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 _show_overview_cbmi;
119 private JMenuItem _choose_minimal_confidence_mi;
120 private JCheckBoxMenuItem _show_branch_length_values_cbmi;
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 JMenuItem _cycle_node_shape_mi;
127 private JMenuItem _cycle_node_fill_mi;
128 private JMenuItem _choose_node_size_mi;
129 private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
130 private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
131 private JMenu _analysis_menu;
132 private JMenuItem _gsdi_item;
133 private JMenuItem _gsdir_item;
134 private Phylogeny _species_tree;
136 private JCheckBoxMenuItem _right_line_up_domains_cbmi;
137 private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
141 public void actionPerformed( final ActionEvent e ) {
142 final Object o = e.getSource();
143 if ( o == _midpoint_root_item ) {
144 getMainPanel().getCurrentTreePanel().midpointRoot();
146 else if ( o == _gsdi_item ) {
147 if ( isSubtreeDisplayed() ) {
152 else if ( o == _gsdir_item ) {
153 if ( isSubtreeDisplayed() ) {
158 else if ( o == _taxcolor_item ) {
159 getMainPanel().getCurrentTreePanel().taxColor();
161 else if ( o == _confcolor_item ) {
162 getMainPanel().getCurrentTreePanel().confColor();
164 else if ( o == _collapse_species_specific_subtrees ) {
165 if ( getCurrentTreePanel() != null ) {
166 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
169 else if ( o == _remove_branch_color_item ) {
170 removeBranchColors();
172 else if ( o == _remove_visual_styles_item ) {
173 removeVisualStyles();
175 else if ( o == _switch_colors_mi ) {
178 else if ( o == _display_basic_information_item ) {
179 displayBasicInformation();
181 else if ( o == _view_as_NH_item ) {
184 else if ( o == _view_as_XML_item ) {
187 else if ( o == _view_as_nexus_item ) {
190 else if ( o == _super_tiny_fonts_mi ) {
191 if ( getCurrentTreePanel() != null ) {
192 getCurrentTreePanel().setSuperTinyFonts();
193 getCurrentTreePanel().repaint();
196 else if ( o == _tiny_fonts_mi ) {
197 if ( getCurrentTreePanel() != null ) {
198 getCurrentTreePanel().setTinyFonts();
199 getCurrentTreePanel().repaint();
202 else if ( o == _small_fonts_mi ) {
203 if ( getCurrentTreePanel() != null ) {
204 getCurrentTreePanel().setSmallFonts();
205 getCurrentTreePanel().repaint();
208 else if ( o == _medium_fonts_mi ) {
209 if ( getCurrentTreePanel() != null ) {
210 getCurrentTreePanel().setMediumFonts();
211 getCurrentTreePanel().repaint();
214 else if ( o == _large_fonts_mi ) {
215 if ( getCurrentTreePanel() != null ) {
216 getCurrentTreePanel().setLargeFonts();
217 getCurrentTreePanel().repaint();
220 else if ( o == _choose_font_mi ) {
223 else if ( o == _choose_minimal_confidence_mi ) {
224 chooseMinimalConfidence();
226 else if ( o == _choose_node_size_mi ) {
227 MainFrame.chooseNodeSize( getOptions(), this );
229 else if ( o == _overview_placment_mi ) {
230 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
232 else if ( o == _cycle_node_fill_mi ) {
233 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
235 else if ( o == _cycle_node_shape_mi ) {
236 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
238 else if ( o == _non_lined_up_cladograms_rbmi ) {
239 updateOptions( getOptions() );
240 _mainpanel.getControlPanel().showWhole();
242 else if ( o == _uniform_cladograms_rbmi ) {
243 updateOptions( getOptions() );
244 _mainpanel.getControlPanel().showWhole();
246 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
247 updateOptions( getOptions() );
248 _mainpanel.getControlPanel().showWhole();
250 else if ( o == _search_case_senstive_cbmi ) {
251 updateOptions( getOptions() );
252 getMainPanel().getControlPanel().search0();
253 getMainPanel().getControlPanel().search1();
255 else if ( o == _search_whole_words_only_cbmi ) {
256 updateOptions( getOptions() );
257 getMainPanel().getControlPanel().search0();
258 getMainPanel().getControlPanel().search1();
260 else if ( o == _inverse_search_result_cbmi ) {
261 updateOptions( getOptions() );
262 getMainPanel().getControlPanel().search0();
263 getMainPanel().getControlPanel().search1();
265 else if ( o == _show_scale_cbmi ) {
266 updateOptions( getOptions() );
268 else if ( o == _show_branch_length_values_cbmi ) {
269 updateOptions( getOptions() );
271 else if ( o == _show_confidence_stddev_cbmi ) {
272 updateOptions( getOptions() );
274 else if ( o == _label_direction_cbmi ) {
275 updateOptions( getOptions() );
277 else if ( o == _abbreviate_scientific_names ) {
278 updateOptions( getOptions() );
280 else if ( o == _show_overview_cbmi ) {
281 updateOptions( getOptions() );
282 if ( getCurrentTreePanel() != null ) {
283 getCurrentTreePanel().updateOvSizes();
286 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
287 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
288 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
291 else if ( o == _screen_antialias_cbmi ) {
292 updateOptions( getOptions() );
293 setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
295 else if ( o == _background_gradient_cbmi ) {
296 updateOptions( getOptions() );
298 else if ( o == _show_domain_labels ) {
299 updateOptions( getOptions() );
301 else if ( o == _color_labels_same_as_parent_branch ) {
302 updateOptions( getOptions() );
304 else if ( o == _show_default_node_shapes_internal_cbmi ) {
305 updateOptions( getOptions() );
307 else if ( o == _show_default_node_shapes_external_cbmi ) {
308 updateOptions( getOptions() );
310 else if ( o == _about_item ) {
313 else if ( o == _help_item ) {
315 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
317 catch ( final IOException e1 ) {
318 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
321 else if ( o == _website_item ) {
323 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
325 catch ( final IOException e1 ) {
326 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
329 else if ( o == _phyloxml_website_item ) {
331 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
333 catch ( final IOException e1 ) {
334 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
337 else if ( o == _aptx_ref_item ) {
339 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
341 catch ( final IOException e1 ) {
342 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
345 else if ( o == _phyloxml_ref_item ) {
347 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
349 catch ( final IOException e1 ) {
350 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
353 else if ( o == _color_by_taxonomic_group_cbmi ) {
354 updateOptions( getOptions() );
356 else if ( o == _right_line_up_domains_cbmi ) {
357 updateOptions( getOptions() );
359 else if ( o == _line_up_renderable_data_cbmi ) {
360 updateOptions( getOptions() );
368 public void destroy() {
369 AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
370 removeAllTextFrames();
371 if ( getMainPanel() != null ) {
372 getMainPanel().terminate();
377 * This method returns the current external node data which
378 * has been selected by the user by clicking the "Return ..."
379 * menu item. This method is expected to be called from Javascript or
382 * @return current external node data as String
384 public String getCurrentExternalNodesDataBuffer() {
385 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
388 public int getCurrentExternalNodesDataBufferChangeCounter() {
389 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
392 public int getCurrentExternalNodesDataBufferLength() {
393 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
397 * This method returns the current phylogeny as a string in the chosen format
399 * @param format must be NH, NHX, NEXUS or PHYLOXML
400 * @return the phylogeny string
401 * @author Herve Menager
403 public String getCurrentPhylogeny( final String format ) {
404 removeAllTextFrames();
405 if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
406 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
409 switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
411 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
413 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
415 return getMainPanel().getCurrentPhylogeny().toNexus();
417 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
425 * This method returns a view of the current phylogeny in a chosen
426 * graphics format, base64-encoded in a string so that in can be used
429 * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
430 * @return the phylogeny string
431 * @author Herve Menager
433 public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
434 final ByteArrayOutputStream baos = new ByteArrayOutputStream();
436 AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
437 _mainpanel.getWidth(),
438 _mainpanel.getHeight(),
439 getCurrentTreePanel(),
440 getCurrentTreePanel().getControlPanel(),
441 GraphicsExportType.valueOf( format ),
444 catch ( final IOException ioe ) {
445 ForesterUtil.printErrorMessage( NAME, ioe.toString() );
446 ioe.printStackTrace();
447 JOptionPane.showMessageDialog( this,
448 NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
449 "Failed to generate graphics",
450 JOptionPane.ERROR_MESSAGE );
453 final byte[] bytes = baos.toByteArray();
454 final String dataImg = Base64.encodeBase64String( bytes );
458 public Options getOptions() {
464 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
465 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
466 final Configuration configuration = new Configuration( config_filename, true, true, true );
467 setConfiguration( configuration );
468 setOptions( Options.createInstance( configuration ) );
470 final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
471 if ( ForesterUtil.isEmpty( tree_url_str ) ) {
472 ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
473 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
474 JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
475 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
478 AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
479 // Get URL to tree file
482 phys_url = new URL( tree_url_str );
484 catch ( final Exception e ) {
485 ForesterUtil.printErrorMessage( NAME, "error: " + e );
487 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
488 + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
490 if ( phys_url == null ) {
491 ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
492 + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
493 JOptionPane.showMessageDialog( this,
494 NAME + ": Could not create URL from: \"" + tree_url_str,
495 "Failed to create URL",
496 JOptionPane.ERROR_MESSAGE );
499 // Load the tree from URL
500 Phylogeny[] phys = null;
502 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
503 getConfiguration().isValidatePhyloXmlAgainstSchema(),
504 getConfiguration().isReplaceUnderscoresInNhParsing(),
505 getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
506 getConfiguration().getTaxonomyExtraction(),
507 getConfiguration().isMidpointReroot() );
509 catch ( final Exception e ) {
510 ForesterUtil.printErrorMessage( NAME, e.toString() );
512 JOptionPane.showMessageDialog( this,
513 NAME + ": Failed to read phylogenies: " + "\nException: " + e,
514 "Failed to read phylogenies",
515 JOptionPane.ERROR_MESSAGE );
517 if ( phys == null ) {
518 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
519 JOptionPane.showMessageDialog( this,
520 NAME + ": phylogenies from [" + phys_url + "] are null",
521 "Failed to read phylogenies",
522 JOptionPane.ERROR_MESSAGE );
525 else if ( phys.length < 1 ) {
526 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
527 JOptionPane.showMessageDialog( this,
528 NAME + ": phylogenies from [" + phys_url + "] are empty",
529 "Failed to read phylogenies",
530 JOptionPane.ERROR_MESSAGE );
534 AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
537 final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
538 if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
539 AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
540 Phylogeny[] species_trees = null;
542 final URL species_tree_url = new URL( species_tree_url_str );
543 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
544 configuration.isValidatePhyloXmlAgainstSchema(),
545 configuration.isReplaceUnderscoresInNhParsing(),
547 TAXONOMY_EXTRACTION.NO,
550 catch ( final IOException e ) {
551 ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
553 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
554 + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
556 if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
557 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
558 if ( species_trees[ 0 ].isEmpty() ) {
559 ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
561 else if ( !species_trees[ 0 ].isRooted() ) {
562 ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
565 setSpeciesTree( species_trees[ 0 ] );
566 AptxUtil.printAppletMessage( NAME, "species tree OK" );
572 setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
573 _jmenubar = new JMenuBar();
574 if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
575 if ( !getConfiguration().isUseNativeUI() ) {
576 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
578 if ( getSpeciesTree() != null ) {
587 setJMenuBar( _jmenubar );
589 final Container contentpane = getContentPane();
590 contentpane.setLayout( new BorderLayout() );
591 contentpane.add( getMainPanel(), BorderLayout.CENTER );
592 addComponentListener( new ComponentAdapter() {
595 public void componentResized( final ComponentEvent e ) {
596 if ( getMainPanel().getCurrentTreePanel() != null ) {
597 getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
598 .getCurrentTreePanel()
601 .getCurrentTreePanel()
604 .isAllowFontSizeChange() );
608 if ( getConfiguration().isUseTabbedDisplay() ) {
609 AptxUtil.printAppletMessage( NAME, "using tabbed display" );
610 AptxUtil.addPhylogeniesToTabs( phys,
611 new File( phys_url.getFile() ).getName(),
617 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
618 if ( getSpeciesTree() != null ) {
619 AptxUtil.printAppletMessage( NAME,
620 "Warning: gsdi (gene duplication inference) only available tabbed display" );
622 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
626 getMainPanel().getControlPanel().showWholeAll();
627 getMainPanel().getControlPanel().showWhole();
629 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
630 for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
631 .getRelevantSequenceRelationTypes() ) {
632 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
634 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
635 if ( default_relation != null ) {
636 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
638 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
639 if ( default_sequence != null ) {
640 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
644 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
648 public void showTextFrame( final String s, final String title ) {
650 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
654 public void start() {
655 if ( getMainPanel() != null ) {
656 getMainPanel().validate();
659 requestFocusInWindow();
661 AptxUtil.printAppletMessage( NAME, "started" );
664 void buildAnalysisMenu() {
665 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
666 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
667 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
668 customizeJMenuItem( _gsdi_item );
669 customizeJMenuItem( _gsdir_item );
670 // _analysis_menu.addSeparator();
671 // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
672 // customizeJMenuItem( _lineage_inference );
673 // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
674 _jmenubar.add( _analysis_menu );
677 void buildFontSizeMenu() {
678 _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
679 _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
680 _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
681 _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
682 _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
683 _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
684 customizeJMenuItem( _super_tiny_fonts_mi );
685 customizeJMenuItem( _tiny_fonts_mi );
686 customizeJMenuItem( _small_fonts_mi );
687 customizeJMenuItem( _medium_fonts_mi );
688 customizeJMenuItem( _large_fonts_mi );
689 _jmenubar.add( _font_size_menu );
692 void buildHelpMenu() {
693 _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
694 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
695 _help_jmenu.addSeparator();
696 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
697 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
698 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
699 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
700 _help_jmenu.addSeparator();
701 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
702 customizeJMenuItem( _help_item );
703 customizeJMenuItem( _website_item );
704 customizeJMenuItem( _phyloxml_website_item );
705 customizeJMenuItem( _aptx_ref_item );
706 customizeJMenuItem( _phyloxml_ref_item );
707 customizeJMenuItem( _about_item );
708 _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
709 _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
710 _jmenubar.add( _help_jmenu );
713 void buildOptionsMenu() {
714 _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
715 _options_jmenu.addChangeListener( new ChangeListener() {
718 public void stateChanged( final ChangeEvent e ) {
719 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
720 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
722 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
723 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
724 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
725 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
727 _show_branch_length_values_cbmi,
728 _non_lined_up_cladograms_rbmi,
729 _uniform_cladograms_rbmi,
730 _ext_node_dependent_cladogram_rbmi,
731 _label_direction_cbmi );
732 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
733 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
734 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
737 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
738 getConfiguration() ) );
740 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
741 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
743 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
744 _radio_group_1 = new ButtonGroup();
745 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
746 _radio_group_1.add( _uniform_cladograms_rbmi );
747 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
749 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
750 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
752 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
754 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
756 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
757 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
758 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
759 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
761 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
762 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
763 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
765 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
767 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
768 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
769 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
770 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
771 _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
772 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
773 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
774 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
775 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
776 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
777 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
778 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
779 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
780 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
782 _options_jmenu.addSeparator();
783 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
784 getConfiguration() ) );
786 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
787 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
789 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
790 customizeJMenuItem( _choose_font_mi );
791 customizeJMenuItem( _choose_minimal_confidence_mi );
792 customizeJMenuItem( _switch_colors_mi );
793 customizeJMenuItem( _overview_placment_mi );
794 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
795 customizeCheckBoxMenuItem( _label_direction_cbmi,
796 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
797 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
798 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
799 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
800 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
801 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
802 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
803 .isShowDefaultNodeShapesExternal() );
804 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
805 .isShowDefaultNodeShapesInternal() );
806 customizeJMenuItem( _cycle_node_shape_mi );
807 customizeJMenuItem( _cycle_node_fill_mi );
808 customizeJMenuItem( _choose_node_size_mi );
809 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
810 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
811 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
812 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
813 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
814 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
815 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
816 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
817 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
818 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
819 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
820 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
821 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
822 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
823 _jmenubar.add( _options_jmenu );
826 void buildToolsMenu() {
827 _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
828 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
829 customizeJMenuItem( _confcolor_item );
830 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
831 customizeJMenuItem( _taxcolor_item );
832 _tools_menu.addSeparator();
833 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
834 _remove_visual_styles_item
835 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
836 customizeJMenuItem( _remove_visual_styles_item );
837 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
838 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
839 customizeJMenuItem( _remove_branch_color_item );
840 _tools_menu.addSeparator();
841 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
842 customizeJMenuItem( _midpoint_root_item );
843 _tools_menu.addSeparator();
844 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
845 customizeJMenuItem( _collapse_species_specific_subtrees );
846 _jmenubar.add( _tools_menu );
849 void buildTypeMenu() {
850 _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
851 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
852 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
853 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
854 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
855 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
856 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
857 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
858 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
859 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
860 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
861 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
862 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
863 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
864 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
865 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
866 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
867 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
868 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
869 initializeTypeMenu( getOptions() );
870 _jmenubar.add( _type_menu );
873 void buildViewMenu() {
874 _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
876 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
877 _view_jmenu.addSeparator();
878 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
879 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
880 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
881 customizeJMenuItem( _display_basic_information_item );
882 customizeJMenuItem( _view_as_NH_item );
883 customizeJMenuItem( _view_as_XML_item );
884 customizeJMenuItem( _view_as_nexus_item );
885 _jmenubar.add( _view_jmenu );
888 void checkTextFrames() {
889 if ( _textframes.size() > 5 ) {
891 if ( _textframes.getFirst() != null ) {
892 _textframes.getFirst().removeMe();
895 _textframes.removeFirst();
898 catch ( final NoSuchElementException e ) {
904 void clearCurrentExternalNodesDataBuffer() {
905 getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
908 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
909 if ( item != null ) {
910 item.setFont( MainFrame.menu_font );
911 if ( !getConfiguration().isUseNativeUI() ) {
912 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
913 item.setForeground( getConfiguration().getGuiMenuTextColor() );
915 item.setSelected( is_selected );
916 item.addActionListener( this );
920 void customizeJMenuItem( final JMenuItem jmi ) {
921 jmi.setFont( MainFrame.menu_font );
922 if ( !getConfiguration().isUseNativeUI() ) {
923 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
924 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
926 jmi.addActionListener( this );
929 void displayBasicInformation() {
930 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
931 String title = "Basic Information";
932 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
933 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
935 showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
940 if ( !isOKforSDI( false, true ) ) {
943 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
944 JOptionPane.showMessageDialog( this,
945 "Gene tree is not rooted.",
946 "Cannot execute GSDI",
947 JOptionPane.ERROR_MESSAGE );
950 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
951 gene_tree.setAllNodesToNotCollapse();
952 gene_tree.recalculateNumberOfExternalDescendants( false );
954 final Phylogeny species_tree = _species_tree.copy();
956 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
958 catch ( final SDIException e ) {
959 JOptionPane.showMessageDialog( this,
960 e.getLocalizedMessage(),
962 JOptionPane.ERROR_MESSAGE );
965 catch ( final Exception e ) {
966 AptxUtil.unexpectedException( e );
969 gene_tree.setRerootable( false );
970 gene_tree.clearHashIdToNodeMap();
971 gene_tree.recalculateNumberOfExternalDescendants( true );
972 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
973 getMainPanel().getControlPanel().setShowEvents( true );
975 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
976 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
978 _mainpanel.getTabbedPane().setSelectedIndex( selected );
980 _mainpanel.getCurrentTreePanel().setEdited( true );
981 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
982 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
983 JOptionPane.showMessageDialog( this,
984 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
985 + "Potential duplications: "
986 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
987 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
988 + "Stripped gene tree nodes: "
989 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
990 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
991 + "Number of polytomies in species tree used: " + poly + "\n",
992 "GSDI successfully completed",
993 JOptionPane.WARNING_MESSAGE );
996 JOptionPane.showMessageDialog( this,
997 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
998 + "Potential duplications: "
999 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1000 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1001 + "Stripped gene tree nodes: "
1002 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1003 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1004 + "Number of polytomies in species tree used: " + poly + "\n",
1005 "GSDI successfully completed",
1006 JOptionPane.INFORMATION_MESSAGE );
1010 void executeGSDIR() {
1011 if ( !isOKforSDI( false, false ) ) {
1014 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1016 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1017 JOptionPane.showMessageDialog( this,
1018 "Gene tree is not completely binary",
1019 "Cannot execute GSDI",
1020 JOptionPane.ERROR_MESSAGE );
1023 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1024 gene_tree.setAllNodesToNotCollapse();
1025 gene_tree.recalculateNumberOfExternalDescendants( false );
1027 final Phylogeny species_tree = _species_tree.copy();
1029 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1031 catch ( final SDIException e ) {
1032 JOptionPane.showMessageDialog( this,
1033 e.getLocalizedMessage(),
1034 "Error during GSDIR",
1035 JOptionPane.ERROR_MESSAGE );
1038 catch ( final Exception e ) {
1039 AptxUtil.unexpectedException( e );
1042 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1043 result_gene_tree.setRerootable( false );
1044 result_gene_tree.clearHashIdToNodeMap();
1045 result_gene_tree.recalculateNumberOfExternalDescendants( true );
1046 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1047 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1048 getMainPanel().getControlPanel().setShowEvents( true );
1050 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1051 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1053 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1055 _mainpanel.getCurrentTreePanel().setEdited( true );
1056 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1057 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1058 JOptionPane.showMessageDialog( this,
1059 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1060 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1061 + "Stripped gene tree nodes: "
1062 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1063 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1064 + "Number of polytomies in species tree used: " + poly + "\n",
1065 "GSDIR successfully completed",
1066 JOptionPane.WARNING_MESSAGE );
1069 JOptionPane.showMessageDialog( this,
1070 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1071 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1072 + "Stripped gene tree nodes: "
1073 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1074 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1075 + "Number of polytomies in species tree used: " + poly + "\n",
1076 "GSDIR successfully completed",
1077 JOptionPane.INFORMATION_MESSAGE );
1081 Configuration getConfiguration() {
1082 return _configuration;
1085 TreePanel getCurrentTreePanel() {
1086 return getMainPanel().getCurrentTreePanel();
1089 JCheckBoxMenuItem getlabelDirectionCbmi() {
1090 return _label_direction_cbmi;
1093 Options getOtions() {
1099 void initializeTypeMenu( final Options options ) {
1100 setTypeMenuToAllUnselected();
1102 switch ( options.getPhylogenyGraphicsType() ) {
1104 _convex_type_cbmi.setSelected( true );
1107 _curved_type_cbmi.setSelected( true );
1110 _euro_type_cbmi.setSelected( true );
1113 _rounded_type_cbmi.setSelected( true );
1116 _triangular_type_cbmi.setSelected( true );
1119 _unrooted_type_cbmi.setSelected( true );
1122 _circular_type_cbmi.setSelected( true );
1125 _rectangular_type_cbmi.setSelected( true );
1129 catch ( final NullPointerException np ) {
1130 // In all likelihood, this is caused by menu-less display.
1134 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1135 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1138 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1139 JOptionPane.showMessageDialog( this,
1140 "No species tree loaded",
1141 "Cannot execute GSDI",
1142 JOptionPane.ERROR_MESSAGE );
1145 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1146 JOptionPane.showMessageDialog( this,
1147 "Species tree is not completely binary",
1148 "Cannot execute GSDI",
1149 JOptionPane.ERROR_MESSAGE );
1152 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1153 JOptionPane.showMessageDialog( this,
1154 "Gene tree is not completely binary",
1155 "Cannot execute GSDI",
1156 JOptionPane.ERROR_MESSAGE );
1164 boolean isSubtreeDisplayed() {
1165 if ( getCurrentTreePanel() != null ) {
1166 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1168 .showMessageDialog( this,
1169 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1170 "Operation can not be exectuted on a sub-tree",
1171 JOptionPane.WARNING_MESSAGE );
1178 void removeAllTextFrames() {
1179 for( final TextFrame tf : _textframes ) {
1184 _textframes.clear();
1187 void setConfiguration( final Configuration configuration ) {
1188 _configuration = configuration;
1191 void setOptions( final Options options ) {
1195 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1196 setTypeMenuToAllUnselected();
1200 _circular_type_cbmi.setSelected( true );
1203 _convex_type_cbmi.setSelected( true );
1206 _curved_type_cbmi.setSelected( true );
1209 _euro_type_cbmi.setSelected( true );
1212 _rounded_type_cbmi.setSelected( true );
1215 _rectangular_type_cbmi.setSelected( true );
1218 _triangular_type_cbmi.setSelected( true );
1221 _unrooted_type_cbmi.setSelected( true );
1224 throw new IllegalArgumentException( "unknown type: " + type );
1227 catch ( final NullPointerException np ) {
1228 // In all likelihood, this is caused by menu-less display.
1232 void setTypeMenuToAllUnselected() {
1233 if ( _convex_type_cbmi != null ) {
1234 _convex_type_cbmi.setSelected( false );
1236 if ( _curved_type_cbmi != null ) {
1237 _curved_type_cbmi.setSelected( false );
1239 if ( _euro_type_cbmi != null ) {
1240 _euro_type_cbmi.setSelected( false );
1242 if ( _rounded_type_cbmi != null ) {
1243 _rounded_type_cbmi.setSelected( false );
1245 if ( _triangular_type_cbmi != null ) {
1246 _triangular_type_cbmi.setSelected( false );
1248 if ( _rectangular_type_cbmi != null ) {
1249 _rectangular_type_cbmi.setSelected( false );
1251 if ( _unrooted_type_cbmi != null ) {
1252 _unrooted_type_cbmi.setSelected( false );
1254 if ( _circular_type_cbmi != null ) {
1255 _circular_type_cbmi.setSelected( false );
1260 _mainpanel.getControlPanel().showWhole();
1263 void switchColors() {
1264 final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1265 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1266 csc.setVisible( true );
1267 getMainPanel().setTreeColorSet( colorset );
1270 void typeChanged( final Object o ) {
1271 updateTypeCheckboxes( getOptions(), o );
1272 updateOptions( getOptions() );
1273 if ( getCurrentTreePanel() != null ) {
1274 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1275 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1276 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1277 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1278 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1279 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1280 getCurrentTreePanel().getControlPanel().showWhole();
1282 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1283 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1286 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1288 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1289 MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1293 void updateOptions( final Options options ) {
1294 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1295 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1296 && _background_gradient_cbmi.isSelected() );
1297 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1298 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1299 && _show_annotation_ref_source.isSelected() );
1300 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1301 && _abbreviate_scientific_names.isSelected() );
1302 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1303 && _color_labels_same_as_parent_branch.isSelected() );
1304 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1305 && _show_default_node_shapes_internal_cbmi.isSelected() );
1306 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1307 && _show_default_node_shapes_external_cbmi.isSelected() );
1308 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1309 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1311 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1312 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1314 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1315 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1317 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1318 && _search_case_senstive_cbmi.isSelected() );
1319 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1320 options.setShowScale( _show_scale_cbmi.isSelected() );
1322 if ( _label_direction_cbmi != null ) {
1323 if ( _label_direction_cbmi.isSelected() ) {
1324 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1327 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1330 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1331 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1332 && _show_confidence_stddev_cbmi.isSelected() );
1333 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1334 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1336 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1337 && _search_whole_words_only_cbmi.isSelected() );
1338 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1339 && _inverse_search_result_cbmi.isSelected() );
1340 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1341 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1343 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1344 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1346 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1347 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1349 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1350 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1352 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1353 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1355 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1356 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1358 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1359 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1361 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1362 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1364 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1365 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1369 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1370 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1374 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1375 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1380 void updateTypeCheckboxes( final Options options, final Object o ) {
1381 setTypeMenuToAllUnselected();
1382 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1385 void viewAsNexus() {
1386 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1387 String title = "Nexus";
1388 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1389 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1391 showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1392 .getNhConversionSupportValueStyle() ),
1398 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1399 String title = "New Hampshire";
1400 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1401 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1403 showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1404 .getNhConversionSupportValueStyle() ),
1410 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1411 String title = "phyloXML";
1412 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1413 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1415 showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1419 private void chooseFont() {
1420 final FontChooser fc = new FontChooser();
1421 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1422 fc.showDialog( this, "Select the Base Font" );
1423 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1426 private void chooseMinimalConfidence() {
1427 final String s = ( String ) JOptionPane
1428 .showInputDialog( this,
1429 "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1430 + getOptions().getMinConfidenceValue() + "]\n",
1431 "Minimal Confidence Value",
1432 JOptionPane.QUESTION_MESSAGE,
1435 getOptions().getMinConfidenceValue() );
1436 if ( !ForesterUtil.isEmpty( s ) ) {
1437 boolean success = true;
1439 final String m_str = s.trim();
1440 if ( !ForesterUtil.isEmpty( m_str ) ) {
1442 m = Double.parseDouble( m_str );
1444 catch ( final Exception ex ) {
1451 if ( success && ( m >= 0.0 ) ) {
1452 getOptions().setMinConfidenceValue( m );
1457 private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1458 if ( item != null ) {
1459 item.setFont( MainFrame.menu_font );
1460 if ( !getConfiguration().isUseNativeUI() ) {
1461 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1462 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1464 item.setSelected( is_selected );
1465 item.addActionListener( this );
1469 private MainPanel getMainPanel() {
1473 private Phylogeny getSpeciesTree() {
1474 return _species_tree;
1477 private boolean isScreenAntialias() {
1481 private void removeBranchColors() {
1482 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1483 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1487 private void removeVisualStyles() {
1488 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1489 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1493 private void setMainPanel( final MainPanelApplets main_panel ) {
1494 _mainpanel = main_panel;
1497 private void setSpeciesTree( final Phylogeny species_tree ) {
1498 _species_tree = species_tree;
1501 private void setupUI() {
1503 if ( getConfiguration().isUseNativeUI() ) {
1504 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1507 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1510 catch ( final UnsupportedLookAndFeelException e ) {
1511 AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1513 catch ( final ClassNotFoundException e ) {
1514 AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1516 catch ( final InstantiationException e ) {
1517 AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1519 catch ( final IllegalAccessException e ) {
1520 AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1522 catch ( final Exception e ) {
1523 AptxUtil.dieWithSystemError( e.toString() );
1527 static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1528 for( final TreePanel tree_panel : treepanels ) {
1529 tree_panel.setTextAntialias();