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;
47 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
48 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
49 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
50 import org.forester.archaeopteryx.tools.ProcessPool;
51 import org.forester.archaeopteryx.tools.ProcessRunning;
52 import org.forester.phylogeny.Phylogeny;
53 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
54 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
55 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
56 import org.forester.util.ForesterConstants;
57 import org.forester.util.ForesterUtil;
59 public abstract class MainFrame extends JFrame implements ActionListener {
61 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
62 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
63 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
64 private static final long serialVersionUID = 3655000897845508358L;
65 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
68 static final String TYPE_MENU_HEADER = "Type";
69 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
70 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
71 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
72 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
73 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
74 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
75 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
76 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
77 static final String OPTIONS_HEADER = "Options";
78 static final String SEARCH_SUBHEADER = "Search:";
79 static final String DISPLAY_SUBHEADER = "Display:";
80 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
81 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
82 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
83 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
84 static final String DISPLAY_SCALE_LABEL = "Display Scale";
85 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
86 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
87 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
88 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
89 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
90 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
91 static final String BG_GRAD_LABEL = "Background Color Gradient";
92 static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
93 static final String SHOW_OVERVIEW_LABEL = "Show Overview";
94 static final String FONT_SIZE_MENU_LABEL = "Font Size";
95 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
96 static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
97 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";
98 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
99 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
100 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
101 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
102 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
103 static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
104 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
105 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
110 JMenu _options_jmenu;
111 JMenu _font_size_menu;
113 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
115 JMenuItem _open_item;
116 JMenuItem _open_url_item;
117 JMenuItem _save_item;
118 JMenuItem _save_all_item;
119 JMenuItem _close_item;
120 JMenuItem _exit_item;
123 JMenuItem _midpoint_root_item;
124 JMenuItem _taxcolor_item;
125 JMenuItem _confcolor_item;
126 JMenuItem _color_rank_jmi;
127 JMenuItem _infer_common_sn_names_item;
128 JMenuItem _collapse_species_specific_subtrees;
129 JMenuItem _collapse_below_threshold; //TODO implememt me
130 JMenuItem _obtain_detailed_taxonomic_information_jmi;
131 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
132 JMenuItem _obtain_uniprot_seq_information_jmi;
133 JMenuItem _move_node_names_to_tax_sn_jmi;
134 JMenuItem _move_node_names_to_seq_names_jmi;
135 JMenuItem _extract_tax_code_from_node_names_jmi;
137 JMenuItem _super_tiny_fonts_item;
138 JMenuItem _tiny_fonts_item;
139 JMenuItem _small_fonts_item;
140 JMenuItem _medium_fonts_item;
141 JMenuItem _large_fonts_item;
143 // _ screen and print
144 JMenuItem _choose_font_mi;
145 JMenuItem _switch_colors_mi;
146 JCheckBoxMenuItem _label_direction_cbmi;
148 JCheckBoxMenuItem _screen_antialias_cbmi;
149 JCheckBoxMenuItem _background_gradient_cbmi;
150 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
151 JRadioButtonMenuItem _uniform_cladograms_rbmi;
152 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
153 JCheckBoxMenuItem _show_branch_length_values_cbmi;
154 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
155 JCheckBoxMenuItem _show_overview_cbmi;
156 JCheckBoxMenuItem _show_domain_labels;
157 JCheckBoxMenuItem _abbreviate_scientific_names;
158 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
159 JMenuItem _overview_placment_mi;
160 JMenuItem _choose_minimal_confidence_mi;
161 JCheckBoxMenuItem _show_default_node_shapes_cbmi;
162 JMenuItem _cycle_node_shape_mi;
163 JMenuItem _cycle_node_fill_mi;
164 JMenuItem _choose_node_size_mi;
165 JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
166 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
168 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
169 JCheckBoxMenuItem _antialias_print_cbmi;
170 JCheckBoxMenuItem _print_black_and_white_cbmi;
171 JCheckBoxMenuItem _print_using_actual_size_cbmi;
172 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
173 JMenuItem _print_size_mi;
174 JMenuItem _choose_pdf_width_mi;
176 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
177 JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
178 JCheckBoxMenuItem _replace_underscores_cbmi;
179 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
180 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
182 JCheckBoxMenuItem _search_case_senstive_cbmi;
183 JCheckBoxMenuItem _search_whole_words_only_cbmi;
184 JCheckBoxMenuItem _inverse_search_result_cbmi;
187 JCheckBoxMenuItem _rectangular_type_cbmi;
188 JCheckBoxMenuItem _triangular_type_cbmi;
189 JCheckBoxMenuItem _curved_type_cbmi;
190 JCheckBoxMenuItem _convex_type_cbmi;
191 JCheckBoxMenuItem _euro_type_cbmi;
192 JCheckBoxMenuItem _rounded_type_cbmi;
193 JCheckBoxMenuItem _unrooted_type_cbmi;
194 JCheckBoxMenuItem _circular_type_cbmi;
195 // view as text menu:
196 JMenuItem _view_as_NH_item;
197 JMenuItem _view_as_NHX_item;
198 JMenuItem _view_as_XML_item;
199 JMenuItem _view_as_nexus_item;
200 JMenuItem _display_basic_information_item;
202 JMenuItem _about_item;
203 JMenuItem _help_item;
204 JMenuItem _website_item;
205 JMenuItem _phyloxml_website_item;
206 JMenuItem _phyloxml_ref_item;
207 JMenuItem _aptx_ref_item;
210 // Handy pointers to child components:
211 MainPanel _mainpanel;
212 Container _contentpane;
213 TextFrame _textframe;
214 Configuration _configuration;
215 JMenuItem _remove_branch_color_item;
217 final ProcessPool _process_pool;
220 _process_pool = ProcessPool.createInstance();
223 public ProcessPool getProcessPool() {
224 return _process_pool;
230 public void actionPerformed( final ActionEvent e ) {
231 final Object o = e.getSource();
232 boolean is_applet = false;
233 JApplet applet = null;
234 if ( getCurrentTreePanel() != null ) {
235 is_applet = getCurrentTreePanel().isApplet();
237 applet = getCurrentTreePanel().obtainApplet();
240 if ( o == _open_url_item ) {
241 readPhylogeniesFromURL();
243 else if ( o == _exit_item ) {
246 else if ( o == _taxcolor_item ) {
249 else if ( o == _confcolor_item ) {
252 else if ( o == _color_rank_jmi ) {
255 else if ( o == _infer_common_sn_names_item ) {
256 if ( isSubtreeDisplayed() ) {
259 if ( getCurrentTreePanel() != null ) {
260 getCurrentTreePanel().inferCommonPartOfScientificNames();
263 else if ( o == _collapse_species_specific_subtrees ) {
264 if ( isSubtreeDisplayed() ) {
267 if ( getCurrentTreePanel() != null ) {
268 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
271 else if ( o == _remove_branch_color_item ) {
272 if ( isSubtreeDisplayed() ) {
275 removeBranchColors();
277 else if ( o == _midpoint_root_item ) {
278 if ( isSubtreeDisplayed() ) {
283 else if ( o == _switch_colors_mi ) {
286 else if ( o == _display_basic_information_item ) {
287 displayBasicInformation();
289 else if ( o == _view_as_NH_item ) {
292 else if ( o == _view_as_NHX_item ) {
295 else if ( o == _view_as_XML_item ) {
298 else if ( o == _view_as_nexus_item ) {
301 else if ( o == _super_tiny_fonts_item ) {
302 if ( getCurrentTreePanel() != null ) {
303 getCurrentTreePanel().setSuperTinyFonts();
304 getCurrentTreePanel().repaint();
307 else if ( o == _tiny_fonts_item ) {
308 if ( getCurrentTreePanel() != null ) {
309 getCurrentTreePanel().setTinyFonts();
310 getCurrentTreePanel().repaint();
313 else if ( o == _small_fonts_item ) {
314 if ( getCurrentTreePanel() != null ) {
315 getCurrentTreePanel().setSmallFonts();
316 getCurrentTreePanel().repaint();
319 else if ( o == _medium_fonts_item ) {
320 if ( getCurrentTreePanel() != null ) {
321 getCurrentTreePanel().setMediumFonts();
322 getCurrentTreePanel().repaint();
325 else if ( o == _large_fonts_item ) {
326 if ( getCurrentTreePanel() != null ) {
327 getCurrentTreePanel().setLargeFonts();
328 getCurrentTreePanel().repaint();
331 else if ( o == _choose_font_mi ) {
334 else if ( o == _choose_minimal_confidence_mi ) {
335 chooseMinimalConfidence();
337 else if ( o == _choose_node_size_mi ) {
338 chooseNodeSize( getOptions(), this );
340 else if ( o == _overview_placment_mi ) {
341 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
343 else if ( o == _cycle_node_fill_mi ) {
344 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
346 else if ( o == _cycle_node_shape_mi ) {
347 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
349 else if ( o == _screen_antialias_cbmi ) {
350 updateOptions( getOptions() );
351 updateScreenTextAntialias( getMainPanel().getTreePanels() );
353 else if ( o == _background_gradient_cbmi ) {
354 updateOptions( getOptions() );
356 else if ( o == _show_domain_labels ) {
357 updateOptions( getOptions() );
359 else if ( o == _abbreviate_scientific_names ) {
360 updateOptions( getOptions() );
362 else if ( o == _color_labels_same_as_parent_branch ) {
363 updateOptions( getOptions() );
365 else if ( o == _show_default_node_shapes_cbmi ) {
366 updateOptions( getOptions() );
368 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
369 updateOptions( getOptions() );
371 else if ( o == _non_lined_up_cladograms_rbmi ) {
372 updateOptions( getOptions() );
375 else if ( o == _uniform_cladograms_rbmi ) {
376 updateOptions( getOptions() );
379 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
380 updateOptions( getOptions() );
383 else if ( o == _search_case_senstive_cbmi ) {
384 updateOptions( getOptions() );
385 getMainPanel().getControlPanel().search();
387 else if ( o == _search_whole_words_only_cbmi ) {
388 updateOptions( getOptions() );
389 getMainPanel().getControlPanel().search();
391 else if ( o == _inverse_search_result_cbmi ) {
392 updateOptions( getOptions() );
393 getMainPanel().getControlPanel().search();
395 else if ( o == _show_scale_cbmi ) {
396 updateOptions( getOptions() );
398 else if ( o == _show_branch_length_values_cbmi ) {
399 updateOptions( getOptions() );
401 else if ( o == _show_confidence_stddev_cbmi ) {
402 updateOptions( getOptions() );
404 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
405 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
406 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
408 updateOptions( getOptions() );
410 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
411 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
412 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
414 updateOptions( getOptions() );
416 else if ( o == _label_direction_cbmi ) {
417 updateOptions( getOptions() );
419 else if ( o == _show_overview_cbmi ) {
420 updateOptions( getOptions() );
421 if ( getCurrentTreePanel() != null ) {
422 getCurrentTreePanel().updateOvSizes();
425 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
426 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
427 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
430 else if ( o == _about_item ) {
433 else if ( o == _help_item ) {
434 help( getConfiguration().getWebLinks() );
436 else if ( o == _website_item ) {
438 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
440 catch ( final IOException e1 ) {
441 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
444 else if ( o == _phyloxml_website_item ) {
446 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
448 catch ( final IOException e1 ) {
449 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
452 else if ( o == _aptx_ref_item ) {
454 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
456 catch ( final IOException e1 ) {
457 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
460 else if ( o == _phyloxml_ref_item ) {
462 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
464 catch ( final IOException e1 ) {
465 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
469 if ( _load_phylogeny_from_webservice_menu_items != null ) {
470 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
471 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
472 readPhylogeniesFromWebservice( i );
477 _contentpane.repaint();
480 boolean isSubtreeDisplayed() {
481 if ( getCurrentTreePanel() != null ) {
482 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
484 .showMessageDialog( this,
485 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
486 "Operation can not be exectuted on a sub-tree",
487 JOptionPane.WARNING_MESSAGE );
494 void activateSaveAllIfNeeded() {
495 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
496 _save_all_item.setEnabled( true );
499 _save_all_item.setEnabled( false );
503 void buildFileMenu() {
504 _file_jmenu = createMenu( "File", getConfiguration() );
505 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
506 _file_jmenu.addSeparator();
507 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
508 customizeJMenuItem( _open_url_item );
509 customizeJMenuItem( _exit_item );
510 _jmenubar.add( _file_jmenu );
513 void buildFontSizeMenu() {
514 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
515 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
516 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
517 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
518 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
519 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
520 customizeJMenuItem( _super_tiny_fonts_item );
521 customizeJMenuItem( _tiny_fonts_item );
522 customizeJMenuItem( _small_fonts_item );
523 customizeJMenuItem( _medium_fonts_item );
524 customizeJMenuItem( _large_fonts_item );
525 _jmenubar.add( _font_size_menu );
528 void buildHelpMenu() {
529 _help_jmenu = createMenu( "Help", getConfiguration() );
530 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
531 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
532 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
533 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
534 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
535 _help_jmenu.addSeparator();
536 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
537 customizeJMenuItem( _help_item );
538 customizeJMenuItem( _website_item );
539 customizeJMenuItem( _phyloxml_website_item );
540 customizeJMenuItem( _aptx_ref_item );
541 customizeJMenuItem( _phyloxml_ref_item );
542 customizeJMenuItem( _about_item );
543 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
544 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
545 _jmenubar.add( _help_jmenu );
548 public synchronized void updateProcessMenu() {
549 System.out.println( "pool size " + _process_pool.size() );
550 if ( _process_pool.size() > 0 ) {
551 if ( _process_menu == null ) {
552 _process_menu = createMenu( "", getConfiguration() );
553 _process_menu.setForeground( Color.RED );
555 _process_menu.removeAll();
556 final String text = "processes running: " + _process_pool.size();
557 _process_menu.setText( text );
558 _jmenubar.add( _process_menu );
559 for( int i = 0; i < _process_pool.size(); ++i ) {
560 final ProcessRunning p = _process_pool.getProcessByIndex( i );
561 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
565 if ( _process_menu != null ) {
566 _process_menu.removeAll();
567 _jmenubar.remove( _process_menu );
570 _jmenubar.validate();
573 // _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
574 // _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
575 // _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
576 // _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
577 // _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
578 // _help_jmenu.addSeparator();
579 // _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
580 // customizeJMenuItem( _help_item );
581 // customizeJMenuItem( _website_item );
582 // customizeJMenuItem( _phyloxml_website_item );
583 // customizeJMenuItem( _aptx_ref_item );
584 // customizeJMenuItem( _phyloxml_ref_item );
585 // customizeJMenuItem( _about_item );
586 // _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
587 // _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
588 // _jmenubar.add( _help_jmenu );
591 void buildTypeMenu() {
592 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
593 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
594 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
595 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
596 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
597 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
598 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
599 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
600 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
601 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
602 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
603 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
604 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
605 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
606 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
607 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
608 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
609 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
610 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
611 initializeTypeMenu( getOptions() );
612 _jmenubar.add( _type_menu );
615 void buildViewMenu() {
616 _view_jmenu = createMenu( "View", getConfiguration() );
617 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
618 _view_jmenu.addSeparator();
619 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
620 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
621 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
622 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
623 customizeJMenuItem( _display_basic_information_item );
624 customizeJMenuItem( _view_as_NH_item );
625 customizeJMenuItem( _view_as_NHX_item );
626 customizeJMenuItem( _view_as_XML_item );
627 customizeJMenuItem( _view_as_nexus_item );
628 _jmenubar.add( _view_jmenu );
631 private void chooseFont() {
632 final FontChooser fc = new FontChooser();
633 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
634 fc.showDialog( this, "Select the Base Font" );
635 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
638 private void chooseMinimalConfidence() {
639 final String s = ( String ) JOptionPane
640 .showInputDialog( this,
641 "Please enter the minimum for confidence values to be displayed.\n"
642 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
643 "Minimal Confidence Value",
644 JOptionPane.QUESTION_MESSAGE,
647 getOptions().getMinConfidenceValue() );
648 if ( !ForesterUtil.isEmpty( s ) ) {
649 boolean success = true;
651 final String m_str = s.trim();
652 if ( !ForesterUtil.isEmpty( m_str ) ) {
654 m = Double.parseDouble( m_str );
656 catch ( final Exception ex ) {
663 if ( success && ( m >= 0.0 ) ) {
664 getOptions().setMinConfidenceValue( m );
669 static void chooseNodeSize( final Options options, final Component parent ) {
670 final String s = ( String ) JOptionPane.showInputDialog( parent,
671 "Please enter the default size for node shapes.\n"
673 + options.getDefaultNodeShapeSize() + "]\n",
675 JOptionPane.QUESTION_MESSAGE,
678 options.getDefaultNodeShapeSize() );
679 if ( !ForesterUtil.isEmpty( s ) ) {
680 boolean success = true;
682 final String m_str = s.trim();
683 if ( !ForesterUtil.isEmpty( m_str ) ) {
685 m = Double.parseDouble( m_str );
687 catch ( final Exception ex ) {
694 if ( success && ( m >= 0.0 ) ) {
695 final short size = ForesterUtil.roundToShort( m );
697 options.setDefaultNodeShapeSize( size );
705 if ( _mainpanel != null ) {
706 _mainpanel.terminate();
708 if ( _contentpane != null ) {
709 _contentpane.removeAll();
716 if ( _mainpanel.getCurrentTreePanel() != null ) {
717 _mainpanel.getCurrentTreePanel().confColor();
722 if ( _mainpanel.getCurrentTreePanel() != null ) {
723 final String[] ranks = AptxUtil.getAllPossibleRanks();
724 final String rank = ( String ) JOptionPane
725 .showInputDialog( this,
726 "What rank should the colorization be based on",
728 JOptionPane.QUESTION_MESSAGE,
732 if ( !ForesterUtil.isEmpty( rank ) ) {
733 _mainpanel.getCurrentTreePanel().colorRank( rank );
738 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
739 if ( item != null ) {
740 item.setFont( MainFrame.menu_font );
741 if ( !getConfiguration().isUseNativeUI() ) {
742 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
743 item.setForeground( getConfiguration().getGuiMenuTextColor() );
745 item.setSelected( is_selected );
746 item.addActionListener( this );
750 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
752 jmi.setFont( MainFrame.menu_font );
753 if ( !getConfiguration().isUseNativeUI() ) {
754 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
755 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
757 jmi.addActionListener( this );
762 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
763 if ( item != null ) {
764 item.setFont( MainFrame.menu_font );
765 if ( !getConfiguration().isUseNativeUI() ) {
766 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
767 item.setForeground( getConfiguration().getGuiMenuTextColor() );
769 item.setSelected( is_selected );
770 item.addActionListener( this );
774 void exceptionOccuredDuringOpenFile( final Exception e ) {
776 _mainpanel.getCurrentTreePanel().setArrowCursor();
778 catch ( final Exception ex ) {
781 JOptionPane.showMessageDialog( this,
782 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
783 "Error during File|Open",
784 JOptionPane.ERROR_MESSAGE );
787 void exceptionOccuredDuringSaveAs( final Exception e ) {
789 _mainpanel.getCurrentTreePanel().setArrowCursor();
791 catch ( final Exception ex ) {
794 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
797 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
798 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
799 JOptionPane.showMessageDialog( this,
800 "Gene tree and species tree have no species in common.",
802 JOptionPane.ERROR_MESSAGE );
805 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
806 JOptionPane.showMessageDialog( this,
807 "Gene tree and species tree have only one species in common.",
809 JOptionPane.ERROR_MESSAGE );
817 public Configuration getConfiguration() {
818 return _configuration;
821 TreePanel getCurrentTreePanel() {
822 return getMainPanel().getCurrentTreePanel();
825 JMenu getHelpMenu() {
829 JCheckBoxMenuItem getlabelDirectionCbmi() {
830 return _label_direction_cbmi;
833 public MainPanel getMainPanel() {
837 JMenuBar getMenuBarOfMainFrame() {
841 public Options getOptions() {
845 void initializeTypeMenu( final Options options ) {
846 setTypeMenuToAllUnselected();
847 switch ( options.getPhylogenyGraphicsType() ) {
849 _convex_type_cbmi.setSelected( true );
852 _curved_type_cbmi.setSelected( true );
855 _euro_type_cbmi.setSelected( true );
858 _rounded_type_cbmi.setSelected( true );
861 _triangular_type_cbmi.setSelected( true );
864 _unrooted_type_cbmi.setSelected( true );
867 _circular_type_cbmi.setSelected( true );
870 _rectangular_type_cbmi.setSelected( true );
875 void midpointRoot() {
876 if ( _mainpanel.getCurrentTreePanel() != null ) {
877 _mainpanel.getCurrentTreePanel().midpointRoot();
881 abstract void readPhylogeniesFromURL();
883 void readPhylogeniesFromWebservice( final int i ) {
884 final UrlTreeReader reader = new UrlTreeReader( this, i );
885 new Thread( reader ).start();
888 private void removeBranchColors() {
889 if ( getMainPanel().getCurrentPhylogeny() != null ) {
890 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
894 void removeTextFrame() {
895 if ( _textframe != null ) {
901 void setConfiguration( final Configuration configuration ) {
902 _configuration = configuration;
905 void setOptions( final Options options ) {
909 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
910 setTypeMenuToAllUnselected();
913 _circular_type_cbmi.setSelected( true );
916 _convex_type_cbmi.setSelected( true );
919 _curved_type_cbmi.setSelected( true );
922 _euro_type_cbmi.setSelected( true );
925 _rounded_type_cbmi.setSelected( true );
928 _rectangular_type_cbmi.setSelected( true );
931 _triangular_type_cbmi.setSelected( true );
934 _unrooted_type_cbmi.setSelected( true );
937 throw new IllegalArgumentException( "unknown type: " + type );
941 void setTypeMenuToAllUnselected() {
942 _convex_type_cbmi.setSelected( false );
943 _curved_type_cbmi.setSelected( false );
944 _euro_type_cbmi.setSelected( false );
945 _rounded_type_cbmi.setSelected( false );
946 _triangular_type_cbmi.setSelected( false );
947 _rectangular_type_cbmi.setSelected( false );
948 _unrooted_type_cbmi.setSelected( false );
949 _circular_type_cbmi.setSelected( false );
952 public void showWhole() {
953 _mainpanel.getControlPanel().showWhole();
956 void switchColors() {
957 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
958 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
959 csc.setVisible( true );
963 if ( _mainpanel.getCurrentTreePanel() != null ) {
964 _mainpanel.getCurrentTreePanel().taxColor();
968 void typeChanged( final Object o ) {
969 updateTypeCheckboxes( getOptions(), o );
970 updateOptions( getOptions() );
971 if ( getCurrentTreePanel() != null ) {
972 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
973 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
974 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
975 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
976 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
977 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
978 getCurrentTreePanel().getControlPanel().showWhole();
980 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
981 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
984 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
986 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
987 updateScreenTextAntialias( getMainPanel().getTreePanels() );
988 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
989 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
990 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
993 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
999 void updateOptions( final Options options ) {
1000 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1001 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1002 && _background_gradient_cbmi.isSelected() );
1003 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1004 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1005 && _abbreviate_scientific_names.isSelected() );
1006 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1007 && _color_labels_same_as_parent_branch.isSelected() );
1008 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1009 && _show_default_node_shapes_cbmi.isSelected() );
1010 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1011 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1012 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1013 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1015 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1016 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1018 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1019 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1021 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1022 && _search_case_senstive_cbmi.isSelected() );
1023 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1024 options.setShowScale( _show_scale_cbmi.isSelected() );
1026 if ( _label_direction_cbmi != null ) {
1027 if ( _label_direction_cbmi.isSelected() ) {
1028 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1031 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1034 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1035 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1036 && _show_confidence_stddev_cbmi.isSelected() );
1037 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1038 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1040 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1041 && ( _print_using_actual_size_cbmi.isSelected() ) );
1042 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1043 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1044 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1045 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1046 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1047 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1049 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1050 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1051 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1054 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1056 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1057 && _print_black_and_white_cbmi.isSelected() );
1058 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1059 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1060 options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
1061 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
1062 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1063 && _replace_underscores_cbmi.isSelected() );
1064 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1065 && _search_whole_words_only_cbmi.isSelected() );
1066 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1067 && _inverse_search_result_cbmi.isSelected() );
1068 if ( _graphics_export_visible_only_cbmi != null ) {
1069 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1070 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1071 _graphics_export_using_actual_size_cbmi.setSelected( true );
1072 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1075 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1078 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1079 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1081 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1082 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1084 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1085 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1087 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1088 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1090 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1091 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1093 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1094 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1096 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1097 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1099 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1100 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1104 void updateTypeCheckboxes( final Options options, final Object o ) {
1105 setTypeMenuToAllUnselected();
1106 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1109 void displayBasicInformation() {
1110 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1113 _textframe = TextFrame.instantiate( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
1116 void viewAsNexus() {
1118 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1119 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
1122 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions()
1123 .getNhConversionSupportValueStyle() ) );
1128 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1129 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
1132 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny()
1133 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) );
1138 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1139 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1142 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
1147 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
1148 && ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
1149 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
1154 * Display the about box.
1156 static void about() {
1157 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1158 about.append( "Copyright (C) 2007-2011 Christian Zmasek\n" );
1159 about.append( "All Rights Reserved\n" );
1160 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1161 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1162 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1163 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1164 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1165 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1167 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1168 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1169 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1170 + ForesterUtil.OS_VERSION + "]\n" );
1172 final Runtime rt = java.lang.Runtime.getRuntime();
1173 final long free_memory = rt.freeMemory() / 1000000;
1174 final long total_memory = rt.totalMemory() / 1000000;
1175 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1176 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1177 about.append( "References:\n" );
1178 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1179 about.append( "For more information & download:\n" );
1180 about.append( Constants.APTX_WEB_SITE + "\n" );
1181 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1182 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1185 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1186 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1189 static JMenu createMenu( final String title, final Configuration conf ) {
1190 final JMenu jmenu = new JMenu( title );
1191 if ( !conf.isUseNativeUI() ) {
1192 jmenu.setFont( MainFrame.menu_font );
1193 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1194 jmenu.setForeground( conf.getGuiMenuTextColor() );
1199 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1200 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1201 if ( !configuration.isUseNativeUI() ) {
1202 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1203 label.setForeground( configuration.getGuiMenuTextColor() );
1204 label.setOpaque( true );
1206 label.setSelected( false );
1207 label.setEnabled( false );
1211 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1212 switch ( op.getOvPlacement() ) {
1214 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1217 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1220 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1223 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1226 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1228 if ( tree_panel != null ) {
1229 tree_panel.updateOvSettings();
1233 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1234 switch ( op.getDefaultNodeFill() ) {
1236 op.setDefaultNodeFill( NodeFill.SOLID );
1239 op.setDefaultNodeFill( NodeFill.GRADIENT );
1242 op.setDefaultNodeFill( NodeFill.NONE );
1245 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1249 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1250 switch ( op.getDefaultNodeShape() ) {
1252 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1255 op.setDefaultNodeShape( NodeShape.CIRCLE );
1258 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1262 static void help( final Map<String, WebLink> weblinks ) {
1263 final StringBuilder sb = new StringBuilder();
1264 sb.append( "Display options\n" );
1265 sb.append( "-------------------\n" );
1266 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1267 sb.append( "Clickable tree nodes\n" );
1268 sb.append( "--------------------\n" );
1269 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1270 sb.append( "or by right clicking:\n" );
1271 sb.append( "o Display Node Data -- display information for a node\n" );
1272 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1273 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1274 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1275 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1276 sb.append( "o Colorize Subtree -- color a subtree\n" );
1277 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1278 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1279 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1280 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1281 sb.append( "Zooming\n" );
1282 sb.append( "---------\n" );
1283 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1284 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1285 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1286 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1287 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1288 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1289 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1290 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1291 sb.append( "Quick tree manipulation:\n" );
1292 sb.append( "------------------------\n" );
1293 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1294 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1295 sb.append( "Memory problems (Java heap space error)\n" );
1296 sb.append( "---------------------------------------\n" );
1297 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1298 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1299 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1300 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1301 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1302 sb.append( "Active web links\n" );
1303 sb.append( "--------------------\n" );
1304 for( final String key : weblinks.keySet() ) {
1305 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1308 // + "General remarks\n"
1309 // + "---------------\n"
1311 // "o The application version permits copying to the clipboard \n"
1313 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1315 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1316 // + " but not any of its parent tree(s).\n"
1318 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1320 // " are likely to be bootstrap values instead of branch length values.\n\n"
1322 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1324 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1326 // " a species: either directly through the \"Species\" field, or the species\n"
1328 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1330 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1332 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1334 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1336 // "o !External nodes of the gene tree associated with species not present in\n"
1338 // " the species tree are REMOVED prior to SDI execution!\n"
1340 // "o Both the gene tree and the species tree must be completely binary.\n"
1342 // "o Duplications and speciations are a function of the position of the root.\n"
1344 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1345 // + " incorrect and need to be inferred again\n"
1347 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1349 sb.append( "phyloXML\n" );
1350 sb.append( "-------------------\n" );
1351 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1352 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1353 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1355 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1356 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1357 TextFrame.instantiate( sb.toString() );
1360 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1361 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1362 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1365 mi.setText( "Cycle Overview Placement..." );
1369 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1370 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1371 mi.setText( "Cycle Node Shape Fill Type... (current: "
1372 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1375 mi.setText( "Cycle Node Shape Fill Type..." );
1379 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1380 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1381 mi.setText( "Cycle Node Shape Fill Type... (current: "
1382 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1385 mi.setText( "Cycle Node Shape Fill Type..." );
1389 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1390 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1391 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1394 mi.setText( "Select Colors..." );
1398 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1399 mi.setText( "Select Font... (current: " + font_desc + ")" );
1402 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1403 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1404 mi.setEnabled( true );
1406 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1407 mi.setEnabled( true );
1410 mi.setEnabled( false );
1412 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1415 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1416 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1419 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1420 final JCheckBoxMenuItem scale,
1421 final JCheckBoxMenuItem branch_lengths,
1422 final JRadioButtonMenuItem non_lined_up,
1423 final JRadioButtonMenuItem uniform_clado,
1424 final JRadioButtonMenuItem nonuniform_clado,
1425 final JCheckBoxMenuItem label_direction_cbmi ) {
1426 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1427 final ControlPanel control = main_panel.getControlPanel();
1428 final Options options = main_panel.getOptions();
1429 scale.setSelected( options.isShowScale() );
1430 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1431 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1432 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1433 scale.setSelected( false );
1434 scale.setEnabled( false );
1435 branch_lengths.setSelected( false );
1436 branch_lengths.setEnabled( false );
1438 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1439 scale.setSelected( false );
1440 scale.setEnabled( false );
1441 branch_lengths.setEnabled( true );
1444 scale.setEnabled( true );
1445 branch_lengths.setEnabled( true );
1447 if ( ( tree_panel != null )
1448 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1449 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1450 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1451 branch_lengths.setSelected( false );
1452 branch_lengths.setEnabled( false );
1454 if ( tree_panel != null ) {
1455 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1456 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1457 non_lined_up.setEnabled( false );
1458 uniform_clado.setEnabled( false );
1459 nonuniform_clado.setEnabled( false );
1462 non_lined_up.setEnabled( true );
1463 uniform_clado.setEnabled( true );
1464 nonuniform_clado.setEnabled( true );
1468 if ( ( tree_panel != null )
1469 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1470 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1471 branch_lengths.setSelected( false );
1472 branch_lengths.setEnabled( false );
1474 if ( ( tree_panel != null )
1475 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1476 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1477 non_lined_up.setEnabled( false );
1480 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1481 non_lined_up.setEnabled( true );
1484 label_direction_cbmi.setEnabled( true );
1485 if ( tree_panel != null ) {
1486 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1487 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1488 label_direction_cbmi.setEnabled( false );
1490 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1491 scale.setSelected( false );
1492 scale.setEnabled( false );
1497 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1498 for( final TreePanel tree_panel : treepanels ) {
1499 tree_panel.setTextAntialias();