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.JFileChooser;
\r
45 import javax.swing.JFrame;
\r
46 import javax.swing.JLabel;
\r
47 import javax.swing.JMenu;
\r
48 import javax.swing.JMenuBar;
\r
49 import javax.swing.JMenuItem;
\r
50 import javax.swing.JOptionPane;
\r
51 import javax.swing.JPanel;
\r
52 import javax.swing.JRadioButtonMenuItem;
\r
53 import javax.swing.JTextField;
\r
54 import javax.swing.SwingUtilities;
\r
55 import javax.swing.filechooser.FileFilter;
\r
57 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
\r
58 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
\r
59 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
\r
60 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
\r
61 import org.forester.archaeopteryx.tools.InferenceManager;
\r
62 import org.forester.archaeopteryx.tools.ProcessPool;
\r
63 import org.forester.archaeopteryx.tools.ProcessRunning;
\r
64 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
\r
65 import org.forester.io.writers.PhylogenyWriter;
\r
66 import org.forester.phylogeny.Phylogeny;
\r
67 import org.forester.phylogeny.PhylogenyMethods;
\r
68 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
\r
69 import org.forester.phylogeny.PhylogenyNode;
\r
70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
\r
71 import org.forester.phylogeny.data.Annotation;
\r
72 import org.forester.phylogeny.data.NodeDataField;
\r
73 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
\r
74 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
\r
75 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
\r
76 import org.forester.sdi.GSDI;
\r
77 import org.forester.sdi.GSDIR;
\r
78 import org.forester.sdi.SDIException;
\r
79 import org.forester.util.ForesterConstants;
\r
80 import org.forester.util.ForesterUtil;
\r
81 import org.forester.util.WindowsUtils;
\r
83 public abstract class MainFrame extends JFrame implements ActionListener {
\r
85 final static NHFilter nhfilter = new NHFilter();
\r
86 final static NHXFilter nhxfilter = new NHXFilter();
\r
87 final static XMLFilter xmlfilter = new XMLFilter();
\r
88 final static TolFilter tolfilter = new TolFilter();
\r
89 final static NexusFilter nexusfilter = new NexusFilter();
\r
90 final static PdfFilter pdffilter = new PdfFilter();
\r
91 final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
\r
92 final static MsaFileFilter msafilter = new MsaFileFilter();
\r
93 final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
\r
94 final static DefaultFilter defaultfilter = new DefaultFilter();
\r
95 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
\r
96 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
\r
97 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
\r
98 private static final long serialVersionUID = 3655000897845508358L;
\r
99 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
\r
102 static final String TYPE_MENU_HEADER = "Type";
\r
103 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
\r
104 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
\r
105 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
\r
106 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
\r
107 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
\r
108 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
\r
109 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
\r
110 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
\r
111 static final String OPTIONS_HEADER = "Options";
\r
112 static final String SEARCH_SUBHEADER = "Search:";
\r
113 static final String DISPLAY_SUBHEADER = "Display:";
\r
114 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
\r
115 static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";
\r
116 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
\r
117 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
\r
118 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
\r
119 static final String DISPLAY_SCALE_LABEL = "Scale";
\r
120 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
\r
121 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
\r
122 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
\r
123 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
\r
124 static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";
\r
125 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
\r
126 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
\r
127 static final String BG_GRAD_LABEL = "Background Color Gradient";
\r
128 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
\r
129 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
\r
130 static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
\r
131 static final String SHOW_OVERVIEW_LABEL = "Overview";
\r
132 static final String FONT_SIZE_MENU_LABEL = "Font Size";
\r
133 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
\r
134 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
\r
135 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
\r
136 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
137 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
\r
138 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
\r
139 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
\r
140 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
\r
141 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
\r
142 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
\r
143 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
\r
144 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
\r
145 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
\r
146 static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
\r
147 static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
\r
148 JMenuBar _jmenubar;
\r
152 JMenu _options_jmenu;
\r
153 JMenu _font_size_menu;
\r
155 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
\r
157 JMenu _analysis_menu;
\r
158 JMenuItem _load_species_tree_item;
\r
159 JMenuItem _gsdi_item;
\r
160 JMenuItem _gsdir_item;
\r
161 JMenuItem _lineage_inference;
\r
163 JMenuItem _open_item;
\r
164 JMenuItem _open_url_item;
\r
165 JMenuItem _save_item;
\r
166 JMenuItem _save_all_item;
\r
167 JMenuItem _close_item;
\r
168 JMenuItem _exit_item;
\r
169 JMenuItem _new_item;
\r
170 JMenuItem _print_item;
\r
171 JMenuItem _write_to_pdf_item;
\r
172 JMenuItem _write_to_jpg_item;
\r
173 JMenuItem _write_to_gif_item;
\r
174 JMenuItem _write_to_tif_item;
\r
175 JMenuItem _write_to_png_item;
\r
176 JMenuItem _write_to_bmp_item;
\r
178 JMenuItem _midpoint_root_item;
\r
179 JMenuItem _taxcolor_item;
\r
180 JMenuItem _confcolor_item;
\r
181 JMenuItem _color_rank_jmi;
\r
182 JMenuItem _collapse_species_specific_subtrees;
\r
183 JMenuItem _obtain_detailed_taxonomic_information_jmi;
\r
184 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
\r
185 JMenuItem _obtain_seq_information_jmi;
\r
186 JMenuItem _move_node_names_to_tax_sn_jmi;
\r
187 JMenuItem _move_node_names_to_seq_names_jmi;
\r
188 JMenuItem _extract_tax_code_from_node_names_jmi;
\r
189 JMenuItem _annotate_item;
\r
190 JMenuItem _remove_branch_color_item;
\r
191 JMenuItem _remove_visual_styles_item;
\r
192 JMenuItem _delete_selected_nodes_item;
\r
193 JMenuItem _delete_not_selected_nodes_item;
\r
195 JMenuItem _super_tiny_fonts_item;
\r
196 JMenuItem _tiny_fonts_item;
\r
197 JMenuItem _small_fonts_item;
\r
198 JMenuItem _medium_fonts_item;
\r
199 JMenuItem _large_fonts_item;
\r
201 // _ screen and print
\r
202 JMenuItem _choose_font_mi;
\r
203 JMenuItem _switch_colors_mi;
\r
204 JCheckBoxMenuItem _label_direction_cbmi;
\r
205 // _ screen display
\r
206 JCheckBoxMenuItem _screen_antialias_cbmi;
\r
207 JCheckBoxMenuItem _background_gradient_cbmi;
\r
208 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
\r
209 JRadioButtonMenuItem _uniform_cladograms_rbmi;
\r
210 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
\r
211 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
\r
212 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
\r
213 JCheckBoxMenuItem _show_overview_cbmi;
\r
214 JCheckBoxMenuItem _show_domain_labels;
\r
215 JCheckBoxMenuItem _show_annotation_ref_source;
\r
216 JCheckBoxMenuItem _abbreviate_scientific_names;
\r
217 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
\r
218 JMenuItem _overview_placment_mi;
\r
219 JMenuItem _choose_minimal_confidence_mi;
\r
220 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
\r
221 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
\r
222 JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
\r
223 JMenuItem _cycle_node_shape_mi;
\r
224 JMenuItem _cycle_node_fill_mi;
\r
225 JMenuItem _choose_node_size_mi;
\r
226 JMenuItem _cycle_data_return;
\r
227 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
\r
228 JCheckBoxMenuItem _right_line_up_domains_cbmi;
\r
229 JCheckBoxMenuItem _line_up_renderable_data_cbmi;
\r
231 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
\r
232 JCheckBoxMenuItem _antialias_print_cbmi;
\r
233 JCheckBoxMenuItem _print_black_and_white_cbmi;
\r
234 JCheckBoxMenuItem _print_using_actual_size_cbmi;
\r
235 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
\r
236 JMenuItem _print_size_mi;
\r
237 JMenuItem _choose_pdf_width_mi;
\r
239 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
\r
240 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
\r
241 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
\r
242 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
\r
243 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
\r
244 JCheckBoxMenuItem _replace_underscores_cbmi;
\r
245 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
\r
246 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
\r
247 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
\r
249 JCheckBoxMenuItem _search_case_senstive_cbmi;
\r
250 JCheckBoxMenuItem _search_whole_words_only_cbmi;
\r
251 JCheckBoxMenuItem _inverse_search_result_cbmi;
\r
252 JCheckBoxMenuItem _search_with_regex_cbmi;
\r
255 JCheckBoxMenuItem _rectangular_type_cbmi;
\r
256 JCheckBoxMenuItem _triangular_type_cbmi;
\r
257 JCheckBoxMenuItem _curved_type_cbmi;
\r
258 JCheckBoxMenuItem _convex_type_cbmi;
\r
259 JCheckBoxMenuItem _euro_type_cbmi;
\r
260 JCheckBoxMenuItem _rounded_type_cbmi;
\r
261 JCheckBoxMenuItem _unrooted_type_cbmi;
\r
262 JCheckBoxMenuItem _circular_type_cbmi;
\r
263 // view as text menu:
\r
264 JMenuItem _view_as_NH_item;
\r
265 JMenuItem _view_as_XML_item;
\r
266 JMenuItem _view_as_nexus_item;
\r
267 JMenuItem _display_basic_information_item;
\r
269 JMenuItem _about_item;
\r
270 JMenuItem _help_item;
\r
271 JMenuItem _website_item;
\r
272 JMenuItem _phyloxml_website_item;
\r
273 JMenuItem _phyloxml_ref_item;
\r
274 JMenuItem _aptx_ref_item;
\r
277 JFileChooser _writetopdf_filechooser;
\r
278 JFileChooser _save_filechooser;
\r
279 JFileChooser _writetographics_filechooser;
\r
281 JMenu _process_menu;
\r
282 MainPanel _mainpanel;
\r
283 Container _contentpane;
\r
284 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
\r
285 Configuration _configuration;
\r
287 private Phylogeny _species_tree;
\r
288 InferenceManager _inference_manager;
\r
289 final ProcessPool _process_pool;
\r
290 private String _previous_node_annotation_ref;
\r
293 _process_pool = ProcessPool.createInstance();
\r
294 _writetopdf_filechooser = new JFileChooser();
\r
295 _writetopdf_filechooser.setMultiSelectionEnabled( false );
\r
296 _writetopdf_filechooser.addChoosableFileFilter( pdffilter );
\r
297 _writetographics_filechooser = new JFileChooser();
\r
298 _writetographics_filechooser.setMultiSelectionEnabled( false );
\r
299 _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter );
\r
300 _save_filechooser = new JFileChooser();
\r
301 _save_filechooser.setMultiSelectionEnabled( false );
\r
302 _save_filechooser.setFileFilter( xmlfilter );
\r
303 _save_filechooser.addChoosableFileFilter( nhfilter );
\r
304 _save_filechooser.addChoosableFileFilter( nexusfilter );
\r
305 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
\r
307 final String home_dir = System.getProperty( "user.home" );
\r
308 _save_filechooser.setCurrentDirectory( new File( home_dir ) );
\r
309 _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
\r
310 _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
\r
312 catch ( final Exception e ) {
\r
313 e.printStackTrace();
\r
314 // Do nothing. Not important.
\r
319 * Action performed.
\r
322 public void actionPerformed( final ActionEvent e ) {
\r
323 final Object o = e.getSource();
\r
324 boolean is_applet = false;
\r
325 JApplet applet = null;
\r
326 if ( getCurrentTreePanel() != null ) {
\r
327 is_applet = getCurrentTreePanel().isApplet();
\r
329 applet = getCurrentTreePanel().obtainApplet();
\r
332 if ( o == _exit_item ) {
\r
335 else if ( o == _gsdi_item ) {
\r
336 if ( isSubtreeDisplayed() ) {
\r
341 else if ( o == _gsdir_item ) {
\r
342 if ( isSubtreeDisplayed() ) {
\r
347 else if ( o == _taxcolor_item ) {
\r
350 else if ( o == _confcolor_item ) {
\r
353 else if ( o == _color_rank_jmi ) {
\r
356 else if ( o == _collapse_species_specific_subtrees ) {
\r
357 if ( isSubtreeDisplayed() ) {
\r
360 if ( getCurrentTreePanel() != null ) {
\r
361 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
\r
364 else if ( o == _remove_branch_color_item ) {
\r
365 if ( isSubtreeDisplayed() ) {
\r
368 removeBranchColors();
\r
370 else if ( o == _remove_visual_styles_item ) {
\r
371 if ( isSubtreeDisplayed() ) {
\r
374 removeVisualStyles();
\r
376 else if ( o == _midpoint_root_item ) {
\r
377 if ( isSubtreeDisplayed() ) {
\r
382 else if ( o == _delete_selected_nodes_item ) {
\r
383 if ( isSubtreeDisplayed() ) {
\r
386 deleteSelectedNodes( true );
\r
388 else if ( o == _delete_not_selected_nodes_item ) {
\r
389 if ( isSubtreeDisplayed() ) {
\r
392 deleteSelectedNodes( false );
\r
394 else if ( o == _annotate_item ) {
\r
395 annotateSequences();
\r
397 else if ( o == _switch_colors_mi ) {
\r
400 else if ( o == _display_basic_information_item ) {
\r
401 if ( getCurrentTreePanel() != null ) {
\r
402 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
\r
405 else if ( o == _view_as_NH_item ) {
\r
408 else if ( o == _view_as_XML_item ) {
\r
411 else if ( o == _view_as_nexus_item ) {
\r
414 else if ( o == _super_tiny_fonts_item ) {
\r
415 if ( getCurrentTreePanel() != null ) {
\r
416 getCurrentTreePanel().setSuperTinyFonts();
\r
417 getCurrentTreePanel().repaint();
\r
420 else if ( o == _tiny_fonts_item ) {
\r
421 if ( getCurrentTreePanel() != null ) {
\r
422 getCurrentTreePanel().setTinyFonts();
\r
423 getCurrentTreePanel().repaint();
\r
426 else if ( o == _small_fonts_item ) {
\r
427 if ( getCurrentTreePanel() != null ) {
\r
428 getCurrentTreePanel().setSmallFonts();
\r
429 getCurrentTreePanel().repaint();
\r
432 else if ( o == _medium_fonts_item ) {
\r
433 if ( getCurrentTreePanel() != null ) {
\r
434 getCurrentTreePanel().setMediumFonts();
\r
435 getCurrentTreePanel().repaint();
\r
438 else if ( o == _large_fonts_item ) {
\r
439 if ( getCurrentTreePanel() != null ) {
\r
440 getCurrentTreePanel().setLargeFonts();
\r
441 getCurrentTreePanel().repaint();
\r
444 else if ( o == _choose_font_mi ) {
\r
447 else if ( o == _choose_minimal_confidence_mi ) {
\r
448 chooseMinimalConfidence();
\r
450 else if ( o == _choose_node_size_mi ) {
\r
451 chooseNodeSize( getOptions(), this );
\r
453 else if ( o == _overview_placment_mi ) {
\r
454 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
\r
456 else if ( o == _cycle_node_fill_mi ) {
\r
457 MainFrame.cycleNodeFill( getOptions() );
\r
459 else if ( o == _cycle_node_shape_mi ) {
\r
460 MainFrame.cycleNodeShape( getOptions() );
\r
462 else if ( o == _cycle_data_return ) {
\r
463 MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
\r
465 else if ( o == _screen_antialias_cbmi ) {
\r
466 updateOptions( getOptions() );
\r
467 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
469 else if ( o == _background_gradient_cbmi ) {
\r
470 updateOptions( getOptions() );
\r
472 else if ( o == _show_domain_labels ) {
\r
473 updateOptions( getOptions() );
\r
475 else if ( o == _show_annotation_ref_source ) {
\r
476 updateOptions( getOptions() );
\r
478 else if ( o == _abbreviate_scientific_names ) {
\r
479 updateOptions( getOptions() );
\r
481 else if ( o == _color_labels_same_as_parent_branch ) {
\r
482 updateOptions( getOptions() );
\r
484 else if ( o == _show_default_node_shapes_internal_cbmi ) {
\r
485 updateOptions( getOptions() );
\r
487 else if ( o == _show_default_node_shapes_external_cbmi ) {
\r
488 updateOptions( getOptions() );
\r
490 else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
\r
491 updateOptions( getOptions() );
\r
493 else if ( o == _non_lined_up_cladograms_rbmi ) {
\r
494 updateOptions( getOptions() );
\r
497 else if ( o == _uniform_cladograms_rbmi ) {
\r
498 updateOptions( getOptions() );
\r
501 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
\r
502 updateOptions( getOptions() );
\r
505 else if ( o == _search_case_senstive_cbmi ) {
\r
506 updateOptions( getOptions() );
\r
507 getMainPanel().getControlPanel().search0();
\r
508 getMainPanel().getControlPanel().search1();
\r
510 else if ( o == _search_whole_words_only_cbmi ) {
\r
511 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
\r
512 _search_with_regex_cbmi.setSelected( false );
\r
514 updateOptions( getOptions() );
\r
515 getMainPanel().getControlPanel().search0();
\r
516 getMainPanel().getControlPanel().search1();
\r
518 else if ( o == _inverse_search_result_cbmi ) {
\r
519 updateOptions( getOptions() );
\r
520 getMainPanel().getControlPanel().search0();
\r
521 getMainPanel().getControlPanel().search1();
\r
523 else if ( o == _search_with_regex_cbmi ) {
\r
524 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
\r
525 _search_whole_words_only_cbmi.setSelected( false );
\r
527 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
\r
528 _search_case_senstive_cbmi.setSelected( true );
\r
530 updateOptions( getOptions() );
\r
531 getMainPanel().getControlPanel().search0();
\r
532 getMainPanel().getControlPanel().search1();
\r
534 else if ( o == _show_scale_cbmi ) {
\r
535 updateOptions( getOptions() );
\r
537 else if ( o == _color_by_taxonomic_group_cbmi ) {
\r
538 updateOptions( getOptions() );
\r
540 else if ( o == _show_confidence_stddev_cbmi ) {
\r
541 updateOptions( getOptions() );
\r
543 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
\r
544 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
545 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
\r
547 updateOptions( getOptions() );
\r
549 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
\r
550 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
551 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
\r
553 updateOptions( getOptions() );
\r
555 else if ( o == _label_direction_cbmi ) {
\r
556 updateOptions( getOptions() );
\r
558 else if ( o == _show_overview_cbmi ) {
\r
559 updateOptions( getOptions() );
\r
560 if ( getCurrentTreePanel() != null ) {
\r
561 getCurrentTreePanel().updateOvSizes();
\r
564 else if ( o == _line_up_renderable_data_cbmi ) {
\r
565 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
\r
566 _right_line_up_domains_cbmi.setSelected( false );
\r
568 updateOptions( getOptions() );
\r
570 else if ( o == _right_line_up_domains_cbmi ) {
\r
571 if ( _right_line_up_domains_cbmi.isSelected() ) {
\r
572 _line_up_renderable_data_cbmi.setSelected( true );
\r
574 updateOptions( getOptions() );
\r
576 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
\r
577 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
\r
578 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
\r
581 else if ( o == _about_item ) {
\r
584 else if ( o == _help_item ) {
\r
586 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );
\r
588 catch ( final IOException e1 ) {
\r
589 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
592 else if ( o == _website_item ) {
\r
594 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
\r
596 catch ( final IOException e1 ) {
\r
597 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
600 else if ( o == _phyloxml_website_item ) {
\r
602 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
\r
604 catch ( final IOException e1 ) {
\r
605 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
608 else if ( o == _aptx_ref_item ) {
\r
610 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
\r
612 catch ( final IOException e1 ) {
\r
613 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
616 else if ( o == _phyloxml_ref_item ) {
\r
618 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
\r
620 catch ( final IOException e1 ) {
\r
621 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
\r
624 else if ( o == _write_to_pdf_item ) {
\r
625 final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(),
\r
627 _writetopdf_filechooser,
\r
631 if ( curr_dir != null ) {
\r
632 setCurrentDir( curr_dir );
\r
635 else if ( o == _save_all_item ) {
\r
638 else if ( o == _write_to_jpg_item ) {
\r
639 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
640 GraphicsExportType.JPG,
\r
642 _writetographics_filechooser,
\r
646 if ( new_dir != null ) {
\r
647 setCurrentDir( new_dir );
\r
650 else if ( o == _write_to_gif_item ) {
\r
651 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
652 GraphicsExportType.GIF,
\r
654 _writetographics_filechooser,
\r
658 if ( new_dir != null ) {
\r
659 setCurrentDir( new_dir );
\r
662 else if ( o == _write_to_tif_item ) {
\r
663 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
664 GraphicsExportType.TIFF,
\r
666 _writetographics_filechooser,
\r
670 if ( new_dir != null ) {
\r
671 setCurrentDir( new_dir );
\r
674 else if ( o == _write_to_bmp_item ) {
\r
675 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
676 GraphicsExportType.BMP,
\r
678 _writetographics_filechooser,
\r
682 if ( new_dir != null ) {
\r
683 setCurrentDir( new_dir );
\r
686 else if ( o == _write_to_png_item ) {
\r
687 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
\r
688 GraphicsExportType.PNG,
\r
690 _writetographics_filechooser,
\r
694 if ( new_dir != null ) {
\r
695 setCurrentDir( new_dir );
\r
698 else if ( o == _print_item ) {
\r
699 print( getCurrentTreePanel(), getOptions(), this );
\r
701 else if ( o == _save_item ) {
\r
702 final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),
\r
708 if ( new_dir != null ) {
\r
709 setCurrentDir( new_dir );
\r
712 else if ( o == _graphics_export_visible_only_cbmi ) {
\r
713 updateOptions( getOptions() );
\r
715 else if ( o == _antialias_print_cbmi ) {
\r
716 updateOptions( getOptions() );
\r
718 else if ( o == _print_black_and_white_cbmi ) {
\r
719 updateOptions( getOptions() );
\r
721 else if ( o == _print_using_actual_size_cbmi ) {
\r
722 updateOptions( getOptions() );
\r
724 else if ( o == _graphics_export_using_actual_size_cbmi ) {
\r
725 updateOptions( getOptions() );
\r
727 else if ( o == _print_size_mi ) {
\r
730 else if ( o == _choose_pdf_width_mi ) {
\r
734 if ( _load_phylogeny_from_webservice_menu_items != null ) {
\r
735 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
\r
736 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
\r
737 readPhylogeniesFromWebservice( i );
\r
742 _contentpane.repaint();
\r
745 public Configuration getConfiguration() {
\r
746 return _configuration;
\r
750 * This method returns the current external node data which
\r
751 * has been selected by the user by clicking the "Return ..."
\r
752 * menu item. This method is expected to be called from Javascript or
\r
753 * something like it.
\r
755 * @return current external node data as String
\r
757 public String getCurrentExternalNodesDataBuffer() {
\r
758 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
\r
761 public int getCurrentExternalNodesDataBufferChangeCounter() {
\r
762 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
\r
765 public int getCurrentExternalNodesDataBufferLength() {
\r
766 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
\r
769 public InferenceManager getInferenceManager() {
\r
770 return _inference_manager;
\r
773 public MainPanel getMainPanel() {
\r
777 public Options getOptions() {
\r
781 public ProcessPool getProcessPool() {
\r
782 return _process_pool;
\r
785 public void showTextFrame( final String s, final String title ) {
\r
787 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
\r
790 public void showWhole() {
\r
791 _mainpanel.getControlPanel().showWhole();
\r
794 public void updateProcessMenu() {
\r
795 // In general Swing is not thread safe.
\r
796 // See "Swing's Threading Policy".
\r
797 SwingUtilities.invokeLater( new Runnable() {
\r
800 public void run() {
\r
801 doUpdateProcessMenu();
\r
806 private void annotateSequences() {
\r
807 if ( getCurrentTreePanel() != null ) {
\r
808 List<PhylogenyNode> nodes = null;
\r
809 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
\r
810 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
811 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
813 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
815 .showMessageDialog( this,
\r
816 "Need to select nodes, either via direct selection or via the \"Search\" function",
\r
817 "No nodes selected for annotation",
\r
818 JOptionPane.ERROR_MESSAGE );
\r
821 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
822 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
823 final JTextField ref_field = new JTextField( 10 );
\r
824 final JTextField desc_filed = new JTextField( 20 );
\r
825 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
\r
826 : getPreviousNodeAnnotationReference() );
\r
827 final JPanel my_panel = new JPanel();
\r
828 my_panel.add( new JLabel( "Reference " ) );
\r
829 my_panel.add( ref_field );
\r
830 my_panel.add( Box.createHorizontalStrut( 15 ) );
\r
831 my_panel.add( new JLabel( "Description " ) );
\r
832 my_panel.add( desc_filed );
\r
833 final int result = JOptionPane.showConfirmDialog( null,
\r
835 "Enter the sequence annotation(s) for the "
\r
836 + nodes.size() + " selected nodes",
\r
837 JOptionPane.OK_CANCEL_OPTION );
\r
838 if ( result == JOptionPane.OK_OPTION ) {
\r
839 String ref = ref_field.getText();
\r
840 String desc = desc_filed.getText();
\r
841 if ( !ForesterUtil.isEmpty( ref ) ) {
\r
843 ref = ref.replaceAll( "\\s+", " " );
\r
844 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
\r
845 || ( ref.length() < 3 ) ) {
\r
846 JOptionPane.showMessageDialog( this,
\r
847 "Reference needs to be in the form of \"GO:1234567\"",
\r
848 "Illegal Format for Annotation Reference",
\r
849 JOptionPane.ERROR_MESSAGE );
\r
853 if ( ref != null ) {
\r
854 setPreviousNodeAnnotationReference( ref );
\r
856 if ( desc != null ) {
\r
857 desc = desc.trim();
\r
858 desc = desc.replaceAll( "\\s+", " " );
\r
860 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
\r
861 for( final PhylogenyNode n : nodes ) {
\r
862 ForesterUtil.ensurePresenceOfSequence( n );
\r
863 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
\r
864 : new Annotation( ref );
\r
865 if ( !ForesterUtil.isEmpty( desc ) ) {
\r
866 ann.setDesc( desc );
\r
868 n.getNodeData().getSequence().addAnnotation( ann );
\r
871 getMainPanel().getControlPanel().showAnnotations();
\r
877 private void chooseFont() {
\r
878 final FontChooser fc = new FontChooser();
\r
879 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
\r
880 fc.showDialog( this, "Select the Base Font" );
\r
881 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
\r
884 private void chooseMinimalConfidence() {
\r
885 final String s = ( String ) JOptionPane
\r
886 .showInputDialog( this,
\r
887 "Please enter the minimum for confidence values to be displayed.\n"
\r
888 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
\r
889 "Minimal Confidence Value",
\r
890 JOptionPane.QUESTION_MESSAGE,
\r
893 getOptions().getMinConfidenceValue() );
\r
894 if ( !ForesterUtil.isEmpty( s ) ) {
\r
895 boolean success = true;
\r
897 final String m_str = s.trim();
\r
898 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
900 m = Double.parseDouble( m_str );
\r
902 catch ( final Exception ex ) {
\r
909 if ( success && ( m >= 0.0 ) ) {
\r
910 getOptions().setMinConfidenceValue( m );
\r
915 private void deleteSelectedNodes( final boolean delete ) {
\r
916 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
\r
917 if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
\r
920 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
921 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
\r
922 final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
\r
923 for( final PhylogenyNode n : all_selected_nodes ) {
\r
924 if ( n.isExternal() ) {
\r
929 String function = "Retain";
\r
931 function = "Delete";
\r
933 if ( ( nodes == null ) || nodes.isEmpty() ) {
\r
935 .showMessageDialog( this,
\r
936 "Need to select external nodes, either via direct selection or via the \"Search\" function",
\r
937 "No external nodes selected to " + function.toLowerCase(),
\r
938 JOptionPane.ERROR_MESSAGE );
\r
941 final int todo = nodes.size();
\r
942 final int ext = phy.getNumberOfExternalNodes();
\r
948 JOptionPane.showMessageDialog( this,
\r
949 "Cannot delete all nodes",
\r
950 "Attempt to delete all nodes ",
\r
951 JOptionPane.ERROR_MESSAGE );
\r
954 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
\r
955 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
\r
956 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
\r
957 if ( result == JOptionPane.OK_OPTION ) {
\r
959 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
\r
960 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
\r
961 final PhylogenyNode n = it.next();
\r
962 if ( !nodes.contains( n ) ) {
\r
963 to_delete.add( n );
\r
966 for( final PhylogenyNode n : to_delete ) {
\r
967 phy.deleteSubtree( n, true );
\r
971 for( final PhylogenyNode n : nodes ) {
\r
972 phy.deleteSubtree( n, true );
\r
976 getCurrentTreePanel().setNodeInPreorderToNull();
\r
977 phy.externalNodesHaveChanged();
\r
978 phy.clearHashIdToNodeMap();
\r
979 phy.recalculateNumberOfExternalDescendants( true );
\r
980 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
981 getCurrentTreePanel().setEdited( true );
\r
986 private void doUpdateProcessMenu() {
\r
987 if ( _process_pool.size() > 0 ) {
\r
988 if ( _process_menu == null ) {
\r
989 _process_menu = createMenu( "", getConfiguration() );
\r
990 _process_menu.setForeground( Color.RED );
\r
992 _process_menu.removeAll();
\r
993 final String text = "processes running: " + _process_pool.size();
\r
994 _process_menu.setText( text );
\r
995 _jmenubar.add( _process_menu );
\r
996 for( int i = 0; i < _process_pool.size(); ++i ) {
\r
997 final ProcessRunning p = _process_pool.getProcessByIndex( i );
\r
998 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
\r
1002 if ( _process_menu != null ) {
\r
1003 _process_menu.removeAll();
\r
1004 _jmenubar.remove( _process_menu );
\r
1007 _jmenubar.validate();
\r
1008 _jmenubar.repaint();
\r
1012 private String getPreviousNodeAnnotationReference() {
\r
1013 return _previous_node_annotation_ref;
\r
1016 private void removeBranchColors() {
\r
1017 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1018 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
\r
1022 private void removeVisualStyles() {
\r
1023 if ( getMainPanel().getCurrentPhylogeny() != null ) {
\r
1024 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
\r
1028 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
\r
1029 _previous_node_annotation_ref = previous_node_annotation_ref;
\r
1032 private void writeAllToFile() {
\r
1033 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
\r
1036 final File my_dir = getCurrentDir();
\r
1037 if ( my_dir != null ) {
\r
1038 _save_filechooser.setCurrentDirectory( my_dir );
\r
1040 _save_filechooser.setSelectedFile( new File( "" ) );
\r
1041 final int result = _save_filechooser.showSaveDialog( _contentpane );
\r
1042 final File file = _save_filechooser.getSelectedFile();
\r
1043 setCurrentDir( _save_filechooser.getCurrentDirectory() );
\r
1044 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1045 if ( file.exists() ) {
\r
1046 final int i = JOptionPane.showConfirmDialog( this,
\r
1047 file + " already exists. Overwrite?",
\r
1049 JOptionPane.OK_CANCEL_OPTION,
\r
1050 JOptionPane.WARNING_MESSAGE );
\r
1051 if ( i != JOptionPane.OK_OPTION ) {
\r
1058 catch ( final Exception e ) {
\r
1059 JOptionPane.showMessageDialog( this,
\r
1060 "Failed to delete: " + file,
\r
1062 JOptionPane.WARNING_MESSAGE );
\r
1066 final int count = getMainPanel().getTabbedPane().getTabCount();
\r
1067 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
\r
1068 for( int i = 0; i < count; ++i ) {
\r
1069 final Phylogeny phy = getMainPanel().getPhylogeny( i );
\r
1070 if ( ForesterUtil.isEmpty( phy.getName() )
\r
1071 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
\r
1072 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
\r
1075 getMainPanel().getTreePanels().get( i ).setEdited( false );
\r
1077 final PhylogenyWriter writer = new PhylogenyWriter();
\r
1079 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
\r
1081 catch ( final IOException e ) {
\r
1082 JOptionPane.showMessageDialog( this,
\r
1083 "Failed to write to: " + file,
\r
1085 JOptionPane.WARNING_MESSAGE );
\r
1090 void activateSaveAllIfNeeded() {
\r
1091 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
\r
1092 _save_all_item.setEnabled( true );
\r
1095 _save_all_item.setEnabled( false );
\r
1099 void buildFileMenu() {
\r
1100 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
1101 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
1102 _file_jmenu.addSeparator();
\r
1103 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
1104 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
1105 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
1107 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
1108 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
1109 if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
1110 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
1112 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
1113 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
1115 _file_jmenu.addSeparator();
\r
1116 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
1117 _file_jmenu.addSeparator();
\r
1118 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
1119 customizeJMenuItem( _save_item );
\r
1120 customizeJMenuItem( _write_to_pdf_item );
\r
1121 customizeJMenuItem( _write_to_png_item );
\r
1122 customizeJMenuItem( _write_to_jpg_item );
\r
1123 customizeJMenuItem( _write_to_gif_item );
\r
1124 customizeJMenuItem( _write_to_tif_item );
\r
1125 customizeJMenuItem( _write_to_bmp_item );
\r
1126 customizeJMenuItem( _print_item );
\r
1127 customizeJMenuItem( _exit_item );
\r
1128 _jmenubar.add( _file_jmenu );
\r
1131 void buildFontSizeMenu() {
\r
1132 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
\r
1133 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
\r
1134 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
\r
1135 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
\r
1136 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
\r
1137 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
\r
1138 customizeJMenuItem( _super_tiny_fonts_item );
\r
1139 customizeJMenuItem( _tiny_fonts_item );
\r
1140 customizeJMenuItem( _small_fonts_item );
\r
1141 customizeJMenuItem( _medium_fonts_item );
\r
1142 customizeJMenuItem( _large_fonts_item );
\r
1143 _jmenubar.add( _font_size_menu );
\r
1146 void buildHelpMenu() {
\r
1147 _help_jmenu = createMenu( "Help", getConfiguration() );
\r
1148 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
\r
1149 _help_jmenu.addSeparator();
\r
1150 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
\r
1151 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
\r
1152 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
\r
1153 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
\r
1154 _help_jmenu.addSeparator();
\r
1155 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
\r
1156 customizeJMenuItem( _help_item );
\r
1157 customizeJMenuItem( _website_item );
\r
1158 customizeJMenuItem( _phyloxml_website_item );
\r
1159 customizeJMenuItem( _aptx_ref_item );
\r
1160 customizeJMenuItem( _phyloxml_ref_item );
\r
1161 customizeJMenuItem( _about_item );
\r
1162 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
\r
1163 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
\r
1164 _jmenubar.add( _help_jmenu );
\r
1167 void buildTypeMenu() {
\r
1168 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
\r
1169 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
\r
1170 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
\r
1171 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
\r
1172 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
\r
1173 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
\r
1174 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
\r
1175 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
\r
1176 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
\r
1177 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
\r
1178 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
\r
1179 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
\r
1180 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
\r
1181 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
\r
1182 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
\r
1183 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
\r
1184 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
\r
1185 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
1186 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
\r
1187 initializeTypeMenu( getOptions() );
\r
1188 _jmenubar.add( _type_menu );
\r
1191 void buildViewMenu() {
\r
1192 _view_jmenu = createMenu( "View", getConfiguration() );
\r
1193 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
\r
1194 _view_jmenu.addSeparator();
\r
1195 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
\r
1196 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
\r
1197 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
\r
1198 customizeJMenuItem( _display_basic_information_item );
\r
1199 customizeJMenuItem( _view_as_NH_item );
\r
1200 customizeJMenuItem( _view_as_XML_item );
\r
1201 customizeJMenuItem( _view_as_nexus_item );
\r
1202 _jmenubar.add( _view_jmenu );
\r
1205 void checkTextFrames() {
\r
1206 if ( _textframes.size() > 5 ) {
\r
1208 if ( _textframes.getFirst() != null ) {
\r
1209 _textframes.getFirst().removeMe();
\r
1212 _textframes.removeFirst();
\r
1215 catch ( final NoSuchElementException e ) {
\r
1221 void choosePdfWidth() {
\r
1222 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1223 "Please enter the default line width for PDF export.\n"
\r
1224 + "[current value: "
\r
1225 + getOptions().getPrintLineWidth() + "]\n",
\r
1226 "Line Width for PDF Export",
\r
1227 JOptionPane.QUESTION_MESSAGE,
\r
1230 getOptions().getPrintLineWidth() );
\r
1231 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1232 boolean success = true;
\r
1234 final String m_str = s.trim();
\r
1235 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1237 f = Float.parseFloat( m_str );
\r
1239 catch ( final Exception ex ) {
\r
1246 if ( success && ( f > 0.0 ) ) {
\r
1247 getOptions().setPrintLineWidth( f );
\r
1252 void choosePrintSize() {
\r
1253 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1254 "Please enter values for width and height,\nseparated by a comma.\n"
\r
1255 + "[current values: "
\r
1256 + getOptions().getPrintSizeX() + ", "
\r
1257 + getOptions().getPrintSizeY() + "]\n"
\r
1258 + "[A4: " + Constants.A4_SIZE_X + ", "
\r
1259 + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
\r
1260 + Constants.US_LETTER_SIZE_X + ", "
\r
1261 + Constants.US_LETTER_SIZE_Y + "]",
\r
1262 "Default Size for Graphics Export",
\r
1263 JOptionPane.QUESTION_MESSAGE,
\r
1266 getOptions().getPrintSizeX() + ", "
\r
1267 + getOptions().getPrintSizeY() );
\r
1268 if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
\r
1269 boolean success = true;
\r
1272 final String[] str_ary = s.split( "," );
\r
1273 if ( str_ary.length == 2 ) {
\r
1274 final String x_str = str_ary[ 0 ].trim();
\r
1275 final String y_str = str_ary[ 1 ].trim();
\r
1276 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
\r
1278 x = Integer.parseInt( x_str );
\r
1279 y = Integer.parseInt( y_str );
\r
1281 catch ( final Exception ex ) {
\r
1292 if ( success && ( x > 1 ) && ( y > 1 ) ) {
\r
1293 getOptions().setPrintSizeX( x );
\r
1294 getOptions().setPrintSizeY( y );
\r
1300 removeAllTextFrames();
\r
1301 if ( _mainpanel != null ) {
\r
1302 _mainpanel.terminate();
\r
1304 if ( _contentpane != null ) {
\r
1305 _contentpane.removeAll();
\r
1307 setVisible( false );
\r
1311 void colorRank() {
\r
1312 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1313 final String[] ranks = AptxUtil.getAllPossibleRanks();
\r
1314 final String rank = ( String ) JOptionPane
\r
1315 .showInputDialog( this,
\r
1316 "What rank should the colorization be based on",
\r
1318 JOptionPane.QUESTION_MESSAGE,
\r
1322 if ( !ForesterUtil.isEmpty( rank ) ) {
\r
1323 _mainpanel.getCurrentTreePanel().colorRank( rank );
\r
1328 void confColor() {
\r
1329 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1330 _mainpanel.getCurrentTreePanel().confColor();
\r
1334 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
\r
1335 if ( item != null ) {
\r
1336 item.setFont( MainFrame.menu_font );
\r
1337 if ( !getConfiguration().isUseNativeUI() ) {
\r
1338 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1339 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1341 item.setSelected( is_selected );
\r
1342 item.addActionListener( this );
\r
1346 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
\r
1347 if ( jmi != null ) {
\r
1348 jmi.setFont( MainFrame.menu_font );
\r
1349 if ( !getConfiguration().isUseNativeUI() ) {
\r
1350 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1351 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1353 jmi.addActionListener( this );
\r
1358 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
\r
1359 if ( item != null ) {
\r
1360 item.setFont( MainFrame.menu_font );
\r
1361 if ( !getConfiguration().isUseNativeUI() ) {
\r
1362 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
\r
1363 item.setForeground( getConfiguration().getGuiMenuTextColor() );
\r
1365 item.setSelected( is_selected );
\r
1366 item.addActionListener( this );
\r
1370 void displayBasicInformation( final File treefile ) {
\r
1371 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1372 String title = "Basic Information";
\r
1373 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1374 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
\r
1376 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
\r
1380 void exceptionOccuredDuringOpenFile( final Exception e ) {
\r
1382 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1384 catch ( final Exception ex ) {
\r
1387 JOptionPane.showMessageDialog( this,
\r
1388 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1389 "Error during File|Open",
\r
1390 JOptionPane.ERROR_MESSAGE );
\r
1393 void executeGSDI() {
\r
1394 if ( !isOKforSDI( false, true ) ) {
\r
1397 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1398 JOptionPane.showMessageDialog( this,
\r
1399 "Gene tree is not rooted.",
\r
1400 "Cannot execute GSDI",
\r
1401 JOptionPane.ERROR_MESSAGE );
\r
1404 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1405 gene_tree.setAllNodesToNotCollapse();
\r
1406 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1408 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1410 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
\r
1412 catch ( final SDIException e ) {
\r
1413 JOptionPane.showMessageDialog( this,
\r
1414 e.getLocalizedMessage(),
\r
1415 "Error during GSDI",
\r
1416 JOptionPane.ERROR_MESSAGE );
\r
1419 catch ( final Exception e ) {
\r
1420 AptxUtil.unexpectedException( e );
\r
1423 gene_tree.setRerootable( false );
\r
1424 gene_tree.clearHashIdToNodeMap();
\r
1425 gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1426 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
\r
1427 getMainPanel().getControlPanel().setShowEvents( true );
\r
1429 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1430 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1432 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1434 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1435 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1436 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1437 JOptionPane.showMessageDialog( this,
\r
1438 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1439 + "Potential duplications: "
\r
1440 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1441 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1442 + "Stripped gene tree nodes: "
\r
1443 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1444 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1445 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1446 "GSDI successfully completed",
\r
1447 JOptionPane.WARNING_MESSAGE );
\r
1450 JOptionPane.showMessageDialog( this,
\r
1451 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
\r
1452 + "Potential duplications: "
\r
1453 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
\r
1454 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
\r
1455 + "Stripped gene tree nodes: "
\r
1456 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1457 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
\r
1458 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1459 "GSDI successfully completed",
\r
1460 JOptionPane.INFORMATION_MESSAGE );
\r
1464 void executeGSDIR() {
\r
1465 if ( !isOKforSDI( false, false ) ) {
\r
1468 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
\r
1470 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
\r
1471 JOptionPane.showMessageDialog( this,
\r
1472 "Gene tree is not completely binary",
\r
1473 "Cannot execute GSDI",
\r
1474 JOptionPane.ERROR_MESSAGE );
\r
1477 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
\r
1478 gene_tree.setAllNodesToNotCollapse();
\r
1479 gene_tree.recalculateNumberOfExternalDescendants( false );
\r
1480 GSDIR gsdir = null;
\r
1481 final Phylogeny species_tree = getSpeciesTree().copy();
\r
1483 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
\r
1485 catch ( final SDIException e ) {
\r
1486 JOptionPane.showMessageDialog( this,
\r
1487 e.getLocalizedMessage(),
\r
1488 "Error during GSDIR",
\r
1489 JOptionPane.ERROR_MESSAGE );
\r
1492 catch ( final Exception e ) {
\r
1493 AptxUtil.unexpectedException( e );
\r
1496 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
\r
1497 result_gene_tree.setRerootable( false );
\r
1498 result_gene_tree.clearHashIdToNodeMap();
\r
1499 result_gene_tree.recalculateNumberOfExternalDescendants( true );
\r
1500 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
\r
1501 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
\r
1502 getMainPanel().getControlPanel().setShowEvents( true );
\r
1504 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
\r
1505 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
\r
1507 _mainpanel.getTabbedPane().setSelectedIndex( selected );
\r
1509 _mainpanel.getCurrentTreePanel().setEdited( true );
\r
1510 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
\r
1511 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
\r
1512 JOptionPane.showMessageDialog( this,
\r
1513 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1514 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1515 + "Stripped gene tree nodes: "
\r
1516 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1517 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1518 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1519 "GSDIR successfully completed",
\r
1520 JOptionPane.WARNING_MESSAGE );
\r
1523 JOptionPane.showMessageDialog( this,
\r
1524 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
\r
1525 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
\r
1526 + "Stripped gene tree nodes: "
\r
1527 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
\r
1528 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
\r
1529 + "Number of polytomies in species tree used: " + poly + "\n",
\r
1530 "GSDIR successfully completed",
\r
1531 JOptionPane.INFORMATION_MESSAGE );
\r
1535 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
\r
1536 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
\r
1537 JOptionPane.showMessageDialog( this,
\r
1538 "Gene tree and species tree have no species in common.",
\r
1539 "Error during SDI",
\r
1540 JOptionPane.ERROR_MESSAGE );
\r
1543 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
\r
1544 JOptionPane.showMessageDialog( this,
\r
1545 "Gene tree and species tree have only one species in common.",
\r
1546 "Error during SDI",
\r
1547 JOptionPane.ERROR_MESSAGE );
\r
1555 ControlPanel getControlPanel() {
\r
1556 return getMainPanel().getControlPanel();
\r
1559 File getCurrentDir() {
\r
1560 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1561 if ( ForesterUtil.isWindows() ) {
\r
1563 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
\r
1565 catch ( final Exception e ) {
\r
1566 _current_dir = null;
\r
1570 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
\r
1571 if ( System.getProperty( "user.home" ) != null ) {
\r
1572 _current_dir = new File( System.getProperty( "user.home" ) );
\r
1574 else if ( System.getProperty( "user.dir" ) != null ) {
\r
1575 _current_dir = new File( System.getProperty( "user.dir" ) );
\r
1578 return _current_dir;
\r
1581 TreePanel getCurrentTreePanel() {
\r
1582 return getMainPanel().getCurrentTreePanel();
\r
1585 JMenu getHelpMenu() {
\r
1586 return _help_jmenu;
\r
1589 JCheckBoxMenuItem getlabelDirectionCbmi() {
\r
1590 return _label_direction_cbmi;
\r
1593 JMenuBar getMenuBarOfMainFrame() {
\r
1597 final Phylogeny getSpeciesTree() {
\r
1598 return _species_tree;
\r
1601 void initializeTypeMenu( final Options options ) {
\r
1602 setTypeMenuToAllUnselected();
\r
1603 switch ( options.getPhylogenyGraphicsType() ) {
\r
1605 _convex_type_cbmi.setSelected( true );
\r
1608 _curved_type_cbmi.setSelected( true );
\r
1611 _euro_type_cbmi.setSelected( true );
\r
1614 _rounded_type_cbmi.setSelected( true );
\r
1617 _triangular_type_cbmi.setSelected( true );
\r
1620 _unrooted_type_cbmi.setSelected( true );
\r
1623 _circular_type_cbmi.setSelected( true );
\r
1626 _rectangular_type_cbmi.setSelected( true );
\r
1631 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
\r
1632 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1635 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
\r
1636 JOptionPane.showMessageDialog( this,
\r
1637 "No species tree loaded",
\r
1638 "Cannot execute GSDI",
\r
1639 JOptionPane.ERROR_MESSAGE );
\r
1642 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
\r
1643 JOptionPane.showMessageDialog( this,
\r
1644 "Species tree is not completely binary",
\r
1645 "Cannot execute GSDI",
\r
1646 JOptionPane.ERROR_MESSAGE );
\r
1649 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
\r
1650 JOptionPane.showMessageDialog( this,
\r
1651 "Gene tree is not completely binary",
\r
1652 "Cannot execute GSDI",
\r
1653 JOptionPane.ERROR_MESSAGE );
\r
1661 boolean isSubtreeDisplayed() {
\r
1662 if ( getCurrentTreePanel() != null ) {
\r
1663 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
\r
1665 .showMessageDialog( this,
\r
1666 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
\r
1667 "Operation can not be exectuted on a sub-tree",
\r
1668 JOptionPane.WARNING_MESSAGE );
\r
1675 void midpointRoot() {
\r
1676 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1677 _mainpanel.getCurrentTreePanel().midpointRoot();
\r
1681 void readPhylogeniesFromWebservice( final int i ) {
\r
1682 final UrlTreeReader reader = new UrlTreeReader( this, i );
\r
1683 new Thread( reader ).start();
\r
1686 void removeAllTextFrames() {
\r
1687 for( final TextFrame tf : _textframes ) {
\r
1688 if ( tf != null ) {
\r
1692 _textframes.clear();
\r
1695 void resetSearch() {
\r
1696 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
\r
1697 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
\r
1698 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
\r
1699 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
\r
1700 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
\r
1701 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
\r
1702 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
\r
1703 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
\r
1704 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
\r
1705 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
\r
1706 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
\r
1707 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
\r
1710 void setConfiguration( final Configuration configuration ) {
\r
1711 _configuration = configuration;
\r
1714 void setCurrentDir( final File current_dir ) {
\r
1715 _current_dir = current_dir;
\r
1718 void setInferenceManager( final InferenceManager i ) {
\r
1719 _inference_manager = i;
\r
1722 void setOptions( final Options options ) {
\r
1723 _options = options;
\r
1726 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
\r
1727 setTypeMenuToAllUnselected();
\r
1730 _circular_type_cbmi.setSelected( true );
\r
1733 _convex_type_cbmi.setSelected( true );
\r
1736 _curved_type_cbmi.setSelected( true );
\r
1739 _euro_type_cbmi.setSelected( true );
\r
1742 _rounded_type_cbmi.setSelected( true );
\r
1745 _rectangular_type_cbmi.setSelected( true );
\r
1748 _triangular_type_cbmi.setSelected( true );
\r
1751 _unrooted_type_cbmi.setSelected( true );
\r
1754 throw new IllegalArgumentException( "unknown type: " + type );
\r
1758 final void setSpeciesTree( final Phylogeny species_tree ) {
\r
1759 _species_tree = species_tree;
\r
1762 void setTypeMenuToAllUnselected() {
\r
1763 _convex_type_cbmi.setSelected( false );
\r
1764 _curved_type_cbmi.setSelected( false );
\r
1765 _euro_type_cbmi.setSelected( false );
\r
1766 _rounded_type_cbmi.setSelected( false );
\r
1767 _triangular_type_cbmi.setSelected( false );
\r
1768 _rectangular_type_cbmi.setSelected( false );
\r
1769 _unrooted_type_cbmi.setSelected( false );
\r
1770 _circular_type_cbmi.setSelected( false );
\r
1773 void switchColors() {
\r
1774 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
\r
1775 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
\r
1776 csc.setVisible( true );
\r
1780 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1781 _mainpanel.getCurrentTreePanel().taxColor();
\r
1785 void typeChanged( final Object o ) {
\r
1786 updateTypeCheckboxes( getOptions(), o );
\r
1787 updateOptions( getOptions() );
\r
1788 if ( getCurrentTreePanel() != null ) {
\r
1789 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
\r
1790 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
\r
1791 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1792 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
\r
1793 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
\r
1794 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
\r
1795 getCurrentTreePanel().getControlPanel().showWhole();
\r
1797 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
\r
1798 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
\r
1801 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
\r
1803 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
\r
1804 updateScreenTextAntialias( getMainPanel().getTreePanels() );
\r
1805 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
\r
1806 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
\r
1807 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
\r
1810 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
\r
1816 void updateOptions( final Options options ) {
\r
1817 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
\r
1818 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
\r
1819 && _background_gradient_cbmi.isSelected() );
\r
1820 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
\r
1821 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
\r
1822 && _show_annotation_ref_source.isSelected() );
\r
1823 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
\r
1824 && _abbreviate_scientific_names.isSelected() );
\r
1825 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
\r
1826 && _color_labels_same_as_parent_branch.isSelected() );
\r
1827 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
\r
1828 && _show_default_node_shapes_internal_cbmi.isSelected() );
\r
1829 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
\r
1830 && _show_default_node_shapes_external_cbmi.isSelected() );
\r
1831 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
\r
1832 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
\r
1833 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
\r
1834 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
\r
1836 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
\r
1837 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1839 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
\r
1840 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1842 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
\r
1843 && _search_case_senstive_cbmi.isSelected() );
\r
1844 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
\r
1845 options.setShowScale( _show_scale_cbmi.isSelected() );
\r
1847 if ( _label_direction_cbmi != null ) {
\r
1848 if ( _label_direction_cbmi.isSelected() ) {
\r
1849 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
\r
1852 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
\r
1855 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
\r
1856 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
\r
1857 && _show_confidence_stddev_cbmi.isSelected() );
\r
1858 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
\r
1859 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
\r
1861 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
\r
1862 && ( _print_using_actual_size_cbmi.isSelected() ) );
\r
1863 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
\r
1864 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
\r
1865 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
\r
1866 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
\r
1867 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1868 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1870 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
\r
1871 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
\r
1872 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1875 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
\r
1877 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
\r
1878 && _print_black_and_white_cbmi.isSelected() );
\r
1879 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
\r
1880 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
\r
1881 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
\r
1882 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1884 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
\r
1885 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1887 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
\r
1888 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1890 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
\r
1891 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
\r
1893 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
\r
1894 && _replace_underscores_cbmi.isSelected() );
\r
1895 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
\r
1896 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
\r
1897 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
\r
1898 && _search_whole_words_only_cbmi.isSelected() );
\r
1899 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
\r
1900 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
\r
1901 && _inverse_search_result_cbmi.isSelected() );
\r
1902 if ( _graphics_export_visible_only_cbmi != null ) {
\r
1903 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
\r
1904 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
\r
1905 _graphics_export_using_actual_size_cbmi.setSelected( true );
\r
1906 _graphics_export_using_actual_size_cbmi.setEnabled( false );
\r
1909 _graphics_export_using_actual_size_cbmi.setEnabled( true );
\r
1912 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
\r
1913 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1915 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
\r
1916 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
\r
1918 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
\r
1919 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
\r
1921 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
\r
1922 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
\r
1924 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
\r
1925 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
\r
1927 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
\r
1928 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
\r
1930 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
\r
1931 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
\r
1933 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
\r
1934 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
\r
1936 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
\r
1937 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
\r
1939 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
\r
1940 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
\r
1944 void updateTypeCheckboxes( final Options options, final Object o ) {
\r
1945 setTypeMenuToAllUnselected();
\r
1946 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
\r
1949 void viewAsNexus() {
\r
1950 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1951 String title = "Nexus";
\r
1952 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1953 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1955 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
\r
1961 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1962 String title = "New Hampshire";
\r
1963 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1964 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1966 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
\r
1967 .getNhConversionSupportValueStyle() ),
\r
1972 void viewAsXML() {
\r
1973 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
\r
1974 String title = "phyloXML";
\r
1975 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
\r
1976 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
\r
1978 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
\r
1982 private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {
\r
1983 switch ( op.getExtDescNodeDataToReturn() ) {
\r
1985 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
\r
1988 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
\r
1990 case DOMAINS_COLLAPSED_PER_PROTEIN:
\r
1991 op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
\r
1993 case SEQ_ANNOTATIONS:
\r
1994 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
\r
1997 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
\r
1999 case SEQUENCE_MOL_SEQ_FASTA:
\r
2000 if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )
\r
2001 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )
\r
2002 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
\r
2003 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )
\r
2004 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )
\r
2005 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {
\r
2006 op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
\r
2009 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
2013 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
\r
2018 * Display the about box.
\r
2020 static void about() {
\r
2021 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
\r
2022 about.append( "Copyright (C) 2014 Christian M Zmasek\n" );
\r
2023 about.append( "All Rights Reserved\n" );
\r
2024 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
\r
2025 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
\r
2026 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
\r
2027 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
\r
2028 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
\r
2029 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
\r
2030 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
\r
2032 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
\r
2033 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
\r
2034 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
\r
2035 + ForesterUtil.OS_VERSION + "]\n" );
\r
2037 final Runtime rt = java.lang.Runtime.getRuntime();
\r
2038 final long free_memory = rt.freeMemory() / 1000000;
\r
2039 final long total_memory = rt.totalMemory() / 1000000;
\r
2040 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
\r
2041 about.append( "[locale: " + Locale.getDefault() + "]\n" );
\r
2042 about.append( "References:\n" );
\r
2043 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
\r
2044 about.append( "For more information & download:\n" );
\r
2045 about.append( Constants.APTX_WEB_SITE + "\n" );
\r
2046 about.append( "Documentation:\n" );
\r
2047 about.append( Constants.APTX_DOC_SITE + "\n" );
\r
2048 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
\r
2049 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
\r
2052 static void chooseNodeSize( final Options options, final Component parent ) {
\r
2053 final String s = ( String ) JOptionPane.showInputDialog( parent,
\r
2054 "Please enter the default size for node shapes.\n"
\r
2055 + "[current value: "
\r
2056 + options.getDefaultNodeShapeSize() + "]\n",
\r
2057 "Node Shape Size",
\r
2058 JOptionPane.QUESTION_MESSAGE,
\r
2061 options.getDefaultNodeShapeSize() );
\r
2062 if ( !ForesterUtil.isEmpty( s ) ) {
\r
2063 boolean success = true;
\r
2065 final String m_str = s.trim();
\r
2066 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
2068 m = Double.parseDouble( m_str );
\r
2070 catch ( final Exception ex ) {
\r
2077 if ( success && ( m >= 0.0 ) ) {
\r
2078 final short size = ForesterUtil.roundToShort( m );
\r
2079 if ( size >= 0.0 ) {
\r
2080 options.setDefaultNodeShapeSize( size );
\r
2086 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
\r
2087 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
\r
2090 static JMenu createMenu( final String title, final Configuration conf ) {
\r
2091 final JMenu jmenu = new JMenu( title );
\r
2092 if ( !conf.isUseNativeUI() ) {
\r
2093 jmenu.setFont( MainFrame.menu_font );
\r
2094 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
\r
2095 jmenu.setForeground( conf.getGuiMenuTextColor() );
\r
2100 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
\r
2101 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
\r
2102 if ( !configuration.isUseNativeUI() ) {
\r
2103 label.setBackground( configuration.getGuiMenuBackgroundColor() );
\r
2104 label.setForeground( configuration.getGuiMenuTextColor() );
\r
2105 label.setOpaque( true );
\r
2107 label.setSelected( false );
\r
2108 label.setEnabled( false );
\r
2112 static void cycleNodeFill( final Options op ) {
\r
2113 switch ( op.getDefaultNodeFill() ) {
\r
2115 op.setDefaultNodeFill( NodeFill.SOLID );
\r
2118 op.setDefaultNodeFill( NodeFill.GRADIENT );
\r
2121 op.setDefaultNodeFill( NodeFill.NONE );
\r
2124 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
\r
2128 static void cycleNodeShape( final Options op ) {
\r
2129 switch ( op.getDefaultNodeShape() ) {
\r
2131 op.setDefaultNodeShape( NodeShape.RECTANGLE );
\r
2134 op.setDefaultNodeShape( NodeShape.CIRCLE );
\r
2137 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
\r
2141 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
\r
2142 switch ( op.getOvPlacement() ) {
\r
2144 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
\r
2147 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
\r
2150 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
\r
2153 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
\r
2156 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
\r
2158 if ( tree_panel != null ) {
\r
2159 tree_panel.updateOvSettings();
\r
2163 static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {
\r
2165 tp.setArrowCursor();
\r
2167 catch ( final Exception ex ) {
\r
2170 JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
\r
2173 static void print( final TreePanel tp, final Options op, final Component c ) {
\r
2174 if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {
\r
2177 if ( !op.isPrintUsingActualSize() ) {
\r
2178 tp.calcParametersForPainting( op.getPrintSizeX() - 80, op.getPrintSizeY() - 140 );
\r
2179 tp.resetPreferredSize();
\r
2182 final String job_name = Constants.PRG_NAME;
\r
2183 boolean error = false;
\r
2184 String printer_name = null;
\r
2186 printer_name = Printer.print( tp, job_name );
\r
2188 catch ( final Exception e ) {
\r
2190 JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
\r
2192 if ( !error && ( printer_name != null ) ) {
\r
2193 String msg = "Printing data sent to printer";
\r
2194 if ( printer_name.length() > 1 ) {
\r
2195 msg += " [" + printer_name + "]";
\r
2197 JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
\r
2199 if ( !op.isPrintUsingActualSize() ) {
\r
2200 tp.getControlPanel().showWhole();
\r
2204 static void printPhylogenyToPdf( final String file_name,
\r
2205 final Options opts,
\r
2206 final TreePanel tp,
\r
2207 final Component comp ) {
\r
2208 if ( !opts.isPrintUsingActualSize() ) {
\r
2209 tp.calcParametersForPainting( opts.getPrintSizeX(), opts.getPrintSizeY() );
\r
2210 tp.resetPreferredSize();
\r
2213 String pdf_written_to = "";
\r
2214 boolean error = false;
\r
2216 if ( opts.isPrintUsingActualSize() ) {
\r
2217 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth(), tp.getHeight() );
\r
2220 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
\r
2222 opts.getPrintSizeX(),
\r
2223 opts.getPrintSizeY() );
\r
2226 catch ( final IOException e ) {
\r
2228 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
2231 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
\r
2232 JOptionPane.showMessageDialog( comp,
\r
2233 "Wrote PDF to: " + pdf_written_to,
\r
2235 JOptionPane.INFORMATION_MESSAGE );
\r
2238 JOptionPane.showMessageDialog( comp,
\r
2239 "There was an unknown problem when attempting to write to PDF file: \""
\r
2240 + file_name + "\"",
\r
2242 JOptionPane.ERROR_MESSAGE );
\r
2245 if ( !opts.isPrintUsingActualSize() ) {
\r
2246 tp.getControlPanel().showWhole();
\r
2250 static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
\r
2251 if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
\r
2252 mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );
\r
2255 mi.setText( "Cycle Node Return Data..." );
\r
2259 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
\r
2260 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
\r
2261 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
2262 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
\r
2265 mi.setText( "Cycle Node Shape Fill Type..." );
\r
2269 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
\r
2270 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
\r
2271 mi.setText( "Cycle Node Shape Fill Type... (current: "
\r
2272 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
\r
2275 mi.setText( "Cycle Node Shape Fill Type..." );
\r
2279 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
\r
2280 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
\r
2281 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
\r
2284 mi.setText( "Cycle Overview Placement..." );
\r
2288 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
\r
2289 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
\r
2290 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
\r
2294 mi.setText( "Select Color Scheme..." );
\r
2298 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
\r
2299 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
\r
2302 static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2303 mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
\r
2304 + o.getPrintSizeY() + ")" );
\r
2307 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
\r
2308 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
\r
2311 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
\r
2312 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
\r
2313 mi.setEnabled( true );
\r
2315 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
\r
2316 mi.setEnabled( true );
\r
2319 mi.setEnabled( false );
\r
2321 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
\r
2324 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
\r
2325 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
\r
2328 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
\r
2329 for( final TreePanel tree_panel : treepanels ) {
\r
2330 tree_panel.setTextAntialias();
\r
2334 static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) {
\r
2336 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2337 writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file );
\r
2339 catch ( final Exception e ) {
\r
2341 exceptionOccuredDuringSaveAs( e, tp, tp );
\r
2346 static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) {
\r
2348 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2349 writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() );
\r
2351 catch ( final Exception e ) {
\r
2353 exceptionOccuredDuringSaveAs( e, tp, tp );
\r
2358 static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) {
\r
2360 final PhylogenyWriter writer = new PhylogenyWriter();
\r
2361 writer.toPhyloXML( file, tp.getPhylogeny(), 0 );
\r
2363 catch ( final Exception e ) {
\r
2365 exceptionOccuredDuringSaveAs( e, tp, tp );
\r
2370 static void writePhylogenyToGraphicsFile( final String file_name,
\r
2371 final GraphicsExportType type,
\r
2372 final MainPanel mp,
\r
2373 final Component comp,
\r
2374 final Container contentpane ) {
\r
2375 mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),
\r
2376 mp.getCurrentTreePanel().getHeight() );
\r
2377 String file_written_to = "";
\r
2378 boolean error = false;
\r
2380 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
\r
2381 mp.getCurrentTreePanel().getWidth(),
\r
2382 mp.getCurrentTreePanel().getHeight(),
\r
2383 mp.getCurrentTreePanel(),
\r
2384 mp.getControlPanel(),
\r
2386 mp.getOptions() );
\r
2388 catch ( final IOException e ) {
\r
2390 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
\r
2393 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
\r
2394 JOptionPane.showMessageDialog( comp,
\r
2395 "Wrote image to: " + file_written_to,
\r
2396 "Graphics Export",
\r
2397 JOptionPane.INFORMATION_MESSAGE );
\r
2400 JOptionPane.showMessageDialog( comp,
\r
2401 "There was an unknown problem when attempting to write to an image file: \""
\r
2402 + file_name + "\"",
\r
2404 JOptionPane.ERROR_MESSAGE );
\r
2407 contentpane.repaint();
\r
2410 static File writeToFile( final Phylogeny t,
\r
2411 final MainPanel mp,
\r
2412 final JFileChooser save_filechooser,
\r
2413 final File current_dir,
\r
2414 final Container contentpane,
\r
2415 final Component comp ) {
\r
2416 File new_file = null;
\r
2417 if ( t == null ) {
\r
2420 String initial_filename = null;
\r
2421 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
2423 initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath();
\r
2425 catch ( final IOException e ) {
\r
2426 initial_filename = null;
\r
2429 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
\r
2430 save_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2433 save_filechooser.setSelectedFile( new File( "" ) );
\r
2435 final File my_dir = current_dir;
\r
2436 if ( my_dir != null ) {
\r
2437 save_filechooser.setCurrentDirectory( my_dir );
\r
2439 final int result = save_filechooser.showSaveDialog( contentpane );
\r
2440 final File file = save_filechooser.getSelectedFile();
\r
2441 new_file = save_filechooser.getCurrentDirectory();
\r
2442 boolean exception = false;
\r
2443 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2444 if ( file.exists() ) {
\r
2445 final int i = JOptionPane.showConfirmDialog( comp,
\r
2446 file + " already exists.\nOverwrite?",
\r
2448 JOptionPane.OK_CANCEL_OPTION,
\r
2449 JOptionPane.QUESTION_MESSAGE );
\r
2450 if ( i != JOptionPane.OK_OPTION ) {
\r
2454 final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
\r
2456 ForesterUtil.copyFile( file, to );
\r
2458 catch ( final Exception e ) {
\r
2459 JOptionPane.showMessageDialog( comp,
\r
2460 "Failed to create backup copy " + to,
\r
2461 "Failed to Create Backup Copy",
\r
2462 JOptionPane.WARNING_MESSAGE );
\r
2467 catch ( final Exception e ) {
\r
2468 JOptionPane.showMessageDialog( comp,
\r
2469 "Failed to delete: " + file,
\r
2470 "Failed to Delete",
\r
2471 JOptionPane.WARNING_MESSAGE );
\r
2475 if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) {
\r
2476 exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2478 else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
\r
2479 exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2481 else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
\r
2482 exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2486 final String file_name = file.getName().trim().toLowerCase();
\r
2487 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2488 || file_name.endsWith( ".tree" ) ) {
\r
2489 exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2491 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
\r
2492 exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2494 // XML is default:
\r
2496 exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
\r
2499 if ( !exception ) {
\r
2500 mp.setTitleOfSelectedTab( file.getName() );
\r
2501 mp.getCurrentTreePanel().setTreeFile( file );
\r
2502 mp.getCurrentTreePanel().setEdited( false );
\r
2508 static File writeToGraphicsFile( final Phylogeny t,
\r
2509 final GraphicsExportType type,
\r
2510 final MainPanel mp,
\r
2511 final JFileChooser writetographics_filechooser,
\r
2512 final Component component,
\r
2513 final Container contentpane,
\r
2514 final File current_dir ) {
\r
2515 File new_dir = null;
\r
2516 if ( ( t == null ) || t.isEmpty() ) {
\r
2519 String initial_filename = "";
\r
2520 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
2521 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
\r
2523 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2524 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2526 initial_filename = initial_filename + "." + type;
\r
2527 writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2528 final File my_dir = current_dir;
\r
2529 if ( my_dir != null ) {
\r
2530 writetographics_filechooser.setCurrentDirectory( my_dir );
\r
2532 final int result = writetographics_filechooser.showSaveDialog( contentpane );
\r
2533 File file = writetographics_filechooser.getSelectedFile();
\r
2534 //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );
\r
2535 new_dir = writetographics_filechooser.getCurrentDirectory();
\r
2536 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2537 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
\r
2538 file = new File( file.toString() + "." + type );
\r
2540 if ( file.exists() ) {
\r
2541 final int i = JOptionPane.showConfirmDialog( component,
\r
2542 file + " already exists. Overwrite?",
\r
2544 JOptionPane.OK_CANCEL_OPTION,
\r
2545 JOptionPane.WARNING_MESSAGE );
\r
2546 if ( i != JOptionPane.OK_OPTION ) {
\r
2553 catch ( final Exception e ) {
\r
2554 JOptionPane.showMessageDialog( component,
\r
2555 "Failed to delete: " + file,
\r
2557 JOptionPane.WARNING_MESSAGE );
\r
2561 writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );
\r
2566 static File writeToPdf( final Phylogeny t,
\r
2567 final MainPanel mp,
\r
2568 final JFileChooser writetopdf_filechooser,
\r
2569 final File curr_dir,
\r
2570 final Container contentpane,
\r
2571 final Component component ) {
\r
2572 if ( ( t == null ) || t.isEmpty() ) {
\r
2575 String initial_filename = "";
\r
2576 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
\r
2577 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
\r
2579 if ( initial_filename.indexOf( '.' ) > 0 ) {
\r
2580 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
\r
2582 initial_filename = initial_filename + ".pdf";
\r
2583 writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
\r
2584 final File my_dir = curr_dir;
\r
2585 if ( my_dir != null ) {
\r
2586 writetopdf_filechooser.setCurrentDirectory( my_dir );
\r
2588 final int result = writetopdf_filechooser.showSaveDialog( contentpane );
\r
2589 File file = writetopdf_filechooser.getSelectedFile();
\r
2590 // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );
\r
2591 final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();
\r
2592 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2593 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
\r
2594 file = new File( file.toString() + ".pdf" );
\r
2596 if ( file.exists() ) {
\r
2597 final int i = JOptionPane.showConfirmDialog( component,
\r
2598 file + " already exists. Overwrite?",
\r
2600 JOptionPane.OK_CANCEL_OPTION,
\r
2601 JOptionPane.WARNING_MESSAGE );
\r
2602 if ( i != JOptionPane.OK_OPTION ) {
\r
2606 printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );
\r
2608 return new_current_dir;
\r
2612 class DefaultFilter extends FileFilter {
\r
2615 public boolean accept( final File f ) {
\r
2616 final String file_name = f.getName().trim().toLowerCase();
\r
2617 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2618 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
\r
2619 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
\r
2620 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
\r
2621 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
\r
2622 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
\r
2623 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
\r
2624 || file_name.endsWith( ".con" ) || f.isDirectory();
\r
2628 public String getDescription() {
\r
2629 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
\r
2633 class GraphicsFileFilter extends FileFilter {
\r
2636 public boolean accept( final File f ) {
\r
2637 final String file_name = f.getName().trim().toLowerCase();
\r
2638 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
\r
2639 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
\r
2643 public String getDescription() {
\r
2644 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
\r
2648 class MsaFileFilter extends FileFilter {
\r
2651 public boolean accept( final File f ) {
\r
2652 final String file_name = f.getName().trim().toLowerCase();
\r
2653 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
\r
2654 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
\r
2658 public String getDescription() {
\r
2659 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
\r
2663 class NexusFilter extends FileFilter {
\r
2666 public boolean accept( final File f ) {
\r
2667 final String file_name = f.getName().trim().toLowerCase();
\r
2668 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
\r
2669 || file_name.endsWith( ".tre" ) || f.isDirectory();
\r
2673 public String getDescription() {
\r
2674 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
\r
2678 class NHFilter extends FileFilter {
\r
2681 public boolean accept( final File f ) {
\r
2682 final String file_name = f.getName().trim().toLowerCase();
\r
2683 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
\r
2684 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
\r
2685 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
\r
2686 || f.isDirectory();
\r
2690 public String getDescription() {
\r
2691 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
\r
2695 class NHXFilter extends FileFilter {
\r
2698 public boolean accept( final File f ) {
\r
2699 final String file_name = f.getName().trim().toLowerCase();
\r
2700 return file_name.endsWith( ".nhx" ) || f.isDirectory();
\r
2704 public String getDescription() {
\r
2705 return "NHX files (*.nhx) [deprecated]";
\r
2709 class PdfFilter extends FileFilter {
\r
2712 public boolean accept( final File f ) {
\r
2713 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
\r
2717 public String getDescription() {
\r
2718 return "PDF files (*.pdf)";
\r
2722 class SequencesFileFilter extends FileFilter {
\r
2725 public boolean accept( final File f ) {
\r
2726 final String file_name = f.getName().trim().toLowerCase();
\r
2727 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
\r
2728 || file_name.endsWith( ".seqs" ) || f.isDirectory();
\r
2732 public String getDescription() {
\r
2733 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
\r
2737 class TolFilter extends FileFilter {
\r
2740 public boolean accept( final File f ) {
\r
2741 final String file_name = f.getName().trim().toLowerCase();
\r
2742 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
\r
2743 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
\r
2747 public String getDescription() {
\r
2748 return "Tree of Life files (*.tol, *.tolxml)";
\r
2752 class XMLFilter extends FileFilter {
\r
2755 public boolean accept( final File f ) {
\r
2756 final String file_name = f.getName().trim().toLowerCase();
\r
2757 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
\r
2758 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
\r
2762 public String getDescription() {
\r
2763 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
\r
git://source.jalview.org / jalview.git / blob