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.net.MalformedURLException;
41 import java.util.ArrayList;
42 import java.util.HashSet;
43 import java.util.List;
46 import javax.swing.ButtonGroup;
47 import javax.swing.JCheckBoxMenuItem;
48 import javax.swing.JFileChooser;
49 import javax.swing.JMenu;
50 import javax.swing.JMenuBar;
51 import javax.swing.JMenuItem;
52 import javax.swing.JOptionPane;
53 import javax.swing.JRadioButtonMenuItem;
54 import javax.swing.UIManager;
55 import javax.swing.UnsupportedLookAndFeelException;
56 import javax.swing.WindowConstants;
57 import javax.swing.event.ChangeEvent;
58 import javax.swing.event.ChangeListener;
59 import javax.swing.filechooser.FileFilter;
60 import javax.swing.plaf.synth.SynthLookAndFeel;
62 import org.forester.analysis.TaxonomyDataObtainer;
63 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
64 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
65 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
66 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
67 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
68 import org.forester.archaeopteryx.tools.GoAnnotation;
69 import org.forester.archaeopteryx.tools.InferenceManager;
70 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
71 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
72 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
73 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
74 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
75 import org.forester.archaeopteryx.webservices.WebservicesManager;
76 import org.forester.io.parsers.FastaParser;
77 import org.forester.io.parsers.GeneralMsaParser;
78 import org.forester.io.parsers.PhylogenyParser;
79 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
80 import org.forester.io.parsers.nhx.NHXParser;
81 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
82 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
83 import org.forester.io.parsers.tol.TolParser;
84 import org.forester.io.parsers.util.ParserUtils;
85 import org.forester.io.writers.PhylogenyWriter;
86 import org.forester.io.writers.SequenceWriter;
87 import org.forester.msa.Msa;
88 import org.forester.msa.MsaFormatException;
89 import org.forester.phylogeny.Phylogeny;
90 import org.forester.phylogeny.PhylogenyMethods;
91 import org.forester.phylogeny.PhylogenyNode;
92 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
93 import org.forester.phylogeny.data.Confidence;
94 import org.forester.phylogeny.data.Taxonomy;
95 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
96 import org.forester.phylogeny.factories.PhylogenyFactory;
97 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
98 import org.forester.sdi.GSDI;
99 import org.forester.sdi.SDI;
100 import org.forester.sdi.SDIR;
101 import org.forester.sdi.SDIse;
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 _sdi_item;
206 private JMenuItem _gsdi_item;
207 private JMenuItem _root_min_dups_item;
208 private JMenuItem _root_min_cost_l_item;
209 private JMenuItem _lineage_inference;
210 private JMenuItem _function_analysis;
211 // Application-only print menu items
212 private JMenuItem _print_item;
213 private JMenuItem _write_to_pdf_item;
214 private JMenuItem _write_to_jpg_item;
215 private JMenuItem _write_to_gif_item;
216 private JMenuItem _write_to_tif_item;
217 private JMenuItem _write_to_png_item;
218 private JMenuItem _write_to_bmp_item;
219 private Phylogeny _species_tree;
220 private File _current_dir;
221 private ButtonGroup _radio_group_1;
223 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
224 // Phylogeny Inference menu
225 private JMenu _inference_menu;
226 private JMenuItem _inference_from_msa_item;
227 private JMenuItem _inference_from_seqs_item;
228 // Phylogeny Inference
229 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
230 private Msa _msa = null;
231 private File _msa_file = null;
232 private List<Sequence> _seqs = null;
233 private File _seqs_file = null;
234 // expression values menu:
235 JMenuItem _read_values_jmi;
237 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
238 this( phys, config, title, null );
241 private MainFrameApplication( final Phylogeny[] phys,
242 final Configuration config,
244 final File current_dir ) {
246 _configuration = config;
247 if ( _configuration == null ) {
248 throw new IllegalArgumentException( "configuration is null" );
251 boolean synth_exception = false;
252 if ( Constants.__SYNTH_LF ) {
254 final SynthLookAndFeel synth = new SynthLookAndFeel();
255 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
256 MainFrameApplication.class );
257 UIManager.setLookAndFeel( synth );
259 catch ( final Exception ex ) {
260 synth_exception = true;
261 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
262 "could not create synth look and feel: "
263 + ex.getLocalizedMessage() );
266 if ( !Constants.__SYNTH_LF || synth_exception ) {
267 if ( _configuration.isUseNativeUI() ) {
268 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
271 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
274 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
276 catch ( final UnsupportedLookAndFeelException e ) {
277 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
279 catch ( final ClassNotFoundException e ) {
280 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
282 catch ( final InstantiationException e ) {
283 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
285 catch ( final IllegalAccessException e ) {
286 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
288 catch ( final Exception e ) {
289 AptxUtil.dieWithSystemError( e.toString() );
291 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
292 setCurrentDir( current_dir );
294 // hide until everything is ready
296 setOptions( Options.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 == _sdi_item ) {
534 if ( isSubtreeDisplayed() ) {
539 else if ( o == _lineage_inference ) {
540 if ( isSubtreeDisplayed() ) {
541 JOptionPane.showMessageDialog( this,
543 "Cannot infer ancestral taxonomies",
544 JOptionPane.ERROR_MESSAGE );
547 executeLineageInference();
549 else if ( o == _function_analysis ) {
550 executeFunctionAnalysis();
552 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
553 if ( isSubtreeDisplayed() ) {
556 obtainDetailedTaxonomicInformation();
558 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
559 if ( isSubtreeDisplayed() ) {
562 obtainDetailedTaxonomicInformationDelete();
564 else if ( o == _obtain_uniprot_seq_information_jmi ) {
565 obtainUniProtSequenceInformation();
567 else if ( o == _read_values_jmi ) {
568 if ( isSubtreeDisplayed() ) {
571 addExpressionValuesFromFile();
573 else if ( o == _move_node_names_to_tax_sn_jmi ) {
574 moveNodeNamesToTaxSn();
576 else if ( o == _move_node_names_to_seq_names_jmi ) {
577 moveNodeNamesToSeqNames();
579 else if ( o == _extract_tax_code_from_node_names_jmi ) {
580 extractTaxCodeFromNodeNames();
582 else if ( o == _gsdi_item ) {
583 if ( isSubtreeDisplayed() ) {
588 else if ( o == _root_min_dups_item ) {
589 if ( isSubtreeDisplayed() ) {
592 executeSDIR( false );
594 else if ( o == _root_min_cost_l_item ) {
595 if ( isSubtreeDisplayed() ) {
600 else if ( o == _graphics_export_visible_only_cbmi ) {
601 updateOptions( getOptions() );
603 else if ( o == _antialias_print_cbmi ) {
604 updateOptions( getOptions() );
606 else if ( o == _print_black_and_white_cbmi ) {
607 updateOptions( getOptions() );
609 else if ( o == _print_using_actual_size_cbmi ) {
610 updateOptions( getOptions() );
612 else if ( o == _graphics_export_using_actual_size_cbmi ) {
613 updateOptions( getOptions() );
615 else if ( o == _print_size_mi ) {
618 else if ( o == _choose_pdf_width_mi ) {
621 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
622 updateOptions( getOptions() );
624 else if ( o == _replace_underscores_cbmi ) {
625 if ( ( _extract_pfam_style_tax_codes_cbmi != null ) && _replace_underscores_cbmi.isSelected() ) {
626 _extract_pfam_style_tax_codes_cbmi.setSelected( false );
628 updateOptions( getOptions() );
630 else if ( o == _collapse_below_threshold ) {
631 if ( isSubtreeDisplayed() ) {
634 collapseBelowThreshold();
636 else if ( o == _extract_pfam_style_tax_codes_cbmi ) {
637 if ( ( _replace_underscores_cbmi != null ) && _extract_pfam_style_tax_codes_cbmi.isSelected() ) {
638 _replace_underscores_cbmi.setSelected( false );
640 updateOptions( getOptions() );
642 else if ( o == _inference_from_msa_item ) {
643 executePhyleneticInference( false );
645 else if ( o == _inference_from_seqs_item ) {
646 executePhyleneticInference( true );
648 _contentpane.repaint();
650 catch ( final Exception ex ) {
651 AptxUtil.unexpectedException( ex );
653 catch ( final Error err ) {
654 AptxUtil.unexpectedError( err );
658 void buildAnalysisMenu() {
659 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
660 _analysis_menu.add( _sdi_item = new JMenuItem( "SDI (Speciation Duplication Inference)" ) );
661 if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
662 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
664 _analysis_menu.addSeparator();
665 _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
666 _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
667 _analysis_menu.addSeparator();
668 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
669 customizeJMenuItem( _sdi_item );
670 customizeJMenuItem( _gsdi_item );
671 customizeJMenuItem( _root_min_dups_item );
672 customizeJMenuItem( _root_min_cost_l_item );
673 customizeJMenuItem( _load_species_tree_item );
674 _analysis_menu.addSeparator();
675 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
676 customizeJMenuItem( _lineage_inference );
677 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
678 _jmenubar.add( _analysis_menu );
681 void buildPhylogeneticInferenceMenu() {
682 final InferenceManager inference_manager = InferenceManager.getInstance();
683 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
684 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
685 customizeJMenuItem( _inference_from_msa_item );
686 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
687 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
688 customizeJMenuItem( _inference_from_seqs_item );
689 _inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
690 _jmenubar.add( _inference_menu );
694 void buildFileMenu() {
695 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
696 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
697 _file_jmenu.addSeparator();
698 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
699 _file_jmenu.addSeparator();
700 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
701 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
702 .getAvailablePhylogeniesWebserviceClients().size() ];
703 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
704 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
705 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
706 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
708 if ( getConfiguration().isEditable() ) {
709 _file_jmenu.addSeparator();
710 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
711 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
713 _file_jmenu.addSeparator();
714 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
715 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
716 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
717 _save_all_item.setEnabled( false );
718 _file_jmenu.addSeparator();
719 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
720 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
721 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
723 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
724 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
725 if ( AptxUtil.canWriteFormat( "gif" ) ) {
726 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
728 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
729 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
731 _file_jmenu.addSeparator();
732 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
733 _file_jmenu.addSeparator();
734 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
735 _close_item.setToolTipText( "To close the current pane." );
736 _close_item.setEnabled( true );
737 _file_jmenu.addSeparator();
738 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
739 // For print in color option item
740 customizeJMenuItem( _open_item );
742 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
743 customizeJMenuItem( _open_url_item );
744 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
745 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
747 customizeJMenuItem( _save_item );
748 if ( getConfiguration().isEditable() ) {
749 customizeJMenuItem( _new_item );
751 customizeJMenuItem( _close_item );
752 customizeJMenuItem( _save_all_item );
753 customizeJMenuItem( _write_to_pdf_item );
754 customizeJMenuItem( _write_to_png_item );
755 customizeJMenuItem( _write_to_jpg_item );
756 customizeJMenuItem( _write_to_gif_item );
757 customizeJMenuItem( _write_to_tif_item );
758 customizeJMenuItem( _write_to_bmp_item );
759 customizeJMenuItem( _print_item );
760 customizeJMenuItem( _exit_item );
761 _jmenubar.add( _file_jmenu );
764 void buildOptionsMenu() {
765 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
766 _options_jmenu.addChangeListener( new ChangeListener() {
769 public void stateChanged( final ChangeEvent e ) {
770 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
771 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
773 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
774 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
775 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
776 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
777 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
778 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
780 _show_branch_length_values_cbmi,
781 _non_lined_up_cladograms_rbmi,
782 _uniform_cladograms_rbmi,
783 _ext_node_dependent_cladogram_rbmi,
784 _label_direction_cbmi );
785 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
786 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
787 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
790 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
792 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
793 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
794 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
795 _radio_group_1 = new ButtonGroup();
796 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
797 _radio_group_1.add( _uniform_cladograms_rbmi );
798 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
799 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
800 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
802 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
803 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
804 _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
806 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
807 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
808 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
809 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
810 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
811 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
812 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
813 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
814 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
815 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
816 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
817 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
818 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
820 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
821 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
822 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
823 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
824 _options_jmenu.addSeparator();
825 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
826 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
827 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
828 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
829 _options_jmenu.addSeparator();
830 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
831 getConfiguration() ) );
832 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
833 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
835 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
837 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
839 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
840 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
841 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
842 _options_jmenu.addSeparator();
843 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
845 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
846 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
848 .add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
849 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
851 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
852 _use_brackets_for_conf_in_nh_export_cbmi
853 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
855 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
856 customizeJMenuItem( _choose_font_mi );
857 customizeJMenuItem( _choose_minimal_confidence_mi );
858 customizeJMenuItem( _switch_colors_mi );
859 customizeJMenuItem( _print_size_mi );
860 customizeJMenuItem( _choose_pdf_width_mi );
861 customizeJMenuItem( _overview_placment_mi );
862 customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
863 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
864 customizeJMenuItem( _cycle_node_shape_mi );
865 customizeJMenuItem( _cycle_node_fill_mi );
866 customizeJMenuItem( _choose_node_size_mi );
867 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
868 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
869 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
870 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
871 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
872 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
873 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
874 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
875 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
876 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
877 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
878 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
879 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
880 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
881 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
882 customizeCheckBoxMenuItem( _label_direction_cbmi,
883 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
884 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
885 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
886 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
887 .isInternalNumberAreConfidenceForNhParsing() );
888 customizeCheckBoxMenuItem( _extract_pfam_style_tax_codes_cbmi, getOptions()
889 .isExtractPfamTaxonomyCodesInNhParsing() );
890 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
891 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
892 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
893 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
894 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
895 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
896 .isGraphicsExportUsingActualSize() );
897 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
898 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
899 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
900 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
901 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
902 _jmenubar.add( _options_jmenu );
905 void buildToolsMenu() {
906 _tools_menu = createMenu( "Tools", getConfiguration() );
907 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
908 customizeJMenuItem( _confcolor_item );
909 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
910 customizeJMenuItem( _color_rank_jmi );
911 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
912 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
913 customizeJMenuItem( _taxcolor_item );
914 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
915 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
916 customizeJMenuItem( _remove_branch_color_item );
917 _tools_menu.addSeparator();
918 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
919 customizeJMenuItem( _midpoint_root_item );
920 _tools_menu.addSeparator();
921 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
922 customizeJMenuItem( _collapse_species_specific_subtrees );
924 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
925 customizeJMenuItem( _collapse_below_threshold );
926 _collapse_below_threshold
927 .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)" );
928 _tools_menu.addSeparator();
930 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
931 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
932 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
933 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
934 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
935 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
937 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes from Node Names" ) );
938 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
939 _extract_tax_code_from_node_names_jmi
940 .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" );
941 _tools_menu.addSeparator();
943 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
944 customizeJMenuItem( _infer_common_sn_names_item );
945 _tools_menu.addSeparator();
947 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
948 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
949 _obtain_detailed_taxonomic_information_jmi
950 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
952 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
953 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
954 _obtain_detailed_taxonomic_information_deleting_jmi
955 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
957 .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
958 customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
959 _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
960 _tools_menu.addSeparator();
961 if ( !Constants.__RELEASE ) {
962 _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
963 customizeJMenuItem( _function_analysis );
965 .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
966 _tools_menu.addSeparator();
968 _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
969 customizeJMenuItem( _read_values_jmi );
970 _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
971 _jmenubar.add( _tools_menu );
974 private void choosePdfWidth() {
975 final String s = ( String ) JOptionPane.showInputDialog( this,
976 "Please enter the default line width for PDF export.\n"
978 + getOptions().getPrintLineWidth() + "]\n",
979 "Line Width for PDF Export",
980 JOptionPane.QUESTION_MESSAGE,
983 getOptions().getPrintLineWidth() );
984 if ( !ForesterUtil.isEmpty( s ) ) {
985 boolean success = true;
987 final String m_str = s.trim();
988 if ( !ForesterUtil.isEmpty( m_str ) ) {
990 f = Float.parseFloat( m_str );
992 catch ( final Exception ex ) {
999 if ( success && ( f > 0.0 ) ) {
1000 getOptions().setPrintLineWidth( f );
1005 private void choosePrintSize() {
1006 final String s = ( String ) JOptionPane.showInputDialog( this,
1007 "Please enter values for width and height,\nseparated by a comma.\n"
1008 + "[current values: "
1009 + getOptions().getPrintSizeX() + ", "
1010 + getOptions().getPrintSizeY() + "]\n"
1011 + "[A4: " + Constants.A4_SIZE_X + ", "
1012 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1013 + Constants.US_LETTER_SIZE_X + ", "
1014 + Constants.US_LETTER_SIZE_Y + "]",
1015 "Default Size for Graphics Export",
1016 JOptionPane.QUESTION_MESSAGE,
1019 getOptions().getPrintSizeX() + ", "
1020 + getOptions().getPrintSizeY() );
1021 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1022 boolean success = true;
1025 final String[] str_ary = s.split( "," );
1026 if ( str_ary.length == 2 ) {
1027 final String x_str = str_ary[ 0 ].trim();
1028 final String y_str = str_ary[ 1 ].trim();
1029 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1031 x = Integer.parseInt( x_str );
1032 y = Integer.parseInt( y_str );
1034 catch ( final Exception ex ) {
1045 if ( success && ( x > 1 ) && ( y > 1 ) ) {
1046 getOptions().setPrintSizeX( x );
1047 getOptions().setPrintSizeY( y );
1054 if ( isUnsavedDataPresent() ) {
1055 final int r = JOptionPane.showConfirmDialog( this,
1056 "Exit despite potentially unsaved changes?",
1058 JOptionPane.YES_NO_OPTION );
1059 if ( r != JOptionPane.YES_OPTION ) {
1066 private void closeCurrentPane() {
1067 if ( getMainPanel().getCurrentTreePanel() != null ) {
1068 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1069 final int r = JOptionPane.showConfirmDialog( this,
1070 "Close tab despite potentially unsaved changes?",
1072 JOptionPane.YES_NO_OPTION );
1073 if ( r != JOptionPane.YES_OPTION ) {
1077 getMainPanel().closeCurrentPane();
1078 activateSaveAllIfNeeded();
1082 private void collapse( final Phylogeny phy, final double m ) {
1083 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1084 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1085 double min_support = Double.MAX_VALUE;
1086 boolean conf_present = false;
1087 while ( it.hasNext() ) {
1088 final PhylogenyNode n = it.next();
1089 if ( !n.isExternal() && !n.isRoot() ) {
1090 final List<Confidence> c = n.getBranchData().getConfidences();
1091 if ( ( c != null ) && ( c.size() > 0 ) ) {
1092 conf_present = true;
1094 for( final Confidence confidence : c ) {
1095 if ( confidence.getValue() > max ) {
1096 max = confidence.getValue();
1099 if ( max < getMinNotCollapseConfidenceValue() ) {
1100 to_be_removed.add( n );
1102 if ( max < min_support ) {
1108 if ( conf_present ) {
1109 for( final PhylogenyNode node : to_be_removed ) {
1110 PhylogenyMethods.removeNode( node, phy );
1112 if ( to_be_removed.size() > 0 ) {
1113 phy.externalNodesHaveChanged();
1115 phy.recalculateNumberOfExternalDescendants( true );
1116 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1117 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1118 getCurrentTreePanel().calculateLongestExtNodeInfo();
1119 getCurrentTreePanel().setNodeInPreorderToNull();
1120 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1121 getCurrentTreePanel().resetPreferredSize();
1122 getCurrentTreePanel().setEdited( true );
1123 getCurrentTreePanel().repaint();
1126 if ( to_be_removed.size() > 0 ) {
1127 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1128 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1129 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1132 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1133 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1137 JOptionPane.showMessageDialog( this,
1138 "No branch collapsed because no confidence values present",
1139 "No confidence values present",
1140 JOptionPane.INFORMATION_MESSAGE );
1144 private void collapseBelowThreshold() {
1145 if ( getCurrentTreePanel() != null ) {
1146 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1147 if ( ( phy != null ) && !phy.isEmpty() ) {
1148 final String s = ( String ) JOptionPane.showInputDialog( this,
1149 "Please enter the minimum confidence value\n",
1150 "Minimal Confidence Value",
1151 JOptionPane.QUESTION_MESSAGE,
1154 getMinNotCollapseConfidenceValue() );
1155 if ( !ForesterUtil.isEmpty( s ) ) {
1156 boolean success = true;
1158 final String m_str = s.trim();
1159 if ( !ForesterUtil.isEmpty( m_str ) ) {
1161 m = Double.parseDouble( m_str );
1163 catch ( final Exception ex ) {
1170 if ( success && ( m >= 0.0 ) ) {
1171 setMinNotCollapseConfidenceValue( m );
1179 private PhyloXmlParser createPhyloXmlParser() {
1180 PhyloXmlParser xml_parser = null;
1181 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1183 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1185 catch ( final Exception e ) {
1186 JOptionPane.showMessageDialog( this,
1187 e.getLocalizedMessage(),
1188 "failed to create validating XML parser",
1189 JOptionPane.WARNING_MESSAGE );
1192 if ( xml_parser == null ) {
1193 xml_parser = new PhyloXmlParser();
1198 void executeGSDI() {
1199 if ( !isOKforSDI( false, true ) ) {
1202 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1203 JOptionPane.showMessageDialog( this,
1204 "Gene tree is not rooted.",
1205 "Cannot execute GSDI",
1206 JOptionPane.ERROR_MESSAGE );
1209 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1210 gene_tree.setAllNodesToNotCollapse();
1211 gene_tree.recalculateNumberOfExternalDescendants( false );
1213 int duplications = -1;
1215 gsdi = new GSDI( gene_tree, _species_tree.copy(), true );
1216 duplications = gsdi.getDuplicationsSum();
1218 catch ( final Exception e ) {
1219 JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
1221 gene_tree.setRerootable( false );
1222 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1223 getControlPanel().setShowEvents( true );
1225 _mainpanel.getCurrentTreePanel().setEdited( true );
1226 JOptionPane.showMessageDialog( this,
1227 "Number of duplications: " + duplications,
1228 "GSDI successfully completed",
1229 JOptionPane.INFORMATION_MESSAGE );
1232 void executeFunctionAnalysis() {
1233 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1236 final GoAnnotation a = new GoAnnotation( this,
1237 _mainpanel.getCurrentTreePanel(),
1238 _mainpanel.getCurrentPhylogeny() );
1239 new Thread( a ).start();
1242 void executeLineageInference() {
1243 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1246 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1247 JOptionPane.showMessageDialog( this,
1248 "Phylogeny is not rooted.",
1249 "Cannot infer ancestral taxonomies",
1250 JOptionPane.ERROR_MESSAGE );
1253 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1254 _mainpanel.getCurrentTreePanel(),
1255 _mainpanel.getCurrentPhylogeny()
1257 new Thread( inferrer ).start();
1260 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1261 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1262 getPhylogeneticInferenceOptions(),
1263 from_unaligned_seqs );
1265 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1266 if ( !from_unaligned_seqs ) {
1267 if ( getMsa() != null ) {
1268 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1269 getPhylogeneticInferenceOptions()
1271 new Thread( inferrer ).start();
1274 JOptionPane.showMessageDialog( this,
1275 "No multiple sequence alignment selected",
1276 "Phylogenetic Inference Not Launched",
1277 JOptionPane.WARNING_MESSAGE );
1281 if ( getSeqs() != null ) {
1282 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1283 getPhylogeneticInferenceOptions()
1285 new Thread( inferrer ).start();
1288 JOptionPane.showMessageDialog( this,
1289 "No input sequences selected",
1290 "Phylogenetic Inference Not Launched",
1291 JOptionPane.WARNING_MESSAGE );
1298 if ( !isOKforSDI( true, true ) ) {
1301 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1302 JOptionPane.showMessageDialog( this,
1303 "Gene tree is not rooted",
1304 "Cannot execute SDI",
1305 JOptionPane.ERROR_MESSAGE );
1308 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1309 gene_tree.setAllNodesToNotCollapse();
1310 gene_tree.recalculateNumberOfExternalDescendants( false );
1312 int duplications = -1;
1314 sdi = new SDIse( gene_tree, _species_tree.copy() );
1315 duplications = sdi.getDuplicationsSum();
1317 catch ( final Exception e ) {
1318 JOptionPane.showMessageDialog( this, e.toString(), "Error during SDI", JOptionPane.ERROR_MESSAGE );
1320 gene_tree.setRerootable( false );
1321 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1322 getControlPanel().setShowEvents( true );
1324 _mainpanel.getCurrentTreePanel().setEdited( true );
1325 JOptionPane.showMessageDialog( this,
1326 "Number of duplications: " + duplications,
1327 "SDI successfully completed",
1328 JOptionPane.INFORMATION_MESSAGE );
1331 void executeSDIR( final boolean minimize_cost ) {
1332 if ( !isOKforSDI( true, true ) ) {
1335 Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1336 final SDIR sdiunrooted = new SDIR();
1337 gene_tree.setAllNodesToNotCollapse();
1338 gene_tree.recalculateNumberOfExternalDescendants( false );
1340 gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1341 !minimize_cost, // minimize sum of dups
1342 true, // minimize height
1343 true, // return tree(s)
1344 1 )[ 0 ]; // # of trees to return
1346 catch ( final Exception e ) {
1347 JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1350 final int duplications = sdiunrooted.getMinimalDuplications();
1351 gene_tree.setRerootable( false );
1352 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1353 getControlPanel().setShowEvents( true );
1355 _mainpanel.getCurrentTreePanel().setEdited( true );
1356 JOptionPane.showMessageDialog( this,
1357 "Number of duplications: " + duplications,
1358 "SDIR successfully completed",
1359 JOptionPane.INFORMATION_MESSAGE );
1364 _mainpanel.terminate();
1365 _contentpane.removeAll();
1366 setVisible( false );
1372 _mainpanel.terminate();
1373 _contentpane.removeAll();
1374 setVisible( false );
1378 private void extractTaxCodeFromNodeNames() {
1379 if ( getCurrentTreePanel() != null ) {
1380 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1381 if ( ( phy != null ) && !phy.isEmpty() ) {
1382 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1383 while ( it.hasNext() ) {
1384 final PhylogenyNode n = it.next();
1385 final String name = n.getName().trim();
1386 if ( !ForesterUtil.isEmpty( name ) ) {
1387 final String code = ParserUtils
1388 .extractTaxonomyCodeFromNodeName( name, false, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
1389 if ( !ForesterUtil.isEmpty( code ) ) {
1390 PhylogenyMethods.setTaxonomyCode( n, code );
1398 private ControlPanel getControlPanel() {
1399 return getMainPanel().getControlPanel();
1402 private File getCurrentDir() {
1403 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1404 if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1 ) {
1406 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1408 catch ( final Exception e ) {
1409 _current_dir = null;
1413 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1414 if ( System.getProperty( "user.home" ) != null ) {
1415 _current_dir = new File( System.getProperty( "user.home" ) );
1417 else if ( System.getProperty( "user.dir" ) != null ) {
1418 _current_dir = new File( System.getProperty( "user.dir" ) );
1421 return _current_dir;
1425 public MainPanel getMainPanel() {
1429 private double getMinNotCollapseConfidenceValue() {
1430 return _min_not_collapse;
1433 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1434 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1437 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1438 JOptionPane.showMessageDialog( this,
1439 "No species tree loaded",
1440 "Cannot execute SDI",
1441 JOptionPane.ERROR_MESSAGE );
1444 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1445 JOptionPane.showMessageDialog( this,
1446 "Species tree is not completely binary",
1447 "Cannot execute SDI",
1448 JOptionPane.ERROR_MESSAGE );
1451 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1452 JOptionPane.showMessageDialog( this,
1453 "Gene tree is not completely binary",
1454 "Cannot execute SDI",
1455 JOptionPane.ERROR_MESSAGE );
1463 private boolean isUnsavedDataPresent() {
1464 final List<TreePanel> tps = getMainPanel().getTreePanels();
1465 for( final TreePanel tp : tps ) {
1466 if ( tp.isEdited() ) {
1473 private void moveNodeNamesToSeqNames() {
1474 if ( getCurrentTreePanel() != null ) {
1475 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1476 if ( ( phy != null ) && !phy.isEmpty() ) {
1477 PhylogenyMethods.transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME );
1482 private void moveNodeNamesToTaxSn() {
1483 if ( getCurrentTreePanel() != null ) {
1484 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1485 if ( ( phy != null ) && !phy.isEmpty() ) {
1486 PhylogenyMethods.transferNodeNameToField( phy,
1487 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
1492 private void newTree() {
1493 final Phylogeny[] phys = new Phylogeny[ 1 ];
1494 final Phylogeny phy = new Phylogeny();
1495 final PhylogenyNode node = new PhylogenyNode();
1496 phy.setRoot( node );
1497 phy.setRooted( true );
1499 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1500 _mainpanel.getControlPanel().showWhole();
1501 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1502 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1503 if ( getMainPanel().getMainFrame() == null ) {
1504 // Must be "E" applet version.
1505 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1506 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1509 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1511 activateSaveAllIfNeeded();
1515 private void obtainDetailedTaxonomicInformation() {
1516 if ( getCurrentTreePanel() != null ) {
1517 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1518 if ( ( phy != null ) && !phy.isEmpty() ) {
1519 final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
1520 _mainpanel.getCurrentTreePanel(),
1522 new Thread( t ).start();
1527 private void obtainDetailedTaxonomicInformationDelete() {
1528 if ( getCurrentTreePanel() != null ) {
1529 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1530 if ( ( phy != null ) && !phy.isEmpty() ) {
1531 final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
1532 _mainpanel.getCurrentTreePanel(),
1535 new Thread( t ).start();
1540 private void obtainUniProtSequenceInformation() {
1541 if ( getCurrentTreePanel() != null ) {
1542 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1543 if ( ( phy != null ) && !phy.isEmpty() ) {
1544 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1545 _mainpanel.getCurrentTreePanel(),
1547 new Thread( u ).start();
1552 private void print() {
1553 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
1554 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
1557 if ( !getOptions().isPrintUsingActualSize() ) {
1558 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
1559 getOptions().getPrintSizeY() - 140,
1561 getCurrentTreePanel().resetPreferredSize();
1562 getCurrentTreePanel().repaint();
1564 final String job_name = Constants.PRG_NAME;
1565 boolean error = false;
1566 String printer_name = null;
1568 printer_name = Printer.print( getCurrentTreePanel(), job_name );
1570 catch ( final Exception e ) {
1572 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
1574 if ( !error && ( printer_name != null ) ) {
1575 String msg = "Printing data sent to printer";
1576 if ( printer_name.length() > 1 ) {
1577 msg += " [" + printer_name + "]";
1579 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
1581 if ( !getOptions().isPrintUsingActualSize() ) {
1582 getControlPanel().showWhole();
1586 private void printPhylogenyToPdf( final String file_name ) {
1587 if ( !getOptions().isPrintUsingActualSize() ) {
1588 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
1589 getOptions().getPrintSizeY(),
1591 getCurrentTreePanel().resetPreferredSize();
1592 getCurrentTreePanel().repaint();
1594 String pdf_written_to = "";
1595 boolean error = false;
1597 if ( getOptions().isPrintUsingActualSize() ) {
1598 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
1599 getCurrentTreePanel(),
1600 getCurrentTreePanel().getWidth(),
1601 getCurrentTreePanel().getHeight() );
1604 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
1605 .getPrintSizeX(), getOptions().getPrintSizeY() );
1608 catch ( final IOException e ) {
1610 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1613 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
1614 JOptionPane.showMessageDialog( this,
1615 "Wrote PDF to: " + pdf_written_to,
1617 JOptionPane.INFORMATION_MESSAGE );
1620 JOptionPane.showMessageDialog( this,
1621 "There was an unknown problem when attempting to write to PDF file: \""
1624 JOptionPane.ERROR_MESSAGE );
1627 if ( !getOptions().isPrintUsingActualSize() ) {
1628 getControlPanel().showWhole();
1632 private void addExpressionValuesFromFile() {
1633 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1634 JOptionPane.showMessageDialog( this,
1635 "Need to load evolutionary tree first",
1636 "Can Not Read Expression Values",
1637 JOptionPane.WARNING_MESSAGE );
1640 final File my_dir = getCurrentDir();
1641 if ( my_dir != null ) {
1642 _values_filechooser.setCurrentDirectory( my_dir );
1644 final int result = _values_filechooser.showOpenDialog( _contentpane );
1645 final File file = _values_filechooser.getSelectedFile();
1646 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1647 BasicTable<String> t = null;
1649 t = BasicTableParser.parse( file, "\t" );
1650 if ( t.getNumberOfColumns() < 2 ) {
1651 t = BasicTableParser.parse( file, "," );
1653 if ( t.getNumberOfColumns() < 2 ) {
1654 t = BasicTableParser.parse( file, " " );
1657 catch ( final IOException e ) {
1658 JOptionPane.showMessageDialog( this,
1660 "Could Not Read Expression Value Table",
1661 JOptionPane.ERROR_MESSAGE );
1664 if ( t.getNumberOfColumns() < 2 ) {
1665 JOptionPane.showMessageDialog( this,
1666 "Table contains " + t.getNumberOfColumns() + " column(s)",
1667 "Problem with Expression Value Table",
1668 JOptionPane.ERROR_MESSAGE );
1671 if ( t.getNumberOfRows() < 1 ) {
1672 JOptionPane.showMessageDialog( this,
1673 "Table contains zero rows",
1674 "Problem with Expression Value Table",
1675 JOptionPane.ERROR_MESSAGE );
1678 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1679 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1680 JOptionPane.showMessageDialog( this,
1681 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1682 + phy.getNumberOfExternalNodes() + " external nodes",
1684 JOptionPane.WARNING_MESSAGE );
1686 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1688 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1689 final PhylogenyNode node = iter.next();
1690 final String node_name = node.getName();
1691 if ( !ForesterUtil.isEmpty( node_name ) ) {
1694 row = t.findRow( node_name );
1696 catch ( final IllegalArgumentException e ) {
1698 .showMessageDialog( this,
1700 "Error Mapping Node Identifiers to Expression Value Identifiers",
1701 JOptionPane.ERROR_MESSAGE );
1705 if ( node.isExternal() ) {
1710 final List<Double> l = new ArrayList<Double>();
1711 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1714 d = Double.parseDouble( t.getValueAsString( col, row ) );
1716 catch ( final NumberFormatException e ) {
1717 JOptionPane.showMessageDialog( this,
1718 "Could not parse \"" + t.getValueAsString( col, row )
1719 + "\" into a decimal value",
1720 "Issue with Expression Value Table",
1721 JOptionPane.ERROR_MESSAGE );
1724 stats.addValue( d );
1727 if ( !l.isEmpty() ) {
1728 if ( node.getNodeData().getProperties() != null ) {
1729 node.getNodeData().getProperties()
1730 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1732 node.getNodeData().setVector( l );
1736 if ( not_found > 0 ) {
1737 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1738 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1740 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1744 private void readPhylogeniesFromFile() {
1745 boolean exception = false;
1746 Phylogeny[] phys = null;
1747 // Set an initial directory if none set yet
1748 final File my_dir = getCurrentDir();
1749 _open_filechooser.setMultiSelectionEnabled( true );
1750 // Open file-open dialog and set current directory
1751 if ( my_dir != null ) {
1752 _open_filechooser.setCurrentDirectory( my_dir );
1754 final int result = _open_filechooser.showOpenDialog( _contentpane );
1755 // All done: get the file
1756 final File[] files = _open_filechooser.getSelectedFiles();
1757 setCurrentDir( _open_filechooser.getCurrentDirectory() );
1758 boolean nhx_or_nexus = false;
1759 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1760 for( final File file : files ) {
1761 if ( ( file != null ) && !file.isDirectory() ) {
1762 if ( _mainpanel.getCurrentTreePanel() != null ) {
1763 _mainpanel.getCurrentTreePanel().setWaitCursor();
1766 _mainpanel.setWaitCursor();
1768 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
1769 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
1771 final NHXParser nhx = new NHXParser();
1772 setSpecialOptionsForNhxParser( nhx );
1773 phys = PhylogenyMethods.readPhylogenies( nhx, file );
1774 nhx_or_nexus = true;
1776 catch ( final Exception e ) {
1778 exceptionOccuredDuringOpenFile( e );
1781 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
1782 warnIfNotPhyloXmlValidation( getConfiguration() );
1784 final PhyloXmlParser xml_parser = createPhyloXmlParser();
1785 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
1787 catch ( final Exception e ) {
1789 exceptionOccuredDuringOpenFile( e );
1792 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
1794 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1796 catch ( final Exception e ) {
1798 exceptionOccuredDuringOpenFile( e );
1801 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
1803 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
1804 setSpecialOptionsForNexParser( nex );
1805 phys = PhylogenyMethods.readPhylogenies( nex, file );
1806 nhx_or_nexus = true;
1808 catch ( final Exception e ) {
1810 exceptionOccuredDuringOpenFile( e );
1816 final PhylogenyParser parser = ParserUtils
1817 .createParserDependingOnFileType( file, getConfiguration()
1818 .isValidatePhyloXmlAgainstSchema() );
1819 if ( parser instanceof NexusPhylogeniesParser ) {
1820 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
1821 setSpecialOptionsForNexParser( nex );
1822 nhx_or_nexus = true;
1824 else if ( parser instanceof NHXParser ) {
1825 final NHXParser nhx = ( NHXParser ) parser;
1826 setSpecialOptionsForNhxParser( nhx );
1827 nhx_or_nexus = true;
1829 else if ( parser instanceof PhyloXmlParser ) {
1830 warnIfNotPhyloXmlValidation( getConfiguration() );
1832 phys = PhylogenyMethods.readPhylogenies( parser, file );
1834 catch ( final Exception e ) {
1836 exceptionOccuredDuringOpenFile( e );
1839 if ( _mainpanel.getCurrentTreePanel() != null ) {
1840 _mainpanel.getCurrentTreePanel().setArrowCursor();
1843 _mainpanel.setArrowCursor();
1845 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
1846 boolean one_desc = false;
1847 if ( nhx_or_nexus ) {
1848 for( final Phylogeny phy : phys ) {
1849 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1850 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1852 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
1858 AptxUtil.addPhylogeniesToTabs( phys,
1860 file.getAbsolutePath(),
1863 _mainpanel.getControlPanel().showWhole();
1864 if ( nhx_or_nexus && one_desc ) {
1866 .showMessageDialog( this,
1867 "One or more trees contain (a) node(s) with one descendant, "
1868 + ForesterUtil.LINE_SEPARATOR
1869 + "possibly indicating illegal parentheses within node names.",
1870 "Warning: Possible Error in New Hampshire Formatted Data",
1871 JOptionPane.WARNING_MESSAGE );
1877 activateSaveAllIfNeeded();
1881 public void readSeqsFromFile() {
1882 // Set an initial directory if none set yet
1883 final File my_dir = getCurrentDir();
1884 _seqs_filechooser.setMultiSelectionEnabled( false );
1885 // Open file-open dialog and set current directory
1886 if ( my_dir != null ) {
1887 _seqs_filechooser.setCurrentDirectory( my_dir );
1889 final int result = _seqs_filechooser.showOpenDialog( _contentpane );
1890 // All done: get the seqs
1891 final File file = _seqs_filechooser.getSelectedFile();
1892 setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
1893 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1894 setSeqsFile( null );
1896 List<Sequence> seqs = null;
1898 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1899 seqs = FastaParser.parse( new FileInputStream( file ) );
1900 for( final Sequence seq : seqs ) {
1901 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
1908 catch ( final MsaFormatException e ) {
1910 _mainpanel.getCurrentTreePanel().setArrowCursor();
1912 catch ( final Exception ex ) {
1915 JOptionPane.showMessageDialog( this,
1916 e.getLocalizedMessage(),
1917 "Multiple sequence file format error",
1918 JOptionPane.ERROR_MESSAGE );
1921 catch ( final IOException e ) {
1923 _mainpanel.getCurrentTreePanel().setArrowCursor();
1925 catch ( final Exception ex ) {
1928 JOptionPane.showMessageDialog( this,
1929 e.getLocalizedMessage(),
1930 "Failed to read multiple sequence file",
1931 JOptionPane.ERROR_MESSAGE );
1934 catch ( final IllegalArgumentException e ) {
1936 _mainpanel.getCurrentTreePanel().setArrowCursor();
1938 catch ( final Exception ex ) {
1941 JOptionPane.showMessageDialog( this,
1942 e.getLocalizedMessage(),
1943 "Unexpected error during reading of multiple sequence file",
1944 JOptionPane.ERROR_MESSAGE );
1947 catch ( final Exception e ) {
1949 _mainpanel.getCurrentTreePanel().setArrowCursor();
1951 catch ( final Exception ex ) {
1954 e.printStackTrace();
1955 JOptionPane.showMessageDialog( this,
1956 e.getLocalizedMessage(),
1957 "Unexpected error during reading of multiple sequence file",
1958 JOptionPane.ERROR_MESSAGE );
1961 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1962 JOptionPane.showMessageDialog( this,
1963 "Multiple sequence file is empty",
1964 "Illegal multiple sequence file",
1965 JOptionPane.ERROR_MESSAGE );
1968 if ( seqs.size() < 4 ) {
1969 JOptionPane.showMessageDialog( this,
1970 "Multiple sequence file needs to contain at least 3 sequences",
1971 "Illegal multiple sequence file",
1972 JOptionPane.ERROR_MESSAGE );
1975 // if ( msa.getLength() < 2 ) {
1976 // JOptionPane.showMessageDialog( this,
1977 // "Multiple sequence alignment needs to contain at least 2 residues",
1978 // "Illegal multiple sequence file",
1979 // JOptionPane.ERROR_MESSAGE );
1983 setSeqsFile( _seqs_filechooser.getSelectedFile() );
1988 public void readMsaFromFile() {
1989 // Set an initial directory if none set yet
1990 final File my_dir = getCurrentDir();
1991 _msa_filechooser.setMultiSelectionEnabled( false );
1992 // Open file-open dialog and set current directory
1993 if ( my_dir != null ) {
1994 _msa_filechooser.setCurrentDirectory( my_dir );
1996 final int result = _msa_filechooser.showOpenDialog( _contentpane );
1997 // All done: get the msa
1998 final File file = _msa_filechooser.getSelectedFile();
1999 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
2000 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
2005 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
2006 msa = FastaParser.parseMsa( new FileInputStream( file ) );
2007 System.out.println( msa.toString() );
2010 msa = GeneralMsaParser.parse( new FileInputStream( file ) );
2013 catch ( final MsaFormatException e ) {
2015 _mainpanel.getCurrentTreePanel().setArrowCursor();
2017 catch ( final Exception ex ) {
2020 JOptionPane.showMessageDialog( this,
2021 e.getLocalizedMessage(),
2022 "Multiple sequence alignment format error",
2023 JOptionPane.ERROR_MESSAGE );
2026 catch ( final IOException e ) {
2028 _mainpanel.getCurrentTreePanel().setArrowCursor();
2030 catch ( final Exception ex ) {
2033 JOptionPane.showMessageDialog( this,
2034 e.getLocalizedMessage(),
2035 "Failed to read multiple sequence alignment",
2036 JOptionPane.ERROR_MESSAGE );
2039 catch ( final IllegalArgumentException e ) {
2041 _mainpanel.getCurrentTreePanel().setArrowCursor();
2043 catch ( final Exception ex ) {
2046 JOptionPane.showMessageDialog( this,
2047 e.getLocalizedMessage(),
2048 "Unexpected error during reading of multiple sequence alignment",
2049 JOptionPane.ERROR_MESSAGE );
2052 catch ( final Exception e ) {
2054 _mainpanel.getCurrentTreePanel().setArrowCursor();
2056 catch ( final Exception ex ) {
2059 e.printStackTrace();
2060 JOptionPane.showMessageDialog( this,
2061 e.getLocalizedMessage(),
2062 "Unexpected error during reading of multiple sequence alignment",
2063 JOptionPane.ERROR_MESSAGE );
2066 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
2067 JOptionPane.showMessageDialog( this,
2068 "Multiple sequence alignment is empty",
2069 "Illegal Multiple Sequence Alignment",
2070 JOptionPane.ERROR_MESSAGE );
2073 if ( msa.getNumberOfSequences() < 4 ) {
2074 JOptionPane.showMessageDialog( this,
2075 "Multiple sequence alignment needs to contain at least 3 sequences",
2076 "Illegal multiple sequence alignment",
2077 JOptionPane.ERROR_MESSAGE );
2080 if ( msa.getLength() < 2 ) {
2081 JOptionPane.showMessageDialog( this,
2082 "Multiple sequence alignment needs to contain at least 2 residues",
2083 "Illegal multiple sequence alignment",
2084 JOptionPane.ERROR_MESSAGE );
2088 setMsaFile( _msa_filechooser.getSelectedFile() );
2094 void readPhylogeniesFromURL() {
2096 Phylogeny[] phys = null;
2097 final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
2098 final String url_string = JOptionPane.showInputDialog( this,
2100 "Use URL/webservice to obtain a phylogeny",
2101 JOptionPane.QUESTION_MESSAGE );
2102 boolean nhx_or_nexus = false;
2103 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
2105 url = new URL( url_string );
2106 PhylogenyParser parser = null;
2107 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
2108 parser = new TolParser();
2111 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
2112 .isValidatePhyloXmlAgainstSchema() );
2114 if ( parser instanceof NexusPhylogeniesParser ) {
2115 nhx_or_nexus = true;
2117 else if ( parser instanceof NHXParser ) {
2118 nhx_or_nexus = true;
2120 if ( _mainpanel.getCurrentTreePanel() != null ) {
2121 _mainpanel.getCurrentTreePanel().setWaitCursor();
2124 _mainpanel.setWaitCursor();
2126 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2127 phys = factory.create( url.openStream(), parser );
2129 catch ( final MalformedURLException e ) {
2130 JOptionPane.showMessageDialog( this,
2131 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
2133 JOptionPane.ERROR_MESSAGE );
2135 catch ( final IOException e ) {
2136 JOptionPane.showMessageDialog( this,
2137 "Could not read from " + url + "\n"
2138 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2139 "Failed to read URL",
2140 JOptionPane.ERROR_MESSAGE );
2142 catch ( final Exception e ) {
2143 JOptionPane.showMessageDialog( this,
2144 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2145 "Unexpected Exception",
2146 JOptionPane.ERROR_MESSAGE );
2149 if ( _mainpanel.getCurrentTreePanel() != null ) {
2150 _mainpanel.getCurrentTreePanel().setArrowCursor();
2153 _mainpanel.setArrowCursor();
2156 if ( ( phys != null ) && ( phys.length > 0 ) ) {
2157 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2158 for( final Phylogeny phy : phys ) {
2159 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2162 AptxUtil.addPhylogeniesToTabs( phys,
2163 new File( url.getFile() ).getName(),
2164 new File( url.getFile() ).toString(),
2167 _mainpanel.getControlPanel().showWhole();
2170 activateSaveAllIfNeeded();
2174 private void readSpeciesTreeFromFile() {
2176 boolean exception = false;
2177 final File my_dir = getCurrentDir();
2178 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2179 if ( my_dir != null ) {
2180 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2182 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2183 final File file = _open_filechooser_for_species_tree.getSelectedFile();
2184 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2185 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2187 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2190 catch ( final Exception e ) {
2192 exceptionOccuredDuringOpenFile( e );
2195 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2197 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2200 catch ( final Exception e ) {
2202 exceptionOccuredDuringOpenFile( e );
2208 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2211 catch ( final Exception e ) {
2213 exceptionOccuredDuringOpenFile( e );
2216 if ( !exception && ( t != null ) && !t.isRooted() ) {
2219 JOptionPane.showMessageDialog( this,
2220 "Species tree is not rooted",
2221 "Species tree not loaded",
2222 JOptionPane.ERROR_MESSAGE );
2224 if ( !exception && ( t != null ) ) {
2225 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2226 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2227 final PhylogenyNode node = it.next();
2228 if ( !node.getNodeData().isHasTaxonomy() ) {
2232 .showMessageDialog( this,
2233 "Species tree contains external node(s) without taxonomy information",
2234 "Species tree not loaded",
2235 JOptionPane.ERROR_MESSAGE );
2239 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2242 JOptionPane.showMessageDialog( this,
2244 + node.getNodeData().getTaxonomy().asSimpleText()
2245 + "] is not unique in species tree",
2246 "Species tree not loaded",
2247 JOptionPane.ERROR_MESSAGE );
2251 tax_set.add( node.getNodeData().getTaxonomy() );
2256 if ( !exception && ( t != null ) ) {
2258 JOptionPane.showMessageDialog( this,
2259 "Species tree successfully loaded",
2260 "Species tree loaded",
2261 JOptionPane.INFORMATION_MESSAGE );
2263 _contentpane.repaint();
2268 private void setCurrentDir( final File current_dir ) {
2269 _current_dir = current_dir;
2272 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2273 _min_not_collapse = min_not_collapse;
2276 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2277 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2280 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2281 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2282 PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
2283 if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
2284 te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
2286 nhx.setTaxonomyExtraction( te );
2289 private void writeAllToFile() {
2290 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2293 final File my_dir = getCurrentDir();
2294 if ( my_dir != null ) {
2295 _save_filechooser.setCurrentDirectory( my_dir );
2297 _save_filechooser.setSelectedFile( new File( "" ) );
2298 final int result = _save_filechooser.showSaveDialog( _contentpane );
2299 final File file = _save_filechooser.getSelectedFile();
2300 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2301 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2302 if ( file.exists() ) {
2303 final int i = JOptionPane.showConfirmDialog( this,
2304 file + " already exists. Overwrite?",
2306 JOptionPane.OK_CANCEL_OPTION,
2307 JOptionPane.WARNING_MESSAGE );
2308 if ( i != JOptionPane.OK_OPTION ) {
2315 catch ( final Exception e ) {
2316 JOptionPane.showMessageDialog( this,
2317 "Failed to delete: " + file,
2319 JOptionPane.WARNING_MESSAGE );
2323 final int count = getMainPanel().getTabbedPane().getTabCount();
2324 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2325 for( int i = 0; i < count; ++i ) {
2326 trees.add( getMainPanel().getPhylogeny( i ) );
2327 getMainPanel().getTreePanels().get( i ).setEdited( false );
2329 final PhylogenyWriter writer = new PhylogenyWriter();
2331 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2333 catch ( final IOException e ) {
2334 JOptionPane.showMessageDialog( this,
2335 "Failed to write to: " + file,
2337 JOptionPane.WARNING_MESSAGE );
2342 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2344 final PhylogenyWriter writer = new PhylogenyWriter();
2345 writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2347 catch ( final Exception e ) {
2349 exceptionOccuredDuringSaveAs( e );
2354 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2356 final PhylogenyWriter writer = new PhylogenyWriter();
2357 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2359 catch ( final Exception e ) {
2361 exceptionOccuredDuringSaveAs( e );
2366 private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
2368 final PhylogenyWriter writer = new PhylogenyWriter();
2369 writer.toNewHampshireX( t, file );
2371 catch ( final Exception e ) {
2373 exceptionOccuredDuringSaveAs( e );
2378 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2380 final PhylogenyWriter writer = new PhylogenyWriter();
2381 writer.toPhyloXML( file, t, 0 );
2383 catch ( final Exception e ) {
2385 exceptionOccuredDuringSaveAs( e );
2390 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
2391 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
2392 _mainpanel.getCurrentTreePanel().getHeight(),
2394 String file_written_to = "";
2395 boolean error = false;
2397 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
2398 _mainpanel.getCurrentTreePanel().getWidth(),
2399 _mainpanel.getCurrentTreePanel().getHeight(),
2400 _mainpanel.getCurrentTreePanel(),
2401 _mainpanel.getControlPanel(),
2405 catch ( final IOException e ) {
2407 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2410 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
2411 JOptionPane.showMessageDialog( this,
2412 "Wrote image to: " + file_written_to,
2414 JOptionPane.INFORMATION_MESSAGE );
2417 JOptionPane.showMessageDialog( this,
2418 "There was an unknown problem when attempting to write to an image file: \""
2421 JOptionPane.ERROR_MESSAGE );
2424 _contentpane.repaint();
2427 private void writeToFile( final Phylogeny t ) {
2431 String initial_filename = null;
2432 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2434 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2436 catch ( final IOException e ) {
2437 initial_filename = null;
2440 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2441 _save_filechooser.setSelectedFile( new File( initial_filename ) );
2444 _save_filechooser.setSelectedFile( new File( "" ) );
2446 final File my_dir = getCurrentDir();
2447 if ( my_dir != null ) {
2448 _save_filechooser.setCurrentDirectory( my_dir );
2450 final int result = _save_filechooser.showSaveDialog( _contentpane );
2451 final File file = _save_filechooser.getSelectedFile();
2452 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2453 boolean exception = false;
2454 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2455 if ( file.exists() ) {
2456 final int i = JOptionPane.showConfirmDialog( this,
2457 file + " already exists.\nOverwrite?",
2459 JOptionPane.OK_CANCEL_OPTION,
2460 JOptionPane.QUESTION_MESSAGE );
2461 if ( i != JOptionPane.OK_OPTION ) {
2465 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2467 ForesterUtil.copyFile( file, to );
2469 catch ( final Exception e ) {
2470 JOptionPane.showMessageDialog( this,
2471 "Failed to create backup copy " + to,
2472 "Failed to Create Backup Copy",
2473 JOptionPane.WARNING_MESSAGE );
2478 catch ( final Exception e ) {
2479 JOptionPane.showMessageDialog( this,
2480 "Failed to delete: " + file,
2482 JOptionPane.WARNING_MESSAGE );
2486 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2487 exception = writeAsNewHampshire( t, exception, file );
2489 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
2490 exception = writeAsNHX( t, exception, file );
2492 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2493 exception = writeAsPhyloXml( t, exception, file );
2495 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2496 exception = writeAsNexus( t, exception, file );
2500 final String file_name = file.getName().trim().toLowerCase();
2501 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2502 || file_name.endsWith( ".tree" ) ) {
2503 exception = writeAsNewHampshire( t, exception, file );
2505 else if ( file_name.endsWith( ".nhx" ) ) {
2506 exception = writeAsNHX( t, exception, file );
2508 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2509 exception = writeAsNexus( t, exception, file );
2513 exception = writeAsPhyloXml( t, exception, file );
2517 getMainPanel().setTitleOfSelectedTab( file.getName() );
2518 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2519 getMainPanel().getCurrentTreePanel().setEdited( false );
2524 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2525 if ( ( t == null ) || t.isEmpty() ) {
2528 String initial_filename = "";
2529 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2530 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2532 if ( initial_filename.indexOf( '.' ) > 0 ) {
2533 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2535 initial_filename = initial_filename + "." + type;
2536 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2537 final File my_dir = getCurrentDir();
2538 if ( my_dir != null ) {
2539 _writetographics_filechooser.setCurrentDirectory( my_dir );
2541 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2542 File file = _writetographics_filechooser.getSelectedFile();
2543 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2544 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2545 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2546 file = new File( file.toString() + "." + type );
2548 if ( file.exists() ) {
2549 final int i = JOptionPane.showConfirmDialog( this,
2550 file + " already exists. Overwrite?",
2552 JOptionPane.OK_CANCEL_OPTION,
2553 JOptionPane.WARNING_MESSAGE );
2554 if ( i != JOptionPane.OK_OPTION ) {
2561 catch ( final Exception e ) {
2562 JOptionPane.showMessageDialog( this,
2563 "Failed to delete: " + file,
2565 JOptionPane.WARNING_MESSAGE );
2569 writePhylogenyToGraphicsFile( file.toString(), type );
2573 private void writeToPdf( final Phylogeny t ) {
2574 if ( ( t == null ) || t.isEmpty() ) {
2577 String initial_filename = "";
2578 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2579 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2581 if ( initial_filename.indexOf( '.' ) > 0 ) {
2582 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2584 initial_filename = initial_filename + ".pdf";
2585 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2586 final File my_dir = getCurrentDir();
2587 if ( my_dir != null ) {
2588 _writetopdf_filechooser.setCurrentDirectory( my_dir );
2590 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2591 File file = _writetopdf_filechooser.getSelectedFile();
2592 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2593 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2594 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2595 file = new File( file.toString() + ".pdf" );
2597 if ( file.exists() ) {
2598 final int i = JOptionPane.showConfirmDialog( this,
2599 file + " already exists. Overwrite?",
2601 JOptionPane.OK_CANCEL_OPTION,
2602 JOptionPane.WARNING_MESSAGE );
2603 if ( i != JOptionPane.OK_OPTION ) {
2607 printPhylogenyToPdf( file.toString() );
2611 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2612 return new MainFrameApplication( phys, config, title );
2615 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2616 return new MainFrameApplication( phys, config );
2619 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2620 return new MainFrameApplication( phys, config_file_name, title );
2623 public static MainFrame createInstance( final Phylogeny[] phys,
2624 final Configuration config,
2626 final File current_dir ) {
2627 return new MainFrameApplication( phys, config, title, current_dir );
2630 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2631 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2632 + o.getPrintSizeY() + ")" );
2635 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2636 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2639 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2640 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2642 .showMessageDialog( null,
2644 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2647 JOptionPane.WARNING_MESSAGE );
2651 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2652 _phylogenetic_inference_options = phylogenetic_inference_options;
2655 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
2656 if ( _phylogenetic_inference_options == null ) {
2657 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
2659 return _phylogenetic_inference_options;
2662 public Msa getMsa() {
2666 void setMsa( final Msa msa ) {
2670 void setMsaFile( final File msa_file ) {
2671 _msa_file = msa_file;
2674 public File getMsaFile() {
2678 public List<Sequence> getSeqs() {
2682 void setSeqs( final List<Sequence> seqs ) {
2686 void setSeqsFile( final File seqs_file ) {
2687 _seqs_file = seqs_file;
2690 public File getSeqsFile() {
2693 } // MainFrameApplication.
2695 class NexusFilter extends FileFilter {
2698 public boolean accept( final File f ) {
2699 final String file_name = f.getName().trim().toLowerCase();
2700 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2701 || file_name.endsWith( ".tre" ) || f.isDirectory();
2705 public String getDescription() {
2706 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2710 class NHFilter extends FileFilter {
2713 public boolean accept( final File f ) {
2714 final String file_name = f.getName().trim().toLowerCase();
2715 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2716 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2717 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2722 public String getDescription() {
2723 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2727 class NHXFilter extends FileFilter {
2730 public boolean accept( final File f ) {
2731 final String file_name = f.getName().trim().toLowerCase();
2732 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2736 public String getDescription() {
2737 return "NHX files (*.nhx)";
2741 class PdfFilter extends FileFilter {
2744 public boolean accept( final File f ) {
2745 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2749 public String getDescription() {
2750 return "PDF files (*.pdf)";
2754 class TolFilter extends FileFilter {
2757 public boolean accept( final File f ) {
2758 final String file_name = f.getName().trim().toLowerCase();
2759 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2760 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2764 public String getDescription() {
2765 return "Tree of Life files (*.tol, *.tolxml)";
2769 class XMLFilter extends FileFilter {
2772 public boolean accept( final File f ) {
2773 final String file_name = f.getName().trim().toLowerCase();
2774 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2775 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2779 public String getDescription() {
2780 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";