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;
17 import java.util.NoSuchElementException;
19 import javax.swing.ButtonGroup;
20 import javax.swing.JApplet;
21 import javax.swing.JCheckBoxMenuItem;
22 import javax.swing.JMenu;
23 import javax.swing.JMenuBar;
24 import javax.swing.JMenuItem;
25 import javax.swing.JOptionPane;
26 import javax.swing.JRadioButtonMenuItem;
27 import javax.swing.UIManager;
28 import javax.swing.UnsupportedLookAndFeelException;
29 import javax.swing.event.ChangeEvent;
30 import javax.swing.event.ChangeListener;
32 import org.apache.commons.codec.binary.Base64;
33 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
34 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
35 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
36 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
37 import org.forester.phylogeny.Phylogeny;
38 import org.forester.phylogeny.data.SequenceRelation;
39 import org.forester.util.ForesterConstants;
40 import org.forester.util.ForesterUtil;
43 // <applet archive="forester.jar"
44 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
45 // codebase="http://www.myserver.org/path/to/forester"
48 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
49 // <param name="url_of_tree_to_load"
50 // value="http://www.myserver.org/examples/data/apaf.xml">
51 // <param name="config_file"
52 // value="http://www.myserver.org/examples/config/config_file.txt">
54 public class ArchaeopteryxE extends JApplet implements ActionListener {
56 private final static String NAME = "ArchaeopteryxE";
57 private static final long serialVersionUID = -1220055577935759443L;
58 private Configuration _configuration;
59 private MainPanelApplets _main_panel;
60 private JMenuBar _jmenubar;
61 private JMenu _options_jmenu;
62 private JMenu _font_size_menu;
63 private JMenuItem _super_tiny_fonts_mi;
64 private JMenuItem _tiny_fonts_mi;
65 private JMenuItem _small_fonts_mi;
66 private JMenuItem _medium_fonts_mi;
67 private JMenuItem _large_fonts_mi;
68 private JMenu _tools_menu;
69 private JMenuItem _taxcolor_item;
70 private JMenuItem _confcolor_item;
71 private JMenuItem _midpoint_root_item;
72 private JMenu _view_jmenu;
73 private JMenuItem _view_as_XML_item;
74 private JMenuItem _view_as_NH_item;
75 private JMenuItem _view_as_NHX_item;
76 private JMenuItem _view_as_nexus_item;
77 private JMenuItem _display_basic_information_item;
78 private JMenu _type_menu;
79 private JCheckBoxMenuItem _rectangular_type_cbmi;
80 private JCheckBoxMenuItem _triangular_type_cbmi;
81 private JCheckBoxMenuItem _curved_type_cbmi;
82 private JCheckBoxMenuItem _convex_type_cbmi;
83 private JCheckBoxMenuItem _euro_type_cbmi;
84 private JCheckBoxMenuItem _rounded_type_cbmi;
85 private JCheckBoxMenuItem _unrooted_type_cbmi;
86 private JCheckBoxMenuItem _circular_type_cbmi;
87 private JMenuItem _help_item;
88 private JMenuItem _about_item;
89 private JMenu _help_jmenu;
90 private JMenuItem _website_item;
91 private JMenuItem _phyloxml_website_item;
92 private JMenuItem _phyloxml_ref_item;
93 private JMenuItem _aptx_ref_item;
94 private JMenuItem _remove_branch_color_item;
95 private JMenuItem _infer_common_sn_names_item;
96 private JCheckBoxMenuItem _show_domain_labels;
97 private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
98 private JCheckBoxMenuItem _abbreviate_scientific_names;
99 private JCheckBoxMenuItem _screen_antialias_cbmi;
100 private JCheckBoxMenuItem _background_gradient_cbmi;
101 private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
102 private JRadioButtonMenuItem _uniform_cladograms_rbmi;
103 private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
104 private Options _options;
105 private JMenuItem _choose_font_mi;
106 private JMenuItem _switch_colors_mi;
107 JCheckBoxMenuItem _label_direction_cbmi;
108 private JCheckBoxMenuItem _show_scale_cbmi;
109 private JCheckBoxMenuItem _search_case_senstive_cbmi;
110 private JCheckBoxMenuItem _search_whole_words_only_cbmi;
111 private JCheckBoxMenuItem _inverse_search_result_cbmi;
112 private JCheckBoxMenuItem _show_overview_cbmi;
113 private JMenuItem _choose_minimal_confidence_mi;
114 private JCheckBoxMenuItem _show_branch_length_values_cbmi;
115 private JMenuItem _collapse_species_specific_subtrees;
116 private JMenuItem _overview_placment_mi;
117 private ButtonGroup _radio_group_1;
118 private JCheckBoxMenuItem _show_default_node_shapes_cbmi;
119 private JMenuItem _cycle_node_shape_mi;
120 private JMenuItem _cycle_node_fill_mi;
121 private JMenuItem _choose_node_size_mi;
122 private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
123 private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
124 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
127 public void actionPerformed( final ActionEvent e ) {
128 final Object o = e.getSource();
129 if ( o == _midpoint_root_item ) {
130 getMainPanel().getCurrentTreePanel().midpointRoot();
132 else if ( o == _taxcolor_item ) {
133 getMainPanel().getCurrentTreePanel().taxColor();
135 else if ( o == _confcolor_item ) {
136 getMainPanel().getCurrentTreePanel().confColor();
138 else if ( o == _infer_common_sn_names_item ) {
139 if ( getCurrentTreePanel() != null ) {
140 getCurrentTreePanel().inferCommonPartOfScientificNames();
143 else if ( o == _collapse_species_specific_subtrees ) {
144 if ( getCurrentTreePanel() != null ) {
145 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
148 else if ( o == _remove_branch_color_item ) {
149 removeBranchColors();
151 else if ( o == _switch_colors_mi ) {
154 else if ( o == _display_basic_information_item ) {
155 displayBasicInformation();
157 else if ( o == _view_as_NH_item ) {
160 else if ( o == _view_as_NHX_item ) {
163 else if ( o == _view_as_XML_item ) {
166 else if ( o == _view_as_nexus_item ) {
169 else if ( o == _super_tiny_fonts_mi ) {
170 if ( getCurrentTreePanel() != null ) {
171 getCurrentTreePanel().setSuperTinyFonts();
172 getCurrentTreePanel().repaint();
175 else if ( o == _tiny_fonts_mi ) {
176 if ( getCurrentTreePanel() != null ) {
177 getCurrentTreePanel().setTinyFonts();
178 getCurrentTreePanel().repaint();
181 else if ( o == _small_fonts_mi ) {
182 if ( getCurrentTreePanel() != null ) {
183 getCurrentTreePanel().setSmallFonts();
184 getCurrentTreePanel().repaint();
187 else if ( o == _medium_fonts_mi ) {
188 if ( getCurrentTreePanel() != null ) {
189 getCurrentTreePanel().setMediumFonts();
190 getCurrentTreePanel().repaint();
193 else if ( o == _large_fonts_mi ) {
194 if ( getCurrentTreePanel() != null ) {
195 getCurrentTreePanel().setLargeFonts();
196 getCurrentTreePanel().repaint();
199 else if ( o == _choose_font_mi ) {
202 else if ( o == _choose_minimal_confidence_mi ) {
203 chooseMinimalConfidence();
205 else if ( o == _choose_node_size_mi ) {
206 MainFrame.chooseNodeSize( getOptions(), this );
208 else if ( o == _overview_placment_mi ) {
209 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
211 else if ( o == _cycle_node_fill_mi ) {
212 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
214 else if ( o == _cycle_node_shape_mi ) {
215 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
217 else if ( o == _non_lined_up_cladograms_rbmi ) {
218 updateOptions( getOptions() );
219 _main_panel.getControlPanel().showWhole();
221 else if ( o == _uniform_cladograms_rbmi ) {
222 updateOptions( getOptions() );
223 _main_panel.getControlPanel().showWhole();
225 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
226 updateOptions( getOptions() );
227 _main_panel.getControlPanel().showWhole();
229 else if ( o == _search_case_senstive_cbmi ) {
230 updateOptions( getOptions() );
231 getMainPanel().getControlPanel().search();
233 else if ( o == _search_whole_words_only_cbmi ) {
234 updateOptions( getOptions() );
235 getMainPanel().getControlPanel().search();
237 else if ( o == _inverse_search_result_cbmi ) {
238 updateOptions( getOptions() );
239 getMainPanel().getControlPanel().search();
241 else if ( o == _show_scale_cbmi ) {
242 updateOptions( getOptions() );
244 else if ( o == _show_branch_length_values_cbmi ) {
245 updateOptions( getOptions() );
247 else if ( o == _show_confidence_stddev_cbmi ) {
248 updateOptions( getOptions() );
250 else if ( o == _label_direction_cbmi ) {
251 updateOptions( getOptions() );
253 else if ( o == _show_overview_cbmi ) {
254 updateOptions( getOptions() );
255 if ( getCurrentTreePanel() != null ) {
256 getCurrentTreePanel().updateOvSizes();
259 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
260 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
261 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
264 else if ( o == _screen_antialias_cbmi ) {
265 updateOptions( getOptions() );
266 setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
268 else if ( o == _background_gradient_cbmi ) {
269 updateOptions( getOptions() );
271 else if ( o == _show_domain_labels ) {
272 updateOptions( getOptions() );
274 else if ( o == _color_labels_same_as_parent_branch ) {
275 updateOptions( getOptions() );
277 else if ( o == _show_default_node_shapes_cbmi ) {
278 updateOptions( getOptions() );
280 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
281 updateOptions( getOptions() );
283 else if ( o == _about_item ) {
286 else if ( o == _help_item ) {
287 help( getConfiguration().getWebLinks() );
289 else if ( o == _website_item ) {
291 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
293 catch ( final IOException e1 ) {
294 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
297 else if ( o == _phyloxml_website_item ) {
299 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
301 catch ( final IOException e1 ) {
302 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
305 else if ( o == _aptx_ref_item ) {
307 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
309 catch ( final IOException e1 ) {
310 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
313 else if ( o == _phyloxml_ref_item ) {
315 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
317 catch ( final IOException e1 ) {
318 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
324 void help( final Map<String, WebLink> weblinks ) {
325 final StringBuilder sb = new StringBuilder();
326 sb.append( "Display options\n" );
327 sb.append( "-------------------\n" );
328 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
329 sb.append( "Clickable tree nodes\n" );
330 sb.append( "--------------------\n" );
331 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
332 sb.append( "or by right clicking:\n" );
333 sb.append( "o Display Node Data -- display information for a node\n" );
334 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
335 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
336 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
337 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
338 sb.append( "o Colorize Subtree -- color a subtree\n" );
339 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
340 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
341 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
342 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
343 sb.append( "Zooming\n" );
344 sb.append( "---------\n" );
345 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
346 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
347 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
348 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
349 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
350 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
351 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
352 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
353 sb.append( "Quick tree manipulation:\n" );
354 sb.append( "------------------------\n" );
355 sb.append( "Order Subtrees -- order the tree by branch length\n" );
356 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
357 sb.append( "Memory problems (Java heap space error)\n" );
358 sb.append( "---------------------------------------\n" );
359 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
360 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
361 sb.append( "the '-Xmx' Java command line option. For example:\n" );
362 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
363 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
364 sb.append( "Active web links\n" );
365 sb.append( "--------------------\n" );
366 for( final String key : weblinks.keySet() ) {
367 sb.append( " " + weblinks.get( key ).toString() + "\n" );
371 sb.append( "phyloXML\n" );
372 sb.append( "-------------------\n" );
373 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
374 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
375 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
377 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
378 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
379 TextFrame.instantiate( sb.toString(), "Help", _textframes );
383 * This method returns the current phylogeny as a string in the chosen format
385 * @param format must be NH, NHX, NEXUS or PHYLOXML
386 * @return the phylogeny string
387 * @author Herve Menager
389 public String getCurrentPhylogeny( final String format ) {
390 removeAllTextFrames();
391 if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
392 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
395 switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
397 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
399 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
401 return getMainPanel().getCurrentPhylogeny().toNexus();
403 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
411 * This method returns a view of the current phylogeny in a chosen
412 * graphics format, base64-encoded in a string so that in can be used
415 * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
416 * @return the phylogeny string
417 * @author Herve Menager
419 public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
420 final ByteArrayOutputStream baos = new ByteArrayOutputStream();
422 AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
423 _main_panel.getWidth(),
424 _main_panel.getHeight(),
425 getCurrentTreePanel(),
426 getCurrentTreePanel().getControlPanel(),
427 GraphicsExportType.valueOf( format ),
430 catch ( final IOException ioe ) {
431 ForesterUtil.printErrorMessage( NAME, ioe.toString() );
432 ioe.printStackTrace();
433 JOptionPane.showMessageDialog( this,
434 NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
435 "Failed to generate graphics",
436 JOptionPane.ERROR_MESSAGE );
439 final byte[] bytes = baos.toByteArray();
440 final String dataImg = Base64.encodeBase64String( bytes );
444 void buildFontSizeMenu() {
445 _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
446 _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
447 _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
448 _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
449 _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
450 _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
451 customizeJMenuItem( _super_tiny_fonts_mi );
452 customizeJMenuItem( _tiny_fonts_mi );
453 customizeJMenuItem( _small_fonts_mi );
454 customizeJMenuItem( _medium_fonts_mi );
455 customizeJMenuItem( _large_fonts_mi );
456 _jmenubar.add( _font_size_menu );
459 void buildHelpMenu() {
460 _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
461 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
462 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
463 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
464 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
465 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
466 _help_jmenu.addSeparator();
467 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
468 customizeJMenuItem( _help_item );
469 customizeJMenuItem( _website_item );
470 customizeJMenuItem( _phyloxml_website_item );
471 customizeJMenuItem( _aptx_ref_item );
472 customizeJMenuItem( _phyloxml_ref_item );
473 customizeJMenuItem( _about_item );
474 _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
475 _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
476 _jmenubar.add( _help_jmenu );
479 void buildOptionsMenu() {
480 _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
481 _options_jmenu.addChangeListener( new ChangeListener() {
484 public void stateChanged( final ChangeEvent e ) {
485 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
486 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
488 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
489 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
490 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
491 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
493 _show_branch_length_values_cbmi,
494 _non_lined_up_cladograms_rbmi,
495 _uniform_cladograms_rbmi,
496 _ext_node_dependent_cladogram_rbmi,
497 _label_direction_cbmi );
498 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
499 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
500 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
503 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
504 getConfiguration() ) );
506 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
507 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
509 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
510 _radio_group_1 = new ButtonGroup();
511 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
512 _radio_group_1.add( _uniform_cladograms_rbmi );
513 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
514 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
515 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
517 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
518 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
520 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
522 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
523 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
524 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
525 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
526 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
528 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
529 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
530 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
531 _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
532 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
533 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
534 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
535 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
537 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
538 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
539 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
540 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
541 _options_jmenu.addSeparator();
542 _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
543 getConfiguration() ) );
545 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
546 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
548 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
549 customizeJMenuItem( _choose_font_mi );
550 customizeJMenuItem( _choose_minimal_confidence_mi );
551 customizeJMenuItem( _switch_colors_mi );
552 customizeJMenuItem( _overview_placment_mi );
553 customizeCheckBoxMenuItem( _label_direction_cbmi,
554 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
555 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
556 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
557 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
558 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
559 customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
560 customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
561 customizeJMenuItem( _cycle_node_shape_mi );
562 customizeJMenuItem( _cycle_node_fill_mi );
563 customizeJMenuItem( _choose_node_size_mi );
564 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
565 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
566 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
567 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
568 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
569 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
570 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
571 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
572 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
573 customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
574 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
575 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
576 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
577 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
578 _jmenubar.add( _options_jmenu );
581 void buildToolsMenu() {
582 _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
583 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
584 customizeJMenuItem( _confcolor_item );
585 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
586 customizeJMenuItem( _taxcolor_item );
587 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
588 _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
589 customizeJMenuItem( _remove_branch_color_item );
590 _tools_menu.addSeparator();
591 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
592 customizeJMenuItem( _midpoint_root_item );
593 _tools_menu.addSeparator();
595 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
596 customizeJMenuItem( _infer_common_sn_names_item );
597 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
598 customizeJMenuItem( _collapse_species_specific_subtrees );
599 _jmenubar.add( _tools_menu );
602 void buildTypeMenu() {
603 _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
604 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
605 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
606 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
607 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
608 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
609 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
610 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
611 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
612 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
613 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
614 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
615 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
616 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
617 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
618 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
619 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
620 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
621 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
622 initializeTypeMenu( getOptions() );
623 _jmenubar.add( _type_menu );
626 void buildViewMenu() {
627 _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
628 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
629 _view_jmenu.addSeparator();
630 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
631 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
632 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
633 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
634 customizeJMenuItem( _display_basic_information_item );
635 customizeJMenuItem( _view_as_NH_item );
636 customizeJMenuItem( _view_as_NHX_item );
637 customizeJMenuItem( _view_as_XML_item );
638 customizeJMenuItem( _view_as_nexus_item );
639 _jmenubar.add( _view_jmenu );
642 private void chooseFont() {
643 final FontChooser fc = new FontChooser();
644 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
645 fc.showDialog( this, "Select the Base Font" );
646 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
649 private void chooseMinimalConfidence() {
650 final String s = ( String ) JOptionPane
651 .showInputDialog( this,
652 "Please the minimum for confidence values to be displayed.\n" + "[current value: "
653 + getOptions().getMinConfidenceValue() + "]\n",
654 "Minimal Confidence Value",
655 JOptionPane.QUESTION_MESSAGE,
658 getOptions().getMinConfidenceValue() );
659 if ( !ForesterUtil.isEmpty( s ) ) {
660 boolean success = true;
662 final String m_str = s.trim();
663 if ( !ForesterUtil.isEmpty( m_str ) ) {
665 m = Double.parseDouble( m_str );
667 catch ( final Exception ex ) {
674 if ( success && ( m >= 0.0 ) ) {
675 getOptions().setMinConfidenceValue( m );
680 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
681 if ( item != null ) {
682 item.setFont( MainFrame.menu_font );
683 if ( !getConfiguration().isUseNativeUI() ) {
684 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
685 item.setForeground( getConfiguration().getGuiMenuTextColor() );
687 item.setSelected( is_selected );
688 item.addActionListener( this );
692 void customizeJMenuItem( final JMenuItem jmi ) {
693 jmi.setFont( MainFrame.menu_font );
694 if ( !getConfiguration().isUseNativeUI() ) {
695 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
696 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
698 jmi.addActionListener( this );
701 private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
702 if ( item != null ) {
703 item.setFont( MainFrame.menu_font );
704 if ( !getConfiguration().isUseNativeUI() ) {
705 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
706 item.setForeground( getConfiguration().getGuiMenuTextColor() );
708 item.setSelected( is_selected );
709 item.addActionListener( this );
714 public void destroy() {
715 AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
716 removeAllTextFrames();
717 if ( getMainPanel() != null ) {
718 getMainPanel().terminate();
722 Configuration getConfiguration() {
723 return _configuration;
726 TreePanel getCurrentTreePanel() {
727 return getMainPanel().getCurrentTreePanel();
730 JCheckBoxMenuItem getlabelDirectionCbmi() {
731 return _label_direction_cbmi;
734 private MainPanel getMainPanel() {
738 public Options getOptions() {
742 Options getOtions() {
748 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
749 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
750 final Configuration configuration = new Configuration( config_filename, true, true, true );
751 setConfiguration( configuration );
752 setOptions( Options.createInstance( configuration ) );
755 Phylogeny[] phys = null;
756 final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
757 AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
758 // Get URL to tree file
759 if ( phys_url_string != null ) {
761 phys_url = new URL( phys_url_string );
763 catch ( final Exception e ) {
764 ForesterUtil.printErrorMessage( NAME, "error: " + e );
766 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
767 + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
770 // Load the tree from URL
771 if ( phys_url != null ) {
773 phys = AptxUtil.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
775 catch ( final Exception e ) {
776 ForesterUtil.printErrorMessage( NAME, e.toString() );
778 JOptionPane.showMessageDialog( this,
779 NAME + ": Failed to read phylogenies: " + "\nException: " + e,
780 "Failed to read phylogenies",
781 JOptionPane.ERROR_MESSAGE );
784 if ( ( phys == null ) || ( phys.length < 1 ) ) {
785 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
786 JOptionPane.showMessageDialog( this,
787 NAME + ": phylogenies from [" + phys_url + "] are null or empty",
788 "Failed to read phylogenies",
789 JOptionPane.ERROR_MESSAGE );
793 AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
796 setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
797 _jmenubar = new JMenuBar();
798 if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
799 if ( !getConfiguration().isUseNativeUI() ) {
800 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
808 setJMenuBar( _jmenubar );
810 final Container contentpane = getContentPane();
811 contentpane.setLayout( new BorderLayout() );
812 contentpane.add( getMainPanel(), BorderLayout.CENTER );
813 addComponentListener( new ComponentAdapter() {
816 public void componentResized( final ComponentEvent e ) {
817 if ( getMainPanel().getCurrentTreePanel() != null ) {
818 getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
820 getMainPanel().getCurrentTreePanel()
826 if ( getConfiguration().isUseTabbedDisplay() ) {
827 AptxUtil.printAppletMessage( NAME, "using tabbed display" );
828 AptxUtil.addPhylogeniesToTabs( phys,
829 new File( phys_url.getFile() ).getName(),
835 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
836 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
840 getMainPanel().getControlPanel().showWholeAll();
841 getMainPanel().getControlPanel().showWhole();
843 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
845 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
846 for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
847 .getRelevantSequenceRelationTypes() ) {
848 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
850 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
851 if ( default_relation != null ) {
852 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
854 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
855 if ( default_sequence != null ) {
856 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
862 void initializeTypeMenu( final Options options ) {
863 setTypeMenuToAllUnselected();
865 switch ( options.getPhylogenyGraphicsType() ) {
867 _convex_type_cbmi.setSelected( true );
870 _curved_type_cbmi.setSelected( true );
873 _euro_type_cbmi.setSelected( true );
876 _rounded_type_cbmi.setSelected( true );
879 _triangular_type_cbmi.setSelected( true );
882 _unrooted_type_cbmi.setSelected( true );
885 _circular_type_cbmi.setSelected( true );
888 _rectangular_type_cbmi.setSelected( true );
892 catch ( final NullPointerException np ) {
893 // In all likelihood, this is caused by menu-less display.
897 private boolean isScreenAntialias() {
901 private void removeBranchColors() {
902 if ( getMainPanel().getCurrentPhylogeny() != null ) {
903 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
907 void setConfiguration( final Configuration configuration ) {
908 _configuration = configuration;
911 private void setMainPanel( final MainPanelApplets main_panel ) {
912 _main_panel = main_panel;
915 void setOptions( final Options options ) {
919 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
920 setTypeMenuToAllUnselected();
924 _circular_type_cbmi.setSelected( true );
927 _convex_type_cbmi.setSelected( true );
930 _curved_type_cbmi.setSelected( true );
933 _euro_type_cbmi.setSelected( true );
936 _rounded_type_cbmi.setSelected( true );
939 _rectangular_type_cbmi.setSelected( true );
942 _triangular_type_cbmi.setSelected( true );
945 _unrooted_type_cbmi.setSelected( true );
948 throw new IllegalArgumentException( "unknown type: " + type );
951 catch ( final NullPointerException np ) {
952 // In all likelihood, this is caused by menu-less display.
956 void setTypeMenuToAllUnselected() {
957 if ( _convex_type_cbmi != null ) {
958 _convex_type_cbmi.setSelected( false );
960 if ( _curved_type_cbmi != null ) {
961 _curved_type_cbmi.setSelected( false );
963 if ( _euro_type_cbmi != null ) {
964 _euro_type_cbmi.setSelected( false );
966 if ( _rounded_type_cbmi != null ) {
967 _rounded_type_cbmi.setSelected( false );
969 if ( _triangular_type_cbmi != null ) {
970 _triangular_type_cbmi.setSelected( false );
972 if ( _rectangular_type_cbmi != null ) {
973 _rectangular_type_cbmi.setSelected( false );
975 if ( _unrooted_type_cbmi != null ) {
976 _unrooted_type_cbmi.setSelected( false );
978 if ( _circular_type_cbmi != null ) {
979 _circular_type_cbmi.setSelected( false );
983 private void setupUI() {
985 if ( getConfiguration().isUseNativeUI() ) {
986 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
989 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
992 catch ( final UnsupportedLookAndFeelException e ) {
993 AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
995 catch ( final ClassNotFoundException e ) {
996 AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
998 catch ( final InstantiationException e ) {
999 AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1001 catch ( final IllegalAccessException e ) {
1002 AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1004 catch ( final Exception e ) {
1005 AptxUtil.dieWithSystemError( e.toString() );
1010 public void start() {
1011 if ( getMainPanel() != null ) {
1012 getMainPanel().validate();
1015 requestFocusInWindow();
1017 AptxUtil.printAppletMessage( NAME, "started" );
1020 void switchColors() {
1021 final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1022 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1023 csc.setVisible( true );
1024 getMainPanel().setTreeColorSet( colorset );
1027 void typeChanged( final Object o ) {
1028 updateTypeCheckboxes( getOptions(), o );
1029 updateOptions( getOptions() );
1030 if ( getCurrentTreePanel() != null ) {
1031 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1032 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1033 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1034 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1035 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1036 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1037 getCurrentTreePanel().getControlPanel().showWhole();
1039 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1040 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1043 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1045 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1046 MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1050 void updateOptions( final Options options ) {
1051 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1052 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1053 && _background_gradient_cbmi.isSelected() );
1054 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1055 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1056 && _abbreviate_scientific_names.isSelected() );
1057 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1058 && _color_labels_same_as_parent_branch.isSelected() );
1059 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1060 && _show_default_node_shapes_cbmi.isSelected() );
1061 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1062 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1063 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1064 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1066 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1067 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1069 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1070 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1072 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1073 && _search_case_senstive_cbmi.isSelected() );
1074 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1075 options.setShowScale( _show_scale_cbmi.isSelected() );
1077 if ( _label_direction_cbmi != null ) {
1078 if ( _label_direction_cbmi.isSelected() ) {
1079 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1082 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1085 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1086 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1087 && _show_confidence_stddev_cbmi.isSelected() );
1088 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1089 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1091 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1092 && _search_whole_words_only_cbmi.isSelected() );
1093 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1094 && _inverse_search_result_cbmi.isSelected() );
1095 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1096 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1098 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1099 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1101 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1102 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1104 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1105 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1107 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1108 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1110 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1111 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1113 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1114 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1116 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1117 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1121 void updateTypeCheckboxes( final Options options, final Object o ) {
1122 setTypeMenuToAllUnselected();
1123 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1126 void displayBasicInformation() {
1127 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1128 String title = "Basic Information";
1129 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1130 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1132 showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
1136 void viewAsNexus() {
1137 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1138 String title = "Nexus";
1139 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1140 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1142 showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1143 .getNhConversionSupportValueStyle() ),
1149 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1150 String title = "New Hampshire";
1151 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1152 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1154 showTextFrame( getMainPanel().getCurrentPhylogeny()
1155 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1161 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1162 String title = "NHX";
1163 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1164 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1166 showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title );
1171 if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1172 String title = "phyloXML";
1173 if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1174 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1176 showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1180 public void showTextFrame( final String s, final String title ) {
1182 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
1185 void checkTextFrames() {
1186 if ( _textframes.size() > 5 ) {
1188 if ( _textframes.getFirst() != null ) {
1189 _textframes.getFirst().removeMe();
1192 _textframes.removeFirst();
1195 catch ( final NoSuchElementException e ) {
1201 void removeAllTextFrames() {
1202 for( final TextFrame tf : _textframes ) {
1207 _textframes.clear();
1210 static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1211 for( final TreePanel tree_panel : treepanels ) {
1212 tree_panel.setTextAntialias();