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;
236 public void actionPerformed( final ActionEvent e ) {
237 final Object o = e.getSource();
238 boolean is_applet = false;
239 JApplet applet = null;
240 if ( getCurrentTreePanel() != null ) {
241 is_applet = getCurrentTreePanel().isApplet();
243 applet = getCurrentTreePanel().obtainApplet();
246 if ( o == _open_url_item ) {
247 readPhylogeniesFromURL();
249 else if ( o == _exit_item ) {
252 else if ( o == _taxcolor_item ) {
255 else if ( o == _confcolor_item ) {
258 else if ( o == _color_rank_jmi ) {
261 else if ( o == _infer_common_sn_names_item ) {
262 if ( isSubtreeDisplayed() ) {
265 if ( getCurrentTreePanel() != null ) {
266 getCurrentTreePanel().inferCommonPartOfScientificNames();
269 else if ( o == _collapse_species_specific_subtrees ) {
270 if ( isSubtreeDisplayed() ) {
273 if ( getCurrentTreePanel() != null ) {
274 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
277 else if ( o == _remove_branch_color_item ) {
278 if ( isSubtreeDisplayed() ) {
281 removeBranchColors();
283 else if ( o == _midpoint_root_item ) {
284 if ( isSubtreeDisplayed() ) {
289 else if ( o == _switch_colors_mi ) {
292 else if ( o == _display_basic_information_item ) {
293 displayBasicInformation();
295 else if ( o == _view_as_NH_item ) {
298 else if ( o == _view_as_NHX_item ) {
301 else if ( o == _view_as_XML_item ) {
304 else if ( o == _view_as_nexus_item ) {
307 else if ( o == _super_tiny_fonts_item ) {
308 if ( getCurrentTreePanel() != null ) {
309 getCurrentTreePanel().setSuperTinyFonts();
310 getCurrentTreePanel().repaint();
313 else if ( o == _tiny_fonts_item ) {
314 if ( getCurrentTreePanel() != null ) {
315 getCurrentTreePanel().setTinyFonts();
316 getCurrentTreePanel().repaint();
319 else if ( o == _small_fonts_item ) {
320 if ( getCurrentTreePanel() != null ) {
321 getCurrentTreePanel().setSmallFonts();
322 getCurrentTreePanel().repaint();
325 else if ( o == _medium_fonts_item ) {
326 if ( getCurrentTreePanel() != null ) {
327 getCurrentTreePanel().setMediumFonts();
328 getCurrentTreePanel().repaint();
331 else if ( o == _large_fonts_item ) {
332 if ( getCurrentTreePanel() != null ) {
333 getCurrentTreePanel().setLargeFonts();
334 getCurrentTreePanel().repaint();
337 else if ( o == _choose_font_mi ) {
340 else if ( o == _choose_minimal_confidence_mi ) {
341 chooseMinimalConfidence();
343 else if ( o == _choose_node_size_mi ) {
344 chooseNodeSize( getOptions(), this );
346 else if ( o == _overview_placment_mi ) {
347 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
349 else if ( o == _cycle_node_fill_mi ) {
350 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
352 else if ( o == _cycle_node_shape_mi ) {
353 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
355 else if ( o == _screen_antialias_cbmi ) {
356 updateOptions( getOptions() );
357 updateScreenTextAntialias( getMainPanel().getTreePanels() );
359 else if ( o == _background_gradient_cbmi ) {
360 updateOptions( getOptions() );
362 else if ( o == _show_domain_labels ) {
363 updateOptions( getOptions() );
365 else if ( o == _abbreviate_scientific_names ) {
366 updateOptions( getOptions() );
368 else if ( o == _color_labels_same_as_parent_branch ) {
369 updateOptions( getOptions() );
371 else if ( o == _show_default_node_shapes_cbmi ) {
372 updateOptions( getOptions() );
374 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
375 updateOptions( getOptions() );
377 else if ( o == _non_lined_up_cladograms_rbmi ) {
378 updateOptions( getOptions() );
381 else if ( o == _uniform_cladograms_rbmi ) {
382 updateOptions( getOptions() );
385 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
386 updateOptions( getOptions() );
389 else if ( o == _search_case_senstive_cbmi ) {
390 updateOptions( getOptions() );
391 getMainPanel().getControlPanel().search();
393 else if ( o == _search_whole_words_only_cbmi ) {
394 updateOptions( getOptions() );
395 getMainPanel().getControlPanel().search();
397 else if ( o == _inverse_search_result_cbmi ) {
398 updateOptions( getOptions() );
399 getMainPanel().getControlPanel().search();
401 else if ( o == _show_scale_cbmi ) {
402 updateOptions( getOptions() );
404 else if ( o == _show_branch_length_values_cbmi ) {
405 updateOptions( getOptions() );
407 else if ( o == _show_confidence_stddev_cbmi ) {
408 updateOptions( getOptions() );
410 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
411 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
412 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
414 updateOptions( getOptions() );
416 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
417 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
418 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
420 updateOptions( getOptions() );
422 else if ( o == _label_direction_cbmi ) {
423 updateOptions( getOptions() );
425 else if ( o == _show_overview_cbmi ) {
426 updateOptions( getOptions() );
427 if ( getCurrentTreePanel() != null ) {
428 getCurrentTreePanel().updateOvSizes();
431 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
432 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
433 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
436 else if ( o == _about_item ) {
439 else if ( o == _help_item ) {
440 help( getConfiguration().getWebLinks() );
442 else if ( o == _website_item ) {
444 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
446 catch ( final IOException e1 ) {
447 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
450 else if ( o == _phyloxml_website_item ) {
452 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
454 catch ( final IOException e1 ) {
455 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
458 else if ( o == _aptx_ref_item ) {
460 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
462 catch ( final IOException e1 ) {
463 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
466 else if ( o == _phyloxml_ref_item ) {
468 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
470 catch ( final IOException e1 ) {
471 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
475 if ( _load_phylogeny_from_webservice_menu_items != null ) {
476 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
477 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
478 readPhylogeniesFromWebservice( i );
483 _contentpane.repaint();
486 boolean isSubtreeDisplayed() {
487 if ( getCurrentTreePanel() != null ) {
488 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
490 .showMessageDialog( this,
491 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
492 "Operation can not be exectuted on a sub-tree",
493 JOptionPane.WARNING_MESSAGE );
500 void activateSaveAllIfNeeded() {
501 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
502 _save_all_item.setEnabled( true );
505 _save_all_item.setEnabled( false );
509 void buildFileMenu() {
510 _file_jmenu = createMenu( "File", getConfiguration() );
511 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
512 _file_jmenu.addSeparator();
513 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
514 customizeJMenuItem( _open_url_item );
515 customizeJMenuItem( _exit_item );
516 _jmenubar.add( _file_jmenu );
519 void buildFontSizeMenu() {
520 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
521 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
522 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
523 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
524 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
525 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
526 customizeJMenuItem( _super_tiny_fonts_item );
527 customizeJMenuItem( _tiny_fonts_item );
528 customizeJMenuItem( _small_fonts_item );
529 customizeJMenuItem( _medium_fonts_item );
530 customizeJMenuItem( _large_fonts_item );
531 _jmenubar.add( _font_size_menu );
534 void buildHelpMenu() {
535 _help_jmenu = createMenu( "Help", getConfiguration() );
536 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
537 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
538 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
539 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
540 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
541 _help_jmenu.addSeparator();
542 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
543 customizeJMenuItem( _help_item );
544 customizeJMenuItem( _website_item );
545 customizeJMenuItem( _phyloxml_website_item );
546 customizeJMenuItem( _aptx_ref_item );
547 customizeJMenuItem( _phyloxml_ref_item );
548 customizeJMenuItem( _about_item );
549 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
550 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
551 _jmenubar.add( _help_jmenu );
554 public void updateProcessMenu() {
555 // In general Swing is not thread safe.
556 // See "Swing's Threading Policy".
557 SwingUtilities.invokeLater( new Runnable() {
561 doUpdateProcessMenu();
566 private void doUpdateProcessMenu() {
567 if ( _process_pool.size() > 0 ) {
568 if ( _process_menu == null ) {
569 _process_menu = createMenu( "", getConfiguration() );
570 _process_menu.setForeground( Color.RED );
572 _process_menu.removeAll();
573 final String text = "processes running: " + _process_pool.size();
574 _process_menu.setText( text );
575 _jmenubar.add( _process_menu );
576 for( int i = 0; i < _process_pool.size(); ++i ) {
577 final ProcessRunning p = _process_pool.getProcessByIndex( i );
578 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
582 if ( _process_menu != null ) {
583 _process_menu.removeAll();
584 _jmenubar.remove( _process_menu );
587 _jmenubar.validate();
592 void buildTypeMenu() {
593 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
594 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
595 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
596 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
597 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
598 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
599 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
600 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
601 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
602 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
603 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
604 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
605 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
606 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
607 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
608 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
609 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
610 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
611 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
612 initializeTypeMenu( getOptions() );
613 _jmenubar.add( _type_menu );
616 void buildViewMenu() {
617 _view_jmenu = createMenu( "View", getConfiguration() );
618 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
619 _view_jmenu.addSeparator();
620 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
621 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
622 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
623 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
624 customizeJMenuItem( _display_basic_information_item );
625 customizeJMenuItem( _view_as_NH_item );
626 customizeJMenuItem( _view_as_NHX_item );
627 customizeJMenuItem( _view_as_XML_item );
628 customizeJMenuItem( _view_as_nexus_item );
629 _jmenubar.add( _view_jmenu );
632 private void chooseFont() {
633 final FontChooser fc = new FontChooser();
634 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
635 fc.showDialog( this, "Select the Base Font" );
636 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
639 private void chooseMinimalConfidence() {
640 final String s = ( String ) JOptionPane
641 .showInputDialog( this,
642 "Please enter the minimum for confidence values to be displayed.\n"
643 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
644 "Minimal Confidence Value",
645 JOptionPane.QUESTION_MESSAGE,
648 getOptions().getMinConfidenceValue() );
649 if ( !ForesterUtil.isEmpty( s ) ) {
650 boolean success = true;
652 final String m_str = s.trim();
653 if ( !ForesterUtil.isEmpty( m_str ) ) {
655 m = Double.parseDouble( m_str );
657 catch ( final Exception ex ) {
664 if ( success && ( m >= 0.0 ) ) {
665 getOptions().setMinConfidenceValue( m );
670 static void chooseNodeSize( final Options options, final Component parent ) {
671 final String s = ( String ) JOptionPane.showInputDialog( parent,
672 "Please enter the default size for node shapes.\n"
674 + options.getDefaultNodeShapeSize() + "]\n",
676 JOptionPane.QUESTION_MESSAGE,
679 options.getDefaultNodeShapeSize() );
680 if ( !ForesterUtil.isEmpty( s ) ) {
681 boolean success = true;
683 final String m_str = s.trim();
684 if ( !ForesterUtil.isEmpty( m_str ) ) {
686 m = Double.parseDouble( m_str );
688 catch ( final Exception ex ) {
695 if ( success && ( m >= 0.0 ) ) {
696 final short size = ForesterUtil.roundToShort( m );
698 options.setDefaultNodeShapeSize( size );
705 removeAllTextFrames();
706 if ( _mainpanel != null ) {
707 _mainpanel.terminate();
709 if ( _contentpane != null ) {
710 _contentpane.removeAll();
717 if ( _mainpanel.getCurrentTreePanel() != null ) {
718 _mainpanel.getCurrentTreePanel().confColor();
723 if ( _mainpanel.getCurrentTreePanel() != null ) {
724 final String[] ranks = AptxUtil.getAllPossibleRanks();
725 final String rank = ( String ) JOptionPane
726 .showInputDialog( this,
727 "What rank should the colorization be based on",
729 JOptionPane.QUESTION_MESSAGE,
733 if ( !ForesterUtil.isEmpty( rank ) ) {
734 _mainpanel.getCurrentTreePanel().colorRank( rank );
739 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
740 if ( item != null ) {
741 item.setFont( MainFrame.menu_font );
742 if ( !getConfiguration().isUseNativeUI() ) {
743 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
744 item.setForeground( getConfiguration().getGuiMenuTextColor() );
746 item.setSelected( is_selected );
747 item.addActionListener( this );
751 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
753 jmi.setFont( MainFrame.menu_font );
754 if ( !getConfiguration().isUseNativeUI() ) {
755 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
756 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
758 jmi.addActionListener( this );
763 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
764 if ( item != null ) {
765 item.setFont( MainFrame.menu_font );
766 if ( !getConfiguration().isUseNativeUI() ) {
767 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
768 item.setForeground( getConfiguration().getGuiMenuTextColor() );
770 item.setSelected( is_selected );
771 item.addActionListener( this );
775 void exceptionOccuredDuringOpenFile( final Exception e ) {
777 _mainpanel.getCurrentTreePanel().setArrowCursor();
779 catch ( final Exception ex ) {
782 JOptionPane.showMessageDialog( this,
783 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
784 "Error during File|Open",
785 JOptionPane.ERROR_MESSAGE );
788 void exceptionOccuredDuringSaveAs( final Exception e ) {
790 _mainpanel.getCurrentTreePanel().setArrowCursor();
792 catch ( final Exception ex ) {
795 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
798 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
799 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
800 JOptionPane.showMessageDialog( this,
801 "Gene tree and species tree have no species in common.",
803 JOptionPane.ERROR_MESSAGE );
806 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
807 JOptionPane.showMessageDialog( this,
808 "Gene tree and species tree have only one species in common.",
810 JOptionPane.ERROR_MESSAGE );
818 public Configuration getConfiguration() {
819 return _configuration;
822 TreePanel getCurrentTreePanel() {
823 return getMainPanel().getCurrentTreePanel();
826 JMenu getHelpMenu() {
830 JCheckBoxMenuItem getlabelDirectionCbmi() {
831 return _label_direction_cbmi;
834 public MainPanel getMainPanel() {
838 JMenuBar getMenuBarOfMainFrame() {
842 public Options getOptions() {
846 void initializeTypeMenu( final Options options ) {
847 setTypeMenuToAllUnselected();
848 switch ( options.getPhylogenyGraphicsType() ) {
850 _convex_type_cbmi.setSelected( true );
853 _curved_type_cbmi.setSelected( true );
856 _euro_type_cbmi.setSelected( true );
859 _rounded_type_cbmi.setSelected( true );
862 _triangular_type_cbmi.setSelected( true );
865 _unrooted_type_cbmi.setSelected( true );
868 _circular_type_cbmi.setSelected( true );
871 _rectangular_type_cbmi.setSelected( true );
876 void midpointRoot() {
877 if ( _mainpanel.getCurrentTreePanel() != null ) {
878 _mainpanel.getCurrentTreePanel().midpointRoot();
882 abstract void readPhylogeniesFromURL();
884 void readPhylogeniesFromWebservice( final int i ) {
885 final UrlTreeReader reader = new UrlTreeReader( this, i );
886 new Thread( reader ).start();
889 private void removeBranchColors() {
890 if ( getMainPanel().getCurrentPhylogeny() != null ) {
891 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
895 void checkTextFrames() {
896 if ( _textframes.size() > 5 ) {
898 if ( _textframes.getFirst() != null ) {
899 _textframes.getFirst().removeMe();
902 _textframes.removeFirst();
905 catch ( final NoSuchElementException e ) {
911 void removeAllTextFrames() {
912 for( final TextFrame tf : _textframes ) {
920 void setConfiguration( final Configuration configuration ) {
921 _configuration = configuration;
924 void setOptions( final Options options ) {
928 void setInferenceManager( final InferenceManager i ) {
929 _inference_manager = i;
932 public InferenceManager getInferenceManager() {
933 return _inference_manager;
936 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
937 setTypeMenuToAllUnselected();
940 _circular_type_cbmi.setSelected( true );
943 _convex_type_cbmi.setSelected( true );
946 _curved_type_cbmi.setSelected( true );
949 _euro_type_cbmi.setSelected( true );
952 _rounded_type_cbmi.setSelected( true );
955 _rectangular_type_cbmi.setSelected( true );
958 _triangular_type_cbmi.setSelected( true );
961 _unrooted_type_cbmi.setSelected( true );
964 throw new IllegalArgumentException( "unknown type: " + type );
968 void setTypeMenuToAllUnselected() {
969 _convex_type_cbmi.setSelected( false );
970 _curved_type_cbmi.setSelected( false );
971 _euro_type_cbmi.setSelected( false );
972 _rounded_type_cbmi.setSelected( false );
973 _triangular_type_cbmi.setSelected( false );
974 _rectangular_type_cbmi.setSelected( false );
975 _unrooted_type_cbmi.setSelected( false );
976 _circular_type_cbmi.setSelected( false );
979 public void showWhole() {
980 _mainpanel.getControlPanel().showWhole();
983 void switchColors() {
984 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
985 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
986 csc.setVisible( true );
990 if ( _mainpanel.getCurrentTreePanel() != null ) {
991 _mainpanel.getCurrentTreePanel().taxColor();
995 void typeChanged( final Object o ) {
996 updateTypeCheckboxes( getOptions(), o );
997 updateOptions( getOptions() );
998 if ( getCurrentTreePanel() != null ) {
999 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1000 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1001 if ( ( ( 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 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1004 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1005 getCurrentTreePanel().getControlPanel().showWhole();
1007 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1008 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1011 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1013 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1014 updateScreenTextAntialias( getMainPanel().getTreePanels() );
1015 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1016 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1017 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1020 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1026 void updateOptions( final Options options ) {
1027 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1028 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1029 && _background_gradient_cbmi.isSelected() );
1030 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1031 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1032 && _abbreviate_scientific_names.isSelected() );
1033 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1034 && _color_labels_same_as_parent_branch.isSelected() );
1035 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1036 && _show_default_node_shapes_cbmi.isSelected() );
1037 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1038 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1039 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1040 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1042 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1043 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1045 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1046 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1048 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1049 && _search_case_senstive_cbmi.isSelected() );
1050 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1051 options.setShowScale( _show_scale_cbmi.isSelected() );
1053 if ( _label_direction_cbmi != null ) {
1054 if ( _label_direction_cbmi.isSelected() ) {
1055 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1058 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1061 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1062 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1063 && _show_confidence_stddev_cbmi.isSelected() );
1064 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1065 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1067 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1068 && ( _print_using_actual_size_cbmi.isSelected() ) );
1069 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1070 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1071 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1072 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1073 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1074 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1076 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1077 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1078 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1081 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1083 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1084 && _print_black_and_white_cbmi.isSelected() );
1085 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1086 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1087 options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
1088 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
1089 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1090 && _replace_underscores_cbmi.isSelected() );
1091 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1092 && _search_whole_words_only_cbmi.isSelected() );
1093 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1094 && _inverse_search_result_cbmi.isSelected() );
1095 if ( _graphics_export_visible_only_cbmi != null ) {
1096 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1097 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1098 _graphics_export_using_actual_size_cbmi.setSelected( true );
1099 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1102 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1105 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1106 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1108 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1109 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1111 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1112 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1114 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1115 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1117 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1118 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1120 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1121 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1123 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1124 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1126 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1127 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1131 void updateTypeCheckboxes( final Options options, final Object o ) {
1132 setTypeMenuToAllUnselected();
1133 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1136 void displayBasicInformation() {
1137 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1138 String title = "Basic Information";
1139 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1140 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1142 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
1146 void viewAsNexus() {
1147 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1148 String title = "Nexus";
1149 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1150 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1152 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1158 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1159 String title = "New Hampshire";
1160 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1161 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1163 showTextFrame( _mainpanel.getCurrentPhylogeny()
1164 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1170 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1171 String title = "NHX";
1172 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1173 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1175 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
1180 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1181 String title = "phyloXML";
1182 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1183 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1185 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1189 public void showTextFrame( final String s, final String title ) {
1191 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
1195 * Display the about box.
1197 static void about() {
1198 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1199 about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
1200 about.append( "All Rights Reserved\n" );
1201 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1202 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1203 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1204 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1205 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1206 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1207 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1209 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1210 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1211 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1212 + ForesterUtil.OS_VERSION + "]\n" );
1214 final Runtime rt = java.lang.Runtime.getRuntime();
1215 final long free_memory = rt.freeMemory() / 1000000;
1216 final long total_memory = rt.totalMemory() / 1000000;
1217 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1218 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1219 about.append( "References:\n" );
1220 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1221 about.append( "For more information & download:\n" );
1222 about.append( Constants.APTX_WEB_SITE + "\n" );
1223 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1224 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1227 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1228 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1231 static JMenu createMenu( final String title, final Configuration conf ) {
1232 final JMenu jmenu = new JMenu( title );
1233 if ( !conf.isUseNativeUI() ) {
1234 jmenu.setFont( MainFrame.menu_font );
1235 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1236 jmenu.setForeground( conf.getGuiMenuTextColor() );
1241 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1242 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1243 if ( !configuration.isUseNativeUI() ) {
1244 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1245 label.setForeground( configuration.getGuiMenuTextColor() );
1246 label.setOpaque( true );
1248 label.setSelected( false );
1249 label.setEnabled( false );
1253 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1254 switch ( op.getOvPlacement() ) {
1256 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1259 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1262 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1265 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1268 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1270 if ( tree_panel != null ) {
1271 tree_panel.updateOvSettings();
1275 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1276 switch ( op.getDefaultNodeFill() ) {
1278 op.setDefaultNodeFill( NodeFill.SOLID );
1281 op.setDefaultNodeFill( NodeFill.GRADIENT );
1284 op.setDefaultNodeFill( NodeFill.NONE );
1287 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1291 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1292 switch ( op.getDefaultNodeShape() ) {
1294 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1297 op.setDefaultNodeShape( NodeShape.CIRCLE );
1300 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1304 void help( final Map<String, WebLink> weblinks ) {
1305 final StringBuilder sb = new StringBuilder();
1306 sb.append( "Display options\n" );
1307 sb.append( "-------------------\n" );
1308 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1309 sb.append( "Clickable tree nodes\n" );
1310 sb.append( "--------------------\n" );
1311 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1312 sb.append( "or by right clicking:\n" );
1313 sb.append( "o Display Node Data -- display information for a node\n" );
1314 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1315 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1316 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1317 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1318 sb.append( "o Colorize Subtree -- color a subtree\n" );
1319 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1320 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1321 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1322 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1323 sb.append( "Zooming\n" );
1324 sb.append( "---------\n" );
1325 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1326 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1327 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1328 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1329 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1330 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1331 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1332 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1333 sb.append( "Quick tree manipulation:\n" );
1334 sb.append( "------------------------\n" );
1335 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1336 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1337 sb.append( "Memory problems (Java heap space error)\n" );
1338 sb.append( "---------------------------------------\n" );
1339 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1340 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1341 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1342 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1343 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1344 sb.append( "Active web links\n" );
1345 sb.append( "--------------------\n" );
1346 for( final String key : weblinks.keySet() ) {
1347 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1350 // + "General remarks\n"
1351 // + "---------------\n"
1353 // "o The application version permits copying to the clipboard \n"
1355 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1357 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1358 // + " but not any of its parent tree(s).\n"
1360 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1362 // " are likely to be bootstrap values instead of branch length values.\n\n"
1364 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1366 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1368 // " a species: either directly through the \"Species\" field, or the species\n"
1370 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1372 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1374 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1376 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1378 // "o !External nodes of the gene tree associated with species not present in\n"
1380 // " the species tree are REMOVED prior to SDI execution!\n"
1382 // "o Both the gene tree and the species tree must be completely binary.\n"
1384 // "o Duplications and speciations are a function of the position of the root.\n"
1386 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1387 // + " incorrect and need to be inferred again\n"
1389 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1391 sb.append( "phyloXML\n" );
1392 sb.append( "-------------------\n" );
1393 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1394 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1395 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1397 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1398 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1399 TextFrame.instantiate( sb.toString(), "Help", _textframes );
1402 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1403 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1404 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1407 mi.setText( "Cycle Overview Placement..." );
1411 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1412 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1413 mi.setText( "Cycle Node Shape Fill Type... (current: "
1414 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1417 mi.setText( "Cycle Node Shape Fill Type..." );
1421 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1422 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1423 mi.setText( "Cycle Node Shape Fill Type... (current: "
1424 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1427 mi.setText( "Cycle Node Shape Fill Type..." );
1431 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1432 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1433 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1436 mi.setText( "Select Colors..." );
1440 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1441 mi.setText( "Select Font... (current: " + font_desc + ")" );
1444 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1445 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1446 mi.setEnabled( true );
1448 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1449 mi.setEnabled( true );
1452 mi.setEnabled( false );
1454 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1457 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1458 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1461 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1462 final JCheckBoxMenuItem scale,
1463 final JCheckBoxMenuItem branch_lengths,
1464 final JRadioButtonMenuItem non_lined_up,
1465 final JRadioButtonMenuItem uniform_clado,
1466 final JRadioButtonMenuItem nonuniform_clado,
1467 final JCheckBoxMenuItem label_direction_cbmi ) {
1468 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1469 final ControlPanel control = main_panel.getControlPanel();
1470 final Options options = main_panel.getOptions();
1471 scale.setSelected( options.isShowScale() );
1472 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1473 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1474 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1475 scale.setSelected( false );
1476 scale.setEnabled( false );
1477 branch_lengths.setSelected( false );
1478 branch_lengths.setEnabled( false );
1480 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1481 scale.setSelected( false );
1482 scale.setEnabled( false );
1483 branch_lengths.setEnabled( true );
1486 scale.setEnabled( true );
1487 branch_lengths.setEnabled( true );
1489 if ( ( tree_panel != null )
1490 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1491 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1492 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1493 branch_lengths.setSelected( false );
1494 branch_lengths.setEnabled( false );
1496 if ( tree_panel != null ) {
1497 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1498 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1499 non_lined_up.setEnabled( false );
1500 uniform_clado.setEnabled( false );
1501 nonuniform_clado.setEnabled( false );
1504 non_lined_up.setEnabled( true );
1505 uniform_clado.setEnabled( true );
1506 nonuniform_clado.setEnabled( true );
1510 if ( ( tree_panel != null )
1511 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1512 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1513 branch_lengths.setSelected( false );
1514 branch_lengths.setEnabled( false );
1516 if ( ( tree_panel != null )
1517 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1518 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1519 non_lined_up.setEnabled( false );
1522 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1523 non_lined_up.setEnabled( true );
1526 label_direction_cbmi.setEnabled( true );
1527 if ( tree_panel != null ) {
1528 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1529 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1530 label_direction_cbmi.setEnabled( false );
1532 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1533 scale.setSelected( false );
1534 scale.setEnabled( false );
1539 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1540 for( final TreePanel tree_panel : treepanels ) {
1541 tree_panel.setTextAntialias();