2 package org.forester.archaeopteryx;
4 import java.awt.BorderLayout;
5 import java.awt.Container;
7 import java.awt.event.ActionEvent;
8 import java.awt.event.ActionListener;
9 import java.awt.event.ComponentAdapter;
10 import java.awt.event.ComponentEvent;
11 import java.io.ByteArrayOutputStream;
13 import java.io.IOException;
15 import java.util.LinkedList;
16 import java.util.List;
17 import java.util.NoSuchElementException;
19 import javax.swing.ButtonGroup;
20 import javax.swing.JApplet;
21 import javax.swing.JCheckBoxMenuItem;
22 import javax.swing.JFileChooser;
23 import javax.swing.JMenu;
24 import javax.swing.JMenuBar;
25 import javax.swing.JMenuItem;
26 import javax.swing.JOptionPane;
27 import javax.swing.JRadioButtonMenuItem;
28 import javax.swing.UIManager;
29 import javax.swing.UnsupportedLookAndFeelException;
30 import javax.swing.event.ChangeEvent;
31 import javax.swing.event.ChangeListener;
33 import org.apache.commons.codec.binary.Base64;
34 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
35 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
36 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
37 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
38 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
39 import org.forester.archaeopteryx.webservices.WebservicesManager;
40 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
41 import org.forester.phylogeny.Phylogeny;
42 import org.forester.phylogeny.PhylogenyMethods;
43 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
44 import org.forester.phylogeny.data.SequenceRelation;
45 import org.forester.sdi.GSDI;
46 import org.forester.sdi.GSDIR;
47 import org.forester.sdi.SDIException;
48 import org.forester.util.ForesterConstants;
49 import org.forester.util.ForesterUtil;
50 import org.forester.util.WindowsUtils;
53 // <applet archive="forester.jar"
54 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
55 // codebase="http://www.myserver.org/path/to/forester"
58 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
59 // <param name="url_of_tree_to_load"
60 // value="http://www.myserver.org/examples/data/apaf.xml">
61 // <param name="config_file"
62 // value="http://www.myserver.org/examples/config/config_file.txt">
64 public class ArchaeopteryxE extends JApplet implements ActionListener {
66 private final static String NAME = "ArchaeopteryxE";
67 private static final long serialVersionUID = -1220055577935759443L;
68 private Configuration _configuration;
69 private MainPanelApplets _mainpanel;
70 private JMenuBar _jmenubar;
71 private JMenu _options_jmenu;
72 private JMenu _font_size_menu;
73 private JMenuItem _super_tiny_fonts_mi;
74 private JMenuItem _tiny_fonts_mi;
75 private JMenuItem _small_fonts_mi;
76 private JMenuItem _medium_fonts_mi;
77 private JMenuItem _large_fonts_mi;
78 private JMenu _tools_menu;
79 private JMenuItem _taxcolor_item;
80 private JMenuItem _confcolor_item;
81 private JMenuItem _midpoint_root_item;
82 private JMenu _view_jmenu;
83 private JMenuItem _view_as_XML_item;
84 private JMenuItem _view_as_NH_item;
85 private JMenuItem _view_as_nexus_item;
86 private JMenuItem _display_basic_information_item;
87 private JMenu _type_menu;
88 private JCheckBoxMenuItem _rectangular_type_cbmi;
89 private JCheckBoxMenuItem _triangular_type_cbmi;
90 private JCheckBoxMenuItem _curved_type_cbmi;
91 private JCheckBoxMenuItem _convex_type_cbmi;
92 private JCheckBoxMenuItem _euro_type_cbmi;
93 private JCheckBoxMenuItem _rounded_type_cbmi;
94 private JCheckBoxMenuItem _unrooted_type_cbmi;
95 private JCheckBoxMenuItem _circular_type_cbmi;
96 private JMenuItem _help_item;
97 private JMenuItem _about_item;
98 private JMenu _help_jmenu;
99 private JMenuItem _website_item;
100 private JMenuItem _phyloxml_website_item;
101 private JMenuItem _phyloxml_ref_item;
102 private JMenuItem _aptx_ref_item;
103 private JMenuItem _remove_branch_color_item;
104 private JMenuItem _remove_visual_styles_item;
105 private JCheckBoxMenuItem _show_domain_labels;
106 private JCheckBoxMenuItem _show_annotation_ref_source;
107 private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
108 private JCheckBoxMenuItem _abbreviate_scientific_names;
109 private JCheckBoxMenuItem _screen_antialias_cbmi;
110 private JCheckBoxMenuItem _background_gradient_cbmi;
111 private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
112 private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
113 private JRadioButtonMenuItem _uniform_cladograms_rbmi;
114 private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
115 private Options _options;
116 private JMenuItem _choose_font_mi;
117 private JMenuItem _switch_colors_mi;
118 JCheckBoxMenuItem _label_direction_cbmi;
119 private JCheckBoxMenuItem _show_scale_cbmi;
120 private JCheckBoxMenuItem _search_case_senstive_cbmi;
121 private JCheckBoxMenuItem _search_whole_words_only_cbmi;
122 private JCheckBoxMenuItem _inverse_search_result_cbmi;
123 private JCheckBoxMenuItem _search_with_regex_cbmi;
124 private JCheckBoxMenuItem _show_overview_cbmi;
125 private JMenuItem _choose_minimal_confidence_mi;
126 private JMenuItem _collapse_species_specific_subtrees;
127 private JMenuItem _overview_placment_mi;
128 private ButtonGroup _radio_group_1;
129 private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
130 private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
131 private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
132 private JMenuItem _cycle_node_shape_mi;
133 private JMenuItem _cycle_node_fill_mi;
134 private JMenuItem _choose_node_size_mi;
135 private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
136 private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
137 private JMenu _analysis_menu;
138 private JMenuItem _gsdi_item;
139 private JMenuItem _gsdir_item;
140 private Phylogeny _species_tree;
141 private JCheckBoxMenuItem _right_line_up_domains_cbmi;
142 private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
144 private JMenuItem _open_item;
145 private JMenuItem _open_url_item;
146 private JMenuItem _save_item;
147 private JMenuItem _save_all_item;
148 private JMenuItem _close_item;
149 private JMenuItem _exit_item;
150 private JMenuItem _new_item;
151 private JMenuItem _print_item;
152 private JMenuItem _write_to_pdf_item;
153 private JMenuItem _write_to_jpg_item;
154 private JMenuItem _write_to_gif_item;
155 private JMenuItem _write_to_tif_item;
156 private JMenuItem _write_to_png_item;
157 private JMenuItem _write_to_bmp_item;
158 private JMenu _file_jmenu;
159 private JFileChooser _writetopdf_filechooser;
160 private File _current_dir;
161 private JFileChooser _save_filechooser;
162 private JFileChooser _writetographics_filechooser;
165 void setCurrentDir( final File current_dir ) {
166 _current_dir = current_dir;
169 File getCurrentDir() {
170 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
171 if ( ForesterUtil.isWindows() ) {
173 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
175 catch ( final Exception e ) {
180 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
181 if ( System.getProperty( "user.home" ) != null ) {
182 _current_dir = new File( System.getProperty( "user.home" ) );
184 else if ( System.getProperty( "user.dir" ) != null ) {
185 _current_dir = new File( System.getProperty( "user.dir" ) );
194 void buildFileMenu() {
195 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
196 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
197 _file_jmenu.addSeparator();
198 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
199 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
200 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
202 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
203 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
204 if ( AptxUtil.canWriteFormat( "gif" ) ) {
205 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
207 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
208 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
210 _file_jmenu.addSeparator();
211 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
212 _file_jmenu.addSeparator();
213 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
214 customizeJMenuItem( _save_item );
215 customizeJMenuItem( _write_to_pdf_item );
216 customizeJMenuItem( _write_to_png_item );
217 customizeJMenuItem( _write_to_jpg_item );
218 customizeJMenuItem( _write_to_gif_item );
219 customizeJMenuItem( _write_to_tif_item );
220 customizeJMenuItem( _write_to_bmp_item );
221 customizeJMenuItem( _print_item );
222 customizeJMenuItem( _exit_item );
223 _jmenubar.add( _file_jmenu );
227 public void actionPerformed( final ActionEvent e ) {
228 final Object o = e.getSource();
229 if ( o == _midpoint_root_item ) {
230 getMainPanel().getCurrentTreePanel().midpointRoot();
232 else if ( o == _gsdi_item ) {
233 if ( isSubtreeDisplayed() ) {
238 else if ( o == _gsdir_item ) {
239 if ( isSubtreeDisplayed() ) {
244 else if ( o == _taxcolor_item ) {
245 getMainPanel().getCurrentTreePanel().taxColor();
247 else if ( o == _confcolor_item ) {
248 getMainPanel().getCurrentTreePanel().confColor();
250 else if ( o == _collapse_species_specific_subtrees ) {
251 if ( getCurrentTreePanel() != null ) {
252 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
255 else if ( o == _remove_branch_color_item ) {
256 removeBranchColors();
258 else if ( o == _remove_visual_styles_item ) {
259 removeVisualStyles();
261 else if ( o == _switch_colors_mi ) {
264 else if ( o == _display_basic_information_item ) {
265 displayBasicInformation();
267 else if ( o == _view_as_NH_item ) {
270 else if ( o == _view_as_XML_item ) {
273 else if ( o == _view_as_nexus_item ) {
276 else if ( o == _super_tiny_fonts_mi ) {
277 if ( getCurrentTreePanel() != null ) {
278 getCurrentTreePanel().setSuperTinyFonts();
279 getCurrentTreePanel().repaint();
282 else if ( o == _tiny_fonts_mi ) {
283 if ( getCurrentTreePanel() != null ) {
284 getCurrentTreePanel().setTinyFonts();
285 getCurrentTreePanel().repaint();
288 else if ( o == _small_fonts_mi ) {
289 if ( getCurrentTreePanel() != null ) {
290 getCurrentTreePanel().setSmallFonts();
291 getCurrentTreePanel().repaint();
294 else if ( o == _medium_fonts_mi ) {
295 if ( getCurrentTreePanel() != null ) {
296 getCurrentTreePanel().setMediumFonts();
297 getCurrentTreePanel().repaint();
300 else if ( o == _large_fonts_mi ) {
301 if ( getCurrentTreePanel() != null ) {
302 getCurrentTreePanel().setLargeFonts();
303 getCurrentTreePanel().repaint();
306 else if ( o == _choose_font_mi ) {
309 else if ( o == _choose_minimal_confidence_mi ) {
310 chooseMinimalConfidence();
312 else if ( o == _choose_node_size_mi ) {
313 MainFrame.chooseNodeSize( getOptions(), this );
315 else if ( o == _overview_placment_mi ) {
316 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
318 else if ( o == _cycle_node_fill_mi ) {
319 MainFrame.cycleNodeFill( getOptions() );
321 else if ( o == _cycle_node_shape_mi ) {
322 MainFrame.cycleNodeShape( getOptions() );
324 else if ( o == _non_lined_up_cladograms_rbmi ) {
325 updateOptions( getOptions() );
326 _mainpanel.getControlPanel().showWhole();
328 else if ( o == _uniform_cladograms_rbmi ) {
329 updateOptions( getOptions() );
330 _mainpanel.getControlPanel().showWhole();
332 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
333 updateOptions( getOptions() );
334 _mainpanel.getControlPanel().showWhole();
336 else if ( o == _search_case_senstive_cbmi ) {
337 updateOptions( getOptions() );
338 getMainPanel().getControlPanel().search0();
339 getMainPanel().getControlPanel().search1();
341 else if ( o == _search_whole_words_only_cbmi ) {
342 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
343 _search_with_regex_cbmi.setSelected( false );
345 updateOptions( getOptions() );
346 getMainPanel().getControlPanel().search0();
347 getMainPanel().getControlPanel().search1();
349 else if ( o == _inverse_search_result_cbmi ) {
350 updateOptions( getOptions() );
351 getMainPanel().getControlPanel().search0();
352 getMainPanel().getControlPanel().search1();
354 else if ( o == _search_with_regex_cbmi ) {
355 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
356 _search_whole_words_only_cbmi.setSelected( false );
358 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
359 _search_case_senstive_cbmi.setSelected( true );
361 updateOptions( getOptions() );
362 getMainPanel().getControlPanel().search0();
363 getMainPanel().getControlPanel().search1();
365 else if ( o == _show_scale_cbmi ) {
366 updateOptions( getOptions() );
368 else if ( o == _show_confidence_stddev_cbmi ) {
369 updateOptions( getOptions() );
371 else if ( o == _label_direction_cbmi ) {
372 updateOptions( getOptions() );
374 else if ( o == _abbreviate_scientific_names ) {
375 updateOptions( getOptions() );
377 else if ( o == _show_overview_cbmi ) {
378 updateOptions( getOptions() );
379 if ( getCurrentTreePanel() != null ) {
380 getCurrentTreePanel().updateOvSizes();
383 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
384 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
385 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
388 else if ( o == _screen_antialias_cbmi ) {
389 updateOptions( getOptions() );
390 setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
392 else if ( o == _background_gradient_cbmi ) {
393 updateOptions( getOptions() );
395 else if ( o == _show_domain_labels ) {
396 updateOptions( getOptions() );
398 else if ( o == _color_labels_same_as_parent_branch ) {
399 updateOptions( getOptions() );
401 else if ( o == _show_default_node_shapes_internal_cbmi ) {
402 updateOptions( getOptions() );
404 else if ( o == _show_default_node_shapes_external_cbmi ) {
405 updateOptions( getOptions() );
407 else if ( o == _about_item ) {
410 else if ( o == _help_item ) {
412 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
414 catch ( final IOException e1 ) {
415 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
418 else if ( o == _website_item ) {
420 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
422 catch ( final IOException e1 ) {
423 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
426 else if ( o == _phyloxml_website_item ) {
428 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
430 catch ( final IOException e1 ) {
431 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
434 else if ( o == _aptx_ref_item ) {
436 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
438 catch ( final IOException e1 ) {
439 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
442 else if ( o == _phyloxml_ref_item ) {
444 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
446 catch ( final IOException e1 ) {
447 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
450 else if ( o == _color_by_taxonomic_group_cbmi ) {
451 updateOptions( getOptions() );
453 else if ( o == _line_up_renderable_data_cbmi ) {
454 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
455 _right_line_up_domains_cbmi.setSelected( false );
457 updateOptions( getOptions() );
459 else if ( o == _right_line_up_domains_cbmi ) {
460 if ( _right_line_up_domains_cbmi.isSelected() ) {
461 _line_up_renderable_data_cbmi.setSelected( true );
463 updateOptions( getOptions() );
466 else if ( o == _write_to_pdf_item ) {
467 // writeToPdf( _mainpanel.getCurrentPhylogeny() );
468 final File curr_dir =MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(),
470 _writetopdf_filechooser,
476 if ( curr_dir != null ) {
477 setCurrentDir( curr_dir );
482 else if ( o == _write_to_jpg_item ) {
484 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
486 else if ( o == _write_to_gif_item ) {
487 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
489 else if ( o == _write_to_tif_item ) {
490 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
492 else if ( o == _write_to_bmp_item ) {
493 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
495 else if ( o == _write_to_png_item ) {
496 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
498 else if ( o == _print_item ) {
499 MainFrame.print( getCurrentTreePanel(),
505 else if ( o == _save_item ) {
506 writeToFile( _mainpanel.getCurrentPhylogeny() );
509 // else if ( o == _graphics_export_visible_only_cbmi ) {
510 // updateOptions( getOptions() );
512 // else if ( o == _antialias_print_cbmi ) {
513 // updateOptions( getOptions() );
515 // else if ( o == _print_black_and_white_cbmi ) {
516 // updateOptions( getOptions() );
518 // else if ( o == _print_using_actual_size_cbmi ) {
519 // updateOptions( getOptions() );
521 // else if ( o == _graphics_export_using_actual_size_cbmi ) {
522 // updateOptions( getOptions() );
524 // else if ( o == _print_size_mi ) {
525 // choosePrintSize();
527 // else if ( o == _choose_pdf_width_mi ) {
535 public void destroy() {
536 AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
537 removeAllTextFrames();
538 if ( getMainPanel() != null ) {
539 getMainPanel().terminate();
544 * This method returns the current external node data which
545 * has been selected by the user by clicking the "Return ..."
546 * menu item. This method is expected to be called from Javascript or
549 * @return current external node data as String
551 public String getCurrentExternalNodesDataBuffer() {
552 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
555 public int getCurrentExternalNodesDataBufferChangeCounter() {
556 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
559 public int getCurrentExternalNodesDataBufferLength() {
560 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
564 * This method returns the current phylogeny as a string in the chosen format
566 * @param format must be NH, NHX, NEXUS or PHYLOXML
567 * @return the phylogeny string
568 * @author Herve Menager
570 public String getCurrentPhylogeny( final String format ) {
571 removeAllTextFrames();
572 if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
573 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
576 switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
578 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
580 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
582 return getMainPanel().getCurrentPhylogeny().toNexus();
584 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
592 * This method returns a view of the current phylogeny in a chosen
593 * graphics format, base64-encoded in a string so that in can be used
596 * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
597 * @return the phylogeny string
598 * @author Herve Menager
600 public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
601 final ByteArrayOutputStream baos = new ByteArrayOutputStream();
603 AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
604 _mainpanel.getWidth(),
605 _mainpanel.getHeight(),
606 getCurrentTreePanel(),
607 getCurrentTreePanel().getControlPanel(),
608 GraphicsExportType.valueOf( format ),
611 catch ( final IOException ioe ) {
612 ForesterUtil.printErrorMessage( NAME, ioe.toString() );
613 ioe.printStackTrace();
614 JOptionPane.showMessageDialog( this,
615 NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
616 "Failed to generate graphics",
617 JOptionPane.ERROR_MESSAGE );
620 final byte[] bytes = baos.toByteArray();
621 final String dataImg = Base64.encodeBase64String( bytes );
625 public Options getOptions() {
631 _writetopdf_filechooser = new JFileChooser();
632 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
633 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
634 final Configuration configuration = new Configuration( config_filename, true, true, true );
635 setConfiguration( configuration );
636 setOptions( Options.createInstance( configuration ) );
638 final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
639 if ( ForesterUtil.isEmpty( tree_url_str ) ) {
640 ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
641 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
642 JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
643 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
646 AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
647 // Get URL to tree file
650 phys_url = new URL( tree_url_str );
652 catch ( final Exception e ) {
653 ForesterUtil.printErrorMessage( NAME, "error: " + e );
655 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
656 + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
658 if ( phys_url == null ) {
659 ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
660 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
661 JOptionPane.showMessageDialog( this,
662 NAME + ": Could not create URL from: \"" + tree_url_str,
663 "Failed to create URL",
664 JOptionPane.ERROR_MESSAGE );
667 // Load the tree from URL
668 Phylogeny[] phys = null;
670 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
671 getConfiguration().isValidatePhyloXmlAgainstSchema(),
672 getConfiguration().isReplaceUnderscoresInNhParsing(),
673 getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
674 getConfiguration().getTaxonomyExtraction(),
675 getConfiguration().isMidpointReroot() );
677 catch ( final Exception e ) {
678 ForesterUtil.printErrorMessage( NAME, e.toString() );
680 JOptionPane.showMessageDialog( this,
681 NAME + ": Failed to read phylogenies: " + "\nException: " + e,
682 "Failed to read phylogenies",
683 JOptionPane.ERROR_MESSAGE );
685 if ( phys == null ) {
686 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
687 JOptionPane.showMessageDialog( this,
688 NAME + ": phylogenies from [" + phys_url + "] are null",
689 "Failed to read phylogenies",
690 JOptionPane.ERROR_MESSAGE );
693 else if ( phys.length < 1 ) {
694 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
695 JOptionPane.showMessageDialog( this,
696 NAME + ": phylogenies from [" + phys_url + "] are empty",
697 "Failed to read phylogenies",
698 JOptionPane.ERROR_MESSAGE );
702 AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
705 final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
706 if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
707 AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
708 Phylogeny[] species_trees = null;
710 final URL species_tree_url = new URL( species_tree_url_str );
711 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
712 configuration.isValidatePhyloXmlAgainstSchema(),
713 configuration.isReplaceUnderscoresInNhParsing(),
715 TAXONOMY_EXTRACTION.NO,
718 catch ( final IOException e ) {
719 ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
721 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
722 + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
724 if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
725 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
726 if ( species_trees[ 0 ].isEmpty() ) {
727 ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
729 else if ( !species_trees[ 0 ].isRooted() ) {
730 ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
733 setSpeciesTree( species_trees[ 0 ] );
734 AptxUtil.printAppletMessage( NAME, "species tree OK" );
741 setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
742 _jmenubar = new JMenuBar();
743 if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
745 if ( !getConfiguration().isUseNativeUI() ) {
746 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
748 if ( getSpeciesTree() != null ) {
757 setJMenuBar( _jmenubar );
759 final Container contentpane = getContentPane();
760 contentpane.setLayout( new BorderLayout() );
761 contentpane.add( getMainPanel(), BorderLayout.CENTER );
762 addComponentListener( new ComponentAdapter() {
765 public void componentResized( final ComponentEvent e ) {
766 if ( getMainPanel().getCurrentTreePanel() != null ) {
767 getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
768 .getCurrentTreePanel()
771 .getCurrentTreePanel()
776 if ( getConfiguration().isUseTabbedDisplay() ) {
778 AptxUtil.printAppletMessage( NAME, "using tabbed display" );
779 AptxUtil.addPhylogeniesToTabs( phys,
780 new File( phys_url.getFile() ).getName(),
785 catch ( final Exception e ) {
786 ForesterUtil.printErrorMessage( NAME, e.toString() );
791 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
792 if ( getSpeciesTree() != null ) {
793 AptxUtil.printAppletMessage( NAME,
794 "Warning: gsdi (gene duplication inference) only available tabbed display" );
796 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
800 getMainPanel().getControlPanel().showWholeAll();
801 getMainPanel().getControlPanel().showWhole();
803 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
804 for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
805 .getRelevantSequenceRelationTypes() ) {
806 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
808 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
809 if ( default_relation != null ) {
810 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
812 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
813 if ( default_sequence != null ) {
814 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
818 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
821 catch ( final Exception e ) {
822 ForesterUtil.printErrorMessage( NAME, e.toString() );
827 public void showTextFrame( final String s, final String title ) {
829 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
833 public void start() {
834 if ( getMainPanel() != null ) {
835 getMainPanel().validate();
838 requestFocusInWindow();
840 AptxUtil.printAppletMessage( NAME, "started" );
843 void buildAnalysisMenu() {
844 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
845 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
846 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
847 customizeJMenuItem( _gsdi_item );
848 customizeJMenuItem( _gsdir_item );
849 // _analysis_menu.addSeparator();
850 // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
851 // customizeJMenuItem( _lineage_inference );
852 // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
853 _jmenubar.add( _analysis_menu );
856 void buildFontSizeMenu() {
857 _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
858 _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
859 _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
860 _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
861 _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
862 _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
863 customizeJMenuItem( _super_tiny_fonts_mi );
864 customizeJMenuItem( _tiny_fonts_mi );
865 customizeJMenuItem( _small_fonts_mi );
866 customizeJMenuItem( _medium_fonts_mi );
867 customizeJMenuItem( _large_fonts_mi );
868 _jmenubar.add( _font_size_menu );
871 void buildHelpMenu() {
872 _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
873 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
874 _help_jmenu.addSeparator();
875 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
876 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
877 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
878 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
879 _help_jmenu.addSeparator();
880 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
881 customizeJMenuItem( _help_item );
882 customizeJMenuItem( _website_item );
883 customizeJMenuItem( _phyloxml_website_item );
884 customizeJMenuItem( _aptx_ref_item );
885 customizeJMenuItem( _phyloxml_ref_item );
886 customizeJMenuItem( _about_item );
887 _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
888 _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
889 _jmenubar.add( _help_jmenu );
892 void buildOptionsMenu() {
893 _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
894 _options_jmenu.addChangeListener( new ChangeListener() {
897 public void stateChanged( final ChangeEvent e ) {
898 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
899 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
901 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
902 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
903 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
904 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
905 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
906 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
908 getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
909 getMainPanel().getControlPanel().setVisibilityOfX();
911 catch ( final Exception ignore ) {
912 // do nothing, not important.
916 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
917 getConfiguration() ) );
919 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
920 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
922 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
923 _radio_group_1 = new ButtonGroup();
924 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
925 _radio_group_1.add( _uniform_cladograms_rbmi );
926 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
927 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
928 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
930 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
932 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
934 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
935 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
936 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
937 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
938 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
940 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
941 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
943 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
945 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
946 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
947 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
948 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
949 _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
950 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
951 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
952 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
953 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
954 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
955 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
956 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
957 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
958 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
959 _options_jmenu.addSeparator();
960 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
961 getConfiguration() ) );
963 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
964 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
965 _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
966 _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
968 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
969 customizeJMenuItem( _choose_font_mi );
970 customizeJMenuItem( _choose_minimal_confidence_mi );
971 customizeJMenuItem( _switch_colors_mi );
972 customizeJMenuItem( _overview_placment_mi );
973 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
974 customizeCheckBoxMenuItem( _label_direction_cbmi,
975 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
976 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
977 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
978 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
979 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
980 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
981 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
982 .isShowDefaultNodeShapesExternal() );
983 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
984 .isShowDefaultNodeShapesInternal() );
985 customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
986 .isShowDefaultNodeShapesForMarkedNodes() );
987 customizeJMenuItem( _cycle_node_shape_mi );
988 customizeJMenuItem( _cycle_node_fill_mi );
989 customizeJMenuItem( _choose_node_size_mi );
990 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
991 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
992 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
993 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
994 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
995 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
996 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
997 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
998 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
999 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1000 customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
1001 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1002 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1003 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1004 customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
1005 customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
1006 _jmenubar.add( _options_jmenu );
1009 void buildToolsMenu() {
1010 _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
1011 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1012 customizeJMenuItem( _confcolor_item );
1013 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1014 customizeJMenuItem( _taxcolor_item );
1015 _tools_menu.addSeparator();
1016 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
1017 _remove_visual_styles_item
1018 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
1019 customizeJMenuItem( _remove_visual_styles_item );
1020 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
1021 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
1022 customizeJMenuItem( _remove_branch_color_item );
1023 _tools_menu.addSeparator();
1024 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1025 customizeJMenuItem( _midpoint_root_item );
1026 _tools_menu.addSeparator();
1027 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1028 customizeJMenuItem( _collapse_species_specific_subtrees );
1029 _jmenubar.add( _tools_menu );
1032 void buildTypeMenu() {
1033 _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
1034 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
1035 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
1036 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
1037 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
1038 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
1039 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
1040 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
1041 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
1042 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
1043 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
1044 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
1045 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
1046 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
1047 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
1048 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
1049 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
1050 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1051 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1052 initializeTypeMenu( getOptions() );
1053 _jmenubar.add( _type_menu );
1056 void buildViewMenu() {
1057 _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
1059 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
1060 _view_jmenu.addSeparator();
1061 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
1062 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
1063 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
1064 customizeJMenuItem( _display_basic_information_item );
1065 customizeJMenuItem( _view_as_NH_item );
1066 customizeJMenuItem( _view_as_XML_item );
1067 customizeJMenuItem( _view_as_nexus_item );
1068 _jmenubar.add( _view_jmenu );
1071 void checkTextFrames() {
1072 if ( _textframes.size() > 5 ) {
1074 if ( _textframes.getFirst() != null ) {
1075 _textframes.getFirst().removeMe();
1078 _textframes.removeFirst();
1081 catch ( final NoSuchElementException e ) {
1087 void clearCurrentExternalNodesDataBuffer() {
1088 getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
1091 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
1092 if ( item != null ) {
1093 item.setFont( MainFrame.menu_font );
1094 if ( !getConfiguration().isUseNativeUI() ) {
1095 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1096 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1098 item.setSelected( is_selected );
1099 item.addActionListener( this );
1103 void customizeJMenuItem( final JMenuItem jmi ) {
1104 if ( jmi != null ) {
1105 jmi.setFont( MainFrame.menu_font );
1106 if ( !getConfiguration().isUseNativeUI() ) {
1107 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1108 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
1110 jmi.addActionListener( this );
1114 void displayBasicInformation() {
1115 if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
1116 && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1117 String title = "Basic Information";
1118 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1119 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
1121 showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
1125 void executeGSDI() {
1126 if ( !isOKforSDI( false, true ) ) {
1129 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1130 JOptionPane.showMessageDialog( this,
1131 "Gene tree is not rooted.",
1132 "Cannot execute GSDI",
1133 JOptionPane.ERROR_MESSAGE );
1136 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1137 gene_tree.setAllNodesToNotCollapse();
1138 gene_tree.recalculateNumberOfExternalDescendants( false );
1140 final Phylogeny species_tree = _species_tree.copy();
1142 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
1144 catch ( final SDIException e ) {
1145 JOptionPane.showMessageDialog( this,
1146 e.getLocalizedMessage(),
1147 "Error during GSDI",
1148 JOptionPane.ERROR_MESSAGE );
1151 catch ( final Exception e ) {
1152 AptxUtil.unexpectedException( e );
1155 gene_tree.setRerootable( false );
1156 gene_tree.clearHashIdToNodeMap();
1157 gene_tree.recalculateNumberOfExternalDescendants( true );
1158 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
1159 getMainPanel().getControlPanel().setShowEvents( true );
1161 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1162 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1164 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1166 _mainpanel.getCurrentTreePanel().setEdited( true );
1167 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1168 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1169 JOptionPane.showMessageDialog( this,
1170 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1171 + "Potential duplications: "
1172 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1173 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1174 + "Stripped gene tree nodes: "
1175 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1176 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1177 + "Number of polytomies in species tree used: " + poly + "\n",
1178 "GSDI successfully completed",
1179 JOptionPane.WARNING_MESSAGE );
1182 JOptionPane.showMessageDialog( this,
1183 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1184 + "Potential duplications: "
1185 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1186 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1187 + "Stripped gene tree nodes: "
1188 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1189 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1190 + "Number of polytomies in species tree used: " + poly + "\n",
1191 "GSDI successfully completed",
1192 JOptionPane.INFORMATION_MESSAGE );
1196 void executeGSDIR() {
1197 if ( !isOKforSDI( false, false ) ) {
1200 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1202 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1203 JOptionPane.showMessageDialog( this,
1204 "Gene tree is not completely binary",
1205 "Cannot execute GSDI",
1206 JOptionPane.ERROR_MESSAGE );
1209 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1210 gene_tree.setAllNodesToNotCollapse();
1211 gene_tree.recalculateNumberOfExternalDescendants( false );
1213 final Phylogeny species_tree = _species_tree.copy();
1215 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1217 catch ( final SDIException e ) {
1218 JOptionPane.showMessageDialog( this,
1219 e.getLocalizedMessage(),
1220 "Error during GSDIR",
1221 JOptionPane.ERROR_MESSAGE );
1224 catch ( final Exception e ) {
1225 AptxUtil.unexpectedException( e );
1228 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1229 result_gene_tree.setRerootable( false );
1230 result_gene_tree.clearHashIdToNodeMap();
1231 result_gene_tree.recalculateNumberOfExternalDescendants( true );
1232 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1233 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1234 getMainPanel().getControlPanel().setShowEvents( true );
1236 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1237 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1239 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1241 _mainpanel.getCurrentTreePanel().setEdited( true );
1242 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1243 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1244 JOptionPane.showMessageDialog( this,
1245 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1246 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1247 + "Stripped gene tree nodes: "
1248 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1249 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1250 + "Number of polytomies in species tree used: " + poly + "\n",
1251 "GSDIR successfully completed",
1252 JOptionPane.WARNING_MESSAGE );
1255 JOptionPane.showMessageDialog( this,
1256 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1257 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1258 + "Stripped gene tree nodes: "
1259 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1260 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1261 + "Number of polytomies in species tree used: " + poly + "\n",
1262 "GSDIR successfully completed",
1263 JOptionPane.INFORMATION_MESSAGE );
1267 Configuration getConfiguration() {
1268 return _configuration;
1271 TreePanel getCurrentTreePanel() {
1272 return getMainPanel().getCurrentTreePanel();
1275 JCheckBoxMenuItem getlabelDirectionCbmi() {
1276 return _label_direction_cbmi;
1279 Options getOtions() {
1283 void initializeTypeMenu( final Options options ) {
1284 setTypeMenuToAllUnselected();
1286 switch ( options.getPhylogenyGraphicsType() ) {
1288 _convex_type_cbmi.setSelected( true );
1291 _curved_type_cbmi.setSelected( true );
1294 _euro_type_cbmi.setSelected( true );
1297 _rounded_type_cbmi.setSelected( true );
1300 _triangular_type_cbmi.setSelected( true );
1303 _unrooted_type_cbmi.setSelected( true );
1306 _circular_type_cbmi.setSelected( true );
1309 _rectangular_type_cbmi.setSelected( true );
1313 catch ( final NullPointerException np ) {
1314 // In all likelihood, this is caused by menu-less display.
1318 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1319 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1322 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1323 JOptionPane.showMessageDialog( this,
1324 "No species tree loaded",
1325 "Cannot execute GSDI",
1326 JOptionPane.ERROR_MESSAGE );
1329 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1330 JOptionPane.showMessageDialog( this,
1331 "Species tree is not completely binary",
1332 "Cannot execute GSDI",
1333 JOptionPane.ERROR_MESSAGE );
1336 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1337 JOptionPane.showMessageDialog( this,
1338 "Gene tree is not completely binary",
1339 "Cannot execute GSDI",
1340 JOptionPane.ERROR_MESSAGE );
1348 boolean isSubtreeDisplayed() {
1349 if ( getCurrentTreePanel() != null ) {
1350 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1352 .showMessageDialog( this,
1353 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1354 "Operation can not be exectuted on a sub-tree",
1355 JOptionPane.WARNING_MESSAGE );
1362 void removeAllTextFrames() {
1363 for( final TextFrame tf : _textframes ) {
1368 _textframes.clear();
1371 void setConfiguration( final Configuration configuration ) {
1372 _configuration = configuration;
1375 void setOptions( final Options options ) {
1379 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1380 setTypeMenuToAllUnselected();
1384 _circular_type_cbmi.setSelected( true );
1387 _convex_type_cbmi.setSelected( true );
1390 _curved_type_cbmi.setSelected( true );
1393 _euro_type_cbmi.setSelected( true );
1396 _rounded_type_cbmi.setSelected( true );
1399 _rectangular_type_cbmi.setSelected( true );
1402 _triangular_type_cbmi.setSelected( true );
1405 _unrooted_type_cbmi.setSelected( true );
1408 throw new IllegalArgumentException( "unknown type: " + type );
1411 catch ( final NullPointerException np ) {
1412 // In all likelihood, this is caused by menu-less display.
1416 void setTypeMenuToAllUnselected() {
1417 if ( _convex_type_cbmi != null ) {
1418 _convex_type_cbmi.setSelected( false );
1420 if ( _curved_type_cbmi != null ) {
1421 _curved_type_cbmi.setSelected( false );
1423 if ( _euro_type_cbmi != null ) {
1424 _euro_type_cbmi.setSelected( false );
1426 if ( _rounded_type_cbmi != null ) {
1427 _rounded_type_cbmi.setSelected( false );
1429 if ( _triangular_type_cbmi != null ) {
1430 _triangular_type_cbmi.setSelected( false );
1432 if ( _rectangular_type_cbmi != null ) {
1433 _rectangular_type_cbmi.setSelected( false );
1435 if ( _unrooted_type_cbmi != null ) {
1436 _unrooted_type_cbmi.setSelected( false );
1438 if ( _circular_type_cbmi != null ) {
1439 _circular_type_cbmi.setSelected( false );
1444 _mainpanel.getControlPanel().showWhole();
1447 void switchColors() {
1448 final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1449 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1450 csc.setVisible( true );
1451 getMainPanel().setTreeColorSet( colorset );
1454 void typeChanged( final Object o ) {
1455 updateTypeCheckboxes( getOptions(), o );
1456 updateOptions( getOptions() );
1457 if ( getCurrentTreePanel() != null ) {
1458 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1459 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1460 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1461 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1462 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1463 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1464 getCurrentTreePanel().getControlPanel().showWhole();
1466 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1467 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1470 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1472 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1473 MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1477 void updateOptions( final Options options ) {
1478 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1479 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1480 && _background_gradient_cbmi.isSelected() );
1481 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1482 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1483 && _show_annotation_ref_source.isSelected() );
1484 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1485 && _abbreviate_scientific_names.isSelected() );
1486 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1487 && _color_labels_same_as_parent_branch.isSelected() );
1488 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1489 && _show_default_node_shapes_internal_cbmi.isSelected() );
1490 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1491 && _show_default_node_shapes_external_cbmi.isSelected() );
1492 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1493 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1494 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1495 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1497 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1498 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1500 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1501 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1503 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1504 && _search_case_senstive_cbmi.isSelected() );
1505 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1506 options.setShowScale( _show_scale_cbmi.isSelected() );
1508 if ( _label_direction_cbmi != null ) {
1509 if ( _label_direction_cbmi.isSelected() ) {
1510 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1513 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1516 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1517 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1518 && _show_confidence_stddev_cbmi.isSelected() );
1519 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1520 && _search_whole_words_only_cbmi.isSelected() );
1521 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
1522 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1523 && _inverse_search_result_cbmi.isSelected() );
1524 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1525 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1527 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1528 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1530 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1531 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1533 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1534 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1536 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1537 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1539 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1540 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1542 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1543 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1545 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1546 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1548 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1549 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1551 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1552 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1554 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1555 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1559 void updateTypeCheckboxes( final Options options, final Object o ) {
1560 setTypeMenuToAllUnselected();
1561 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1564 void viewAsNexus() {
1565 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1566 String title = "Nexus";
1567 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1568 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1570 showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1571 .getNhConversionSupportValueStyle() ),
1577 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1578 String title = "New Hampshire";
1579 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1580 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1582 showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1583 .getNhConversionSupportValueStyle() ),
1589 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1590 String title = "phyloXML";
1591 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1592 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1594 showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1598 private void chooseFont() {
1599 final FontChooser fc = new FontChooser();
1600 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1601 fc.showDialog( this, "Select the Base Font" );
1602 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1605 private void chooseMinimalConfidence() {
1606 final String s = ( String ) JOptionPane
1607 .showInputDialog( this,
1608 "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1609 + getOptions().getMinConfidenceValue() + "]\n",
1610 "Minimal Confidence Value",
1611 JOptionPane.QUESTION_MESSAGE,
1614 getOptions().getMinConfidenceValue() );
1615 if ( !ForesterUtil.isEmpty( s ) ) {
1616 boolean success = true;
1618 final String m_str = s.trim();
1619 if ( !ForesterUtil.isEmpty( m_str ) ) {
1621 m = Double.parseDouble( m_str );
1623 catch ( final Exception ex ) {
1630 if ( success && ( m >= 0.0 ) ) {
1631 getOptions().setMinConfidenceValue( m );
1636 private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1637 if ( item != null ) {
1638 item.setFont( MainFrame.menu_font );
1639 if ( !getConfiguration().isUseNativeUI() ) {
1640 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1641 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1643 item.setSelected( is_selected );
1644 item.addActionListener( this );
1648 MainPanel getMainPanel() {
1652 private Phylogeny getSpeciesTree() {
1653 return _species_tree;
1656 private boolean isScreenAntialias() {
1660 private void removeBranchColors() {
1661 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1662 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1666 private void removeVisualStyles() {
1667 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1668 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1672 private void setMainPanel( final MainPanelApplets main_panel ) {
1673 _mainpanel = main_panel;
1676 private void setSpeciesTree( final Phylogeny species_tree ) {
1677 _species_tree = species_tree;
1680 private void setupUI() {
1682 if ( getConfiguration().isUseNativeUI() ) {
1683 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1686 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1689 catch ( final UnsupportedLookAndFeelException e ) {
1690 AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1692 catch ( final ClassNotFoundException e ) {
1693 AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1695 catch ( final InstantiationException e ) {
1696 AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1698 catch ( final IllegalAccessException e ) {
1699 AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1701 catch ( final Exception e ) {
1702 AptxUtil.dieWithSystemError( e.toString() );
1706 static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1707 for( final TreePanel tree_panel : treepanels ) {
1708 tree_panel.setTextAntialias();