2 package org.forester.archaeopteryx;
4 import java.awt.BorderLayout;
5 import java.awt.Container;
6 import java.awt.event.ActionEvent;
7 import java.awt.event.ActionListener;
8 import java.awt.event.ComponentAdapter;
9 import java.awt.event.ComponentEvent;
10 import java.io.ByteArrayOutputStream;
12 import java.io.IOException;
14 import java.util.LinkedList;
15 import java.util.List;
16 import java.util.NoSuchElementException;
18 import javax.swing.ButtonGroup;
19 import javax.swing.JApplet;
20 import javax.swing.JCheckBoxMenuItem;
21 import javax.swing.JMenu;
22 import javax.swing.JMenuBar;
23 import javax.swing.JMenuItem;
24 import javax.swing.JOptionPane;
25 import javax.swing.JRadioButtonMenuItem;
26 import javax.swing.UIManager;
27 import javax.swing.UnsupportedLookAndFeelException;
28 import javax.swing.event.ChangeEvent;
29 import javax.swing.event.ChangeListener;
31 import org.apache.commons.codec.binary.Base64;
32 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
33 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
34 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
35 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
36 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
37 import org.forester.phylogeny.Phylogeny;
38 import org.forester.phylogeny.PhylogenyMethods;
39 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
40 import org.forester.phylogeny.data.SequenceRelation;
41 import org.forester.sdi.GSDI;
42 import org.forester.sdi.GSDIR;
43 import org.forester.sdi.SDIException;
44 import org.forester.util.ForesterConstants;
45 import org.forester.util.ForesterUtil;
48 // <applet archive="forester.jar"
49 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
50 // codebase="http://www.myserver.org/path/to/forester"
53 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
54 // <param name="url_of_tree_to_load"
55 // value="http://www.myserver.org/examples/data/apaf.xml">
56 // <param name="config_file"
57 // value="http://www.myserver.org/examples/config/config_file.txt">
59 public class ArchaeopteryxE extends JApplet implements ActionListener {
61 private final static String NAME = "ArchaeopteryxE";
62 private static final long serialVersionUID = -1220055577935759443L;
63 private Configuration _configuration;
64 private MainPanelApplets _mainpanel;
65 private JMenuBar _jmenubar;
66 private JMenu _options_jmenu;
67 private JMenu _font_size_menu;
68 private JMenuItem _super_tiny_fonts_mi;
69 private JMenuItem _tiny_fonts_mi;
70 private JMenuItem _small_fonts_mi;
71 private JMenuItem _medium_fonts_mi;
72 private JMenuItem _large_fonts_mi;
73 private JMenu _tools_menu;
74 private JMenuItem _taxcolor_item;
75 private JMenuItem _confcolor_item;
76 private JMenuItem _midpoint_root_item;
77 private JMenu _view_jmenu;
78 private JMenuItem _view_as_XML_item;
79 private JMenuItem _view_as_NH_item;
80 private JMenuItem _view_as_nexus_item;
81 private JMenuItem _display_basic_information_item;
82 private JMenu _type_menu;
83 private JCheckBoxMenuItem _rectangular_type_cbmi;
84 private JCheckBoxMenuItem _triangular_type_cbmi;
85 private JCheckBoxMenuItem _curved_type_cbmi;
86 private JCheckBoxMenuItem _convex_type_cbmi;
87 private JCheckBoxMenuItem _euro_type_cbmi;
88 private JCheckBoxMenuItem _rounded_type_cbmi;
89 private JCheckBoxMenuItem _unrooted_type_cbmi;
90 private JCheckBoxMenuItem _circular_type_cbmi;
91 private JMenuItem _help_item;
92 private JMenuItem _about_item;
93 private JMenu _help_jmenu;
94 private JMenuItem _website_item;
95 private JMenuItem _phyloxml_website_item;
96 private JMenuItem _phyloxml_ref_item;
97 private JMenuItem _aptx_ref_item;
98 private JMenuItem _remove_branch_color_item;
99 private JMenuItem _remove_visual_styles_item;
100 private JCheckBoxMenuItem _show_domain_labels;
101 private JCheckBoxMenuItem _show_annotation_ref_source;
102 private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
103 private JCheckBoxMenuItem _abbreviate_scientific_names;
104 private JCheckBoxMenuItem _screen_antialias_cbmi;
105 private JCheckBoxMenuItem _background_gradient_cbmi;
106 private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
107 private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
108 private JRadioButtonMenuItem _uniform_cladograms_rbmi;
109 private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
110 private Options _options;
111 private JMenuItem _choose_font_mi;
112 private JMenuItem _switch_colors_mi;
113 JCheckBoxMenuItem _label_direction_cbmi;
114 private JCheckBoxMenuItem _show_scale_cbmi;
115 private JCheckBoxMenuItem _search_case_senstive_cbmi;
116 private JCheckBoxMenuItem _search_whole_words_only_cbmi;
117 private JCheckBoxMenuItem _inverse_search_result_cbmi;
118 private JCheckBoxMenuItem _search_with_regex_cbmi;
119 private JCheckBoxMenuItem _show_overview_cbmi;
120 private JMenuItem _choose_minimal_confidence_mi;
121 private JMenuItem _collapse_species_specific_subtrees;
122 private JMenuItem _overview_placment_mi;
123 private ButtonGroup _radio_group_1;
124 private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
125 private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
126 private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
127 private JMenuItem _cycle_node_shape_mi;
128 private JMenuItem _cycle_node_fill_mi;
129 private JMenuItem _choose_node_size_mi;
130 private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
131 private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
132 private JMenu _analysis_menu;
133 private JMenuItem _gsdi_item;
134 private JMenuItem _gsdir_item;
135 private Phylogeny _species_tree;
136 private JCheckBoxMenuItem _right_line_up_domains_cbmi;
137 private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
140 public void actionPerformed( final ActionEvent e ) {
141 final Object o = e.getSource();
142 if ( o == _midpoint_root_item ) {
143 getMainPanel().getCurrentTreePanel().midpointRoot();
145 else if ( o == _gsdi_item ) {
146 if ( isSubtreeDisplayed() ) {
151 else if ( o == _gsdir_item ) {
152 if ( isSubtreeDisplayed() ) {
157 else if ( o == _taxcolor_item ) {
158 getMainPanel().getCurrentTreePanel().taxColor();
160 else if ( o == _confcolor_item ) {
161 getMainPanel().getCurrentTreePanel().confColor();
163 else if ( o == _collapse_species_specific_subtrees ) {
164 if ( getCurrentTreePanel() != null ) {
165 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
168 else if ( o == _remove_branch_color_item ) {
169 removeBranchColors();
171 else if ( o == _remove_visual_styles_item ) {
172 removeVisualStyles();
174 else if ( o == _switch_colors_mi ) {
177 else if ( o == _display_basic_information_item ) {
178 displayBasicInformation();
180 else if ( o == _view_as_NH_item ) {
183 else if ( o == _view_as_XML_item ) {
186 else if ( o == _view_as_nexus_item ) {
189 else if ( o == _super_tiny_fonts_mi ) {
190 if ( getCurrentTreePanel() != null ) {
191 getCurrentTreePanel().setSuperTinyFonts();
192 getCurrentTreePanel().repaint();
195 else if ( o == _tiny_fonts_mi ) {
196 if ( getCurrentTreePanel() != null ) {
197 getCurrentTreePanel().setTinyFonts();
198 getCurrentTreePanel().repaint();
201 else if ( o == _small_fonts_mi ) {
202 if ( getCurrentTreePanel() != null ) {
203 getCurrentTreePanel().setSmallFonts();
204 getCurrentTreePanel().repaint();
207 else if ( o == _medium_fonts_mi ) {
208 if ( getCurrentTreePanel() != null ) {
209 getCurrentTreePanel().setMediumFonts();
210 getCurrentTreePanel().repaint();
213 else if ( o == _large_fonts_mi ) {
214 if ( getCurrentTreePanel() != null ) {
215 getCurrentTreePanel().setLargeFonts();
216 getCurrentTreePanel().repaint();
219 else if ( o == _choose_font_mi ) {
222 else if ( o == _choose_minimal_confidence_mi ) {
223 chooseMinimalConfidence();
225 else if ( o == _choose_node_size_mi ) {
226 MainFrame.chooseNodeSize( getOptions(), this );
228 else if ( o == _overview_placment_mi ) {
229 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
231 else if ( o == _cycle_node_fill_mi ) {
232 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
234 else if ( o == _cycle_node_shape_mi ) {
235 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
237 else if ( o == _non_lined_up_cladograms_rbmi ) {
238 updateOptions( getOptions() );
239 _mainpanel.getControlPanel().showWhole();
241 else if ( o == _uniform_cladograms_rbmi ) {
242 updateOptions( getOptions() );
243 _mainpanel.getControlPanel().showWhole();
245 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
246 updateOptions( getOptions() );
247 _mainpanel.getControlPanel().showWhole();
249 else if ( o == _search_case_senstive_cbmi ) {
250 updateOptions( getOptions() );
251 getMainPanel().getControlPanel().search0();
252 getMainPanel().getControlPanel().search1();
254 else if ( o == _search_whole_words_only_cbmi ) {
255 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
256 _search_with_regex_cbmi.setSelected( false );
258 updateOptions( getOptions() );
259 getMainPanel().getControlPanel().search0();
260 getMainPanel().getControlPanel().search1();
262 else if ( o == _inverse_search_result_cbmi ) {
263 updateOptions( getOptions() );
264 getMainPanel().getControlPanel().search0();
265 getMainPanel().getControlPanel().search1();
267 else if ( o == _search_with_regex_cbmi ) {
268 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
269 _search_whole_words_only_cbmi.setSelected( false );
271 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
272 _search_case_senstive_cbmi.setSelected( true );
274 updateOptions( getOptions() );
275 getMainPanel().getControlPanel().search0();
276 getMainPanel().getControlPanel().search1();
278 else if ( o == _show_scale_cbmi ) {
279 updateOptions( getOptions() );
281 else if ( o == _show_confidence_stddev_cbmi ) {
282 updateOptions( getOptions() );
284 else if ( o == _label_direction_cbmi ) {
285 updateOptions( getOptions() );
287 else if ( o == _abbreviate_scientific_names ) {
288 updateOptions( getOptions() );
290 else if ( o == _show_overview_cbmi ) {
291 updateOptions( getOptions() );
292 if ( getCurrentTreePanel() != null ) {
293 getCurrentTreePanel().updateOvSizes();
296 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
297 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
298 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
301 else if ( o == _screen_antialias_cbmi ) {
302 updateOptions( getOptions() );
303 setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
305 else if ( o == _background_gradient_cbmi ) {
306 updateOptions( getOptions() );
308 else if ( o == _show_domain_labels ) {
309 updateOptions( getOptions() );
311 else if ( o == _color_labels_same_as_parent_branch ) {
312 updateOptions( getOptions() );
314 else if ( o == _show_default_node_shapes_internal_cbmi ) {
315 updateOptions( getOptions() );
317 else if ( o == _show_default_node_shapes_external_cbmi ) {
318 updateOptions( getOptions() );
320 else if ( o == _about_item ) {
323 else if ( o == _help_item ) {
325 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
327 catch ( final IOException e1 ) {
328 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
331 else if ( o == _website_item ) {
333 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
335 catch ( final IOException e1 ) {
336 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
339 else if ( o == _phyloxml_website_item ) {
341 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
343 catch ( final IOException e1 ) {
344 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
347 else if ( o == _aptx_ref_item ) {
349 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
351 catch ( final IOException e1 ) {
352 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
355 else if ( o == _phyloxml_ref_item ) {
357 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
359 catch ( final IOException e1 ) {
360 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
363 else if ( o == _color_by_taxonomic_group_cbmi ) {
364 updateOptions( getOptions() );
366 else if ( o == _line_up_renderable_data_cbmi ) {
367 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
368 _right_line_up_domains_cbmi.setSelected( false );
370 updateOptions( getOptions() );
372 else if ( o == _right_line_up_domains_cbmi ) {
373 if ( _right_line_up_domains_cbmi.isSelected() ) {
374 _line_up_renderable_data_cbmi.setSelected( true );
376 updateOptions( getOptions() );
382 public void destroy() {
383 AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
384 removeAllTextFrames();
385 if ( getMainPanel() != null ) {
386 getMainPanel().terminate();
391 * This method returns the current external node data which
392 * has been selected by the user by clicking the "Return ..."
393 * menu item. This method is expected to be called from Javascript or
396 * @return current external node data as String
398 public String getCurrentExternalNodesDataBuffer() {
399 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
402 public int getCurrentExternalNodesDataBufferChangeCounter() {
403 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
406 public int getCurrentExternalNodesDataBufferLength() {
407 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
411 * This method returns the current phylogeny as a string in the chosen format
413 * @param format must be NH, NHX, NEXUS or PHYLOXML
414 * @return the phylogeny string
415 * @author Herve Menager
417 public String getCurrentPhylogeny( final String format ) {
418 removeAllTextFrames();
419 if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
420 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
423 switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
425 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
427 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
429 return getMainPanel().getCurrentPhylogeny().toNexus();
431 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
439 * This method returns a view of the current phylogeny in a chosen
440 * graphics format, base64-encoded in a string so that in can be used
443 * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
444 * @return the phylogeny string
445 * @author Herve Menager
447 public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
448 final ByteArrayOutputStream baos = new ByteArrayOutputStream();
450 AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
451 _mainpanel.getWidth(),
452 _mainpanel.getHeight(),
453 getCurrentTreePanel(),
454 getCurrentTreePanel().getControlPanel(),
455 GraphicsExportType.valueOf( format ),
458 catch ( final IOException ioe ) {
459 ForesterUtil.printErrorMessage( NAME, ioe.toString() );
460 ioe.printStackTrace();
461 JOptionPane.showMessageDialog( this,
462 NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
463 "Failed to generate graphics",
464 JOptionPane.ERROR_MESSAGE );
467 final byte[] bytes = baos.toByteArray();
468 final String dataImg = Base64.encodeBase64String( bytes );
472 public Options getOptions() {
478 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
479 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
480 final Configuration configuration = new Configuration( config_filename, true, true, true );
481 setConfiguration( configuration );
482 setOptions( Options.createInstance( configuration ) );
484 final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
485 if ( ForesterUtil.isEmpty( tree_url_str ) ) {
486 ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
487 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
488 JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
489 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
492 AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
493 // Get URL to tree file
496 phys_url = new URL( tree_url_str );
498 catch ( final Exception e ) {
499 ForesterUtil.printErrorMessage( NAME, "error: " + e );
501 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
502 + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
504 if ( phys_url == null ) {
505 ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
506 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
507 JOptionPane.showMessageDialog( this,
508 NAME + ": Could not create URL from: \"" + tree_url_str,
509 "Failed to create URL",
510 JOptionPane.ERROR_MESSAGE );
513 // Load the tree from URL
514 Phylogeny[] phys = null;
516 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
517 getConfiguration().isValidatePhyloXmlAgainstSchema(),
518 getConfiguration().isReplaceUnderscoresInNhParsing(),
519 getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
520 getConfiguration().getTaxonomyExtraction(),
521 getConfiguration().isMidpointReroot() );
523 catch ( final Exception e ) {
524 ForesterUtil.printErrorMessage( NAME, e.toString() );
526 JOptionPane.showMessageDialog( this,
527 NAME + ": Failed to read phylogenies: " + "\nException: " + e,
528 "Failed to read phylogenies",
529 JOptionPane.ERROR_MESSAGE );
531 if ( phys == null ) {
532 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
533 JOptionPane.showMessageDialog( this,
534 NAME + ": phylogenies from [" + phys_url + "] are null",
535 "Failed to read phylogenies",
536 JOptionPane.ERROR_MESSAGE );
539 else if ( phys.length < 1 ) {
540 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
541 JOptionPane.showMessageDialog( this,
542 NAME + ": phylogenies from [" + phys_url + "] are empty",
543 "Failed to read phylogenies",
544 JOptionPane.ERROR_MESSAGE );
548 AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
551 final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
552 if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
553 AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
554 Phylogeny[] species_trees = null;
556 final URL species_tree_url = new URL( species_tree_url_str );
557 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
558 configuration.isValidatePhyloXmlAgainstSchema(),
559 configuration.isReplaceUnderscoresInNhParsing(),
561 TAXONOMY_EXTRACTION.NO,
564 catch ( final IOException e ) {
565 ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
567 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
568 + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
570 if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
571 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
572 if ( species_trees[ 0 ].isEmpty() ) {
573 ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
575 else if ( !species_trees[ 0 ].isRooted() ) {
576 ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
579 setSpeciesTree( species_trees[ 0 ] );
580 AptxUtil.printAppletMessage( NAME, "species tree OK" );
587 setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
588 _jmenubar = new JMenuBar();
589 if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
590 if ( !getConfiguration().isUseNativeUI() ) {
591 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
593 if ( getSpeciesTree() != null ) {
602 setJMenuBar( _jmenubar );
604 final Container contentpane = getContentPane();
605 contentpane.setLayout( new BorderLayout() );
606 contentpane.add( getMainPanel(), BorderLayout.CENTER );
607 addComponentListener( new ComponentAdapter() {
610 public void componentResized( final ComponentEvent e ) {
611 if ( getMainPanel().getCurrentTreePanel() != null ) {
612 getMainPanel().getCurrentTreePanel()
613 .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
614 getMainPanel().getCurrentTreePanel().getHeight(),
615 getOptions().isAllowFontSizeChange() );
619 if ( getConfiguration().isUseTabbedDisplay() ) {
621 AptxUtil.printAppletMessage( NAME, "using tabbed display" );
622 AptxUtil.addPhylogeniesToTabs( phys,
623 new File( phys_url.getFile() ).getName(),
628 catch ( final Exception e ) {
629 ForesterUtil.printErrorMessage( NAME, e.toString() );
634 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
635 if ( getSpeciesTree() != null ) {
636 AptxUtil.printAppletMessage( NAME,
637 "Warning: gsdi (gene duplication inference) only available tabbed display" );
639 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
643 getMainPanel().getControlPanel().showWholeAll();
644 getMainPanel().getControlPanel().showWhole();
646 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
647 for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
648 .getRelevantSequenceRelationTypes() ) {
649 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
651 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
652 if ( default_relation != null ) {
653 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
655 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
656 if ( default_sequence != null ) {
657 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
661 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
664 catch ( final Exception e ) {
665 ForesterUtil.printErrorMessage( NAME, e.toString() );
670 public void showTextFrame( final String s, final String title ) {
672 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
676 public void start() {
677 if ( getMainPanel() != null ) {
678 getMainPanel().validate();
681 requestFocusInWindow();
683 AptxUtil.printAppletMessage( NAME, "started" );
686 void buildAnalysisMenu() {
687 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
688 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
689 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
690 customizeJMenuItem( _gsdi_item );
691 customizeJMenuItem( _gsdir_item );
692 // _analysis_menu.addSeparator();
693 // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
694 // customizeJMenuItem( _lineage_inference );
695 // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
696 _jmenubar.add( _analysis_menu );
699 void buildFontSizeMenu() {
700 _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
701 _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
702 _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
703 _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
704 _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
705 _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
706 customizeJMenuItem( _super_tiny_fonts_mi );
707 customizeJMenuItem( _tiny_fonts_mi );
708 customizeJMenuItem( _small_fonts_mi );
709 customizeJMenuItem( _medium_fonts_mi );
710 customizeJMenuItem( _large_fonts_mi );
711 _jmenubar.add( _font_size_menu );
714 void buildHelpMenu() {
715 _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
716 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
717 _help_jmenu.addSeparator();
718 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
719 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
720 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
721 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
722 _help_jmenu.addSeparator();
723 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
724 customizeJMenuItem( _help_item );
725 customizeJMenuItem( _website_item );
726 customizeJMenuItem( _phyloxml_website_item );
727 customizeJMenuItem( _aptx_ref_item );
728 customizeJMenuItem( _phyloxml_ref_item );
729 customizeJMenuItem( _about_item );
730 _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
731 _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
732 _jmenubar.add( _help_jmenu );
735 void buildOptionsMenu() {
736 _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
737 _options_jmenu.addChangeListener( new ChangeListener() {
740 public void stateChanged( final ChangeEvent e ) {
741 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
742 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
744 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
745 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
746 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
747 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
748 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
749 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
751 getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
752 getMainPanel().getControlPanel().setVisibilityOfX();
754 catch ( final Exception ignore ) {
755 // do nothing, not important.
759 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
760 getConfiguration() ) );
762 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
763 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
765 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
766 _radio_group_1 = new ButtonGroup();
767 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
768 _radio_group_1.add( _uniform_cladograms_rbmi );
769 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
770 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
771 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
773 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
775 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
777 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
778 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
779 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
780 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
781 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
783 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
784 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
786 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
788 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
789 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
790 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
791 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
792 _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
793 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
794 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
795 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
796 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
797 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
798 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
799 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
800 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
801 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
802 _options_jmenu.addSeparator();
803 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
804 getConfiguration() ) );
806 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
807 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
808 _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
810 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
811 customizeJMenuItem( _choose_font_mi );
812 customizeJMenuItem( _choose_minimal_confidence_mi );
813 customizeJMenuItem( _switch_colors_mi );
814 customizeJMenuItem( _overview_placment_mi );
815 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
816 customizeCheckBoxMenuItem( _label_direction_cbmi,
817 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
818 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
819 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
820 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
821 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
822 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
823 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
824 .isShowDefaultNodeShapesExternal() );
825 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
826 .isShowDefaultNodeShapesInternal() );
827 customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
828 .isShowDefaultNodeShapesForMarkedNodes() );
829 customizeJMenuItem( _cycle_node_shape_mi );
830 customizeJMenuItem( _cycle_node_fill_mi );
831 customizeJMenuItem( _choose_node_size_mi );
832 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
833 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
834 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
835 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
836 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
837 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
838 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
839 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
840 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
841 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
842 customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
843 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
844 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
845 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
846 customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
847 customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
848 _jmenubar.add( _options_jmenu );
851 void buildToolsMenu() {
852 _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
853 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
854 customizeJMenuItem( _confcolor_item );
855 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
856 customizeJMenuItem( _taxcolor_item );
857 _tools_menu.addSeparator();
858 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
859 _remove_visual_styles_item
860 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
861 customizeJMenuItem( _remove_visual_styles_item );
862 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
863 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
864 customizeJMenuItem( _remove_branch_color_item );
865 _tools_menu.addSeparator();
866 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
867 customizeJMenuItem( _midpoint_root_item );
868 _tools_menu.addSeparator();
869 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
870 customizeJMenuItem( _collapse_species_specific_subtrees );
871 _jmenubar.add( _tools_menu );
874 void buildTypeMenu() {
875 _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
876 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
877 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
878 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
879 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
880 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
881 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
882 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
883 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
884 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
885 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
886 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
887 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
888 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
889 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
890 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
891 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
892 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
893 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
894 initializeTypeMenu( getOptions() );
895 _jmenubar.add( _type_menu );
898 void buildViewMenu() {
899 _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
901 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
902 _view_jmenu.addSeparator();
903 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
904 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
905 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
906 customizeJMenuItem( _display_basic_information_item );
907 customizeJMenuItem( _view_as_NH_item );
908 customizeJMenuItem( _view_as_XML_item );
909 customizeJMenuItem( _view_as_nexus_item );
910 _jmenubar.add( _view_jmenu );
913 void checkTextFrames() {
914 if ( _textframes.size() > 5 ) {
916 if ( _textframes.getFirst() != null ) {
917 _textframes.getFirst().removeMe();
920 _textframes.removeFirst();
923 catch ( final NoSuchElementException e ) {
929 void clearCurrentExternalNodesDataBuffer() {
930 getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
933 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
934 if ( item != null ) {
935 item.setFont( MainFrame.menu_font );
936 if ( !getConfiguration().isUseNativeUI() ) {
937 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
938 item.setForeground( getConfiguration().getGuiMenuTextColor() );
940 item.setSelected( is_selected );
941 item.addActionListener( this );
945 void customizeJMenuItem( final JMenuItem jmi ) {
946 jmi.setFont( MainFrame.menu_font );
947 if ( !getConfiguration().isUseNativeUI() ) {
948 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
949 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
951 jmi.addActionListener( this );
954 void displayBasicInformation() {
955 if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
956 && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
957 String title = "Basic Information";
958 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
959 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
961 showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
966 if ( !isOKforSDI( false, true ) ) {
969 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
970 JOptionPane.showMessageDialog( this,
971 "Gene tree is not rooted.",
972 "Cannot execute GSDI",
973 JOptionPane.ERROR_MESSAGE );
976 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
977 gene_tree.setAllNodesToNotCollapse();
978 gene_tree.recalculateNumberOfExternalDescendants( false );
980 final Phylogeny species_tree = _species_tree.copy();
982 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
984 catch ( final SDIException e ) {
985 JOptionPane.showMessageDialog( this,
986 e.getLocalizedMessage(),
988 JOptionPane.ERROR_MESSAGE );
991 catch ( final Exception e ) {
992 AptxUtil.unexpectedException( e );
995 gene_tree.setRerootable( false );
996 gene_tree.clearHashIdToNodeMap();
997 gene_tree.recalculateNumberOfExternalDescendants( true );
998 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
999 getMainPanel().getControlPanel().setShowEvents( true );
1001 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1002 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1004 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1006 _mainpanel.getCurrentTreePanel().setEdited( true );
1007 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1008 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1009 JOptionPane.showMessageDialog( this,
1010 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1011 + "Potential duplications: "
1012 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1013 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1014 + "Stripped gene tree nodes: "
1015 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1016 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1017 + "Number of polytomies in species tree used: " + poly + "\n",
1018 "GSDI successfully completed",
1019 JOptionPane.WARNING_MESSAGE );
1022 JOptionPane.showMessageDialog( this,
1023 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1024 + "Potential duplications: "
1025 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1026 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1027 + "Stripped gene tree nodes: "
1028 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1029 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1030 + "Number of polytomies in species tree used: " + poly + "\n",
1031 "GSDI successfully completed",
1032 JOptionPane.INFORMATION_MESSAGE );
1036 void executeGSDIR() {
1037 if ( !isOKforSDI( false, false ) ) {
1040 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1042 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1043 JOptionPane.showMessageDialog( this,
1044 "Gene tree is not completely binary",
1045 "Cannot execute GSDI",
1046 JOptionPane.ERROR_MESSAGE );
1049 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1050 gene_tree.setAllNodesToNotCollapse();
1051 gene_tree.recalculateNumberOfExternalDescendants( false );
1053 final Phylogeny species_tree = _species_tree.copy();
1055 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1057 catch ( final SDIException e ) {
1058 JOptionPane.showMessageDialog( this,
1059 e.getLocalizedMessage(),
1060 "Error during GSDIR",
1061 JOptionPane.ERROR_MESSAGE );
1064 catch ( final Exception e ) {
1065 AptxUtil.unexpectedException( e );
1068 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1069 result_gene_tree.setRerootable( false );
1070 result_gene_tree.clearHashIdToNodeMap();
1071 result_gene_tree.recalculateNumberOfExternalDescendants( true );
1072 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1073 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1074 getMainPanel().getControlPanel().setShowEvents( true );
1076 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1077 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1079 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1081 _mainpanel.getCurrentTreePanel().setEdited( true );
1082 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1083 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1084 JOptionPane.showMessageDialog( this,
1085 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1086 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1087 + "Stripped gene tree nodes: "
1088 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1089 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1090 + "Number of polytomies in species tree used: " + poly + "\n",
1091 "GSDIR successfully completed",
1092 JOptionPane.WARNING_MESSAGE );
1095 JOptionPane.showMessageDialog( this,
1096 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1097 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1098 + "Stripped gene tree nodes: "
1099 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1100 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1101 + "Number of polytomies in species tree used: " + poly + "\n",
1102 "GSDIR successfully completed",
1103 JOptionPane.INFORMATION_MESSAGE );
1107 Configuration getConfiguration() {
1108 return _configuration;
1111 TreePanel getCurrentTreePanel() {
1112 return getMainPanel().getCurrentTreePanel();
1115 JCheckBoxMenuItem getlabelDirectionCbmi() {
1116 return _label_direction_cbmi;
1119 Options getOtions() {
1123 void initializeTypeMenu( final Options options ) {
1124 setTypeMenuToAllUnselected();
1126 switch ( options.getPhylogenyGraphicsType() ) {
1128 _convex_type_cbmi.setSelected( true );
1131 _curved_type_cbmi.setSelected( true );
1134 _euro_type_cbmi.setSelected( true );
1137 _rounded_type_cbmi.setSelected( true );
1140 _triangular_type_cbmi.setSelected( true );
1143 _unrooted_type_cbmi.setSelected( true );
1146 _circular_type_cbmi.setSelected( true );
1149 _rectangular_type_cbmi.setSelected( true );
1153 catch ( final NullPointerException np ) {
1154 // In all likelihood, this is caused by menu-less display.
1158 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1159 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1162 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1163 JOptionPane.showMessageDialog( this,
1164 "No species tree loaded",
1165 "Cannot execute GSDI",
1166 JOptionPane.ERROR_MESSAGE );
1169 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1170 JOptionPane.showMessageDialog( this,
1171 "Species tree is not completely binary",
1172 "Cannot execute GSDI",
1173 JOptionPane.ERROR_MESSAGE );
1176 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1177 JOptionPane.showMessageDialog( this,
1178 "Gene tree is not completely binary",
1179 "Cannot execute GSDI",
1180 JOptionPane.ERROR_MESSAGE );
1188 boolean isSubtreeDisplayed() {
1189 if ( getCurrentTreePanel() != null ) {
1190 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1192 .showMessageDialog( this,
1193 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1194 "Operation can not be exectuted on a sub-tree",
1195 JOptionPane.WARNING_MESSAGE );
1202 void removeAllTextFrames() {
1203 for( final TextFrame tf : _textframes ) {
1208 _textframes.clear();
1211 void setConfiguration( final Configuration configuration ) {
1212 _configuration = configuration;
1215 void setOptions( final Options options ) {
1219 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1220 setTypeMenuToAllUnselected();
1224 _circular_type_cbmi.setSelected( true );
1227 _convex_type_cbmi.setSelected( true );
1230 _curved_type_cbmi.setSelected( true );
1233 _euro_type_cbmi.setSelected( true );
1236 _rounded_type_cbmi.setSelected( true );
1239 _rectangular_type_cbmi.setSelected( true );
1242 _triangular_type_cbmi.setSelected( true );
1245 _unrooted_type_cbmi.setSelected( true );
1248 throw new IllegalArgumentException( "unknown type: " + type );
1251 catch ( final NullPointerException np ) {
1252 // In all likelihood, this is caused by menu-less display.
1256 void setTypeMenuToAllUnselected() {
1257 if ( _convex_type_cbmi != null ) {
1258 _convex_type_cbmi.setSelected( false );
1260 if ( _curved_type_cbmi != null ) {
1261 _curved_type_cbmi.setSelected( false );
1263 if ( _euro_type_cbmi != null ) {
1264 _euro_type_cbmi.setSelected( false );
1266 if ( _rounded_type_cbmi != null ) {
1267 _rounded_type_cbmi.setSelected( false );
1269 if ( _triangular_type_cbmi != null ) {
1270 _triangular_type_cbmi.setSelected( false );
1272 if ( _rectangular_type_cbmi != null ) {
1273 _rectangular_type_cbmi.setSelected( false );
1275 if ( _unrooted_type_cbmi != null ) {
1276 _unrooted_type_cbmi.setSelected( false );
1278 if ( _circular_type_cbmi != null ) {
1279 _circular_type_cbmi.setSelected( false );
1284 _mainpanel.getControlPanel().showWhole();
1287 void switchColors() {
1288 final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1289 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1290 csc.setVisible( true );
1291 getMainPanel().setTreeColorSet( colorset );
1294 void typeChanged( final Object o ) {
1295 updateTypeCheckboxes( getOptions(), o );
1296 updateOptions( getOptions() );
1297 if ( getCurrentTreePanel() != null ) {
1298 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1299 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1300 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1301 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1302 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1303 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1304 getCurrentTreePanel().getControlPanel().showWhole();
1306 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1307 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1310 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1312 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1313 MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1317 void updateOptions( final Options options ) {
1318 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1319 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1320 && _background_gradient_cbmi.isSelected() );
1321 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1322 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1323 && _show_annotation_ref_source.isSelected() );
1324 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1325 && _abbreviate_scientific_names.isSelected() );
1326 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1327 && _color_labels_same_as_parent_branch.isSelected() );
1328 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1329 && _show_default_node_shapes_internal_cbmi.isSelected() );
1330 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1331 && _show_default_node_shapes_external_cbmi.isSelected() );
1332 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1333 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1334 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1335 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1337 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1338 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1340 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1341 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1343 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1344 && _search_case_senstive_cbmi.isSelected() );
1345 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1346 options.setShowScale( _show_scale_cbmi.isSelected() );
1348 if ( _label_direction_cbmi != null ) {
1349 if ( _label_direction_cbmi.isSelected() ) {
1350 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1353 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1356 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1357 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1358 && _show_confidence_stddev_cbmi.isSelected() );
1359 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1360 && _search_whole_words_only_cbmi.isSelected() );
1361 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
1362 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1363 && _inverse_search_result_cbmi.isSelected() );
1364 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1365 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1367 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1368 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1370 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1371 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1373 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1374 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1376 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1377 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1379 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1380 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1382 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1383 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1385 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1386 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1388 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1389 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1391 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1392 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1394 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1395 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1399 void updateTypeCheckboxes( final Options options, final Object o ) {
1400 setTypeMenuToAllUnselected();
1401 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1404 void viewAsNexus() {
1405 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1406 String title = "Nexus";
1407 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1408 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1410 showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1411 .getNhConversionSupportValueStyle() ),
1417 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1418 String title = "New Hampshire";
1419 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1420 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1422 showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1423 .getNhConversionSupportValueStyle() ),
1429 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1430 String title = "phyloXML";
1431 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1432 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1434 showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1438 private void chooseFont() {
1439 final FontChooser fc = new FontChooser();
1440 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1441 fc.showDialog( this, "Select the Base Font" );
1442 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1445 private void chooseMinimalConfidence() {
1446 final String s = ( String ) JOptionPane
1447 .showInputDialog( this,
1448 "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1449 + getOptions().getMinConfidenceValue() + "]\n",
1450 "Minimal Confidence Value",
1451 JOptionPane.QUESTION_MESSAGE,
1454 getOptions().getMinConfidenceValue() );
1455 if ( !ForesterUtil.isEmpty( s ) ) {
1456 boolean success = true;
1458 final String m_str = s.trim();
1459 if ( !ForesterUtil.isEmpty( m_str ) ) {
1461 m = Double.parseDouble( m_str );
1463 catch ( final Exception ex ) {
1470 if ( success && ( m >= 0.0 ) ) {
1471 getOptions().setMinConfidenceValue( m );
1476 private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1477 if ( item != null ) {
1478 item.setFont( MainFrame.menu_font );
1479 if ( !getConfiguration().isUseNativeUI() ) {
1480 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1481 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1483 item.setSelected( is_selected );
1484 item.addActionListener( this );
1488 MainPanel getMainPanel() {
1492 private Phylogeny getSpeciesTree() {
1493 return _species_tree;
1496 private boolean isScreenAntialias() {
1500 private void removeBranchColors() {
1501 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1502 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1506 private void removeVisualStyles() {
1507 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1508 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1512 private void setMainPanel( final MainPanelApplets main_panel ) {
1513 _mainpanel = main_panel;
1516 private void setSpeciesTree( final Phylogeny species_tree ) {
1517 _species_tree = species_tree;
1520 private void setupUI() {
1522 if ( getConfiguration().isUseNativeUI() ) {
1523 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1526 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1529 catch ( final UnsupportedLookAndFeelException e ) {
1530 AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1532 catch ( final ClassNotFoundException e ) {
1533 AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1535 catch ( final InstantiationException e ) {
1536 AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1538 catch ( final IllegalAccessException e ) {
1539 AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1541 catch ( final Exception e ) {
1542 AptxUtil.dieWithSystemError( e.toString() );
1546 static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1547 for( final TreePanel tree_panel : treepanels ) {
1548 tree_panel.setTextAntialias();