2 // FORESTER -- software libraries and applications
\r
3 // for evolutionary biology research and applications.
\r
5 // Copyright (C) 2008-2009 Christian M. Zmasek
\r
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
\r
7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
\r
8 // All rights reserved
\r
10 // This library is free software; you can redistribute it and/or
\r
11 // modify it under the terms of the GNU Lesser General Public
\r
12 // License as published by the Free Software Foundation; either
\r
13 // version 2.1 of the License, or (at your option) any later version.
\r
15 // This library is distributed in the hope that it will be useful,
\r
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
\r
18 // Lesser General Public License for more details.
\r
20 // You should have received a copy of the GNU Lesser General Public
\r
21 // License along with this library; if not, write to the Free Software
\r
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
24 // Contact: phylosoft @ gmail . com
\r
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
\r
27 package org.forester.archaeopteryx;
\r
29 import java.awt.BorderLayout;
\r
30 import java.awt.Font;
\r
31 import java.awt.event.ActionEvent;
\r
32 import java.awt.event.ComponentAdapter;
\r
33 import java.awt.event.ComponentEvent;
\r
34 import java.awt.event.WindowAdapter;
\r
35 import java.awt.event.WindowEvent;
\r
36 import java.io.File;
\r
37 import java.io.FileInputStream;
\r
38 import java.io.IOException;
\r
39 import java.io.InputStream;
\r
40 import java.net.MalformedURLException;
\r
41 import java.net.URL;
\r
42 import java.util.ArrayList;
\r
43 import java.util.HashSet;
\r
44 import java.util.List;
\r
45 import java.util.Set;
\r
47 import javax.swing.ButtonGroup;
\r
48 import javax.swing.JCheckBoxMenuItem;
\r
49 import javax.swing.JFileChooser;
\r
50 import javax.swing.JMenu;
\r
51 import javax.swing.JMenuBar;
\r
52 import javax.swing.JMenuItem;
\r
53 import javax.swing.JOptionPane;
\r
54 import javax.swing.JRadioButtonMenuItem;
\r
55 import javax.swing.UIManager;
\r
56 import javax.swing.UnsupportedLookAndFeelException;
\r
57 import javax.swing.WindowConstants;
\r
58 import javax.swing.event.ChangeEvent;
\r
59 import javax.swing.event.ChangeListener;
\r
60 import javax.swing.filechooser.FileFilter;
\r
61 import javax.swing.plaf.synth.SynthLookAndFeel;
\r
63 import org.forester.analysis.TaxonomyDataManager;
\r
64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
\r
65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
\r
66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
\r
67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
\r
68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
\r
69 import org.forester.archaeopteryx.tools.InferenceManager;
\r
70 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
\r
71 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
\r
72 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
\r
73 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
\r
74 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
\r
75 import org.forester.archaeopteryx.webservices.WebservicesManager;
\r
76 import org.forester.io.parsers.FastaParser;
\r
77 import org.forester.io.parsers.GeneralMsaParser;
\r
78 import org.forester.io.parsers.PhylogenyParser;
\r
79 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
\r
80 import org.forester.io.parsers.nhx.NHXParser;
\r
81 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
\r
82 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
\r
83 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
\r
84 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
\r
85 import org.forester.io.parsers.tol.TolParser;
\r
86 import org.forester.io.parsers.util.ParserUtils;
\r
87 import org.forester.io.writers.PhylogenyWriter;
\r
88 import org.forester.io.writers.SequenceWriter;
\r
89 import org.forester.msa.Msa;
\r
90 import org.forester.msa.MsaFormatException;
\r
91 import org.forester.phylogeny.Phylogeny;
\r
92 import org.forester.phylogeny.PhylogenyMethods;
\r
93 import org.forester.phylogeny.PhylogenyNode;
\r
94 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
\r
95 import org.forester.phylogeny.data.Confidence;
\r
96 import org.forester.phylogeny.data.Taxonomy;
\r
97 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
\r
98 import org.forester.phylogeny.factories.PhylogenyFactory;
\r
99 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
\r
100 import org.forester.sequence.Sequence;
\r
101 import org.forester.util.BasicDescriptiveStatistics;
\r
102 import org.forester.util.BasicTable;
\r
103 import org.forester.util.BasicTableParser;
\r
104 import org.forester.util.DescriptiveStatistics;
\r
105 import org.forester.util.ForesterUtil;
\r
106 import org.forester.util.WindowsUtils;
\r
108 public final class MainFrameApplication extends MainFrame {
\r
110 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
\r
111 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
\r
112 private final static int FRAME_X_SIZE = 800;
\r
113 private final static int FRAME_Y_SIZE = 800;
\r
114 // Filters for the file-open dialog (classes defined in this file)
\r
115 private final static NHFilter nhfilter = new NHFilter();
\r
116 private final static NHXFilter nhxfilter = new NHXFilter();
\r
117 private final static XMLFilter xmlfilter = new XMLFilter();
\r
118 private final static TolFilter tolfilter = new TolFilter();
\r
119 private final static NexusFilter nexusfilter = new NexusFilter();
\r
120 private final static PdfFilter pdffilter = new PdfFilter();
\r
121 private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
\r
122 private final static MsaFileFilter msafilter = new MsaFileFilter();
\r
123 private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
\r
124 private final static DefaultFilter defaultfilter = new DefaultFilter();
\r
125 private static final long serialVersionUID = -799735726778865234L;
\r
126 private final JFileChooser _values_filechooser;
\r
127 private final JFileChooser _sequences_filechooser;
\r
128 private final JFileChooser _open_filechooser;
\r
129 private final JFileChooser _msa_filechooser;
\r
130 private final JFileChooser _seqs_pi_filechooser;
\r
131 private final JFileChooser _open_filechooser_for_species_tree;
\r
132 private final JFileChooser _save_filechooser;
\r
133 private final JFileChooser _writetopdf_filechooser;
\r
134 private final JFileChooser _writetographics_filechooser;
\r
135 // Application-only print menu items
\r
136 private JMenuItem _print_item;
\r
137 private JMenuItem _write_to_pdf_item;
\r
138 private JMenuItem _write_to_jpg_item;
\r
139 private JMenuItem _write_to_gif_item;
\r
140 private JMenuItem _write_to_tif_item;
\r
141 private JMenuItem _write_to_png_item;
\r
142 private JMenuItem _write_to_bmp_item;
\r
143 private File _current_dir;
\r
144 private ButtonGroup _radio_group_1;
\r
145 private ButtonGroup _radio_group_2;
\r
147 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
\r
148 // Phylogeny Inference menu
\r
149 private JMenu _inference_menu;
\r
150 private JMenuItem _inference_from_msa_item;
\r
151 private JMenuItem _inference_from_seqs_item;
\r
152 // Phylogeny Inference
\r
153 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
\r
154 private Msa _msa = null;
\r
155 private File _msa_file = null;
\r
156 private List<Sequence> _seqs = null;
\r
157 private File _seqs_file = null;
\r
158 JMenuItem _read_values_jmi;
\r
159 JMenuItem _read_seqs_jmi;
\r
162 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
\r
163 _configuration = config;
\r
164 if ( _configuration == null ) {
\r
165 throw new IllegalArgumentException( "configuration is null" );
\r
167 setVisible( false );
\r
168 setOptions( Options.createInstance( _configuration ) );
\r
169 _mainpanel = new MainPanel( _configuration, this );
\r
170 _open_filechooser = null;
\r
171 _open_filechooser_for_species_tree = null;
\r
172 _save_filechooser = null;
\r
173 _writetopdf_filechooser = null;
\r
174 _writetographics_filechooser = null;
\r
175 _msa_filechooser = null;
\r
176 _seqs_pi_filechooser = null;
\r
177 _values_filechooser = null;
\r
178 _sequences_filechooser = null;
\r
179 _jmenubar = new JMenuBar();
\r
182 _contentpane = getContentPane();
\r
183 _contentpane.setLayout( new BorderLayout() );
\r
184 _contentpane.add( _mainpanel, BorderLayout.CENTER );
\r
186 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
\r
187 // The window listener
\r
188 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
\r
189 addWindowListener( new WindowAdapter() {
\r
192 public void windowClosing( final WindowEvent e ) {
\r
196 // setVisible( true );
\r
197 if ( ( phys != null ) && ( phys.length > 0 ) ) {
\r
198 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
\r
200 getMainPanel().getControlPanel().showWholeAll();
\r
201 getMainPanel().getControlPanel().showWhole();
\r
203 //activateSaveAllIfNeeded();
\r
204 // ...and its children
\r
205 _contentpane.repaint();
\r
208 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
\r
209 this( phys, config, title, null );
\r
212 private MainFrameApplication( final Phylogeny[] phys,
\r
213 final Configuration config,
\r
214 final String title,
\r
215 final File current_dir ) {
\r
217 _configuration = config;
\r
218 if ( _configuration == null ) {
\r
219 throw new IllegalArgumentException( "configuration is null" );
\r
222 boolean synth_exception = false;
\r
223 if ( Constants.__SYNTH_LF ) {
\r
225 final SynthLookAndFeel synth = new SynthLookAndFeel();
\r
226 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
\r
227 MainFrameApplication.class );
\r
228 UIManager.setLookAndFeel( synth );
\r
230 catch ( final Exception ex ) {
\r
231 synth_exception = true;
\r
232 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
\r
233 "could not create synth look and feel: "
\r
234 + ex.getLocalizedMessage() );
\r
237 if ( !Constants.__SYNTH_LF || synth_exception ) {
\r
238 if ( _configuration.isUseNativeUI() ) {
\r
239 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
\r
242 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
\r
245 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
\r
247 catch ( final UnsupportedLookAndFeelException e ) {
\r
248 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
\r
250 catch ( final ClassNotFoundException e ) {
\r
251 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
\r
253 catch ( final InstantiationException e ) {
\r
254 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
\r
256 catch ( final IllegalAccessException e ) {
\r
257 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
\r
259 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
\r
260 setCurrentDir( current_dir );
\r
262 // hide until everything is ready
\r
263 setVisible( false );
\r
264 setOptions( Options.createInstance( _configuration ) );
\r
265 setInferenceManager( InferenceManager.createInstance( _configuration ) );
\r
266 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
\r
267 // _textframe = null; #~~~~
\r
269 setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
\r
270 _mainpanel = new MainPanel( _configuration, this );
\r
271 // The file dialogs
\r
272 _open_filechooser = new JFileChooser();
\r
273 _open_filechooser.setCurrentDirectory( new File( "." ) );
\r
274 _open_filechooser.setMultiSelectionEnabled( false );
\r
275 _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
\r
276 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
\r
277 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
\r
278 _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
\r
279 _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
\r
280 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
\r
281 _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
\r
282 _open_filechooser_for_species_tree = new JFileChooser();
\r
283 _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
\r
284 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
\r
285 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
\r
286 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
\r
287 _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
\r
288 _save_filechooser = new JFileChooser();
\r
289 _save_filechooser.setCurrentDirectory( new File( "." ) );
\r
290 _save_filechooser.setMultiSelectionEnabled( false );
\r
291 _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
\r
292 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
\r
293 _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
\r
294 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
\r
295 _writetopdf_filechooser = new JFileChooser();
\r
296 _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
\r
297 _writetographics_filechooser = new JFileChooser();
\r
298 _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
\r
300 _msa_filechooser = new JFileChooser();
\r
301 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
\r
302 _msa_filechooser.setCurrentDirectory( new File( "." ) );
\r
303 _msa_filechooser.setMultiSelectionEnabled( false );
\r
304 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
\r
305 _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
\r
307 _seqs_pi_filechooser = new JFileChooser();
\r
308 _seqs_pi_filechooser.setName( "Read Sequences File" );
\r
309 _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
\r
310 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
\r
311 _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
\r
312 _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
\r
314 _values_filechooser = new JFileChooser();
\r
315 _values_filechooser.setCurrentDirectory( new File( "." ) );
\r
316 _values_filechooser.setMultiSelectionEnabled( false );
\r
318 _sequences_filechooser = new JFileChooser();
\r
319 _sequences_filechooser.setCurrentDirectory( new File( "." ) );
\r
320 _sequences_filechooser.setMultiSelectionEnabled( false );
\r
321 // build the menu bar
\r
322 _jmenubar = new JMenuBar();
\r
323 if ( !_configuration.isUseNativeUI() ) {
\r
324 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
327 if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
\r
328 buildPhylogeneticInferenceMenu();
\r
330 buildAnalysisMenu();
\r
333 buildFontSizeMenu();
\r
334 buildOptionsMenu();
\r
337 setJMenuBar( _jmenubar );
\r
338 _jmenubar.add( _help_jmenu );
\r
339 _contentpane = getContentPane();
\r
340 _contentpane.setLayout( new BorderLayout() );
\r
341 _contentpane.add( _mainpanel, BorderLayout.CENTER );
\r
343 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
\r
344 // addWindowFocusListener( new WindowAdapter() {
\r
347 // public void windowGainedFocus( WindowEvent e ) {
\r
348 // requestFocusInWindow();
\r
351 // The window listener
\r
352 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
\r
353 addWindowListener( new WindowAdapter() {
\r
356 public void windowClosing( final WindowEvent e ) {
\r
357 if ( isUnsavedDataPresent() ) {
\r
358 final int r = JOptionPane.showConfirmDialog( null,
\r
359 "Exit despite potentially unsaved changes?",
\r
361 JOptionPane.YES_NO_OPTION );
\r
362 if ( r != JOptionPane.YES_OPTION ) {
\r
367 final int r = JOptionPane.showConfirmDialog( null,
\r
368 "Exit Archaeopteryx?",
\r
370 JOptionPane.YES_NO_OPTION );
\r
371 if ( r != JOptionPane.YES_OPTION ) {
\r
378 // The component listener
\r
379 addComponentListener( new ComponentAdapter() {
\r
382 public void componentResized( final ComponentEvent e ) {
\r
383 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
384 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
\r
386 _mainpanel.getCurrentTreePanel()
\r
388 getOptions().isAllowFontSizeChange() );
\r
392 requestFocusInWindow();
\r
393 // addKeyListener( this );
\r
394 setVisible( true );
\r
395 if ( ( phys != null ) && ( phys.length > 0 ) ) {
\r
396 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
\r
398 getMainPanel().getControlPanel().showWholeAll();
\r
399 getMainPanel().getControlPanel().showWhole();
\r
401 activateSaveAllIfNeeded();
\r
402 // ...and its children
\r
403 _contentpane.repaint();
\r
407 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
\r
408 // Reads the config file (false, false => not url, not applet):
\r
409 this( phys, new Configuration( config_file, false, false, true ), title );
\r
413 public void actionPerformed( final ActionEvent e ) {
\r
415 super.actionPerformed( e );
\r
416 final Object o = e.getSource();
\r
417 // Handle app-specific actions here:
\r
418 if ( o == _open_item ) {
\r
419 readPhylogeniesFromFile();
\r
421 if ( o == _open_url_item ) {
\r
422 readPhylogeniesFromURL();
\r
424 else if ( o == _save_item ) {
\r
425 writeToFile( _mainpanel.getCurrentPhylogeny() );
\r
426 // If subtree currently displayed, save it, instead of complete
\r
429 else if ( o == _new_item ) {
\r
432 else if ( o == _save_all_item ) {
\r
435 else if ( o == _close_item ) {
\r
436 closeCurrentPane();
\r
438 else if ( o == _write_to_pdf_item ) {
\r
439 writeToPdf( _mainpanel.getCurrentPhylogeny() );
\r
441 else if ( o == _write_to_jpg_item ) {
\r
442 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
\r
444 else if ( o == _write_to_png_item ) {
\r
445 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
\r
447 else if ( o == _write_to_gif_item ) {
\r
448 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
\r
450 else if ( o == _write_to_tif_item ) {
\r
451 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
\r
453 else if ( o == _write_to_bmp_item ) {
\r
454 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
\r
456 else if ( o == _print_item ) {
\r
459 else if ( o == _load_species_tree_item ) {
\r
460 readSpeciesTreeFromFile();
\r
462 else if ( o == _lineage_inference ) {
\r
463 if ( isSubtreeDisplayed() ) {
\r
464 JOptionPane.showMessageDialog( this,
\r
465 "Subtree is shown.",
\r
466 "Cannot infer ancestral taxonomies",
\r
467 JOptionPane.ERROR_MESSAGE );
\r
470 executeLineageInference();
\r
472 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
\r
473 if ( isSubtreeDisplayed() ) {
\r
476 obtainDetailedTaxonomicInformation();
\r
478 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
\r
479 if ( isSubtreeDisplayed() ) {
\r
482 obtainDetailedTaxonomicInformationDelete();
\r
484 else if ( o == _obtain_seq_information_jmi ) {
\r
485 obtainSequenceInformation();
\r
487 else if ( o == _read_values_jmi ) {
\r
488 if ( isSubtreeDisplayed() ) {
\r
491 addExpressionValuesFromFile();
\r
493 else if ( o == _read_seqs_jmi ) {
\r
494 if ( isSubtreeDisplayed() ) {
\r
497 addSequencesFromFile();
\r
499 else if ( o == _move_node_names_to_tax_sn_jmi ) {
\r
500 moveNodeNamesToTaxSn();
\r
502 else if ( o == _move_node_names_to_seq_names_jmi ) {
\r
503 moveNodeNamesToSeqNames();
\r
505 else if ( o == _extract_tax_code_from_node_names_jmi ) {
\r
506 extractTaxDataFromNodeNames();
\r
508 else if ( o == _graphics_export_visible_only_cbmi ) {
\r
509 updateOptions( getOptions() );
\r
511 else if ( o == _antialias_print_cbmi ) {
\r
512 updateOptions( getOptions() );
\r
514 else if ( o == _print_black_and_white_cbmi ) {
\r
515 updateOptions( getOptions() );
\r
517 else if ( o == _print_using_actual_size_cbmi ) {
\r
518 updateOptions( getOptions() );
\r
520 else if ( o == _graphics_export_using_actual_size_cbmi ) {
\r
521 updateOptions( getOptions() );
\r
523 else if ( o == _print_size_mi ) {
\r
526 else if ( o == _choose_pdf_width_mi ) {
\r
529 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
\r
530 updateOptions( getOptions() );
\r
532 else if ( o == _replace_underscores_cbmi ) {
\r
533 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
\r
534 _extract_taxonomy_no_rbmi.setSelected( true );
\r
536 updateOptions( getOptions() );
\r
538 else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
\r
539 updateOptions( getOptions() );
\r
541 else if ( o == _collapse_below_threshold ) {
\r
542 if ( isSubtreeDisplayed() ) {
\r
545 collapseBelowThreshold();
\r
547 else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
\r
548 || ( o == _extract_taxonomy_agressive_rbmi ) ) {
\r
549 if ( _replace_underscores_cbmi != null ) {
\r
550 _replace_underscores_cbmi.setSelected( false );
\r
552 updateOptions( getOptions() );
\r
554 else if ( o == _extract_taxonomy_no_rbmi ) {
\r
555 updateOptions( getOptions() );
\r
557 else if ( o == _inference_from_msa_item ) {
\r
558 executePhyleneticInference( false );
\r
560 else if ( o == _inference_from_seqs_item ) {
\r
561 executePhyleneticInference( true );
\r
563 _contentpane.repaint();
\r
565 catch ( final Exception ex ) {
\r
566 AptxUtil.unexpectedException( ex );
\r
568 catch ( final Error err ) {
\r
569 AptxUtil.unexpectedError( err );
\r
573 public void end() {
\r
574 _mainpanel.terminate();
\r
575 _contentpane.removeAll();
\r
576 setVisible( false );
\r
581 public MainPanel getMainPanel() {
\r
585 public Msa getMsa() {
\r
589 public File getMsaFile() {
\r
593 public List<Sequence> getSeqs() {
\r
597 public File getSeqsFile() {
\r
601 public void readMsaFromFile() {
\r
602 // Set an initial directory if none set yet
\r
603 final File my_dir = getCurrentDir();
\r
604 _msa_filechooser.setMultiSelectionEnabled( false );
\r
605 // Open file-open dialog and set current directory
\r
606 if ( my_dir != null ) {
\r
607 _msa_filechooser.setCurrentDirectory( my_dir );
\r
609 final int result = _msa_filechooser.showOpenDialog( _contentpane );
\r
610 // All done: get the msa
\r
611 final File file = _msa_filechooser.getSelectedFile();
\r
612 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
\r
613 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
614 setMsaFile( null );
\r
618 final InputStream is = new FileInputStream( file );
\r
619 if ( FastaParser.isLikelyFasta( file ) ) {
\r
620 msa = FastaParser.parseMsa( is );
\r
623 msa = GeneralMsaParser.parse( is );
\r
626 catch ( final MsaFormatException e ) {
\r
628 JOptionPane.showMessageDialog( this,
\r
629 e.getLocalizedMessage(),
\r
630 "Multiple sequence alignment format error",
\r
631 JOptionPane.ERROR_MESSAGE );
\r
634 catch ( final IOException e ) {
\r
636 JOptionPane.showMessageDialog( this,
\r
637 e.getLocalizedMessage(),
\r
638 "Failed to read multiple sequence alignment",
\r
639 JOptionPane.ERROR_MESSAGE );
\r
642 catch ( final IllegalArgumentException e ) {
\r
644 JOptionPane.showMessageDialog( this,
\r
645 e.getLocalizedMessage(),
\r
646 "Unexpected error during reading of multiple sequence alignment",
\r
647 JOptionPane.ERROR_MESSAGE );
\r
650 catch ( final Exception e ) {
\r
652 e.printStackTrace();
\r
653 JOptionPane.showMessageDialog( this,
\r
654 e.getLocalizedMessage(),
\r
655 "Unexpected error during reading of multiple sequence alignment",
\r
656 JOptionPane.ERROR_MESSAGE );
\r
659 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
\r
660 JOptionPane.showMessageDialog( this,
\r
661 "Multiple sequence alignment is empty",
\r
662 "Illegal Multiple Sequence Alignment",
\r
663 JOptionPane.ERROR_MESSAGE );
\r
666 if ( msa.getNumberOfSequences() < 4 ) {
\r
667 JOptionPane.showMessageDialog( this,
\r
668 "Multiple sequence alignment needs to contain at least 3 sequences",
\r
669 "Illegal multiple sequence alignment",
\r
670 JOptionPane.ERROR_MESSAGE );
\r
673 if ( msa.getLength() < 2 ) {
\r
674 JOptionPane.showMessageDialog( this,
\r
675 "Multiple sequence alignment needs to contain at least 2 residues",
\r
676 "Illegal multiple sequence alignment",
\r
677 JOptionPane.ERROR_MESSAGE );
\r
681 setMsaFile( _msa_filechooser.getSelectedFile() );
\r
686 public void readSeqsFromFileforPI() {
\r
687 // Set an initial directory if none set yet
\r
688 final File my_dir = getCurrentDir();
\r
689 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
\r
690 // Open file-open dialog and set current directory
\r
691 if ( my_dir != null ) {
\r
692 _seqs_pi_filechooser.setCurrentDirectory( my_dir );
\r
694 final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
\r
695 // All done: get the seqs
\r
696 final File file = _seqs_pi_filechooser.getSelectedFile();
\r
697 setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
\r
698 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
699 setSeqsFile( null );
\r
701 List<Sequence> seqs = null;
\r
703 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
\r
704 seqs = FastaParser.parse( new FileInputStream( file ) );
\r
705 for( final Sequence seq : seqs ) {
\r
706 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
\r
713 catch ( final MsaFormatException e ) {
\r
715 JOptionPane.showMessageDialog( this,
\r
716 e.getLocalizedMessage(),
\r
717 "Multiple sequence file format error",
\r
718 JOptionPane.ERROR_MESSAGE );
\r
721 catch ( final IOException e ) {
\r
723 JOptionPane.showMessageDialog( this,
\r
724 e.getLocalizedMessage(),
\r
725 "Failed to read multiple sequence file",
\r
726 JOptionPane.ERROR_MESSAGE );
\r
729 catch ( final IllegalArgumentException e ) {
\r
731 JOptionPane.showMessageDialog( this,
\r
732 e.getLocalizedMessage(),
\r
733 "Unexpected error during reading of multiple sequence file",
\r
734 JOptionPane.ERROR_MESSAGE );
\r
737 catch ( final Exception e ) {
\r
739 e.printStackTrace();
\r
740 JOptionPane.showMessageDialog( this,
\r
741 e.getLocalizedMessage(),
\r
742 "Unexpected error during reading of multiple sequence file",
\r
743 JOptionPane.ERROR_MESSAGE );
\r
746 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
747 JOptionPane.showMessageDialog( this,
\r
748 "Multiple sequence file is empty",
\r
749 "Illegal multiple sequence file",
\r
750 JOptionPane.ERROR_MESSAGE );
\r
753 if ( seqs.size() < 4 ) {
\r
754 JOptionPane.showMessageDialog( this,
\r
755 "Multiple sequence file needs to contain at least 3 sequences",
\r
756 "Illegal multiple sequence file",
\r
757 JOptionPane.ERROR_MESSAGE );
\r
760 // if ( msa.getLength() < 2 ) {
\r
761 // JOptionPane.showMessageDialog( this,
\r
762 // "Multiple sequence alignment needs to contain at least 2 residues",
\r
763 // "Illegal multiple sequence file",
\r
764 // JOptionPane.ERROR_MESSAGE );
\r
768 setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
\r
773 void buildAnalysisMenu() {
\r
774 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
\r
775 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
\r
776 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
\r
777 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
\r
778 customizeJMenuItem( _gsdi_item );
\r
779 customizeJMenuItem( _gsdir_item );
\r
780 customizeJMenuItem( _load_species_tree_item );
\r
781 _analysis_menu.addSeparator();
\r
782 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
\r
783 customizeJMenuItem( _lineage_inference );
\r
784 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
\r
785 _jmenubar.add( _analysis_menu );
\r
789 void buildFileMenu() {
\r
790 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
791 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
\r
792 _file_jmenu.addSeparator();
\r
793 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
\r
794 _file_jmenu.addSeparator();
\r
795 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
\r
796 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
\r
797 .getAvailablePhylogeniesWebserviceClients().size() ];
\r
798 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
799 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
\r
800 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
\r
801 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
803 if ( getConfiguration().isEditable() ) {
\r
804 _file_jmenu.addSeparator();
\r
805 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
\r
806 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
\r
808 _file_jmenu.addSeparator();
\r
809 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
810 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
\r
811 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
\r
812 _save_all_item.setEnabled( false );
\r
813 _file_jmenu.addSeparator();
\r
814 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
815 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
816 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
818 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
819 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
820 if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
821 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
823 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
824 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
826 _file_jmenu.addSeparator();
\r
827 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
828 _file_jmenu.addSeparator();
\r
829 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
\r
830 _close_item.setToolTipText( "To close the current pane." );
\r
831 _close_item.setEnabled( true );
\r
832 _file_jmenu.addSeparator();
\r
833 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
834 customizeJMenuItem( _open_item );
\r
836 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
\r
837 customizeJMenuItem( _open_url_item );
\r
838 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
839 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
841 customizeJMenuItem( _save_item );
\r
842 if ( getConfiguration().isEditable() ) {
\r
843 customizeJMenuItem( _new_item );
\r
845 customizeJMenuItem( _close_item );
\r
846 customizeJMenuItem( _save_all_item );
\r
847 customizeJMenuItem( _write_to_pdf_item );
\r
848 customizeJMenuItem( _write_to_png_item );
\r
849 customizeJMenuItem( _write_to_jpg_item );
\r
850 customizeJMenuItem( _write_to_gif_item );
\r
851 customizeJMenuItem( _write_to_tif_item );
\r
852 customizeJMenuItem( _write_to_bmp_item );
\r
853 customizeJMenuItem( _print_item );
\r
854 customizeJMenuItem( _exit_item );
\r
855 _jmenubar.add( _file_jmenu );
\r
858 void buildOptionsMenu() {
\r
859 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
\r
860 _options_jmenu.addChangeListener( new ChangeListener() {
\r
863 public void stateChanged( final ChangeEvent e ) {
\r
864 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
\r
865 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
\r
867 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
\r
868 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
\r
869 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
\r
870 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
\r
871 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
\r
872 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
\r
874 _show_branch_length_values_cbmi,
\r
875 _non_lined_up_cladograms_rbmi,
\r
876 _uniform_cladograms_rbmi,
\r
877 _ext_node_dependent_cladogram_rbmi,
\r
878 _label_direction_cbmi );
\r
879 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
\r
880 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
\r
881 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
\r
884 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
\r
886 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
\r
887 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
\r
888 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
\r
889 _radio_group_1 = new ButtonGroup();
\r
890 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
\r
891 _radio_group_1.add( _uniform_cladograms_rbmi );
\r
892 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
\r
894 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
\r
895 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
\r
897 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
\r
899 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
\r
901 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
\r
902 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
\r
903 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
\r
904 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
\r
906 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
\r
908 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
\r
909 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
\r
910 _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
\r
911 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
\r
912 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
\r
913 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
\r
914 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
\r
915 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
\r
916 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
\r
917 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
\r
918 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
\r
919 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
\r
920 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
\r
921 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
\r
922 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
\r
923 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
\r
924 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
\r
926 _options_jmenu.addSeparator();
\r
927 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
\r
928 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
\r
929 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
\r
930 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
\r
931 _options_jmenu.addSeparator();
\r
932 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
\r
933 getConfiguration() ) );
\r
934 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
\r
935 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
\r
937 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
\r
939 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
\r
941 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
\r
942 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
\r
943 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
\r
944 _options_jmenu.addSeparator();
\r
945 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
\r
947 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
\r
948 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
\r
950 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
\r
952 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
\r
954 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
\r
956 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
\r
958 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
\r
959 _extract_taxonomy_pfam_strict_rbmi
\r
960 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
\r
961 _extract_taxonomy_pfam_relaxed_rbmi
\r
962 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
\r
963 _extract_taxonomy_agressive_rbmi
\r
964 .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
\r
965 _radio_group_2 = new ButtonGroup();
\r
966 _radio_group_2.add( _extract_taxonomy_no_rbmi );
\r
967 _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
\r
968 _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
\r
969 _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
\r
971 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
\r
973 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
\r
974 _use_brackets_for_conf_in_nh_export_cbmi
\r
975 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
\r
977 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
\r
978 customizeJMenuItem( _choose_font_mi );
\r
979 customizeJMenuItem( _choose_minimal_confidence_mi );
\r
980 customizeJMenuItem( _switch_colors_mi );
\r
981 customizeJMenuItem( _print_size_mi );
\r
982 customizeJMenuItem( _choose_pdf_width_mi );
\r
983 customizeJMenuItem( _overview_placment_mi );
\r
984 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
\r
985 .isShowDefaultNodeShapesExternal() );
\r
986 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
\r
987 .isShowDefaultNodeShapesInternal() );
\r
988 customizeJMenuItem( _cycle_node_shape_mi );
\r
989 customizeJMenuItem( _cycle_node_fill_mi );
\r
990 customizeJMenuItem( _choose_node_size_mi );
\r
991 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
\r
992 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
\r
993 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
\r
994 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
\r
995 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
\r
996 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
\r
997 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
\r
998 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
\r
999 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
\r
1000 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
\r
1001 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
\r
1002 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
\r
1003 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1004 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
\r
1005 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1006 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
\r
1007 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
\r
1008 customizeCheckBoxMenuItem( _label_direction_cbmi,
\r
1009 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
\r
1010 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
\r
1011 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
\r
1012 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
\r
1013 .isInternalNumberAreConfidenceForNhParsing() );
\r
1014 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
\r
1015 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
\r
1016 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
\r
1017 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1018 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
\r
1019 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1020 customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
\r
1021 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1022 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
\r
1023 customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
\r
1024 .isReplaceUnderscoresInNhParsing() );
\r
1025 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
\r
1026 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
\r
1027 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
\r
1028 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
\r
1029 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
\r
1030 .isGraphicsExportUsingActualSize() );
\r
1031 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
\r
1032 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
\r
1033 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1034 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
\r
1035 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1038 customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData()
\r
1041 customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
\r
1042 _jmenubar.add( _options_jmenu );
\r
1045 void buildPhylogeneticInferenceMenu() {
\r
1046 final InferenceManager im = getInferenceManager();
\r
1047 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
\r
1048 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
\r
1049 customizeJMenuItem( _inference_from_msa_item );
\r
1050 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
\r
1051 if ( im.canDoMsa() ) {
\r
1052 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
\r
1053 customizeJMenuItem( _inference_from_seqs_item );
\r
1054 _inference_from_seqs_item
\r
1055 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
\r
1059 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
\r
1060 customizeJMenuItem( _inference_from_seqs_item );
\r
1061 _inference_from_seqs_item.setEnabled( false );
\r
1063 _jmenubar.add( _inference_menu );
\r
1066 void buildToolsMenu() {
\r
1067 _tools_menu = createMenu( "Tools", getConfiguration() );
\r
1068 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
\r
1069 customizeJMenuItem( _confcolor_item );
\r
1070 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
\r
1071 customizeJMenuItem( _color_rank_jmi );
\r
1072 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
\r
1073 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
\r
1074 customizeJMenuItem( _taxcolor_item );
\r
1075 _tools_menu.addSeparator();
\r
1076 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
\r
1077 _remove_visual_styles_item
\r
1078 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
\r
1079 customizeJMenuItem( _remove_visual_styles_item );
\r
1080 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
\r
1081 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
\r
1082 customizeJMenuItem( _remove_branch_color_item );
\r
1083 _tools_menu.addSeparator();
\r
1084 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
\r
1085 customizeJMenuItem( _annotate_item );
\r
1086 _tools_menu.addSeparator();
\r
1087 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
\r
1088 customizeJMenuItem( _midpoint_root_item );
\r
1089 _tools_menu.addSeparator();
\r
1090 _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );
\r
1091 _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );
\r
1092 customizeJMenuItem( _delete_selected_nodes_item );
\r
1093 _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );
\r
1094 _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
\r
1096 customizeJMenuItem( _delete_not_selected_nodes_item );
\r
1097 _tools_menu.addSeparator();
\r
1098 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
\r
1099 customizeJMenuItem( _collapse_species_specific_subtrees );
\r
1101 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
\r
1102 customizeJMenuItem( _collapse_below_threshold );
\r
1103 _collapse_below_threshold
\r
1104 .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)" );
\r
1105 _tools_menu.addSeparator();
\r
1107 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
\r
1108 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
\r
1109 _extract_tax_code_from_node_names_jmi
\r
1110 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
\r
1112 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
\r
1113 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
\r
1114 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
\r
1115 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
\r
1116 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
\r
1117 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
\r
1118 _tools_menu.addSeparator();
\r
1119 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
\r
1120 customizeJMenuItem( _obtain_seq_information_jmi );
\r
1121 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
\r
1123 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
\r
1124 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
\r
1125 _obtain_detailed_taxonomic_information_jmi
\r
1126 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
\r
1128 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
\r
1129 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
\r
1130 _obtain_detailed_taxonomic_information_deleting_jmi
\r
1131 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
\r
1132 _tools_menu.addSeparator();
\r
1133 _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
\r
1134 customizeJMenuItem( _read_values_jmi );
\r
1135 _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
\r
1136 _jmenubar.add( _tools_menu );
\r
1137 _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
\r
1138 customizeJMenuItem( _read_seqs_jmi );
\r
1140 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
\r
1141 _jmenubar.add( _tools_menu );
\r
1146 if ( isUnsavedDataPresent() ) {
\r
1147 final int r = JOptionPane.showConfirmDialog( this,
\r
1148 "Exit despite potentially unsaved changes?",
\r
1150 JOptionPane.YES_NO_OPTION );
\r
1151 if ( r != JOptionPane.YES_OPTION ) {
\r
1158 void executeLineageInference() {
\r
1159 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
\r
1162 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1163 JOptionPane.showMessageDialog( this,
\r
1164 "Phylogeny is not rooted.",
\r
1165 "Cannot infer ancestral taxonomies",
\r
1166 JOptionPane.ERROR_MESSAGE );
\r
1169 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
\r
1170 _mainpanel.getCurrentTreePanel(),
\r
1171 _mainpanel.getCurrentPhylogeny()
\r
1173 new Thread( inferrer ).start();
\r
1177 removeAllTextFrames();
\r
1178 _mainpanel.terminate();
\r
1179 _contentpane.removeAll();
\r
1180 setVisible( false );
\r
1185 void readPhylogeniesFromURL() {
\r
1187 Phylogeny[] phys = null;
\r
1188 final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
\r
1189 final String url_string = JOptionPane.showInputDialog( this,
\r
1191 "Use URL/webservice to obtain a phylogeny",
\r
1192 JOptionPane.QUESTION_MESSAGE );
\r
1193 boolean nhx_or_nexus = false;
\r
1194 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
\r
1196 url = new URL( url_string );
\r
1197 PhylogenyParser parser = null;
\r
1198 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
\r
1199 parser = new TolParser();
\r
1202 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
\r
1203 .isValidatePhyloXmlAgainstSchema() );
\r
1205 if ( parser instanceof NexusPhylogeniesParser ) {
\r
1206 nhx_or_nexus = true;
\r
1208 else if ( parser instanceof NHXParser ) {
\r
1209 nhx_or_nexus = true;
\r
1211 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1212 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
1215 _mainpanel.setWaitCursor();
\r
1217 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
1218 phys = factory.create( url.openStream(), parser );
\r
1220 catch ( final MalformedURLException e ) {
\r
1221 JOptionPane.showMessageDialog( this,
\r
1222 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
\r
1224 JOptionPane.ERROR_MESSAGE );
\r
1226 catch ( final IOException e ) {
\r
1227 JOptionPane.showMessageDialog( this,
\r
1228 "Could not read from " + url + "\n"
\r
1229 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1230 "Failed to read URL",
\r
1231 JOptionPane.ERROR_MESSAGE );
\r
1233 catch ( final Exception e ) {
\r
1234 JOptionPane.showMessageDialog( this,
\r
1235 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1236 "Unexpected Exception",
\r
1237 JOptionPane.ERROR_MESSAGE );
\r
1240 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1241 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1244 _mainpanel.setArrowCursor();
\r
1247 if ( ( phys != null ) && ( phys.length > 0 ) ) {
\r
1248 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
1249 for( final Phylogeny phy : phys ) {
\r
1251 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
1254 AptxUtil.addPhylogeniesToTabs( phys,
\r
1255 new File( url.getFile() ).getName(),
\r
1256 new File( url.getFile() ).toString(),
\r
1257 getConfiguration(),
\r
1259 _mainpanel.getControlPanel().showWhole();
\r
1262 activateSaveAllIfNeeded();
\r
1266 void setMsa( final Msa msa ) {
\r
1270 void setMsaFile( final File msa_file ) {
\r
1271 _msa_file = msa_file;
\r
1274 void setSeqs( final List<Sequence> seqs ) {
\r
1278 void setSeqsFile( final File seqs_file ) {
\r
1279 _seqs_file = seqs_file;
\r
1282 void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
\r
1283 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
\r
1284 _mainpanel.getCurrentTreePanel().getHeight(),
\r
1286 String file_written_to = "";
\r
1287 boolean error = false;
\r
1289 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
\r
1290 _mainpanel.getCurrentTreePanel().getWidth(),
\r
1291 _mainpanel.getCurrentTreePanel().getHeight(),
\r
1292 _mainpanel.getCurrentTreePanel(),
\r
1293 _mainpanel.getControlPanel(),
\r
1297 catch ( final IOException e ) {
\r
1299 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
1302 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
\r
1303 JOptionPane.showMessageDialog( this,
\r
1304 "Wrote image to: " + file_written_to,
\r
1305 "Graphics Export",
\r
1306 JOptionPane.INFORMATION_MESSAGE );
\r
1309 JOptionPane.showMessageDialog( this,
\r
1310 "There was an unknown problem when attempting to write to an image file: \""
\r
1311 + file_name + "\"",
\r
1313 JOptionPane.ERROR_MESSAGE );
\r
1316 _contentpane.repaint();
\r
1319 private void addExpressionValuesFromFile() {
\r
1320 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
1321 JOptionPane.showMessageDialog( this,
\r
1322 "Need to load evolutionary tree first",
\r
1323 "Can Not Read Expression Values",
\r
1324 JOptionPane.WARNING_MESSAGE );
\r
1327 final File my_dir = getCurrentDir();
\r
1328 if ( my_dir != null ) {
\r
1329 _values_filechooser.setCurrentDirectory( my_dir );
\r
1331 final int result = _values_filechooser.showOpenDialog( _contentpane );
\r
1332 final File file = _values_filechooser.getSelectedFile();
\r
1333 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1334 BasicTable<String> t = null;
\r
1336 t = BasicTableParser.parse( file, '\t' );
\r
1337 if ( t.getNumberOfColumns() < 2 ) {
\r
1338 t = BasicTableParser.parse( file, ',' );
\r
1340 if ( t.getNumberOfColumns() < 2 ) {
\r
1341 t = BasicTableParser.parse( file, ' ' );
\r
1344 catch ( final IOException e ) {
\r
1345 JOptionPane.showMessageDialog( this,
\r
1347 "Could Not Read Expression Value Table",
\r
1348 JOptionPane.ERROR_MESSAGE );
\r
1351 if ( t.getNumberOfColumns() < 2 ) {
\r
1352 JOptionPane.showMessageDialog( this,
\r
1353 "Table contains " + t.getNumberOfColumns() + " column(s)",
\r
1354 "Problem with Expression Value Table",
\r
1355 JOptionPane.ERROR_MESSAGE );
\r
1358 if ( t.getNumberOfRows() < 1 ) {
\r
1359 JOptionPane.showMessageDialog( this,
\r
1360 "Table contains zero rows",
\r
1361 "Problem with Expression Value Table",
\r
1362 JOptionPane.ERROR_MESSAGE );
\r
1365 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1366 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
\r
1367 JOptionPane.showMessageDialog( this,
\r
1368 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
\r
1369 + phy.getNumberOfExternalNodes() + " external nodes",
\r
1371 JOptionPane.WARNING_MESSAGE );
\r
1373 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
\r
1374 int not_found = 0;
\r
1375 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
1376 final PhylogenyNode node = iter.next();
\r
1377 final String node_name = node.getName();
\r
1378 if ( !ForesterUtil.isEmpty( node_name ) ) {
\r
1381 row = t.findRow( node_name );
\r
1383 catch ( final IllegalArgumentException e ) {
\r
1385 .showMessageDialog( this,
\r
1387 "Error Mapping Node Identifiers to Expression Value Identifiers",
\r
1388 JOptionPane.ERROR_MESSAGE );
\r
1392 if ( node.isExternal() ) {
\r
1397 final List<Double> l = new ArrayList<Double>();
\r
1398 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
\r
1401 d = Double.parseDouble( t.getValueAsString( col, row ) );
\r
1403 catch ( final NumberFormatException e ) {
\r
1404 JOptionPane.showMessageDialog( this,
\r
1405 "Could not parse \"" + t.getValueAsString( col, row )
\r
1406 + "\" into a decimal value",
\r
1407 "Issue with Expression Value Table",
\r
1408 JOptionPane.ERROR_MESSAGE );
\r
1411 stats.addValue( d );
\r
1414 if ( !l.isEmpty() ) {
\r
1415 if ( node.getNodeData().getProperties() != null ) {
\r
1416 node.getNodeData().getProperties()
\r
1417 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
\r
1419 node.getNodeData().setVector( l );
\r
1423 if ( not_found > 0 ) {
\r
1424 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
\r
1425 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
\r
1427 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
\r
1431 private void addSequencesFromFile() {
\r
1432 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
1433 JOptionPane.showMessageDialog( this,
\r
1434 "Need to load evolutionary tree first",
\r
1435 "Can Not Read Sequences",
\r
1436 JOptionPane.WARNING_MESSAGE );
\r
1439 final File my_dir = getCurrentDir();
\r
1440 if ( my_dir != null ) {
\r
1441 _sequences_filechooser.setCurrentDirectory( my_dir );
\r
1443 final int result = _sequences_filechooser.showOpenDialog( _contentpane );
\r
1444 final File file = _sequences_filechooser.getSelectedFile();
\r
1445 List<Sequence> seqs = null;
\r
1446 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1448 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
\r
1449 seqs = FastaParser.parse( new FileInputStream( file ) );
\r
1452 JOptionPane.showMessageDialog( this,
\r
1453 "Format does not appear to be Fasta",
\r
1454 "Multiple sequence file format error",
\r
1455 JOptionPane.ERROR_MESSAGE );
\r
1459 catch ( final MsaFormatException e ) {
\r
1461 JOptionPane.showMessageDialog( this,
\r
1462 e.getLocalizedMessage(),
\r
1463 "Multiple sequence file format error",
\r
1464 JOptionPane.ERROR_MESSAGE );
\r
1467 catch ( final IOException e ) {
\r
1469 JOptionPane.showMessageDialog( this,
\r
1470 e.getLocalizedMessage(),
\r
1471 "Failed to read multiple sequence file",
\r
1472 JOptionPane.ERROR_MESSAGE );
\r
1475 catch ( final Exception e ) {
\r
1477 e.printStackTrace();
\r
1478 JOptionPane.showMessageDialog( this,
\r
1479 e.getLocalizedMessage(),
\r
1480 "Unexpected error during reading of multiple sequence file",
\r
1481 JOptionPane.ERROR_MESSAGE );
\r
1484 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
1485 JOptionPane.showMessageDialog( this,
\r
1486 "Multiple sequence file is empty",
\r
1487 "Empty multiple sequence file",
\r
1488 JOptionPane.ERROR_MESSAGE );
\r
1493 if ( seqs != null ) {
\r
1494 for( final Sequence seq : seqs ) {
\r
1495 System.out.println( seq.getIdentifier() );
\r
1497 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1498 int total_counter = 0;
\r
1499 int attached_counter = 0;
\r
1500 for( final Sequence seq : seqs ) {
\r
1502 final String seq_name = seq.getIdentifier();
\r
1503 if ( !ForesterUtil.isEmpty( seq_name ) ) {
\r
1504 List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
\r
1505 if ( nodes.isEmpty() ) {
\r
1506 nodes = phy.getNodesViaSequenceSymbol( seq_name );
\r
1508 if ( nodes.isEmpty() ) {
\r
1509 nodes = phy.getNodesViaGeneName( seq_name );
\r
1511 if ( nodes.isEmpty() ) {
\r
1512 nodes = phy.getNodes( seq_name );
\r
1514 if ( nodes.size() > 1 ) {
\r
1515 JOptionPane.showMessageDialog( this,
\r
1516 "Sequence name \"" + seq_name + "\" is not unique",
\r
1517 "Sequence name not unique",
\r
1518 JOptionPane.ERROR_MESSAGE );
\r
1522 final String[] a = seq_name.split( "\\s" );
\r
1523 if ( nodes.isEmpty() && ( a.length > 1 ) ) {
\r
1524 final String seq_name_split = a[ 0 ];
\r
1525 nodes = phy.getNodesViaSequenceName( seq_name_split );
\r
1526 if ( nodes.isEmpty() ) {
\r
1527 nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
\r
1529 if ( nodes.isEmpty() ) {
\r
1530 nodes = phy.getNodes( seq_name_split );
\r
1532 if ( nodes.size() > 1 ) {
\r
1533 JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
\r
1534 + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
\r
1539 if ( nodes.size() == 1 ) {
\r
1540 ++attached_counter;
\r
1541 final PhylogenyNode n = nodes.get( 0 );
\r
1542 if ( !n.getNodeData().isHasSequence() ) {
\r
1543 n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
\r
1545 n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
\r
1546 if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
\r
1547 n.getNodeData().getSequence().setName( seq_name );
\r
1552 if ( attached_counter > 0 ) {
\r
1553 int ext_nodes = 0;
\r
1554 int ext_nodes_with_seq = 0;
\r
1555 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
\r
1557 final PhylogenyNode n = iter.next();
\r
1558 if ( n.getNodeData().isHasSequence()
\r
1559 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
\r
1560 ++ext_nodes_with_seq;
\r
1564 if ( ext_nodes == ext_nodes_with_seq ) {
\r
1565 s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
\r
1568 s = ext_nodes_with_seq + " out of " + ext_nodes
\r
1569 + " external nodes now have a molecular sequence attached to them.";
\r
1571 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
\r
1572 JOptionPane.showMessageDialog( this,
\r
1573 "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
\r
1574 "All sequences attached",
\r
1575 JOptionPane.INFORMATION_MESSAGE );
\r
1578 JOptionPane.showMessageDialog( this, "Attached " + attached_counter
\r
1579 + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
\r
1580 + " sequences attached", JOptionPane.WARNING_MESSAGE );
\r
1584 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
\r
1585 + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
\r
1590 private void choosePdfWidth() {
\r
1591 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1592 "Please enter the default line width for PDF export.\n"
\r
1593 + "[current value: "
\r
1594 + getOptions().getPrintLineWidth() + "]\n",
\r
1595 "Line Width for PDF Export",
\r
1596 JOptionPane.QUESTION_MESSAGE,
\r
1599 getOptions().getPrintLineWidth() );
\r
1600 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1601 boolean success = true;
\r
1603 final String m_str = s.trim();
\r
1604 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1606 f = Float.parseFloat( m_str );
\r
1608 catch ( final Exception ex ) {
\r
1615 if ( success && ( f > 0.0 ) ) {
\r
1616 getOptions().setPrintLineWidth( f );
\r
1621 private void choosePrintSize() {
\r
1622 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1623 "Please enter values for width and height,\nseparated by a comma.\n"
\r
1624 + "[current values: "
\r
1625 + getOptions().getPrintSizeX() + ", "
\r
1626 + getOptions().getPrintSizeY() + "]\n"
\r
1627 + "[A4: " + Constants.A4_SIZE_X + ", "
\r
1628 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
\r
1629 + Constants.US_LETTER_SIZE_X + ", "
\r
1630 + Constants.US_LETTER_SIZE_Y + "]",
\r
1631 "Default Size for Graphics Export",
\r
1632 JOptionPane.QUESTION_MESSAGE,
\r
1635 getOptions().getPrintSizeX() + ", "
\r
1636 + getOptions().getPrintSizeY() );
\r
1637 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
\r
1638 boolean success = true;
\r
1641 final String[] str_ary = s.split( "," );
\r
1642 if ( str_ary.length == 2 ) {
\r
1643 final String x_str = str_ary[ 0 ].trim();
\r
1644 final String y_str = str_ary[ 1 ].trim();
\r
1645 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
\r
1647 x = Integer.parseInt( x_str );
\r
1648 y = Integer.parseInt( y_str );
\r
1650 catch ( final Exception ex ) {
\r
1661 if ( success && ( x > 1 ) && ( y > 1 ) ) {
\r
1662 getOptions().setPrintSizeX( x );
\r
1663 getOptions().setPrintSizeY( y );
\r
1668 private void closeCurrentPane() {
\r
1669 if ( getMainPanel().getCurrentTreePanel() != null ) {
\r
1670 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
\r
1671 final int r = JOptionPane.showConfirmDialog( this,
\r
1672 "Close tab despite potentially unsaved changes?",
\r
1674 JOptionPane.YES_NO_OPTION );
\r
1675 if ( r != JOptionPane.YES_OPTION ) {
\r
1679 getMainPanel().closeCurrentPane();
\r
1680 activateSaveAllIfNeeded();
\r
1684 private void collapse( final Phylogeny phy, final double m ) {
\r
1685 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1686 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
\r
1687 double min_support = Double.MAX_VALUE;
\r
1688 boolean conf_present = false;
\r
1689 while ( it.hasNext() ) {
\r
1690 final PhylogenyNode n = it.next();
\r
1691 if ( !n.isExternal() && !n.isRoot() ) {
\r
1692 final List<Confidence> c = n.getBranchData().getConfidences();
\r
1693 if ( ( c != null ) && ( c.size() > 0 ) ) {
\r
1694 conf_present = true;
\r
1696 for( final Confidence confidence : c ) {
\r
1697 if ( confidence.getValue() > max ) {
\r
1698 max = confidence.getValue();
\r
1701 if ( max < getMinNotCollapseConfidenceValue() ) {
\r
1702 to_be_removed.add( n );
\r
1704 if ( max < min_support ) {
\r
1705 min_support = max;
\r
1710 if ( conf_present ) {
\r
1711 for( final PhylogenyNode node : to_be_removed ) {
\r
1712 PhylogenyMethods.removeNode( node, phy );
\r
1714 if ( to_be_removed.size() > 0 ) {
\r
1715 phy.externalNodesHaveChanged();
\r
1716 phy.clearHashIdToNodeMap();
\r
1717 phy.recalculateNumberOfExternalDescendants( true );
\r
1718 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1719 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
\r
1720 getCurrentTreePanel().calculateLongestExtNodeInfo();
\r
1721 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1722 getCurrentTreePanel().recalculateMaxDistanceToRoot();
\r
1723 getCurrentTreePanel().resetPreferredSize();
\r
1724 getCurrentTreePanel().setEdited( true );
\r
1725 getCurrentTreePanel().repaint();
\r
1728 if ( to_be_removed.size() > 0 ) {
\r
1729 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
\r
1730 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
\r
1731 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
\r
1734 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
\r
1735 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
\r
1739 JOptionPane.showMessageDialog( this,
\r
1740 "No branch collapsed because no confidence values present",
\r
1741 "No confidence values present",
\r
1742 JOptionPane.INFORMATION_MESSAGE );
\r
1746 private void collapseBelowThreshold() {
\r
1747 if ( getCurrentTreePanel() != null ) {
\r
1748 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1749 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1750 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1751 "Please enter the minimum confidence value\n",
\r
1752 "Minimal Confidence Value",
\r
1753 JOptionPane.QUESTION_MESSAGE,
\r
1756 getMinNotCollapseConfidenceValue() );
\r
1757 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1758 boolean success = true;
\r
1760 final String m_str = s.trim();
\r
1761 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1763 m = Double.parseDouble( m_str );
\r
1765 catch ( final Exception ex ) {
\r
1772 if ( success && ( m >= 0.0 ) ) {
\r
1773 setMinNotCollapseConfidenceValue( m );
\r
1774 collapse( phy, m );
\r
1781 private PhyloXmlParser createPhyloXmlParser() {
\r
1782 PhyloXmlParser xml_parser = null;
\r
1783 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
\r
1785 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
\r
1787 catch ( final Exception e ) {
\r
1788 JOptionPane.showMessageDialog( this,
\r
1789 e.getLocalizedMessage(),
\r
1790 "failed to create validating XML parser",
\r
1791 JOptionPane.WARNING_MESSAGE );
\r
1794 if ( xml_parser == null ) {
\r
1795 xml_parser = PhyloXmlParser.createPhyloXmlParser();
\r
1797 return xml_parser;
\r
1800 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
\r
1801 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
\r
1802 getPhylogeneticInferenceOptions(),
\r
1803 from_unaligned_seqs );
\r
1804 dialog.activate();
\r
1805 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
\r
1806 if ( !from_unaligned_seqs ) {
\r
1807 if ( getMsa() != null ) {
\r
1808 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
\r
1809 getPhylogeneticInferenceOptions()
\r
1811 new Thread( inferrer ).start();
\r
1814 JOptionPane.showMessageDialog( this,
\r
1815 "No multiple sequence alignment selected",
\r
1816 "Phylogenetic Inference Not Launched",
\r
1817 JOptionPane.WARNING_MESSAGE );
\r
1821 if ( getSeqs() != null ) {
\r
1822 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
\r
1823 getPhylogeneticInferenceOptions()
\r
1825 new Thread( inferrer ).start();
\r
1828 JOptionPane.showMessageDialog( this,
\r
1829 "No input sequences selected",
\r
1830 "Phylogenetic Inference Not Launched",
\r
1831 JOptionPane.WARNING_MESSAGE );
\r
1837 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
\r
1838 final StringBuilder sb = new StringBuilder();
\r
1839 final StringBuilder sb_failed = new StringBuilder();
\r
1841 int counter_failed = 0;
\r
1842 if ( getCurrentTreePanel() != null ) {
\r
1843 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1844 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1845 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
\r
1846 while ( it.hasNext() ) {
\r
1847 final PhylogenyNode n = it.next();
\r
1848 final String name = n.getName().trim();
\r
1849 if ( !ForesterUtil.isEmpty( name ) ) {
\r
1850 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
\r
1851 TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1852 if ( !ForesterUtil.isEmpty( nt ) ) {
\r
1853 if ( counter < 15 ) {
\r
1854 sb.append( name + ": " + nt + "\n" );
\r
1856 else if ( counter == 15 ) {
\r
1857 sb.append( "...\n" );
\r
1862 if ( counter_failed < 15 ) {
\r
1863 sb_failed.append( name + "\n" );
\r
1865 else if ( counter_failed == 15 ) {
\r
1866 sb_failed.append( "...\n" );
\r
1872 if ( counter > 0 ) {
\r
1873 String failed = "";
\r
1874 String all = "all ";
\r
1875 if ( counter_failed > 0 ) {
\r
1877 failed = "\nCould not extract taxonomic data for " + counter_failed
\r
1878 + " named external nodes:\n" + sb_failed;
\r
1880 JOptionPane.showMessageDialog( this,
\r
1881 "Extracted taxonomic data from " + all + counter
\r
1882 + " named external nodes:\n" + sb.toString() + failed,
\r
1883 "Taxonomic Data Extraction Completed",
\r
1884 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
\r
1885 : JOptionPane.INFORMATION_MESSAGE );
\r
1889 .showMessageDialog( this,
\r
1890 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
\r
1891 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
\r
1892 + "or nodes already have taxonomic data?\n",
\r
1893 "No Taxonomic Data Extracted",
\r
1894 JOptionPane.ERROR_MESSAGE );
\r
1900 private ControlPanel getControlPanel() {
\r
1901 return getMainPanel().getControlPanel();
\r
1904 private File getCurrentDir() {
\r
1905 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1906 if ( ForesterUtil.isWindows() ) {
\r
1908 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
\r
1910 catch ( final Exception e ) {
\r
1911 _current_dir = null;
\r
1915 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1916 if ( System.getProperty( "user.home" ) != null ) {
\r
1917 _current_dir = new File( System.getProperty( "user.home" ) );
\r
1919 else if ( System.getProperty( "user.dir" ) != null ) {
\r
1920 _current_dir = new File( System.getProperty( "user.dir" ) );
\r
1923 return _current_dir;
\r
1926 private double getMinNotCollapseConfidenceValue() {
\r
1927 return _min_not_collapse;
\r
1930 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
\r
1931 if ( _phylogenetic_inference_options == null ) {
\r
1932 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
\r
1934 return _phylogenetic_inference_options;
\r
1937 private boolean isUnsavedDataPresent() {
\r
1938 final List<TreePanel> tps = getMainPanel().getTreePanels();
\r
1939 for( final TreePanel tp : tps ) {
\r
1940 if ( tp.isEdited() ) {
\r
1947 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
\r
1948 if ( getCurrentTreePanel() != null ) {
\r
1949 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1950 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1952 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
\r
1957 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
\r
1958 if ( getCurrentTreePanel() != null ) {
\r
1959 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1960 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1961 PhylogenyMethods.transferNodeNameToField( phy,
\r
1962 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
\r
1968 private void newTree() {
\r
1969 final Phylogeny[] phys = new Phylogeny[ 1 ];
\r
1970 final Phylogeny phy = new Phylogeny();
\r
1971 final PhylogenyNode node = new PhylogenyNode();
\r
1972 phy.setRoot( node );
\r
1973 phy.setRooted( true );
\r
1975 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
\r
1976 _mainpanel.getControlPanel().showWhole();
\r
1977 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1978 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1979 if ( getMainPanel().getMainFrame() == null ) {
\r
1980 // Must be "E" applet version.
\r
1981 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
\r
1982 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1985 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1987 activateSaveAllIfNeeded();
\r
1991 private void obtainDetailedTaxonomicInformation() {
\r
1992 if ( getCurrentTreePanel() != null ) {
\r
1993 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1994 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1995 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
1996 _mainpanel.getCurrentTreePanel(),
\r
2000 new Thread( t ).start();
\r
2005 private void obtainDetailedTaxonomicInformationDelete() {
\r
2006 if ( getCurrentTreePanel() != null ) {
\r
2007 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
2008 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2009 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
2010 _mainpanel.getCurrentTreePanel(),
\r
2014 new Thread( t ).start();
\r
2019 private void obtainSequenceInformation() {
\r
2020 if ( getCurrentTreePanel() != null ) {
\r
2021 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
2022 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
2023 final SequenceDataRetriver u = new SequenceDataRetriver( this,
\r
2024 _mainpanel.getCurrentTreePanel(),
\r
2026 new Thread( u ).start();
\r
2031 private void print() {
\r
2032 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
\r
2033 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
\r
2036 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2037 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
\r
2038 getOptions().getPrintSizeY() - 140,
\r
2040 getCurrentTreePanel().resetPreferredSize();
\r
2041 getCurrentTreePanel().repaint();
\r
2043 final String job_name = Constants.PRG_NAME;
\r
2044 boolean error = false;
\r
2045 String printer_name = null;
\r
2047 printer_name = Printer.print( getCurrentTreePanel(), job_name );
\r
2049 catch ( final Exception e ) {
\r
2051 JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
\r
2053 if ( !error && ( printer_name != null ) ) {
\r
2054 String msg = "Printing data sent to printer";
\r
2055 if ( printer_name.length() > 1 ) {
\r
2056 msg += " [" + printer_name + "]";
\r
2058 JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
\r
2060 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2061 getControlPanel().showWhole();
\r
2065 private void printPhylogenyToPdf( final String file_name ) {
\r
2066 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2067 getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
\r
2068 getOptions().getPrintSizeY(),
\r
2070 getCurrentTreePanel().resetPreferredSize();
\r
2071 getCurrentTreePanel().repaint();
\r
2073 String pdf_written_to = "";
\r
2074 boolean error = false;
\r
2076 if ( getOptions().isPrintUsingActualSize() ) {
\r
2077 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
\r
2078 getCurrentTreePanel(),
\r
2079 getCurrentTreePanel().getWidth(),
\r
2080 getCurrentTreePanel().getHeight() );
\r
2083 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
\r
2084 .getPrintSizeX(), getOptions().getPrintSizeY() );
\r
2087 catch ( final IOException e ) {
\r
2089 JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
2092 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
\r
2093 JOptionPane.showMessageDialog( this,
\r
2094 "Wrote PDF to: " + pdf_written_to,
\r
2096 JOptionPane.INFORMATION_MESSAGE );
\r
2099 JOptionPane.showMessageDialog( this,
\r
2100 "There was an unknown problem when attempting to write to PDF file: \""
\r
2101 + file_name + "\"",
\r
2103 JOptionPane.ERROR_MESSAGE );
\r
2106 if ( !getOptions().isPrintUsingActualSize() ) {
\r
2107 getControlPanel().showWhole();
\r
2111 private void readPhylogeniesFromFile() {
\r
2112 boolean exception = false;
\r
2113 Phylogeny[] phys = null;
\r
2114 // Set an initial directory if none set yet
\r
2115 final File my_dir = getCurrentDir();
\r
2116 _open_filechooser.setMultiSelectionEnabled( true );
\r
2117 // Open file-open dialog and set current directory
\r
2118 if ( my_dir != null ) {
\r
2119 _open_filechooser.setCurrentDirectory( my_dir );
\r
2121 final int result = _open_filechooser.showOpenDialog( _contentpane );
\r
2122 // All done: get the file
\r
2123 final File[] files = _open_filechooser.getSelectedFiles();
\r
2124 setCurrentDir( _open_filechooser.getCurrentDirectory() );
\r
2125 boolean nhx_or_nexus = false;
\r
2126 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2127 for( final File file : files ) {
\r
2128 if ( ( file != null ) && !file.isDirectory() ) {
\r
2129 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
2130 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
2133 _mainpanel.setWaitCursor();
\r
2135 if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
\r
2136 || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
\r
2138 final NHXParser nhx = new NHXParser();
\r
2139 setSpecialOptionsForNhxParser( nhx );
\r
2140 phys = PhylogenyMethods.readPhylogenies( nhx, file );
\r
2141 nhx_or_nexus = true;
\r
2143 catch ( final Exception e ) {
\r
2145 exceptionOccuredDuringOpenFile( e );
\r
2148 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
\r
2149 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
2151 final PhyloXmlParser xml_parser = createPhyloXmlParser();
\r
2152 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
\r
2154 catch ( final Exception e ) {
\r
2156 exceptionOccuredDuringOpenFile( e );
\r
2159 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
\r
2161 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
2163 catch ( final Exception e ) {
\r
2165 exceptionOccuredDuringOpenFile( e );
\r
2168 else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
\r
2170 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
\r
2171 setSpecialOptionsForNexParser( nex );
\r
2172 phys = PhylogenyMethods.readPhylogenies( nex, file );
\r
2173 nhx_or_nexus = true;
\r
2175 catch ( final Exception e ) {
\r
2177 exceptionOccuredDuringOpenFile( e );
\r
2183 final PhylogenyParser parser = ParserUtils
\r
2184 .createParserDependingOnFileType( file, getConfiguration()
\r
2185 .isValidatePhyloXmlAgainstSchema() );
\r
2186 if ( parser instanceof NexusPhylogeniesParser ) {
\r
2187 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
\r
2188 setSpecialOptionsForNexParser( nex );
\r
2189 nhx_or_nexus = true;
\r
2191 else if ( parser instanceof NHXParser ) {
\r
2192 final NHXParser nhx = ( NHXParser ) parser;
\r
2193 setSpecialOptionsForNhxParser( nhx );
\r
2194 nhx_or_nexus = true;
\r
2196 else if ( parser instanceof PhyloXmlParser ) {
\r
2197 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
2199 phys = PhylogenyMethods.readPhylogenies( parser, file );
\r
2201 catch ( final Exception e ) {
\r
2203 exceptionOccuredDuringOpenFile( e );
\r
2206 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
2207 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
2210 _mainpanel.setArrowCursor();
\r
2212 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
\r
2213 boolean one_desc = false;
\r
2214 if ( nhx_or_nexus ) {
\r
2215 for( final Phylogeny phy : phys ) {
\r
2216 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
2217 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
2219 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
\r
2225 AptxUtil.addPhylogeniesToTabs( phys,
\r
2227 file.getAbsolutePath(),
\r
2228 getConfiguration(),
\r
2230 _mainpanel.getControlPanel().showWhole();
\r
2231 if ( nhx_or_nexus && one_desc ) {
\r
2233 .showMessageDialog( this,
\r
2234 "One or more trees contain (a) node(s) with one descendant, "
\r
2235 + ForesterUtil.LINE_SEPARATOR
\r
2236 + "possibly indicating illegal parentheses within node names.",
\r
2237 "Warning: Possible Error in New Hampshire Formatted Data",
\r
2238 JOptionPane.WARNING_MESSAGE );
\r
2244 activateSaveAllIfNeeded();
\r
2248 private void readSpeciesTreeFromFile() {
\r
2249 Phylogeny t = null;
\r
2250 boolean exception = false;
\r
2251 final File my_dir = getCurrentDir();
\r
2252 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
\r
2253 if ( my_dir != null ) {
\r
2254 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
\r
2256 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
\r
2257 final File file = _open_filechooser_for_species_tree.getSelectedFile();
\r
2258 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2259 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
\r
2261 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
2262 .createPhyloXmlParserXsdValidating(), file );
\r
2265 catch ( final Exception e ) {
\r
2267 exceptionOccuredDuringOpenFile( e );
\r
2270 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
\r
2272 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
2275 catch ( final Exception e ) {
\r
2277 exceptionOccuredDuringOpenFile( e );
\r
2283 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
2284 .createPhyloXmlParserXsdValidating(), file );
\r
2287 catch ( final Exception e ) {
\r
2289 exceptionOccuredDuringOpenFile( e );
\r
2292 if ( !exception && ( t != null ) && !t.isRooted() ) {
\r
2295 JOptionPane.showMessageDialog( this,
\r
2296 "Species tree is not rooted",
\r
2297 "Species tree not loaded",
\r
2298 JOptionPane.ERROR_MESSAGE );
\r
2300 if ( !exception && ( t != null ) ) {
\r
2301 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
\r
2302 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
\r
2303 final PhylogenyNode node = it.next();
\r
2304 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
2308 .showMessageDialog( this,
\r
2309 "Species tree contains external node(s) without taxonomy information",
\r
2310 "Species tree not loaded",
\r
2311 JOptionPane.ERROR_MESSAGE );
\r
2315 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
\r
2318 JOptionPane.showMessageDialog( this,
\r
2320 + node.getNodeData().getTaxonomy().asSimpleText()
\r
2321 + "] is not unique in species tree",
\r
2322 "Species tree not loaded",
\r
2323 JOptionPane.ERROR_MESSAGE );
\r
2327 tax_set.add( node.getNodeData().getTaxonomy() );
\r
2332 if ( !exception && ( t != null ) ) {
\r
2333 setSpeciesTree( t );
\r
2334 JOptionPane.showMessageDialog( this,
\r
2335 "Species tree successfully loaded",
\r
2336 "Species tree loaded",
\r
2337 JOptionPane.INFORMATION_MESSAGE );
\r
2339 _contentpane.repaint();
\r
2344 private void setArrowCursor() {
\r
2346 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
2348 catch ( final Exception ex ) {
\r
2353 private void setCurrentDir( final File current_dir ) {
\r
2354 _current_dir = current_dir;
\r
2357 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
\r
2358 _min_not_collapse = min_not_collapse;
\r
2361 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
\r
2362 _phylogenetic_inference_options = phylogenetic_inference_options;
\r
2365 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
\r
2366 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
2367 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
2370 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
\r
2371 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
2372 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
2373 nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
\r
2376 private void writeAllToFile() {
\r
2377 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
\r
2380 final File my_dir = getCurrentDir();
\r
2381 if ( my_dir != null ) {
\r
2382 _save_filechooser.setCurrentDirectory( my_dir );
\r
2384 _save_filechooser.setSelectedFile( new File( "" ) );
\r
2385 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
2386 final File file = _save_filechooser.getSelectedFile();
\r
2387 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
2388 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2389 if ( file.exists() ) {
\r
2390 final int i = JOptionPane.showConfirmDialog( this,
\r
2391 file + " already exists. Overwrite?",
\r
2393 JOptionPane.OK_CANCEL_OPTION,
\r
2394 JOptionPane.WARNING_MESSAGE );
\r
2395 if ( i != JOptionPane.OK_OPTION ) {
\r
2402 catch ( final Exception e ) {
\r
2403 JOptionPane.showMessageDialog( this,
\r
2404 "Failed to delete: " + file,
\r
2406 JOptionPane.WARNING_MESSAGE );
\r
2410 final int count = getMainPanel().getTabbedPane().getTabCount();
\r
2411 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
\r
2412 for( int i = 0; i < count; ++i ) {
\r
2413 final Phylogeny phy = getMainPanel().getPhylogeny( i );
\r
2414 if ( ForesterUtil.isEmpty( phy.getName() )
\r
2415 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
\r
2416 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
\r
2419 getMainPanel().getTreePanels().get( i ).setEdited( false );
\r
2421 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2423 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
\r
2425 catch ( final IOException e ) {
\r
2426 JOptionPane.showMessageDialog( this,
\r
2427 "Failed to write to: " + file,
\r
2429 JOptionPane.WARNING_MESSAGE );
\r
2434 private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
\r
2436 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2437 writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );
\r
2439 catch ( final Exception e ) {
\r
2441 exceptionOccuredDuringSaveAs( e );
\r
2446 private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
\r
2448 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2449 writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
\r
2451 catch ( final Exception e ) {
\r
2453 exceptionOccuredDuringSaveAs( e );
\r
2458 private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
\r
2460 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2461 writer.toPhyloXML( file, t, 0 );
\r
2463 catch ( final Exception e ) {
\r
2465 exceptionOccuredDuringSaveAs( e );
\r
2470 private void writeToFile( final Phylogeny t ) {
\r
2471 if ( t == null ) {
\r
2474 String initial_filename = null;
\r
2475 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2477 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
\r
2479 catch ( final IOException e ) {
\r
2480 initial_filename = null;
\r
2483 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
\r
2484 _save_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2487 _save_filechooser.setSelectedFile( new File( "" ) );
\r
2489 final File my_dir = getCurrentDir();
\r
2490 if ( my_dir != null ) {
\r
2491 _save_filechooser.setCurrentDirectory( my_dir );
\r
2493 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
2494 final File file = _save_filechooser.getSelectedFile();
\r
2495 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
2496 boolean exception = false;
\r
2497 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2498 if ( file.exists() ) {
\r
2499 final int i = JOptionPane.showConfirmDialog( this,
\r
2500 file + " already exists.\nOverwrite?",
\r
2502 JOptionPane.OK_CANCEL_OPTION,
\r
2503 JOptionPane.QUESTION_MESSAGE );
\r
2504 if ( i != JOptionPane.OK_OPTION ) {
\r
2508 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
\r
2510 ForesterUtil.copyFile( file, to );
\r
2512 catch ( final Exception e ) {
\r
2513 JOptionPane.showMessageDialog( this,
\r
2514 "Failed to create backup copy " + to,
\r
2515 "Failed to Create Backup Copy",
\r
2516 JOptionPane.WARNING_MESSAGE );
\r
2521 catch ( final Exception e ) {
\r
2522 JOptionPane.showMessageDialog( this,
\r
2523 "Failed to delete: " + file,
\r
2524 "Failed to Delete",
\r
2525 JOptionPane.WARNING_MESSAGE );
\r
2529 if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
\r
2530 exception = writeAsNewHampshire( t, exception, file );
\r
2532 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
\r
2533 exception = writeAsPhyloXml( t, exception, file );
\r
2535 else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
\r
2536 exception = writeAsNexus( t, exception, file );
\r
2540 final String file_name = file.getName().trim().toLowerCase();
\r
2541 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2542 || file_name.endsWith( ".tree" ) ) {
\r
2543 exception = writeAsNewHampshire( t, exception, file );
\r
2545 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
\r
2546 exception = writeAsNexus( t, exception, file );
\r
2548 // XML is default:
\r
2550 exception = writeAsPhyloXml( t, exception, file );
\r
2553 if ( !exception ) {
\r
2554 getMainPanel().setTitleOfSelectedTab( file.getName() );
\r
2555 getMainPanel().getCurrentTreePanel().setTreeFile( file );
\r
2556 getMainPanel().getCurrentTreePanel().setEdited( false );
\r
2561 private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
\r
2562 if ( ( t == null ) || t.isEmpty() ) {
\r
2565 String initial_filename = "";
\r
2566 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2567 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
\r
2569 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2570 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2572 initial_filename = initial_filename + "." + type;
\r
2573 _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2574 final File my_dir = getCurrentDir();
\r
2575 if ( my_dir != null ) {
\r
2576 _writetographics_filechooser.setCurrentDirectory( my_dir );
\r
2578 final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
\r
2579 File file = _writetographics_filechooser.getSelectedFile();
\r
2580 setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
\r
2581 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2582 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
\r
2583 file = new File( file.toString() + "." + type );
\r
2585 if ( file.exists() ) {
\r
2586 final int i = JOptionPane.showConfirmDialog( this,
\r
2587 file + " already exists. Overwrite?",
\r
2589 JOptionPane.OK_CANCEL_OPTION,
\r
2590 JOptionPane.WARNING_MESSAGE );
\r
2591 if ( i != JOptionPane.OK_OPTION ) {
\r
2598 catch ( final Exception e ) {
\r
2599 JOptionPane.showMessageDialog( this,
\r
2600 "Failed to delete: " + file,
\r
2602 JOptionPane.WARNING_MESSAGE );
\r
2606 writePhylogenyToGraphicsFile( file.toString(), type );
\r
2610 private void writeToPdf( final Phylogeny t ) {
\r
2611 if ( ( t == null ) || t.isEmpty() ) {
\r
2614 String initial_filename = "";
\r
2615 if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
\r
2616 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
\r
2618 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2619 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2621 initial_filename = initial_filename + ".pdf";
\r
2622 _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2623 final File my_dir = getCurrentDir();
\r
2624 if ( my_dir != null ) {
\r
2625 _writetopdf_filechooser.setCurrentDirectory( my_dir );
\r
2627 final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
\r
2628 File file = _writetopdf_filechooser.getSelectedFile();
\r
2629 setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
\r
2630 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2631 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
\r
2632 file = new File( file.toString() + ".pdf" );
\r
2634 if ( file.exists() ) {
\r
2635 final int i = JOptionPane.showConfirmDialog( this,
\r
2636 file + " already exists. Overwrite?",
\r
2638 JOptionPane.OK_CANCEL_OPTION,
\r
2639 JOptionPane.WARNING_MESSAGE );
\r
2640 if ( i != JOptionPane.OK_OPTION ) {
\r
2644 printPhylogenyToPdf( file.toString() );
\r
2648 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
\r
2649 return new MainFrameApplication( phys, config );
\r
2652 public static MainFrame createInstance( final Phylogeny[] phys,
\r
2653 final Configuration config,
\r
2654 final String title,
\r
2655 final File current_dir ) {
\r
2656 return new MainFrameApplication( phys, config, title, current_dir );
\r
2659 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
\r
2660 return new MainFrameApplication( phys, config, title );
\r
2663 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
\r
2664 return new MainFrameApplication( phys, config_file_name, title );
\r
2667 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2668 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
\r
2669 + o.getPrintSizeY() + ")" );
\r
2672 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2673 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
\r
2676 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
\r
2677 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
\r
2679 .showMessageDialog( null,
\r
2681 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
\r
2684 JOptionPane.WARNING_MESSAGE );
\r
2687 } // MainFrameApplication.
\r
2689 class DefaultFilter extends FileFilter {
\r
2692 public boolean accept( final File f ) {
\r
2693 final String file_name = f.getName().trim().toLowerCase();
\r
2694 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2695 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
\r
2696 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
\r
2697 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
\r
2698 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
\r
2699 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
\r
2700 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
\r
2701 || file_name.endsWith( ".con" ) || f.isDirectory();
\r
2705 public String getDescription() {
\r
2706 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
\r
2710 class GraphicsFileFilter extends FileFilter {
\r
2713 public boolean accept( final File f ) {
\r
2714 final String file_name = f.getName().trim().toLowerCase();
\r
2715 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
\r
2716 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
\r
2720 public String getDescription() {
\r
2721 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
\r
2725 class MsaFileFilter extends FileFilter {
\r
2728 public boolean accept( final File f ) {
\r
2729 final String file_name = f.getName().trim().toLowerCase();
\r
2730 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
\r
2731 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
\r
2735 public String getDescription() {
\r
2736 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
\r
2740 class NexusFilter extends FileFilter {
\r
2743 public boolean accept( final File f ) {
\r
2744 final String file_name = f.getName().trim().toLowerCase();
\r
2745 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
\r
2746 || file_name.endsWith( ".tre" ) || f.isDirectory();
\r
2750 public String getDescription() {
\r
2751 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
\r
2755 class NHFilter extends FileFilter {
\r
2758 public boolean accept( final File f ) {
\r
2759 final String file_name = f.getName().trim().toLowerCase();
\r
2760 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2761 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
\r
2762 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
\r
2763 || f.isDirectory();
\r
2767 public String getDescription() {
\r
2768 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
\r
2772 class NHXFilter extends FileFilter {
\r
2775 public boolean accept( final File f ) {
\r
2776 final String file_name = f.getName().trim().toLowerCase();
\r
2777 return file_name.endsWith( ".nhx" ) || f.isDirectory();
\r
2781 public String getDescription() {
\r
2782 return "NHX files (*.nhx) [deprecated]";
\r
2786 class PdfFilter extends FileFilter {
\r
2789 public boolean accept( final File f ) {
\r
2790 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
\r
2794 public String getDescription() {
\r
2795 return "PDF files (*.pdf)";
\r
2799 class SequencesFileFilter extends FileFilter {
\r
2802 public boolean accept( final File f ) {
\r
2803 final String file_name = f.getName().trim().toLowerCase();
\r
2804 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
\r
2805 || file_name.endsWith( ".seqs" ) || f.isDirectory();
\r
2809 public String getDescription() {
\r
2810 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
\r
2814 class TolFilter extends FileFilter {
\r
2817 public boolean accept( final File f ) {
\r
2818 final String file_name = f.getName().trim().toLowerCase();
\r
2819 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
\r
2820 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
\r
2824 public String getDescription() {
\r
2825 return "Tree of Life files (*.tol, *.tolxml)";
\r
2829 class XMLFilter extends FileFilter {
\r
2832 public boolean accept( final File f ) {
\r
2833 final String file_name = f.getName().trim().toLowerCase();
\r
2834 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
\r
2835 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
\r
2839 public String getDescription() {
\r
2840 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
\r
git://source.jalview.org / jalview.git / blob