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.ArrayList;
\r
36 import java.util.LinkedList;
\r
37 import java.util.List;
\r
38 import java.util.Locale;
\r
39 import java.util.NoSuchElementException;
\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.phylogeny.iterators.PhylogenyNodeIterator;
\r
71 import org.forester.sdi.GSDI;
\r
72 import org.forester.sdi.GSDIR;
\r
73 import org.forester.sdi.SDIException;
\r
74 import org.forester.util.ForesterConstants;
\r
75 import org.forester.util.ForesterUtil;
\r
77 public abstract class MainFrame extends JFrame implements ActionListener {
\r
79 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
\r
80 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
\r
81 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
\r
82 private static final long serialVersionUID = 3655000897845508358L;
\r
83 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
\r
86 static final String TYPE_MENU_HEADER = "Type";
\r
87 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
\r
88 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
\r
89 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
\r
90 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
\r
91 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
\r
92 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
\r
93 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
\r
94 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
\r
95 static final String OPTIONS_HEADER = "Options";
\r
96 static final String SEARCH_SUBHEADER = "Search:";
\r
97 static final String DISPLAY_SUBHEADER = "Display:";
\r
98 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
\r
99 static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";
\r
100 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
\r
101 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
\r
102 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
\r
103 static final String DISPLAY_SCALE_LABEL = "Scale";
\r
104 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
\r
105 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
\r
106 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
\r
107 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
\r
108 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
\r
109 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
\r
110 static final String BG_GRAD_LABEL = "Background Color Gradient";
\r
111 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
\r
112 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
\r
113 static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
\r
114 static final String SHOW_OVERVIEW_LABEL = "Overview";
\r
115 static final String FONT_SIZE_MENU_LABEL = "Font Size";
\r
116 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
\r
117 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
\r
118 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
\r
119 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
120 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
\r
121 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
\r
122 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
\r
123 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
\r
124 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
\r
125 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
\r
126 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
\r
127 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
\r
128 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
\r
129 static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
\r
130 static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
\r
131 JMenuBar _jmenubar;
\r
135 JMenu _options_jmenu;
\r
136 JMenu _font_size_menu;
\r
138 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
\r
140 JMenu _analysis_menu;
\r
141 JMenuItem _load_species_tree_item;
\r
142 JMenuItem _gsdi_item;
\r
143 JMenuItem _gsdir_item;
\r
144 JMenuItem _lineage_inference;
\r
146 JMenuItem _open_item;
\r
147 JMenuItem _open_url_item;
\r
148 JMenuItem _save_item;
\r
149 JMenuItem _save_all_item;
\r
150 JMenuItem _close_item;
\r
151 JMenuItem _exit_item;
\r
152 JMenuItem _new_item;
\r
154 JMenuItem _midpoint_root_item;
\r
155 JMenuItem _taxcolor_item;
\r
156 JMenuItem _confcolor_item;
\r
157 JMenuItem _color_rank_jmi;
\r
158 JMenuItem _collapse_species_specific_subtrees;
\r
159 JMenuItem _obtain_detailed_taxonomic_information_jmi;
\r
160 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
\r
161 JMenuItem _obtain_seq_information_jmi;
\r
162 JMenuItem _move_node_names_to_tax_sn_jmi;
\r
163 JMenuItem _move_node_names_to_seq_names_jmi;
\r
164 JMenuItem _extract_tax_code_from_node_names_jmi;
\r
165 JMenuItem _annotate_item;
\r
166 JMenuItem _remove_branch_color_item;
\r
167 JMenuItem _remove_visual_styles_item;
\r
168 JMenuItem _delete_selected_nodes_item;
\r
169 JMenuItem _delete_not_selected_nodes_item;
\r
171 JMenuItem _super_tiny_fonts_item;
\r
172 JMenuItem _tiny_fonts_item;
\r
173 JMenuItem _small_fonts_item;
\r
174 JMenuItem _medium_fonts_item;
\r
175 JMenuItem _large_fonts_item;
\r
177 // _ screen and print
\r
178 JMenuItem _choose_font_mi;
\r
179 JMenuItem _switch_colors_mi;
\r
180 JCheckBoxMenuItem _label_direction_cbmi;
\r
181 // _ screen display
\r
182 JCheckBoxMenuItem _screen_antialias_cbmi;
\r
183 JCheckBoxMenuItem _background_gradient_cbmi;
\r
184 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
\r
185 JRadioButtonMenuItem _uniform_cladograms_rbmi;
\r
186 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
\r
187 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
\r
188 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
\r
189 JCheckBoxMenuItem _show_overview_cbmi;
\r
190 JCheckBoxMenuItem _show_domain_labels;
\r
191 JCheckBoxMenuItem _show_annotation_ref_source;
\r
192 JCheckBoxMenuItem _abbreviate_scientific_names;
\r
193 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
\r
194 JMenuItem _overview_placment_mi;
\r
195 JMenuItem _choose_minimal_confidence_mi;
\r
196 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
\r
197 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
\r
198 JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
\r
199 JMenuItem _cycle_node_shape_mi;
\r
200 JMenuItem _cycle_node_fill_mi;
\r
201 JMenuItem _choose_node_size_mi;
\r
202 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
\r
203 JCheckBoxMenuItem _right_line_up_domains_cbmi;
\r
204 JCheckBoxMenuItem _line_up_renderable_data_cbmi;
\r
206 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
\r
207 JCheckBoxMenuItem _antialias_print_cbmi;
\r
208 JCheckBoxMenuItem _print_black_and_white_cbmi;
\r
209 JCheckBoxMenuItem _print_using_actual_size_cbmi;
\r
210 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
\r
211 JMenuItem _print_size_mi;
\r
212 JMenuItem _choose_pdf_width_mi;
\r
214 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
\r
215 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
\r
216 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
\r
217 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
\r
218 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
\r
219 JCheckBoxMenuItem _replace_underscores_cbmi;
\r
220 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
\r
221 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
\r
222 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
\r
224 JCheckBoxMenuItem _search_case_senstive_cbmi;
\r
225 JCheckBoxMenuItem _search_whole_words_only_cbmi;
\r
226 JCheckBoxMenuItem _inverse_search_result_cbmi;
\r
227 JCheckBoxMenuItem _search_with_regex_cbmi;
\r
230 JCheckBoxMenuItem _rectangular_type_cbmi;
\r
231 JCheckBoxMenuItem _triangular_type_cbmi;
\r
232 JCheckBoxMenuItem _curved_type_cbmi;
\r
233 JCheckBoxMenuItem _convex_type_cbmi;
\r
234 JCheckBoxMenuItem _euro_type_cbmi;
\r
235 JCheckBoxMenuItem _rounded_type_cbmi;
\r
236 JCheckBoxMenuItem _unrooted_type_cbmi;
\r
237 JCheckBoxMenuItem _circular_type_cbmi;
\r
238 // view as text menu:
\r
239 JMenuItem _view_as_NH_item;
\r
240 JMenuItem _view_as_XML_item;
\r
241 JMenuItem _view_as_nexus_item;
\r
242 JMenuItem _display_basic_information_item;
\r
244 JMenuItem _about_item;
\r
245 JMenuItem _help_item;
\r
246 JMenuItem _website_item;
\r
247 JMenuItem _phyloxml_website_item;
\r
248 JMenuItem _phyloxml_ref_item;
\r
249 JMenuItem _aptx_ref_item;
\r
251 JMenu _process_menu;
\r
252 // Handy pointers to child components:
\r
253 MainPanel _mainpanel;
\r
254 Container _contentpane;
\r
255 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
\r
256 Configuration _configuration;
\r
258 private Phylogeny _species_tree;
\r
259 InferenceManager _inference_manager;
\r
260 final ProcessPool _process_pool;
\r
261 private String _previous_node_annotation_ref;
\r
264 _process_pool = ProcessPool.createInstance();
\r
268 * Action performed.
\r
271 public void actionPerformed( final ActionEvent e ) {
\r
272 final Object o = e.getSource();
\r
273 boolean is_applet = false;
\r
274 JApplet applet = null;
\r
275 if ( getCurrentTreePanel() != null ) {
\r
276 is_applet = getCurrentTreePanel().isApplet();
\r
278 applet = getCurrentTreePanel().obtainApplet();
\r
281 if ( o == _exit_item ) {
\r
284 else if ( o == _gsdi_item ) {
\r
285 if ( isSubtreeDisplayed() ) {
\r
290 else if ( o == _gsdir_item ) {
\r
291 if ( isSubtreeDisplayed() ) {
\r
296 else if ( o == _taxcolor_item ) {
\r
299 else if ( o == _confcolor_item ) {
\r
302 else if ( o == _color_rank_jmi ) {
\r
305 else if ( o == _collapse_species_specific_subtrees ) {
\r
306 if ( isSubtreeDisplayed() ) {
\r
309 if ( getCurrentTreePanel() != null ) {
\r
310 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
\r
313 else if ( o == _remove_branch_color_item ) {
\r
314 if ( isSubtreeDisplayed() ) {
\r
317 removeBranchColors();
\r
319 else if ( o == _remove_visual_styles_item ) {
\r
320 if ( isSubtreeDisplayed() ) {
\r
323 removeVisualStyles();
\r
325 else if ( o == _midpoint_root_item ) {
\r
326 if ( isSubtreeDisplayed() ) {
\r
331 else if ( o == _delete_selected_nodes_item ) {
\r
332 if ( isSubtreeDisplayed() ) {
\r
335 deleteSelectedNodes( true );
\r
337 else if ( o == _delete_not_selected_nodes_item ) {
\r
338 if ( isSubtreeDisplayed() ) {
\r
341 deleteSelectedNodes( false );
\r
343 else if ( o == _annotate_item ) {
\r
344 annotateSequences();
\r
346 else if ( o == _switch_colors_mi ) {
\r
349 else if ( o == _display_basic_information_item ) {
\r
350 if ( getCurrentTreePanel() != null ) {
\r
351 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
\r
354 else if ( o == _view_as_NH_item ) {
\r
357 else if ( o == _view_as_XML_item ) {
\r
360 else if ( o == _view_as_nexus_item ) {
\r
363 else if ( o == _super_tiny_fonts_item ) {
\r
364 if ( getCurrentTreePanel() != null ) {
\r
365 getCurrentTreePanel().setSuperTinyFonts();
\r
366 getCurrentTreePanel().repaint();
\r
369 else if ( o == _tiny_fonts_item ) {
\r
370 if ( getCurrentTreePanel() != null ) {
\r
371 getCurrentTreePanel().setTinyFonts();
\r
372 getCurrentTreePanel().repaint();
\r
375 else if ( o == _small_fonts_item ) {
\r
376 if ( getCurrentTreePanel() != null ) {
\r
377 getCurrentTreePanel().setSmallFonts();
\r
378 getCurrentTreePanel().repaint();
\r
381 else if ( o == _medium_fonts_item ) {
\r
382 if ( getCurrentTreePanel() != null ) {
\r
383 getCurrentTreePanel().setMediumFonts();
\r
384 getCurrentTreePanel().repaint();
\r
387 else if ( o == _large_fonts_item ) {
\r
388 if ( getCurrentTreePanel() != null ) {
\r
389 getCurrentTreePanel().setLargeFonts();
\r
390 getCurrentTreePanel().repaint();
\r
393 else if ( o == _choose_font_mi ) {
\r
396 else if ( o == _choose_minimal_confidence_mi ) {
\r
397 chooseMinimalConfidence();
\r
399 else if ( o == _choose_node_size_mi ) {
\r
400 chooseNodeSize( getOptions(), this );
\r
402 else if ( o == _overview_placment_mi ) {
\r
403 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
\r
405 else if ( o == _cycle_node_fill_mi ) {
\r
406 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
\r
408 else if ( o == _cycle_node_shape_mi ) {
\r
409 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
\r
411 else if ( o == _screen_antialias_cbmi ) {
\r
412 updateOptions( getOptions() );
\r
413 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
415 else if ( o == _background_gradient_cbmi ) {
\r
416 updateOptions( getOptions() );
\r
418 else if ( o == _show_domain_labels ) {
\r
419 updateOptions( getOptions() );
\r
421 else if ( o == _show_annotation_ref_source ) {
\r
422 updateOptions( getOptions() );
\r
424 else if ( o == _abbreviate_scientific_names ) {
\r
425 updateOptions( getOptions() );
\r
427 else if ( o == _color_labels_same_as_parent_branch ) {
\r
428 updateOptions( getOptions() );
\r
430 else if ( o == _show_default_node_shapes_internal_cbmi ) {
\r
431 updateOptions( getOptions() );
\r
433 else if ( o == _show_default_node_shapes_external_cbmi ) {
\r
434 updateOptions( getOptions() );
\r
436 else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
\r
437 updateOptions( getOptions() );
\r
439 else if ( o == _non_lined_up_cladograms_rbmi ) {
\r
440 updateOptions( getOptions() );
\r
443 else if ( o == _uniform_cladograms_rbmi ) {
\r
444 updateOptions( getOptions() );
\r
447 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
\r
448 updateOptions( getOptions() );
\r
451 else if ( o == _search_case_senstive_cbmi ) {
\r
452 updateOptions( getOptions() );
\r
453 getMainPanel().getControlPanel().search0();
\r
454 getMainPanel().getControlPanel().search1();
\r
456 else if ( o == _search_whole_words_only_cbmi ) {
\r
457 updateOptions( getOptions() );
\r
458 getMainPanel().getControlPanel().search0();
\r
459 getMainPanel().getControlPanel().search1();
\r
461 else if ( o == _inverse_search_result_cbmi ) {
\r
462 updateOptions( getOptions() );
\r
463 getMainPanel().getControlPanel().search0();
\r
464 getMainPanel().getControlPanel().search1();
\r
466 else if ( o == _search_with_regex_cbmi ) {
\r
467 updateOptions( getOptions() );
\r
468 getMainPanel().getControlPanel().search0();
\r
469 getMainPanel().getControlPanel().search1();
\r
471 else if ( o == _show_scale_cbmi ) {
\r
472 updateOptions( getOptions() );
\r
474 else if ( o == _color_by_taxonomic_group_cbmi ) {
\r
475 updateOptions( getOptions() );
\r
477 else if ( o == _show_confidence_stddev_cbmi ) {
\r
478 updateOptions( getOptions() );
\r
480 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
\r
481 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
482 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
\r
484 updateOptions( getOptions() );
\r
486 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
487 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
488 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
490 updateOptions( getOptions() );
\r
492 else if ( o == _label_direction_cbmi ) {
\r
493 updateOptions( getOptions() );
\r
495 else if ( o == _show_overview_cbmi ) {
\r
496 updateOptions( getOptions() );
\r
497 if ( getCurrentTreePanel() != null ) {
\r
498 getCurrentTreePanel().updateOvSizes();
\r
501 else if ( o == _line_up_renderable_data_cbmi ) {
\r
502 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
\r
503 _right_line_up_domains_cbmi.setSelected( false );
\r
505 updateOptions( getOptions() );
\r
507 else if ( o == _right_line_up_domains_cbmi ) {
\r
508 if ( _right_line_up_domains_cbmi.isSelected() ) {
\r
509 _line_up_renderable_data_cbmi.setSelected( true );
\r
511 updateOptions( getOptions() );
\r
513 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
514 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
515 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
518 else if ( o == _about_item ) {
\r
521 else if ( o == _help_item ) {
\r
523 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );
\r
525 catch ( final IOException e1 ) {
\r
526 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
529 else if ( o == _website_item ) {
\r
531 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
\r
533 catch ( final IOException e1 ) {
\r
534 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
537 else if ( o == _phyloxml_website_item ) {
\r
539 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
541 catch ( final IOException e1 ) {
\r
542 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
545 else if ( o == _aptx_ref_item ) {
\r
547 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
\r
549 catch ( final IOException e1 ) {
\r
550 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
553 else if ( o == _phyloxml_ref_item ) {
\r
555 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
557 catch ( final IOException e1 ) {
\r
558 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
562 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
563 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
564 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
565 readPhylogeniesFromWebservice( i );
\r
570 _contentpane.repaint();
\r
573 private void deleteSelectedNodes( final boolean delete ) {
\r
574 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
575 if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
\r
578 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
579 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
580 final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
581 for( final PhylogenyNode n : all_selected_nodes ) {
\r
582 if ( n.isExternal() ) {
\r
587 String function = "Retain";
\r
589 function = "Delete";
\r
591 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
593 .showMessageDialog( this,
\r
594 "Need to select external nodes, either via direct selection or via the \"Search\" function",
\r
595 "No external nodes selected to " + function.toLowerCase(),
\r
596 JOptionPane.ERROR_MESSAGE );
\r
599 final int todo = nodes.size();
\r
600 final int ext = phy.getNumberOfExternalNodes();
\r
606 JOptionPane.showMessageDialog( this,
\r
607 "Cannot delete all nodes",
\r
608 "Attempt to delete all nodes ",
\r
609 JOptionPane.ERROR_MESSAGE );
\r
612 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
\r
613 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
\r
614 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
\r
615 if ( result == JOptionPane.OK_OPTION ) {
\r
617 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
\r
618 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
\r
619 final PhylogenyNode n = it.next();
\r
620 if ( !nodes.contains( n ) ) {
\r
621 to_delete.add( n );
\r
624 for( final PhylogenyNode n : to_delete ) {
\r
625 phy.deleteSubtree( n, true );
\r
629 for( final PhylogenyNode n : nodes ) {
\r
630 phy.deleteSubtree( n, true );
\r
634 getCurrentTreePanel().setNodeInPreorderToNull();
\r
635 phy.externalNodesHaveChanged();
\r
636 phy.clearHashIdToNodeMap();
\r
637 phy.recalculateNumberOfExternalDescendants( true );
\r
638 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
639 getCurrentTreePanel().setEdited( true );
\r
644 void resetSearch() {
\r
645 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
\r
646 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
\r
647 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
\r
648 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
\r
649 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
\r
650 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
\r
651 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
\r
652 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
\r
653 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
\r
654 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
\r
655 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
\r
656 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
\r
659 public Configuration getConfiguration() {
\r
660 return _configuration;
\r
664 * This method returns the current external node data which
\r
665 * has been selected by the user by clicking the "Return ..."
\r
666 * menu item. This method is expected to be called from Javascript or
\r
667 * something like it.
\r
669 * @return current external node data as String
\r
671 public String getCurrentExternalNodesDataBuffer() {
\r
672 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
675 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
676 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
679 public int getCurrentExternalNodesDataBufferLength() {
\r
680 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
683 public InferenceManager getInferenceManager() {
\r
684 return _inference_manager;
\r
687 public MainPanel getMainPanel() {
\r
691 public Options getOptions() {
\r
695 public ProcessPool getProcessPool() {
\r
696 return _process_pool;
\r
699 public void showTextFrame( final String s, final String title ) {
\r
701 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
704 public void showWhole() {
\r
705 _mainpanel.getControlPanel().showWhole();
\r
708 public void updateProcessMenu() {
\r
709 // In general Swing is not thread safe.
\r
710 // See "Swing's Threading Policy".
\r
711 SwingUtilities.invokeLater( new Runnable() {
\r
714 public void run() {
\r
715 doUpdateProcessMenu();
\r
720 void activateSaveAllIfNeeded() {
\r
721 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
722 _save_all_item.setEnabled( true );
\r
725 _save_all_item.setEnabled( false );
\r
729 void buildFileMenu() {
\r
730 _file_jmenu = createMenu( "File", getConfiguration() );
\r
731 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
732 customizeJMenuItem( _exit_item );
\r
733 _jmenubar.add( _file_jmenu );
\r
736 void buildFontSizeMenu() {
\r
737 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
738 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
739 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
740 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
741 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
742 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
743 customizeJMenuItem( _super_tiny_fonts_item );
\r
744 customizeJMenuItem( _tiny_fonts_item );
\r
745 customizeJMenuItem( _small_fonts_item );
\r
746 customizeJMenuItem( _medium_fonts_item );
\r
747 customizeJMenuItem( _large_fonts_item );
\r
748 _jmenubar.add( _font_size_menu );
\r
751 void buildHelpMenu() {
\r
752 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
753 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
\r
754 _help_jmenu.addSeparator();
\r
755 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
756 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
\r
757 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
758 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
759 _help_jmenu.addSeparator();
\r
760 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
761 customizeJMenuItem( _help_item );
\r
762 customizeJMenuItem( _website_item );
\r
763 customizeJMenuItem( _phyloxml_website_item );
\r
764 customizeJMenuItem( _aptx_ref_item );
\r
765 customizeJMenuItem( _phyloxml_ref_item );
\r
766 customizeJMenuItem( _about_item );
\r
767 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
768 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
769 _jmenubar.add( _help_jmenu );
\r
772 void buildTypeMenu() {
\r
773 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
774 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
775 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
776 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
777 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
778 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
779 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
780 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
781 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
782 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
783 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
784 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
785 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
786 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
787 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
788 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
789 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
790 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
791 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
792 initializeTypeMenu( getOptions() );
\r
793 _jmenubar.add( _type_menu );
\r
796 void buildViewMenu() {
\r
797 _view_jmenu = createMenu( "View", getConfiguration() );
\r
798 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
799 _view_jmenu.addSeparator();
\r
800 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
801 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
802 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
803 customizeJMenuItem( _display_basic_information_item );
\r
804 customizeJMenuItem( _view_as_NH_item );
\r
805 customizeJMenuItem( _view_as_XML_item );
\r
806 customizeJMenuItem( _view_as_nexus_item );
\r
807 _jmenubar.add( _view_jmenu );
\r
810 void checkTextFrames() {
\r
811 if ( _textframes.size() > 5 ) {
\r
813 if ( _textframes.getFirst() != null ) {
\r
814 _textframes.getFirst().removeMe();
\r
817 _textframes.removeFirst();
\r
820 catch ( final NoSuchElementException e ) {
\r
827 removeAllTextFrames();
\r
828 if ( _mainpanel != null ) {
\r
829 _mainpanel.terminate();
\r
831 if ( _contentpane != null ) {
\r
832 _contentpane.removeAll();
\r
834 setVisible( false );
\r
839 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
840 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
841 final String rank = ( String ) JOptionPane
\r
842 .showInputDialog( this,
\r
843 "What rank should the colorization be based on",
\r
845 JOptionPane.QUESTION_MESSAGE,
\r
849 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
850 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
856 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
857 _mainpanel.getCurrentTreePanel().confColor();
\r
861 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
862 if ( item != null ) {
\r
863 item.setFont( MainFrame.menu_font );
\r
864 if ( !getConfiguration().isUseNativeUI() ) {
\r
865 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
866 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
868 item.setSelected( is_selected );
\r
869 item.addActionListener( this );
\r
873 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
874 if ( jmi != null ) {
\r
875 jmi.setFont( MainFrame.menu_font );
\r
876 if ( !getConfiguration().isUseNativeUI() ) {
\r
877 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
878 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
880 jmi.addActionListener( this );
\r
885 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
886 if ( item != null ) {
\r
887 item.setFont( MainFrame.menu_font );
\r
888 if ( !getConfiguration().isUseNativeUI() ) {
\r
889 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
890 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
892 item.setSelected( is_selected );
\r
893 item.addActionListener( this );
\r
897 void displayBasicInformation( final File treefile ) {
\r
898 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
899 String title = "Basic Information";
\r
900 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
901 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
903 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
907 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
909 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
911 catch ( final Exception ex ) {
\r
914 JOptionPane.showMessageDialog( this,
\r
915 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
916 "Error during File|Open",
\r
917 JOptionPane.ERROR_MESSAGE );
\r
920 void exceptionOccuredDuringSaveAs( final Exception e ) {
\r
922 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
924 catch ( final Exception ex ) {
\r
927 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
930 void executeGSDI() {
\r
931 if ( !isOKforSDI( false, true ) ) {
\r
934 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
935 JOptionPane.showMessageDialog( this,
\r
936 "Gene tree is not rooted.",
\r
937 "Cannot execute GSDI",
\r
938 JOptionPane.ERROR_MESSAGE );
\r
941 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
942 gene_tree.setAllNodesToNotCollapse();
\r
943 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
945 final Phylogeny species_tree = getSpeciesTree().copy();
\r
947 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
949 catch ( final SDIException e ) {
\r
950 JOptionPane.showMessageDialog( this,
\r
951 e.getLocalizedMessage(),
\r
952 "Error during GSDI",
\r
953 JOptionPane.ERROR_MESSAGE );
\r
956 catch ( final Exception e ) {
\r
957 AptxUtil.unexpectedException( e );
\r
960 gene_tree.setRerootable( false );
\r
961 gene_tree.clearHashIdToNodeMap();
\r
962 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
963 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
964 getMainPanel().getControlPanel().setShowEvents( true );
\r
966 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
967 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
969 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
971 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
972 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
973 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
974 JOptionPane.showMessageDialog( this,
\r
975 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
976 + "Potential duplications: "
\r
977 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
978 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
979 + "Stripped gene tree nodes: "
\r
980 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
981 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
982 + "Number of polytomies in species tree used: " + poly + "\n",
\r
983 "GSDI successfully completed",
\r
984 JOptionPane.WARNING_MESSAGE );
\r
987 JOptionPane.showMessageDialog( this,
\r
988 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
989 + "Potential duplications: "
\r
990 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
991 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
992 + "Stripped gene tree nodes: "
\r
993 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
994 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
995 + "Number of polytomies in species tree used: " + poly + "\n",
\r
996 "GSDI successfully completed",
\r
997 JOptionPane.INFORMATION_MESSAGE );
\r
1001 void executeGSDIR() {
\r
1002 if ( !isOKforSDI( false, false ) ) {
\r
1005 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
1007 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
1008 JOptionPane.showMessageDialog( this,
\r
1009 "Gene tree is not completely binary",
\r
1010 "Cannot execute GSDI",
\r
1011 JOptionPane.ERROR_MESSAGE );
\r
1014 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1015 gene_tree.setAllNodesToNotCollapse();
\r
1016 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1017 GSDIR gsdir = null;
\r
1018 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1020 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
1022 catch ( final SDIException e ) {
\r
1023 JOptionPane.showMessageDialog( this,
\r
1024 e.getLocalizedMessage(),
\r
1025 "Error during GSDIR",
\r
1026 JOptionPane.ERROR_MESSAGE );
\r
1029 catch ( final Exception e ) {
\r
1030 AptxUtil.unexpectedException( e );
\r
1033 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
1034 result_gene_tree.setRerootable( false );
\r
1035 result_gene_tree.clearHashIdToNodeMap();
\r
1036 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1037 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
1038 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
1039 getMainPanel().getControlPanel().setShowEvents( true );
\r
1041 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1042 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1044 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1046 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1047 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1048 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1049 JOptionPane.showMessageDialog( this,
\r
1050 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1051 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1052 + "Stripped gene tree nodes: "
\r
1053 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1054 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1055 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1056 "GSDIR successfully completed",
\r
1057 JOptionPane.WARNING_MESSAGE );
\r
1060 JOptionPane.showMessageDialog( this,
\r
1061 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1062 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1063 + "Stripped gene tree nodes: "
\r
1064 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1065 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1066 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1067 "GSDIR successfully completed",
\r
1068 JOptionPane.INFORMATION_MESSAGE );
\r
1072 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
1073 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
1074 JOptionPane.showMessageDialog( this,
\r
1075 "Gene tree and species tree have no species in common.",
\r
1076 "Error during SDI",
\r
1077 JOptionPane.ERROR_MESSAGE );
\r
1080 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
1081 JOptionPane.showMessageDialog( this,
\r
1082 "Gene tree and species tree have only one species in common.",
\r
1083 "Error during SDI",
\r
1084 JOptionPane.ERROR_MESSAGE );
\r
1092 TreePanel getCurrentTreePanel() {
\r
1093 return getMainPanel().getCurrentTreePanel();
\r
1096 JMenu getHelpMenu() {
\r
1097 return _help_jmenu;
\r
1100 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
1101 return _label_direction_cbmi;
\r
1104 JMenuBar getMenuBarOfMainFrame() {
\r
1108 final Phylogeny getSpeciesTree() {
\r
1109 return _species_tree;
\r
1112 void initializeTypeMenu( final Options options ) {
\r
1113 setTypeMenuToAllUnselected();
\r
1114 switch ( options.getPhylogenyGraphicsType() ) {
\r
1116 _convex_type_cbmi.setSelected( true );
\r
1119 _curved_type_cbmi.setSelected( true );
\r
1122 _euro_type_cbmi.setSelected( true );
\r
1125 _rounded_type_cbmi.setSelected( true );
\r
1128 _triangular_type_cbmi.setSelected( true );
\r
1131 _unrooted_type_cbmi.setSelected( true );
\r
1134 _circular_type_cbmi.setSelected( true );
\r
1137 _rectangular_type_cbmi.setSelected( true );
\r
1142 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1143 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1146 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1147 JOptionPane.showMessageDialog( this,
\r
1148 "No species tree loaded",
\r
1149 "Cannot execute GSDI",
\r
1150 JOptionPane.ERROR_MESSAGE );
\r
1153 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1154 JOptionPane.showMessageDialog( this,
\r
1155 "Species tree is not completely binary",
\r
1156 "Cannot execute GSDI",
\r
1157 JOptionPane.ERROR_MESSAGE );
\r
1160 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1161 JOptionPane.showMessageDialog( this,
\r
1162 "Gene tree is not completely binary",
\r
1163 "Cannot execute GSDI",
\r
1164 JOptionPane.ERROR_MESSAGE );
\r
1172 boolean isSubtreeDisplayed() {
\r
1173 if ( getCurrentTreePanel() != null ) {
\r
1174 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1176 .showMessageDialog( this,
\r
1177 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1178 "Operation can not be exectuted on a sub-tree",
\r
1179 JOptionPane.WARNING_MESSAGE );
\r
1186 void midpointRoot() {
\r
1187 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1188 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1192 void readPhylogeniesFromWebservice( final int i ) {
\r
1193 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1194 new Thread( reader ).start();
\r
1197 void removeAllTextFrames() {
\r
1198 for( final TextFrame tf : _textframes ) {
\r
1199 if ( tf != null ) {
\r
1203 _textframes.clear();
\r
1206 void setConfiguration( final Configuration configuration ) {
\r
1207 _configuration = configuration;
\r
1210 void setInferenceManager( final InferenceManager i ) {
\r
1211 _inference_manager = i;
\r
1214 void setOptions( final Options options ) {
\r
1215 _options = options;
\r
1218 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1219 setTypeMenuToAllUnselected();
\r
1222 _circular_type_cbmi.setSelected( true );
\r
1225 _convex_type_cbmi.setSelected( true );
\r
1228 _curved_type_cbmi.setSelected( true );
\r
1231 _euro_type_cbmi.setSelected( true );
\r
1234 _rounded_type_cbmi.setSelected( true );
\r
1237 _rectangular_type_cbmi.setSelected( true );
\r
1240 _triangular_type_cbmi.setSelected( true );
\r
1243 _unrooted_type_cbmi.setSelected( true );
\r
1246 throw new IllegalArgumentException( "unknown type: " + type );
\r
1250 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1251 _species_tree = species_tree;
\r
1254 void setTypeMenuToAllUnselected() {
\r
1255 _convex_type_cbmi.setSelected( false );
\r
1256 _curved_type_cbmi.setSelected( false );
\r
1257 _euro_type_cbmi.setSelected( false );
\r
1258 _rounded_type_cbmi.setSelected( false );
\r
1259 _triangular_type_cbmi.setSelected( false );
\r
1260 _rectangular_type_cbmi.setSelected( false );
\r
1261 _unrooted_type_cbmi.setSelected( false );
\r
1262 _circular_type_cbmi.setSelected( false );
\r
1265 void switchColors() {
\r
1266 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1267 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1268 csc.setVisible( true );
\r
1272 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1273 _mainpanel.getCurrentTreePanel().taxColor();
\r
1277 void typeChanged( final Object o ) {
\r
1278 updateTypeCheckboxes( getOptions(), o );
\r
1279 updateOptions( getOptions() );
\r
1280 if ( getCurrentTreePanel() != null ) {
\r
1281 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1282 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1283 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1284 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
1285 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1286 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
1287 getCurrentTreePanel().getControlPanel().showWhole();
\r
1289 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1290 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
1293 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
1295 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
1296 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
1297 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
1298 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
1299 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
1302 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
1308 void updateOptions( final Options options ) {
\r
1309 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
1310 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
1311 && _background_gradient_cbmi.isSelected() );
\r
1312 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
1313 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
1314 && _show_annotation_ref_source.isSelected() );
\r
1315 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
1316 && _abbreviate_scientific_names.isSelected() );
\r
1317 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
1318 && _color_labels_same_as_parent_branch.isSelected() );
\r
1319 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
1320 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
1321 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
1322 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
1323 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
\r
1324 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
\r
1325 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
1326 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
1328 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
1329 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1331 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
1332 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1334 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
1335 && _search_case_senstive_cbmi.isSelected() );
\r
1336 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
1337 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
1339 if ( _label_direction_cbmi != null ) {
\r
1340 if ( _label_direction_cbmi.isSelected() ) {
\r
1341 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
1344 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
1347 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
1348 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
1349 && _show_confidence_stddev_cbmi.isSelected() );
\r
1350 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
1351 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
1353 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
\r
1354 && ( _print_using_actual_size_cbmi.isSelected() ) );
\r
1355 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
\r
1356 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
\r
1357 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
1358 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
1359 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1360 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1362 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
1363 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1364 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1367 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
1369 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
1370 && _print_black_and_white_cbmi.isSelected() );
\r
1371 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
1372 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
1373 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
1374 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1376 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
1377 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1379 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
1380 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1382 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
1383 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
1385 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
1386 && _replace_underscores_cbmi.isSelected() );
\r
1387 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
1388 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
1389 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
1390 && _search_whole_words_only_cbmi.isSelected() );
\r
1391 options.setSearchWithRegex( ( _search_with_regex_cbmi != null )
\r
1392 && _search_with_regex_cbmi.isSelected() );
\r
1394 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
1395 && _inverse_search_result_cbmi.isSelected() );
\r
1396 if ( _graphics_export_visible_only_cbmi != null ) {
\r
1397 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
1398 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
\r
1399 _graphics_export_using_actual_size_cbmi.setSelected( true );
\r
1400 _graphics_export_using_actual_size_cbmi.setEnabled( false );
\r
1403 _graphics_export_using_actual_size_cbmi.setEnabled( true );
\r
1406 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
1407 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1409 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
1410 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
1412 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
1413 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
1415 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
1416 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
1418 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
1419 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
1421 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
1422 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
1424 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
1425 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
1427 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
1428 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
1430 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
\r
1431 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
\r
1433 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
\r
1434 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
\r
1438 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
1439 setTypeMenuToAllUnselected();
\r
1440 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
1443 void viewAsNexus() {
\r
1444 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1445 String title = "Nexus";
\r
1446 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1447 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1449 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
1455 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1456 String title = "New Hampshire";
\r
1457 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1458 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1460 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
1461 .getNhConversionSupportValueStyle() ),
\r
1466 void viewAsXML() {
\r
1467 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1468 String title = "phyloXML";
\r
1469 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1470 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1472 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
1476 private void annotateSequences() {
\r
1477 if ( getCurrentTreePanel() != null ) {
\r
1478 List<PhylogenyNode> nodes = null;
\r
1479 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
\r
1480 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
1481 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
1483 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
1485 .showMessageDialog( this,
\r
1486 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
1487 "No nodes selected for annotation",
\r
1488 JOptionPane.ERROR_MESSAGE );
\r
1491 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
1492 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1493 final JTextField ref_field = new JTextField( 10 );
\r
1494 final JTextField desc_filed = new JTextField( 20 );
\r
1495 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
1496 : getPreviousNodeAnnotationReference() );
\r
1497 final JPanel my_panel = new JPanel();
\r
1498 my_panel.add( new JLabel( "Reference " ) );
\r
1499 my_panel.add( ref_field );
\r
1500 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
1501 my_panel.add( new JLabel( "Description " ) );
\r
1502 my_panel.add( desc_filed );
\r
1503 final int result = JOptionPane.showConfirmDialog( null,
\r
1505 "Enter the sequence annotation(s) for the "
\r
1506 + nodes.size() + " selected nodes",
\r
1507 JOptionPane.OK_CANCEL_OPTION );
\r
1508 if ( result == JOptionPane.OK_OPTION ) {
\r
1509 String ref = ref_field.getText();
\r
1510 String desc = desc_filed.getText();
\r
1511 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
1513 ref = ref.replaceAll( "\\s+", " " );
\r
1514 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
1515 || ( ref.length() < 3 ) ) {
\r
1516 JOptionPane.showMessageDialog( this,
\r
1517 "Reference needs to be in the form of \"GO:1234567\"",
\r
1518 "Illegal Format for Annotation Reference",
\r
1519 JOptionPane.ERROR_MESSAGE );
\r
1523 if ( ref != null ) {
\r
1524 setPreviousNodeAnnotationReference( ref );
\r
1526 if ( desc != null ) {
\r
1527 desc = desc.trim();
\r
1528 desc = desc.replaceAll( "\\s+", " " );
\r
1530 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
1531 for( final PhylogenyNode n : nodes ) {
\r
1532 ForesterUtil.ensurePresenceOfSequence( n );
\r
1533 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
1534 : new Annotation( ref );
\r
1535 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
1536 ann.setDesc( desc );
\r
1538 n.getNodeData().getSequence().addAnnotation( ann );
\r
1541 getMainPanel().getControlPanel().showAnnotations();
\r
1547 private void chooseFont() {
\r
1548 final FontChooser fc = new FontChooser();
\r
1549 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
1550 fc.showDialog( this, "Select the Base Font" );
\r
1551 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
1554 private void chooseMinimalConfidence() {
\r
1555 final String s = ( String ) JOptionPane
\r
1556 .showInputDialog( this,
\r
1557 "Please enter the minimum for confidence values to be displayed.\n"
\r
1558 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
1559 "Minimal Confidence Value",
\r
1560 JOptionPane.QUESTION_MESSAGE,
\r
1563 getOptions().getMinConfidenceValue() );
\r
1564 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1565 boolean success = true;
\r
1567 final String m_str = s.trim();
\r
1568 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1570 m = Double.parseDouble( m_str );
\r
1572 catch ( final Exception ex ) {
\r
1579 if ( success && ( m >= 0.0 ) ) {
\r
1580 getOptions().setMinConfidenceValue( m );
\r
1585 private void doUpdateProcessMenu() {
\r
1586 if ( _process_pool.size() > 0 ) {
\r
1587 if ( _process_menu == null ) {
\r
1588 _process_menu = createMenu( "", getConfiguration() );
\r
1589 _process_menu.setForeground( Color.RED );
\r
1591 _process_menu.removeAll();
\r
1592 final String text = "processes running: " + _process_pool.size();
\r
1593 _process_menu.setText( text );
\r
1594 _jmenubar.add( _process_menu );
\r
1595 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
1596 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
1597 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
1601 if ( _process_menu != null ) {
\r
1602 _process_menu.removeAll();
\r
1603 _jmenubar.remove( _process_menu );
\r
1606 _jmenubar.validate();
\r
1607 _jmenubar.repaint();
\r
1611 private String getPreviousNodeAnnotationReference() {
\r
1612 return _previous_node_annotation_ref;
\r
1615 private void removeBranchColors() {
\r
1616 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1617 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
1621 private void removeVisualStyles() {
\r
1622 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1623 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
1627 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
1628 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
1632 * Display the about box.
\r
1634 static void about() {
\r
1635 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
\r
1636 about.append( "Copyright (C) 2014 Christian M Zmasek\n" );
\r
1637 about.append( "All Rights Reserved\n" );
\r
1638 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
\r
1639 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
\r
1640 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
\r
1641 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
1642 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
\r
1643 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
\r
1644 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
\r
1646 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
\r
1647 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
\r
1648 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
\r
1649 + ForesterUtil.OS_VERSION + "]\n" );
\r
1651 final Runtime rt = java.lang.Runtime.getRuntime();
\r
1652 final long free_memory = rt.freeMemory() / 1000000;
\r
1653 final long total_memory = rt.totalMemory() / 1000000;
\r
1654 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
\r
1655 about.append( "[locale: " + Locale.getDefault() + "]\n" );
\r
1656 about.append( "References:\n" );
\r
1657 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
\r
1658 about.append( "For more information & download:\n" );
\r
1659 about.append( Constants.APTX_WEB_SITE + "\n" );
\r
1660 about.append( "Documentation:\n" );
\r
1661 about.append( Constants.APTX_DOC_SITE + "\n" );
\r
1662 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
\r
1663 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
\r
1666 static void chooseNodeSize( final Options options, final Component parent ) {
\r
1667 final String s = ( String ) JOptionPane.showInputDialog( parent,
\r
1668 "Please enter the default size for node shapes.\n"
\r
1669 + "[current value: "
\r
1670 + options.getDefaultNodeShapeSize() + "]\n",
\r
1671 "Node Shape Size",
\r
1672 JOptionPane.QUESTION_MESSAGE,
\r
1675 options.getDefaultNodeShapeSize() );
\r
1676 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1677 boolean success = true;
\r
1679 final String m_str = s.trim();
\r
1680 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1682 m = Double.parseDouble( m_str );
\r
1684 catch ( final Exception ex ) {
\r
1691 if ( success && ( m >= 0.0 ) ) {
\r
1692 final short size = ForesterUtil.roundToShort( m );
\r
1693 if ( size >= 0.0 ) {
\r
1694 options.setDefaultNodeShapeSize( size );
\r
1700 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
\r
1701 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
\r
1704 static JMenu createMenu( final String title, final Configuration conf ) {
\r
1705 final JMenu jmenu = new JMenu( title );
\r
1706 if ( !conf.isUseNativeUI() ) {
\r
1707 jmenu.setFont( MainFrame.menu_font );
\r
1708 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
\r
1709 jmenu.setForeground( conf.getGuiMenuTextColor() );
\r
1714 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
\r
1715 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
\r
1716 if ( !configuration.isUseNativeUI() ) {
\r
1717 label.setBackground( configuration.getGuiMenuBackgroundColor() );
\r
1718 label.setForeground( configuration.getGuiMenuTextColor() );
\r
1719 label.setOpaque( true );
\r
1721 label.setSelected( false );
\r
1722 label.setEnabled( false );
\r
1726 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
\r
1727 switch ( op.getDefaultNodeFill() ) {
\r
1729 op.setDefaultNodeFill( NodeFill.SOLID );
\r
1732 op.setDefaultNodeFill( NodeFill.GRADIENT );
\r
1735 op.setDefaultNodeFill( NodeFill.NONE );
\r
1738 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
\r
1742 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
\r
1743 switch ( op.getDefaultNodeShape() ) {
\r
1745 op.setDefaultNodeShape( NodeShape.RECTANGLE );
\r
1748 op.setDefaultNodeShape( NodeShape.CIRCLE );
\r
1751 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
\r
1755 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
\r
1756 switch ( op.getOvPlacement() ) {
\r
1758 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
\r
1761 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
\r
1764 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
\r
1767 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
\r
1770 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
\r
1772 if ( tree_panel != null ) {
\r
1773 tree_panel.updateOvSettings();
\r
1777 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
\r
1778 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
\r
1779 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1780 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
\r
1783 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1787 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
\r
1788 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
\r
1789 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
1790 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
\r
1793 mi.setText( "Cycle Node Shape Fill Type..." );
\r
1797 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
\r
1798 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
\r
1799 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
\r
1802 mi.setText( "Cycle Overview Placement..." );
\r
1806 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
\r
1807 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
\r
1808 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
\r
1812 mi.setText( "Select Color Scheme..." );
\r
1816 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
\r
1817 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
\r
1820 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
\r
1821 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
\r
1822 mi.setEnabled( true );
\r
1824 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
\r
1825 mi.setEnabled( true );
\r
1828 mi.setEnabled( false );
\r
1830 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
\r
1833 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
\r
1834 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
\r
1837 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
\r
1838 for( final TreePanel tree_panel : treepanels ) {
\r
1839 tree_panel.setTextAntialias();
\r