2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/forester
27 package org.forester.archaeopteryx;
29 import java.awt.BorderLayout;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.ComponentAdapter;
33 import java.awt.event.ComponentEvent;
34 import java.awt.event.WindowAdapter;
35 import java.awt.event.WindowEvent;
37 import java.io.FileInputStream;
38 import java.io.IOException;
39 import java.io.InputStream;
40 import java.net.MalformedURLException;
42 import java.util.ArrayList;
43 import java.util.HashSet;
44 import java.util.List;
47 import javax.swing.ButtonGroup;
48 import javax.swing.JCheckBoxMenuItem;
49 import javax.swing.JFileChooser;
50 import javax.swing.JMenu;
51 import javax.swing.JMenuBar;
52 import javax.swing.JMenuItem;
53 import javax.swing.JOptionPane;
54 import javax.swing.JRadioButtonMenuItem;
55 import javax.swing.UIManager;
56 import javax.swing.UnsupportedLookAndFeelException;
57 import javax.swing.WindowConstants;
58 import javax.swing.event.ChangeEvent;
59 import javax.swing.event.ChangeListener;
60 import javax.swing.filechooser.FileFilter;
61 import javax.swing.plaf.synth.SynthLookAndFeel;
63 import org.forester.analysis.TaxonomyDataManager;
64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
69 import org.forester.archaeopteryx.tools.GoAnnotation;
70 import org.forester.archaeopteryx.tools.InferenceManager;
71 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
72 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
73 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
74 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
75 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
76 import org.forester.archaeopteryx.webservices.WebservicesManager;
77 import org.forester.io.parsers.FastaParser;
78 import org.forester.io.parsers.GeneralMsaParser;
79 import org.forester.io.parsers.PhylogenyParser;
80 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
81 import org.forester.io.parsers.nhx.NHXParser;
82 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
83 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
84 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
85 import org.forester.io.parsers.tol.TolParser;
86 import org.forester.io.parsers.util.ParserUtils;
87 import org.forester.io.writers.PhylogenyWriter;
88 import org.forester.io.writers.SequenceWriter;
89 import org.forester.msa.Msa;
90 import org.forester.msa.MsaFormatException;
91 import org.forester.phylogeny.Phylogeny;
92 import org.forester.phylogeny.PhylogenyMethods;
93 import org.forester.phylogeny.PhylogenyNode;
94 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
95 import org.forester.phylogeny.data.Confidence;
96 import org.forester.phylogeny.data.Taxonomy;
97 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
98 import org.forester.phylogeny.factories.PhylogenyFactory;
99 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
100 import org.forester.sdi.GSDI;
101 import org.forester.sdi.SDIR;
102 import org.forester.sequence.Sequence;
103 import org.forester.util.BasicDescriptiveStatistics;
104 import org.forester.util.BasicTable;
105 import org.forester.util.BasicTableParser;
106 import org.forester.util.DescriptiveStatistics;
107 import org.forester.util.ForesterUtil;
108 import org.forester.util.WindowsUtils;
110 class DefaultFilter extends FileFilter {
113 public boolean accept( final File f ) {
114 final String file_name = f.getName().trim().toLowerCase();
115 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
116 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
117 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
118 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
119 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
120 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
121 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
122 || file_name.endsWith( ".con" ) || f.isDirectory();
126 public String getDescription() {
127 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
131 class GraphicsFileFilter extends FileFilter {
134 public boolean accept( final File f ) {
135 final String file_name = f.getName().trim().toLowerCase();
136 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
137 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
141 public String getDescription() {
142 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
146 class MsaFileFilter extends FileFilter {
149 public boolean accept( final File f ) {
150 final String file_name = f.getName().trim().toLowerCase();
151 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
152 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
156 public String getDescription() {
157 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
161 class SequencesFileFilter extends FileFilter {
164 public boolean accept( final File f ) {
165 final String file_name = f.getName().trim().toLowerCase();
166 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
167 || file_name.endsWith( ".seqs" ) || f.isDirectory();
171 public String getDescription() {
172 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
176 public final class MainFrameApplication extends MainFrame {
178 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
179 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
180 private final static int FRAME_X_SIZE = 800;
181 private final static int FRAME_Y_SIZE = 800;
182 // Filters for the file-open dialog (classes defined in this file)
183 private final static NHFilter nhfilter = new NHFilter();
184 private final static NHXFilter nhxfilter = new NHXFilter();
185 private final static XMLFilter xmlfilter = new XMLFilter();
186 private final static TolFilter tolfilter = new TolFilter();
187 private final static NexusFilter nexusfilter = new NexusFilter();
188 private final static PdfFilter pdffilter = new PdfFilter();
189 private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
190 private final static MsaFileFilter msafilter = new MsaFileFilter();
191 private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
192 private final static DefaultFilter defaultfilter = new DefaultFilter();
193 private static final long serialVersionUID = -799735726778865234L;
194 private final JFileChooser _values_filechooser;
195 private final JFileChooser _open_filechooser;
196 private final JFileChooser _msa_filechooser;
197 private final JFileChooser _seqs_filechooser;
198 private final JFileChooser _open_filechooser_for_species_tree;
199 private final JFileChooser _save_filechooser;
200 private final JFileChooser _writetopdf_filechooser;
201 private final JFileChooser _writetographics_filechooser;
203 private JMenu _analysis_menu;
204 private JMenuItem _load_species_tree_item;
205 private JMenuItem _gsdi_item;
206 private JMenuItem _root_min_dups_item;
207 private JMenuItem _root_min_cost_l_item;
208 private JMenuItem _lineage_inference;
209 private JMenuItem _function_analysis;
210 // Application-only print menu items
211 private JMenuItem _print_item;
212 private JMenuItem _write_to_pdf_item;
213 private JMenuItem _write_to_jpg_item;
214 private JMenuItem _write_to_gif_item;
215 private JMenuItem _write_to_tif_item;
216 private JMenuItem _write_to_png_item;
217 private JMenuItem _write_to_bmp_item;
218 private Phylogeny _species_tree;
219 private File _current_dir;
220 private ButtonGroup _radio_group_1;
222 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
223 // Phylogeny Inference menu
224 private JMenu _inference_menu;
225 private JMenuItem _inference_from_msa_item;
226 private JMenuItem _inference_from_seqs_item;
227 // Phylogeny Inference
228 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
229 private Msa _msa = null;
230 private File _msa_file = null;
231 private List<Sequence> _seqs = null;
232 private File _seqs_file = null;
233 // expression values menu:
234 JMenuItem _read_values_jmi;
236 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
237 this( phys, config, title, null );
240 private MainFrameApplication( final Phylogeny[] phys,
241 final Configuration config,
243 final File current_dir ) {
245 _configuration = config;
246 if ( _configuration == null ) {
247 throw new IllegalArgumentException( "configuration is null" );
250 boolean synth_exception = false;
251 if ( Constants.__SYNTH_LF ) {
253 final SynthLookAndFeel synth = new SynthLookAndFeel();
254 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
255 MainFrameApplication.class );
256 UIManager.setLookAndFeel( synth );
258 catch ( final Exception ex ) {
259 synth_exception = true;
260 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
261 "could not create synth look and feel: "
262 + ex.getLocalizedMessage() );
265 if ( !Constants.__SYNTH_LF || synth_exception ) {
266 if ( _configuration.isUseNativeUI() ) {
267 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
270 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
273 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
275 catch ( final UnsupportedLookAndFeelException e ) {
276 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
278 catch ( final ClassNotFoundException e ) {
279 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
281 catch ( final InstantiationException e ) {
282 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
284 catch ( final IllegalAccessException e ) {
285 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
287 catch ( final Exception e ) {
288 AptxUtil.dieWithSystemError( e.toString() );
290 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
291 setCurrentDir( current_dir );
293 // hide until everything is ready
295 setOptions( Options.createInstance( _configuration ) );
296 setInferenceManager( InferenceManager.createInstance( _configuration ) );
297 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
298 // _textframe = null; #~~~~
299 _species_tree = null;
301 setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
302 _mainpanel = new MainPanel( _configuration, this );
304 _open_filechooser = new JFileChooser();
305 _open_filechooser.setCurrentDirectory( new File( "." ) );
306 _open_filechooser.setMultiSelectionEnabled( false );
307 _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
308 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
309 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
310 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
311 _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
312 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
313 _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
314 _open_filechooser_for_species_tree = new JFileChooser();
315 _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
316 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
317 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
318 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
319 _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
320 _save_filechooser = new JFileChooser();
321 _save_filechooser.setCurrentDirectory( new File( "." ) );
322 _save_filechooser.setMultiSelectionEnabled( false );
323 _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
324 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
325 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
326 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
327 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
328 _writetopdf_filechooser = new JFileChooser();
329 _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
330 _writetographics_filechooser = new JFileChooser();
331 _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
333 _msa_filechooser = new JFileChooser();
334 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
335 _msa_filechooser.setCurrentDirectory( new File( "." ) );
336 _msa_filechooser.setMultiSelectionEnabled( false );
337 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
338 _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
340 _seqs_filechooser = new JFileChooser();
341 _seqs_filechooser.setName( "Read Sequences File" );
342 _seqs_filechooser.setCurrentDirectory( new File( "." ) );
343 _seqs_filechooser.setMultiSelectionEnabled( false );
344 _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() );
345 _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
347 _values_filechooser = new JFileChooser();
348 _values_filechooser.setCurrentDirectory( new File( "." ) );
349 _values_filechooser.setMultiSelectionEnabled( false );
350 // build the menu bar
351 _jmenubar = new JMenuBar();
352 if ( !_configuration.isUseNativeUI() ) {
353 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
356 if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
357 buildPhylogeneticInferenceMenu();
366 setJMenuBar( _jmenubar );
367 _jmenubar.add( _help_jmenu );
368 _contentpane = getContentPane();
369 _contentpane.setLayout( new BorderLayout() );
370 _contentpane.add( _mainpanel, BorderLayout.CENTER );
372 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
373 // addWindowFocusListener( new WindowAdapter() {
376 // public void windowGainedFocus( WindowEvent e ) {
377 // requestFocusInWindow();
380 // The window listener
381 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
382 addWindowListener( new WindowAdapter() {
385 public void windowClosing( final WindowEvent e ) {
386 if ( isUnsavedDataPresent() ) {
387 final int r = JOptionPane.showConfirmDialog( null,
388 "Exit despite potentially unsaved changes?",
390 JOptionPane.YES_NO_OPTION );
391 if ( r != JOptionPane.YES_OPTION ) {
396 final int r = JOptionPane.showConfirmDialog( null,
397 "Exit Archaeopteryx?",
399 JOptionPane.YES_NO_OPTION );
400 if ( r != JOptionPane.YES_OPTION ) {
407 // The component listener
408 addComponentListener( new ComponentAdapter() {
411 public void componentResized( final ComponentEvent e ) {
412 if ( _mainpanel.getCurrentTreePanel() != null ) {
413 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
415 _mainpanel.getCurrentTreePanel()
421 requestFocusInWindow();
422 // addKeyListener( this );
424 if ( ( phys != null ) && ( phys.length > 0 ) ) {
425 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
427 getMainPanel().getControlPanel().showWholeAll();
428 getMainPanel().getControlPanel().showWhole();
430 activateSaveAllIfNeeded();
431 // ...and its children
432 _contentpane.repaint();
436 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
437 _configuration = config;
438 if ( _configuration == null ) {
439 throw new IllegalArgumentException( "configuration is null" );
442 setOptions( Options.createInstance( _configuration ) );
443 _mainpanel = new MainPanel( _configuration, this );
444 _open_filechooser = null;
445 _open_filechooser_for_species_tree = null;
446 _save_filechooser = null;
447 _writetopdf_filechooser = null;
448 _writetographics_filechooser = null;
449 _msa_filechooser = null;
450 _seqs_filechooser = null;
451 _values_filechooser = null;
452 _jmenubar = new JMenuBar();
455 _contentpane = getContentPane();
456 _contentpane.setLayout( new BorderLayout() );
457 _contentpane.add( _mainpanel, BorderLayout.CENTER );
459 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
460 // The window listener
461 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
462 addWindowListener( new WindowAdapter() {
465 public void windowClosing( final WindowEvent e ) {
469 // setVisible( true );
470 if ( ( phys != null ) && ( phys.length > 0 ) ) {
471 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
473 getMainPanel().getControlPanel().showWholeAll();
474 getMainPanel().getControlPanel().showWhole();
476 //activateSaveAllIfNeeded();
477 // ...and its children
478 _contentpane.repaint();
481 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
482 // Reads the config file (false, false => not url, not applet):
483 this( phys, new Configuration( config_file, false, false, true ), title );
487 public void actionPerformed( final ActionEvent e ) {
489 super.actionPerformed( e );
490 final Object o = e.getSource();
491 // Handle app-specific actions here:
492 if ( o == _open_item ) {
493 readPhylogeniesFromFile();
495 else if ( o == _save_item ) {
496 writeToFile( _mainpanel.getCurrentPhylogeny() );
497 // If subtree currently displayed, save it, instead of complete
500 else if ( o == _new_item ) {
503 else if ( o == _save_all_item ) {
506 else if ( o == _close_item ) {
509 else if ( o == _write_to_pdf_item ) {
510 writeToPdf( _mainpanel.getCurrentPhylogeny() );
512 else if ( o == _write_to_jpg_item ) {
513 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
515 else if ( o == _write_to_png_item ) {
516 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
518 else if ( o == _write_to_gif_item ) {
519 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
521 else if ( o == _write_to_tif_item ) {
522 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
524 else if ( o == _write_to_bmp_item ) {
525 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
527 else if ( o == _print_item ) {
530 else if ( o == _load_species_tree_item ) {
531 readSpeciesTreeFromFile();
533 else if ( o == _lineage_inference ) {
534 if ( isSubtreeDisplayed() ) {
535 JOptionPane.showMessageDialog( this,
537 "Cannot infer ancestral taxonomies",
538 JOptionPane.ERROR_MESSAGE );
541 executeLineageInference();
543 else if ( o == _function_analysis ) {
544 executeFunctionAnalysis();
546 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
547 if ( isSubtreeDisplayed() ) {
550 obtainDetailedTaxonomicInformation();
552 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
553 if ( isSubtreeDisplayed() ) {
556 obtainDetailedTaxonomicInformationDelete();
558 else if ( o == _obtain_seq_information_jmi ) {
559 obtainSequenceInformation();
561 else if ( o == _read_values_jmi ) {
562 if ( isSubtreeDisplayed() ) {
565 addExpressionValuesFromFile();
567 else if ( o == _move_node_names_to_tax_sn_jmi ) {
568 moveNodeNamesToTaxSn();
570 else if ( o == _move_node_names_to_seq_names_jmi ) {
571 moveNodeNamesToSeqNames();
573 else if ( o == _extract_tax_code_from_node_names_jmi ) {
574 extractTaxCodeFromNodeNames();
576 else if ( o == _gsdi_item ) {
577 if ( isSubtreeDisplayed() ) {
582 else if ( o == _root_min_dups_item ) {
583 if ( isSubtreeDisplayed() ) {
586 executeSDIR( false );
588 else if ( o == _root_min_cost_l_item ) {
589 if ( isSubtreeDisplayed() ) {
594 else if ( o == _graphics_export_visible_only_cbmi ) {
595 updateOptions( getOptions() );
597 else if ( o == _antialias_print_cbmi ) {
598 updateOptions( getOptions() );
600 else if ( o == _print_black_and_white_cbmi ) {
601 updateOptions( getOptions() );
603 else if ( o == _print_using_actual_size_cbmi ) {
604 updateOptions( getOptions() );
606 else if ( o == _graphics_export_using_actual_size_cbmi ) {
607 updateOptions( getOptions() );
609 else if ( o == _print_size_mi ) {
612 else if ( o == _choose_pdf_width_mi ) {
615 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
616 updateOptions( getOptions() );
618 else if ( o == _replace_underscores_cbmi ) {
619 if ( ( _extract_pfam_style_tax_codes_cbmi != null ) && _replace_underscores_cbmi.isSelected() ) {
620 _extract_pfam_style_tax_codes_cbmi.setSelected( false );
622 updateOptions( getOptions() );
624 else if ( o == _collapse_below_threshold ) {
625 if ( isSubtreeDisplayed() ) {
628 collapseBelowThreshold();
630 else if ( o == _extract_pfam_style_tax_codes_cbmi ) {
631 if ( ( _replace_underscores_cbmi != null ) && _extract_pfam_style_tax_codes_cbmi.isSelected() ) {
632 _replace_underscores_cbmi.setSelected( false );
634 updateOptions( getOptions() );
636 else if ( o == _inference_from_msa_item ) {
637 executePhyleneticInference( false );
639 else if ( o == _inference_from_seqs_item ) {
640 executePhyleneticInference( true );
642 _contentpane.repaint();
644 catch ( final Exception ex ) {
645 AptxUtil.unexpectedException( ex );
647 catch ( final Error err ) {
648 AptxUtil.unexpectedError( err );
652 void buildAnalysisMenu() {
653 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
654 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
655 _analysis_menu.addSeparator();
656 _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
657 _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
658 _analysis_menu.addSeparator();
659 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
660 customizeJMenuItem( _gsdi_item );
661 customizeJMenuItem( _root_min_dups_item );
662 customizeJMenuItem( _root_min_cost_l_item );
663 customizeJMenuItem( _load_species_tree_item );
664 _analysis_menu.addSeparator();
665 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
666 customizeJMenuItem( _lineage_inference );
667 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
668 _jmenubar.add( _analysis_menu );
671 void buildPhylogeneticInferenceMenu() {
672 final InferenceManager im = getInferenceManager();
673 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
674 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
675 customizeJMenuItem( _inference_from_msa_item );
676 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
677 if ( im.canDoMsa() ) {
678 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
679 customizeJMenuItem( _inference_from_seqs_item );
680 _inference_from_seqs_item
681 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
685 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
686 customizeJMenuItem( _inference_from_seqs_item );
687 _inference_from_seqs_item.setEnabled( false );
689 _jmenubar.add( _inference_menu );
693 void buildFileMenu() {
694 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
695 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
696 _file_jmenu.addSeparator();
697 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
698 _file_jmenu.addSeparator();
699 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
700 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
701 .getAvailablePhylogeniesWebserviceClients().size() ];
702 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
703 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
704 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
705 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
707 if ( getConfiguration().isEditable() ) {
708 _file_jmenu.addSeparator();
709 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
710 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
712 _file_jmenu.addSeparator();
713 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
714 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
715 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
716 _save_all_item.setEnabled( false );
717 _file_jmenu.addSeparator();
718 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
719 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
720 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
722 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
723 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
724 if ( AptxUtil.canWriteFormat( "gif" ) ) {
725 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
727 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
728 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
730 _file_jmenu.addSeparator();
731 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
732 _file_jmenu.addSeparator();
733 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
734 _close_item.setToolTipText( "To close the current pane." );
735 _close_item.setEnabled( true );
736 _file_jmenu.addSeparator();
737 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
738 // For print in color option item
739 customizeJMenuItem( _open_item );
741 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
742 customizeJMenuItem( _open_url_item );
743 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
744 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
746 customizeJMenuItem( _save_item );
747 if ( getConfiguration().isEditable() ) {
748 customizeJMenuItem( _new_item );
750 customizeJMenuItem( _close_item );
751 customizeJMenuItem( _save_all_item );
752 customizeJMenuItem( _write_to_pdf_item );
753 customizeJMenuItem( _write_to_png_item );
754 customizeJMenuItem( _write_to_jpg_item );
755 customizeJMenuItem( _write_to_gif_item );
756 customizeJMenuItem( _write_to_tif_item );
757 customizeJMenuItem( _write_to_bmp_item );
758 customizeJMenuItem( _print_item );
759 customizeJMenuItem( _exit_item );
760 _jmenubar.add( _file_jmenu );
763 void buildOptionsMenu() {
764 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
765 _options_jmenu.addChangeListener( new ChangeListener() {
768 public void stateChanged( final ChangeEvent e ) {
769 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
770 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
772 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
773 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
774 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
775 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
776 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
777 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
779 _show_branch_length_values_cbmi,
780 _non_lined_up_cladograms_rbmi,
781 _uniform_cladograms_rbmi,
782 _ext_node_dependent_cladogram_rbmi,
783 _label_direction_cbmi );
784 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
785 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
786 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
789 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
791 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
792 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
793 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
794 _radio_group_1 = new ButtonGroup();
795 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
796 _radio_group_1.add( _uniform_cladograms_rbmi );
797 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
798 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
799 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
801 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
802 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
803 _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
805 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
806 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
807 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
808 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
809 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
810 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
811 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
812 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
813 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
814 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
815 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
816 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
817 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
819 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
820 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
821 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
822 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
823 _options_jmenu.addSeparator();
824 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
825 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
826 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
827 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
828 _options_jmenu.addSeparator();
829 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
830 getConfiguration() ) );
831 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
832 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
834 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
836 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
838 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
839 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
840 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
841 _options_jmenu.addSeparator();
842 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
844 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
845 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
847 .add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
848 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
850 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
851 _use_brackets_for_conf_in_nh_export_cbmi
852 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
854 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
855 customizeJMenuItem( _choose_font_mi );
856 customizeJMenuItem( _choose_minimal_confidence_mi );
857 customizeJMenuItem( _switch_colors_mi );
858 customizeJMenuItem( _print_size_mi );
859 customizeJMenuItem( _choose_pdf_width_mi );
860 customizeJMenuItem( _overview_placment_mi );
861 customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
862 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
863 customizeJMenuItem( _cycle_node_shape_mi );
864 customizeJMenuItem( _cycle_node_fill_mi );
865 customizeJMenuItem( _choose_node_size_mi );
866 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
867 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
868 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
869 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
870 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
871 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
872 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
873 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
874 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
875 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
876 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
877 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
878 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
879 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
880 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
881 customizeCheckBoxMenuItem( _label_direction_cbmi,
882 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
883 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
884 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
885 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
886 .isInternalNumberAreConfidenceForNhParsing() );
887 customizeCheckBoxMenuItem( _extract_pfam_style_tax_codes_cbmi, getOptions()
888 .isExtractPfamTaxonomyCodesInNhParsing() );
889 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
890 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
891 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
892 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
893 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
894 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
895 .isGraphicsExportUsingActualSize() );
896 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
897 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
898 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
899 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
900 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
901 _jmenubar.add( _options_jmenu );
904 void buildToolsMenu() {
905 _tools_menu = createMenu( "Tools", getConfiguration() );
906 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
907 customizeJMenuItem( _confcolor_item );
908 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
909 customizeJMenuItem( _color_rank_jmi );
910 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
911 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
912 customizeJMenuItem( _taxcolor_item );
913 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
914 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
915 customizeJMenuItem( _remove_branch_color_item );
916 _tools_menu.addSeparator();
917 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
918 customizeJMenuItem( _annotate_item );
919 _tools_menu.addSeparator();
920 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
921 customizeJMenuItem( _midpoint_root_item );
922 _tools_menu.addSeparator();
923 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
924 customizeJMenuItem( _collapse_species_specific_subtrees );
926 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
927 customizeJMenuItem( _collapse_below_threshold );
928 _collapse_below_threshold
929 .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)" );
930 _tools_menu.addSeparator();
932 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
933 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
934 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
935 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
936 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
937 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
939 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes from Node Names" ) );
940 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
941 _extract_tax_code_from_node_names_jmi
942 .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" );
943 _tools_menu.addSeparator();
945 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
946 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
947 _obtain_detailed_taxonomic_information_jmi
948 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
950 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
951 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
952 _obtain_detailed_taxonomic_information_deleting_jmi
953 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
954 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
955 customizeJMenuItem( _obtain_seq_information_jmi );
956 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
957 _tools_menu.addSeparator();
958 if ( !Constants.__RELEASE ) {
959 _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
960 customizeJMenuItem( _function_analysis );
962 .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
963 _tools_menu.addSeparator();
965 _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
966 customizeJMenuItem( _read_values_jmi );
967 _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
968 _jmenubar.add( _tools_menu );
971 private void choosePdfWidth() {
972 final String s = ( String ) JOptionPane.showInputDialog( this,
973 "Please enter the default line width for PDF export.\n"
975 + getOptions().getPrintLineWidth() + "]\n",
976 "Line Width for PDF Export",
977 JOptionPane.QUESTION_MESSAGE,
980 getOptions().getPrintLineWidth() );
981 if ( !ForesterUtil.isEmpty( s ) ) {
982 boolean success = true;
984 final String m_str = s.trim();
985 if ( !ForesterUtil.isEmpty( m_str ) ) {
987 f = Float.parseFloat( m_str );
989 catch ( final Exception ex ) {
996 if ( success && ( f > 0.0 ) ) {
997 getOptions().setPrintLineWidth( f );
1002 private void choosePrintSize() {
1003 final String s = ( String ) JOptionPane.showInputDialog( this,
1004 "Please enter values for width and height,\nseparated by a comma.\n"
1005 + "[current values: "
1006 + getOptions().getPrintSizeX() + ", "
1007 + getOptions().getPrintSizeY() + "]\n"
1008 + "[A4: " + Constants.A4_SIZE_X + ", "
1009 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1010 + Constants.US_LETTER_SIZE_X + ", "
1011 + Constants.US_LETTER_SIZE_Y + "]",
1012 "Default Size for Graphics Export",
1013 JOptionPane.QUESTION_MESSAGE,
1016 getOptions().getPrintSizeX() + ", "
1017 + getOptions().getPrintSizeY() );
1018 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1019 boolean success = true;
1022 final String[] str_ary = s.split( "," );
1023 if ( str_ary.length == 2 ) {
1024 final String x_str = str_ary[ 0 ].trim();
1025 final String y_str = str_ary[ 1 ].trim();
1026 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1028 x = Integer.parseInt( x_str );
1029 y = Integer.parseInt( y_str );
1031 catch ( final Exception ex ) {
1042 if ( success && ( x > 1 ) && ( y > 1 ) ) {
1043 getOptions().setPrintSizeX( x );
1044 getOptions().setPrintSizeY( y );
1051 if ( isUnsavedDataPresent() ) {
1052 final int r = JOptionPane.showConfirmDialog( this,
1053 "Exit despite potentially unsaved changes?",
1055 JOptionPane.YES_NO_OPTION );
1056 if ( r != JOptionPane.YES_OPTION ) {
1063 private void closeCurrentPane() {
1064 if ( getMainPanel().getCurrentTreePanel() != null ) {
1065 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1066 final int r = JOptionPane.showConfirmDialog( this,
1067 "Close tab despite potentially unsaved changes?",
1069 JOptionPane.YES_NO_OPTION );
1070 if ( r != JOptionPane.YES_OPTION ) {
1074 getMainPanel().closeCurrentPane();
1075 activateSaveAllIfNeeded();
1079 private void collapse( final Phylogeny phy, final double m ) {
1080 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1081 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1082 double min_support = Double.MAX_VALUE;
1083 boolean conf_present = false;
1084 while ( it.hasNext() ) {
1085 final PhylogenyNode n = it.next();
1086 if ( !n.isExternal() && !n.isRoot() ) {
1087 final List<Confidence> c = n.getBranchData().getConfidences();
1088 if ( ( c != null ) && ( c.size() > 0 ) ) {
1089 conf_present = true;
1091 for( final Confidence confidence : c ) {
1092 if ( confidence.getValue() > max ) {
1093 max = confidence.getValue();
1096 if ( max < getMinNotCollapseConfidenceValue() ) {
1097 to_be_removed.add( n );
1099 if ( max < min_support ) {
1105 if ( conf_present ) {
1106 for( final PhylogenyNode node : to_be_removed ) {
1107 PhylogenyMethods.removeNode( node, phy );
1109 if ( to_be_removed.size() > 0 ) {
1110 phy.externalNodesHaveChanged();
1111 phy.clearHashIdToNodeMap();
1112 phy.recalculateNumberOfExternalDescendants( true );
1113 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1114 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1115 getCurrentTreePanel().calculateLongestExtNodeInfo();
1116 getCurrentTreePanel().setNodeInPreorderToNull();
1117 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1118 getCurrentTreePanel().resetPreferredSize();
1119 getCurrentTreePanel().setEdited( true );
1120 getCurrentTreePanel().repaint();
1123 if ( to_be_removed.size() > 0 ) {
1124 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1125 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1126 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1129 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1130 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1134 JOptionPane.showMessageDialog( this,
1135 "No branch collapsed because no confidence values present",
1136 "No confidence values present",
1137 JOptionPane.INFORMATION_MESSAGE );
1141 private void collapseBelowThreshold() {
1142 if ( getCurrentTreePanel() != null ) {
1143 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1144 if ( ( phy != null ) && !phy.isEmpty() ) {
1145 final String s = ( String ) JOptionPane.showInputDialog( this,
1146 "Please enter the minimum confidence value\n",
1147 "Minimal Confidence Value",
1148 JOptionPane.QUESTION_MESSAGE,
1151 getMinNotCollapseConfidenceValue() );
1152 if ( !ForesterUtil.isEmpty( s ) ) {
1153 boolean success = true;
1155 final String m_str = s.trim();
1156 if ( !ForesterUtil.isEmpty( m_str ) ) {
1158 m = Double.parseDouble( m_str );
1160 catch ( final Exception ex ) {
1167 if ( success && ( m >= 0.0 ) ) {
1168 setMinNotCollapseConfidenceValue( m );
1176 private PhyloXmlParser createPhyloXmlParser() {
1177 PhyloXmlParser xml_parser = null;
1178 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1180 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1182 catch ( final Exception e ) {
1183 JOptionPane.showMessageDialog( this,
1184 e.getLocalizedMessage(),
1185 "failed to create validating XML parser",
1186 JOptionPane.WARNING_MESSAGE );
1189 if ( xml_parser == null ) {
1190 xml_parser = new PhyloXmlParser();
1195 void executeGSDI() {
1196 if ( !isOKforSDI( false, true ) ) {
1199 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1200 JOptionPane.showMessageDialog( this,
1201 "Gene tree is not rooted.",
1202 "Cannot execute GSDI",
1203 JOptionPane.ERROR_MESSAGE );
1206 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1207 gene_tree.setAllNodesToNotCollapse();
1208 gene_tree.recalculateNumberOfExternalDescendants( false );
1211 gsdi = new GSDI( gene_tree, _species_tree.copy(), false, true, true );
1213 catch ( final Exception e ) {
1214 JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
1216 gene_tree.setRerootable( false );
1217 _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1218 _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
1219 _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
1220 _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1221 _mainpanel.getCurrentTreePanel().setEdited( true );
1222 getControlPanel().setShowEvents( true );
1224 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1225 _mainpanel.addPhylogenyInNewTab( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null );
1227 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1229 _mainpanel.getCurrentTreePanel().setEdited( true );
1230 JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1231 + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
1232 + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
1235 void executeFunctionAnalysis() {
1236 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1239 final GoAnnotation a = new GoAnnotation( this,
1240 _mainpanel.getCurrentTreePanel(),
1241 _mainpanel.getCurrentPhylogeny() );
1242 new Thread( a ).start();
1245 void executeLineageInference() {
1246 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1249 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1250 JOptionPane.showMessageDialog( this,
1251 "Phylogeny is not rooted.",
1252 "Cannot infer ancestral taxonomies",
1253 JOptionPane.ERROR_MESSAGE );
1256 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1257 _mainpanel.getCurrentTreePanel(),
1258 _mainpanel.getCurrentPhylogeny()
1260 new Thread( inferrer ).start();
1263 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1264 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1265 getPhylogeneticInferenceOptions(),
1266 from_unaligned_seqs );
1268 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1269 if ( !from_unaligned_seqs ) {
1270 if ( getMsa() != null ) {
1271 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1272 getPhylogeneticInferenceOptions()
1274 new Thread( inferrer ).start();
1277 JOptionPane.showMessageDialog( this,
1278 "No multiple sequence alignment selected",
1279 "Phylogenetic Inference Not Launched",
1280 JOptionPane.WARNING_MESSAGE );
1284 if ( getSeqs() != null ) {
1285 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1286 getPhylogeneticInferenceOptions()
1288 new Thread( inferrer ).start();
1291 JOptionPane.showMessageDialog( this,
1292 "No input sequences selected",
1293 "Phylogenetic Inference Not Launched",
1294 JOptionPane.WARNING_MESSAGE );
1300 void executeSDIR( final boolean minimize_cost ) {
1301 if ( !isOKforSDI( true, true ) ) {
1304 Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1305 final SDIR sdiunrooted = new SDIR();
1306 gene_tree.setAllNodesToNotCollapse();
1307 gene_tree.recalculateNumberOfExternalDescendants( false );
1309 gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1310 !minimize_cost, // minimize sum of dups
1311 true, // minimize height
1312 true, // return tree(s)
1313 1 )[ 0 ]; // # of trees to return
1315 catch ( final Exception e ) {
1316 JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1319 final int duplications = sdiunrooted.getMinimalDuplications();
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 "SDIR successfully completed",
1328 JOptionPane.INFORMATION_MESSAGE );
1332 removeAllTextFrames();
1333 _mainpanel.terminate();
1334 _contentpane.removeAll();
1335 setVisible( false );
1341 _mainpanel.terminate();
1342 _contentpane.removeAll();
1343 setVisible( false );
1347 private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
1348 if ( getCurrentTreePanel() != null ) {
1349 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1350 if ( ( phy != null ) && !phy.isEmpty() ) {
1351 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1352 while ( it.hasNext() ) {
1353 final PhylogenyNode n = it.next();
1354 final String name = n.getName().trim();
1355 if ( !ForesterUtil.isEmpty( name ) ) {
1356 final String code = ParserUtils
1357 .extractTaxonomyCodeFromNodeName( name, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
1358 if ( !ForesterUtil.isEmpty( code ) ) {
1359 PhylogenyMethods.setTaxonomyCode( n, code );
1367 private ControlPanel getControlPanel() {
1368 return getMainPanel().getControlPanel();
1371 private File getCurrentDir() {
1372 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1373 if ( ForesterUtil.isWindowns() ) {
1375 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1377 catch ( final Exception e ) {
1378 _current_dir = null;
1382 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1383 if ( System.getProperty( "user.home" ) != null ) {
1384 _current_dir = new File( System.getProperty( "user.home" ) );
1386 else if ( System.getProperty( "user.dir" ) != null ) {
1387 _current_dir = new File( System.getProperty( "user.dir" ) );
1390 return _current_dir;
1394 public MainPanel getMainPanel() {
1398 private double getMinNotCollapseConfidenceValue() {
1399 return _min_not_collapse;
1402 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1403 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1406 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1407 JOptionPane.showMessageDialog( this,
1408 "No species tree loaded",
1409 "Cannot execute SDI",
1410 JOptionPane.ERROR_MESSAGE );
1413 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1414 JOptionPane.showMessageDialog( this,
1415 "Species tree is not completely binary",
1416 "Cannot execute SDI",
1417 JOptionPane.ERROR_MESSAGE );
1420 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1421 JOptionPane.showMessageDialog( this,
1422 "Gene tree is not completely binary",
1423 "Cannot execute SDI",
1424 JOptionPane.ERROR_MESSAGE );
1432 private boolean isUnsavedDataPresent() {
1433 final List<TreePanel> tps = getMainPanel().getTreePanels();
1434 for( final TreePanel tp : tps ) {
1435 if ( tp.isEdited() ) {
1442 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1443 if ( getCurrentTreePanel() != null ) {
1444 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1445 if ( ( phy != null ) && !phy.isEmpty() ) {
1447 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1452 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1453 if ( getCurrentTreePanel() != null ) {
1454 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1455 if ( ( phy != null ) && !phy.isEmpty() ) {
1456 PhylogenyMethods.transferNodeNameToField( phy,
1457 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1463 private void newTree() {
1464 final Phylogeny[] phys = new Phylogeny[ 1 ];
1465 final Phylogeny phy = new Phylogeny();
1466 final PhylogenyNode node = new PhylogenyNode();
1467 phy.setRoot( node );
1468 phy.setRooted( true );
1470 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1471 _mainpanel.getControlPanel().showWhole();
1472 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1473 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1474 if ( getMainPanel().getMainFrame() == null ) {
1475 // Must be "E" applet version.
1476 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1477 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1480 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1482 activateSaveAllIfNeeded();
1486 private void obtainDetailedTaxonomicInformation() {
1487 if ( getCurrentTreePanel() != null ) {
1488 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1489 if ( ( phy != null ) && !phy.isEmpty() ) {
1490 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1491 _mainpanel.getCurrentTreePanel(),
1495 new Thread( t ).start();
1500 private void obtainDetailedTaxonomicInformationDelete() {
1501 if ( getCurrentTreePanel() != null ) {
1502 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1503 if ( ( phy != null ) && !phy.isEmpty() ) {
1504 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1505 _mainpanel.getCurrentTreePanel(),
1509 new Thread( t ).start();
1514 private void obtainSequenceInformation() {
1515 if ( getCurrentTreePanel() != null ) {
1516 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1517 if ( ( phy != null ) && !phy.isEmpty() ) {
1518 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1519 _mainpanel.getCurrentTreePanel(),
1521 new Thread( u ).start();
1526 private void print() {
1527 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
1528 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
1531 if ( !getOptions().isPrintUsingActualSize() ) {
1532 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
1533 getOptions().getPrintSizeY() - 140,
1535 getCurrentTreePanel().resetPreferredSize();
1536 getCurrentTreePanel().repaint();
1538 final String job_name = Constants.PRG_NAME;
1539 boolean error = false;
1540 String printer_name = null;
1542 printer_name = Printer.print( getCurrentTreePanel(), job_name );
1544 catch ( final Exception e ) {
1546 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
1548 if ( !error && ( printer_name != null ) ) {
1549 String msg = "Printing data sent to printer";
1550 if ( printer_name.length() > 1 ) {
1551 msg += " [" + printer_name + "]";
1553 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
1555 if ( !getOptions().isPrintUsingActualSize() ) {
1556 getControlPanel().showWhole();
1560 private void printPhylogenyToPdf( final String file_name ) {
1561 if ( !getOptions().isPrintUsingActualSize() ) {
1562 getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
1563 getOptions().getPrintSizeY(),
1565 getCurrentTreePanel().resetPreferredSize();
1566 getCurrentTreePanel().repaint();
1568 String pdf_written_to = "";
1569 boolean error = false;
1571 if ( getOptions().isPrintUsingActualSize() ) {
1572 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
1573 getCurrentTreePanel(),
1574 getCurrentTreePanel().getWidth(),
1575 getCurrentTreePanel().getHeight() );
1578 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
1579 .getPrintSizeX(), getOptions().getPrintSizeY() );
1582 catch ( final IOException e ) {
1584 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1587 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
1588 JOptionPane.showMessageDialog( this,
1589 "Wrote PDF to: " + pdf_written_to,
1591 JOptionPane.INFORMATION_MESSAGE );
1594 JOptionPane.showMessageDialog( this,
1595 "There was an unknown problem when attempting to write to PDF file: \""
1598 JOptionPane.ERROR_MESSAGE );
1601 if ( !getOptions().isPrintUsingActualSize() ) {
1602 getControlPanel().showWhole();
1606 private void addExpressionValuesFromFile() {
1607 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1608 JOptionPane.showMessageDialog( this,
1609 "Need to load evolutionary tree first",
1610 "Can Not Read Expression Values",
1611 JOptionPane.WARNING_MESSAGE );
1614 final File my_dir = getCurrentDir();
1615 if ( my_dir != null ) {
1616 _values_filechooser.setCurrentDirectory( my_dir );
1618 final int result = _values_filechooser.showOpenDialog( _contentpane );
1619 final File file = _values_filechooser.getSelectedFile();
1620 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1621 BasicTable<String> t = null;
1623 t = BasicTableParser.parse( file, "\t" );
1624 if ( t.getNumberOfColumns() < 2 ) {
1625 t = BasicTableParser.parse( file, "," );
1627 if ( t.getNumberOfColumns() < 2 ) {
1628 t = BasicTableParser.parse( file, " " );
1631 catch ( final IOException e ) {
1632 JOptionPane.showMessageDialog( this,
1634 "Could Not Read Expression Value Table",
1635 JOptionPane.ERROR_MESSAGE );
1638 if ( t.getNumberOfColumns() < 2 ) {
1639 JOptionPane.showMessageDialog( this,
1640 "Table contains " + t.getNumberOfColumns() + " column(s)",
1641 "Problem with Expression Value Table",
1642 JOptionPane.ERROR_MESSAGE );
1645 if ( t.getNumberOfRows() < 1 ) {
1646 JOptionPane.showMessageDialog( this,
1647 "Table contains zero rows",
1648 "Problem with Expression Value Table",
1649 JOptionPane.ERROR_MESSAGE );
1652 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1653 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1654 JOptionPane.showMessageDialog( this,
1655 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1656 + phy.getNumberOfExternalNodes() + " external nodes",
1658 JOptionPane.WARNING_MESSAGE );
1660 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1662 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1663 final PhylogenyNode node = iter.next();
1664 final String node_name = node.getName();
1665 if ( !ForesterUtil.isEmpty( node_name ) ) {
1668 row = t.findRow( node_name );
1670 catch ( final IllegalArgumentException e ) {
1672 .showMessageDialog( this,
1674 "Error Mapping Node Identifiers to Expression Value Identifiers",
1675 JOptionPane.ERROR_MESSAGE );
1679 if ( node.isExternal() ) {
1684 final List<Double> l = new ArrayList<Double>();
1685 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1688 d = Double.parseDouble( t.getValueAsString( col, row ) );
1690 catch ( final NumberFormatException e ) {
1691 JOptionPane.showMessageDialog( this,
1692 "Could not parse \"" + t.getValueAsString( col, row )
1693 + "\" into a decimal value",
1694 "Issue with Expression Value Table",
1695 JOptionPane.ERROR_MESSAGE );
1698 stats.addValue( d );
1701 if ( !l.isEmpty() ) {
1702 if ( node.getNodeData().getProperties() != null ) {
1703 node.getNodeData().getProperties()
1704 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1706 node.getNodeData().setVector( l );
1710 if ( not_found > 0 ) {
1711 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1712 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1714 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1718 private void readPhylogeniesFromFile() {
1719 boolean exception = false;
1720 Phylogeny[] phys = null;
1721 // Set an initial directory if none set yet
1722 final File my_dir = getCurrentDir();
1723 _open_filechooser.setMultiSelectionEnabled( true );
1724 // Open file-open dialog and set current directory
1725 if ( my_dir != null ) {
1726 _open_filechooser.setCurrentDirectory( my_dir );
1728 final int result = _open_filechooser.showOpenDialog( _contentpane );
1729 // All done: get the file
1730 final File[] files = _open_filechooser.getSelectedFiles();
1731 setCurrentDir( _open_filechooser.getCurrentDirectory() );
1732 boolean nhx_or_nexus = false;
1733 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1734 for( final File file : files ) {
1735 if ( ( file != null ) && !file.isDirectory() ) {
1736 if ( _mainpanel.getCurrentTreePanel() != null ) {
1737 _mainpanel.getCurrentTreePanel().setWaitCursor();
1740 _mainpanel.setWaitCursor();
1742 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
1743 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
1745 final NHXParser nhx = new NHXParser();
1746 setSpecialOptionsForNhxParser( nhx );
1747 phys = PhylogenyMethods.readPhylogenies( nhx, file );
1748 nhx_or_nexus = true;
1750 catch ( final Exception e ) {
1752 exceptionOccuredDuringOpenFile( e );
1755 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
1756 warnIfNotPhyloXmlValidation( getConfiguration() );
1758 final PhyloXmlParser xml_parser = createPhyloXmlParser();
1759 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
1761 catch ( final Exception e ) {
1763 exceptionOccuredDuringOpenFile( e );
1766 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
1768 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1770 catch ( final Exception e ) {
1772 exceptionOccuredDuringOpenFile( e );
1775 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
1777 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
1778 setSpecialOptionsForNexParser( nex );
1779 phys = PhylogenyMethods.readPhylogenies( nex, file );
1780 nhx_or_nexus = true;
1782 catch ( final Exception e ) {
1784 exceptionOccuredDuringOpenFile( e );
1790 final PhylogenyParser parser = ParserUtils
1791 .createParserDependingOnFileType( file, getConfiguration()
1792 .isValidatePhyloXmlAgainstSchema() );
1793 if ( parser instanceof NexusPhylogeniesParser ) {
1794 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
1795 setSpecialOptionsForNexParser( nex );
1796 nhx_or_nexus = true;
1798 else if ( parser instanceof NHXParser ) {
1799 final NHXParser nhx = ( NHXParser ) parser;
1800 setSpecialOptionsForNhxParser( nhx );
1801 nhx_or_nexus = true;
1803 else if ( parser instanceof PhyloXmlParser ) {
1804 warnIfNotPhyloXmlValidation( getConfiguration() );
1806 phys = PhylogenyMethods.readPhylogenies( parser, file );
1808 catch ( final Exception e ) {
1810 exceptionOccuredDuringOpenFile( e );
1813 if ( _mainpanel.getCurrentTreePanel() != null ) {
1814 _mainpanel.getCurrentTreePanel().setArrowCursor();
1817 _mainpanel.setArrowCursor();
1819 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
1820 boolean one_desc = false;
1821 if ( nhx_or_nexus ) {
1822 for( final Phylogeny phy : phys ) {
1823 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1824 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1826 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
1832 AptxUtil.addPhylogeniesToTabs( phys,
1834 file.getAbsolutePath(),
1837 _mainpanel.getControlPanel().showWhole();
1838 if ( nhx_or_nexus && one_desc ) {
1840 .showMessageDialog( this,
1841 "One or more trees contain (a) node(s) with one descendant, "
1842 + ForesterUtil.LINE_SEPARATOR
1843 + "possibly indicating illegal parentheses within node names.",
1844 "Warning: Possible Error in New Hampshire Formatted Data",
1845 JOptionPane.WARNING_MESSAGE );
1851 activateSaveAllIfNeeded();
1855 public void readSeqsFromFile() {
1856 // Set an initial directory if none set yet
1857 final File my_dir = getCurrentDir();
1858 _seqs_filechooser.setMultiSelectionEnabled( false );
1859 // Open file-open dialog and set current directory
1860 if ( my_dir != null ) {
1861 _seqs_filechooser.setCurrentDirectory( my_dir );
1863 final int result = _seqs_filechooser.showOpenDialog( _contentpane );
1864 // All done: get the seqs
1865 final File file = _seqs_filechooser.getSelectedFile();
1866 setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
1867 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1868 setSeqsFile( null );
1870 List<Sequence> seqs = null;
1872 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1873 seqs = FastaParser.parse( new FileInputStream( file ) );
1874 for( final Sequence seq : seqs ) {
1875 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
1882 catch ( final MsaFormatException e ) {
1884 _mainpanel.getCurrentTreePanel().setArrowCursor();
1886 catch ( final Exception ex ) {
1889 JOptionPane.showMessageDialog( this,
1890 e.getLocalizedMessage(),
1891 "Multiple sequence file format error",
1892 JOptionPane.ERROR_MESSAGE );
1895 catch ( final IOException e ) {
1897 _mainpanel.getCurrentTreePanel().setArrowCursor();
1899 catch ( final Exception ex ) {
1902 JOptionPane.showMessageDialog( this,
1903 e.getLocalizedMessage(),
1904 "Failed to read multiple sequence file",
1905 JOptionPane.ERROR_MESSAGE );
1908 catch ( final IllegalArgumentException e ) {
1910 _mainpanel.getCurrentTreePanel().setArrowCursor();
1912 catch ( final Exception ex ) {
1915 JOptionPane.showMessageDialog( this,
1916 e.getLocalizedMessage(),
1917 "Unexpected error during reading of multiple sequence file",
1918 JOptionPane.ERROR_MESSAGE );
1921 catch ( final Exception e ) {
1923 _mainpanel.getCurrentTreePanel().setArrowCursor();
1925 catch ( final Exception ex ) {
1928 e.printStackTrace();
1929 JOptionPane.showMessageDialog( this,
1930 e.getLocalizedMessage(),
1931 "Unexpected error during reading of multiple sequence file",
1932 JOptionPane.ERROR_MESSAGE );
1935 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1936 JOptionPane.showMessageDialog( this,
1937 "Multiple sequence file is empty",
1938 "Illegal multiple sequence file",
1939 JOptionPane.ERROR_MESSAGE );
1942 if ( seqs.size() < 4 ) {
1943 JOptionPane.showMessageDialog( this,
1944 "Multiple sequence file needs to contain at least 3 sequences",
1945 "Illegal multiple sequence file",
1946 JOptionPane.ERROR_MESSAGE );
1949 // if ( msa.getLength() < 2 ) {
1950 // JOptionPane.showMessageDialog( this,
1951 // "Multiple sequence alignment needs to contain at least 2 residues",
1952 // "Illegal multiple sequence file",
1953 // JOptionPane.ERROR_MESSAGE );
1957 setSeqsFile( _seqs_filechooser.getSelectedFile() );
1962 public void readMsaFromFile() {
1963 // Set an initial directory if none set yet
1964 final File my_dir = getCurrentDir();
1965 _msa_filechooser.setMultiSelectionEnabled( false );
1966 // Open file-open dialog and set current directory
1967 if ( my_dir != null ) {
1968 _msa_filechooser.setCurrentDirectory( my_dir );
1970 final int result = _msa_filechooser.showOpenDialog( _contentpane );
1971 // All done: get the msa
1972 final File file = _msa_filechooser.getSelectedFile();
1973 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
1974 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1979 final InputStream is = new FileInputStream( file );
1980 if ( FastaParser.isLikelyFasta( file ) ) {
1981 msa = FastaParser.parseMsa( is );
1984 msa = GeneralMsaParser.parse( is );
1987 catch ( final MsaFormatException e ) {
1989 _mainpanel.getCurrentTreePanel().setArrowCursor();
1991 catch ( final Exception ex ) {
1994 JOptionPane.showMessageDialog( this,
1995 e.getLocalizedMessage(),
1996 "Multiple sequence alignment format error",
1997 JOptionPane.ERROR_MESSAGE );
2000 catch ( final IOException e ) {
2002 _mainpanel.getCurrentTreePanel().setArrowCursor();
2004 catch ( final Exception ex ) {
2007 JOptionPane.showMessageDialog( this,
2008 e.getLocalizedMessage(),
2009 "Failed to read multiple sequence alignment",
2010 JOptionPane.ERROR_MESSAGE );
2013 catch ( final IllegalArgumentException e ) {
2015 _mainpanel.getCurrentTreePanel().setArrowCursor();
2017 catch ( final Exception ex ) {
2020 JOptionPane.showMessageDialog( this,
2021 e.getLocalizedMessage(),
2022 "Unexpected error during reading of multiple sequence alignment",
2023 JOptionPane.ERROR_MESSAGE );
2026 catch ( final Exception e ) {
2028 _mainpanel.getCurrentTreePanel().setArrowCursor();
2030 catch ( final Exception ex ) {
2033 e.printStackTrace();
2034 JOptionPane.showMessageDialog( this,
2035 e.getLocalizedMessage(),
2036 "Unexpected error during reading of multiple sequence alignment",
2037 JOptionPane.ERROR_MESSAGE );
2040 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
2041 JOptionPane.showMessageDialog( this,
2042 "Multiple sequence alignment is empty",
2043 "Illegal Multiple Sequence Alignment",
2044 JOptionPane.ERROR_MESSAGE );
2047 if ( msa.getNumberOfSequences() < 4 ) {
2048 JOptionPane.showMessageDialog( this,
2049 "Multiple sequence alignment needs to contain at least 3 sequences",
2050 "Illegal multiple sequence alignment",
2051 JOptionPane.ERROR_MESSAGE );
2054 if ( msa.getLength() < 2 ) {
2055 JOptionPane.showMessageDialog( this,
2056 "Multiple sequence alignment needs to contain at least 2 residues",
2057 "Illegal multiple sequence alignment",
2058 JOptionPane.ERROR_MESSAGE );
2062 setMsaFile( _msa_filechooser.getSelectedFile() );
2068 void readPhylogeniesFromURL() {
2070 Phylogeny[] phys = null;
2071 final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
2072 final String url_string = JOptionPane.showInputDialog( this,
2074 "Use URL/webservice to obtain a phylogeny",
2075 JOptionPane.QUESTION_MESSAGE );
2076 boolean nhx_or_nexus = false;
2077 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
2079 url = new URL( url_string );
2080 PhylogenyParser parser = null;
2081 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
2082 parser = new TolParser();
2085 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
2086 .isValidatePhyloXmlAgainstSchema() );
2088 if ( parser instanceof NexusPhylogeniesParser ) {
2089 nhx_or_nexus = true;
2091 else if ( parser instanceof NHXParser ) {
2092 nhx_or_nexus = true;
2094 if ( _mainpanel.getCurrentTreePanel() != null ) {
2095 _mainpanel.getCurrentTreePanel().setWaitCursor();
2098 _mainpanel.setWaitCursor();
2100 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2101 phys = factory.create( url.openStream(), parser );
2103 catch ( final MalformedURLException e ) {
2104 JOptionPane.showMessageDialog( this,
2105 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
2107 JOptionPane.ERROR_MESSAGE );
2109 catch ( final IOException e ) {
2110 JOptionPane.showMessageDialog( this,
2111 "Could not read from " + url + "\n"
2112 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2113 "Failed to read URL",
2114 JOptionPane.ERROR_MESSAGE );
2116 catch ( final Exception e ) {
2117 JOptionPane.showMessageDialog( this,
2118 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2119 "Unexpected Exception",
2120 JOptionPane.ERROR_MESSAGE );
2123 if ( _mainpanel.getCurrentTreePanel() != null ) {
2124 _mainpanel.getCurrentTreePanel().setArrowCursor();
2127 _mainpanel.setArrowCursor();
2130 if ( ( phys != null ) && ( phys.length > 0 ) ) {
2131 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2132 for( final Phylogeny phy : phys ) {
2133 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2136 AptxUtil.addPhylogeniesToTabs( phys,
2137 new File( url.getFile() ).getName(),
2138 new File( url.getFile() ).toString(),
2141 _mainpanel.getControlPanel().showWhole();
2144 activateSaveAllIfNeeded();
2148 private void readSpeciesTreeFromFile() {
2150 boolean exception = false;
2151 final File my_dir = getCurrentDir();
2152 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2153 if ( my_dir != null ) {
2154 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2156 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2157 final File file = _open_filechooser_for_species_tree.getSelectedFile();
2158 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2159 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2161 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2164 catch ( final Exception e ) {
2166 exceptionOccuredDuringOpenFile( e );
2169 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2171 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2174 catch ( final Exception e ) {
2176 exceptionOccuredDuringOpenFile( e );
2182 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2185 catch ( final Exception e ) {
2187 exceptionOccuredDuringOpenFile( e );
2190 if ( !exception && ( t != null ) && !t.isRooted() ) {
2193 JOptionPane.showMessageDialog( this,
2194 "Species tree is not rooted",
2195 "Species tree not loaded",
2196 JOptionPane.ERROR_MESSAGE );
2198 if ( !exception && ( t != null ) ) {
2199 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2200 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2201 final PhylogenyNode node = it.next();
2202 if ( !node.getNodeData().isHasTaxonomy() ) {
2206 .showMessageDialog( this,
2207 "Species tree contains external node(s) without taxonomy information",
2208 "Species tree not loaded",
2209 JOptionPane.ERROR_MESSAGE );
2213 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2216 JOptionPane.showMessageDialog( this,
2218 + node.getNodeData().getTaxonomy().asSimpleText()
2219 + "] is not unique in species tree",
2220 "Species tree not loaded",
2221 JOptionPane.ERROR_MESSAGE );
2225 tax_set.add( node.getNodeData().getTaxonomy() );
2230 if ( !exception && ( t != null ) ) {
2232 JOptionPane.showMessageDialog( this,
2233 "Species tree successfully loaded",
2234 "Species tree loaded",
2235 JOptionPane.INFORMATION_MESSAGE );
2237 _contentpane.repaint();
2242 private void setCurrentDir( final File current_dir ) {
2243 _current_dir = current_dir;
2246 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2247 _min_not_collapse = min_not_collapse;
2250 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2251 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2254 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2255 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2256 PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
2257 if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
2258 te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
2260 nhx.setTaxonomyExtraction( te );
2263 private void writeAllToFile() {
2264 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2267 final File my_dir = getCurrentDir();
2268 if ( my_dir != null ) {
2269 _save_filechooser.setCurrentDirectory( my_dir );
2271 _save_filechooser.setSelectedFile( new File( "" ) );
2272 final int result = _save_filechooser.showSaveDialog( _contentpane );
2273 final File file = _save_filechooser.getSelectedFile();
2274 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2275 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2276 if ( file.exists() ) {
2277 final int i = JOptionPane.showConfirmDialog( this,
2278 file + " already exists. Overwrite?",
2280 JOptionPane.OK_CANCEL_OPTION,
2281 JOptionPane.WARNING_MESSAGE );
2282 if ( i != JOptionPane.OK_OPTION ) {
2289 catch ( final Exception e ) {
2290 JOptionPane.showMessageDialog( this,
2291 "Failed to delete: " + file,
2293 JOptionPane.WARNING_MESSAGE );
2297 final int count = getMainPanel().getTabbedPane().getTabCount();
2298 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2299 for( int i = 0; i < count; ++i ) {
2300 trees.add( getMainPanel().getPhylogeny( i ) );
2301 getMainPanel().getTreePanels().get( i ).setEdited( false );
2303 final PhylogenyWriter writer = new PhylogenyWriter();
2305 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2307 catch ( final IOException e ) {
2308 JOptionPane.showMessageDialog( this,
2309 "Failed to write to: " + file,
2311 JOptionPane.WARNING_MESSAGE );
2316 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2318 final PhylogenyWriter writer = new PhylogenyWriter();
2319 writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2321 catch ( final Exception e ) {
2323 exceptionOccuredDuringSaveAs( e );
2328 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2330 final PhylogenyWriter writer = new PhylogenyWriter();
2331 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2333 catch ( final Exception e ) {
2335 exceptionOccuredDuringSaveAs( e );
2340 private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
2342 final PhylogenyWriter writer = new PhylogenyWriter();
2343 writer.toNewHampshireX( t, file );
2345 catch ( final Exception e ) {
2347 exceptionOccuredDuringSaveAs( e );
2352 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2354 final PhylogenyWriter writer = new PhylogenyWriter();
2355 writer.toPhyloXML( file, t, 0 );
2357 catch ( final Exception e ) {
2359 exceptionOccuredDuringSaveAs( e );
2364 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
2365 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
2366 _mainpanel.getCurrentTreePanel().getHeight(),
2368 String file_written_to = "";
2369 boolean error = false;
2371 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
2372 _mainpanel.getCurrentTreePanel().getWidth(),
2373 _mainpanel.getCurrentTreePanel().getHeight(),
2374 _mainpanel.getCurrentTreePanel(),
2375 _mainpanel.getControlPanel(),
2379 catch ( final IOException e ) {
2381 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2384 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
2385 JOptionPane.showMessageDialog( this,
2386 "Wrote image to: " + file_written_to,
2388 JOptionPane.INFORMATION_MESSAGE );
2391 JOptionPane.showMessageDialog( this,
2392 "There was an unknown problem when attempting to write to an image file: \""
2395 JOptionPane.ERROR_MESSAGE );
2398 _contentpane.repaint();
2401 private void writeToFile( final Phylogeny t ) {
2405 String initial_filename = null;
2406 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2408 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2410 catch ( final IOException e ) {
2411 initial_filename = null;
2414 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2415 _save_filechooser.setSelectedFile( new File( initial_filename ) );
2418 _save_filechooser.setSelectedFile( new File( "" ) );
2420 final File my_dir = getCurrentDir();
2421 if ( my_dir != null ) {
2422 _save_filechooser.setCurrentDirectory( my_dir );
2424 final int result = _save_filechooser.showSaveDialog( _contentpane );
2425 final File file = _save_filechooser.getSelectedFile();
2426 setCurrentDir( _save_filechooser.getCurrentDirectory() );
2427 boolean exception = false;
2428 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2429 if ( file.exists() ) {
2430 final int i = JOptionPane.showConfirmDialog( this,
2431 file + " already exists.\nOverwrite?",
2433 JOptionPane.OK_CANCEL_OPTION,
2434 JOptionPane.QUESTION_MESSAGE );
2435 if ( i != JOptionPane.OK_OPTION ) {
2439 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2441 ForesterUtil.copyFile( file, to );
2443 catch ( final Exception e ) {
2444 JOptionPane.showMessageDialog( this,
2445 "Failed to create backup copy " + to,
2446 "Failed to Create Backup Copy",
2447 JOptionPane.WARNING_MESSAGE );
2452 catch ( final Exception e ) {
2453 JOptionPane.showMessageDialog( this,
2454 "Failed to delete: " + file,
2456 JOptionPane.WARNING_MESSAGE );
2460 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2461 exception = writeAsNewHampshire( t, exception, file );
2463 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
2464 exception = writeAsNHX( t, exception, file );
2466 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2467 exception = writeAsPhyloXml( t, exception, file );
2469 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2470 exception = writeAsNexus( t, exception, file );
2474 final String file_name = file.getName().trim().toLowerCase();
2475 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2476 || file_name.endsWith( ".tree" ) ) {
2477 exception = writeAsNewHampshire( t, exception, file );
2479 else if ( file_name.endsWith( ".nhx" ) ) {
2480 exception = writeAsNHX( t, exception, file );
2482 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2483 exception = writeAsNexus( t, exception, file );
2487 exception = writeAsPhyloXml( t, exception, file );
2491 getMainPanel().setTitleOfSelectedTab( file.getName() );
2492 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2493 getMainPanel().getCurrentTreePanel().setEdited( false );
2498 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2499 if ( ( t == null ) || t.isEmpty() ) {
2502 String initial_filename = "";
2503 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2504 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2506 if ( initial_filename.indexOf( '.' ) > 0 ) {
2507 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2509 initial_filename = initial_filename + "." + type;
2510 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2511 final File my_dir = getCurrentDir();
2512 if ( my_dir != null ) {
2513 _writetographics_filechooser.setCurrentDirectory( my_dir );
2515 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2516 File file = _writetographics_filechooser.getSelectedFile();
2517 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2518 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2519 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2520 file = new File( file.toString() + "." + type );
2522 if ( file.exists() ) {
2523 final int i = JOptionPane.showConfirmDialog( this,
2524 file + " already exists. Overwrite?",
2526 JOptionPane.OK_CANCEL_OPTION,
2527 JOptionPane.WARNING_MESSAGE );
2528 if ( i != JOptionPane.OK_OPTION ) {
2535 catch ( final Exception e ) {
2536 JOptionPane.showMessageDialog( this,
2537 "Failed to delete: " + file,
2539 JOptionPane.WARNING_MESSAGE );
2543 writePhylogenyToGraphicsFile( file.toString(), type );
2547 private void writeToPdf( final Phylogeny t ) {
2548 if ( ( t == null ) || t.isEmpty() ) {
2551 String initial_filename = "";
2552 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2553 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2555 if ( initial_filename.indexOf( '.' ) > 0 ) {
2556 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2558 initial_filename = initial_filename + ".pdf";
2559 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2560 final File my_dir = getCurrentDir();
2561 if ( my_dir != null ) {
2562 _writetopdf_filechooser.setCurrentDirectory( my_dir );
2564 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2565 File file = _writetopdf_filechooser.getSelectedFile();
2566 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2567 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2568 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2569 file = new File( file.toString() + ".pdf" );
2571 if ( file.exists() ) {
2572 final int i = JOptionPane.showConfirmDialog( this,
2573 file + " already exists. Overwrite?",
2575 JOptionPane.OK_CANCEL_OPTION,
2576 JOptionPane.WARNING_MESSAGE );
2577 if ( i != JOptionPane.OK_OPTION ) {
2581 printPhylogenyToPdf( file.toString() );
2585 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2586 return new MainFrameApplication( phys, config, title );
2589 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2590 return new MainFrameApplication( phys, config );
2593 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2594 return new MainFrameApplication( phys, config_file_name, title );
2597 public static MainFrame createInstance( final Phylogeny[] phys,
2598 final Configuration config,
2600 final File current_dir ) {
2601 return new MainFrameApplication( phys, config, title, current_dir );
2604 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2605 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2606 + o.getPrintSizeY() + ")" );
2609 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2610 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2613 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2614 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2616 .showMessageDialog( null,
2618 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2621 JOptionPane.WARNING_MESSAGE );
2625 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2626 _phylogenetic_inference_options = phylogenetic_inference_options;
2629 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
2630 if ( _phylogenetic_inference_options == null ) {
2631 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
2633 return _phylogenetic_inference_options;
2636 public Msa getMsa() {
2640 void setMsa( final Msa msa ) {
2644 void setMsaFile( final File msa_file ) {
2645 _msa_file = msa_file;
2648 public File getMsaFile() {
2652 public List<Sequence> getSeqs() {
2656 void setSeqs( final List<Sequence> seqs ) {
2660 void setSeqsFile( final File seqs_file ) {
2661 _seqs_file = seqs_file;
2664 public File getSeqsFile() {
2667 } // MainFrameApplication.
2669 class NexusFilter extends FileFilter {
2672 public boolean accept( final File f ) {
2673 final String file_name = f.getName().trim().toLowerCase();
2674 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2675 || file_name.endsWith( ".tre" ) || f.isDirectory();
2679 public String getDescription() {
2680 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2684 class NHFilter extends FileFilter {
2687 public boolean accept( final File f ) {
2688 final String file_name = f.getName().trim().toLowerCase();
2689 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2690 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2691 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2696 public String getDescription() {
2697 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2701 class NHXFilter extends FileFilter {
2704 public boolean accept( final File f ) {
2705 final String file_name = f.getName().trim().toLowerCase();
2706 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2710 public String getDescription() {
2711 return "NHX files (*.nhx)";
2715 class PdfFilter extends FileFilter {
2718 public boolean accept( final File f ) {
2719 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2723 public String getDescription() {
2724 return "PDF files (*.pdf)";
2728 class TolFilter extends FileFilter {
2731 public boolean accept( final File f ) {
2732 final String file_name = f.getName().trim().toLowerCase();
2733 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2734 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2738 public String getDescription() {
2739 return "Tree of Life files (*.tol, *.tolxml)";
2743 class XMLFilter extends FileFilter {
2746 public boolean accept( final File f ) {
2747 final String file_name = f.getName().trim().toLowerCase();
2748 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2749 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2753 public String getDescription() {
2754 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";