportedLookAndFeelException e ) {
276 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
278 catch ( final ClassNotFoundException e ) {
279 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
281 catch ( final InstantiationException e ) {
282 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
284 catch ( final IllegalAccessException e ) {
285 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
287 catch ( final Exception e ) {
288 AptxUtil.dieWithSystemError( e.toString() );
290 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
291 setCurrentDir( current_dir );
293 // hide until everything is ready
295 setOptions( Options.createInstance( _configuration ) );
296 setInferenceManager( InferenceManager.createInstance( _configuration ) );
297 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
299 _species_tree = null;
301 setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
302 _mainpanel = new MainPanel( _configuration, this );
304 _open_filechooser = new JFileChooser();
305 _open_filechooser.setCurrentDirectory( new File( "." ) );
306 _open_filechooser.setMultiSelectionEnabled( false );
307 _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
308 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
309 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
310 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
311 _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
312 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
313 _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
314 _open_filechooser_for_species_tree = new JFileChooser();
315 _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
316 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
317 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
318 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
319 _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
320 _save_filechooser = new JFileChooser();
321 _save_filechooser.setCurrentDirectory( new File( "." ) );
322 _save_filechooser.setMultiSelectionEnabled( false );
323 _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
324 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
325 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
326 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
327 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
328 _writetopdf_filechooser = new JFileChooser();
329 _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
330 _writetographics_filechooser = new JFileChooser();
331 _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
333 _msa_filechooser = new JFileChooser();
334 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
335 _msa_filechooser.setCurrentDirectory( new File( "." ) );
336 _msa_filechooser.setMultiSelectionEnabled( false );
337 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
338 _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
340 _seqs_filechooser = new JFileChooser();
341 _seqs_filechooser.setName( "Read Sequences File" );
342 _seqs_filechooser.setCurrentDirectory( new File( "." ) );
343 _seqs_filechooser.setMultiSelectionEnabled( false );
344 _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() );
345 _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
347 _values_filechooser = new JFileChooser();
348 _values_filechooser.setCurrentDirectory( new File( "." ) );
349 _values_filechooser.setMultiSelectionEnabled( false );
350 // build the menu bar
351 _jmenubar = new JMenuBar();
352 if ( !_configuration.isUseNativeUI() ) {
353 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
356 if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
357 buildPhylogeneticInferenceMenu();
366 setJMenuBar( _jmenubar );
367 _jmenubar.add( _help_jmenu );
368 _contentpane = getContentPane();
369 _contentpane.setLayout( new BorderLayout() );
370 _contentpane.add( _mainpanel, BorderLayout.CENTER );
372 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
373 // addWindowFocusListener( new WindowAdapter() {
376 // public void windowGainedFocus( WindowEvent e ) {
377 // requestFocusInWindow();
380 // The window listener
381 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
382 addWindowListener( new WindowAdapter() {
385 public void windowClosing( final WindowEvent e ) {
386 if ( isUnsavedDataPresent() ) {
387 final int r = JOptionPane.showConfirmDialog( null,
388 "Exit despite potentially unsaved changes?",
390 JOptionPane.YES_NO_OPTION );
391 if ( r != JOptionPane.YES_OPTION ) {
396 final int r = JOptionPane.showConfirmDialog( null,
397 "Exit Archaeopteryx?",
399 JOptionPane.YES_NO_OPTION );
400 if ( r != JOptionPane.YES_OPTION ) {
407 // The component listener
408 addComponentListener( new ComponentAdapter() {
411 public void componentResized( final ComponentEvent e ) {
412 if ( _mainpanel.getCurrentTreePanel() != null ) {
413 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
415 _mainpanel.getCurrentTreePanel()
421 requestFocusInWindow();
422 // addKeyListener( this );
424 if ( ( phys != null ) && ( phys.length > 0 ) ) {
425 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
427 getMainPanel().getControlPanel().showWholeAll();
428 getMainPanel().getControlPanel().showWhole();
430 activateSaveAllIfNeeded();
431 // ...and its children
432 _contentpane.repaint();
436 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
437 _configuration = config;
438 if ( _configuration == null ) {
439 throw new IllegalArgumentException( "configuration is null" );
442 setOptions( Options.createInstance( _configuration ) );
443 _mainpanel = new MainPanel( _configuration, this );
444 _open_filechooser = null;
445 _open_filechooser_for_species_tree = null;
446 _save_filechooser = null;
447 _writetopdf_filechooser = null;
448 _writetographics_filechooser = null;
449 _msa_filechooser = null;
450 _seqs_filechooser = null;
451 _values_filechooser = null;
452 _jmenubar = new JMenuBar();
455 _contentpane = getContentPane();
456 _contentpane.setLayout( new BorderLayout() );
457 _contentpane.add( _mainpanel, BorderLayout.CENTER );
459 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
460 // The window listener
461 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
462 addWindowListener( new WindowAdapter() {
465 public void windowClosing( final WindowEvent e ) {
469 // setVisible( true );
470 if ( ( phys != null ) && ( phys.length > 0 ) ) {
471 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
473 getMainPanel().getControlPanel().showWholeAll();
474 getMainPanel().getControlPanel().showWhole();
476 //activateSaveAllIfNeeded();
477 // ...and its children
478 _contentpane.repaint();
481 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
482 // Reads the config file (false, false => not url, not applet):
483 this( phys, new Configuration( config_file, false, false, true ), title );
487 public void actionPerformed( final ActionEvent e ) {
489 super.actionPerformed( e );
490 final Object o = e.getSource();
491 // Handle app-specific actions here:
492 if ( o == _open_item ) {
493 readPhylogeniesFromFile();
495 else if ( o == _save_item ) {
496 writeToFile( _mainpanel.getCurrentPhylogeny() );
497 // If subtree currently displayed, save it, instead of complete
500 else if ( o == _new_item ) {
503 else if ( o == _save_all_item ) {
506 else if ( o == _close_item ) {
509 else if ( o == _write_to_pdf_item ) {
510 writeToPdf( _mainpanel.getCurrentPhylogeny() );
512 else if ( o == _write_to_jpg_item ) {
513 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
515 else if ( o == _write_to_png_item ) {
516 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
518 else if ( o == _write_to_gif_item ) {
519 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
521 else if ( o == _write_to_tif_item ) {
522 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
524 else if ( o == _write_to_bmp_item ) {
525 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
527 else if ( o == _print_item ) {
530 else if ( o == _load_species_tree_item ) {
531 readSpeciesTreeFromFile();
533 else if ( o == _lineage_inference ) {
534 if ( isSubtreeDisplayed() ) {
535 JOptionPane.showMessageDialog( this,
537 "Cannot infer ancestral taxonomies",
538 JOptionPane.ERROR_MESSAGE );
541 executeLineageInference();
543 else if ( o == _function_analysis ) {
544 executeFunctionAnalysis();
546 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
547 if ( isSubtreeDisplayed() ) {
550 obtainDetailedTaxonomicInformation();
552 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
553 if ( isSubtreeDisplayed() ) {
556 obtainDetailedTaxonomicInformationDelete();
558 else if ( o == _obtain_uniprot_seq_information_jmi ) {
559 obtainUniProtSequenceInformation();
561 else if ( o == _read_values_jmi ) {
562 if ( isSubtreeDisplayed() ) {
565 addExpressionValuesFromFile();
567 else if ( o == _move_node_names_to_tax_sn_jmi ) {
568 moveNodeNamesToTaxSn();
570 else if ( o == _move_node_names_to_seq_names_jmi ) {
571 moveNodeNamesToSeqNames();
573 else if ( o == _extract_tax_code_from_node_names_jmi ) {
574 extractTaxCodeFromNodeNames();
576 else if ( o == _gsdi_item ) {
577 if ( isSubtreeDisplayed() ) {
582 else if ( o == _root_min_dups_item ) {
583 if ( isSubtreeDisplayed() ) {
586 executeSDIR( false );
588 else if ( o == _root_min_cost_l_item ) {
589 if ( isSubtreeDisplayed() ) {
594 else if ( o == _graphics_export_visible_only_cbmi ) {
595 updateOptions( getOptions() );
597 else if ( o == _antialias_print_cbmi ) {
598 updateOptions( getOptions() );
600 else if ( o == _print_black_and_white_cbmi ) {
601 updateOptions( getOptions() );
603 else if ( o == _print_using_actual_size_cbmi ) {
604 updateOptions( getOptions() );
606 else if ( o == _graphics_export_using_actual_size_cbmi ) {
607 updateOptions( getOptions() );
609 else if ( o == _print_size_mi ) {
612 else if ( o == _choose_pdf_width_mi ) {
615 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
616 updateOptions( getOptions() );
618 else if ( o == _replace_underscores_cbmi ) {
619 if ( ( _extract_pfam_style_tax_codes_cbmi != null ) && _replace_underscores_cbmi.isSelected() ) {
620 _extract_pfam_style_tax_codes_cbmi.setSelected( false );
622 updateOptions( getOptions() );
624 else if ( o == _collapse_below_threshold ) {
625 if ( isSubtreeDisplayed() ) {
628 collapseBelowThreshold();
630 else if ( o == _extract_pfam_style_tax_codes_cbmi ) {
631 if ( ( _replace_underscores_cbmi != null ) && _extract_pfam_style_tax_codes_cbmi.isSelected() ) {
632 _replace_underscores_cbmi.setSelected( false );
634 updateOptions( getOptions() );
636 else if ( o == _inference_from_msa_item ) {
637 executePhyleneticInference( false );
639 else if ( o == _inference_from_seqs_item ) {
640 executePhyleneticInference( true );
642 _contentpane.repaint();
644 catch ( final Exception ex ) {
645 AptxUtil.unexpectedException( ex );
647 catch ( final Error err ) {
648 AptxUtil.unexpectedError( err );
652 void buildAnalysisMenu() {
653 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
654 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
655 _analysis_menu.addSeparator();
656 _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
657 _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
658 _analysis_menu.addSeparator();
659 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
660 customizeJMenuItem( _gsdi_item );
661 customizeJMenuItem( _root_min_dups_item );
662 customizeJMenuItem( _root_min_cost_l_item );
663 customizeJMenuItem( _load_species_tree_item );
664 _analysis_menu.addSeparator();
665 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
666 customizeJMenuItem( _lineage_inference );
667 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
668 _jmenubar.add( _analysis_menu );
671 void buildPhylogeneticInferenceMenu() {
672 final InferenceManager im = getInferenceManager();
673 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
674 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
675 customizeJMenuItem( _inference_from_msa_item );
676 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
677 if ( im.canDoMsa() ) {
678 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
679 customizeJMenuItem( _inference_from_seqs_item );
680 _inference_from_seqs_item
681 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
685 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
686 customizeJMenuItem( _inference_from_seqs_item );
687 _inference_from_seqs_item.setEnabled( false );
689 _jmenubar.add( _inference_menu );
693 void buildFileMenu() {
694 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
695 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
696 _file_jmenu.addSeparator();
697 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
698 _file_jmenu.addSeparator();
699 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
700 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
701 .getAvailablePhylogeniesWebserviceClients().size() ];
702 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
703 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
704 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
705 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
707 if ( getConfiguration().isEditable() ) {
708 _file_jmenu.addSeparator();
709 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
710 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
712 _file_jmenu.addSeparator();
713 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
714 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
715 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
716 _save_all_item.setEnabled( false );
717 _file_jmenu.addSeparator();
718 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
719 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
720 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
722 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
723 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
724 if ( AptxUtil.canWriteFormat( "gif" ) ) {
725 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
727 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
728 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
730 _file_jmenu.addSeparator();
731 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
732 _file_jmenu.addSeparator();
733 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
734 _close_item.setToolTipText( "To close the current pane." );
735 _close_item.setEnabled( true );
736 _file_jmenu.addSeparator();
737 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
738 // For print in color option item
739 customizeJMenuItem( _open_item );
741 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
742 customizeJMenuItem( _open_url_item );
743 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
744 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
746 customizeJMenuItem( _save_item );
747 if ( getConfiguration().isEditable() ) {
748 customizeJMenuItem( _new_item );
750 customizeJMenuItem( _close_item );
751 customizeJMenuItem( _save_all_item );
752 customizeJMenuItem( _write_to_pdf_item );
753 customizeJMenuItem( _write_to_png_item );
754 customizeJMenuItem( _write_to_jpg_item );
755 customizeJMenuItem( _write_to_gif_item );
756 customizeJMenuItem( _write_to_tif_item );
757 customizeJMenuItem( _write_to_bmp_item );
758 customizeJMenuItem( _print_item );
759 customizeJMenuItem( _exit_item );
760 _jmenubar.add( _file_jmenu );
763 void buildOptionsMenu() {
764 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
765 _options_jmenu.addChangeListener( new ChangeListener() {
768 public void stateChanged( final ChangeEvent e ) {
769 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
770 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
772 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
773 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
774 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
775 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
776 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
777 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
779 _show_branch_length_values_cbmi,
780 _non_lined_up_cladograms_rbmi,
781 _uniform_cladograms_rbmi,
782 _ext_node_dependent_cladogram_rbmi,
783 _label_direction_cbmi );
784 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
785 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
786 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
789 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
791 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
792 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
793 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
794 _radio_group_1 = new ButtonGroup();
795 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
796 _radio_group_1.add( _uniform_cladograms_rbmi );
797 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
798 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
799 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
801 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
802 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
803 _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
805 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
806 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
807 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
808 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
809 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
810 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
811 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
812 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
813 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
814 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
815 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
816 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
817 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
819 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
820 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
821 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
822 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
823 _options_jmenu.addSeparator();
824 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
825 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
826 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
827 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
828 _options_jmenu.addSeparator();
829 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
830 getConfiguration() ) );
831 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
832 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
834 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
836 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
838 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
839 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
840 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
841 _options_jmenu.addSeparator();
842 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
844 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
845 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
847 .add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
848 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
850 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
851 _use_brackets_for_conf_in_nh_export_cbmi
852 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
854 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
855 customizeJMenuItem( _choose_font_mi );
856 customizeJMenuItem( _choose_minimal_confidence_mi );
857 customizeJMenuItem( _switch_colors_mi );
858 customizeJMenuItem( _print_size_mi );
859 customizeJMenuItem( _choose_pdf_width_mi );
860 customizeJMenuItem( _overview_placment_mi );
861 customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
862 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
863 customizeJMenuItem( _cycle_node_shape_mi );
864 customizeJMenuItem( _cycle_node_fill_mi );
865 customizeJMenuItem( _choose_node_size_mi );
866 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
867 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
868 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
869 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
870 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
871 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
872 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
873 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
874 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
875 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
876 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
877 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
878 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
879 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
880 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
881 customizeCheckBoxMenuItem( _label_direction_cbmi,
882 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
883 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
884 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
885 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
886 .isInternalNumberAreConfidenceForNhParsing() );
887 customizeCheckBoxMenuItem( _extract_pfam_style_tax_codes_cbmi, getOptions()
888 .isExtractPfamTaxonomyCodesInNhParsing() );
889 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
890 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
891 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
892 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
893 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
894 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
895 .isGraphicsExportUsingActualSize() );
896 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
897 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
898 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
899 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
900 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
901 _jmenubar.add( _options_jmenu );
904 void buildToolsMenu() {
905 _tools_menu = createMenu( "Tools", getConfiguration() );
906 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
907 customizeJMenuItem( _confcolor_item );
908 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
909 customizeJMenuItem( _color_rank_jmi );
910 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
911 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
912 customizeJMenuItem( _taxcolor_item );
913 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
914 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
915 customizeJMenuItem( _remove_branch_color_item );
916 _tools_menu.addSeparator();
917 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
918 customizeJMenuItem( _midpoint_root_item );
919 _tools_menu.addSeparator();
920 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
921 customizeJMenuItem( _collapse_species_specific_subtrees );
923 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
924 customizeJMenuItem( _collapse_below_threshold );
925 _collapse_below_threshold
926 .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)" );
927 _tools_menu.addSeparator();
929 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
930 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
931 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
932 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
933 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
934 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
936 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes from Node Names" ) );
937 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
938 _extract_tax_code_from_node_names_jmi
939 .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" );
940 _tools_menu.addSeparator();
942 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
943 customizeJMenuItem( _infer_common_sn_names_item );
944 _tools_menu.addSeparator();
946 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
947 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
948 _obtain_detailed_taxonomic_information_jmi
949 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
951 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
952 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
953 _obtain_detailed_taxonomic_information_deleting_jmi
954 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
955 _tools_menu.add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
956 customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
957 _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
958 _tools_menu.addSeparator();
959 if ( !Constants.__RELEASE ) {
960 _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
961 customizeJMenuItem( _function_analysis );
963 .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
964 _tools_menu.addSeparator();
966 _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
967 customizeJMenuItem( _read_values_jmi );
968 _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
969 _jmenubar.add( _tools_menu );
972 private void choosePdfWidth() {
973 final String s = ( String ) JOptionPane.showInputDialog( this,
974 "Please enter the default line width for PDF export.\n"
976 + getOptions().getPrintLineWidth() + "]\n",
977 "Line Width for PDF Export",
978 JOptionPane.QUESTION_MESSAGE,
981 getOptions().getPrintLineWidth() );
982 if ( !ForesterUtil.isEmpty( s ) ) {
983 boolean success = true;
985 final String m_str = s.trim();
986 if ( !ForesterUtil.isEmpty( m_str ) ) {
988 f = Float.parseFloat( m_str );
990 catch ( final Exception ex ) {
997 if ( success && ( f > 0.0 ) ) {
998 getOptions().setPrintLineWidth( f );
1003 private void choosePrintSize() {
1004 final String s = ( String ) JOptionPane.showInputDialog( this,
1005 "Please enter values for width and height,\nseparated by a comma.\n"
1006 + "[current values: "
1007 + getOptions().getPrintSizeX() + ", "
1008 + getOptions().getPrintSizeY() + "]\n"
1009 + "[A4: " + Constants.A4_SIZE_X + ", "
1010 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1011 + Constants.US_LETTER_SIZE_X + ", "
1012 + Constants.US_LETTER_SIZE_Y + "]",
1013 "Default Size for Graphics Export",
1014 JOptionPane.QUESTION_MESSAGE,
1017 getOptions().getPrintSizeX() + ", "
1018 + getOptions().getPrintSizeY() );
1019 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1020 boolean success = true;
1023 final String[] str_ary = s.split( "," );
1024 if ( str_ary.length == 2 ) {
1025 final String x_str = str_ary[ 0 ].trim();
1026 final String y_str = str_ary[ 1 ].trim();
1027 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1029 x = Integer.parseInt( x_str );
1030 y = Integer.parseInt( y_str );
1032 catch ( final Exception ex ) {
1043 if ( success && ( x > 1 ) && ( y > 1 ) ) {
1044 getOptions().setPrintSizeX( x );
1045 getOptions().setPrintSizeY( y );
1052 if ( isUnsavedDataPresent() ) {
1053 final int r = JOptionPane.showConfirmDialog( this,
1054 "Exit despite potentially unsaved changes?",
1056 JOptionPane.YES_NO_OPTION );
1057 if ( r != JOptionPane.YES_OPTION ) {
1064 private void closeCurrentPane() {
1065 if ( getMainPanel().getCurrentTreePanel() != null ) {
1066 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1067 final int r = JOptionPane.showConfirmDialog( this,
1068 "Close tab despite potentially unsaved changes?",
1070 JOptionPane.YES_NO_OPTION );
1071 if ( r != JOptionPane.YES_OPTION ) {
1075 getMainPanel().closeCurrentPane();
1076 activateSaveAllIfNeeded();
1080 private void collapse( final Phylogeny phy, final double m ) {
1081 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1082 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1083 double min_support = Double.MAX_VALUE;
1084 boolean conf_present = false;
1085 while ( it.hasNext() ) {
1086 final PhylogenyNode n = it.next();
1087 if ( !n.isExternal() && !n.isRoot() ) {
1088 final List<Confidence> c = n.getBranchData().getConfidences();
1089 if ( ( c != null ) && ( c.size() > 0 ) ) {
1090 conf_present = true;
1092 for( final Confidence confidence : c ) {
1093 if ( confidence.getValue() > max ) {
1094 max = confidence.getValue();
1097 if ( max < getMinNotCollapseConfidenceValue() ) {
1098 to_be_removed.add( n );
1100 if ( max < min_support ) {
1106 if ( conf_present ) {
1107 for( final PhylogenyNode node : to_be_removed ) {
1108 PhylogenyMethods.removeNode( node, phy );
1110 if ( to_be_removed.size() > 0 ) {
1111 phy.externalNodesHaveChanged();
1112 phy.clearHashIdToNodeMap();
1113 phy.recalculateNumberOfExternalDescendants( true );
1114 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1115 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1116 getCurrentTreePanel().calculateLongestExtNodeInfo();
1117 getCurrentTreePanel().setNodeInPreorderToNull();
1118 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1119 getCurrentTreePanel().resetPreferredSize();
1120 getCurrentTreePanel().setEdited( true );
1121 getCurrentTreePanel().repaint();
1124 if ( to_be_removed.size() > 0 ) {
1125 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1126 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1127 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1130 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1131 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1135 JOptionPane.showMessageDialog( this,
1136 "No branch collapsed because no confidence values present",
1137 "No confidence values present",
1138 JOptionPane.INFORMATION_MESSAGE );
1142 private void collapseBelowThreshold() {
1143 if ( getCurrentTreePanel() != null ) {
1144 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1145 if ( ( phy != null ) && !phy.isEmpty() ) {
1146 final String s = ( String ) JOptionPane.showInputDialog( this,
1147 "Please enter the minimum confidence value\n",
1148 "Minimal Confidence Value",
1149 JOptionPane.QUESTION_MESSAGE,
1152 getMinNotCollapseConfidenceValue() );
1153 if ( !ForesterUtil.isEmpty( s ) ) {
1154 boolean success = true;
1156 final String m_str = s.trim();
1157 if ( !ForesterUtil.isEmpty( m_str ) ) {
1159 m = Double.parseDouble( m_str );
1161 catch ( final Exception ex ) {
1168 if ( success && ( m >= 0.0 ) ) {
1169 setMinNotCollapseConfidenceValue( m );
1177 private PhyloXmlParser createPhyloXmlParser() {
1178 PhyloXmlParser xml_parser = null;
1179 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1181 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1183 catch ( final Exception e ) {
1184 JOptionPane.showMessageDialog( this,
1185 e.getLocalizedMessage(),
1186 "failed to create validating XML parser",
1187 JOptionPane.WARNING_MESSAGE );
1190 if ( xml_parser == null ) {
1191 xml_parser = new PhyloXmlParser();
1196 void executeGSDI() {
1197 if ( !isOKforSDI( false, true ) ) {
1200 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1201 JOptionPane.showMessageDialog( this,
1202 "Gene tree is not rooted.",
1203 "Cannot execute GSDI",
1204 JOptionPane.ERROR_MESSAGE );
1207 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1208 gene_tree.setAllNodesToNotCollapse();
1209 gene_tree.recalculateNumberOfExternalDescendants( false );
1212 gsdi = new GSDI( gene_tree, _species_tree.copy(), false, true, true );
1214 catch ( final Exception e ) {
1215 JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
1217 gene_tree.setRerootable( false );
1218 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1219 _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
1220 _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
1221 _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1222 _mainpanel.getCurrentTreePanel().setEdited( true );
1223 getControlPanel().setShowEvents( true );
1225 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1226 _mainpanel.addPhylogenyInNewTab( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null );
1228 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1230 _mainpanel.getCurrentTreePanel().setEdited( true );
1231 JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1232 + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
1233 + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
1236 void executeFunctionAnalysis() {
1237 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1240 final GoAnnotation a = new GoAnnotation( this,
1241 _mainpanel.getCurrentTreePanel(),
1242 _mainpanel.getCurrentPhylogeny() );
1243 new Thread( a ).start();
1246 void executeLineageInference() {
1247 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1250 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1251 JOptionPane.showMessageDialog( this,
1252 "Phylogeny is not rooted.",
1253 "Cannot infer ancestral taxonomies",
1254 JOptionPane.ERROR_MESSAGE );
1257 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1258 _mainpanel.getCurrentTreePanel(),
1259 _mainpanel.getCurrentPhylogeny()
1261 new Thread( inferrer ).start();
1264 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1265 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1266 getPhylogeneticInferenceOptions(),
1267 from_unaligned_seqs );
1269 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1270 if ( !from_unaligned_seqs ) {
1271 if ( getMsa() != null ) {
1272 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1273 getPhylogeneticInferenceOptions()
1275 new Thread( inferrer ).start();
1278 JOptionPane.showMessageDialog( this,
1279 "No multiple sequence alignment selected",
1280 "Phylogenetic Inference Not Launched",
1281 JOptionPane.WARNING_MESSAGE );
1285 if ( getSeqs() != null ) {
1286 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1287 getPhylogeneticInferenceOptions()
1289 new Thread( inferrer ).start();
1292 JOptionPane.showMessageDialog( this,
1293 "No input sequences selected",
1294 "Phylogenetic Inference Not Launched",
1295 JOptionPane.WARNING_MESSAGE );
1301 void executeSDIR( final boolean minimize_cost ) {
1302 if ( !isOKforSDI( true, true ) ) {
1305 Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1306 final SDIR sdiunrooted = new SDIR();
1307 gene_tree.setAllNodesToNotCollapse();
1308 gene_tree.recalculateNumberOfExternalDescendants( false );
1310 gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1311 !minimize_cost, // minimize sum of dups
1312 true, // minimize height
1313 true, // return tree(s)
1314 1 )[ 0 ]; // # of trees to return
1316 catch ( final Exception e ) {
1317 JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1320 final int duplications = sdiunrooted.getMinimalDuplications();
1321 gene_tree.setRerootable( false );
1322 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1323 getControlPanel().setShowEvents( true );
1325 _mainpanel.getCurrentTreePanel().setEdited( true );
1326 JOptionPane.showMessageDialog( this,
1327 "Number of duplications: " + duplications,
1328 "SDIR successfully completed",
1329 JOptionPane.INFORMATION_MESSAGE );
1334 _mainpanel.terminate();
1335 _contentpane.removeAll();
1336 setVisible( false );
1342 _mainpanel.terminate();
1343 _contentpane.removeAll();
1344 setVisible( false );
1348 private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
1349 if ( getCurrentTreePanel() != null ) {
1350 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1351 if ( ( phy != null ) && !phy.isEmpty() ) {
1352 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1353 while ( it.hasNext() ) {
1354 final PhylogenyNode n = it.next();
1355 final String name = n.getName().trim();
1356 if ( !ForesterUtil.isEmpty( name ) ) {
1357 final String code = ParserUtils
1358 .extractTaxonomyCodeFromNodeName( name, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
1359 if ( !ForesterUtil.isEmpty( code ) ) {
1360 PhylogenyMethods.setTaxonomyCode( n, code );
1368 private ControlPanel getControlPanel() {
1369 return getMainPanel().getControlPanel();
1372 private File getCurrentDir() {
1373 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1374 if ( ForesterUtil.isWindowns() ) {
1376 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1378 catch ( final Exception e ) {
1379 _current_dir = null;
1383 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1384 if ( System.getProperty( "user.home" ) != null ) {
1385 _current_dir = new File( System.getProperty( "user.home" ) );
1387 else if ( System.getProperty( "user.dir" ) != null ) {
1388 _current_dir = new File( System.getProperty( "user.dir" ) );
1391 return _current_dir;
1395 public MainPanel getMainPanel() {
1399 private double getMinNotCollapseConfidenceValue() {
1400 return _min_not_collapse;
1403 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1404 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1407 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1408 JOptionPane.showMessageDialog( this,
1409 "No species tree loaded",
1410 "Cannot execute SDI",
1411 JOptionPane.ERROR_MESSAGE );
1414 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1415 JOptionPane.showMessageDialog( this,
1416 "Species tree is not completely binary",
1417 "Cannot execute SDI",
1418 JOptionPane.ERROR_MESSAGE );
1421 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1422 JOptionPane.showMessageDialog( this,
1423 "Gene tree is not completely binary",
1424 "Cannot execute SDI",
1425 JOptionPane.ERROR_MESSAGE );
1433 private boolean isUnsavedDataPresent() {
1434 final List<TreePanel> tps = getMainPanel().getTreePanels();
1435 for( final TreePanel tp : tps ) {
1436 if ( tp.isEdited() ) {
1443 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1444 if ( getCurrentTreePanel() != null ) {
1445 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1446 if ( ( phy != null ) && !phy.isEmpty() ) {
1448 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1453 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1454 if ( getCurrentTreePanel() != null ) {
1455 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1456 if ( ( phy != null ) && !phy.isEmpty() ) {
1457 PhylogenyMethods.transferNodeNameToField( phy,
1458 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1464 private void newTree() {
1465 final Phylogeny[] phys = new Phylogeny[ 1 ];
1466 final Phylogeny phy = new Phylogeny();
1467 final PhylogenyNode node = new PhylogenyNode();
1468 phy.setRoot( node );
1469 phy.setRooted( true );
1471 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1472 _mainpanel.getControlPanel().showWhole();
1473 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1474 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1475 if ( getMainPanel().getMainFrame() == null ) {
1476 // Must be "E" applet version.
1477 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1478 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1481 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1483 activateSaveAllIfNeeded();
1487 private void obtainDetailedTaxonomicInformation() {
1488 if ( getCurrentTreePanel() != null ) {
1489 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1490 if ( ( phy != null ) && !phy.isEmpty() ) {
1491 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1492 _mainpanel.getCurrentTreePanel(),
1496 new Thread( t ).start();
1501 private void obtainDetailedTaxonomicInformationDelete() {
1502 if ( getCurrentTreePanel() != null ) {
1503 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1504 if ( ( phy != null ) && !phy.isEmpty() ) {
1505 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1506 _mainpanel.getCurrentTreePanel(),
1510 new Thread( t ).start();
1515 private void obtainUniProtSequenceInformation() {
1516 if ( getCurrentTreePanel() != null ) {
1517 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1518 if ( ( phy != null ) && !phy.isEmpty() ) {
1519 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1520 _mainpanel.getCurrentTreePanel(),
1522 new Thread( u ).start();
1527 private void print() {
1528 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
1529 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
1532 if ( !getOptions().isPrintUsingActualSize() ) {
1533 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
1534 getOptions().getPrintSizeY() - 140,
1536 getCurrentTreePanel().resetPreferredSize();
1537 getCurrentTreePanel().repaint();
1539 final String job_name = Constants.PRG_NAME;
1540 boolean error = false;
1541 String printer_name = null;
1543 printer_name = Printer.print( getCurrentTreePanel(), job_name );
1545 catch ( final Exception e ) {
1547 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
1549 if ( !error && ( printer_name != null ) ) {
1550 String msg = "Printing data sent to printer";
1551 if ( printer_name.length() > 1 ) {
1552 msg += " [" + printer_name + "]";
1554 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
1556 if ( !getOptions().isPrintUsingActualSize() ) {
1557 getControlPanel().showWhole();
1561 private void printPhylogenyToPdf( final String file_name ) {
1562 if ( !getOptions().isPrintUsingActualSize() ) {
1563 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
1564 getOptions().getPrintSizeY(),
1566 getCurrentTreePanel().resetPreferredSize();
1567 getCurrentTreePanel().repaint();
1569 String pdf_written_to = "";
1570 boolean error = false;
1572 if ( getOptions().isPrintUsingActualSize() ) {
1573 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
1574 getCurrentTreePanel(),
1575 getCurrentTreePanel().getWidth(),
1576 getCurrentTreePanel().getHeight() );
1579 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
1580 .getPrintSizeX(), getOptions().getPrintSizeY() );
1583 catch ( final IOException e ) {
1585 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1588 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
1589 JOptionPane.showMessageDialog( this,
1590 "Wrote PDF to: " + pdf_written_to,
1592 JOptionPane.INFORMATION_MESSAGE );
1595 JOptionPane.showMessageDialog( this,
1596 "There was an unknown problem when attempting to write to PDF file: \""
1599 JOptionPane.ERROR_MESSAGE );
1602 if ( !getOptions().isPrintUsingActualSize() ) {
1603 getControlPanel().showWhole();
1607 private void addExpressionValuesFromFile() {
1608 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1609 JOptionPane.showMessageDialog( this,
1610 "Need to load evolutionary tree first",
1611 "Can Not Read Expression Values",
1612 JOptionPane.WARNING_MESSAGE );
1615 final File my_dir = getCurrentDir();
1616 if ( my_dir != null ) {
1617 _values_filechooser.setCurrentDirectory( my_dir );
1619 final int result = _values_filechooser.showOpenDialog( _contentpane );
1620 final File file = _values_filechooser.getSelectedFile();
1621 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1622 BasicTable<String> t = null;
1624 t = BasicTableParser.parse( file, "\t" );
1625 if ( t.getNumberOfColumns() < 2 ) {
1626 t = BasicTableParser.parse( file, "," );
1628 if ( t.getNumberOfColumns() < 2 ) {
1629 t = BasicTableParser.parse( file, " " );
1632 catch ( final IOException e ) {
1633 JOptionPane.showMessageDialog( this,
1635 "Could Not Read Expression Value Table",
1636 JOptionPane.ERROR_MESSAGE );
1639 if ( t.getNumberOfColumns() < 2 ) {
1640 JOptionPane.showMessageDialog( this,
1641 "Table contains " + t.getNumberOfColumns() + " column(s)",
1642 "Problem with Expression Value Table",
1643 JOptionPane.ERROR_MESSAGE );
1646 if ( t.getNumberOfRows() < 1 ) {
1647 JOptionPane.showMessageDialog( this,
1648 "Table contains zero rows",
1649 "Problem with Expression Value Table",
1650 JOptionPane.ERROR_MESSAGE );
1653 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1654 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1655 JOptionPane.showMessageDialog( this,
1656 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1657 + phy.getNumberOfExternalNodes() + " external nodes",
1659 JOptionPane.WARNING_MESSAGE );
1661 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1663 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1664 final PhylogenyNode node = iter.next();
1665 final String node_name = node.getName();
1666 if ( !ForesterUtil.isEmpty( node_name ) ) {
1669 row = t.findRow( node_name );
1671 catch ( final IllegalArgumentException e ) {
1673 .showMessageDialog( this,
1675 "Error Mapping Node Identifiers to Expression Value Identifiers",
1676 JOptionPane.ERROR_MESSAGE );
1680 if ( node.isExternal() ) {
1685 final List<Double> l = new ArrayList<Double>();
1686 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1689 d = Double.parseDouble( t.getValueAsString( col, row ) );
1691 catch ( final NumberFormatException e ) {
1692 JOptionPane.showMessageDialog( this,
1693 "Could not parse \"" + t.getValueAsString( col, row )
1694 + "\" into a decimal value",
1695 "Issue with Expression Value Table",
1696 JOptionPane.ERROR_MESSAGE );
1699 stats.addValue( d );
1702 if ( !l.isEmpty() ) {
1703 if ( node.getNodeData().getProperties() != null ) {
1704 node.getNodeData().getProperties()
1705 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1707 node.getNodeData().setVector( l );
1711 if ( not_found > 0 ) {
1712 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1713 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1715 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1719 private void readPhylogeniesFromFile() {
1720 boolean exception = false;
1721 Phylogeny[] phys = null;
1722 // Set an initial directory if none set yet
1723 final File my_dir = getCurrentDir();
1724 _open_filechooser.setMultiSelectionEnabled( true );
1725 // Open file-open dialog and set current directory
1726 if ( my_dir != null ) {
1727 _open_filechooser.setCurrentDirectory( my_dir );
1729 final int result = _open_filechooser.showOpenDialog( _contentpane );
1730 // All done: get the file
1731 final File[] files = _open_filechooser.getSelectedFiles();
1732 setCurrentDir( _open_filechooser.getCurrentDirectory() );
1733 boolean nhx_or_nexus = false;
1734 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1735 for( final File file : files ) {
1736 if ( ( file != null ) && !file.isDirectory() ) {
1737 if ( _mainpanel.getCurrentTreePanel() != null ) {
1738 _mainpanel.getCurrentTreePanel().setWaitCursor();
1741 _mainpanel.setWaitCursor();
1743 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
1744 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
1746 final NHXParser nhx = new NHXParser();
1747 setSpecialOptionsForNhxParser( nhx );
1748 phys = PhylogenyMethods.readPhylogenies( nhx, file );
1749 nhx_or_nexus = true;
1751 catch ( final Exception e ) {
1753 exceptionOccuredDuringOpenFile( e );
1756 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
1757 warnIfNotPhyloXmlValidation( getConfiguration() );
1759 final PhyloXmlParser xml_parser = createPhyloXmlParser();
1760 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
1762 catch ( final Exception e ) {
1764 exceptionOccuredDuringOpenFile( e );
1767 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
1769 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1771 catch ( final Exception e ) {
1773 exceptionOccuredDuringOpenFile( e );
1776 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
1778 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
1779 setSpecialOptionsForNexParser( nex );
1780 phys = PhylogenyMethods.readPhylogenies( nex, file );
1781 nhx_or_nexus = true;
1783 catch ( final Exception e ) {
1785 exceptionOccuredDuringOpenFile( e );
1791 final PhylogenyParser parser = ParserUtils
1792 .createParserDependingOnFileType( file, getConfiguration()
1793 .isValidatePhyloXmlAgainstSchema() );
1794 if ( parser instanceof NexusPhylogeniesParser ) {
1795 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
1796 setSpecialOptionsForNexParser( nex );
1797 nhx_or_nexus = true;
1799 else if ( parser instanceof NHXParser ) {
1800 final NHXParser nhx = ( NHXParser ) parser;
1801 setSpecialOptionsForNhxParser( nhx );
1802 nhx_or_nexus = true;
1804 else if ( parser instanceof PhyloXmlParser ) {
1805 warnIfNotPhyloXmlValidation( getConfiguration() );
1807 phys = PhylogenyMethods.readPhylogenies( parser, file );
1809 catch ( final Exception e ) {
1811 exceptionOccuredDuringOpenFile( e );
1814 if ( _mainpanel.getCurrentTreePanel() != null ) {
1815 _mainpanel.getCurrentTreePanel().setArrowCursor();
1818 _mainpanel.setArrowCursor();
1820 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
1821 boolean one_desc = false;
1822 if ( nhx_or_nexus ) {
1823 for( final Phylogeny phy : phys ) {
1824 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1825 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1827 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
1833 AptxUtil.addPhylogeniesToTabs( phys,
1835 file.getAbsolutePath(),
1838 _mainpanel.getControlPanel().showWhole();
1839 if ( nhx_or_nexus && one_desc ) {
1841 .showMessageDialog( this,
1842 "One or more trees contain (a) node(s) with one descendant, "
1843 + ForesterUtil.LINE_SEPARATOR
1844 + "possibly indicating illegal parentheses within node names.",
1845 "Warning: Possible Error in New Hampshire Formatted Data",
1846 JOptionPane.WARNING_MESSAGE );
1852 activateSaveAllIfNeeded();
1856 public void readSeqsFromFile() {
1857 // Set an initial directory if none set yet
1858 final File my_dir = getCurrentDir();
1859 _seqs_filechooser.setMultiSelectionEnabled( false );
1860 // Open file-open dialog and set current directory
1861 if ( my_dir != null ) {
1862 _seqs_filechooser.setCurrentDirectory( my_dir );
1864 final int result = _seqs_filechooser.showOpenDialog( _contentpane );
1865 // All done: get the seqs
1866 final File file = _seqs_filechooser.getSelectedFile();
1867 setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
1868 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1869 setSeqsFile( null );
1871 List<Sequence> seqs = null;
1873 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1874 seqs = FastaParser.parse( new FileInputStream( file ) );
1875 for( final Sequence seq : seqs ) {
1876 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
1883 catch ( final MsaFormatException e ) {
1885 _mainpanel.getCurrentTreePanel().setArrowCursor();
1887 catch ( final Exception ex ) {
1890 JOptionPane.showMessageDialog( this,
1891 e.getLocalizedMessage(),
1892 "Multiple sequence file format error",
1893 JOptionPane.ERROR_MESSAGE );
1896 catch ( final IOException e ) {
1898 _mainpanel.getCurrentTreePanel().setArrowCursor();
1900 catch ( final Exception ex ) {
1903 JOptionPane.showMessageDialog( this,
1904 e.getLocalizedMessage(),
1905 "Failed to read multiple sequence file",
1906 JOptionPane.ERROR_MESSAGE );
1909 catch ( final IllegalArgumentException e ) {
1911 _mainpanel.getCurrentTreePanel().setArrowCursor();
1913 catch ( final Exception ex ) {
1916 JOptionPane.showMessageDialog( this,
1917 e.getLocalizedMessage(),
1918 "Unexpected error during reading of multiple sequence file",
1919 JOptionPane.ERROR_MESSAGE );
1922 catch ( final Exception e ) {
1924 _mainpanel.getCurrentTreePanel().setArrowCursor();
1926 catch ( final Exception ex ) {
1929 e.printStackTrace();
1930 JOptionPane.showMessageDialog( this,
1931 e.getLocalizedMessage(),
1932 "Unexpected error during reading of multiple sequence file",
1933 JOptionPane.ERROR_MESSAGE );
1936 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1937 JOptionPane.showMessageDialog( this,
1938 "Multiple sequence file is empty",
1939 "Illegal multiple sequence file",
1940 JOptionPane.ERROR_MESSAGE );
1943 if ( seqs.size() < 4 ) {
1944 JOptionPane.showMessageDialog( this,
1945 "Multiple sequence file needs to contain at least 3 sequences",
1946 "Illegal multiple sequence file",
1947 JOptionPane.ERROR_MESSAGE );
1950 // if ( msa.getLength() < 2 ) {
1951 // JOptionPane.showMessageDialog( this,
1952 // "Multiple sequence alignment needs to contain at least 2 residues",
1953 // "Illegal multiple sequence file",
1954 // JOptionPane.ERROR_MESSAGE );
1958 setSeqsFile( _seqs_filechooser.getSelectedFile() );
1963 public void readMsaFromFile() {
1964 // Set an initial directory if none set yet
1965 final File my_dir = getCurrentDir();
1966 _msa_filechooser.setMultiSelectionEnabled( false );
1967 // Open file-open dialog and set current directory
1968 if ( my_dir != null ) {
1969 _msa_filechooser.setCurrentDirectory( my_dir );
1971 final int result = _msa_filechooser.showOpenDialog( _contentpane );
1972 // All done: get the msa
1973 final File file = _msa_filechooser.getSelectedFile();
1974 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
1975 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1980 final InputStream is = new FileInputStream( file );
1981 if ( FastaParser.isLikelyFasta( file ) ) {
1982 msa = FastaParser.parseMsa( is );
1985 msa = GeneralMsaParser.parse( is );
1988 catch ( final MsaFormatException e ) {
1990 _mainpanel.getCurrentTreePanel().setArrowCursor();
1992 catch ( final Exception ex ) {
1995 JOptionPane.showMessageDialog( this,
1996 e.getLocalizedMessage(),
1997 "Multiple sequence alignment format error",
1998 JOptionPane.ERROR_MESSAGE );
2001 catch ( final IOException e ) {
2003 _mainpanel.getCurrentTreePanel().setArrowCursor();
2005 catch ( final Exception ex ) {
2008 JOptionPane.showMessageDialog( this,
2009 e.getLocalizedMessage(),
2010 "Failed to read multiple sequence alignment",
2011 JOptionPane.ERROR_MESSAGE );
2014 catch ( final IllegalArgumentException e ) {
2016 _mainpanel.getCurrentTreePanel().setArrowCursor();
2018 catch ( final Exception ex ) {
2021 JOptionPane.showMessageDialog( this,
2022 e.getLocalizedMessage(),
2023 "Unexpected error during reading of multiple sequence alignment",
2024 JOptionPane.ERROR_MESSAGE );
2027 catch ( final Exception e ) {
2029 _mainpanel.getCurrentTreePanel().setArrowCursor();
2031 catch ( final Exception ex ) {
2034 e.printStackTrace();
2035 JOptionPane.showMessageDialog( this,
2036 e.getLocalizedMessage(),
2037 "Unexpected error during reading of multiple sequence alignment",
2038 JOptionPane.ERROR_MESSAGE );
2041 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
2042 JOptionPane.showMessageDialog( this,
2043 "Multiple sequence alignment is empty",
2044 "Illegal Multiple Sequence Alignment",
2045 JOptionPane.ERROR_MESSAGE );
2048 if ( msa.getNumberOfSequences() < 4 ) {
2049 JOptionPane.showMessageDialog( this,
2050 "Multiple sequence alignment needs to contain at least 3 sequences",
2051 "Illegal multiple sequence alignment",
2052 JOptionPane.ERROR_MESSAGE );
2055 if ( msa.getLength() < 2 ) {
2056 JOptionPane.showMessageDialog( this,
2057 "Multiple sequence alignment needs to contain at least 2 residues",
2058 "Illegal multiple sequence alignment",
2059 JOptionPane.ERROR_MESSAGE );
2063 setMsaFile( _msa_filechooser.getSelectedFile() );
2069 void readPhylogeniesFromURL() {
2071 Phylogeny[] phys = null;
2072 final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
2073 final String url_string = JOptionPane.showInputDialog( this,
2075 "Use URL/webservice to obtain a phylogeny",
2076 JOptionPane.QUESTION_MESSAGE );
2077 boolean nhx_or_nexus = false;
2078 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
2080 url = new URL( url_string );
2081 PhylogenyParser parser = null;
2082 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
2083 parser = new TolParser();
2086 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
2087 .isValidatePhyloXmlAgainstSchema() );
2089 if ( parser instanceof NexusPhylogeniesParser ) {
2090 nhx_or_nexus = true;
2092 else if ( parser instanceof NHXParser ) {
2093 nhx_or_nexus = true;
2095 if ( _mainpanel.getCurrentTreePanel() != null ) {
2096 _mainpanel.getCurrentTreePanel().setWaitCursor();
2099 _mainpanel.setWaitCursor();
2101 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2102 phys = factory.create( url.openStream(), parser );
2104 catch ( final MalformedURLException e ) {
2105 JOptionPane.showMessageDialog( this,
2106 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
2108 JOptionPane.ERROR_MESSAGE );
2110 catch ( final IOException e ) {
2111 JOptionPane.showMessageDialog( this,
2112 "Could not read from " + url + "\n"
2113 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2114 "Failed to read URL",
2115 JOptionPane.ERROR_MESSAGE );
2117 catch ( final Exception e ) {
2118 JOptionPane.showMessageDialog( this,
2119 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2120 "Unexpected Exception",
2121 JOptionPane.ERROR_MESSAGE );
2124 if ( _mainpanel.getCurrentTreePanel() != null ) {
2125 _mainpanel.getCurrentTreePanel().setArrowCursor();
2128 _mainpanel.setArrowCursor();
2131 if ( ( phys != null ) && ( phys.length > 0 ) ) {
2132 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2133 for( final Phylogeny phy : phys ) {
2134 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2137 AptxUtil.addPhylogeniesToTabs( phys,
2138 new File( url.getFile() ).getName(),
2139 new File( url.getFile() ).toString(),
2142 _mainpanel.getControlPanel().showWhole();
2145 activateSaveAllIfNeeded();
2149 private void readSpeciesTreeFromFile() {
2151 boolean exception = false;
2152 final File my_dir = getCurrentDir();
2153 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2154 if ( my_dir != null ) {
2155 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2157 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2158 final File file = _open_filechooser_for_species_tree.getSelectedFile();
2159 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2160 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2162 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2165 catch ( final Exception e ) {
2167 exceptionOccuredDuringOpenFile( e );
2170 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2172 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2175 catch ( final Exception e ) {
2177 exceptionOccuredDuringOpenFile( e );
2183 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2186 catch ( final Exception e ) {
2188 exceptionOccuredDuringOpenFile( e );
2191 if ( !exception && ( t != null ) && !t.isRooted() ) {
2194 JOptionPane.showMessageDialog( this,
2195 "Species tree is not rooted",
2196 "Species tree not loaded",
2197 JOptionPane.ERROR_MESSAGE );
2199 if ( !exception && ( t != null ) ) {
2200 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2201 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2202 final PhylogenyNode node = it.next();
2203 if ( !node.getNodeData().isHasTaxonomy() ) {
2207 .showMessageDialog( this,
2208 "Species tree contains external node(s) without taxonomy information",
2209 "Species tree not loaded",
2210 JOptionPane.ERROR_MESSAGE );
2214 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2217 JOptionPane.showMessageDialog( this,
2219 + node.getNodeData().getTaxonomy().asSimpleText()
2220 + "] is not unique in species tree",
2221 "Species tree not loaded",
2222 JOptionPane.ERROR_MESSAGE );
2226 tax_set.add( node.getNodeData().getTaxonomy() );
2231 if ( !exception && ( t != null ) ) {
2233 JOptionPane.showMessageDialog( this,
2234 "Species tree successfully loaded",
2235 "Species tree loaded",
2236 JOptionPane.INFORMATION_MESSAGE );
2238 _contentpane.repaint();
2243 private void setCurrentDir( final File current_dir ) {
2244 _current_dir = current_dir;
2247 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2248 _min_not_collapse = min_not_collapse;
2251 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2252 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2255 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2256 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2257 PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
2258 if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
2259 te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
2261 nhx.setTaxonomyExtraction( te );
2264 private void writeAllToFile() {
2265 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2268 final File my_dir = getCurrentDir();
2269 if ( my_dir != null ) {
2270 _save_filechooser.setCurrentDirectory( my_dir );
2272 _save_filechooser.setSelectedFile( new File( "" ) );
2273 final int result = _save_filechooser.showSaveDialog( _contentpane );
2274 final File file = _save_filechooser.getSelectedFile();
2275 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2276 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2277 if ( file.exists() ) {
2278 final int i = JOptionPane.showConfirmDialog( this,
2279 file + " already exists. Overwrite?",
2281 JOptionPane.OK_CANCEL_OPTION,
2282 JOptionPane.WARNING_MESSAGE );
2283 if ( i != JOptionPane.OK_OPTION ) {
2290 catch ( final Exception e ) {
2291 JOptionPane.showMessageDialog( this,
2292 "Failed to delete: " + file,
2294 JOptionPane.WARNING_MESSAGE );
2298 final int count = getMainPanel().getTabbedPane().getTabCount();
2299 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2300 for( int i = 0; i < count; ++i ) {
2301 trees.add( getMainPanel().getPhylogeny( i ) );
2302 getMainPanel().getTreePanels().get( i ).setEdited( false );
2304 final PhylogenyWriter writer = new PhylogenyWriter();
2306 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2308 catch ( final IOException e ) {
2309 JOptionPane.showMessageDialog( this,
2310 "Failed to write to: " + file,
2312 JOptionPane.WARNING_MESSAGE );
2317 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2319 final PhylogenyWriter writer = new PhylogenyWriter();
2320 writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2322 catch ( final Exception e ) {
2324 exceptionOccuredDuringSaveAs( e );
2329 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2331 final PhylogenyWriter writer = new PhylogenyWriter();
2332 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2334 catch ( final Exception e ) {
2336 exceptionOccuredDuringSaveAs( e );
2341 private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
2343 final PhylogenyWriter writer = new PhylogenyWriter();
2344 writer.toNewHampshireX( t, file );
2346 catch ( final Exception e ) {
2348 exceptionOccuredDuringSaveAs( e );
2353 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2355 final PhylogenyWriter writer = new PhylogenyWriter();
2356 writer.toPhyloXML( file, t, 0 );
2358 catch ( final Exception e ) {
2360 exceptionOccuredDuringSaveAs( e );
2365 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
2366 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
2367 _mainpanel.getCurrentTreePanel().getHeight(),
2369 String file_written_to = "";
2370 boolean error = false;
2372 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
2373 _mainpanel.getCurrentTreePanel().getWidth(),
2374 _mainpanel.getCurrentTreePanel().getHeight(),
2375 _mainpanel.getCurrentTreePanel(),
2376 _mainpanel.getControlPanel(),
2380 catch ( final IOException e ) {
2382 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2385 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
2386 JOptionPane.showMessageDialog( this,
2387 "Wrote image to: " + file_written_to,
2389 JOptionPane.INFORMATION_MESSAGE );
2392 JOptionPane.showMessageDialog( this,
2393 "There was an unknown problem when attempting to write to an image file: \""
2396 JOptionPane.ERROR_MESSAGE );
2399 _contentpane.repaint();
2402 private void writeToFile( final Phylogeny t ) {
2406 String initial_filename = null;
2407 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2409 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2411 catch ( final IOException e ) {
2412 initial_filename = null;
2415 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2416 _save_filechooser.setSelectedFile( new File( initial_filename ) );
2419 _save_filechooser.setSelectedFile( new File( "" ) );
2421 final File my_dir = getCurrentDir();
2422 if ( my_dir != null ) {
2423 _save_filechooser.setCurrentDirectory( my_dir );
2425 final int result = _save_filechooser.showSaveDialog( _contentpane );
2426 final File file = _save_filechooser.getSelectedFile();
2427 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2428 boolean exception = false;
2429 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2430 if ( file.exists() ) {
2431 final int i = JOptionPane.showConfirmDialog( this,
2432 file + " already exists.\nOverwrite?",
2434 JOptionPane.OK_CANCEL_OPTION,
2435 JOptionPane.QUESTION_MESSAGE );
2436 if ( i != JOptionPane.OK_OPTION ) {
2440 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2442 ForesterUtil.copyFile( file, to );
2444 catch ( final Exception e ) {
2445 JOptionPane.showMessageDialog( this,
2446 "Failed to create backup copy " + to,
2447 "Failed to Create Backup Copy",
2448 JOptionPane.WARNING_MESSAGE );
2453 catch ( final Exception e ) {
2454 JOptionPane.showMessageDialog( this,
2455 "Failed to delete: " + file,
2457 JOptionPane.WARNING_MESSAGE );
2461 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2462 exception = writeAsNewHampshire( t, exception, file );
2464 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
2465 exception = writeAsNHX( t, exception, file );
2467 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2468 exception = writeAsPhyloXml( t, exception, file );
2470 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2471 exception = writeAsNexus( t, exception, file );
2475 final String file_name = file.getName().trim().toLowerCase();
2476 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2477 || file_name.endsWith( ".tree" ) ) {
2478 exception = writeAsNewHampshire( t, exception, file );
2480 else if ( file_name.endsWith( ".nhx" ) ) {
2481 exception = writeAsNHX( t, exception, file );
2483 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2484 exception = writeAsNexus( t, exception, file );
2488 exception = writeAsPhyloXml( t, exception, file );
2492 getMainPanel().setTitleOfSelectedTab( file.getName() );
2493 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2494 getMainPanel().getCurrentTreePanel().setEdited( false );
2499 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2500 if ( ( t == null ) || t.isEmpty() ) {
2503 String initial_filename = "";
2504 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2505 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2507 if ( initial_filename.indexOf( '.' ) > 0 ) {
2508 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2510 initial_filename = initial_filename + "." + type;
2511 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2512 final File my_dir = getCurrentDir();
2513 if ( my_dir != null ) {
2514 _writetographics_filechooser.setCurrentDirectory( my_dir );
2516 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2517 File file = _writetographics_filechooser.getSelectedFile();
2518 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2519 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2520 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2521 file = new File( file.toString() + "." + type );
2523 if ( file.exists() ) {
2524 final int i = JOptionPane.showConfirmDialog( this,
2525 file + " already exists. Overwrite?",
2527 JOptionPane.OK_CANCEL_OPTION,
2528 JOptionPane.WARNING_MESSAGE );
2529 if ( i != JOptionPane.OK_OPTION ) {
2536 catch ( final Exception e ) {
2537 JOptionPane.showMessageDialog( this,
2538 "Failed to delete: " + file,
2540 JOptionPane.WARNING_MESSAGE );
2544 writePhylogenyToGraphicsFile( file.toString(), type );
2548 private void writeToPdf( final Phylogeny t ) {
2549 if ( ( t == null ) || t.isEmpty() ) {
2552 String initial_filename = "";
2553 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2554 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2556 if ( initial_filename.indexOf( '.' ) > 0 ) {
2557 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2559 initial_filename = initial_filename + ".pdf";
2560 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2561 final File my_dir = getCurrentDir();
2562 if ( my_dir != null ) {
2563 _writetopdf_filechooser.setCurrentDirectory( my_dir );
2565 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2566 File file = _writetopdf_filechooser.getSelectedFile();
2567 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2568 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2569 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2570 file = new File( file.toString() + ".pdf" );
2572 if ( file.exists() ) {
2573 final int i = JOptionPane.showConfirmDialog( this,
2574 file + " already exists. Overwrite?",
2576 JOptionPane.OK_CANCEL_OPTION,
2577 JOptionPane.WARNING_MESSAGE );
2578 if ( i != JOptionPane.OK_OPTION ) {
2582 printPhylogenyToPdf( file.toString() );
2586 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2587 return new MainFrameApplication( phys, config, title );
2590 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2591 return new MainFrameApplication( phys, config );
2594 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2595 return new MainFrameApplication( phys, config_file_name, title );
2598 public static MainFrame createInstance( final Phylogeny[] phys,
2599 final Configuration config,
2601 final File current_dir ) {
2602 return new MainFrameApplication( phys, config, title, current_dir );
2605 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2606 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2607 + o.getPrintSizeY() + ")" );
2610 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2611 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2614 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2615 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2617 .showMessageDialog( null,
2619 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2622 JOptionPane.WARNING_MESSAGE );
2626 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2627 _phylogenetic_inference_options = phylogenetic_inference_options;
2630 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
2631 if ( _phylogenetic_inference_options == null ) {
2632 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
2634 return _phylogenetic_inference_options;
2637 public Msa getMsa() {
2641 void setMsa( final Msa msa ) {
2645 void setMsaFile( final File msa_file ) {
2646 _msa_file = msa_file;
2649 public File getMsaFile() {
2653 public List<Sequence> getSeqs() {
2657 void setSeqs( final List<Sequence> seqs ) {
2661 void setSeqsFile( final File seqs_file ) {
2662 _seqs_file = seqs_file;
2665 public File getSeqsFile() {
2668 } // MainFrameApplication.
2670 class NexusFilter extends FileFilter {
2673 public boolean accept( final File f ) {
2674 final String file_name = f.getName().trim().toLowerCase();
2675 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2676 || file_name.endsWith( ".tre" ) || f.isDirectory();
2680 public String getDescription() {
2681 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2685 class NHFilter extends FileFilter {
2688 public boolean accept( final File f ) {
2689 final String file_name = f.getName().trim().toLowerCase();
2690 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2691 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2692 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2697 public String getDescription() {
2698 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2702 class NHXFilter extends FileFilter {
2705 public boolean accept( final File f ) {
2706 final String file_name = f.getName().trim().toLowerCase();
2707 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2711 public String getDescription() {
2712 return "NHX files (*.nhx)";
2716 class PdfFilter extends FileFilter {
2719 public boolean accept( final File f ) {
2720 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2724 public String getDescription() {
2725 return "PDF files (*.pdf)";
2729 class TolFilter extends FileFilter {
2732 public boolean accept( final File f ) {
2733 final String file_name = f.getName().trim().toLowerCase();
2734 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2735 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2739 public String getDescription() {
2740 return "Tree of Life files (*.tol, *.tolxml)";
2744 class XMLFilter extends FileFilter {
2747 public boolean accept( final File f ) {
2748 final String file_name = f.getName().trim().toLowerCase();
2749 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2750 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2754 public String getDescription() {
2755 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";