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.LinkedList;
35 import java.util.List;
36 import java.util.Locale;
38 import java.util.NoSuchElementException;
40 import javax.swing.JApplet;
41 import javax.swing.JCheckBoxMenuItem;
42 import javax.swing.JFrame;
43 import javax.swing.JMenu;
44 import javax.swing.JMenuBar;
45 import javax.swing.JMenuItem;
46 import javax.swing.JOptionPane;
47 import javax.swing.JRadioButtonMenuItem;
48 import javax.swing.SwingUtilities;
50 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
51 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
52 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
53 import org.forester.archaeopteryx.tools.InferenceManager;
54 import org.forester.archaeopteryx.tools.ProcessPool;
55 import org.forester.archaeopteryx.tools.ProcessRunning;
56 import org.forester.phylogeny.Phylogeny;
57 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
58 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
59 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
60 import org.forester.util.ForesterConstants;
61 import org.forester.util.ForesterUtil;
63 public abstract class MainFrame extends JFrame implements ActionListener {
65 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
66 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
67 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
68 private static final long serialVersionUID = 3655000897845508358L;
69 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
72 static final String TYPE_MENU_HEADER = "Type";
73 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
74 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
75 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
76 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
77 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
78 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
79 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
80 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
81 static final String OPTIONS_HEADER = "Options";
82 static final String SEARCH_SUBHEADER = "Search:";
83 static final String DISPLAY_SUBHEADER = "Display:";
84 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
85 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
86 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
87 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
88 static final String DISPLAY_SCALE_LABEL = "Display Scale";
89 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
90 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
91 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
92 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
93 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
94 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
95 static final String BG_GRAD_LABEL = "Background Color Gradient";
96 static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
97 static final String SHOW_OVERVIEW_LABEL = "Show Overview";
98 static final String FONT_SIZE_MENU_LABEL = "Font Size";
99 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
100 static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
101 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";
102 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
103 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
104 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
105 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
106 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
107 static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
108 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
109 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
114 JMenu _options_jmenu;
115 JMenu _font_size_menu;
117 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
119 JMenuItem _open_item;
120 JMenuItem _open_url_item;
121 JMenuItem _save_item;
122 JMenuItem _save_all_item;
123 JMenuItem _close_item;
124 JMenuItem _exit_item;
127 JMenuItem _midpoint_root_item;
128 JMenuItem _taxcolor_item;
129 JMenuItem _confcolor_item;
130 JMenuItem _color_rank_jmi;
131 JMenuItem _infer_common_sn_names_item;
132 JMenuItem _collapse_species_specific_subtrees;
133 JMenuItem _collapse_below_threshold; //TODO implememt me
134 JMenuItem _obtain_detailed_taxonomic_information_jmi;
135 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
136 JMenuItem _obtain_uniprot_seq_information_jmi;
137 JMenuItem _move_node_names_to_tax_sn_jmi;
138 JMenuItem _move_node_names_to_seq_names_jmi;
139 JMenuItem _extract_tax_code_from_node_names_jmi;
141 JMenuItem _super_tiny_fonts_item;
142 JMenuItem _tiny_fonts_item;
143 JMenuItem _small_fonts_item;
144 JMenuItem _medium_fonts_item;
145 JMenuItem _large_fonts_item;
147 // _ screen and print
148 JMenuItem _choose_font_mi;
149 JMenuItem _switch_colors_mi;
150 JCheckBoxMenuItem _label_direction_cbmi;
152 JCheckBoxMenuItem _screen_antialias_cbmi;
153 JCheckBoxMenuItem _background_gradient_cbmi;
154 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
155 JRadioButtonMenuItem _uniform_cladograms_rbmi;
156 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
157 JCheckBoxMenuItem _show_branch_length_values_cbmi;
158 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
159 JCheckBoxMenuItem _show_overview_cbmi;
160 JCheckBoxMenuItem _show_domain_labels;
161 JCheckBoxMenuItem _abbreviate_scientific_names;
162 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
163 JMenuItem _overview_placment_mi;
164 JMenuItem _choose_minimal_confidence_mi;
165 JCheckBoxMenuItem _show_default_node_shapes_cbmi;
166 JMenuItem _cycle_node_shape_mi;
167 JMenuItem _cycle_node_fill_mi;
168 JMenuItem _choose_node_size_mi;
169 JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
170 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
172 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
173 JCheckBoxMenuItem _antialias_print_cbmi;
174 JCheckBoxMenuItem _print_black_and_white_cbmi;
175 JCheckBoxMenuItem _print_using_actual_size_cbmi;
176 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
177 JMenuItem _print_size_mi;
178 JMenuItem _choose_pdf_width_mi;
180 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
181 JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
182 JCheckBoxMenuItem _replace_underscores_cbmi;
183 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
184 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
186 JCheckBoxMenuItem _search_case_senstive_cbmi;
187 JCheckBoxMenuItem _search_whole_words_only_cbmi;
188 JCheckBoxMenuItem _inverse_search_result_cbmi;
191 JCheckBoxMenuItem _rectangular_type_cbmi;
192 JCheckBoxMenuItem _triangular_type_cbmi;
193 JCheckBoxMenuItem _curved_type_cbmi;
194 JCheckBoxMenuItem _convex_type_cbmi;
195 JCheckBoxMenuItem _euro_type_cbmi;
196 JCheckBoxMenuItem _rounded_type_cbmi;
197 JCheckBoxMenuItem _unrooted_type_cbmi;
198 JCheckBoxMenuItem _circular_type_cbmi;
199 // view as text menu:
200 JMenuItem _view_as_NH_item;
201 JMenuItem _view_as_NHX_item;
202 JMenuItem _view_as_XML_item;
203 JMenuItem _view_as_nexus_item;
204 JMenuItem _display_basic_information_item;
206 JMenuItem _about_item;
207 JMenuItem _help_item;
208 JMenuItem _website_item;
209 JMenuItem _phyloxml_website_item;
210 JMenuItem _phyloxml_ref_item;
211 JMenuItem _aptx_ref_item;
214 // Handy pointers to child components:
215 MainPanel _mainpanel;
216 Container _contentpane;
217 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
218 Configuration _configuration;
219 JMenuItem _remove_branch_color_item;
221 InferenceManager _inference_manager;
222 final ProcessPool _process_pool;
225 _process_pool = ProcessPool.createInstance();
228 public ProcessPool getProcessPool() {
229 return _process_pool;
235 public void actionPerformed( final ActionEvent e ) {
236 final Object o = e.getSource();
237 boolean is_applet = false;
238 JApplet applet = null;
239 if ( getCurrentTreePanel() != null ) {
240 is_applet = getCurrentTreePanel().isApplet();
242 applet = getCurrentTreePanel().obtainApplet();
245 if ( o == _open_url_item ) {
246 readPhylogeniesFromURL();
248 else if ( o == _exit_item ) {
251 else if ( o == _taxcolor_item ) {
254 else if ( o == _confcolor_item ) {
257 else if ( o == _color_rank_jmi ) {
260 else if ( o == _infer_common_sn_names_item ) {
261 if ( isSubtreeDisplayed() ) {
264 if ( getCurrentTreePanel() != null ) {
265 getCurrentTreePanel().inferCommonPartOfScientificNames();
268 else if ( o == _collapse_species_specific_subtrees ) {
269 if ( isSubtreeDisplayed() ) {
272 if ( getCurrentTreePanel() != null ) {
273 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
276 else if ( o == _remove_branch_color_item ) {
277 if ( isSubtreeDisplayed() ) {
280 removeBranchColors();
282 else if ( o == _midpoint_root_item ) {
283 if ( isSubtreeDisplayed() ) {
288 else if ( o == _switch_colors_mi ) {
291 else if ( o == _display_basic_information_item ) {
292 displayBasicInformation();
294 else if ( o == _view_as_NH_item ) {
297 else if ( o == _view_as_NHX_item ) {
300 else if ( o == _view_as_XML_item ) {
303 else if ( o == _view_as_nexus_item ) {
306 else if ( o == _super_tiny_fonts_item ) {
307 if ( getCurrentTreePanel() != null ) {
308 getCurrentTreePanel().setSuperTinyFonts();
309 getCurrentTreePanel().repaint();
312 else if ( o == _tiny_fonts_item ) {
313 if ( getCurrentTreePanel() != null ) {
314 getCurrentTreePanel().setTinyFonts();
315 getCurrentTreePanel().repaint();
318 else if ( o == _small_fonts_item ) {
319 if ( getCurrentTreePanel() != null ) {
320 getCurrentTreePanel().setSmallFonts();
321 getCurrentTreePanel().repaint();
324 else if ( o == _medium_fonts_item ) {
325 if ( getCurrentTreePanel() != null ) {
326 getCurrentTreePanel().setMediumFonts();
327 getCurrentTreePanel().repaint();
330 else if ( o == _large_fonts_item ) {
331 if ( getCurrentTreePanel() != null ) {
332 getCurrentTreePanel().setLargeFonts();
333 getCurrentTreePanel().repaint();
336 else if ( o == _choose_font_mi ) {
339 else if ( o == _choose_minimal_confidence_mi ) {
340 chooseMinimalConfidence();
342 else if ( o == _choose_node_size_mi ) {
343 chooseNodeSize( getOptions(), this );
345 else if ( o == _overview_placment_mi ) {
346 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
348 else if ( o == _cycle_node_fill_mi ) {
349 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
351 else if ( o == _cycle_node_shape_mi ) {
352 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
354 else if ( o == _screen_antialias_cbmi ) {
355 updateOptions( getOptions() );
356 updateScreenTextAntialias( getMainPanel().getTreePanels() );
358 else if ( o == _background_gradient_cbmi ) {
359 updateOptions( getOptions() );
361 else if ( o == _show_domain_labels ) {
362 updateOptions( getOptions() );
364 else if ( o == _abbreviate_scientific_names ) {
365 updateOptions( getOptions() );
367 else if ( o == _color_labels_same_as_parent_branch ) {
368 updateOptions( getOptions() );
370 else if ( o == _show_default_node_shapes_cbmi ) {
371 updateOptions( getOptions() );
373 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
374 updateOptions( getOptions() );
376 else if ( o == _non_lined_up_cladograms_rbmi ) {
377 updateOptions( getOptions() );
380 else if ( o == _uniform_cladograms_rbmi ) {
381 updateOptions( getOptions() );
384 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
385 updateOptions( getOptions() );
388 else if ( o == _search_case_senstive_cbmi ) {
389 updateOptions( getOptions() );
390 getMainPanel().getControlPanel().search();
392 else if ( o == _search_whole_words_only_cbmi ) {
393 updateOptions( getOptions() );
394 getMainPanel().getControlPanel().search();
396 else if ( o == _inverse_search_result_cbmi ) {
397 updateOptions( getOptions() );
398 getMainPanel().getControlPanel().search();
400 else if ( o == _show_scale_cbmi ) {
401 updateOptions( getOptions() );
403 else if ( o == _show_branch_length_values_cbmi ) {
404 updateOptions( getOptions() );
406 else if ( o == _show_confidence_stddev_cbmi ) {
407 updateOptions( getOptions() );
409 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
410 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
411 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
413 updateOptions( getOptions() );
415 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
416 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
417 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
419 updateOptions( getOptions() );
421 else if ( o == _label_direction_cbmi ) {
422 updateOptions( getOptions() );
424 else if ( o == _show_overview_cbmi ) {
425 updateOptions( getOptions() );
426 if ( getCurrentTreePanel() != null ) {
427 getCurrentTreePanel().updateOvSizes();
430 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
431 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
432 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
435 else if ( o == _about_item ) {
438 else if ( o == _help_item ) {
439 help( getConfiguration().getWebLinks() );
441 else if ( o == _website_item ) {
443 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
445 catch ( final IOException e1 ) {
446 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
449 else if ( o == _phyloxml_website_item ) {
451 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
453 catch ( final IOException e1 ) {
454 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
457 else if ( o == _aptx_ref_item ) {
459 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
461 catch ( final IOException e1 ) {
462 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
465 else if ( o == _phyloxml_ref_item ) {
467 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
469 catch ( final IOException e1 ) {
470 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
474 if ( _load_phylogeny_from_webservice_menu_items != null ) {
475 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
476 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
477 readPhylogeniesFromWebservice( i );
482 _contentpane.repaint();
485 boolean isSubtreeDisplayed() {
486 if ( getCurrentTreePanel() != null ) {
487 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
489 .showMessageDialog( this,
490 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
491 "Operation can not be exectuted on a sub-tree",
492 JOptionPane.WARNING_MESSAGE );
499 void activateSaveAllIfNeeded() {
500 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
501 _save_all_item.setEnabled( true );
504 _save_all_item.setEnabled( false );
508 void buildFileMenu() {
509 _file_jmenu = createMenu( "File", getConfiguration() );
510 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
511 _file_jmenu.addSeparator();
512 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
513 customizeJMenuItem( _open_url_item );
514 customizeJMenuItem( _exit_item );
515 _jmenubar.add( _file_jmenu );
518 void buildFontSizeMenu() {
519 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
520 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
521 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
522 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
523 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
524 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
525 customizeJMenuItem( _super_tiny_fonts_item );
526 customizeJMenuItem( _tiny_fonts_item );
527 customizeJMenuItem( _small_fonts_item );
528 customizeJMenuItem( _medium_fonts_item );
529 customizeJMenuItem( _large_fonts_item );
530 _jmenubar.add( _font_size_menu );
533 void buildHelpMenu() {
534 _help_jmenu = createMenu( "Help", getConfiguration() );
535 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
536 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
537 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
538 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
539 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
540 _help_jmenu.addSeparator();
541 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
542 customizeJMenuItem( _help_item );
543 customizeJMenuItem( _website_item );
544 customizeJMenuItem( _phyloxml_website_item );
545 customizeJMenuItem( _aptx_ref_item );
546 customizeJMenuItem( _phyloxml_ref_item );
547 customizeJMenuItem( _about_item );
548 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
549 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
550 _jmenubar.add( _help_jmenu );
553 public void updateProcessMenu() {
554 // In general Swing is not thread safe.
555 // See "Swing's Threading Policy".
556 SwingUtilities.invokeLater( new Runnable() {
559 doUpdateProcessMenu();
564 private void doUpdateProcessMenu() {
565 if ( _process_pool.size() > 0 ) {
566 if ( _process_menu == null ) {
567 _process_menu = createMenu( "", getConfiguration() );
568 _process_menu.setForeground( Color.RED );
570 _process_menu.removeAll();
571 final String text = "processes running: " + _process_pool.size();
572 _process_menu.setText( text );
573 _jmenubar.add( _process_menu );
574 for( int i = 0; i < _process_pool.size(); ++i ) {
575 final ProcessRunning p = _process_pool.getProcessByIndex( i );
576 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
580 if ( _process_menu != null ) {
581 _process_menu.removeAll();
582 _jmenubar.remove( _process_menu );
585 _jmenubar.validate();
590 void buildTypeMenu() {
591 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
592 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
593 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
594 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
595 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
596 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
597 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
598 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
599 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
600 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
601 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
602 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
603 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
604 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
605 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
606 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
607 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
608 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
609 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
610 initializeTypeMenu( getOptions() );
611 _jmenubar.add( _type_menu );
614 void buildViewMenu() {
615 _view_jmenu = createMenu( "View", getConfiguration() );
616 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
617 _view_jmenu.addSeparator();
618 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
619 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
620 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
621 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
622 customizeJMenuItem( _display_basic_information_item );
623 customizeJMenuItem( _view_as_NH_item );
624 customizeJMenuItem( _view_as_NHX_item );
625 customizeJMenuItem( _view_as_XML_item );
626 customizeJMenuItem( _view_as_nexus_item );
627 _jmenubar.add( _view_jmenu );
630 private void chooseFont() {
631 final FontChooser fc = new FontChooser();
632 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
633 fc.showDialog( this, "Select the Base Font" );
634 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
637 private void chooseMinimalConfidence() {
638 final String s = ( String ) JOptionPane
639 .showInputDialog( this,
640 "Please enter the minimum for confidence values to be displayed.\n"
641 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
642 "Minimal Confidence Value",
643 JOptionPane.QUESTION_MESSAGE,
646 getOptions().getMinConfidenceValue() );
647 if ( !ForesterUtil.isEmpty( s ) ) {
648 boolean success = true;
650 final String m_str = s.trim();
651 if ( !ForesterUtil.isEmpty( m_str ) ) {
653 m = Double.parseDouble( m_str );
655 catch ( final Exception ex ) {
662 if ( success && ( m >= 0.0 ) ) {
663 getOptions().setMinConfidenceValue( m );
668 static void chooseNodeSize( final Options options, final Component parent ) {
669 final String s = ( String ) JOptionPane.showInputDialog( parent,
670 "Please enter the default size for node shapes.\n"
672 + options.getDefaultNodeShapeSize() + "]\n",
674 JOptionPane.QUESTION_MESSAGE,
677 options.getDefaultNodeShapeSize() );
678 if ( !ForesterUtil.isEmpty( s ) ) {
679 boolean success = true;
681 final String m_str = s.trim();
682 if ( !ForesterUtil.isEmpty( m_str ) ) {
684 m = Double.parseDouble( m_str );
686 catch ( final Exception ex ) {
693 if ( success && ( m >= 0.0 ) ) {
694 final short size = ForesterUtil.roundToShort( m );
696 options.setDefaultNodeShapeSize( size );
703 removeAllTextFrames();
704 if ( _mainpanel != null ) {
705 _mainpanel.terminate();
707 if ( _contentpane != null ) {
708 _contentpane.removeAll();
715 if ( _mainpanel.getCurrentTreePanel() != null ) {
716 _mainpanel.getCurrentTreePanel().confColor();
721 if ( _mainpanel.getCurrentTreePanel() != null ) {
722 final String[] ranks = AptxUtil.getAllPossibleRanks();
723 final String rank = ( String ) JOptionPane
724 .showInputDialog( this,
725 "What rank should the colorization be based on",
727 JOptionPane.QUESTION_MESSAGE,
731 if ( !ForesterUtil.isEmpty( rank ) ) {
732 _mainpanel.getCurrentTreePanel().colorRank( rank );
737 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
738 if ( item != null ) {
739 item.setFont( MainFrame.menu_font );
740 if ( !getConfiguration().isUseNativeUI() ) {
741 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
742 item.setForeground( getConfiguration().getGuiMenuTextColor() );
744 item.setSelected( is_selected );
745 item.addActionListener( this );
749 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
751 jmi.setFont( MainFrame.menu_font );
752 if ( !getConfiguration().isUseNativeUI() ) {
753 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
754 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
756 jmi.addActionListener( this );
761 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
762 if ( item != null ) {
763 item.setFont( MainFrame.menu_font );
764 if ( !getConfiguration().isUseNativeUI() ) {
765 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
766 item.setForeground( getConfiguration().getGuiMenuTextColor() );
768 item.setSelected( is_selected );
769 item.addActionListener( this );
773 void exceptionOccuredDuringOpenFile( final Exception e ) {
775 _mainpanel.getCurrentTreePanel().setArrowCursor();
777 catch ( final Exception ex ) {
780 JOptionPane.showMessageDialog( this,
781 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
782 "Error during File|Open",
783 JOptionPane.ERROR_MESSAGE );
786 void exceptionOccuredDuringSaveAs( final Exception e ) {
788 _mainpanel.getCurrentTreePanel().setArrowCursor();
790 catch ( final Exception ex ) {
793 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
796 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
797 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
798 JOptionPane.showMessageDialog( this,
799 "Gene tree and species tree have no species in common.",
801 JOptionPane.ERROR_MESSAGE );
804 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
805 JOptionPane.showMessageDialog( this,
806 "Gene tree and species tree have only one species in common.",
808 JOptionPane.ERROR_MESSAGE );
816 public Configuration getConfiguration() {
817 return _configuration;
820 TreePanel getCurrentTreePanel() {
821 return getMainPanel().getCurrentTreePanel();
824 JMenu getHelpMenu() {
828 JCheckBoxMenuItem getlabelDirectionCbmi() {
829 return _label_direction_cbmi;
832 public MainPanel getMainPanel() {
836 JMenuBar getMenuBarOfMainFrame() {
840 public Options getOptions() {
844 void initializeTypeMenu( final Options options ) {
845 setTypeMenuToAllUnselected();
846 switch ( options.getPhylogenyGraphicsType() ) {
848 _convex_type_cbmi.setSelected( true );
851 _curved_type_cbmi.setSelected( true );
854 _euro_type_cbmi.setSelected( true );
857 _rounded_type_cbmi.setSelected( true );
860 _triangular_type_cbmi.setSelected( true );
863 _unrooted_type_cbmi.setSelected( true );
866 _circular_type_cbmi.setSelected( true );
869 _rectangular_type_cbmi.setSelected( true );
874 void midpointRoot() {
875 if ( _mainpanel.getCurrentTreePanel() != null ) {
876 _mainpanel.getCurrentTreePanel().midpointRoot();
880 abstract void readPhylogeniesFromURL();
882 void readPhylogeniesFromWebservice( final int i ) {
883 final UrlTreeReader reader = new UrlTreeReader( this, i );
884 new Thread( reader ).start();
887 private void removeBranchColors() {
888 if ( getMainPanel().getCurrentPhylogeny() != null ) {
889 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
893 void checkTextFrames() {
894 if ( _textframes.size() > 5 ) {
896 if ( _textframes.getFirst() != null ) {
897 _textframes.getFirst().removeMe();
900 _textframes.removeFirst();
903 catch ( final NoSuchElementException e ) {
909 void removeAllTextFrames() {
910 for( final TextFrame tf : _textframes ) {
918 void setConfiguration( final Configuration configuration ) {
919 _configuration = configuration;
922 void setOptions( final Options options ) {
926 void setInferenceManager( final InferenceManager i ) {
927 _inference_manager = i;
930 public InferenceManager getInferenceManager() {
931 return _inference_manager;
934 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
935 setTypeMenuToAllUnselected();
938 _circular_type_cbmi.setSelected( true );
941 _convex_type_cbmi.setSelected( true );
944 _curved_type_cbmi.setSelected( true );
947 _euro_type_cbmi.setSelected( true );
950 _rounded_type_cbmi.setSelected( true );
953 _rectangular_type_cbmi.setSelected( true );
956 _triangular_type_cbmi.setSelected( true );
959 _unrooted_type_cbmi.setSelected( true );
962 throw new IllegalArgumentException( "unknown type: " + type );
966 void setTypeMenuToAllUnselected() {
967 _convex_type_cbmi.setSelected( false );
968 _curved_type_cbmi.setSelected( false );
969 _euro_type_cbmi.setSelected( false );
970 _rounded_type_cbmi.setSelected( false );
971 _triangular_type_cbmi.setSelected( false );
972 _rectangular_type_cbmi.setSelected( false );
973 _unrooted_type_cbmi.setSelected( false );
974 _circular_type_cbmi.setSelected( false );
977 public void showWhole() {
978 _mainpanel.getControlPanel().showWhole();
981 void switchColors() {
982 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
983 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
984 csc.setVisible( true );
988 if ( _mainpanel.getCurrentTreePanel() != null ) {
989 _mainpanel.getCurrentTreePanel().taxColor();
993 void typeChanged( final Object o ) {
994 updateTypeCheckboxes( getOptions(), o );
995 updateOptions( getOptions() );
996 if ( getCurrentTreePanel() != null ) {
997 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
998 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
999 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1000 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1001 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1002 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1003 getCurrentTreePanel().getControlPanel().showWhole();
1005 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1006 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1009 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1011 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1012 updateScreenTextAntialias( getMainPanel().getTreePanels() );
1013 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1014 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1015 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1018 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1024 void updateOptions( final Options options ) {
1025 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1026 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1027 && _background_gradient_cbmi.isSelected() );
1028 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1029 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1030 && _abbreviate_scientific_names.isSelected() );
1031 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1032 && _color_labels_same_as_parent_branch.isSelected() );
1033 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1034 && _show_default_node_shapes_cbmi.isSelected() );
1035 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1036 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1037 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1038 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1040 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1041 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1043 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1044 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1046 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1047 && _search_case_senstive_cbmi.isSelected() );
1048 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1049 options.setShowScale( _show_scale_cbmi.isSelected() );
1051 if ( _label_direction_cbmi != null ) {
1052 if ( _label_direction_cbmi.isSelected() ) {
1053 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1056 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1059 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1060 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1061 && _show_confidence_stddev_cbmi.isSelected() );
1062 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1063 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1065 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1066 && ( _print_using_actual_size_cbmi.isSelected() ) );
1067 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1068 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1069 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1070 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1071 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1072 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1074 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1075 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1076 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1079 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1081 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1082 && _print_black_and_white_cbmi.isSelected() );
1083 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1084 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1085 options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
1086 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
1087 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1088 && _replace_underscores_cbmi.isSelected() );
1089 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1090 && _search_whole_words_only_cbmi.isSelected() );
1091 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1092 && _inverse_search_result_cbmi.isSelected() );
1093 if ( _graphics_export_visible_only_cbmi != null ) {
1094 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1095 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1096 _graphics_export_using_actual_size_cbmi.setSelected( true );
1097 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1100 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1103 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1104 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1106 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1107 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1109 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1110 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1112 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1113 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1115 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1116 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1118 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1119 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1121 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1122 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1124 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1125 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1129 void updateTypeCheckboxes( final Options options, final Object o ) {
1130 setTypeMenuToAllUnselected();
1131 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1134 void displayBasicInformation() {
1135 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1136 String title = "Basic Information";
1137 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1138 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1140 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
1144 void viewAsNexus() {
1145 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1146 String title = "Nexus";
1147 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1148 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1150 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1156 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1157 String title = "New Hampshire";
1158 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1159 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1161 showTextFrame( _mainpanel.getCurrentPhylogeny()
1162 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1168 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1169 String title = "NHX";
1170 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1171 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1173 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
1178 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1179 String title = "phyloXML";
1180 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1181 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1183 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1187 public void showTextFrame( final String s, final String title ) {
1189 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
1193 * Display the about box.
1195 static void about() {
1196 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1197 about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
1198 about.append( "All Rights Reserved\n" );
1199 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1200 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1201 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1202 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1203 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1204 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1205 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1207 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1208 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1209 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1210 + ForesterUtil.OS_VERSION + "]\n" );
1212 final Runtime rt = java.lang.Runtime.getRuntime();
1213 final long free_memory = rt.freeMemory() / 1000000;
1214 final long total_memory = rt.totalMemory() / 1000000;
1215 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1216 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1217 about.append( "References:\n" );
1218 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1219 about.append( "For more information & download:\n" );
1220 about.append( Constants.APTX_WEB_SITE + "\n" );
1221 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1222 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1225 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1226 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1229 static JMenu createMenu( final String title, final Configuration conf ) {
1230 final JMenu jmenu = new JMenu( title );
1231 if ( !conf.isUseNativeUI() ) {
1232 jmenu.setFont( MainFrame.menu_font );
1233 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1234 jmenu.setForeground( conf.getGuiMenuTextColor() );
1239 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1240 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1241 if ( !configuration.isUseNativeUI() ) {
1242 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1243 label.setForeground( configuration.getGuiMenuTextColor() );
1244 label.setOpaque( true );
1246 label.setSelected( false );
1247 label.setEnabled( false );
1251 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1252 switch ( op.getOvPlacement() ) {
1254 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1257 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1260 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1263 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1266 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1268 if ( tree_panel != null ) {
1269 tree_panel.updateOvSettings();
1273 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1274 switch ( op.getDefaultNodeFill() ) {
1276 op.setDefaultNodeFill( NodeFill.SOLID );
1279 op.setDefaultNodeFill( NodeFill.GRADIENT );
1282 op.setDefaultNodeFill( NodeFill.NONE );
1285 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1289 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1290 switch ( op.getDefaultNodeShape() ) {
1292 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1295 op.setDefaultNodeShape( NodeShape.CIRCLE );
1298 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1302 void help( final Map<String, WebLink> weblinks ) {
1303 final StringBuilder sb = new StringBuilder();
1304 sb.append( "Display options\n" );
1305 sb.append( "-------------------\n" );
1306 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1307 sb.append( "Clickable tree nodes\n" );
1308 sb.append( "--------------------\n" );
1309 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1310 sb.append( "or by right clicking:\n" );
1311 sb.append( "o Display Node Data -- display information for a node\n" );
1312 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1313 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1314 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1315 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1316 sb.append( "o Colorize Subtree -- color a subtree\n" );
1317 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1318 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1319 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1320 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1321 sb.append( "Zooming\n" );
1322 sb.append( "---------\n" );
1323 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1324 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1325 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1326 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1327 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1328 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1329 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1330 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1331 sb.append( "Quick tree manipulation:\n" );
1332 sb.append( "------------------------\n" );
1333 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1334 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1335 sb.append( "Memory problems (Java heap space error)\n" );
1336 sb.append( "---------------------------------------\n" );
1337 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1338 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1339 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1340 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1341 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1342 sb.append( "Active web links\n" );
1343 sb.append( "--------------------\n" );
1344 for( final String key : weblinks.keySet() ) {
1345 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1348 // + "General remarks\n"
1349 // + "---------------\n"
1351 // "o The application version permits copying to the clipboard \n"
1353 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1355 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1356 // + " but not any of its parent tree(s).\n"
1358 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1360 // " are likely to be bootstrap values instead of branch length values.\n\n"
1362 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1364 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1366 // " a species: either directly through the \"Species\" field, or the species\n"
1368 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1370 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1372 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1374 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1376 // "o !External nodes of the gene tree associated with species not present in\n"
1378 // " the species tree are REMOVED prior to SDI execution!\n"
1380 // "o Both the gene tree and the species tree must be completely binary.\n"
1382 // "o Duplications and speciations are a function of the position of the root.\n"
1384 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1385 // + " incorrect and need to be inferred again\n"
1387 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1389 sb.append( "phyloXML\n" );
1390 sb.append( "-------------------\n" );
1391 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1392 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1393 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1395 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1396 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1397 TextFrame.instantiate( sb.toString(), "Help", _textframes );
1400 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1401 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1402 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1405 mi.setText( "Cycle Overview Placement..." );
1409 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1410 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1411 mi.setText( "Cycle Node Shape Fill Type... (current: "
1412 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1415 mi.setText( "Cycle Node Shape Fill Type..." );
1419 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1420 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1421 mi.setText( "Cycle Node Shape Fill Type... (current: "
1422 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1425 mi.setText( "Cycle Node Shape Fill Type..." );
1429 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1430 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1431 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1434 mi.setText( "Select Colors..." );
1438 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1439 mi.setText( "Select Font... (current: " + font_desc + ")" );
1442 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1443 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1444 mi.setEnabled( true );
1446 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1447 mi.setEnabled( true );
1450 mi.setEnabled( false );
1452 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1455 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1456 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1459 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1460 final JCheckBoxMenuItem scale,
1461 final JCheckBoxMenuItem branch_lengths,
1462 final JRadioButtonMenuItem non_lined_up,
1463 final JRadioButtonMenuItem uniform_clado,
1464 final JRadioButtonMenuItem nonuniform_clado,
1465 final JCheckBoxMenuItem label_direction_cbmi ) {
1466 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1467 final ControlPanel control = main_panel.getControlPanel();
1468 final Options options = main_panel.getOptions();
1469 scale.setSelected( options.isShowScale() );
1470 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1471 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1472 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1473 scale.setSelected( false );
1474 scale.setEnabled( false );
1475 branch_lengths.setSelected( false );
1476 branch_lengths.setEnabled( false );
1478 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1479 scale.setSelected( false );
1480 scale.setEnabled( false );
1481 branch_lengths.setEnabled( true );
1484 scale.setEnabled( true );
1485 branch_lengths.setEnabled( true );
1487 if ( ( tree_panel != null )
1488 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1489 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1490 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1491 branch_lengths.setSelected( false );
1492 branch_lengths.setEnabled( false );
1494 if ( tree_panel != null ) {
1495 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1496 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1497 non_lined_up.setEnabled( false );
1498 uniform_clado.setEnabled( false );
1499 nonuniform_clado.setEnabled( false );
1502 non_lined_up.setEnabled( true );
1503 uniform_clado.setEnabled( true );
1504 nonuniform_clado.setEnabled( true );
1508 if ( ( tree_panel != null )
1509 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1510 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1511 branch_lengths.setSelected( false );
1512 branch_lengths.setEnabled( false );
1514 if ( ( tree_panel != null )
1515 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1516 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1517 non_lined_up.setEnabled( false );
1520 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1521 non_lined_up.setEnabled( true );
1524 label_direction_cbmi.setEnabled( true );
1525 if ( tree_panel != null ) {
1526 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1527 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1528 label_direction_cbmi.setEnabled( false );
1530 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1531 scale.setSelected( false );
1532 scale.setEnabled( false );
1537 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1538 for( final TreePanel tree_panel : treepanels ) {
1539 tree_panel.setTextAntialias();