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 JCheckBoxMenuItem _show_domain_labels;
100 private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
101 private JCheckBoxMenuItem _abbreviate_scientific_names;
102 private JCheckBoxMenuItem _screen_antialias_cbmi;
103 private JCheckBoxMenuItem _background_gradient_cbmi;
104 private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
105 private JRadioButtonMenuItem _uniform_cladograms_rbmi;
106 private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
107 private Options _options;
108 private JMenuItem _choose_font_mi;
109 private JMenuItem _switch_colors_mi;
110 JCheckBoxMenuItem _label_direction_cbmi;
111 private JCheckBoxMenuItem _show_scale_cbmi;
112 private JCheckBoxMenuItem _search_case_senstive_cbmi;
113 private JCheckBoxMenuItem _search_whole_words_only_cbmi;
114 private JCheckBoxMenuItem _inverse_search_result_cbmi;
115 private JCheckBoxMenuItem _show_overview_cbmi;
116 private JMenuItem _choose_minimal_confidence_mi;
117 private JCheckBoxMenuItem _show_branch_length_values_cbmi;
118 private JMenuItem _collapse_species_specific_subtrees;
119 private JMenuItem _overview_placment_mi;
120 private ButtonGroup _radio_group_1;
121 private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
122 private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
123 private JMenuItem _cycle_node_shape_mi;
124 private JMenuItem _cycle_node_fill_mi;
125 private JMenuItem _choose_node_size_mi;
126 private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
127 private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
128 private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
129 private JMenu _analysis_menu;
130 private JMenuItem _gsdi_item;
131 private JMenuItem _gsdir_item;
132 private Phylogeny _species_tree;
135 public void actionPerformed( final ActionEvent e ) {
136 final Object o = e.getSource();
137 if ( o == _midpoint_root_item ) {
138 getMainPanel().getCurrentTreePanel().midpointRoot();
140 else if ( o == _gsdi_item ) {
141 if ( isSubtreeDisplayed() ) {
146 else if ( o == _gsdir_item ) {
147 if ( isSubtreeDisplayed() ) {
152 else if ( o == _taxcolor_item ) {
153 getMainPanel().getCurrentTreePanel().taxColor();
155 else if ( o == _confcolor_item ) {
156 getMainPanel().getCurrentTreePanel().confColor();
158 else if ( o == _collapse_species_specific_subtrees ) {
159 if ( getCurrentTreePanel() != null ) {
160 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
163 else if ( o == _remove_branch_color_item ) {
164 removeBranchColors();
166 else if ( o == _switch_colors_mi ) {
169 else if ( o == _display_basic_information_item ) {
170 displayBasicInformation();
172 else if ( o == _view_as_NH_item ) {
175 else if ( o == _view_as_XML_item ) {
178 else if ( o == _view_as_nexus_item ) {
181 else if ( o == _super_tiny_fonts_mi ) {
182 if ( getCurrentTreePanel() != null ) {
183 getCurrentTreePanel().setSuperTinyFonts();
184 getCurrentTreePanel().repaint();
187 else if ( o == _tiny_fonts_mi ) {
188 if ( getCurrentTreePanel() != null ) {
189 getCurrentTreePanel().setTinyFonts();
190 getCurrentTreePanel().repaint();
193 else if ( o == _small_fonts_mi ) {
194 if ( getCurrentTreePanel() != null ) {
195 getCurrentTreePanel().setSmallFonts();
196 getCurrentTreePanel().repaint();
199 else if ( o == _medium_fonts_mi ) {
200 if ( getCurrentTreePanel() != null ) {
201 getCurrentTreePanel().setMediumFonts();
202 getCurrentTreePanel().repaint();
205 else if ( o == _large_fonts_mi ) {
206 if ( getCurrentTreePanel() != null ) {
207 getCurrentTreePanel().setLargeFonts();
208 getCurrentTreePanel().repaint();
211 else if ( o == _choose_font_mi ) {
214 else if ( o == _choose_minimal_confidence_mi ) {
215 chooseMinimalConfidence();
217 else if ( o == _choose_node_size_mi ) {
218 MainFrame.chooseNodeSize( getOptions(), this );
220 else if ( o == _overview_placment_mi ) {
221 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
223 else if ( o == _cycle_node_fill_mi ) {
224 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
226 else if ( o == _cycle_node_shape_mi ) {
227 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
229 else if ( o == _non_lined_up_cladograms_rbmi ) {
230 updateOptions( getOptions() );
231 _mainpanel.getControlPanel().showWhole();
233 else if ( o == _uniform_cladograms_rbmi ) {
234 updateOptions( getOptions() );
235 _mainpanel.getControlPanel().showWhole();
237 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
238 updateOptions( getOptions() );
239 _mainpanel.getControlPanel().showWhole();
241 else if ( o == _search_case_senstive_cbmi ) {
242 updateOptions( getOptions() );
243 getMainPanel().getControlPanel().search();
245 else if ( o == _search_whole_words_only_cbmi ) {
246 updateOptions( getOptions() );
247 getMainPanel().getControlPanel().search();
249 else if ( o == _inverse_search_result_cbmi ) {
250 updateOptions( getOptions() );
251 getMainPanel().getControlPanel().search();
253 else if ( o == _show_scale_cbmi ) {
254 updateOptions( getOptions() );
256 else if ( o == _show_branch_length_values_cbmi ) {
257 updateOptions( getOptions() );
259 else if ( o == _show_confidence_stddev_cbmi ) {
260 updateOptions( getOptions() );
262 else if ( o == _label_direction_cbmi ) {
263 updateOptions( getOptions() );
265 else if ( o == _abbreviate_scientific_names ) {
266 updateOptions( getOptions() );
268 else if ( o == _show_overview_cbmi ) {
269 updateOptions( getOptions() );
270 if ( getCurrentTreePanel() != null ) {
271 getCurrentTreePanel().updateOvSizes();
274 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
275 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
276 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
279 else if ( o == _screen_antialias_cbmi ) {
280 updateOptions( getOptions() );
281 setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
283 else if ( o == _background_gradient_cbmi ) {
284 updateOptions( getOptions() );
286 else if ( o == _show_domain_labels ) {
287 updateOptions( getOptions() );
289 else if ( o == _color_labels_same_as_parent_branch ) {
290 updateOptions( getOptions() );
292 else if ( o == _show_default_node_shapes_internal_cbmi ) {
293 updateOptions( getOptions() );
295 else if ( o == _show_default_node_shapes_external_cbmi ) {
296 updateOptions( getOptions() );
298 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
299 updateOptions( getOptions() );
301 else if ( o == _about_item ) {
304 else if ( o == _help_item ) {
307 else if ( o == _website_item ) {
309 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
311 catch ( final IOException e1 ) {
312 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
315 else if ( o == _phyloxml_website_item ) {
317 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
319 catch ( final IOException e1 ) {
320 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
323 else if ( o == _aptx_ref_item ) {
325 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
327 catch ( final IOException e1 ) {
328 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
331 else if ( o == _phyloxml_ref_item ) {
333 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
335 catch ( final IOException e1 ) {
336 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
343 public void destroy() {
344 AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
345 removeAllTextFrames();
346 if ( getMainPanel() != null ) {
347 getMainPanel().terminate();
352 * This method returns the current external node data which
353 * has been selected by the user by clicking the "Return ..."
354 * menu item. This method is expected to be called from Javascript or
357 * @return current external node data as String
359 public String getCurrentExternalNodesDataBuffer() {
360 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
363 public int getCurrentExternalNodesDataBufferChangeCounter() {
364 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
367 public int getCurrentExternalNodesDataBufferLength() {
368 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
372 * This method returns the current phylogeny as a string in the chosen format
374 * @param format must be NH, NHX, NEXUS or PHYLOXML
375 * @return the phylogeny string
376 * @author Herve Menager
378 public String getCurrentPhylogeny( final String format ) {
379 removeAllTextFrames();
380 if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
381 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
384 switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
386 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
388 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
390 return getMainPanel().getCurrentPhylogeny().toNexus();
392 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
400 * This method returns a view of the current phylogeny in a chosen
401 * graphics format, base64-encoded in a string so that in can be used
404 * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
405 * @return the phylogeny string
406 * @author Herve Menager
408 public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
409 final ByteArrayOutputStream baos = new ByteArrayOutputStream();
411 AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
412 _mainpanel.getWidth(),
413 _mainpanel.getHeight(),
414 getCurrentTreePanel(),
415 getCurrentTreePanel().getControlPanel(),
416 GraphicsExportType.valueOf( format ),
419 catch ( final IOException ioe ) {
420 ForesterUtil.printErrorMessage( NAME, ioe.toString() );
421 ioe.printStackTrace();
422 JOptionPane.showMessageDialog( this,
423 NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
424 "Failed to generate graphics",
425 JOptionPane.ERROR_MESSAGE );
428 final byte[] bytes = baos.toByteArray();
429 final String dataImg = Base64.encodeBase64String( bytes );
433 public Options getOptions() {
439 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
440 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
441 final Configuration configuration = new Configuration( config_filename, true, true, true );
442 setConfiguration( configuration );
443 setOptions( Options.createInstance( configuration ) );
446 Phylogeny[] phys = null;
447 final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
448 AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
449 // Get URL to tree file
450 if ( tree_url_str != null ) {
452 phys_url = new URL( tree_url_str );
454 catch ( final Exception e ) {
455 ForesterUtil.printErrorMessage( NAME, "error: " + e );
457 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
458 + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
461 // Load the tree from URL
462 if ( phys_url != null ) {
464 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
465 getConfiguration().isValidatePhyloXmlAgainstSchema(),
466 getConfiguration().isReplaceUnderscoresInNhParsing(),
467 getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
468 getConfiguration().getTaxonomyExtraction(),
469 getConfiguration().isMidpointReroot() );
471 catch ( final Exception e ) {
472 ForesterUtil.printErrorMessage( NAME, e.toString() );
474 JOptionPane.showMessageDialog( this,
475 NAME + ": Failed to read phylogenies: " + "\nException: " + e,
476 "Failed to read phylogenies",
477 JOptionPane.ERROR_MESSAGE );
480 if ( ( phys == null ) || ( phys.length < 1 ) ) {
481 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
482 JOptionPane.showMessageDialog( this,
483 NAME + ": phylogenies from [" + phys_url + "] are null or empty",
484 "Failed to read phylogenies",
485 JOptionPane.ERROR_MESSAGE );
489 AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
492 final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
493 if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
494 AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
495 Phylogeny[] species_trees = null;
497 final URL species_tree_url = new URL( species_tree_url_str );
498 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
499 configuration.isValidatePhyloXmlAgainstSchema(),
500 configuration.isReplaceUnderscoresInNhParsing(),
502 TAXONOMY_EXTRACTION.NO,
505 catch ( final IOException e ) {
506 ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
508 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
509 + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
511 if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
512 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
513 if ( species_trees[ 0 ].isEmpty() ) {
514 ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
516 else if ( !species_trees[ 0 ].isRooted() ) {
517 ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
520 setSpeciesTree( species_trees[ 0 ] );
521 AptxUtil.printAppletMessage( NAME, "species tree OK" );
527 setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
528 _jmenubar = new JMenuBar();
529 if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
530 if ( !getConfiguration().isUseNativeUI() ) {
531 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
533 if ( getSpeciesTree() != null ) {
542 setJMenuBar( _jmenubar );
544 final Container contentpane = getContentPane();
545 contentpane.setLayout( new BorderLayout() );
546 contentpane.add( getMainPanel(), BorderLayout.CENTER );
547 addComponentListener( new ComponentAdapter() {
550 public void componentResized( final ComponentEvent e ) {
551 if ( getMainPanel().getCurrentTreePanel() != null ) {
552 getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
553 .getCurrentTreePanel()
556 .getCurrentTreePanel()
559 .isAllowFontSizeChange() );
563 if ( getConfiguration().isUseTabbedDisplay() ) {
564 AptxUtil.printAppletMessage( NAME, "using tabbed display" );
565 AptxUtil.addPhylogeniesToTabs( phys,
566 new File( phys_url.getFile() ).getName(),
572 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
573 if ( getSpeciesTree() != null ) {
574 AptxUtil.printAppletMessage( NAME,
575 "Warning: gsdi (gene duplication inference) only available tabbed display" );
577 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
581 getMainPanel().getControlPanel().showWholeAll();
582 getMainPanel().getControlPanel().showWhole();
584 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
586 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
587 for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
588 .getRelevantSequenceRelationTypes() ) {
589 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
591 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
592 if ( default_relation != null ) {
593 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
595 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
596 if ( default_sequence != null ) {
597 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
603 public void showTextFrame( final String s, final String title ) {
605 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
609 public void start() {
610 if ( getMainPanel() != null ) {
611 getMainPanel().validate();
614 requestFocusInWindow();
616 AptxUtil.printAppletMessage( NAME, "started" );
619 void buildAnalysisMenu() {
620 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
621 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
622 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
623 customizeJMenuItem( _gsdi_item );
624 customizeJMenuItem( _gsdir_item );
625 // _analysis_menu.addSeparator();
626 // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
627 // customizeJMenuItem( _lineage_inference );
628 // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
629 _jmenubar.add( _analysis_menu );
632 void buildFontSizeMenu() {
633 _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
634 _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
635 _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
636 _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
637 _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
638 _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
639 customizeJMenuItem( _super_tiny_fonts_mi );
640 customizeJMenuItem( _tiny_fonts_mi );
641 customizeJMenuItem( _small_fonts_mi );
642 customizeJMenuItem( _medium_fonts_mi );
643 customizeJMenuItem( _large_fonts_mi );
644 _jmenubar.add( _font_size_menu );
647 void buildHelpMenu() {
648 _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
649 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
650 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
651 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
652 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
653 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
654 _help_jmenu.addSeparator();
655 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
656 customizeJMenuItem( _help_item );
657 customizeJMenuItem( _website_item );
658 customizeJMenuItem( _phyloxml_website_item );
659 customizeJMenuItem( _aptx_ref_item );
660 customizeJMenuItem( _phyloxml_ref_item );
661 customizeJMenuItem( _about_item );
662 _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
663 _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
664 _jmenubar.add( _help_jmenu );
667 void buildOptionsMenu() {
668 _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
669 _options_jmenu.addChangeListener( new ChangeListener() {
672 public void stateChanged( final ChangeEvent e ) {
673 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
674 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
676 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
677 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
678 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
679 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
681 _show_branch_length_values_cbmi,
682 _non_lined_up_cladograms_rbmi,
683 _uniform_cladograms_rbmi,
684 _ext_node_dependent_cladogram_rbmi,
685 _label_direction_cbmi );
686 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
687 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
688 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
691 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
692 getConfiguration() ) );
694 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
695 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
697 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
698 _radio_group_1 = new ButtonGroup();
699 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
700 _radio_group_1.add( _uniform_cladograms_rbmi );
701 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
702 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
703 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
705 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
706 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
708 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
710 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
712 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
713 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
714 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
715 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
716 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
718 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
719 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
720 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
721 _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
722 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
723 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
724 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
725 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
727 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
728 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
729 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
730 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
731 _options_jmenu.addSeparator();
732 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
733 getConfiguration() ) );
735 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
736 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
738 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
739 customizeJMenuItem( _choose_font_mi );
740 customizeJMenuItem( _choose_minimal_confidence_mi );
741 customizeJMenuItem( _switch_colors_mi );
742 customizeJMenuItem( _overview_placment_mi );
743 customizeCheckBoxMenuItem( _label_direction_cbmi,
744 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
745 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
746 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
747 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
748 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
749 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
750 .isShowDefaultNodeShapesExternal() );
751 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
752 .isShowDefaultNodeShapesInternal() );
753 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
754 customizeJMenuItem( _cycle_node_shape_mi );
755 customizeJMenuItem( _cycle_node_fill_mi );
756 customizeJMenuItem( _choose_node_size_mi );
757 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
758 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
759 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
760 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
761 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
762 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
763 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
764 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
765 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
766 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
767 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
768 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
769 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
770 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
771 _jmenubar.add( _options_jmenu );
774 void buildToolsMenu() {
775 _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
776 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
777 customizeJMenuItem( _confcolor_item );
778 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
779 customizeJMenuItem( _taxcolor_item );
780 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
781 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
782 customizeJMenuItem( _remove_branch_color_item );
783 _tools_menu.addSeparator();
784 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
785 customizeJMenuItem( _midpoint_root_item );
786 _tools_menu.addSeparator();
787 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
788 customizeJMenuItem( _collapse_species_specific_subtrees );
789 _jmenubar.add( _tools_menu );
792 void buildTypeMenu() {
793 _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
794 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
795 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
796 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
797 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
798 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
799 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
800 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
801 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
802 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
803 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
804 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
805 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
806 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
807 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
808 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
809 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
810 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
811 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
812 initializeTypeMenu( getOptions() );
813 _jmenubar.add( _type_menu );
816 void buildViewMenu() {
817 _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
819 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
820 _view_jmenu.addSeparator();
821 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
822 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
823 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
824 customizeJMenuItem( _display_basic_information_item );
825 customizeJMenuItem( _view_as_NH_item );
826 customizeJMenuItem( _view_as_XML_item );
827 customizeJMenuItem( _view_as_nexus_item );
828 _jmenubar.add( _view_jmenu );
831 void checkTextFrames() {
832 if ( _textframes.size() > 5 ) {
834 if ( _textframes.getFirst() != null ) {
835 _textframes.getFirst().removeMe();
838 _textframes.removeFirst();
841 catch ( final NoSuchElementException e ) {
847 void clearCurrentExternalNodesDataBuffer() {
848 getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
851 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
852 if ( item != null ) {
853 item.setFont( MainFrame.menu_font );
854 if ( !getConfiguration().isUseNativeUI() ) {
855 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
856 item.setForeground( getConfiguration().getGuiMenuTextColor() );
858 item.setSelected( is_selected );
859 item.addActionListener( this );
863 void customizeJMenuItem( final JMenuItem jmi ) {
864 jmi.setFont( MainFrame.menu_font );
865 if ( !getConfiguration().isUseNativeUI() ) {
866 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
867 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
869 jmi.addActionListener( this );
872 void displayBasicInformation() {
873 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
874 String title = "Basic Information";
875 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
876 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
878 showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
883 if ( !isOKforSDI( false, true ) ) {
886 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
887 JOptionPane.showMessageDialog( this,
888 "Gene tree is not rooted.",
889 "Cannot execute GSDI",
890 JOptionPane.ERROR_MESSAGE );
893 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
894 gene_tree.setAllNodesToNotCollapse();
895 gene_tree.recalculateNumberOfExternalDescendants( false );
897 final Phylogeny species_tree = _species_tree.copy();
899 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
901 catch ( final SDIException e ) {
902 JOptionPane.showMessageDialog( this,
903 e.getLocalizedMessage(),
905 JOptionPane.ERROR_MESSAGE );
908 catch ( final Exception e ) {
909 AptxUtil.unexpectedException( e );
912 gene_tree.setRerootable( false );
913 gene_tree.clearHashIdToNodeMap();
914 gene_tree.recalculateNumberOfExternalDescendants( true );
915 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
916 getMainPanel().getControlPanel().setShowEvents( true );
918 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
919 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
921 _mainpanel.getTabbedPane().setSelectedIndex( selected );
923 _mainpanel.getCurrentTreePanel().setEdited( true );
924 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
925 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
926 JOptionPane.showMessageDialog( this,
927 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
928 + "Potential duplications: "
929 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
930 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
931 + "Stripped gene tree nodes: "
932 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
933 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
934 + "Number of polytomies in species tree used: " + poly + "\n",
935 "GSDI successfully completed",
936 JOptionPane.WARNING_MESSAGE );
939 JOptionPane.showMessageDialog( this,
940 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
941 + "Potential duplications: "
942 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
943 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
944 + "Stripped gene tree nodes: "
945 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
946 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
947 + "Number of polytomies in species tree used: " + poly + "\n",
948 "GSDI successfully completed",
949 JOptionPane.INFORMATION_MESSAGE );
953 void executeGSDIR() {
954 if ( !isOKforSDI( false, false ) ) {
957 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
959 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
960 JOptionPane.showMessageDialog( this,
961 "Gene tree is not completely binary",
962 "Cannot execute GSDI",
963 JOptionPane.ERROR_MESSAGE );
966 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
967 gene_tree.setAllNodesToNotCollapse();
968 gene_tree.recalculateNumberOfExternalDescendants( false );
970 final Phylogeny species_tree = _species_tree.copy();
972 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
974 catch ( final SDIException e ) {
975 JOptionPane.showMessageDialog( this,
976 e.getLocalizedMessage(),
977 "Error during GSDIR",
978 JOptionPane.ERROR_MESSAGE );
981 catch ( final Exception e ) {
982 AptxUtil.unexpectedException( e );
985 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
986 result_gene_tree.setRerootable( false );
987 result_gene_tree.clearHashIdToNodeMap();
988 result_gene_tree.recalculateNumberOfExternalDescendants( true );
989 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
990 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
991 getMainPanel().getControlPanel().setShowEvents( true );
993 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
994 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
996 _mainpanel.getTabbedPane().setSelectedIndex( selected );
998 _mainpanel.getCurrentTreePanel().setEdited( true );
999 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1000 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1001 JOptionPane.showMessageDialog( this,
1002 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1003 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1004 + "Stripped gene tree nodes: "
1005 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1006 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1007 + "Number of polytomies in species tree used: " + poly + "\n",
1008 "GSDIR successfully completed",
1009 JOptionPane.WARNING_MESSAGE );
1012 JOptionPane.showMessageDialog( this,
1013 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1014 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1015 + "Stripped gene tree nodes: "
1016 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1017 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1018 + "Number of polytomies in species tree used: " + poly + "\n",
1019 "GSDIR successfully completed",
1020 JOptionPane.INFORMATION_MESSAGE );
1024 Configuration getConfiguration() {
1025 return _configuration;
1028 TreePanel getCurrentTreePanel() {
1029 return getMainPanel().getCurrentTreePanel();
1032 JCheckBoxMenuItem getlabelDirectionCbmi() {
1033 return _label_direction_cbmi;
1036 Options getOtions() {
1041 final StringBuilder sb = new StringBuilder();
1042 sb.append( "Display options\n" );
1043 sb.append( "-------------------\n" );
1044 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1045 sb.append( "Clickable tree nodes\n" );
1046 sb.append( "--------------------\n" );
1047 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1048 sb.append( "or by right clicking:\n" );
1049 sb.append( "o Display Node Data -- display information for a node\n" );
1050 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1051 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1052 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1053 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1054 sb.append( "o Colorize Subtree -- color a subtree\n" );
1055 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1056 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1057 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1058 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1059 sb.append( "Zooming\n" );
1060 sb.append( "---------\n" );
1061 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1062 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1063 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1064 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1065 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1066 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1067 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1068 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1069 sb.append( "Quick tree manipulation:\n" );
1070 sb.append( "------------------------\n" );
1071 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1072 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1073 sb.append( "phyloXML\n" );
1074 sb.append( "-------------------\n" );
1075 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1076 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1077 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1079 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1080 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1081 TextFrame.instantiate( sb.toString(), "Help", _textframes );
1084 void initializeTypeMenu( final Options options ) {
1085 setTypeMenuToAllUnselected();
1087 switch ( options.getPhylogenyGraphicsType() ) {
1089 _convex_type_cbmi.setSelected( true );
1092 _curved_type_cbmi.setSelected( true );
1095 _euro_type_cbmi.setSelected( true );
1098 _rounded_type_cbmi.setSelected( true );
1101 _triangular_type_cbmi.setSelected( true );
1104 _unrooted_type_cbmi.setSelected( true );
1107 _circular_type_cbmi.setSelected( true );
1110 _rectangular_type_cbmi.setSelected( true );
1114 catch ( final NullPointerException np ) {
1115 // In all likelihood, this is caused by menu-less display.
1119 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1120 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1123 else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1124 JOptionPane.showMessageDialog( this,
1125 "No species tree loaded",
1126 "Cannot execute GSDI",
1127 JOptionPane.ERROR_MESSAGE );
1130 else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1131 JOptionPane.showMessageDialog( this,
1132 "Species tree is not completely binary",
1133 "Cannot execute GSDI",
1134 JOptionPane.ERROR_MESSAGE );
1137 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1138 JOptionPane.showMessageDialog( this,
1139 "Gene tree is not completely binary",
1140 "Cannot execute GSDI",
1141 JOptionPane.ERROR_MESSAGE );
1149 boolean isSubtreeDisplayed() {
1150 if ( getCurrentTreePanel() != null ) {
1151 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1153 .showMessageDialog( this,
1154 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1155 "Operation can not be exectuted on a sub-tree",
1156 JOptionPane.WARNING_MESSAGE );
1163 void removeAllTextFrames() {
1164 for( final TextFrame tf : _textframes ) {
1169 _textframes.clear();
1172 void setConfiguration( final Configuration configuration ) {
1173 _configuration = configuration;
1176 void setOptions( final Options options ) {
1180 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1181 setTypeMenuToAllUnselected();
1185 _circular_type_cbmi.setSelected( true );
1188 _convex_type_cbmi.setSelected( true );
1191 _curved_type_cbmi.setSelected( true );
1194 _euro_type_cbmi.setSelected( true );
1197 _rounded_type_cbmi.setSelected( true );
1200 _rectangular_type_cbmi.setSelected( true );
1203 _triangular_type_cbmi.setSelected( true );
1206 _unrooted_type_cbmi.setSelected( true );
1209 throw new IllegalArgumentException( "unknown type: " + type );
1212 catch ( final NullPointerException np ) {
1213 // In all likelihood, this is caused by menu-less display.
1217 void setTypeMenuToAllUnselected() {
1218 if ( _convex_type_cbmi != null ) {
1219 _convex_type_cbmi.setSelected( false );
1221 if ( _curved_type_cbmi != null ) {
1222 _curved_type_cbmi.setSelected( false );
1224 if ( _euro_type_cbmi != null ) {
1225 _euro_type_cbmi.setSelected( false );
1227 if ( _rounded_type_cbmi != null ) {
1228 _rounded_type_cbmi.setSelected( false );
1230 if ( _triangular_type_cbmi != null ) {
1231 _triangular_type_cbmi.setSelected( false );
1233 if ( _rectangular_type_cbmi != null ) {
1234 _rectangular_type_cbmi.setSelected( false );
1236 if ( _unrooted_type_cbmi != null ) {
1237 _unrooted_type_cbmi.setSelected( false );
1239 if ( _circular_type_cbmi != null ) {
1240 _circular_type_cbmi.setSelected( false );
1245 _mainpanel.getControlPanel().showWhole();
1248 void switchColors() {
1249 final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1250 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1251 csc.setVisible( true );
1252 getMainPanel().setTreeColorSet( colorset );
1255 void typeChanged( final Object o ) {
1256 updateTypeCheckboxes( getOptions(), o );
1257 updateOptions( getOptions() );
1258 if ( getCurrentTreePanel() != null ) {
1259 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1260 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1261 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1262 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1263 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1264 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1265 getCurrentTreePanel().getControlPanel().showWhole();
1267 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1268 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1271 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1273 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1274 MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1278 void updateOptions( final Options options ) {
1279 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1280 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1281 && _background_gradient_cbmi.isSelected() );
1282 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1283 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1284 && _abbreviate_scientific_names.isSelected() );
1285 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1286 && _color_labels_same_as_parent_branch.isSelected() );
1287 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1288 && _show_default_node_shapes_internal_cbmi.isSelected() );
1289 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1290 && _show_default_node_shapes_external_cbmi.isSelected() );
1291 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1292 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1293 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1294 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1296 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1297 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1299 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1300 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1302 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1303 && _search_case_senstive_cbmi.isSelected() );
1304 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1305 options.setShowScale( _show_scale_cbmi.isSelected() );
1307 if ( _label_direction_cbmi != null ) {
1308 if ( _label_direction_cbmi.isSelected() ) {
1309 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1312 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1315 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1316 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1317 && _show_confidence_stddev_cbmi.isSelected() );
1318 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1319 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1321 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1322 && _search_whole_words_only_cbmi.isSelected() );
1323 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1324 && _inverse_search_result_cbmi.isSelected() );
1325 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1326 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1328 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1329 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1331 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1332 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1334 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1335 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1337 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1338 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1340 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1341 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1343 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1344 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1346 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1347 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1351 void updateTypeCheckboxes( final Options options, final Object o ) {
1352 setTypeMenuToAllUnselected();
1353 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1356 void viewAsNexus() {
1357 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1358 String title = "Nexus";
1359 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1360 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1362 showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1363 .getNhConversionSupportValueStyle() ),
1369 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1370 String title = "New Hampshire";
1371 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1372 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1374 showTextFrame( getMainPanel().getCurrentPhylogeny()
1375 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1381 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1382 String title = "phyloXML";
1383 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1384 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1386 showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1390 private void chooseFont() {
1391 final FontChooser fc = new FontChooser();
1392 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1393 fc.showDialog( this, "Select the Base Font" );
1394 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1397 private void chooseMinimalConfidence() {
1398 final String s = ( String ) JOptionPane
1399 .showInputDialog( this,
1400 "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1401 + getOptions().getMinConfidenceValue() + "]\n",
1402 "Minimal Confidence Value",
1403 JOptionPane.QUESTION_MESSAGE,
1406 getOptions().getMinConfidenceValue() );
1407 if ( !ForesterUtil.isEmpty( s ) ) {
1408 boolean success = true;
1410 final String m_str = s.trim();
1411 if ( !ForesterUtil.isEmpty( m_str ) ) {
1413 m = Double.parseDouble( m_str );
1415 catch ( final Exception ex ) {
1422 if ( success && ( m >= 0.0 ) ) {
1423 getOptions().setMinConfidenceValue( m );
1428 private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1429 if ( item != null ) {
1430 item.setFont( MainFrame.menu_font );
1431 if ( !getConfiguration().isUseNativeUI() ) {
1432 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1433 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1435 item.setSelected( is_selected );
1436 item.addActionListener( this );
1440 private MainPanel getMainPanel() {
1444 private Phylogeny getSpeciesTree() {
1445 return _species_tree;
1448 private boolean isScreenAntialias() {
1452 private void removeBranchColors() {
1453 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1454 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1458 private void setMainPanel( final MainPanelApplets main_panel ) {
1459 _mainpanel = main_panel;
1462 private void setSpeciesTree( final Phylogeny species_tree ) {
1463 _species_tree = species_tree;
1466 private void setupUI() {
1468 if ( getConfiguration().isUseNativeUI() ) {
1469 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1472 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1475 catch ( final UnsupportedLookAndFeelException e ) {
1476 AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1478 catch ( final ClassNotFoundException e ) {
1479 AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1481 catch ( final InstantiationException e ) {
1482 AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1484 catch ( final IllegalAccessException e ) {
1485 AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1487 catch ( final Exception e ) {
1488 AptxUtil.dieWithSystemError( e.toString() );
1492 static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1493 for( final TreePanel tree_panel : treepanels ) {
1494 tree_panel.setTextAntialias();