2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2010 Christian M. Zmasek
8 // This library is free software; you can redistribute it and/or
9 // modify it under the terms of the GNU Lesser General Public
10 // License as published by the Free Software Foundation; either
11 // version 2.1 of the License, or (at your option) any later version.
13 // This library is distributed in the hope that it will be useful,
14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 // Lesser General Public License for more details.
18 // You should have received a copy of the GNU Lesser General Public
19 // License along with this library; if not, write to the Free Software
20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
22 // Contact: phylosoft @ gmail . com
23 // WWW: www.phylosoft.org/forester
25 package org.forester.archaeopteryx;
27 import java.awt.Color;
28 import java.awt.Component;
29 import java.awt.Container;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.ActionListener;
33 import java.io.IOException;
34 import java.util.List;
35 import java.util.Locale;
38 import javax.swing.JApplet;
39 import javax.swing.JCheckBoxMenuItem;
40 import javax.swing.JFrame;
41 import javax.swing.JMenu;
42 import javax.swing.JMenuBar;
43 import javax.swing.JMenuItem;
44 import javax.swing.JOptionPane;
45 import javax.swing.JRadioButtonMenuItem;
46 import javax.swing.SwingUtilities;
48 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
49 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
50 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
51 import org.forester.archaeopteryx.tools.InferenceManager;
52 import org.forester.archaeopteryx.tools.ProcessPool;
53 import org.forester.archaeopteryx.tools.ProcessRunning;
54 import org.forester.phylogeny.Phylogeny;
55 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
56 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
57 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
58 import org.forester.util.ForesterConstants;
59 import org.forester.util.ForesterUtil;
61 public abstract class MainFrame extends JFrame implements ActionListener {
63 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
64 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
65 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
66 private static final long serialVersionUID = 3655000897845508358L;
67 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
70 static final String TYPE_MENU_HEADER = "Type";
71 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
72 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
73 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
74 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
75 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
76 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
77 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
78 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
79 static final String OPTIONS_HEADER = "Options";
80 static final String SEARCH_SUBHEADER = "Search:";
81 static final String DISPLAY_SUBHEADER = "Display:";
82 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
83 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
84 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
85 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
86 static final String DISPLAY_SCALE_LABEL = "Display Scale";
87 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
88 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
89 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
90 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
91 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
92 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
93 static final String BG_GRAD_LABEL = "Background Color Gradient";
94 static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
95 static final String SHOW_OVERVIEW_LABEL = "Show Overview";
96 static final String FONT_SIZE_MENU_LABEL = "Font Size";
97 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
98 static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
99 static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
100 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
101 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
102 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
103 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
104 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
105 static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
106 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
107 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
112 JMenu _options_jmenu;
113 JMenu _font_size_menu;
115 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
117 JMenuItem _open_item;
118 JMenuItem _open_url_item;
119 JMenuItem _save_item;
120 JMenuItem _save_all_item;
121 JMenuItem _close_item;
122 JMenuItem _exit_item;
125 JMenuItem _midpoint_root_item;
126 JMenuItem _taxcolor_item;
127 JMenuItem _confcolor_item;
128 JMenuItem _color_rank_jmi;
129 JMenuItem _infer_common_sn_names_item;
130 JMenuItem _collapse_species_specific_subtrees;
131 JMenuItem _collapse_below_threshold; //TODO implememt me
132 JMenuItem _obtain_detailed_taxonomic_information_jmi;
133 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
134 JMenuItem _obtain_uniprot_seq_information_jmi;
135 JMenuItem _move_node_names_to_tax_sn_jmi;
136 JMenuItem _move_node_names_to_seq_names_jmi;
137 JMenuItem _extract_tax_code_from_node_names_jmi;
139 JMenuItem _super_tiny_fonts_item;
140 JMenuItem _tiny_fonts_item;
141 JMenuItem _small_fonts_item;
142 JMenuItem _medium_fonts_item;
143 JMenuItem _large_fonts_item;
145 // _ screen and print
146 JMenuItem _choose_font_mi;
147 JMenuItem _switch_colors_mi;
148 JCheckBoxMenuItem _label_direction_cbmi;
150 JCheckBoxMenuItem _screen_antialias_cbmi;
151 JCheckBoxMenuItem _background_gradient_cbmi;
152 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
153 JRadioButtonMenuItem _uniform_cladograms_rbmi;
154 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
155 JCheckBoxMenuItem _show_branch_length_values_cbmi;
156 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
157 JCheckBoxMenuItem _show_overview_cbmi;
158 JCheckBoxMenuItem _show_domain_labels;
159 JCheckBoxMenuItem _abbreviate_scientific_names;
160 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
161 JMenuItem _overview_placment_mi;
162 JMenuItem _choose_minimal_confidence_mi;
163 JCheckBoxMenuItem _show_default_node_shapes_cbmi;
164 JMenuItem _cycle_node_shape_mi;
165 JMenuItem _cycle_node_fill_mi;
166 JMenuItem _choose_node_size_mi;
167 JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
168 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
170 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
171 JCheckBoxMenuItem _antialias_print_cbmi;
172 JCheckBoxMenuItem _print_black_and_white_cbmi;
173 JCheckBoxMenuItem _print_using_actual_size_cbmi;
174 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
175 JMenuItem _print_size_mi;
176 JMenuItem _choose_pdf_width_mi;
178 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
179 JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
180 JCheckBoxMenuItem _replace_underscores_cbmi;
181 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
182 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
184 JCheckBoxMenuItem _search_case_senstive_cbmi;
185 JCheckBoxMenuItem _search_whole_words_only_cbmi;
186 JCheckBoxMenuItem _inverse_search_result_cbmi;
189 JCheckBoxMenuItem _rectangular_type_cbmi;
190 JCheckBoxMenuItem _triangular_type_cbmi;
191 JCheckBoxMenuItem _curved_type_cbmi;
192 JCheckBoxMenuItem _convex_type_cbmi;
193 JCheckBoxMenuItem _euro_type_cbmi;
194 JCheckBoxMenuItem _rounded_type_cbmi;
195 JCheckBoxMenuItem _unrooted_type_cbmi;
196 JCheckBoxMenuItem _circular_type_cbmi;
197 // view as text menu:
198 JMenuItem _view_as_NH_item;
199 JMenuItem _view_as_NHX_item;
200 JMenuItem _view_as_XML_item;
201 JMenuItem _view_as_nexus_item;
202 JMenuItem _display_basic_information_item;
204 JMenuItem _about_item;
205 JMenuItem _help_item;
206 JMenuItem _website_item;
207 JMenuItem _phyloxml_website_item;
208 JMenuItem _phyloxml_ref_item;
209 JMenuItem _aptx_ref_item;
212 // Handy pointers to child components:
213 MainPanel _mainpanel;
214 Container _contentpane;
215 TextFrame _textframe;
216 Configuration _configuration;
217 JMenuItem _remove_branch_color_item;
219 InferenceManager _inference_manager;
220 final ProcessPool _process_pool;
223 _process_pool = ProcessPool.createInstance();
226 public ProcessPool getProcessPool() {
227 return _process_pool;
233 public void actionPerformed( final ActionEvent e ) {
234 final Object o = e.getSource();
235 boolean is_applet = false;
236 JApplet applet = null;
237 if ( getCurrentTreePanel() != null ) {
238 is_applet = getCurrentTreePanel().isApplet();
240 applet = getCurrentTreePanel().obtainApplet();
243 if ( o == _open_url_item ) {
244 readPhylogeniesFromURL();
246 else if ( o == _exit_item ) {
249 else if ( o == _taxcolor_item ) {
252 else if ( o == _confcolor_item ) {
255 else if ( o == _color_rank_jmi ) {
258 else if ( o == _infer_common_sn_names_item ) {
259 if ( isSubtreeDisplayed() ) {
262 if ( getCurrentTreePanel() != null ) {
263 getCurrentTreePanel().inferCommonPartOfScientificNames();
266 else if ( o == _collapse_species_specific_subtrees ) {
267 if ( isSubtreeDisplayed() ) {
270 if ( getCurrentTreePanel() != null ) {
271 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
274 else if ( o == _remove_branch_color_item ) {
275 if ( isSubtreeDisplayed() ) {
278 removeBranchColors();
280 else if ( o == _midpoint_root_item ) {
281 if ( isSubtreeDisplayed() ) {
286 else if ( o == _switch_colors_mi ) {
289 else if ( o == _display_basic_information_item ) {
290 displayBasicInformation();
292 else if ( o == _view_as_NH_item ) {
295 else if ( o == _view_as_NHX_item ) {
298 else if ( o == _view_as_XML_item ) {
301 else if ( o == _view_as_nexus_item ) {
304 else if ( o == _super_tiny_fonts_item ) {
305 if ( getCurrentTreePanel() != null ) {
306 getCurrentTreePanel().setSuperTinyFonts();
307 getCurrentTreePanel().repaint();
310 else if ( o == _tiny_fonts_item ) {
311 if ( getCurrentTreePanel() != null ) {
312 getCurrentTreePanel().setTinyFonts();
313 getCurrentTreePanel().repaint();
316 else if ( o == _small_fonts_item ) {
317 if ( getCurrentTreePanel() != null ) {
318 getCurrentTreePanel().setSmallFonts();
319 getCurrentTreePanel().repaint();
322 else if ( o == _medium_fonts_item ) {
323 if ( getCurrentTreePanel() != null ) {
324 getCurrentTreePanel().setMediumFonts();
325 getCurrentTreePanel().repaint();
328 else if ( o == _large_fonts_item ) {
329 if ( getCurrentTreePanel() != null ) {
330 getCurrentTreePanel().setLargeFonts();
331 getCurrentTreePanel().repaint();
334 else if ( o == _choose_font_mi ) {
337 else if ( o == _choose_minimal_confidence_mi ) {
338 chooseMinimalConfidence();
340 else if ( o == _choose_node_size_mi ) {
341 chooseNodeSize( getOptions(), this );
343 else if ( o == _overview_placment_mi ) {
344 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
346 else if ( o == _cycle_node_fill_mi ) {
347 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
349 else if ( o == _cycle_node_shape_mi ) {
350 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
352 else if ( o == _screen_antialias_cbmi ) {
353 updateOptions( getOptions() );
354 updateScreenTextAntialias( getMainPanel().getTreePanels() );
356 else if ( o == _background_gradient_cbmi ) {
357 updateOptions( getOptions() );
359 else if ( o == _show_domain_labels ) {
360 updateOptions( getOptions() );
362 else if ( o == _abbreviate_scientific_names ) {
363 updateOptions( getOptions() );
365 else if ( o == _color_labels_same_as_parent_branch ) {
366 updateOptions( getOptions() );
368 else if ( o == _show_default_node_shapes_cbmi ) {
369 updateOptions( getOptions() );
371 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
372 updateOptions( getOptions() );
374 else if ( o == _non_lined_up_cladograms_rbmi ) {
375 updateOptions( getOptions() );
378 else if ( o == _uniform_cladograms_rbmi ) {
379 updateOptions( getOptions() );
382 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
383 updateOptions( getOptions() );
386 else if ( o == _search_case_senstive_cbmi ) {
387 updateOptions( getOptions() );
388 getMainPanel().getControlPanel().search();
390 else if ( o == _search_whole_words_only_cbmi ) {
391 updateOptions( getOptions() );
392 getMainPanel().getControlPanel().search();
394 else if ( o == _inverse_search_result_cbmi ) {
395 updateOptions( getOptions() );
396 getMainPanel().getControlPanel().search();
398 else if ( o == _show_scale_cbmi ) {
399 updateOptions( getOptions() );
401 else if ( o == _show_branch_length_values_cbmi ) {
402 updateOptions( getOptions() );
404 else if ( o == _show_confidence_stddev_cbmi ) {
405 updateOptions( getOptions() );
407 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
408 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
409 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
411 updateOptions( getOptions() );
413 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
414 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
415 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
417 updateOptions( getOptions() );
419 else if ( o == _label_direction_cbmi ) {
420 updateOptions( getOptions() );
422 else if ( o == _show_overview_cbmi ) {
423 updateOptions( getOptions() );
424 if ( getCurrentTreePanel() != null ) {
425 getCurrentTreePanel().updateOvSizes();
428 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
429 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
430 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
433 else if ( o == _about_item ) {
436 else if ( o == _help_item ) {
437 help( getConfiguration().getWebLinks() );
439 else if ( o == _website_item ) {
441 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
443 catch ( final IOException e1 ) {
444 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
447 else if ( o == _phyloxml_website_item ) {
449 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
451 catch ( final IOException e1 ) {
452 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
455 else if ( o == _aptx_ref_item ) {
457 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
459 catch ( final IOException e1 ) {
460 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
463 else if ( o == _phyloxml_ref_item ) {
465 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
467 catch ( final IOException e1 ) {
468 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
472 if ( _load_phylogeny_from_webservice_menu_items != null ) {
473 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
474 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
475 readPhylogeniesFromWebservice( i );
480 _contentpane.repaint();
483 boolean isSubtreeDisplayed() {
484 if ( getCurrentTreePanel() != null ) {
485 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
487 .showMessageDialog( this,
488 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
489 "Operation can not be exectuted on a sub-tree",
490 JOptionPane.WARNING_MESSAGE );
497 void activateSaveAllIfNeeded() {
498 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
499 _save_all_item.setEnabled( true );
502 _save_all_item.setEnabled( false );
506 void buildFileMenu() {
507 _file_jmenu = createMenu( "File", getConfiguration() );
508 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
509 _file_jmenu.addSeparator();
510 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
511 customizeJMenuItem( _open_url_item );
512 customizeJMenuItem( _exit_item );
513 _jmenubar.add( _file_jmenu );
516 void buildFontSizeMenu() {
517 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
518 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
519 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
520 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
521 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
522 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
523 customizeJMenuItem( _super_tiny_fonts_item );
524 customizeJMenuItem( _tiny_fonts_item );
525 customizeJMenuItem( _small_fonts_item );
526 customizeJMenuItem( _medium_fonts_item );
527 customizeJMenuItem( _large_fonts_item );
528 _jmenubar.add( _font_size_menu );
531 void buildHelpMenu() {
532 _help_jmenu = createMenu( "Help", getConfiguration() );
533 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
534 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
535 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
536 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
537 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
538 _help_jmenu.addSeparator();
539 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
540 customizeJMenuItem( _help_item );
541 customizeJMenuItem( _website_item );
542 customizeJMenuItem( _phyloxml_website_item );
543 customizeJMenuItem( _aptx_ref_item );
544 customizeJMenuItem( _phyloxml_ref_item );
545 customizeJMenuItem( _about_item );
546 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
547 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
548 _jmenubar.add( _help_jmenu );
551 public void updateProcessMenu() {
552 // In general Swing is not thread safe.
553 // See "Swing's Threading Policy".
554 SwingUtilities.invokeLater( new Runnable() {
557 doUpdateProcessMenu();
562 private void doUpdateProcessMenu() {
563 if ( _process_pool.size() > 0 ) {
564 if ( _process_menu == null ) {
565 _process_menu = createMenu( "", getConfiguration() );
566 _process_menu.setForeground( Color.RED );
568 _process_menu.removeAll();
569 final String text = "processes running: " + _process_pool.size();
570 _process_menu.setText( text );
571 _jmenubar.add( _process_menu );
572 for( int i = 0; i < _process_pool.size(); ++i ) {
573 final ProcessRunning p = _process_pool.getProcessByIndex( i );
574 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
578 if ( _process_menu != null ) {
579 _process_menu.removeAll();
580 _jmenubar.remove( _process_menu );
583 _jmenubar.validate();
588 void buildTypeMenu() {
589 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
590 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
591 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
592 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
593 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
594 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
595 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
596 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
597 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
598 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
599 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
600 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
601 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
602 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
603 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
604 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
605 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
606 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
607 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
608 initializeTypeMenu( getOptions() );
609 _jmenubar.add( _type_menu );
612 void buildViewMenu() {
613 _view_jmenu = createMenu( "View", getConfiguration() );
614 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
615 _view_jmenu.addSeparator();
616 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
617 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
618 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
619 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
620 customizeJMenuItem( _display_basic_information_item );
621 customizeJMenuItem( _view_as_NH_item );
622 customizeJMenuItem( _view_as_NHX_item );
623 customizeJMenuItem( _view_as_XML_item );
624 customizeJMenuItem( _view_as_nexus_item );
625 _jmenubar.add( _view_jmenu );
628 private void chooseFont() {
629 final FontChooser fc = new FontChooser();
630 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
631 fc.showDialog( this, "Select the Base Font" );
632 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
635 private void chooseMinimalConfidence() {
636 final String s = ( String ) JOptionPane
637 .showInputDialog( this,
638 "Please enter the minimum for confidence values to be displayed.\n"
639 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
640 "Minimal Confidence Value",
641 JOptionPane.QUESTION_MESSAGE,
644 getOptions().getMinConfidenceValue() );
645 if ( !ForesterUtil.isEmpty( s ) ) {
646 boolean success = true;
648 final String m_str = s.trim();
649 if ( !ForesterUtil.isEmpty( m_str ) ) {
651 m = Double.parseDouble( m_str );
653 catch ( final Exception ex ) {
660 if ( success && ( m >= 0.0 ) ) {
661 getOptions().setMinConfidenceValue( m );
666 static void chooseNodeSize( final Options options, final Component parent ) {
667 final String s = ( String ) JOptionPane.showInputDialog( parent,
668 "Please enter the default size for node shapes.\n"
670 + options.getDefaultNodeShapeSize() + "]\n",
672 JOptionPane.QUESTION_MESSAGE,
675 options.getDefaultNodeShapeSize() );
676 if ( !ForesterUtil.isEmpty( s ) ) {
677 boolean success = true;
679 final String m_str = s.trim();
680 if ( !ForesterUtil.isEmpty( m_str ) ) {
682 m = Double.parseDouble( m_str );
684 catch ( final Exception ex ) {
691 if ( success && ( m >= 0.0 ) ) {
692 final short size = ForesterUtil.roundToShort( m );
694 options.setDefaultNodeShapeSize( size );
702 if ( _mainpanel != null ) {
703 _mainpanel.terminate();
705 if ( _contentpane != null ) {
706 _contentpane.removeAll();
713 if ( _mainpanel.getCurrentTreePanel() != null ) {
714 _mainpanel.getCurrentTreePanel().confColor();
719 if ( _mainpanel.getCurrentTreePanel() != null ) {
720 final String[] ranks = AptxUtil.getAllPossibleRanks();
721 final String rank = ( String ) JOptionPane
722 .showInputDialog( this,
723 "What rank should the colorization be based on",
725 JOptionPane.QUESTION_MESSAGE,
729 if ( !ForesterUtil.isEmpty( rank ) ) {
730 _mainpanel.getCurrentTreePanel().colorRank( rank );
735 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
736 if ( item != null ) {
737 item.setFont( MainFrame.menu_font );
738 if ( !getConfiguration().isUseNativeUI() ) {
739 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
740 item.setForeground( getConfiguration().getGuiMenuTextColor() );
742 item.setSelected( is_selected );
743 item.addActionListener( this );
747 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
749 jmi.setFont( MainFrame.menu_font );
750 if ( !getConfiguration().isUseNativeUI() ) {
751 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
752 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
754 jmi.addActionListener( this );
759 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
760 if ( item != null ) {
761 item.setFont( MainFrame.menu_font );
762 if ( !getConfiguration().isUseNativeUI() ) {
763 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
764 item.setForeground( getConfiguration().getGuiMenuTextColor() );
766 item.setSelected( is_selected );
767 item.addActionListener( this );
771 void exceptionOccuredDuringOpenFile( final Exception e ) {
773 _mainpanel.getCurrentTreePanel().setArrowCursor();
775 catch ( final Exception ex ) {
778 JOptionPane.showMessageDialog( this,
779 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
780 "Error during File|Open",
781 JOptionPane.ERROR_MESSAGE );
784 void exceptionOccuredDuringSaveAs( final Exception e ) {
786 _mainpanel.getCurrentTreePanel().setArrowCursor();
788 catch ( final Exception ex ) {
791 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
794 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
795 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
796 JOptionPane.showMessageDialog( this,
797 "Gene tree and species tree have no species in common.",
799 JOptionPane.ERROR_MESSAGE );
802 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
803 JOptionPane.showMessageDialog( this,
804 "Gene tree and species tree have only one species in common.",
806 JOptionPane.ERROR_MESSAGE );
814 public Configuration getConfiguration() {
815 return _configuration;
818 TreePanel getCurrentTreePanel() {
819 return getMainPanel().getCurrentTreePanel();
822 JMenu getHelpMenu() {
826 JCheckBoxMenuItem getlabelDirectionCbmi() {
827 return _label_direction_cbmi;
830 public MainPanel getMainPanel() {
834 JMenuBar getMenuBarOfMainFrame() {
838 public Options getOptions() {
842 void initializeTypeMenu( final Options options ) {
843 setTypeMenuToAllUnselected();
844 switch ( options.getPhylogenyGraphicsType() ) {
846 _convex_type_cbmi.setSelected( true );
849 _curved_type_cbmi.setSelected( true );
852 _euro_type_cbmi.setSelected( true );
855 _rounded_type_cbmi.setSelected( true );
858 _triangular_type_cbmi.setSelected( true );
861 _unrooted_type_cbmi.setSelected( true );
864 _circular_type_cbmi.setSelected( true );
867 _rectangular_type_cbmi.setSelected( true );
872 void midpointRoot() {
873 if ( _mainpanel.getCurrentTreePanel() != null ) {
874 _mainpanel.getCurrentTreePanel().midpointRoot();
878 abstract void readPhylogeniesFromURL();
880 void readPhylogeniesFromWebservice( final int i ) {
881 final UrlTreeReader reader = new UrlTreeReader( this, i );
882 new Thread( reader ).start();
885 private void removeBranchColors() {
886 if ( getMainPanel().getCurrentPhylogeny() != null ) {
887 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
891 void removeTextFrame() {
892 if ( _textframe != null ) {
898 void setConfiguration( final Configuration configuration ) {
899 _configuration = configuration;
902 void setOptions( final Options options ) {
906 void setInferenceManager( final InferenceManager i ) {
907 _inference_manager = i;
910 public InferenceManager getInferenceManager() {
911 return _inference_manager;
914 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
915 setTypeMenuToAllUnselected();
918 _circular_type_cbmi.setSelected( true );
921 _convex_type_cbmi.setSelected( true );
924 _curved_type_cbmi.setSelected( true );
927 _euro_type_cbmi.setSelected( true );
930 _rounded_type_cbmi.setSelected( true );
933 _rectangular_type_cbmi.setSelected( true );
936 _triangular_type_cbmi.setSelected( true );
939 _unrooted_type_cbmi.setSelected( true );
942 throw new IllegalArgumentException( "unknown type: " + type );
946 void setTypeMenuToAllUnselected() {
947 _convex_type_cbmi.setSelected( false );
948 _curved_type_cbmi.setSelected( false );
949 _euro_type_cbmi.setSelected( false );
950 _rounded_type_cbmi.setSelected( false );
951 _triangular_type_cbmi.setSelected( false );
952 _rectangular_type_cbmi.setSelected( false );
953 _unrooted_type_cbmi.setSelected( false );
954 _circular_type_cbmi.setSelected( false );
957 public void showWhole() {
958 _mainpanel.getControlPanel().showWhole();
961 void switchColors() {
962 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
963 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
964 csc.setVisible( true );
968 if ( _mainpanel.getCurrentTreePanel() != null ) {
969 _mainpanel.getCurrentTreePanel().taxColor();
973 void typeChanged( final Object o ) {
974 updateTypeCheckboxes( getOptions(), o );
975 updateOptions( getOptions() );
976 if ( getCurrentTreePanel() != null ) {
977 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
978 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
979 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
980 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
981 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
982 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
983 getCurrentTreePanel().getControlPanel().showWhole();
985 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
986 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
989 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
991 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
992 updateScreenTextAntialias( getMainPanel().getTreePanels() );
993 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
994 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
995 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
998 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1004 void updateOptions( final Options options ) {
1005 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1006 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1007 && _background_gradient_cbmi.isSelected() );
1008 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1009 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1010 && _abbreviate_scientific_names.isSelected() );
1011 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1012 && _color_labels_same_as_parent_branch.isSelected() );
1013 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1014 && _show_default_node_shapes_cbmi.isSelected() );
1015 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1016 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1017 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1018 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1020 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1021 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1023 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1024 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1026 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1027 && _search_case_senstive_cbmi.isSelected() );
1028 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1029 options.setShowScale( _show_scale_cbmi.isSelected() );
1031 if ( _label_direction_cbmi != null ) {
1032 if ( _label_direction_cbmi.isSelected() ) {
1033 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1036 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1039 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1040 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1041 && _show_confidence_stddev_cbmi.isSelected() );
1042 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1043 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1045 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1046 && ( _print_using_actual_size_cbmi.isSelected() ) );
1047 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1048 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1049 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1050 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1051 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1052 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1054 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1055 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1056 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1059 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1061 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1062 && _print_black_and_white_cbmi.isSelected() );
1063 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1064 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1065 options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
1066 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
1067 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1068 && _replace_underscores_cbmi.isSelected() );
1069 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1070 && _search_whole_words_only_cbmi.isSelected() );
1071 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1072 && _inverse_search_result_cbmi.isSelected() );
1073 if ( _graphics_export_visible_only_cbmi != null ) {
1074 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1075 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1076 _graphics_export_using_actual_size_cbmi.setSelected( true );
1077 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1080 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1083 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1084 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1086 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1087 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1089 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1090 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1092 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1093 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1095 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1096 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1098 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1099 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1101 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1102 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1104 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1105 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1109 void updateTypeCheckboxes( final Options options, final Object o ) {
1110 setTypeMenuToAllUnselected();
1111 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1114 void displayBasicInformation() {
1115 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1118 _textframe = TextFrame.instantiate( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
1121 void viewAsNexus() {
1123 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1124 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
1127 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions()
1128 .getNhConversionSupportValueStyle() ) );
1133 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1134 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
1137 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny()
1138 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) );
1143 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1144 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1147 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
1152 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
1153 && ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
1154 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
1159 * Display the about box.
1161 static void about() {
1162 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1163 about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
1164 about.append( "All Rights Reserved\n" );
1165 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1166 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1167 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1168 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1169 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1170 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1171 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1173 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1174 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1175 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1176 + ForesterUtil.OS_VERSION + "]\n" );
1178 final Runtime rt = java.lang.Runtime.getRuntime();
1179 final long free_memory = rt.freeMemory() / 1000000;
1180 final long total_memory = rt.totalMemory() / 1000000;
1181 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1182 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1183 about.append( "References:\n" );
1184 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1185 about.append( "For more information & download:\n" );
1186 about.append( Constants.APTX_WEB_SITE + "\n" );
1187 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1188 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1191 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1192 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1195 static JMenu createMenu( final String title, final Configuration conf ) {
1196 final JMenu jmenu = new JMenu( title );
1197 if ( !conf.isUseNativeUI() ) {
1198 jmenu.setFont( MainFrame.menu_font );
1199 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1200 jmenu.setForeground( conf.getGuiMenuTextColor() );
1205 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1206 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1207 if ( !configuration.isUseNativeUI() ) {
1208 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1209 label.setForeground( configuration.getGuiMenuTextColor() );
1210 label.setOpaque( true );
1212 label.setSelected( false );
1213 label.setEnabled( false );
1217 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1218 switch ( op.getOvPlacement() ) {
1220 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1223 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1226 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1229 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1232 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1234 if ( tree_panel != null ) {
1235 tree_panel.updateOvSettings();
1239 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1240 switch ( op.getDefaultNodeFill() ) {
1242 op.setDefaultNodeFill( NodeFill.SOLID );
1245 op.setDefaultNodeFill( NodeFill.GRADIENT );
1248 op.setDefaultNodeFill( NodeFill.NONE );
1251 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1255 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1256 switch ( op.getDefaultNodeShape() ) {
1258 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1261 op.setDefaultNodeShape( NodeShape.CIRCLE );
1264 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1268 static void help( final Map<String, WebLink> weblinks ) {
1269 final StringBuilder sb = new StringBuilder();
1270 sb.append( "Display options\n" );
1271 sb.append( "-------------------\n" );
1272 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1273 sb.append( "Clickable tree nodes\n" );
1274 sb.append( "--------------------\n" );
1275 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1276 sb.append( "or by right clicking:\n" );
1277 sb.append( "o Display Node Data -- display information for a node\n" );
1278 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1279 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1280 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1281 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1282 sb.append( "o Colorize Subtree -- color a subtree\n" );
1283 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1284 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1285 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1286 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1287 sb.append( "Zooming\n" );
1288 sb.append( "---------\n" );
1289 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1290 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1291 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1292 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1293 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1294 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1295 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1296 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1297 sb.append( "Quick tree manipulation:\n" );
1298 sb.append( "------------------------\n" );
1299 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1300 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1301 sb.append( "Memory problems (Java heap space error)\n" );
1302 sb.append( "---------------------------------------\n" );
1303 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1304 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1305 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1306 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1307 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1308 sb.append( "Active web links\n" );
1309 sb.append( "--------------------\n" );
1310 for( final String key : weblinks.keySet() ) {
1311 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1314 // + "General remarks\n"
1315 // + "---------------\n"
1317 // "o The application version permits copying to the clipboard \n"
1319 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1321 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1322 // + " but not any of its parent tree(s).\n"
1324 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1326 // " are likely to be bootstrap values instead of branch length values.\n\n"
1328 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1330 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1332 // " a species: either directly through the \"Species\" field, or the species\n"
1334 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1336 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1338 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1340 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1342 // "o !External nodes of the gene tree associated with species not present in\n"
1344 // " the species tree are REMOVED prior to SDI execution!\n"
1346 // "o Both the gene tree and the species tree must be completely binary.\n"
1348 // "o Duplications and speciations are a function of the position of the root.\n"
1350 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1351 // + " incorrect and need to be inferred again\n"
1353 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1355 sb.append( "phyloXML\n" );
1356 sb.append( "-------------------\n" );
1357 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1358 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1359 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1361 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1362 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1363 TextFrame.instantiate( sb.toString() );
1366 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1367 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1368 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1371 mi.setText( "Cycle Overview Placement..." );
1375 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1376 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1377 mi.setText( "Cycle Node Shape Fill Type... (current: "
1378 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1381 mi.setText( "Cycle Node Shape Fill Type..." );
1385 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1386 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1387 mi.setText( "Cycle Node Shape Fill Type... (current: "
1388 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1391 mi.setText( "Cycle Node Shape Fill Type..." );
1395 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1396 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1397 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1400 mi.setText( "Select Colors..." );
1404 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1405 mi.setText( "Select Font... (current: " + font_desc + ")" );
1408 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1409 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1410 mi.setEnabled( true );
1412 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1413 mi.setEnabled( true );
1416 mi.setEnabled( false );
1418 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1421 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1422 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1425 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1426 final JCheckBoxMenuItem scale,
1427 final JCheckBoxMenuItem branch_lengths,
1428 final JRadioButtonMenuItem non_lined_up,
1429 final JRadioButtonMenuItem uniform_clado,
1430 final JRadioButtonMenuItem nonuniform_clado,
1431 final JCheckBoxMenuItem label_direction_cbmi ) {
1432 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1433 final ControlPanel control = main_panel.getControlPanel();
1434 final Options options = main_panel.getOptions();
1435 scale.setSelected( options.isShowScale() );
1436 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1437 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1438 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1439 scale.setSelected( false );
1440 scale.setEnabled( false );
1441 branch_lengths.setSelected( false );
1442 branch_lengths.setEnabled( false );
1444 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1445 scale.setSelected( false );
1446 scale.setEnabled( false );
1447 branch_lengths.setEnabled( true );
1450 scale.setEnabled( true );
1451 branch_lengths.setEnabled( true );
1453 if ( ( tree_panel != null )
1454 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1455 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1456 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1457 branch_lengths.setSelected( false );
1458 branch_lengths.setEnabled( false );
1460 if ( tree_panel != null ) {
1461 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1462 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1463 non_lined_up.setEnabled( false );
1464 uniform_clado.setEnabled( false );
1465 nonuniform_clado.setEnabled( false );
1468 non_lined_up.setEnabled( true );
1469 uniform_clado.setEnabled( true );
1470 nonuniform_clado.setEnabled( true );
1474 if ( ( tree_panel != null )
1475 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1476 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1477 branch_lengths.setSelected( false );
1478 branch_lengths.setEnabled( false );
1480 if ( ( tree_panel != null )
1481 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1482 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1483 non_lined_up.setEnabled( false );
1486 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1487 non_lined_up.setEnabled( true );
1490 label_direction_cbmi.setEnabled( true );
1491 if ( tree_panel != null ) {
1492 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1493 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1494 label_direction_cbmi.setEnabled( false );
1496 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1497 scale.setSelected( false );
1498 scale.setEnabled( false );
1503 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1504 for( final TreePanel tree_panel : treepanels ) {
1505 tree_panel.setTextAntialias();