2 // FORESTER -- software libraries and applications
\r
3 // for evolutionary biology research and applications.
\r
5 // Copyright (C) 2008-2010 Christian M. Zmasek
\r
6 // All rights reserved
\r
8 // This library is free software; you can redistribute it and/or
\r
9 // modify it under the terms of the GNU Lesser General Public
\r
10 // License as published by the Free Software Foundation; either
\r
11 // version 2.1 of the License, or (at your option) any later version.
\r
13 // This library is distributed in the hope that it will be useful,
\r
14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
\r
16 // Lesser General Public License for more details.
\r
18 // You should have received a copy of the GNU Lesser General Public
\r
19 // License along with this library; if not, write to the Free Software
\r
20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
22 // Contact: phylosoft @ gmail . com
\r
23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
\r
25 package org.forester.archaeopteryx;
\r
27 import java.awt.Color;
\r
28 import java.awt.Component;
\r
29 import java.awt.Container;
\r
30 import java.awt.Font;
\r
31 import java.awt.event.ActionEvent;
\r
32 import java.awt.event.ActionListener;
\r
33 import java.io.File;
\r
34 import java.io.IOException;
\r
35 import java.util.LinkedList;
\r
36 import java.util.List;
\r
37 import java.util.Locale;
\r
38 import java.util.NoSuchElementException;
\r
39 import java.util.Set;
\r
41 import javax.swing.Box;
\r
42 import javax.swing.JApplet;
\r
43 import javax.swing.JCheckBoxMenuItem;
\r
44 import javax.swing.JFrame;
\r
45 import javax.swing.JLabel;
\r
46 import javax.swing.JMenu;
\r
47 import javax.swing.JMenuBar;
\r
48 import javax.swing.JMenuItem;
\r
49 import javax.swing.JOptionPane;
\r
50 import javax.swing.JPanel;
\r
51 import javax.swing.JRadioButtonMenuItem;
\r
52 import javax.swing.JTextField;
\r
53 import javax.swing.SwingUtilities;
\r
55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
\r
56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
\r
57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
\r
58 import org.forester.archaeopteryx.tools.InferenceManager;
\r
59 import org.forester.archaeopteryx.tools.ProcessPool;
\r
60 import org.forester.archaeopteryx.tools.ProcessRunning;
\r
61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
\r
62 import org.forester.phylogeny.Phylogeny;
\r
63 import org.forester.phylogeny.PhylogenyMethods;
\r
64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
\r
65 import org.forester.phylogeny.PhylogenyNode;
\r
66 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
\r
67 import org.forester.phylogeny.data.Annotation;
\r
68 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
\r
69 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
\r
70 import org.forester.sdi.GSDI;
\r
71 import org.forester.sdi.GSDIR;
\r
72 import org.forester.sdi.SDIException;
\r
73 import org.forester.util.ForesterConstants;
\r
74 import org.forester.util.ForesterUtil;
\r
76 public abstract class MainFrame extends JFrame implements ActionListener {
\r
78 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
\r
79 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
\r
80 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
\r
81 private static final long serialVersionUID = 3655000897845508358L;
\r
82 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
\r
85 static final String TYPE_MENU_HEADER = "Type";
\r
86 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
\r
87 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
\r
88 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
\r
89 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
\r
90 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
\r
91 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
\r
92 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
\r
93 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
\r
94 static final String OPTIONS_HEADER = "Options";
\r
95 static final String SEARCH_SUBHEADER = "Search:";
\r
96 static final String DISPLAY_SUBHEADER = "Display:";
\r
97 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
\r
98 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
\r
99 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
\r
100 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values";
\r
101 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
\r
102 static final String DISPLAY_SCALE_LABEL = "Scale";
\r
103 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
\r
104 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
\r
105 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
\r
106 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
\r
107 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
\r
108 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
\r
109 static final String BG_GRAD_LABEL = "Background Color Gradient";
\r
110 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";
\r
111 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";
\r
112 static final String SHOW_OVERVIEW_LABEL = "Overview";
\r
113 static final String FONT_SIZE_MENU_LABEL = "Font Size";
\r
114 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
\r
115 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
\r
116 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
\r
117 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";
\r
118 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
\r
119 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
\r
120 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
\r
121 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
\r
122 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
\r
123 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
\r
124 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
\r
125 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
\r
126 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
\r
127 JMenuBar _jmenubar;
\r
131 JMenu _options_jmenu;
\r
132 JMenu _font_size_menu;
\r
134 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
\r
136 JMenu _analysis_menu;
\r
137 JMenuItem _load_species_tree_item;
\r
138 JMenuItem _gsdi_item;
\r
139 JMenuItem _gsdir_item;
\r
140 JMenuItem _lineage_inference;
\r
142 JMenuItem _open_item;
\r
143 JMenuItem _open_url_item;
\r
144 JMenuItem _save_item;
\r
145 JMenuItem _save_all_item;
\r
146 JMenuItem _close_item;
\r
147 JMenuItem _exit_item;
\r
148 JMenuItem _new_item;
\r
150 JMenuItem _midpoint_root_item;
\r
151 JMenuItem _taxcolor_item;
\r
152 JMenuItem _confcolor_item;
\r
153 JMenuItem _color_rank_jmi;
\r
154 JMenuItem _collapse_species_specific_subtrees;
\r
155 JMenuItem _collapse_below_threshold; //TODO implememt me
\r
156 JMenuItem _obtain_detailed_taxonomic_information_jmi;
\r
157 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
\r
158 JMenuItem _obtain_seq_information_jmi;
\r
159 JMenuItem _move_node_names_to_tax_sn_jmi;
\r
160 JMenuItem _move_node_names_to_seq_names_jmi;
\r
161 JMenuItem _extract_tax_code_from_node_names_jmi;
\r
162 JMenuItem _annotate_item;
\r
163 JMenuItem _remove_branch_color_item;
\r
164 JMenuItem _remove_visual_styles_item;
\r
166 JMenuItem _super_tiny_fonts_item;
\r
167 JMenuItem _tiny_fonts_item;
\r
168 JMenuItem _small_fonts_item;
\r
169 JMenuItem _medium_fonts_item;
\r
170 JMenuItem _large_fonts_item;
\r
172 // _ screen and print
\r
173 JMenuItem _choose_font_mi;
\r
174 JMenuItem _switch_colors_mi;
\r
175 JCheckBoxMenuItem _label_direction_cbmi;
\r
176 // _ screen display
\r
177 JCheckBoxMenuItem _screen_antialias_cbmi;
\r
178 JCheckBoxMenuItem _background_gradient_cbmi;
\r
179 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
\r
180 JRadioButtonMenuItem _uniform_cladograms_rbmi;
\r
181 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
\r
182 JCheckBoxMenuItem _show_branch_length_values_cbmi;
\r
183 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
\r
184 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
\r
185 JCheckBoxMenuItem _show_overview_cbmi;
\r
186 JCheckBoxMenuItem _show_domain_labels;
\r
187 JCheckBoxMenuItem _show_annotation_ref_source;
\r
188 JCheckBoxMenuItem _abbreviate_scientific_names;
\r
189 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
\r
190 JMenuItem _overview_placment_mi;
\r
191 JMenuItem _choose_minimal_confidence_mi;
\r
192 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
\r
193 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
\r
194 JMenuItem _cycle_node_shape_mi;
\r
195 JMenuItem _cycle_node_fill_mi;
\r
196 JMenuItem _choose_node_size_mi;
\r
197 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
\r
199 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
\r
200 JCheckBoxMenuItem _antialias_print_cbmi;
\r
201 JCheckBoxMenuItem _print_black_and_white_cbmi;
\r
202 JCheckBoxMenuItem _print_using_actual_size_cbmi;
\r
203 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
\r
204 JMenuItem _print_size_mi;
\r
205 JMenuItem _choose_pdf_width_mi;
\r
207 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
\r
208 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
\r
209 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
\r
210 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
\r
211 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
\r
212 JCheckBoxMenuItem _replace_underscores_cbmi;
\r
213 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
\r
214 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
\r
215 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
\r
217 JCheckBoxMenuItem _search_case_senstive_cbmi;
\r
218 JCheckBoxMenuItem _search_whole_words_only_cbmi;
\r
219 JCheckBoxMenuItem _inverse_search_result_cbmi;
\r
222 JCheckBoxMenuItem _rectangular_type_cbmi;
\r
223 JCheckBoxMenuItem _triangular_type_cbmi;
\r
224 JCheckBoxMenuItem _curved_type_cbmi;
\r
225 JCheckBoxMenuItem _convex_type_cbmi;
\r
226 JCheckBoxMenuItem _euro_type_cbmi;
\r
227 JCheckBoxMenuItem _rounded_type_cbmi;
\r
228 JCheckBoxMenuItem _unrooted_type_cbmi;
\r
229 JCheckBoxMenuItem _circular_type_cbmi;
\r
230 // view as text menu:
\r
231 JMenuItem _view_as_NH_item;
\r
232 JMenuItem _view_as_XML_item;
\r
233 JMenuItem _view_as_nexus_item;
\r
234 JMenuItem _display_basic_information_item;
\r
236 JMenuItem _about_item;
\r
237 JMenuItem _help_item;
\r
238 JMenuItem _website_item;
\r
239 JMenuItem _phyloxml_website_item;
\r
240 JMenuItem _phyloxml_ref_item;
\r
241 JMenuItem _aptx_ref_item;
\r
243 JMenu _process_menu;
\r
244 // Handy pointers to child components:
\r
245 MainPanel _mainpanel;
\r
246 Container _contentpane;
\r
247 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
\r
248 Configuration _configuration;
\r
250 private Phylogeny _species_tree;
\r
251 InferenceManager _inference_manager;
\r
252 final ProcessPool _process_pool;
\r
253 private String _previous_node_annotation_ref;
\r
256 _process_pool = ProcessPool.createInstance();
\r
260 * Action performed.
\r
263 public void actionPerformed( final ActionEvent e ) {
\r
264 final Object o = e.getSource();
\r
265 boolean is_applet = false;
\r
266 JApplet applet = null;
\r
267 if ( getCurrentTreePanel() != null ) {
\r
268 is_applet = getCurrentTreePanel().isApplet();
\r
270 applet = getCurrentTreePanel().obtainApplet();
\r
273 if ( o == _exit_item ) {
\r
276 else if ( o == _gsdi_item ) {
\r
277 if ( isSubtreeDisplayed() ) {
\r
282 else if ( o == _gsdir_item ) {
\r
283 if ( isSubtreeDisplayed() ) {
\r
288 else if ( o == _taxcolor_item ) {
\r
291 else if ( o == _confcolor_item ) {
\r
294 else if ( o == _color_rank_jmi ) {
\r
297 else if ( o == _collapse_species_specific_subtrees ) {
\r
298 if ( isSubtreeDisplayed() ) {
\r
301 if ( getCurrentTreePanel() != null ) {
\r
302 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
\r
305 else if ( o == _remove_branch_color_item ) {
\r
306 if ( isSubtreeDisplayed() ) {
\r
309 removeBranchColors();
\r
311 else if ( o == _remove_visual_styles_item ) {
\r
312 if ( isSubtreeDisplayed() ) {
\r
315 removeVisualStyles();
\r
317 else if ( o == _midpoint_root_item ) {
\r
318 if ( isSubtreeDisplayed() ) {
\r
323 else if ( o == _annotate_item ) {
\r
324 annotateSequences();
\r
326 else if ( o == _switch_colors_mi ) {
\r
329 else if ( o == _display_basic_information_item ) {
\r
330 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
\r
332 else if ( o == _view_as_NH_item ) {
\r
335 else if ( o == _view_as_XML_item ) {
\r
338 else if ( o == _view_as_nexus_item ) {
\r
341 else if ( o == _super_tiny_fonts_item ) {
\r
342 if ( getCurrentTreePanel() != null ) {
\r
343 getCurrentTreePanel().setSuperTinyFonts();
\r
344 getCurrentTreePanel().repaint();
\r
347 else if ( o == _tiny_fonts_item ) {
\r
348 if ( getCurrentTreePanel() != null ) {
\r
349 getCurrentTreePanel().setTinyFonts();
\r
350 getCurrentTreePanel().repaint();
\r
353 else if ( o == _small_fonts_item ) {
\r
354 if ( getCurrentTreePanel() != null ) {
\r
355 getCurrentTreePanel().setSmallFonts();
\r
356 getCurrentTreePanel().repaint();
\r
359 else if ( o == _medium_fonts_item ) {
\r
360 if ( getCurrentTreePanel() != null ) {
\r
361 getCurrentTreePanel().setMediumFonts();
\r
362 getCurrentTreePanel().repaint();
\r
365 else if ( o == _large_fonts_item ) {
\r
366 if ( getCurrentTreePanel() != null ) {
\r
367 getCurrentTreePanel().setLargeFonts();
\r
368 getCurrentTreePanel().repaint();
\r
371 else if ( o == _choose_font_mi ) {
\r
374 else if ( o == _choose_minimal_confidence_mi ) {
\r
375 chooseMinimalConfidence();
\r
377 else if ( o == _choose_node_size_mi ) {
\r
378 chooseNodeSize( getOptions(), this );
\r
380 else if ( o == _overview_placment_mi ) {
\r
381 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
\r
383 else if ( o == _cycle_node_fill_mi ) {
\r
384 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
\r
386 else if ( o == _cycle_node_shape_mi ) {
\r
387 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
\r
389 else if ( o == _screen_antialias_cbmi ) {
\r
390 updateOptions( getOptions() );
\r
391 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
393 else if ( o == _background_gradient_cbmi ) {
\r
394 updateOptions( getOptions() );
\r
396 else if ( o == _show_domain_labels ) {
\r
397 updateOptions( getOptions() );
\r
399 else if ( o == _show_annotation_ref_source ) {
\r
400 updateOptions( getOptions() );
\r
402 else if ( o == _abbreviate_scientific_names ) {
\r
403 updateOptions( getOptions() );
\r
405 else if ( o == _color_labels_same_as_parent_branch ) {
\r
406 updateOptions( getOptions() );
\r
408 else if ( o == _show_default_node_shapes_internal_cbmi ) {
\r
409 updateOptions( getOptions() );
\r
411 else if ( o == _show_default_node_shapes_external_cbmi ) {
\r
412 updateOptions( getOptions() );
\r
414 else if ( o == _non_lined_up_cladograms_rbmi ) {
\r
415 updateOptions( getOptions() );
\r
418 else if ( o == _uniform_cladograms_rbmi ) {
\r
419 updateOptions( getOptions() );
\r
422 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
\r
423 updateOptions( getOptions() );
\r
426 else if ( o == _search_case_senstive_cbmi ) {
\r
427 updateOptions( getOptions() );
\r
428 getMainPanel().getControlPanel().search0();
\r
429 getMainPanel().getControlPanel().search1();
\r
431 else if ( o == _search_whole_words_only_cbmi ) {
\r
432 updateOptions( getOptions() );
\r
433 getMainPanel().getControlPanel().search0();
\r
434 getMainPanel().getControlPanel().search1();
\r
436 else if ( o == _inverse_search_result_cbmi ) {
\r
437 updateOptions( getOptions() );
\r
438 getMainPanel().getControlPanel().search0();
\r
439 getMainPanel().getControlPanel().search1();
\r
441 else if ( o == _show_scale_cbmi ) {
\r
442 updateOptions( getOptions() );
\r
444 else if ( o == _show_branch_length_values_cbmi ) {
\r
445 updateOptions( getOptions() );
\r
447 else if ( o == _color_by_taxonomic_group_cbmi ) {
\r
448 updateOptions( getOptions() );
\r
450 else if ( o == _show_confidence_stddev_cbmi ) {
\r
451 updateOptions( getOptions() );
\r
453 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
\r
454 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
455 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
\r
457 updateOptions( getOptions() );
\r
459 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
460 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
461 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
463 updateOptions( getOptions() );
\r
465 else if ( o == _label_direction_cbmi ) {
\r
466 updateOptions( getOptions() );
\r
468 else if ( o == _show_overview_cbmi ) {
\r
469 updateOptions( getOptions() );
\r
470 if ( getCurrentTreePanel() != null ) {
\r
471 getCurrentTreePanel().updateOvSizes();
\r
474 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
475 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
476 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
479 else if ( o == _about_item ) {
\r
482 else if ( o == _help_item ) {
\r
485 else if ( o == _website_item ) {
\r
487 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
\r
489 catch ( final IOException e1 ) {
\r
490 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
493 else if ( o == _phyloxml_website_item ) {
\r
495 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
497 catch ( final IOException e1 ) {
\r
498 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
501 else if ( o == _aptx_ref_item ) {
\r
503 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
\r
505 catch ( final IOException e1 ) {
\r
506 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
509 else if ( o == _phyloxml_ref_item ) {
\r
511 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
513 catch ( final IOException e1 ) {
\r
514 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
518 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
519 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
520 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
521 readPhylogeniesFromWebservice( i );
\r
526 _contentpane.repaint();
\r
529 public Configuration getConfiguration() {
\r
530 return _configuration;
\r
534 * This method returns the current external node data which
\r
535 * has been selected by the user by clicking the "Return ..."
\r
536 * menu item. This method is expected to be called from Javascript or
\r
537 * something like it.
\r
539 * @return current external node data as String
\r
541 public String getCurrentExternalNodesDataBuffer() {
\r
542 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
545 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
546 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
549 public int getCurrentExternalNodesDataBufferLength() {
\r
550 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
553 public InferenceManager getInferenceManager() {
\r
554 return _inference_manager;
\r
557 public MainPanel getMainPanel() {
\r
561 public Options getOptions() {
\r
565 public ProcessPool getProcessPool() {
\r
566 return _process_pool;
\r
569 public void showTextFrame( final String s, final String title ) {
\r
571 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
574 public void showWhole() {
\r
575 _mainpanel.getControlPanel().showWhole();
\r
578 public void updateProcessMenu() {
\r
579 // In general Swing is not thread safe.
\r
580 // See "Swing's Threading Policy".
\r
581 SwingUtilities.invokeLater( new Runnable() {
\r
584 public void run() {
\r
585 doUpdateProcessMenu();
\r
590 void activateSaveAllIfNeeded() {
\r
591 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
592 _save_all_item.setEnabled( true );
\r
595 _save_all_item.setEnabled( false );
\r
599 void buildFileMenu() {
\r
600 _file_jmenu = createMenu( "File", getConfiguration() );
\r
601 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
602 customizeJMenuItem( _exit_item );
\r
603 _jmenubar.add( _file_jmenu );
\r
606 void buildFontSizeMenu() {
\r
607 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
608 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
609 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
610 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
611 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
612 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
613 customizeJMenuItem( _super_tiny_fonts_item );
\r
614 customizeJMenuItem( _tiny_fonts_item );
\r
615 customizeJMenuItem( _small_fonts_item );
\r
616 customizeJMenuItem( _medium_fonts_item );
\r
617 customizeJMenuItem( _large_fonts_item );
\r
618 _jmenubar.add( _font_size_menu );
\r
621 void buildHelpMenu() {
\r
622 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
623 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
\r
624 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
625 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
\r
626 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
627 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
628 _help_jmenu.addSeparator();
\r
629 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
630 customizeJMenuItem( _help_item );
\r
631 customizeJMenuItem( _website_item );
\r
632 customizeJMenuItem( _phyloxml_website_item );
\r
633 customizeJMenuItem( _aptx_ref_item );
\r
634 customizeJMenuItem( _phyloxml_ref_item );
\r
635 customizeJMenuItem( _about_item );
\r
636 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
637 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
638 _jmenubar.add( _help_jmenu );
\r
641 void buildTypeMenu() {
\r
642 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
643 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
644 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
645 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
646 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
647 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
648 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
649 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
650 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
651 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
652 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
653 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
654 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
655 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
656 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
657 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
658 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
659 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
660 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
661 initializeTypeMenu( getOptions() );
\r
662 _jmenubar.add( _type_menu );
\r
665 void buildViewMenu() {
\r
666 _view_jmenu = createMenu( "View", getConfiguration() );
\r
667 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
668 _view_jmenu.addSeparator();
\r
669 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
670 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
671 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
672 customizeJMenuItem( _display_basic_information_item );
\r
673 customizeJMenuItem( _view_as_NH_item );
\r
674 customizeJMenuItem( _view_as_XML_item );
\r
675 customizeJMenuItem( _view_as_nexus_item );
\r
676 _jmenubar.add( _view_jmenu );
\r
679 void checkTextFrames() {
\r
680 if ( _textframes.size() > 5 ) {
\r
682 if ( _textframes.getFirst() != null ) {
\r
683 _textframes.getFirst().removeMe();
\r
686 _textframes.removeFirst();
\r
689 catch ( final NoSuchElementException e ) {
\r
696 removeAllTextFrames();
\r
697 if ( _mainpanel != null ) {
\r
698 _mainpanel.terminate();
\r
700 if ( _contentpane != null ) {
\r
701 _contentpane.removeAll();
\r
703 setVisible( false );
\r
708 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
709 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
710 final String rank = ( String ) JOptionPane
\r
711 .showInputDialog( this,
\r
712 "What rank should the colorization be based on",
\r
714 JOptionPane.QUESTION_MESSAGE,
\r
718 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
719 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
725 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
726 _mainpanel.getCurrentTreePanel().confColor();
\r
730 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
731 if ( item != null ) {
\r
732 item.setFont( MainFrame.menu_font );
\r
733 if ( !getConfiguration().isUseNativeUI() ) {
\r
734 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
735 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
737 item.setSelected( is_selected );
\r
738 item.addActionListener( this );
\r
742 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
743 if ( jmi != null ) {
\r
744 jmi.setFont( MainFrame.menu_font );
\r
745 if ( !getConfiguration().isUseNativeUI() ) {
\r
746 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
747 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
749 jmi.addActionListener( this );
\r
754 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
755 if ( item != null ) {
\r
756 item.setFont( MainFrame.menu_font );
\r
757 if ( !getConfiguration().isUseNativeUI() ) {
\r
758 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
759 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
761 item.setSelected( is_selected );
\r
762 item.addActionListener( this );
\r
766 void displayBasicInformation( final File treefile ) {
\r
767 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
768 String title = "Basic Information";
\r
769 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
770 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
772 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
776 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
778 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
780 catch ( final Exception ex ) {
\r
783 JOptionPane.showMessageDialog( this,
\r
784 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
785 "Error during File|Open",
\r
786 JOptionPane.ERROR_MESSAGE );
\r
789 void exceptionOccuredDuringSaveAs( final Exception e ) {
\r
791 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
793 catch ( final Exception ex ) {
\r
796 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
799 void executeGSDI() {
\r
800 if ( !isOKforSDI( false, true ) ) {
\r
803 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
804 JOptionPane.showMessageDialog( this,
\r
805 "Gene tree is not rooted.",
\r
806 "Cannot execute GSDI",
\r
807 JOptionPane.ERROR_MESSAGE );
\r
810 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
811 gene_tree.setAllNodesToNotCollapse();
\r
812 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
814 final Phylogeny species_tree = getSpeciesTree().copy();
\r
816 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
818 catch ( final SDIException e ) {
\r
819 JOptionPane.showMessageDialog( this,
\r
820 e.getLocalizedMessage(),
\r
821 "Error during GSDI",
\r
822 JOptionPane.ERROR_MESSAGE );
\r
825 catch ( final Exception e ) {
\r
826 AptxUtil.unexpectedException( e );
\r
829 gene_tree.setRerootable( false );
\r
830 gene_tree.clearHashIdToNodeMap();
\r
831 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
832 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
833 getMainPanel().getControlPanel().setShowEvents( true );
\r
835 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
836 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
838 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
840 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
841 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
842 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
843 JOptionPane.showMessageDialog( this,
\r
844 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
845 + "Potential duplications: "
\r
846 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
847 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
848 + "Stripped gene tree nodes: "
\r
849 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
850 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
851 + "Number of polytomies in species tree used: " + poly + "\n",
\r
852 "GSDI successfully completed",
\r
853 JOptionPane.WARNING_MESSAGE );
\r
856 JOptionPane.showMessageDialog( this,
\r
857 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
858 + "Potential duplications: "
\r
859 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
860 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
861 + "Stripped gene tree nodes: "
\r
862 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
863 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
864 + "Number of polytomies in species tree used: " + poly + "\n",
\r
865 "GSDI successfully completed",
\r
866 JOptionPane.INFORMATION_MESSAGE );
\r
870 void executeGSDIR() {
\r
871 if ( !isOKforSDI( false, false ) ) {
\r
874 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
876 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
877 JOptionPane.showMessageDialog( this,
\r
878 "Gene tree is not completely binary",
\r
879 "Cannot execute GSDI",
\r
880 JOptionPane.ERROR_MESSAGE );
\r
883 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
884 gene_tree.setAllNodesToNotCollapse();
\r
885 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
886 GSDIR gsdir = null;
\r
887 final Phylogeny species_tree = getSpeciesTree().copy();
\r
889 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
891 catch ( final SDIException e ) {
\r
892 JOptionPane.showMessageDialog( this,
\r
893 e.getLocalizedMessage(),
\r
894 "Error during GSDIR",
\r
895 JOptionPane.ERROR_MESSAGE );
\r
898 catch ( final Exception e ) {
\r
899 AptxUtil.unexpectedException( e );
\r
902 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
903 result_gene_tree.setRerootable( false );
\r
904 result_gene_tree.clearHashIdToNodeMap();
\r
905 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
906 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
907 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
908 getMainPanel().getControlPanel().setShowEvents( true );
\r
910 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
911 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
913 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
915 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
916 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
917 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
918 JOptionPane.showMessageDialog( this,
\r
919 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
920 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
921 + "Stripped gene tree nodes: "
\r
922 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
923 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
924 + "Number of polytomies in species tree used: " + poly + "\n",
\r
925 "GSDIR successfully completed",
\r
926 JOptionPane.WARNING_MESSAGE );
\r
929 JOptionPane.showMessageDialog( this,
\r
930 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
931 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
932 + "Stripped gene tree nodes: "
\r
933 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
934 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
935 + "Number of polytomies in species tree used: " + poly + "\n",
\r
936 "GSDIR successfully completed",
\r
937 JOptionPane.INFORMATION_MESSAGE );
\r
941 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
942 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
943 JOptionPane.showMessageDialog( this,
\r
944 "Gene tree and species tree have no species in common.",
\r
945 "Error during SDI",
\r
946 JOptionPane.ERROR_MESSAGE );
\r
949 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
950 JOptionPane.showMessageDialog( this,
\r
951 "Gene tree and species tree have only one species in common.",
\r
952 "Error during SDI",
\r
953 JOptionPane.ERROR_MESSAGE );
\r
961 TreePanel getCurrentTreePanel() {
\r
962 return getMainPanel().getCurrentTreePanel();
\r
965 JMenu getHelpMenu() {
\r
966 return _help_jmenu;
\r
969 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
970 return _label_direction_cbmi;
\r
973 JMenuBar getMenuBarOfMainFrame() {
\r
977 final Phylogeny getSpeciesTree() {
\r
978 return _species_tree;
\r
982 final StringBuilder sb = new StringBuilder();
\r
983 sb.append( "Display options\n" );
\r
984 sb.append( "-------------------\n" );
\r
985 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
\r
986 sb.append( "Clickable tree nodes\n" );
\r
987 sb.append( "--------------------\n" );
\r
988 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
\r
989 sb.append( "or by right clicking:\n" );
\r
990 sb.append( "o Display Node Data -- display information for a node\n" );
\r
991 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
\r
992 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
\r
993 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
\r
994 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
\r
995 sb.append( "o Colorize Subtree -- color a subtree\n" );
\r
996 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
\r
997 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
\r
998 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
\r
999 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
\r
1000 sb.append( "Zooming\n" );
\r
1001 sb.append( "---------\n" );
\r
1002 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
\r
1003 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
\r
1004 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
\r
1005 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
\r
1006 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
\r
1007 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
\r
1008 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
\r
1009 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
\r
1010 sb.append( "Quick tree manipulation:\n" );
\r
1011 sb.append( "------------------------\n" );
\r
1012 sb.append( "Order Subtrees -- order the tree by branch length\n" );
\r
1013 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
\r
1014 sb.append( "Memory problems (Java heap space error)\n" );
\r
1015 sb.append( "---------------------------------------\n" );
\r
1016 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
\r
1017 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
\r
1018 sb.append( "the '-Xmx' Java command line option. For example:\n" );
\r
1019 sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
\r
1020 // + "General remarks\n"
\r
1021 // + "---------------\n"
\r
1023 // "o The application version permits copying to the clipboard \n"
\r
1025 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
\r
1027 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
\r
1028 // + " but not any of its parent tree(s).\n"
\r
1030 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
\r
1032 // " are likely to be bootstrap values instead of branch length values.\n\n"
\r
1034 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
\r
1036 // "o Each external node of the gene tree (in display) needs to be associated with\n"
\r
1038 // " a species: either directly through the \"Species\" field, or the species\n"
\r
1040 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
\r
1042 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
\r
1044 // "o A species tree for each species of the gene tree needs to be loaded with\n"
\r
1046 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
\r
1048 // "o !External nodes of the gene tree associated with species not present in\n"
\r
1050 // " the species tree are REMOVED prior to SDI execution!\n"
\r
1052 // "o Both the gene tree and the species tree must be completely binary.\n"
\r
1054 // "o Duplications and speciations are a function of the position of the root.\n"
\r
1056 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
\r
1057 // + " incorrect and need to be inferred again\n"
\r
1059 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
\r
1060 sb.append( "phyloXML\n" );
\r
1061 sb.append( "-------------------\n" );
\r
1062 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
\r
1063 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
\r
1064 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
1065 sb.append( "\n" );
\r
1066 sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
\r
1067 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
\r
1068 TextFrame.instantiate( sb.toString(), "Help", _textframes );
\r
1071 void initializeTypeMenu( final Options options ) {
\r
1072 setTypeMenuToAllUnselected();
\r
1073 switch ( options.getPhylogenyGraphicsType() ) {
\r
1075 _convex_type_cbmi.setSelected( true );
\r
1078 _curved_type_cbmi.setSelected( true );
\r
1081 _euro_type_cbmi.setSelected( true );
\r
1084 _rounded_type_cbmi.setSelected( true );
\r
1087 _triangular_type_cbmi.setSelected( true );
\r
1090 _unrooted_type_cbmi.setSelected( true );
\r
1093 _circular_type_cbmi.setSelected( true );
\r
1096 _rectangular_type_cbmi.setSelected( true );
\r
1101 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1102 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1105 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1106 JOptionPane.showMessageDialog( this,
\r
1107 "No species tree loaded",
\r
1108 "Cannot execute GSDI",
\r
1109 JOptionPane.ERROR_MESSAGE );
\r
1112 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1113 JOptionPane.showMessageDialog( this,
\r
1114 "Species tree is not completely binary",
\r
1115 "Cannot execute GSDI",
\r
1116 JOptionPane.ERROR_MESSAGE );
\r
1119 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1120 JOptionPane.showMessageDialog( this,
\r
1121 "Gene tree is not completely binary",
\r
1122 "Cannot execute GSDI",
\r
1123 JOptionPane.ERROR_MESSAGE );
\r
1131 boolean isSubtreeDisplayed() {
\r
1132 if ( getCurrentTreePanel() != null ) {
\r
1133 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1135 .showMessageDialog( this,
\r
1136 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1137 "Operation can not be exectuted on a sub-tree",
\r
1138 JOptionPane.WARNING_MESSAGE );
\r
1145 void midpointRoot() {
\r
1146 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1147 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1151 void readPhylogeniesFromWebservice( final int i ) {
\r
1152 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1153 new Thread( reader ).start();
\r
1156 void removeAllTextFrames() {
\r
1157 for( final TextFrame tf : _textframes ) {
\r
1158 if ( tf != null ) {
\r
1162 _textframes.clear();
\r
1165 void setConfiguration( final Configuration configuration ) {
\r
1166 _configuration = configuration;
\r
1169 void setInferenceManager( final InferenceManager i ) {
\r
1170 _inference_manager = i;
\r
1173 void setOptions( final Options options ) {
\r
1174 _options = options;
\r
1177 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1178 setTypeMenuToAllUnselected();
\r
1181 _circular_type_cbmi.setSelected( true );
\r
1184 _convex_type_cbmi.setSelected( true );
\r
1187 _curved_type_cbmi.setSelected( true );
\r
1190 _euro_type_cbmi.setSelected( true );
\r
1193 _rounded_type_cbmi.setSelected( true );
\r
1196 _rectangular_type_cbmi.setSelected( true );
\r
1199 _triangular_type_cbmi.setSelected( true );
\r
1202 _unrooted_type_cbmi.setSelected( true );
\r
1205 throw new IllegalArgumentException( "unknown type: " + type );
\r
1209 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1210 _species_tree = species_tree;
\r
1213 void setTypeMenuToAllUnselected() {
\r
1214 _convex_type_cbmi.setSelected( false );
\r
1215 _curved_type_cbmi.setSelected( false );
\r
1216 _euro_type_cbmi.setSelected( false );
\r
1217 _rounded_type_cbmi.setSelected( false );
\r
1218 _triangular_type_cbmi.setSelected( false );
\r
1219 _rectangular_type_cbmi.setSelected( false );
\r
1220 _unrooted_type_cbmi.setSelected( false );
\r
1221 _circular_type_cbmi.setSelected( false );
\r
1224 void switchColors() {
\r
1225 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1226 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1227 csc.setVisible( true );
\r
1231 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1232 _mainpanel.getCurrentTreePanel().taxColor();
\r
1236 void typeChanged( final Object o ) {
\r
1237 updateTypeCheckboxes( getOptions(), o );
\r
1238 updateOptions( getOptions() );
\r
1239 if ( getCurrentTreePanel() != null ) {
\r
1240 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1241 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1242 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1243 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
1244 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1245 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
1246 getCurrentTreePanel().getControlPanel().showWhole();
\r
1248 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1249 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
1252 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
1254 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
1255 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
1256 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
1257 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
1258 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
1261 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
1267 void updateOptions( final Options options ) {
\r
1268 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
1269 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
1270 && _background_gradient_cbmi.isSelected() );
\r
1271 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
1272 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
1273 && _show_annotation_ref_source.isSelected() );
\r
1274 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
1275 && _abbreviate_scientific_names.isSelected() );
\r
1276 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
1277 && _color_labels_same_as_parent_branch.isSelected() );
\r
1278 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
1279 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
1280 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
1281 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
1282 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
1283 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
1285 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
1286 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1288 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
1289 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1291 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
1292 && _search_case_senstive_cbmi.isSelected() );
\r
1293 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
1294 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
1296 if ( _label_direction_cbmi != null ) {
\r
1297 if ( _label_direction_cbmi.isSelected() ) {
\r
1298 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
1301 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
1304 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
1305 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
1306 && _show_confidence_stddev_cbmi.isSelected() );
\r
1307 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
\r
1308 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
\r
1310 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
1311 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
1313 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
\r
1314 && ( _print_using_actual_size_cbmi.isSelected() ) );
\r
1315 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
\r
1316 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
\r
1317 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
1318 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
1319 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1320 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1322 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
1323 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1324 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1327 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
1329 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
1330 && _print_black_and_white_cbmi.isSelected() );
\r
1331 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
1332 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
1333 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
1334 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1336 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
1337 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1339 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
1340 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1342 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
1343 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
1345 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
1346 && _replace_underscores_cbmi.isSelected() );
\r
1347 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
1348 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
1349 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
1350 && _search_whole_words_only_cbmi.isSelected() );
\r
1351 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
1352 && _inverse_search_result_cbmi.isSelected() );
\r
1353 if ( _graphics_export_visible_only_cbmi != null ) {
\r
1354 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
1355 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
\r
1356 _graphics_export_using_actual_size_cbmi.setSelected( true );
\r
1357 _graphics_export_using_actual_size_cbmi.setEnabled( false );
\r
1360 _graphics_export_using_actual_size_cbmi.setEnabled( true );
\r
1363 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
1364 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1366 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
1367 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
1369 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
1370 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
1372 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
1373 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
1375 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
1376 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
1378 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
1379 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
1381 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
1382 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
1384 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
1385 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
1389 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
1390 setTypeMenuToAllUnselected();
\r
1391 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
1394 void viewAsNexus() {
\r
1395 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1396 String title = "Nexus";
\r
1397 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1398 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1400 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
1406 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1407 String title = "New Hampshire";
\r
1408 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1409 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1411 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
1412 .getNhConversionSupportValueStyle() ),
\r
1417 void viewAsXML() {
\r
1418 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1419 String title = "phyloXML";
\r
1420 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1421 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1423 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
1427 private void annotateSequences() {
\r
1428 if ( getCurrentTreePanel() != null ) {
\r
1429 final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
\r
1430 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
1432 .showMessageDialog( this,
\r
1433 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
1434 "No nodes selected for annotation",
\r
1435 JOptionPane.ERROR_MESSAGE );
\r
1438 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
1439 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1440 final JTextField ref_field = new JTextField( 10 );
\r
1441 final JTextField desc_filed = new JTextField( 20 );
\r
1442 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
1443 : getPreviousNodeAnnotationReference() );
\r
1444 final JPanel my_panel = new JPanel();
\r
1445 my_panel.add( new JLabel( "Reference " ) );
\r
1446 my_panel.add( ref_field );
\r
1447 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
1448 my_panel.add( new JLabel( "Description " ) );
\r
1449 my_panel.add( desc_filed );
\r
1450 final int result = JOptionPane.showConfirmDialog( null,
\r
1452 "Enter the sequence annotation(s) for the "
\r
1453 + nodes.size() + " selected nodes",
\r
1454 JOptionPane.OK_CANCEL_OPTION );
\r
1455 if ( result == JOptionPane.OK_OPTION ) {
\r
1456 String ref = ref_field.getText();
\r
1457 String desc = desc_filed.getText();
\r
1458 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
1460 ref = ref.replaceAll( "\\s+", " " );
\r
1461 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
1462 || ( ref.length() < 3 ) ) {
\r
1463 JOptionPane.showMessageDialog( this,
\r
1464 "Reference needs to be in the form of \"GO:1234567\"",
\r
1465 "Illegal Format for Annotation Reference",
\r
1466 JOptionPane.ERROR_MESSAGE );
\r
1470 if ( ref != null ) {
\r
1471 setPreviousNodeAnnotationReference( ref );
\r
1473 if ( desc != null ) {
\r
1474 desc = desc.trim();
\r
1475 desc = desc.replaceAll( "\\s+", " " );
\r
1477 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
1478 for( final Long id : nodes ) {
\r
1479 final PhylogenyNode n = phy.getNode( id );
\r
1480 ForesterUtil.ensurePresenceOfSequence( n );
\r
1481 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
1482 : new Annotation( ref );
\r
1483 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
1484 ann.setDesc( desc );
\r
1486 n.getNodeData().getSequence().addAnnotation( ann );
\r
1489 getMainPanel().getControlPanel().showAnnotations();
\r
1495 private void chooseFont() {
\r
1496 final FontChooser fc = new FontChooser();
\r
1497 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
1498 fc.showDialog( this, "Select the Base Font" );
\r
1499 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
1502 private void chooseMinimalConfidence() {
\r
1503 final String s = ( String ) JOptionPane
\r
1504 .showInputDialog( this,
\r
1505 "Please enter the minimum for confidence values to be displayed.\n"
\r
1506 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
1507 "Minimal Confidence Value",
\r
1508 JOptionPane.QUESTION_MESSAGE,
\r
1511 getOptions().getMinConfidenceValue() );
\r
1512 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1513 boolean success = true;
\r
1515 final String m_str = s.trim();
\r
1516 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1518 m = Double.parseDouble( m_str );
\r
1520 catch ( final Exception ex ) {
\r
1527 if ( success && ( m >= 0.0 ) ) {
\r
1528 getOptions().setMinConfidenceValue( m );
\r
1533 private void doUpdateProcessMenu() {
\r
1534 if ( _process_pool.size() > 0 ) {
\r
1535 if ( _process_menu == null ) {
\r
1536 _process_menu = createMenu( "", getConfiguration() );
\r
1537 _process_menu.setForeground( Color.RED );
\r
1539 _process_menu.removeAll();
\r
1540 final String text = "processes running: " + _process_pool.size();
\r
1541 _process_menu.setText( text );
\r
1542 _jmenubar.add( _process_menu );
\r
1543 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
1544 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
1545 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
1549 if ( _process_menu != null ) {
\r
1550 _process_menu.removeAll();
\r
1551 _jmenubar.remove( _process_menu );
\r
1554 _jmenubar.validate();
\r
1555 _jmenubar.repaint();
\r
1559 private String getPreviousNodeAnnotationReference() {
\r
1560 return _previous_node_annotation_ref;
\r
1563 private void removeBranchColors() {
\r
1564 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1565 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
1569 private void removeVisualStyles() {
\r
1570 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1571 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
1575 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
1576 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
1580 * Display the about box.
\r
1582 static void about() {
\r
1583 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
\r
1584 about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
\r
1585 about.append( "All Rights Reserved\n" );
\r
1586 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
\r
1587 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
\r
1588 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
\r
1589 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
1590 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
\r
1591 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
\r
1592 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
\r
1594 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
\r
1595 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
\r
1596 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
\r
1597 + ForesterUtil.OS_VERSION + "]\n" );
\r
1599 final Runtime rt = java.lang.Runtime.getRuntime();
\r
1600 final long free_memory = rt.freeMemory() / 1000000;
\r
1601 final long total_memory = rt.totalMemory() / 1000000;
\r
1602 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
\r
1603 about.append( "[locale: " + Locale.getDefault() + "]\n" );
\r
1604 about.append( "References:\n" );
\r
1605 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
\r
1606 about.append( "For more information & download:\n" );
\r
1607 about.append( Constants.APTX_WEB_SITE + "\n" );
\r
1608 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
\r
1609 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
\r
1612 static void chooseNodeSize( final Options options, final Component parent ) {
\r
1613 final String s = ( String ) JOptionPane.showInputDialog( parent,
\r
1614 "Please enter the default size for node shapes.\n"
\r
1615 + "[current value: "
\r
1616 + options.getDefaultNodeShapeSize() + "]\n",
\r
1617 "Node Shape Size",
\r
1618 JOptionPane.QUESTION_MESSAGE,
\r
1621 options.getDefaultNodeShapeSize() );
\r
1622 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1623 boolean success = true;
\r
1625 final String m_str = s.trim();
\r
1626 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1628 m = Double.parseDouble( m_str );
\r
1630 catch ( final Exception ex ) {
\r
1637 if ( success && ( m >= 0.0 ) ) {
\r
1638 final short size = ForesterUtil.roundToShort( m );
\r
1639 if ( size >= 0.0 ) {
\r
1640 options.setDefaultNodeShapeSize( size );
\r
1646 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
\r
1647 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
\r
1650 static JMenu createMenu( final String title, final Configuration conf ) {
\r
1651 final JMenu jmenu = new JMenu( title );
\r
1652 if ( !conf.isUseNativeUI() ) {
\r
1653 jmenu.setFont( MainFrame.menu_font );
\r
1654 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
\r
1655 jmenu.setForeground( conf.getGuiMenuTextColor() );
\r
1660 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
\r
1661 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
\r
1662 if ( !configuration.isUseNativeUI() ) {
\r
1663 label.setBackground( configuration.getGuiMenuBackgroundColor() );
\r
1664 label.setForeground( configuration.getGuiMenuTextColor() );
\r
1665 label.setOpaque( true );
\r
1667 label.setSelected( false );
\r
1668 label.setEnabled( false );
\r
1672 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
\r
1673 switch ( op.getDefaultNodeFill() ) {
\r
1675 op.setDefaultNodeFill( NodeFill.SOLID );
\r
1678 op.setDefaultNodeFill( NodeFill.GRADIENT );
\r
1681 op.setDefaultNodeFill( NodeFill.NONE );
\r
1684 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
\r
1688 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
\r
1689 switch ( op.getDefaultNodeShape() ) {
\r
1691 op.setDefaultNodeShape( NodeShape.RECTANGLE );
\r
1694 op.setDefaultNodeShape( NodeShape.CIRCLE );
\r
1697 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
\r
1701 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
\r
1702 switch ( op.getOvPlacement() ) {
\r
1704 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
\r
1707 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
\r
1710 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
\r
1713 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
\r
1716 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
\r
1718 if ( tree_panel != null ) {
\r
1719 tree_panel.updateOvSettings();
\r
1723 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
\r
1724 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
\r
1725 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1726 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
\r
1729 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1733 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
\r
1734 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
\r
1735 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1736 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
\r
1739 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1743 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
\r
1744 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
\r
1745 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
\r
1748 mi.setText( "Cycle Overview Placement..." );
\r
1752 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
\r
1753 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
\r
1754 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
\r
1758 mi.setText( "Select Color Scheme..." );
\r
1762 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
\r
1763 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
\r
1766 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
\r
1767 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
\r
1768 mi.setEnabled( true );
\r
1770 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
\r
1771 mi.setEnabled( true );
\r
1774 mi.setEnabled( false );
\r
1776 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
\r
1779 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
\r
1780 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
\r
1783 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
\r
1784 final JCheckBoxMenuItem scale,
\r
1785 final JCheckBoxMenuItem branch_lengths,
\r
1786 final JRadioButtonMenuItem non_lined_up,
\r
1787 final JRadioButtonMenuItem uniform_clado,
\r
1788 final JRadioButtonMenuItem nonuniform_clado,
\r
1789 final JCheckBoxMenuItem label_direction_cbmi ) {
\r
1790 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
\r
1791 final ControlPanel control = main_panel.getControlPanel();
\r
1792 final Options options = main_panel.getOptions();
\r
1793 scale.setSelected( options.isShowScale() );
\r
1794 branch_lengths.setSelected( options.isShowBranchLengthValues() );
\r
1795 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
\r
1796 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
\r
1797 scale.setSelected( false );
\r
1798 scale.setEnabled( false );
\r
1799 branch_lengths.setSelected( false );
\r
1800 branch_lengths.setEnabled( false );
\r
1802 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
\r
1803 scale.setSelected( false );
\r
1804 scale.setEnabled( false );
\r
1805 branch_lengths.setEnabled( true );
\r
1808 scale.setEnabled( true );
\r
1809 branch_lengths.setEnabled( true );
\r
1811 if ( ( tree_panel != null )
\r
1812 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
\r
1813 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
\r
1814 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
\r
1815 branch_lengths.setSelected( false );
\r
1816 branch_lengths.setEnabled( false );
\r
1818 if ( tree_panel != null ) {
\r
1819 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
\r
1820 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
\r
1821 non_lined_up.setEnabled( false );
\r
1822 uniform_clado.setEnabled( false );
\r
1823 nonuniform_clado.setEnabled( false );
\r
1826 non_lined_up.setEnabled( true );
\r
1827 uniform_clado.setEnabled( true );
\r
1828 nonuniform_clado.setEnabled( true );
\r
1832 if ( ( tree_panel != null )
\r
1833 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
\r
1834 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
\r
1835 branch_lengths.setSelected( false );
\r
1836 branch_lengths.setEnabled( false );
\r
1838 if ( ( tree_panel != null )
\r
1839 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
\r
1840 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
\r
1841 non_lined_up.setEnabled( false );
\r
1844 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
\r
1845 non_lined_up.setEnabled( true );
\r
1848 label_direction_cbmi.setEnabled( true );
\r
1849 if ( tree_panel != null ) {
\r
1850 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
\r
1851 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1852 label_direction_cbmi.setEnabled( false );
\r
1854 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
\r
1855 scale.setSelected( false );
\r
1856 scale.setEnabled( false );
\r
1861 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
\r
1862 for( final TreePanel tree_panel : treepanels ) {
\r
1863 tree_panel.setTextAntialias();
\r