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.ProcessPool;
52 import org.forester.archaeopteryx.tools.ProcessRunning;
53 import org.forester.phylogeny.Phylogeny;
54 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
55 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
56 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
57 import org.forester.util.ForesterConstants;
58 import org.forester.util.ForesterUtil;
60 public abstract class MainFrame extends JFrame implements ActionListener {
62 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
63 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
64 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
65 private static final long serialVersionUID = 3655000897845508358L;
66 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
69 static final String TYPE_MENU_HEADER = "Type";
70 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
71 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
72 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
73 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
74 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
75 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
76 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
77 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
78 static final String OPTIONS_HEADER = "Options";
79 static final String SEARCH_SUBHEADER = "Search:";
80 static final String DISPLAY_SUBHEADER = "Display:";
81 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
82 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
83 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
84 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
85 static final String DISPLAY_SCALE_LABEL = "Display Scale";
86 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
87 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
88 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
89 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
90 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
91 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
92 static final String BG_GRAD_LABEL = "Background Color Gradient";
93 static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
94 static final String SHOW_OVERVIEW_LABEL = "Show Overview";
95 static final String FONT_SIZE_MENU_LABEL = "Font Size";
96 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
97 static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
98 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";
99 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
100 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
101 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
102 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
103 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
104 static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
105 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
106 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
111 JMenu _options_jmenu;
112 JMenu _font_size_menu;
114 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
116 JMenuItem _open_item;
117 JMenuItem _open_url_item;
118 JMenuItem _save_item;
119 JMenuItem _save_all_item;
120 JMenuItem _close_item;
121 JMenuItem _exit_item;
124 JMenuItem _midpoint_root_item;
125 JMenuItem _taxcolor_item;
126 JMenuItem _confcolor_item;
127 JMenuItem _color_rank_jmi;
128 JMenuItem _infer_common_sn_names_item;
129 JMenuItem _collapse_species_specific_subtrees;
130 JMenuItem _collapse_below_threshold; //TODO implememt me
131 JMenuItem _obtain_detailed_taxonomic_information_jmi;
132 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
133 JMenuItem _obtain_uniprot_seq_information_jmi;
134 JMenuItem _move_node_names_to_tax_sn_jmi;
135 JMenuItem _move_node_names_to_seq_names_jmi;
136 JMenuItem _extract_tax_code_from_node_names_jmi;
138 JMenuItem _super_tiny_fonts_item;
139 JMenuItem _tiny_fonts_item;
140 JMenuItem _small_fonts_item;
141 JMenuItem _medium_fonts_item;
142 JMenuItem _large_fonts_item;
144 // _ screen and print
145 JMenuItem _choose_font_mi;
146 JMenuItem _switch_colors_mi;
147 JCheckBoxMenuItem _label_direction_cbmi;
149 JCheckBoxMenuItem _screen_antialias_cbmi;
150 JCheckBoxMenuItem _background_gradient_cbmi;
151 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
152 JRadioButtonMenuItem _uniform_cladograms_rbmi;
153 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
154 JCheckBoxMenuItem _show_branch_length_values_cbmi;
155 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
156 JCheckBoxMenuItem _show_overview_cbmi;
157 JCheckBoxMenuItem _show_domain_labels;
158 JCheckBoxMenuItem _abbreviate_scientific_names;
159 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
160 JMenuItem _overview_placment_mi;
161 JMenuItem _choose_minimal_confidence_mi;
162 JCheckBoxMenuItem _show_default_node_shapes_cbmi;
163 JMenuItem _cycle_node_shape_mi;
164 JMenuItem _cycle_node_fill_mi;
165 JMenuItem _choose_node_size_mi;
166 JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
167 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
169 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
170 JCheckBoxMenuItem _antialias_print_cbmi;
171 JCheckBoxMenuItem _print_black_and_white_cbmi;
172 JCheckBoxMenuItem _print_using_actual_size_cbmi;
173 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
174 JMenuItem _print_size_mi;
175 JMenuItem _choose_pdf_width_mi;
177 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
178 JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
179 JCheckBoxMenuItem _replace_underscores_cbmi;
180 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
181 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
183 JCheckBoxMenuItem _search_case_senstive_cbmi;
184 JCheckBoxMenuItem _search_whole_words_only_cbmi;
185 JCheckBoxMenuItem _inverse_search_result_cbmi;
188 JCheckBoxMenuItem _rectangular_type_cbmi;
189 JCheckBoxMenuItem _triangular_type_cbmi;
190 JCheckBoxMenuItem _curved_type_cbmi;
191 JCheckBoxMenuItem _convex_type_cbmi;
192 JCheckBoxMenuItem _euro_type_cbmi;
193 JCheckBoxMenuItem _rounded_type_cbmi;
194 JCheckBoxMenuItem _unrooted_type_cbmi;
195 JCheckBoxMenuItem _circular_type_cbmi;
196 // view as text menu:
197 JMenuItem _view_as_NH_item;
198 JMenuItem _view_as_NHX_item;
199 JMenuItem _view_as_XML_item;
200 JMenuItem _view_as_nexus_item;
201 JMenuItem _display_basic_information_item;
203 JMenuItem _about_item;
204 JMenuItem _help_item;
205 JMenuItem _website_item;
206 JMenuItem _phyloxml_website_item;
207 JMenuItem _phyloxml_ref_item;
208 JMenuItem _aptx_ref_item;
211 // Handy pointers to child components:
212 MainPanel _mainpanel;
213 Container _contentpane;
214 TextFrame _textframe;
215 Configuration _configuration;
216 JMenuItem _remove_branch_color_item;
218 final ProcessPool _process_pool;
221 _process_pool = ProcessPool.createInstance();
224 public ProcessPool getProcessPool() {
225 return _process_pool;
231 public void actionPerformed( final ActionEvent e ) {
232 final Object o = e.getSource();
233 boolean is_applet = false;
234 JApplet applet = null;
235 if ( getCurrentTreePanel() != null ) {
236 is_applet = getCurrentTreePanel().isApplet();
238 applet = getCurrentTreePanel().obtainApplet();
241 if ( o == _open_url_item ) {
242 readPhylogeniesFromURL();
244 else if ( o == _exit_item ) {
247 else if ( o == _taxcolor_item ) {
250 else if ( o == _confcolor_item ) {
253 else if ( o == _color_rank_jmi ) {
256 else if ( o == _infer_common_sn_names_item ) {
257 if ( isSubtreeDisplayed() ) {
260 if ( getCurrentTreePanel() != null ) {
261 getCurrentTreePanel().inferCommonPartOfScientificNames();
264 else if ( o == _collapse_species_specific_subtrees ) {
265 if ( isSubtreeDisplayed() ) {
268 if ( getCurrentTreePanel() != null ) {
269 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
272 else if ( o == _remove_branch_color_item ) {
273 if ( isSubtreeDisplayed() ) {
276 removeBranchColors();
278 else if ( o == _midpoint_root_item ) {
279 if ( isSubtreeDisplayed() ) {
284 else if ( o == _switch_colors_mi ) {
287 else if ( o == _display_basic_information_item ) {
288 displayBasicInformation();
290 else if ( o == _view_as_NH_item ) {
293 else if ( o == _view_as_NHX_item ) {
296 else if ( o == _view_as_XML_item ) {
299 else if ( o == _view_as_nexus_item ) {
302 else if ( o == _super_tiny_fonts_item ) {
303 if ( getCurrentTreePanel() != null ) {
304 getCurrentTreePanel().setSuperTinyFonts();
305 getCurrentTreePanel().repaint();
308 else if ( o == _tiny_fonts_item ) {
309 if ( getCurrentTreePanel() != null ) {
310 getCurrentTreePanel().setTinyFonts();
311 getCurrentTreePanel().repaint();
314 else if ( o == _small_fonts_item ) {
315 if ( getCurrentTreePanel() != null ) {
316 getCurrentTreePanel().setSmallFonts();
317 getCurrentTreePanel().repaint();
320 else if ( o == _medium_fonts_item ) {
321 if ( getCurrentTreePanel() != null ) {
322 getCurrentTreePanel().setMediumFonts();
323 getCurrentTreePanel().repaint();
326 else if ( o == _large_fonts_item ) {
327 if ( getCurrentTreePanel() != null ) {
328 getCurrentTreePanel().setLargeFonts();
329 getCurrentTreePanel().repaint();
332 else if ( o == _choose_font_mi ) {
335 else if ( o == _choose_minimal_confidence_mi ) {
336 chooseMinimalConfidence();
338 else if ( o == _choose_node_size_mi ) {
339 chooseNodeSize( getOptions(), this );
341 else if ( o == _overview_placment_mi ) {
342 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
344 else if ( o == _cycle_node_fill_mi ) {
345 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
347 else if ( o == _cycle_node_shape_mi ) {
348 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
350 else if ( o == _screen_antialias_cbmi ) {
351 updateOptions( getOptions() );
352 updateScreenTextAntialias( getMainPanel().getTreePanels() );
354 else if ( o == _background_gradient_cbmi ) {
355 updateOptions( getOptions() );
357 else if ( o == _show_domain_labels ) {
358 updateOptions( getOptions() );
360 else if ( o == _abbreviate_scientific_names ) {
361 updateOptions( getOptions() );
363 else if ( o == _color_labels_same_as_parent_branch ) {
364 updateOptions( getOptions() );
366 else if ( o == _show_default_node_shapes_cbmi ) {
367 updateOptions( getOptions() );
369 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
370 updateOptions( getOptions() );
372 else if ( o == _non_lined_up_cladograms_rbmi ) {
373 updateOptions( getOptions() );
376 else if ( o == _uniform_cladograms_rbmi ) {
377 updateOptions( getOptions() );
380 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
381 updateOptions( getOptions() );
384 else if ( o == _search_case_senstive_cbmi ) {
385 updateOptions( getOptions() );
386 getMainPanel().getControlPanel().search();
388 else if ( o == _search_whole_words_only_cbmi ) {
389 updateOptions( getOptions() );
390 getMainPanel().getControlPanel().search();
392 else if ( o == _inverse_search_result_cbmi ) {
393 updateOptions( getOptions() );
394 getMainPanel().getControlPanel().search();
396 else if ( o == _show_scale_cbmi ) {
397 updateOptions( getOptions() );
399 else if ( o == _show_branch_length_values_cbmi ) {
400 updateOptions( getOptions() );
402 else if ( o == _show_confidence_stddev_cbmi ) {
403 updateOptions( getOptions() );
405 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
406 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
407 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
409 updateOptions( getOptions() );
411 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
412 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
413 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
415 updateOptions( getOptions() );
417 else if ( o == _label_direction_cbmi ) {
418 updateOptions( getOptions() );
420 else if ( o == _show_overview_cbmi ) {
421 updateOptions( getOptions() );
422 if ( getCurrentTreePanel() != null ) {
423 getCurrentTreePanel().updateOvSizes();
426 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
427 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
428 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
431 else if ( o == _about_item ) {
434 else if ( o == _help_item ) {
435 help( getConfiguration().getWebLinks() );
437 else if ( o == _website_item ) {
439 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
441 catch ( final IOException e1 ) {
442 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
445 else if ( o == _phyloxml_website_item ) {
447 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
449 catch ( final IOException e1 ) {
450 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
453 else if ( o == _aptx_ref_item ) {
455 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
457 catch ( final IOException e1 ) {
458 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
461 else if ( o == _phyloxml_ref_item ) {
463 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
465 catch ( final IOException e1 ) {
466 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
470 if ( _load_phylogeny_from_webservice_menu_items != null ) {
471 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
472 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
473 readPhylogeniesFromWebservice( i );
478 _contentpane.repaint();
481 boolean isSubtreeDisplayed() {
482 if ( getCurrentTreePanel() != null ) {
483 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
485 .showMessageDialog( this,
486 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
487 "Operation can not be exectuted on a sub-tree",
488 JOptionPane.WARNING_MESSAGE );
495 void activateSaveAllIfNeeded() {
496 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
497 _save_all_item.setEnabled( true );
500 _save_all_item.setEnabled( false );
504 void buildFileMenu() {
505 _file_jmenu = createMenu( "File", getConfiguration() );
506 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
507 _file_jmenu.addSeparator();
508 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
509 customizeJMenuItem( _open_url_item );
510 customizeJMenuItem( _exit_item );
511 _jmenubar.add( _file_jmenu );
514 void buildFontSizeMenu() {
515 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
516 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
517 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
518 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
519 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
520 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
521 customizeJMenuItem( _super_tiny_fonts_item );
522 customizeJMenuItem( _tiny_fonts_item );
523 customizeJMenuItem( _small_fonts_item );
524 customizeJMenuItem( _medium_fonts_item );
525 customizeJMenuItem( _large_fonts_item );
526 _jmenubar.add( _font_size_menu );
529 void buildHelpMenu() {
530 _help_jmenu = createMenu( "Help", getConfiguration() );
531 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
532 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
533 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
534 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
535 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
536 _help_jmenu.addSeparator();
537 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
538 customizeJMenuItem( _help_item );
539 customizeJMenuItem( _website_item );
540 customizeJMenuItem( _phyloxml_website_item );
541 customizeJMenuItem( _aptx_ref_item );
542 customizeJMenuItem( _phyloxml_ref_item );
543 customizeJMenuItem( _about_item );
544 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
545 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
546 _jmenubar.add( _help_jmenu );
549 public void updateProcessMenu() {
550 // In general Swing is not thread safe.
551 // See "Swing's Threading Policy".
552 SwingUtilities.invokeLater( new Runnable() {
555 doUpdateProcessMenu();
560 private void doUpdateProcessMenu() {
561 if ( _process_pool.size() > 0 ) {
562 if ( _process_menu == null ) {
563 _process_menu = createMenu( "", getConfiguration() );
564 _process_menu.setForeground( Color.RED );
566 _process_menu.removeAll();
567 final String text = "processes running: " + _process_pool.size();
568 _process_menu.setText( text );
569 _jmenubar.add( _process_menu );
570 for( int i = 0; i < _process_pool.size(); ++i ) {
571 final ProcessRunning p = _process_pool.getProcessByIndex( i );
572 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
576 if ( _process_menu != null ) {
577 _process_menu.removeAll();
578 _jmenubar.remove( _process_menu );
581 _jmenubar.validate();
586 void buildTypeMenu() {
587 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
588 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
589 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
590 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
591 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
592 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
593 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
594 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
595 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
596 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
597 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
598 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
599 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
600 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
601 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
602 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
603 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
604 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
605 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
606 initializeTypeMenu( getOptions() );
607 _jmenubar.add( _type_menu );
610 void buildViewMenu() {
611 _view_jmenu = createMenu( "View", getConfiguration() );
612 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
613 _view_jmenu.addSeparator();
614 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
615 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
616 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
617 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
618 customizeJMenuItem( _display_basic_information_item );
619 customizeJMenuItem( _view_as_NH_item );
620 customizeJMenuItem( _view_as_NHX_item );
621 customizeJMenuItem( _view_as_XML_item );
622 customizeJMenuItem( _view_as_nexus_item );
623 _jmenubar.add( _view_jmenu );
626 private void chooseFont() {
627 final FontChooser fc = new FontChooser();
628 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
629 fc.showDialog( this, "Select the Base Font" );
630 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
633 private void chooseMinimalConfidence() {
634 final String s = ( String ) JOptionPane
635 .showInputDialog( this,
636 "Please enter the minimum for confidence values to be displayed.\n"
637 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
638 "Minimal Confidence Value",
639 JOptionPane.QUESTION_MESSAGE,
642 getOptions().getMinConfidenceValue() );
643 if ( !ForesterUtil.isEmpty( s ) ) {
644 boolean success = true;
646 final String m_str = s.trim();
647 if ( !ForesterUtil.isEmpty( m_str ) ) {
649 m = Double.parseDouble( m_str );
651 catch ( final Exception ex ) {
658 if ( success && ( m >= 0.0 ) ) {
659 getOptions().setMinConfidenceValue( m );
664 static void chooseNodeSize( final Options options, final Component parent ) {
665 final String s = ( String ) JOptionPane.showInputDialog( parent,
666 "Please enter the default size for node shapes.\n"
668 + options.getDefaultNodeShapeSize() + "]\n",
670 JOptionPane.QUESTION_MESSAGE,
673 options.getDefaultNodeShapeSize() );
674 if ( !ForesterUtil.isEmpty( s ) ) {
675 boolean success = true;
677 final String m_str = s.trim();
678 if ( !ForesterUtil.isEmpty( m_str ) ) {
680 m = Double.parseDouble( m_str );
682 catch ( final Exception ex ) {
689 if ( success && ( m >= 0.0 ) ) {
690 final short size = ForesterUtil.roundToShort( m );
692 options.setDefaultNodeShapeSize( size );
700 if ( _mainpanel != null ) {
701 _mainpanel.terminate();
703 if ( _contentpane != null ) {
704 _contentpane.removeAll();
711 if ( _mainpanel.getCurrentTreePanel() != null ) {
712 _mainpanel.getCurrentTreePanel().confColor();
717 if ( _mainpanel.getCurrentTreePanel() != null ) {
718 final String[] ranks = AptxUtil.getAllPossibleRanks();
719 final String rank = ( String ) JOptionPane
720 .showInputDialog( this,
721 "What rank should the colorization be based on",
723 JOptionPane.QUESTION_MESSAGE,
727 if ( !ForesterUtil.isEmpty( rank ) ) {
728 _mainpanel.getCurrentTreePanel().colorRank( rank );
733 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
734 if ( item != null ) {
735 item.setFont( MainFrame.menu_font );
736 if ( !getConfiguration().isUseNativeUI() ) {
737 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
738 item.setForeground( getConfiguration().getGuiMenuTextColor() );
740 item.setSelected( is_selected );
741 item.addActionListener( this );
745 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
747 jmi.setFont( MainFrame.menu_font );
748 if ( !getConfiguration().isUseNativeUI() ) {
749 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
750 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
752 jmi.addActionListener( this );
757 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
758 if ( item != null ) {
759 item.setFont( MainFrame.menu_font );
760 if ( !getConfiguration().isUseNativeUI() ) {
761 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
762 item.setForeground( getConfiguration().getGuiMenuTextColor() );
764 item.setSelected( is_selected );
765 item.addActionListener( this );
769 void exceptionOccuredDuringOpenFile( final Exception e ) {
771 _mainpanel.getCurrentTreePanel().setArrowCursor();
773 catch ( final Exception ex ) {
776 JOptionPane.showMessageDialog( this,
777 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
778 "Error during File|Open",
779 JOptionPane.ERROR_MESSAGE );
782 void exceptionOccuredDuringSaveAs( final Exception e ) {
784 _mainpanel.getCurrentTreePanel().setArrowCursor();
786 catch ( final Exception ex ) {
789 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
792 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
793 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
794 JOptionPane.showMessageDialog( this,
795 "Gene tree and species tree have no species in common.",
797 JOptionPane.ERROR_MESSAGE );
800 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
801 JOptionPane.showMessageDialog( this,
802 "Gene tree and species tree have only one species in common.",
804 JOptionPane.ERROR_MESSAGE );
812 public Configuration getConfiguration() {
813 return _configuration;
816 TreePanel getCurrentTreePanel() {
817 return getMainPanel().getCurrentTreePanel();
820 JMenu getHelpMenu() {
824 JCheckBoxMenuItem getlabelDirectionCbmi() {
825 return _label_direction_cbmi;
828 public MainPanel getMainPanel() {
832 JMenuBar getMenuBarOfMainFrame() {
836 public Options getOptions() {
840 void initializeTypeMenu( final Options options ) {
841 setTypeMenuToAllUnselected();
842 switch ( options.getPhylogenyGraphicsType() ) {
844 _convex_type_cbmi.setSelected( true );
847 _curved_type_cbmi.setSelected( true );
850 _euro_type_cbmi.setSelected( true );
853 _rounded_type_cbmi.setSelected( true );
856 _triangular_type_cbmi.setSelected( true );
859 _unrooted_type_cbmi.setSelected( true );
862 _circular_type_cbmi.setSelected( true );
865 _rectangular_type_cbmi.setSelected( true );
870 void midpointRoot() {
871 if ( _mainpanel.getCurrentTreePanel() != null ) {
872 _mainpanel.getCurrentTreePanel().midpointRoot();
876 abstract void readPhylogeniesFromURL();
878 void readPhylogeniesFromWebservice( final int i ) {
879 final UrlTreeReader reader = new UrlTreeReader( this, i );
880 new Thread( reader ).start();
883 private void removeBranchColors() {
884 if ( getMainPanel().getCurrentPhylogeny() != null ) {
885 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
889 void removeTextFrame() {
890 if ( _textframe != null ) {
896 void setConfiguration( final Configuration configuration ) {
897 _configuration = configuration;
900 void setOptions( final Options options ) {
904 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
905 setTypeMenuToAllUnselected();
908 _circular_type_cbmi.setSelected( true );
911 _convex_type_cbmi.setSelected( true );
914 _curved_type_cbmi.setSelected( true );
917 _euro_type_cbmi.setSelected( true );
920 _rounded_type_cbmi.setSelected( true );
923 _rectangular_type_cbmi.setSelected( true );
926 _triangular_type_cbmi.setSelected( true );
929 _unrooted_type_cbmi.setSelected( true );
932 throw new IllegalArgumentException( "unknown type: " + type );
936 void setTypeMenuToAllUnselected() {
937 _convex_type_cbmi.setSelected( false );
938 _curved_type_cbmi.setSelected( false );
939 _euro_type_cbmi.setSelected( false );
940 _rounded_type_cbmi.setSelected( false );
941 _triangular_type_cbmi.setSelected( false );
942 _rectangular_type_cbmi.setSelected( false );
943 _unrooted_type_cbmi.setSelected( false );
944 _circular_type_cbmi.setSelected( false );
947 public void showWhole() {
948 _mainpanel.getControlPanel().showWhole();
951 void switchColors() {
952 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
953 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
954 csc.setVisible( true );
958 if ( _mainpanel.getCurrentTreePanel() != null ) {
959 _mainpanel.getCurrentTreePanel().taxColor();
963 void typeChanged( final Object o ) {
964 updateTypeCheckboxes( getOptions(), o );
965 updateOptions( getOptions() );
966 if ( getCurrentTreePanel() != null ) {
967 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
968 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
969 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
970 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
971 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
972 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
973 getCurrentTreePanel().getControlPanel().showWhole();
975 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
976 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
979 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
981 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
982 updateScreenTextAntialias( getMainPanel().getTreePanels() );
983 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
984 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
985 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
988 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
994 void updateOptions( final Options options ) {
995 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
996 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
997 && _background_gradient_cbmi.isSelected() );
998 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
999 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1000 && _abbreviate_scientific_names.isSelected() );
1001 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1002 && _color_labels_same_as_parent_branch.isSelected() );
1003 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1004 && _show_default_node_shapes_cbmi.isSelected() );
1005 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1006 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1007 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1008 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1010 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1011 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1013 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1014 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1016 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1017 && _search_case_senstive_cbmi.isSelected() );
1018 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1019 options.setShowScale( _show_scale_cbmi.isSelected() );
1021 if ( _label_direction_cbmi != null ) {
1022 if ( _label_direction_cbmi.isSelected() ) {
1023 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1026 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1029 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1030 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1031 && _show_confidence_stddev_cbmi.isSelected() );
1032 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1033 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1035 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1036 && ( _print_using_actual_size_cbmi.isSelected() ) );
1037 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1038 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1039 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1040 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1041 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1042 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1044 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1045 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1046 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1049 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1051 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1052 && _print_black_and_white_cbmi.isSelected() );
1053 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1054 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1055 options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
1056 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
1057 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1058 && _replace_underscores_cbmi.isSelected() );
1059 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1060 && _search_whole_words_only_cbmi.isSelected() );
1061 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1062 && _inverse_search_result_cbmi.isSelected() );
1063 if ( _graphics_export_visible_only_cbmi != null ) {
1064 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1065 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1066 _graphics_export_using_actual_size_cbmi.setSelected( true );
1067 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1070 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1073 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1074 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1076 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1077 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1079 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1080 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1082 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1083 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1085 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1086 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1088 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1089 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1091 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1092 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1094 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1095 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1099 void updateTypeCheckboxes( final Options options, final Object o ) {
1100 setTypeMenuToAllUnselected();
1101 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1104 void displayBasicInformation() {
1105 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1108 _textframe = TextFrame.instantiate( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
1111 void viewAsNexus() {
1113 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1114 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
1117 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions()
1118 .getNhConversionSupportValueStyle() ) );
1123 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1124 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
1127 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny()
1128 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) );
1133 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1134 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1137 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
1142 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
1143 && ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
1144 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
1149 * Display the about box.
1151 static void about() {
1152 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1153 about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
1154 about.append( "All Rights Reserved\n" );
1155 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1156 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1157 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1158 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1159 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1160 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1161 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1163 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1164 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1165 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1166 + ForesterUtil.OS_VERSION + "]\n" );
1168 final Runtime rt = java.lang.Runtime.getRuntime();
1169 final long free_memory = rt.freeMemory() / 1000000;
1170 final long total_memory = rt.totalMemory() / 1000000;
1171 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1172 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1173 about.append( "References:\n" );
1174 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1175 about.append( "For more information & download:\n" );
1176 about.append( Constants.APTX_WEB_SITE + "\n" );
1177 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1178 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1181 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1182 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1185 static JMenu createMenu( final String title, final Configuration conf ) {
1186 final JMenu jmenu = new JMenu( title );
1187 if ( !conf.isUseNativeUI() ) {
1188 jmenu.setFont( MainFrame.menu_font );
1189 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1190 jmenu.setForeground( conf.getGuiMenuTextColor() );
1195 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1196 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1197 if ( !configuration.isUseNativeUI() ) {
1198 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1199 label.setForeground( configuration.getGuiMenuTextColor() );
1200 label.setOpaque( true );
1202 label.setSelected( false );
1203 label.setEnabled( false );
1207 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1208 switch ( op.getOvPlacement() ) {
1210 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1213 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1216 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1219 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1222 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1224 if ( tree_panel != null ) {
1225 tree_panel.updateOvSettings();
1229 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1230 switch ( op.getDefaultNodeFill() ) {
1232 op.setDefaultNodeFill( NodeFill.SOLID );
1235 op.setDefaultNodeFill( NodeFill.GRADIENT );
1238 op.setDefaultNodeFill( NodeFill.NONE );
1241 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1245 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1246 switch ( op.getDefaultNodeShape() ) {
1248 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1251 op.setDefaultNodeShape( NodeShape.CIRCLE );
1254 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1258 static void help( final Map<String, WebLink> weblinks ) {
1259 final StringBuilder sb = new StringBuilder();
1260 sb.append( "Display options\n" );
1261 sb.append( "-------------------\n" );
1262 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1263 sb.append( "Clickable tree nodes\n" );
1264 sb.append( "--------------------\n" );
1265 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1266 sb.append( "or by right clicking:\n" );
1267 sb.append( "o Display Node Data -- display information for a node\n" );
1268 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1269 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1270 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1271 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1272 sb.append( "o Colorize Subtree -- color a subtree\n" );
1273 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1274 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1275 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1276 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1277 sb.append( "Zooming\n" );
1278 sb.append( "---------\n" );
1279 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1280 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1281 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1282 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1283 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1284 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1285 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1286 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1287 sb.append( "Quick tree manipulation:\n" );
1288 sb.append( "------------------------\n" );
1289 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1290 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1291 sb.append( "Memory problems (Java heap space error)\n" );
1292 sb.append( "---------------------------------------\n" );
1293 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1294 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1295 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1296 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1297 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1298 sb.append( "Active web links\n" );
1299 sb.append( "--------------------\n" );
1300 for( final String key : weblinks.keySet() ) {
1301 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1304 // + "General remarks\n"
1305 // + "---------------\n"
1307 // "o The application version permits copying to the clipboard \n"
1309 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1311 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1312 // + " but not any of its parent tree(s).\n"
1314 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1316 // " are likely to be bootstrap values instead of branch length values.\n\n"
1318 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1320 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1322 // " a species: either directly through the \"Species\" field, or the species\n"
1324 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1326 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1328 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1330 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1332 // "o !External nodes of the gene tree associated with species not present in\n"
1334 // " the species tree are REMOVED prior to SDI execution!\n"
1336 // "o Both the gene tree and the species tree must be completely binary.\n"
1338 // "o Duplications and speciations are a function of the position of the root.\n"
1340 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1341 // + " incorrect and need to be inferred again\n"
1343 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1345 sb.append( "phyloXML\n" );
1346 sb.append( "-------------------\n" );
1347 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1348 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1349 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1351 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1352 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1353 TextFrame.instantiate( sb.toString() );
1356 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1357 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1358 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1361 mi.setText( "Cycle Overview Placement..." );
1365 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1366 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1367 mi.setText( "Cycle Node Shape Fill Type... (current: "
1368 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1371 mi.setText( "Cycle Node Shape Fill Type..." );
1375 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1376 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1377 mi.setText( "Cycle Node Shape Fill Type... (current: "
1378 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1381 mi.setText( "Cycle Node Shape Fill Type..." );
1385 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1386 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1387 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1390 mi.setText( "Select Colors..." );
1394 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1395 mi.setText( "Select Font... (current: " + font_desc + ")" );
1398 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1399 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1400 mi.setEnabled( true );
1402 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1403 mi.setEnabled( true );
1406 mi.setEnabled( false );
1408 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1411 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1412 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1415 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1416 final JCheckBoxMenuItem scale,
1417 final JCheckBoxMenuItem branch_lengths,
1418 final JRadioButtonMenuItem non_lined_up,
1419 final JRadioButtonMenuItem uniform_clado,
1420 final JRadioButtonMenuItem nonuniform_clado,
1421 final JCheckBoxMenuItem label_direction_cbmi ) {
1422 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1423 final ControlPanel control = main_panel.getControlPanel();
1424 final Options options = main_panel.getOptions();
1425 scale.setSelected( options.isShowScale() );
1426 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1427 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1428 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1429 scale.setSelected( false );
1430 scale.setEnabled( false );
1431 branch_lengths.setSelected( false );
1432 branch_lengths.setEnabled( false );
1434 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1435 scale.setSelected( false );
1436 scale.setEnabled( false );
1437 branch_lengths.setEnabled( true );
1440 scale.setEnabled( true );
1441 branch_lengths.setEnabled( true );
1443 if ( ( tree_panel != null )
1444 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1445 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1446 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1447 branch_lengths.setSelected( false );
1448 branch_lengths.setEnabled( false );
1450 if ( tree_panel != null ) {
1451 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1452 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1453 non_lined_up.setEnabled( false );
1454 uniform_clado.setEnabled( false );
1455 nonuniform_clado.setEnabled( false );
1458 non_lined_up.setEnabled( true );
1459 uniform_clado.setEnabled( true );
1460 nonuniform_clado.setEnabled( true );
1464 if ( ( tree_panel != null )
1465 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1466 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1467 branch_lengths.setSelected( false );
1468 branch_lengths.setEnabled( false );
1470 if ( ( tree_panel != null )
1471 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1472 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1473 non_lined_up.setEnabled( false );
1476 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1477 non_lined_up.setEnabled( true );
1480 label_direction_cbmi.setEnabled( true );
1481 if ( tree_panel != null ) {
1482 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1483 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1484 label_direction_cbmi.setEnabled( false );
1486 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1487 scale.setSelected( false );
1488 scale.setEnabled( false );
1493 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1494 for( final TreePanel tree_panel : treepanels ) {
1495 tree_panel.setTextAntialias();