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: https://sites.google.com/site/cmzmasek/home/software/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;
37 import java.util.NoSuchElementException;
40 import javax.swing.Box;
41 import javax.swing.JApplet;
42 import javax.swing.JCheckBoxMenuItem;
43 import javax.swing.JFrame;
44 import javax.swing.JLabel;
45 import javax.swing.JMenu;
46 import javax.swing.JMenuBar;
47 import javax.swing.JMenuItem;
48 import javax.swing.JOptionPane;
49 import javax.swing.JPanel;
50 import javax.swing.JRadioButtonMenuItem;
51 import javax.swing.JTextField;
52 import javax.swing.SwingUtilities;
54 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
55 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
56 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
57 import org.forester.archaeopteryx.tools.InferenceManager;
58 import org.forester.archaeopteryx.tools.ProcessPool;
59 import org.forester.archaeopteryx.tools.ProcessRunning;
60 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
61 import org.forester.phylogeny.Phylogeny;
62 import org.forester.phylogeny.PhylogenyMethods;
63 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
64 import org.forester.phylogeny.PhylogenyNode;
65 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
66 import org.forester.phylogeny.data.Annotation;
67 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
68 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
69 import org.forester.sdi.GSDI;
70 import org.forester.sdi.GSDIR;
71 import org.forester.sdi.SDIException;
72 import org.forester.util.ForesterConstants;
73 import org.forester.util.ForesterUtil;
75 public abstract class MainFrame extends JFrame implements ActionListener {
77 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
78 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
79 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
80 private static final long serialVersionUID = 3655000897845508358L;
81 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
84 static final String TYPE_MENU_HEADER = "Type";
85 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
86 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
87 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
88 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
89 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
90 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
91 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
92 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
93 static final String OPTIONS_HEADER = "Options";
94 static final String SEARCH_SUBHEADER = "Search:";
95 static final String DISPLAY_SUBHEADER = "Display:";
96 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
97 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
98 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
99 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
100 static final String DISPLAY_SCALE_LABEL = "Display Scale";
101 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
102 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
103 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
104 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
105 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
106 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
107 static final String BG_GRAD_LABEL = "Background Color Gradient";
108 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Show External Node Shapes";
109 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal Node Shapes";
110 static final String SHOW_OVERVIEW_LABEL = "Show Overview";
111 static final String FONT_SIZE_MENU_LABEL = "Font Size";
112 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
113 static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
114 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";
115 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
116 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
117 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
118 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
119 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
120 static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
121 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
122 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
123 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Show Basic Tree Information";
128 JMenu _options_jmenu;
129 JMenu _font_size_menu;
131 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
133 JMenu _analysis_menu;
134 JMenuItem _load_species_tree_item;
135 JMenuItem _gsdi_item;
136 JMenuItem _gsdir_item;
137 JMenuItem _lineage_inference;
138 JMenuItem _function_analysis;
140 JMenuItem _open_item;
141 JMenuItem _open_url_item;
142 JMenuItem _save_item;
143 JMenuItem _save_all_item;
144 JMenuItem _close_item;
145 JMenuItem _exit_item;
148 JMenuItem _midpoint_root_item;
149 JMenuItem _taxcolor_item;
150 JMenuItem _confcolor_item;
151 JMenuItem _color_rank_jmi;
152 JMenuItem _collapse_species_specific_subtrees;
153 JMenuItem _collapse_below_threshold; //TODO implememt me
154 JMenuItem _obtain_detailed_taxonomic_information_jmi;
155 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
156 JMenuItem _obtain_seq_information_jmi;
157 JMenuItem _move_node_names_to_tax_sn_jmi;
158 JMenuItem _move_node_names_to_seq_names_jmi;
159 JMenuItem _extract_tax_code_from_node_names_jmi;
160 JMenuItem _annotate_item;
162 JMenuItem _super_tiny_fonts_item;
163 JMenuItem _tiny_fonts_item;
164 JMenuItem _small_fonts_item;
165 JMenuItem _medium_fonts_item;
166 JMenuItem _large_fonts_item;
168 // _ screen and print
169 JMenuItem _choose_font_mi;
170 JMenuItem _switch_colors_mi;
171 JCheckBoxMenuItem _label_direction_cbmi;
173 JCheckBoxMenuItem _screen_antialias_cbmi;
174 JCheckBoxMenuItem _background_gradient_cbmi;
175 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
176 JRadioButtonMenuItem _uniform_cladograms_rbmi;
177 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
178 JCheckBoxMenuItem _show_branch_length_values_cbmi;
179 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
180 JCheckBoxMenuItem _show_overview_cbmi;
181 JCheckBoxMenuItem _show_domain_labels;
182 JCheckBoxMenuItem _abbreviate_scientific_names;
183 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
184 JMenuItem _overview_placment_mi;
185 JMenuItem _choose_minimal_confidence_mi;
186 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
187 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
188 JMenuItem _cycle_node_shape_mi;
189 JMenuItem _cycle_node_fill_mi;
190 JMenuItem _choose_node_size_mi;
191 JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
192 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
194 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
195 JCheckBoxMenuItem _antialias_print_cbmi;
196 JCheckBoxMenuItem _print_black_and_white_cbmi;
197 JCheckBoxMenuItem _print_using_actual_size_cbmi;
198 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
199 JMenuItem _print_size_mi;
200 JMenuItem _choose_pdf_width_mi;
202 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
203 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
204 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
205 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
206 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
207 JCheckBoxMenuItem _replace_underscores_cbmi;
208 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
209 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
211 JCheckBoxMenuItem _search_case_senstive_cbmi;
212 JCheckBoxMenuItem _search_whole_words_only_cbmi;
213 JCheckBoxMenuItem _inverse_search_result_cbmi;
216 JCheckBoxMenuItem _rectangular_type_cbmi;
217 JCheckBoxMenuItem _triangular_type_cbmi;
218 JCheckBoxMenuItem _curved_type_cbmi;
219 JCheckBoxMenuItem _convex_type_cbmi;
220 JCheckBoxMenuItem _euro_type_cbmi;
221 JCheckBoxMenuItem _rounded_type_cbmi;
222 JCheckBoxMenuItem _unrooted_type_cbmi;
223 JCheckBoxMenuItem _circular_type_cbmi;
224 // view as text menu:
225 JMenuItem _view_as_NH_item;
226 JMenuItem _view_as_XML_item;
227 JMenuItem _view_as_nexus_item;
228 JMenuItem _display_basic_information_item;
230 JMenuItem _about_item;
231 JMenuItem _help_item;
232 JMenuItem _website_item;
233 JMenuItem _phyloxml_website_item;
234 JMenuItem _phyloxml_ref_item;
235 JMenuItem _aptx_ref_item;
238 // Handy pointers to child components:
239 MainPanel _mainpanel;
240 Container _contentpane;
241 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
242 Configuration _configuration;
243 JMenuItem _remove_branch_color_item;
245 private Phylogeny _species_tree;
246 InferenceManager _inference_manager;
247 final ProcessPool _process_pool;
248 private String _previous_node_annotation_ref;
251 _process_pool = ProcessPool.createInstance();
258 public void actionPerformed( final ActionEvent e ) {
259 final Object o = e.getSource();
260 boolean is_applet = false;
261 JApplet applet = null;
262 if ( getCurrentTreePanel() != null ) {
263 is_applet = getCurrentTreePanel().isApplet();
265 applet = getCurrentTreePanel().obtainApplet();
268 if ( o == _open_url_item ) {
269 readPhylogeniesFromURL();
271 else if ( o == _exit_item ) {
274 else if ( o == _gsdi_item ) {
275 if ( isSubtreeDisplayed() ) {
280 else if ( o == _gsdir_item ) {
281 if ( isSubtreeDisplayed() ) {
286 else if ( o == _taxcolor_item ) {
289 else if ( o == _confcolor_item ) {
292 else if ( o == _color_rank_jmi ) {
295 else if ( o == _collapse_species_specific_subtrees ) {
296 if ( isSubtreeDisplayed() ) {
299 if ( getCurrentTreePanel() != null ) {
300 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
303 else if ( o == _remove_branch_color_item ) {
304 if ( isSubtreeDisplayed() ) {
307 removeBranchColors();
309 else if ( o == _midpoint_root_item ) {
310 if ( isSubtreeDisplayed() ) {
315 else if ( o == _annotate_item ) {
318 else if ( o == _switch_colors_mi ) {
321 else if ( o == _display_basic_information_item ) {
322 displayBasicInformation();
324 else if ( o == _view_as_NH_item ) {
327 else if ( o == _view_as_XML_item ) {
330 else if ( o == _view_as_nexus_item ) {
333 else if ( o == _super_tiny_fonts_item ) {
334 if ( getCurrentTreePanel() != null ) {
335 getCurrentTreePanel().setSuperTinyFonts();
336 getCurrentTreePanel().repaint();
339 else if ( o == _tiny_fonts_item ) {
340 if ( getCurrentTreePanel() != null ) {
341 getCurrentTreePanel().setTinyFonts();
342 getCurrentTreePanel().repaint();
345 else if ( o == _small_fonts_item ) {
346 if ( getCurrentTreePanel() != null ) {
347 getCurrentTreePanel().setSmallFonts();
348 getCurrentTreePanel().repaint();
351 else if ( o == _medium_fonts_item ) {
352 if ( getCurrentTreePanel() != null ) {
353 getCurrentTreePanel().setMediumFonts();
354 getCurrentTreePanel().repaint();
357 else if ( o == _large_fonts_item ) {
358 if ( getCurrentTreePanel() != null ) {
359 getCurrentTreePanel().setLargeFonts();
360 getCurrentTreePanel().repaint();
363 else if ( o == _choose_font_mi ) {
366 else if ( o == _choose_minimal_confidence_mi ) {
367 chooseMinimalConfidence();
369 else if ( o == _choose_node_size_mi ) {
370 chooseNodeSize( getOptions(), this );
372 else if ( o == _overview_placment_mi ) {
373 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
375 else if ( o == _cycle_node_fill_mi ) {
376 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
378 else if ( o == _cycle_node_shape_mi ) {
379 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
381 else if ( o == _screen_antialias_cbmi ) {
382 updateOptions( getOptions() );
383 updateScreenTextAntialias( getMainPanel().getTreePanels() );
385 else if ( o == _background_gradient_cbmi ) {
386 updateOptions( getOptions() );
388 else if ( o == _show_domain_labels ) {
389 updateOptions( getOptions() );
391 else if ( o == _abbreviate_scientific_names ) {
392 updateOptions( getOptions() );
394 else if ( o == _color_labels_same_as_parent_branch ) {
395 updateOptions( getOptions() );
397 else if ( o == _show_default_node_shapes_internal_cbmi ) {
398 updateOptions( getOptions() );
400 else if ( o == _show_default_node_shapes_external_cbmi ) {
401 updateOptions( getOptions() );
403 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
404 updateOptions( getOptions() );
406 else if ( o == _non_lined_up_cladograms_rbmi ) {
407 updateOptions( getOptions() );
410 else if ( o == _uniform_cladograms_rbmi ) {
411 updateOptions( getOptions() );
414 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
415 updateOptions( getOptions() );
418 else if ( o == _search_case_senstive_cbmi ) {
419 updateOptions( getOptions() );
420 getMainPanel().getControlPanel().search();
422 else if ( o == _search_whole_words_only_cbmi ) {
423 updateOptions( getOptions() );
424 getMainPanel().getControlPanel().search();
426 else if ( o == _inverse_search_result_cbmi ) {
427 updateOptions( getOptions() );
428 getMainPanel().getControlPanel().search();
430 else if ( o == _show_scale_cbmi ) {
431 updateOptions( getOptions() );
433 else if ( o == _show_branch_length_values_cbmi ) {
434 updateOptions( getOptions() );
436 else if ( o == _show_confidence_stddev_cbmi ) {
437 updateOptions( getOptions() );
439 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
440 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
441 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
443 updateOptions( getOptions() );
445 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
446 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
447 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
449 updateOptions( getOptions() );
451 else if ( o == _label_direction_cbmi ) {
452 updateOptions( getOptions() );
454 else if ( o == _show_overview_cbmi ) {
455 updateOptions( getOptions() );
456 if ( getCurrentTreePanel() != null ) {
457 getCurrentTreePanel().updateOvSizes();
460 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
461 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
462 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
465 else if ( o == _about_item ) {
468 else if ( o == _help_item ) {
471 else if ( o == _website_item ) {
473 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
475 catch ( final IOException e1 ) {
476 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
479 else if ( o == _phyloxml_website_item ) {
481 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
483 catch ( final IOException e1 ) {
484 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
487 else if ( o == _aptx_ref_item ) {
489 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
491 catch ( final IOException e1 ) {
492 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
495 else if ( o == _phyloxml_ref_item ) {
497 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
499 catch ( final IOException e1 ) {
500 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
504 if ( _load_phylogeny_from_webservice_menu_items != null ) {
505 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
506 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
507 readPhylogeniesFromWebservice( i );
512 _contentpane.repaint();
515 public Configuration getConfiguration() {
516 return _configuration;
520 * This method returns the current external node data which
521 * has been selected by the user by clicking the "Return ..."
522 * menu item. This method is expected to be called from Javascript or
525 * @return current external node data as String
527 public String getCurrentExternalNodesDataBuffer() {
528 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
531 public int getCurrentExternalNodesDataBufferChangeCounter() {
532 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
535 public int getCurrentExternalNodesDataBufferLength() {
536 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
539 public InferenceManager getInferenceManager() {
540 return _inference_manager;
543 public MainPanel getMainPanel() {
547 public Options getOptions() {
551 public ProcessPool getProcessPool() {
552 return _process_pool;
555 public void showTextFrame( final String s, final String title ) {
557 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
560 public void showWhole() {
561 _mainpanel.getControlPanel().showWhole();
564 public void updateProcessMenu() {
565 // In general Swing is not thread safe.
566 // See "Swing's Threading Policy".
567 SwingUtilities.invokeLater( new Runnable() {
571 doUpdateProcessMenu();
576 void activateSaveAllIfNeeded() {
577 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
578 _save_all_item.setEnabled( true );
581 _save_all_item.setEnabled( false );
585 void buildFileMenu() {
586 _file_jmenu = createMenu( "File", getConfiguration() );
587 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
588 _file_jmenu.addSeparator();
589 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
590 customizeJMenuItem( _open_url_item );
591 customizeJMenuItem( _exit_item );
592 _jmenubar.add( _file_jmenu );
595 void buildFontSizeMenu() {
596 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
597 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
598 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
599 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
600 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
601 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
602 customizeJMenuItem( _super_tiny_fonts_item );
603 customizeJMenuItem( _tiny_fonts_item );
604 customizeJMenuItem( _small_fonts_item );
605 customizeJMenuItem( _medium_fonts_item );
606 customizeJMenuItem( _large_fonts_item );
607 _jmenubar.add( _font_size_menu );
610 void buildHelpMenu() {
611 _help_jmenu = createMenu( "Help", getConfiguration() );
612 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
613 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
614 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
615 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
616 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
617 _help_jmenu.addSeparator();
618 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
619 customizeJMenuItem( _help_item );
620 customizeJMenuItem( _website_item );
621 customizeJMenuItem( _phyloxml_website_item );
622 customizeJMenuItem( _aptx_ref_item );
623 customizeJMenuItem( _phyloxml_ref_item );
624 customizeJMenuItem( _about_item );
625 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
626 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
627 _jmenubar.add( _help_jmenu );
630 void buildTypeMenu() {
631 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
632 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
633 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
634 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
635 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
636 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
637 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
638 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
639 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
640 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
641 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
642 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
643 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
644 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
645 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
646 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
647 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
648 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
649 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
650 initializeTypeMenu( getOptions() );
651 _jmenubar.add( _type_menu );
654 void buildViewMenu() {
655 _view_jmenu = createMenu( "View", getConfiguration() );
656 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
657 _view_jmenu.addSeparator();
658 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
659 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
660 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
661 customizeJMenuItem( _display_basic_information_item );
662 customizeJMenuItem( _view_as_NH_item );
663 customizeJMenuItem( _view_as_XML_item );
664 customizeJMenuItem( _view_as_nexus_item );
665 _jmenubar.add( _view_jmenu );
668 void checkTextFrames() {
669 if ( _textframes.size() > 5 ) {
671 if ( _textframes.getFirst() != null ) {
672 _textframes.getFirst().removeMe();
675 _textframes.removeFirst();
678 catch ( final NoSuchElementException e ) {
685 removeAllTextFrames();
686 if ( _mainpanel != null ) {
687 _mainpanel.terminate();
689 if ( _contentpane != null ) {
690 _contentpane.removeAll();
697 if ( _mainpanel.getCurrentTreePanel() != null ) {
698 final String[] ranks = AptxUtil.getAllPossibleRanks();
699 final String rank = ( String ) JOptionPane
700 .showInputDialog( this,
701 "What rank should the colorization be based on",
703 JOptionPane.QUESTION_MESSAGE,
707 if ( !ForesterUtil.isEmpty( rank ) ) {
708 _mainpanel.getCurrentTreePanel().colorRank( rank );
714 if ( _mainpanel.getCurrentTreePanel() != null ) {
715 _mainpanel.getCurrentTreePanel().confColor();
719 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
720 if ( item != null ) {
721 item.setFont( MainFrame.menu_font );
722 if ( !getConfiguration().isUseNativeUI() ) {
723 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
724 item.setForeground( getConfiguration().getGuiMenuTextColor() );
726 item.setSelected( is_selected );
727 item.addActionListener( this );
731 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
733 jmi.setFont( MainFrame.menu_font );
734 if ( !getConfiguration().isUseNativeUI() ) {
735 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
736 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
738 jmi.addActionListener( this );
743 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
744 if ( item != null ) {
745 item.setFont( MainFrame.menu_font );
746 if ( !getConfiguration().isUseNativeUI() ) {
747 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
748 item.setForeground( getConfiguration().getGuiMenuTextColor() );
750 item.setSelected( is_selected );
751 item.addActionListener( this );
755 void displayBasicInformation() {
756 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
757 String title = "Basic Information";
758 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
759 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
761 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
765 void exceptionOccuredDuringOpenFile( final Exception e ) {
767 _mainpanel.getCurrentTreePanel().setArrowCursor();
769 catch ( final Exception ex ) {
772 JOptionPane.showMessageDialog( this,
773 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
774 "Error during File|Open",
775 JOptionPane.ERROR_MESSAGE );
778 void exceptionOccuredDuringSaveAs( final Exception e ) {
780 _mainpanel.getCurrentTreePanel().setArrowCursor();
782 catch ( final Exception ex ) {
785 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
789 if ( !isOKforSDI( false, true ) ) {
792 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
793 JOptionPane.showMessageDialog( this,
794 "Gene tree is not rooted.",
795 "Cannot execute GSDI",
796 JOptionPane.ERROR_MESSAGE );
799 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
800 gene_tree.setAllNodesToNotCollapse();
801 gene_tree.recalculateNumberOfExternalDescendants( false );
803 final Phylogeny species_tree = getSpeciesTree().copy();
805 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
807 catch ( final SDIException e ) {
808 JOptionPane.showMessageDialog( this,
809 e.getLocalizedMessage(),
811 JOptionPane.ERROR_MESSAGE );
814 catch ( final Exception e ) {
815 AptxUtil.unexpectedException( e );
818 gene_tree.setRerootable( false );
819 gene_tree.clearHashIdToNodeMap();
820 gene_tree.recalculateNumberOfExternalDescendants( true );
821 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
822 getMainPanel().getControlPanel().setShowEvents( true );
824 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
825 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
827 _mainpanel.getTabbedPane().setSelectedIndex( selected );
829 _mainpanel.getCurrentTreePanel().setEdited( true );
830 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
831 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
832 JOptionPane.showMessageDialog( this,
833 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
834 + "Potential duplications: "
835 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
836 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
837 + "Stripped gene tree nodes: "
838 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
839 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
840 + "Number of polytomies in species tree used: " + poly + "\n",
841 "GSDI successfully completed",
842 JOptionPane.WARNING_MESSAGE );
845 JOptionPane.showMessageDialog( this,
846 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
847 + "Potential duplications: "
848 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
849 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
850 + "Stripped gene tree nodes: "
851 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
852 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
853 + "Number of polytomies in species tree used: " + poly + "\n",
854 "GSDI successfully completed",
855 JOptionPane.INFORMATION_MESSAGE );
859 void executeGSDIR() {
860 if ( !isOKforSDI( false, false ) ) {
863 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
865 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
866 JOptionPane.showMessageDialog( this,
867 "Gene tree is not completely binary",
868 "Cannot execute GSDI",
869 JOptionPane.ERROR_MESSAGE );
872 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
873 gene_tree.setAllNodesToNotCollapse();
874 gene_tree.recalculateNumberOfExternalDescendants( false );
876 final Phylogeny species_tree = getSpeciesTree().copy();
878 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
880 catch ( final SDIException e ) {
881 JOptionPane.showMessageDialog( this,
882 e.getLocalizedMessage(),
883 "Error during GSDIR",
884 JOptionPane.ERROR_MESSAGE );
887 catch ( final Exception e ) {
888 AptxUtil.unexpectedException( e );
891 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
892 result_gene_tree.setRerootable( false );
893 result_gene_tree.clearHashIdToNodeMap();
894 result_gene_tree.recalculateNumberOfExternalDescendants( true );
895 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
896 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
897 getMainPanel().getControlPanel().setShowEvents( true );
899 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
900 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
902 _mainpanel.getTabbedPane().setSelectedIndex( selected );
904 _mainpanel.getCurrentTreePanel().setEdited( true );
905 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
906 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
907 JOptionPane.showMessageDialog( this,
908 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
909 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
910 + "Stripped gene tree nodes: "
911 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
912 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
913 + "Number of polytomies in species tree used: " + poly + "\n",
914 "GSDIR successfully completed",
915 JOptionPane.WARNING_MESSAGE );
918 JOptionPane.showMessageDialog( this,
919 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
920 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
921 + "Stripped gene tree nodes: "
922 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
923 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
924 + "Number of polytomies in species tree used: " + poly + "\n",
925 "GSDIR successfully completed",
926 JOptionPane.INFORMATION_MESSAGE );
930 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
931 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
932 JOptionPane.showMessageDialog( this,
933 "Gene tree and species tree have no species in common.",
935 JOptionPane.ERROR_MESSAGE );
938 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
939 JOptionPane.showMessageDialog( this,
940 "Gene tree and species tree have only one species in common.",
942 JOptionPane.ERROR_MESSAGE );
950 TreePanel getCurrentTreePanel() {
951 return getMainPanel().getCurrentTreePanel();
954 JMenu getHelpMenu() {
958 JCheckBoxMenuItem getlabelDirectionCbmi() {
959 return _label_direction_cbmi;
962 JMenuBar getMenuBarOfMainFrame() {
966 final Phylogeny getSpeciesTree() {
967 return _species_tree;
971 final StringBuilder sb = new StringBuilder();
972 sb.append( "Display options\n" );
973 sb.append( "-------------------\n" );
974 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
975 sb.append( "Clickable tree nodes\n" );
976 sb.append( "--------------------\n" );
977 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
978 sb.append( "or by right clicking:\n" );
979 sb.append( "o Display Node Data -- display information for a node\n" );
980 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
981 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
982 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
983 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
984 sb.append( "o Colorize Subtree -- color a subtree\n" );
985 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
986 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
987 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
988 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
989 sb.append( "Zooming\n" );
990 sb.append( "---------\n" );
991 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
992 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
993 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
994 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
995 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
996 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
997 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
998 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
999 sb.append( "Quick tree manipulation:\n" );
1000 sb.append( "------------------------\n" );
1001 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1002 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1003 sb.append( "Memory problems (Java heap space error)\n" );
1004 sb.append( "---------------------------------------\n" );
1005 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1006 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1007 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1008 sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1009 // + "General remarks\n"
1010 // + "---------------\n"
1012 // "o The application version permits copying to the clipboard \n"
1014 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1016 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1017 // + " but not any of its parent tree(s).\n"
1019 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1021 // " are likely to be bootstrap values instead of branch length values.\n\n"
1023 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1025 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1027 // " a species: either directly through the \"Species\" field, or the species\n"
1029 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1031 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1033 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1035 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1037 // "o !External nodes of the gene tree associated with species not present in\n"
1039 // " the species tree are REMOVED prior to SDI execution!\n"
1041 // "o Both the gene tree and the species tree must be completely binary.\n"
1043 // "o Duplications and speciations are a function of the position of the root.\n"
1045 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1046 // + " incorrect and need to be inferred again\n"
1048 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1049 sb.append( "phyloXML\n" );
1050 sb.append( "-------------------\n" );
1051 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1052 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1053 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1055 sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
1056 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1057 TextFrame.instantiate( sb.toString(), "Help", _textframes );
1060 void initializeTypeMenu( final Options options ) {
1061 setTypeMenuToAllUnselected();
1062 switch ( options.getPhylogenyGraphicsType() ) {
1064 _convex_type_cbmi.setSelected( true );
1067 _curved_type_cbmi.setSelected( true );
1070 _euro_type_cbmi.setSelected( true );
1073 _rounded_type_cbmi.setSelected( true );
1076 _triangular_type_cbmi.setSelected( true );
1079 _unrooted_type_cbmi.setSelected( true );
1082 _circular_type_cbmi.setSelected( true );
1085 _rectangular_type_cbmi.setSelected( true );
1090 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1091 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1094 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
1095 JOptionPane.showMessageDialog( this,
1096 "No species tree loaded",
1097 "Cannot execute GSDI",
1098 JOptionPane.ERROR_MESSAGE );
1101 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
1102 JOptionPane.showMessageDialog( this,
1103 "Species tree is not completely binary",
1104 "Cannot execute GSDI",
1105 JOptionPane.ERROR_MESSAGE );
1108 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1109 JOptionPane.showMessageDialog( this,
1110 "Gene tree is not completely binary",
1111 "Cannot execute GSDI",
1112 JOptionPane.ERROR_MESSAGE );
1120 boolean isSubtreeDisplayed() {
1121 if ( getCurrentTreePanel() != null ) {
1122 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1124 .showMessageDialog( this,
1125 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1126 "Operation can not be exectuted on a sub-tree",
1127 JOptionPane.WARNING_MESSAGE );
1134 void midpointRoot() {
1135 if ( _mainpanel.getCurrentTreePanel() != null ) {
1136 _mainpanel.getCurrentTreePanel().midpointRoot();
1140 abstract void readPhylogeniesFromURL();
1142 void readPhylogeniesFromWebservice( final int i ) {
1143 final UrlTreeReader reader = new UrlTreeReader( this, i );
1144 new Thread( reader ).start();
1147 void removeAllTextFrames() {
1148 for( final TextFrame tf : _textframes ) {
1153 _textframes.clear();
1156 void setConfiguration( final Configuration configuration ) {
1157 _configuration = configuration;
1160 void setInferenceManager( final InferenceManager i ) {
1161 _inference_manager = i;
1164 void setOptions( final Options options ) {
1168 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1169 setTypeMenuToAllUnselected();
1172 _circular_type_cbmi.setSelected( true );
1175 _convex_type_cbmi.setSelected( true );
1178 _curved_type_cbmi.setSelected( true );
1181 _euro_type_cbmi.setSelected( true );
1184 _rounded_type_cbmi.setSelected( true );
1187 _rectangular_type_cbmi.setSelected( true );
1190 _triangular_type_cbmi.setSelected( true );
1193 _unrooted_type_cbmi.setSelected( true );
1196 throw new IllegalArgumentException( "unknown type: " + type );
1200 final void setSpeciesTree( final Phylogeny species_tree ) {
1201 _species_tree = species_tree;
1204 void setTypeMenuToAllUnselected() {
1205 _convex_type_cbmi.setSelected( false );
1206 _curved_type_cbmi.setSelected( false );
1207 _euro_type_cbmi.setSelected( false );
1208 _rounded_type_cbmi.setSelected( false );
1209 _triangular_type_cbmi.setSelected( false );
1210 _rectangular_type_cbmi.setSelected( false );
1211 _unrooted_type_cbmi.setSelected( false );
1212 _circular_type_cbmi.setSelected( false );
1215 void switchColors() {
1216 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
1217 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1218 csc.setVisible( true );
1222 if ( _mainpanel.getCurrentTreePanel() != null ) {
1223 _mainpanel.getCurrentTreePanel().taxColor();
1227 void typeChanged( final Object o ) {
1228 updateTypeCheckboxes( getOptions(), o );
1229 updateOptions( getOptions() );
1230 if ( getCurrentTreePanel() != null ) {
1231 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1232 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1233 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1234 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1235 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1236 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1237 getCurrentTreePanel().getControlPanel().showWhole();
1239 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1240 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1243 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1245 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1246 updateScreenTextAntialias( getMainPanel().getTreePanels() );
1247 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1248 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1249 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1252 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1258 void updateOptions( final Options options ) {
1259 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1260 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1261 && _background_gradient_cbmi.isSelected() );
1262 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1263 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1264 && _abbreviate_scientific_names.isSelected() );
1265 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1266 && _color_labels_same_as_parent_branch.isSelected() );
1267 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1268 && _show_default_node_shapes_internal_cbmi.isSelected() );
1269 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1270 && _show_default_node_shapes_external_cbmi.isSelected() );
1271 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1272 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1273 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1274 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1276 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1277 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1279 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1280 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1282 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1283 && _search_case_senstive_cbmi.isSelected() );
1284 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1285 options.setShowScale( _show_scale_cbmi.isSelected() );
1287 if ( _label_direction_cbmi != null ) {
1288 if ( _label_direction_cbmi.isSelected() ) {
1289 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1292 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1295 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1296 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1297 && _show_confidence_stddev_cbmi.isSelected() );
1298 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1299 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1301 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1302 && ( _print_using_actual_size_cbmi.isSelected() ) );
1303 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1304 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1305 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1306 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1307 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1308 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1310 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1311 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1312 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1315 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1317 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1318 && _print_black_and_white_cbmi.isSelected() );
1319 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1320 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1321 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
1322 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1324 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
1325 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1327 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
1328 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1330 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
1331 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1333 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1334 && _replace_underscores_cbmi.isSelected() );
1335 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1336 && _search_whole_words_only_cbmi.isSelected() );
1337 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1338 && _inverse_search_result_cbmi.isSelected() );
1339 if ( _graphics_export_visible_only_cbmi != null ) {
1340 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1341 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1342 _graphics_export_using_actual_size_cbmi.setSelected( true );
1343 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1346 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1349 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1350 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1352 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1353 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1355 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1356 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1358 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1359 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1361 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1362 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1364 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1365 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1367 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1368 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1370 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1371 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1375 void updateTypeCheckboxes( final Options options, final Object o ) {
1376 setTypeMenuToAllUnselected();
1377 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1380 void viewAsNexus() {
1381 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1382 String title = "Nexus";
1383 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1384 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1386 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1392 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1393 String title = "New Hampshire";
1394 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1395 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1397 showTextFrame( _mainpanel.getCurrentPhylogeny()
1398 .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1404 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1405 String title = "phyloXML";
1406 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1407 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1409 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1413 private void annotateSequences() {
1414 if ( getCurrentTreePanel() != null ) {
1415 final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
1416 if ( ( nodes == null ) || nodes.isEmpty() ) {
1418 .showMessageDialog( this,
1419 "Need to select nodes, either via direct selection or via the \"Search\" function",
1420 "No nodes selected for annotation",
1421 JOptionPane.ERROR_MESSAGE );
1424 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
1425 if ( ( phy != null ) && !phy.isEmpty() ) {
1426 final JTextField ref_field = new JTextField( 10 );
1427 final JTextField desc_filed = new JTextField( 20 );
1428 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
1429 : getPreviousNodeAnnotationReference() );
1430 final JPanel my_panel = new JPanel();
1431 my_panel.add( new JLabel( "Reference " ) );
1432 my_panel.add( ref_field );
1433 my_panel.add( Box.createHorizontalStrut( 15 ) );
1434 my_panel.add( new JLabel( "Description " ) );
1435 my_panel.add( desc_filed );
1436 final int result = JOptionPane.showConfirmDialog( null,
1438 "Enter the sequence annotation(s) for the "
1439 + nodes.size() + " selected nodes",
1440 JOptionPane.OK_CANCEL_OPTION );
1441 if ( result == JOptionPane.OK_OPTION ) {
1442 String ref = ref_field.getText();
1443 String desc = desc_filed.getText();
1444 if ( !ForesterUtil.isEmpty( ref ) ) {
1446 ref = ref.replaceAll( "\\s+", " " );
1447 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
1448 || ( ref.length() < 3 ) ) {
1449 JOptionPane.showMessageDialog( this,
1450 "Reference needs to be in the form of \"GO:1234567\"",
1451 "Illegal Format for Annotation Reference",
1452 JOptionPane.ERROR_MESSAGE );
1456 if ( ref != null ) {
1457 setPreviousNodeAnnotationReference( ref );
1459 if ( desc != null ) {
1461 desc = desc.replaceAll( "\\s+", " " );
1463 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
1464 for( final Long id : nodes ) {
1465 final PhylogenyNode n = phy.getNode( id );
1466 ForesterUtil.ensurePresenceOfSequence( n );
1467 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
1468 : new Annotation( ref );
1469 if ( !ForesterUtil.isEmpty( desc ) ) {
1470 ann.setDesc( desc );
1472 n.getNodeData().getSequence().addAnnotation( ann );
1475 getMainPanel().getControlPanel().showAnnotations();
1481 private void chooseFont() {
1482 final FontChooser fc = new FontChooser();
1483 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1484 fc.showDialog( this, "Select the Base Font" );
1485 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1488 private void chooseMinimalConfidence() {
1489 final String s = ( String ) JOptionPane
1490 .showInputDialog( this,
1491 "Please enter the minimum for confidence values to be displayed.\n"
1492 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
1493 "Minimal Confidence Value",
1494 JOptionPane.QUESTION_MESSAGE,
1497 getOptions().getMinConfidenceValue() );
1498 if ( !ForesterUtil.isEmpty( s ) ) {
1499 boolean success = true;
1501 final String m_str = s.trim();
1502 if ( !ForesterUtil.isEmpty( m_str ) ) {
1504 m = Double.parseDouble( m_str );
1506 catch ( final Exception ex ) {
1513 if ( success && ( m >= 0.0 ) ) {
1514 getOptions().setMinConfidenceValue( m );
1519 private void doUpdateProcessMenu() {
1520 if ( _process_pool.size() > 0 ) {
1521 if ( _process_menu == null ) {
1522 _process_menu = createMenu( "", getConfiguration() );
1523 _process_menu.setForeground( Color.RED );
1525 _process_menu.removeAll();
1526 final String text = "processes running: " + _process_pool.size();
1527 _process_menu.setText( text );
1528 _jmenubar.add( _process_menu );
1529 for( int i = 0; i < _process_pool.size(); ++i ) {
1530 final ProcessRunning p = _process_pool.getProcessByIndex( i );
1531 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
1535 if ( _process_menu != null ) {
1536 _process_menu.removeAll();
1537 _jmenubar.remove( _process_menu );
1540 _jmenubar.validate();
1541 _jmenubar.repaint();
1545 private String getPreviousNodeAnnotationReference() {
1546 return _previous_node_annotation_ref;
1549 private void removeBranchColors() {
1550 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1551 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1555 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
1556 _previous_node_annotation_ref = previous_node_annotation_ref;
1560 * Display the about box.
1562 static void about() {
1563 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1564 about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
1565 about.append( "All Rights Reserved\n" );
1566 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1567 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1568 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1569 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1570 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1571 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1572 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1574 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1575 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1576 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1577 + ForesterUtil.OS_VERSION + "]\n" );
1579 final Runtime rt = java.lang.Runtime.getRuntime();
1580 final long free_memory = rt.freeMemory() / 1000000;
1581 final long total_memory = rt.totalMemory() / 1000000;
1582 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1583 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1584 about.append( "References:\n" );
1585 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1586 about.append( "For more information & download:\n" );
1587 about.append( Constants.APTX_WEB_SITE + "\n" );
1588 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1589 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1592 static void chooseNodeSize( final Options options, final Component parent ) {
1593 final String s = ( String ) JOptionPane.showInputDialog( parent,
1594 "Please enter the default size for node shapes.\n"
1595 + "[current value: "
1596 + options.getDefaultNodeShapeSize() + "]\n",
1598 JOptionPane.QUESTION_MESSAGE,
1601 options.getDefaultNodeShapeSize() );
1602 if ( !ForesterUtil.isEmpty( s ) ) {
1603 boolean success = true;
1605 final String m_str = s.trim();
1606 if ( !ForesterUtil.isEmpty( m_str ) ) {
1608 m = Double.parseDouble( m_str );
1610 catch ( final Exception ex ) {
1617 if ( success && ( m >= 0.0 ) ) {
1618 final short size = ForesterUtil.roundToShort( m );
1619 if ( size >= 0.0 ) {
1620 options.setDefaultNodeShapeSize( size );
1626 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1627 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1630 static JMenu createMenu( final String title, final Configuration conf ) {
1631 final JMenu jmenu = new JMenu( title );
1632 if ( !conf.isUseNativeUI() ) {
1633 jmenu.setFont( MainFrame.menu_font );
1634 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1635 jmenu.setForeground( conf.getGuiMenuTextColor() );
1640 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1641 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1642 if ( !configuration.isUseNativeUI() ) {
1643 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1644 label.setForeground( configuration.getGuiMenuTextColor() );
1645 label.setOpaque( true );
1647 label.setSelected( false );
1648 label.setEnabled( false );
1652 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1653 switch ( op.getDefaultNodeFill() ) {
1655 op.setDefaultNodeFill( NodeFill.SOLID );
1658 op.setDefaultNodeFill( NodeFill.GRADIENT );
1661 op.setDefaultNodeFill( NodeFill.NONE );
1664 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1668 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1669 switch ( op.getDefaultNodeShape() ) {
1671 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1674 op.setDefaultNodeShape( NodeShape.CIRCLE );
1677 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1681 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1682 switch ( op.getOvPlacement() ) {
1684 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1687 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1690 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1693 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1696 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1698 if ( tree_panel != null ) {
1699 tree_panel.updateOvSettings();
1703 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1704 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1705 mi.setText( "Cycle Node Shape Fill Type... (current: "
1706 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1709 mi.setText( "Cycle Node Shape Fill Type..." );
1713 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1714 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1715 mi.setText( "Cycle Node Shape Fill Type... (current: "
1716 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1719 mi.setText( "Cycle Node Shape Fill Type..." );
1723 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1724 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1725 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1728 mi.setText( "Cycle Overview Placement..." );
1732 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1733 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1734 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1737 mi.setText( "Select Colors..." );
1741 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1742 mi.setText( "Select Font... (current: " + font_desc + ")" );
1745 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1746 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1747 mi.setEnabled( true );
1749 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1750 mi.setEnabled( true );
1753 mi.setEnabled( false );
1755 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1758 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1759 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1762 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1763 final JCheckBoxMenuItem scale,
1764 final JCheckBoxMenuItem branch_lengths,
1765 final JRadioButtonMenuItem non_lined_up,
1766 final JRadioButtonMenuItem uniform_clado,
1767 final JRadioButtonMenuItem nonuniform_clado,
1768 final JCheckBoxMenuItem label_direction_cbmi ) {
1769 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1770 final ControlPanel control = main_panel.getControlPanel();
1771 final Options options = main_panel.getOptions();
1772 scale.setSelected( options.isShowScale() );
1773 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1774 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1775 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1776 scale.setSelected( false );
1777 scale.setEnabled( false );
1778 branch_lengths.setSelected( false );
1779 branch_lengths.setEnabled( false );
1781 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1782 scale.setSelected( false );
1783 scale.setEnabled( false );
1784 branch_lengths.setEnabled( true );
1787 scale.setEnabled( true );
1788 branch_lengths.setEnabled( true );
1790 if ( ( tree_panel != null )
1791 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1792 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1793 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1794 branch_lengths.setSelected( false );
1795 branch_lengths.setEnabled( false );
1797 if ( tree_panel != null ) {
1798 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1799 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1800 non_lined_up.setEnabled( false );
1801 uniform_clado.setEnabled( false );
1802 nonuniform_clado.setEnabled( false );
1805 non_lined_up.setEnabled( true );
1806 uniform_clado.setEnabled( true );
1807 nonuniform_clado.setEnabled( true );
1811 if ( ( tree_panel != null )
1812 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1813 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1814 branch_lengths.setSelected( false );
1815 branch_lengths.setEnabled( false );
1817 if ( ( tree_panel != null )
1818 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1819 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1820 non_lined_up.setEnabled( false );
1823 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1824 non_lined_up.setEnabled( true );
1827 label_direction_cbmi.setEnabled( true );
1828 if ( tree_panel != null ) {
1829 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1830 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1831 label_direction_cbmi.setEnabled( false );
1833 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1834 scale.setSelected( false );
1835 scale.setEnabled( false );
1840 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1841 for( final TreePanel tree_panel : treepanels ) {
1842 tree_panel.setTextAntialias();