2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2010 Christian M. Zmasek
8 // This library is free software; you can redistribute it and/or
9 // modify it under the terms of the GNU Lesser General Public
10 // License as published by the Free Software Foundation; either
11 // version 2.1 of the License, or (at your option) any later version.
13 // This library is distributed in the hope that it will be useful,
14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 // Lesser General Public License for more details.
18 // You should have received a copy of the GNU Lesser General Public
19 // License along with this library; if not, write to the Free Software
20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
22 // Contact: phylosoft @ gmail . com
23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
25 package org.forester.archaeopteryx;
27 import java.awt.Color;
28 import java.awt.Component;
29 import java.awt.Container;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.ActionListener;
34 import java.io.IOException;
35 import java.util.ArrayList;
36 import java.util.LinkedList;
37 import java.util.List;
38 import java.util.Locale;
40 import java.util.NoSuchElementException;
42 import javax.swing.Box;
43 import javax.swing.JApplet;
44 import javax.swing.JCheckBoxMenuItem;
45 import javax.swing.JFileChooser;
46 import javax.swing.JFrame;
47 import javax.swing.JLabel;
48 import javax.swing.JMenu;
49 import javax.swing.JMenuBar;
50 import javax.swing.JMenuItem;
51 import javax.swing.JOptionPane;
52 import javax.swing.JPanel;
53 import javax.swing.JRadioButtonMenuItem;
54 import javax.swing.JTextField;
55 import javax.swing.SwingUtilities;
56 import javax.swing.filechooser.FileFilter;
58 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
59 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
60 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
61 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
62 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
63 import org.forester.archaeopteryx.tools.InferenceManager;
64 import org.forester.archaeopteryx.tools.ProcessPool;
65 import org.forester.archaeopteryx.tools.ProcessRunning;
66 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
67 import org.forester.io.writers.PhylogenyWriter;
68 import org.forester.phylogeny.Phylogeny;
69 import org.forester.phylogeny.PhylogenyMethods;
70 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
71 import org.forester.phylogeny.PhylogenyNode;
72 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
73 import org.forester.phylogeny.data.Annotation;
74 import org.forester.phylogeny.data.NodeDataField;
75 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
76 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
77 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
78 import org.forester.sdi.GSDI;
79 import org.forester.sdi.GSDIR;
80 import org.forester.sdi.SDIException;
81 import org.forester.util.ForesterConstants;
82 import org.forester.util.ForesterUtil;
83 import org.forester.util.WindowsUtils;
85 public abstract class MainFrame extends JFrame implements ActionListener {
87 final static NHFilter nhfilter = new NHFilter();
88 final static NHXFilter nhxfilter = new NHXFilter();
89 final static XMLFilter xmlfilter = new XMLFilter();
90 final static TolFilter tolfilter = new TolFilter();
91 final static NexusFilter nexusfilter = new NexusFilter();
92 final static PdfFilter pdffilter = new PdfFilter();
93 final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
94 final static MsaFileFilter msafilter = new MsaFileFilter();
95 final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
96 final static DefaultFilter defaultfilter = new DefaultFilter();
97 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "rotate with mousewheel + Shift (or A and S), D toggles between horizontal and radial labels";
98 static final String PHYLOXML_REF_TOOL_TIP = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME
99 static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE;
100 private static final long serialVersionUID = 3655000897845508358L;
101 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
104 static final String TYPE_MENU_HEADER = "Type";
105 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
106 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
107 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
108 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
109 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
110 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
111 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
112 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
113 static final String OPTIONS_HEADER = "Options";
114 static final String SEARCH_SUBHEADER = "Search:";
115 static final String DISPLAY_SUBHEADER = "Display:";
116 static final String SEARCH_TERMS_ONLY_LABEL = "Words";
117 static final String SEARCH_REGEX_LABEL = "Regex";
118 static final String SEARCH_CASE_SENSITIVE_LABEL = "Match Case";
119 static final String INVERSE_SEARCH_RESULT_LABEL = "Inverse";
120 static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
121 static final String DISPLAY_SCALE_LABEL = "Scale";
122 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladogram";
123 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
124 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
125 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.";
126 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
127 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
128 static final String BG_GRAD_LABEL = "Background Color Gradient";
129 static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
130 static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
131 static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
132 static final String SHOW_OVERVIEW_LABEL = "Overview";
133 static final String FONT_SIZE_MENU_LABEL = "Font Size";
134 static final String NONUNIFORM_CLADOGRAMS_LABEL = "Lined Up Cladogram";
135 static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
136 static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
137 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";
138 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
139 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
140 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
141 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
142 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
143 static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
144 static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
145 static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
146 static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
147 static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
148 static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
149 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
150 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
155 JMenu _options_jmenu;
156 JMenu _font_size_menu;
158 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
160 JMenu _analysis_menu;
161 JMenuItem _load_species_tree_item;
162 JMenuItem _gsdi_item;
163 JMenuItem _gsdir_item;
164 JMenuItem _lineage_inference;
166 JMenuItem _open_item;
167 JMenuItem _open_url_item;
168 JMenuItem _save_item;
169 JMenuItem _save_all_item;
170 JMenuItem _close_item;
171 JMenuItem _exit_item;
173 JMenuItem _print_item;
174 JMenuItem _write_to_pdf_item;
175 JMenuItem _write_to_jpg_item;
176 JMenuItem _write_to_gif_item;
177 JMenuItem _write_to_tif_item;
178 JMenuItem _write_to_png_item;
179 JMenuItem _write_to_bmp_item;
181 JMenuItem _midpoint_root_item;
182 JMenuItem _taxcolor_item;
183 JMenuItem _confcolor_item;
184 JMenuItem _color_rank_jmi;
185 JMenuItem _collapse_species_specific_subtrees;
187 JMenuItem _obtain_detailed_taxonomic_information_jmi;
188 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
189 JMenuItem _obtain_seq_information_jmi;
190 JMenuItem _move_node_names_to_tax_sn_jmi;
191 JMenuItem _move_node_names_to_seq_names_jmi;
192 JMenuItem _extract_tax_code_from_node_names_jmi;
193 JMenuItem _annotate_item;
194 JMenuItem _remove_branch_color_item;
195 JMenuItem _remove_visual_styles_item;
196 JMenuItem _delete_selected_nodes_item;
197 JMenuItem _delete_not_selected_nodes_item;
199 JMenuItem _super_tiny_fonts_item;
200 JMenuItem _tiny_fonts_item;
201 JMenuItem _small_fonts_item;
202 JMenuItem _medium_fonts_item;
203 JMenuItem _large_fonts_item;
205 // _ screen and print
206 JMenuItem _choose_font_mi;
207 JMenuItem _switch_colors_mi;
208 JCheckBoxMenuItem _label_direction_cbmi;
210 JCheckBoxMenuItem _screen_antialias_cbmi;
211 JCheckBoxMenuItem _background_gradient_cbmi;
212 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
213 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
214 JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
215 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
216 JCheckBoxMenuItem _show_overview_cbmi;
217 JCheckBoxMenuItem _show_domain_labels;
218 JCheckBoxMenuItem _show_annotation_ref_source;
219 JCheckBoxMenuItem _abbreviate_scientific_names;
220 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
221 JMenuItem _overview_placment_mi;
222 JMenuItem _choose_minimal_confidence_mi;
223 JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
224 JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
225 JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
226 JMenuItem _cycle_node_shape_mi;
227 JMenuItem _cycle_node_fill_mi;
228 JMenuItem _choose_node_size_mi;
229 JMenuItem _cycle_data_return;
230 JCheckBoxMenuItem _show_confidence_stddev_cbmi;
231 JCheckBoxMenuItem _right_line_up_domains_cbmi;
232 JCheckBoxMenuItem _line_up_renderable_data_cbmi;
233 JCheckBoxMenuItem _collapsed_with_average_height_cbmi;
234 JCheckBoxMenuItem _show_abbreviated_labels_for_collapsed_nodes_cbmi;
236 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
237 JCheckBoxMenuItem _antialias_print_cbmi;
238 JCheckBoxMenuItem _print_black_and_white_cbmi;
239 //JMenuItem _print_size_mi;
240 JMenuItem _choose_pdf_width_mi;
242 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
243 JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
244 JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
245 JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
246 JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
247 JCheckBoxMenuItem _replace_underscores_cbmi;
248 JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
249 JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
250 JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
251 JCheckBoxMenuItem _parse_beast_style_extended_nexus_tags_cbmi;
253 JCheckBoxMenuItem _search_case_senstive_cbmi;
254 JCheckBoxMenuItem _search_whole_words_only_cbmi;
255 JCheckBoxMenuItem _inverse_search_result_cbmi;
256 JCheckBoxMenuItem _search_with_regex_cbmi;
257 JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_cbmi;
260 JCheckBoxMenuItem _rectangular_type_cbmi;
261 JCheckBoxMenuItem _triangular_type_cbmi;
262 JCheckBoxMenuItem _curved_type_cbmi;
263 JCheckBoxMenuItem _convex_type_cbmi;
264 JCheckBoxMenuItem _euro_type_cbmi;
265 JCheckBoxMenuItem _rounded_type_cbmi;
266 JCheckBoxMenuItem _unrooted_type_cbmi;
267 JCheckBoxMenuItem _circular_type_cbmi;
268 // view as text menu:
269 JMenuItem _view_as_NH_item;
270 JMenuItem _view_as_XML_item;
271 JMenuItem _view_as_nexus_item;
272 JMenuItem _display_basic_information_item;
274 JMenuItem _about_item;
275 JMenuItem _help_item;
276 JMenuItem _website_item;
277 JMenuItem _mailing_list_item;
278 JMenuItem _phyloxml_website_item;
279 JMenuItem _phyloxml_ref_item;
280 JMenuItem _aptx_ref_item;
283 JFileChooser _writetopdf_filechooser;
284 JFileChooser _save_filechooser;
285 JFileChooser _writetographics_filechooser;
288 MainPanel _mainpanel;
289 Container _contentpane;
290 final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
291 Configuration _configuration;
293 private Phylogeny _species_tree;
294 InferenceManager _inference_manager;
295 final ProcessPool _process_pool;
296 private String _previous_node_annotation_ref;
299 _process_pool = ProcessPool.createInstance();
300 _writetopdf_filechooser = new JFileChooser();
301 _writetopdf_filechooser.setMultiSelectionEnabled( false );
302 _writetopdf_filechooser.addChoosableFileFilter( pdffilter );
303 _writetographics_filechooser = new JFileChooser();
304 _writetographics_filechooser.setMultiSelectionEnabled( false );
305 _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter );
306 _save_filechooser = new JFileChooser();
307 _save_filechooser.setMultiSelectionEnabled( false );
308 _save_filechooser.setFileFilter( xmlfilter );
309 _save_filechooser.addChoosableFileFilter( nhfilter );
310 _save_filechooser.addChoosableFileFilter( nexusfilter );
311 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
313 final String home_dir = System.getProperty( "user.home" );
314 _save_filechooser.setCurrentDirectory( new File( home_dir ) );
315 _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
316 _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
318 catch ( final Exception e ) {
320 // Do nothing. Not important.
328 public void actionPerformed( final ActionEvent e ) {
329 final Object o = e.getSource();
330 boolean is_applet = false;
331 JApplet applet = null;
332 if ( getCurrentTreePanel() != null ) {
333 is_applet = getCurrentTreePanel().isApplet();
335 applet = getCurrentTreePanel().obtainApplet();
338 if ( o == _exit_item ) {
341 else if ( o == _gsdi_item ) {
342 if ( isSubtreeDisplayed() ) {
347 else if ( o == _gsdir_item ) {
348 if ( isSubtreeDisplayed() ) {
353 else if ( o == _taxcolor_item ) {
356 else if ( o == _confcolor_item ) {
359 else if ( o == _color_rank_jmi ) {
362 else if ( o == _collapse_species_specific_subtrees ) {
363 if ( isSubtreeDisplayed() ) {
366 if ( getCurrentTreePanel() != null ) {
367 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
370 else if ( o == _remove_branch_color_item ) {
371 if ( isSubtreeDisplayed() ) {
374 removeBranchColors();
376 else if ( o == _remove_visual_styles_item ) {
377 if ( isSubtreeDisplayed() ) {
380 removeVisualStyles();
382 else if ( o == _midpoint_root_item ) {
383 if ( isSubtreeDisplayed() ) {
388 else if ( o == _delete_selected_nodes_item ) {
389 if ( isSubtreeDisplayed() ) {
392 deleteSelectedNodes( true );
394 else if ( o == _delete_not_selected_nodes_item ) {
395 if ( isSubtreeDisplayed() ) {
398 deleteSelectedNodes( false );
400 else if ( o == _annotate_item ) {
403 else if ( o == _switch_colors_mi ) {
406 else if ( o == _display_basic_information_item ) {
407 if ( getCurrentTreePanel() != null ) {
408 displayBasicInformation( getCurrentTreePanel().getTreeFile() );
411 else if ( o == _view_as_NH_item ) {
414 else if ( o == _view_as_XML_item ) {
417 else if ( o == _view_as_nexus_item ) {
420 else if ( o == _super_tiny_fonts_item ) {
421 if ( getCurrentTreePanel() != null ) {
422 getCurrentTreePanel().setSuperTinyFonts();
423 getCurrentTreePanel().repaint();
426 else if ( o == _tiny_fonts_item ) {
427 if ( getCurrentTreePanel() != null ) {
428 getCurrentTreePanel().setTinyFonts();
429 getCurrentTreePanel().repaint();
432 else if ( o == _small_fonts_item ) {
433 if ( getCurrentTreePanel() != null ) {
434 getCurrentTreePanel().setSmallFonts();
435 getCurrentTreePanel().repaint();
438 else if ( o == _medium_fonts_item ) {
439 if ( getCurrentTreePanel() != null ) {
440 getCurrentTreePanel().setMediumFonts();
441 getCurrentTreePanel().repaint();
444 else if ( o == _large_fonts_item ) {
445 if ( getCurrentTreePanel() != null ) {
446 getCurrentTreePanel().setLargeFonts();
447 getCurrentTreePanel().repaint();
450 else if ( o == _choose_font_mi ) {
453 else if ( o == _choose_minimal_confidence_mi ) {
454 chooseMinimalConfidence();
456 else if ( o == _choose_node_size_mi ) {
457 chooseNodeSize( getOptions(), this );
459 else if ( o == _overview_placment_mi ) {
460 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
462 else if ( o == _cycle_node_fill_mi ) {
463 MainFrame.cycleNodeFill( getOptions() );
465 else if ( o == _cycle_node_shape_mi ) {
466 MainFrame.cycleNodeShape( getOptions() );
468 else if ( o == _cycle_data_return ) {
469 MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
471 else if ( o == _screen_antialias_cbmi ) {
472 updateOptions( getOptions() );
473 updateScreenTextAntialias( getMainPanel().getTreePanels() );
475 else if ( o == _background_gradient_cbmi ) {
476 updateOptions( getOptions() );
478 else if ( o == _show_domain_labels ) {
479 updateOptions( getOptions() );
481 else if ( o == _show_annotation_ref_source ) {
482 updateOptions( getOptions() );
484 else if ( o == _abbreviate_scientific_names ) {
485 updateOptions( getOptions() );
487 else if ( o == _color_labels_same_as_parent_branch ) {
488 updateOptions( getOptions() );
490 else if ( o == _show_default_node_shapes_internal_cbmi ) {
491 updateOptions( getOptions() );
493 else if ( o == _show_default_node_shapes_external_cbmi ) {
494 updateOptions( getOptions() );
496 else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
497 updateOptions( getOptions() );
499 else if ( o == _non_lined_up_cladograms_rbmi ) {
500 updateOptions( getOptions() );
503 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
504 updateOptions( getOptions() );
507 else if ( o == _search_case_senstive_cbmi ) {
508 if ( ( _search_with_regex_cbmi != null ) && _search_case_senstive_cbmi.isSelected() ) {
509 _search_with_regex_cbmi.setSelected( false );
511 updateOptions( getOptions() );
512 getMainPanel().getControlPanel().search0();
513 getMainPanel().getControlPanel().search1();
515 else if ( o == _search_whole_words_only_cbmi ) {
516 if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
517 _search_with_regex_cbmi.setSelected( false );
519 updateOptions( getOptions() );
520 getMainPanel().getControlPanel().search0();
521 getMainPanel().getControlPanel().search1();
523 else if ( o == _inverse_search_result_cbmi ) {
524 updateOptions( getOptions() );
525 getMainPanel().getControlPanel().search0();
526 getMainPanel().getControlPanel().search1();
528 else if ( o == _search_with_regex_cbmi ) {
529 if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
530 _search_whole_words_only_cbmi.setSelected( false );
532 if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
533 _search_case_senstive_cbmi.setSelected( false );
535 updateOptions( getOptions() );
536 getMainPanel().getControlPanel().search0();
537 getMainPanel().getControlPanel().search1();
539 else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) {
540 updateOptions( getOptions() );
542 else if ( o == _parse_beast_style_extended_nexus_tags_cbmi ) {
543 updateOptions( getOptions() );
545 else if ( o == _show_scale_cbmi ) {
546 updateOptions( getOptions() );
548 else if ( o == _color_by_taxonomic_group_cbmi ) {
549 updateOptions( getOptions() );
551 else if ( o == _show_confidence_stddev_cbmi ) {
552 updateOptions( getOptions() );
554 else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
555 if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
556 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
558 updateOptions( getOptions() );
560 else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
561 if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
562 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
564 updateOptions( getOptions() );
566 else if ( o == _label_direction_cbmi ) {
567 updateOptions( getOptions() );
569 else if ( o == _show_overview_cbmi ) {
570 updateOptions( getOptions() );
571 if ( getCurrentTreePanel() != null ) {
572 getCurrentTreePanel().updateOvSizes();
575 else if ( o == _line_up_renderable_data_cbmi ) {
576 if ( !_line_up_renderable_data_cbmi.isSelected() ) {
577 _right_line_up_domains_cbmi.setSelected( false );
579 updateOptions( getOptions() );
582 else if ( o == _collapsed_with_average_height_cbmi ) {
583 if ( _collapsed_with_average_height_cbmi.isSelected() ) {
584 _collapsed_with_average_height_cbmi.setSelected( true );
586 updateOptions( getOptions() );
588 else if ( o == _show_abbreviated_labels_for_collapsed_nodes_cbmi ) {
589 if ( _show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() ) {
590 _show_abbreviated_labels_for_collapsed_nodes_cbmi.setSelected( true );
592 updateOptions( getOptions() );
594 else if ( o == _right_line_up_domains_cbmi ) {
595 if ( _right_line_up_domains_cbmi.isSelected() ) {
596 _line_up_renderable_data_cbmi.setSelected( true );
598 updateOptions( getOptions() );
600 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
601 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
602 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
605 else if ( o == _about_item ) {
608 else if ( o == _help_item ) {
610 AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, is_applet, applet );
612 catch ( final IOException e1 ) {
613 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
616 else if ( o == _website_item ) {
618 AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, is_applet, applet );
620 catch ( final IOException e1 ) {
621 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
624 else if ( o == _mailing_list_item ) {
626 AptxUtil.openWebsite( AptxConstants.APTX_MAILING_LIST, is_applet, applet );
628 catch ( final IOException e1 ) {
629 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
632 else if ( o == _phyloxml_website_item ) {
634 AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet );
636 catch ( final IOException e1 ) {
637 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
640 else if ( o == _aptx_ref_item ) {
642 AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, is_applet, applet );
644 catch ( final IOException e1 ) {
645 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
648 else if ( o == _phyloxml_ref_item ) {
650 AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, is_applet, applet );
652 catch ( final IOException e1 ) {
653 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
656 else if ( o == _write_to_pdf_item ) {
657 final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(),
659 _writetopdf_filechooser,
663 if ( curr_dir != null ) {
664 setCurrentDir( curr_dir );
667 else if ( o == _save_all_item ) {
670 else if ( o == _write_to_jpg_item ) {
671 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
672 GraphicsExportType.JPG,
674 _writetographics_filechooser,
678 if ( new_dir != null ) {
679 setCurrentDir( new_dir );
682 else if ( o == _write_to_gif_item ) {
683 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
684 GraphicsExportType.GIF,
686 _writetographics_filechooser,
690 if ( new_dir != null ) {
691 setCurrentDir( new_dir );
694 else if ( o == _write_to_tif_item ) {
695 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
696 GraphicsExportType.TIFF,
698 _writetographics_filechooser,
702 if ( new_dir != null ) {
703 setCurrentDir( new_dir );
706 else if ( o == _write_to_bmp_item ) {
707 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
708 GraphicsExportType.BMP,
710 _writetographics_filechooser,
714 if ( new_dir != null ) {
715 setCurrentDir( new_dir );
718 else if ( o == _write_to_png_item ) {
719 final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
720 GraphicsExportType.PNG,
722 _writetographics_filechooser,
726 if ( new_dir != null ) {
727 setCurrentDir( new_dir );
730 else if ( o == _print_item ) {
731 print( getCurrentTreePanel(), getOptions(), this );
733 else if ( o == _save_item ) {
734 final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),
740 if ( new_dir != null ) {
741 setCurrentDir( new_dir );
744 else if ( o == _graphics_export_visible_only_cbmi ) {
745 updateOptions( getOptions() );
747 else if ( o == _antialias_print_cbmi ) {
748 updateOptions( getOptions() );
750 else if ( o == _print_black_and_white_cbmi ) {
751 updateOptions( getOptions() );
753 else if ( o == _choose_pdf_width_mi ) {
756 else if ( o == _lineage_inference ) {
757 if ( isSubtreeDisplayed() ) {
758 JOptionPane.showMessageDialog( this,
760 "Cannot infer ancestral taxonomies",
761 JOptionPane.ERROR_MESSAGE );
764 executeLineageInference();
767 if ( _load_phylogeny_from_webservice_menu_items != null ) {
768 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
769 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
770 readPhylogeniesFromWebservice( i );
775 _contentpane.repaint();
778 public Configuration getConfiguration() {
779 return _configuration;
783 * This method returns the current external node data which
784 * has been selected by the user by clicking the "Return ..."
785 * menu item. This method is expected to be called from Javascript or
788 * @return current external node data as String
790 public String getCurrentExternalNodesDataBuffer() {
791 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
794 public int getCurrentExternalNodesDataBufferChangeCounter() {
795 return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
798 public int getCurrentExternalNodesDataBufferLength() {
799 return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
802 public InferenceManager getInferenceManager() {
803 return _inference_manager;
806 public MainPanel getMainPanel() {
810 public Options getOptions() {
814 public ProcessPool getProcessPool() {
815 return _process_pool;
818 public void showTextFrame( final String s, final String title ) {
820 _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
823 public void showWhole() {
824 _mainpanel.getControlPanel().showWhole();
827 public void updateProcessMenu() {
828 // In general Swing is not thread safe.
829 // See "Swing's Threading Policy".
830 SwingUtilities.invokeLater( new Runnable() {
834 doUpdateProcessMenu();
839 private void annotateSequences() {
840 if ( getCurrentTreePanel() != null ) {
841 List<PhylogenyNode> nodes = null;
842 if ( ( getCurrentTreePanel().getFoundNodes0() != null )
843 || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
844 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
846 if ( ( nodes == null ) || nodes.isEmpty() ) {
848 .showMessageDialog( this,
849 "Need to select nodes, either via direct selection or via the \"Search\" function",
850 "No nodes selected for annotation",
851 JOptionPane.ERROR_MESSAGE );
854 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
855 if ( ( phy != null ) && !phy.isEmpty() ) {
856 final JTextField ref_field = new JTextField( 10 );
857 final JTextField desc_filed = new JTextField( 20 );
858 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
859 : getPreviousNodeAnnotationReference() );
860 final JPanel my_panel = new JPanel();
861 my_panel.add( new JLabel( "Reference " ) );
862 my_panel.add( ref_field );
863 my_panel.add( Box.createHorizontalStrut( 15 ) );
864 my_panel.add( new JLabel( "Description " ) );
865 my_panel.add( desc_filed );
866 final int result = JOptionPane.showConfirmDialog( null,
868 "Enter the sequence annotation(s) for the "
869 + nodes.size() + " selected nodes",
870 JOptionPane.OK_CANCEL_OPTION );
871 if ( result == JOptionPane.OK_OPTION ) {
872 String ref = ref_field.getText();
873 String desc = desc_filed.getText();
874 if ( !ForesterUtil.isEmpty( ref ) ) {
876 ref = ref.replaceAll( "\\s+", " " );
877 if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
878 || ( ref.length() < 3 ) ) {
879 JOptionPane.showMessageDialog( this,
880 "Reference needs to be in the form of \"GO:1234567\"",
881 "Illegal Format for Annotation Reference",
882 JOptionPane.ERROR_MESSAGE );
887 setPreviousNodeAnnotationReference( ref );
889 if ( desc != null ) {
891 desc = desc.replaceAll( "\\s+", " " );
893 if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
894 for( final PhylogenyNode n : nodes ) {
895 ForesterUtil.ensurePresenceOfSequence( n );
896 final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
897 : new Annotation( ref );
898 if ( !ForesterUtil.isEmpty( desc ) ) {
901 n.getNodeData().getSequence().addAnnotation( ann );
904 getMainPanel().getControlPanel().showAnnotations();
910 private void chooseFont() {
911 final FontChooser fc = new FontChooser();
912 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
913 fc.showDialog( this, "Select the Base Font" );
914 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
915 getControlPanel().displayedPhylogenyMightHaveChanged( true );
916 if ( getMainPanel().getCurrentTreePanel() != null ) {
917 getMainPanel().getCurrentTreePanel().resetPreferredSize();
918 getMainPanel().getCurrentTreePanel().updateOvSizes();
924 private void chooseMinimalConfidence() {
925 final String s = ( String ) JOptionPane
926 .showInputDialog( this,
927 "Please enter the minimum for confidence values to be displayed.\n"
928 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
929 "Minimal Confidence Value",
930 JOptionPane.QUESTION_MESSAGE,
933 getOptions().getMinConfidenceValue() );
934 if ( !ForesterUtil.isEmpty( s ) ) {
935 boolean success = true;
937 final String m_str = s.trim();
938 if ( !ForesterUtil.isEmpty( m_str ) ) {
940 m = Double.parseDouble( m_str );
942 catch ( final Exception ex ) {
949 if ( success && ( m >= 0.0 ) ) {
950 getOptions().setMinConfidenceValue( m );
955 private void deleteSelectedNodes( final boolean delete ) {
956 final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
957 if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
960 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
961 if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
962 final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
963 for( final PhylogenyNode n : all_selected_nodes ) {
964 if ( n.isExternal() ) {
969 String function = "Retain";
973 if ( ( nodes == null ) || nodes.isEmpty() ) {
975 .showMessageDialog( this,
976 "Need to select external nodes, either via direct selection or via the \"Search\" function",
977 "No external nodes selected to " + function.toLowerCase(),
978 JOptionPane.ERROR_MESSAGE );
981 final int todo = nodes.size();
982 final int ext = phy.getNumberOfExternalNodes();
988 JOptionPane.showMessageDialog( this,
989 "Cannot delete all nodes",
990 "Attempt to delete all nodes ",
991 JOptionPane.ERROR_MESSAGE );
994 final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
995 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
996 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
997 if ( result == JOptionPane.OK_OPTION ) {
999 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
1000 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1001 final PhylogenyNode n = it.next();
1002 if ( !nodes.contains( n ) ) {
1006 for( final PhylogenyNode n : to_delete ) {
1007 phy.deleteSubtree( n, true );
1011 for( final PhylogenyNode n : nodes ) {
1012 phy.deleteSubtree( n, true );
1016 getCurrentTreePanel().setNodeInPreorderToNull();
1017 phy.externalNodesHaveChanged();
1018 phy.clearHashIdToNodeMap();
1019 phy.recalculateNumberOfExternalDescendants( true );
1020 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1021 getCurrentTreePanel().setEdited( true );
1026 private void doUpdateProcessMenu() {
1027 if ( _process_pool.size() > 0 ) {
1028 if ( _process_menu == null ) {
1029 _process_menu = createMenu( "", getConfiguration() );
1030 _process_menu.setForeground( Color.RED );
1032 _process_menu.removeAll();
1033 final String text = "processes running: " + _process_pool.size();
1034 _process_menu.setText( text );
1035 _jmenubar.add( _process_menu );
1036 for( int i = 0; i < _process_pool.size(); ++i ) {
1037 final ProcessRunning p = _process_pool.getProcessByIndex( i );
1038 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
1042 if ( _process_menu != null ) {
1043 _process_menu.removeAll();
1044 _jmenubar.remove( _process_menu );
1047 _jmenubar.validate();
1048 _jmenubar.repaint();
1052 private String getPreviousNodeAnnotationReference() {
1053 return _previous_node_annotation_ref;
1056 private void removeBranchColors() {
1057 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1058 AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1062 private void removeVisualStyles() {
1063 if ( getMainPanel().getCurrentPhylogeny() != null ) {
1064 AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1068 private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
1069 _previous_node_annotation_ref = previous_node_annotation_ref;
1072 private void writeAllToFile() {
1073 if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
1076 final File my_dir = getCurrentDir();
1077 if ( my_dir != null ) {
1078 _save_filechooser.setCurrentDirectory( my_dir );
1080 _save_filechooser.setSelectedFile( new File( "" ) );
1081 final int result = _save_filechooser.showSaveDialog( _contentpane );
1082 final File file = _save_filechooser.getSelectedFile();
1083 setCurrentDir( _save_filechooser.getCurrentDirectory() );
1084 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1085 if ( file.exists() ) {
1086 final int i = JOptionPane.showConfirmDialog( this,
1087 file + " already exists. Overwrite?",
1089 JOptionPane.OK_CANCEL_OPTION,
1090 JOptionPane.WARNING_MESSAGE );
1091 if ( i != JOptionPane.OK_OPTION ) {
1098 catch ( final Exception e ) {
1099 JOptionPane.showMessageDialog( this,
1100 "Failed to delete: " + file,
1102 JOptionPane.WARNING_MESSAGE );
1106 final int count = getMainPanel().getTabbedPane().getTabCount();
1107 final List<Phylogeny> trees = new ArrayList<Phylogeny>();
1108 for( int i = 0; i < count; ++i ) {
1109 final Phylogeny phy = getMainPanel().getPhylogeny( i );
1110 if ( ForesterUtil.isEmpty( phy.getName() )
1111 && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
1112 phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
1115 getMainPanel().getTreePanels().get( i ).setEdited( false );
1117 final PhylogenyWriter writer = new PhylogenyWriter();
1119 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
1121 catch ( final IOException e ) {
1122 JOptionPane.showMessageDialog( this,
1123 "Failed to write to: " + file,
1125 JOptionPane.WARNING_MESSAGE );
1130 void activateSaveAllIfNeeded() {
1131 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
1132 _save_all_item.setEnabled( true );
1135 _save_all_item.setEnabled( false );
1139 void buildFileMenu() {
1140 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
1141 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
1142 _file_jmenu.addSeparator();
1143 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
1144 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
1145 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
1147 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
1148 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
1149 if ( AptxUtil.canWriteFormat( "gif" ) ) {
1150 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
1152 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
1153 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
1155 _file_jmenu.addSeparator();
1156 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
1157 _file_jmenu.addSeparator();
1158 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
1159 customizeJMenuItem( _save_item );
1160 customizeJMenuItem( _write_to_pdf_item );
1161 customizeJMenuItem( _write_to_png_item );
1162 customizeJMenuItem( _write_to_jpg_item );
1163 customizeJMenuItem( _write_to_gif_item );
1164 customizeJMenuItem( _write_to_tif_item );
1165 customizeJMenuItem( _write_to_bmp_item );
1166 customizeJMenuItem( _print_item );
1167 customizeJMenuItem( _exit_item );
1168 _jmenubar.add( _file_jmenu );
1171 void buildFontSizeMenu() {
1172 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
1173 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
1174 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
1175 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
1176 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
1177 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
1178 customizeJMenuItem( _super_tiny_fonts_item );
1179 customizeJMenuItem( _tiny_fonts_item );
1180 customizeJMenuItem( _small_fonts_item );
1181 customizeJMenuItem( _medium_fonts_item );
1182 customizeJMenuItem( _large_fonts_item );
1183 _jmenubar.add( _font_size_menu );
1186 void buildHelpMenu() {
1187 _help_jmenu = createMenu( "Help", getConfiguration() );
1188 _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
1189 _help_jmenu.addSeparator();
1190 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
1191 _help_jmenu.add( _mailing_list_item = new JMenuItem( "Mailing List" ) );
1192 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
1193 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
1194 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
1195 _help_jmenu.addSeparator();
1196 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
1197 customizeJMenuItem( _help_item );
1198 customizeJMenuItem( _website_item );
1199 customizeJMenuItem( _mailing_list_item );
1200 customizeJMenuItem( _phyloxml_website_item );
1201 customizeJMenuItem( _aptx_ref_item );
1202 customizeJMenuItem( _phyloxml_ref_item );
1203 customizeJMenuItem( _about_item );
1204 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
1205 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
1206 _jmenubar.add( _help_jmenu );
1209 void buildTypeMenu() {
1210 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
1211 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
1212 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
1213 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
1214 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
1215 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
1216 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
1217 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
1218 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
1219 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
1220 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
1221 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
1222 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
1223 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
1224 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
1225 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
1226 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
1227 _triangular_type_cbmi.setToolTipText( "not suitable for phylograms" );
1228 _curved_type_cbmi.setToolTipText( "not suitable for phylograms" );
1229 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1230 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1231 initializeTypeMenu( getOptions() );
1232 _jmenubar.add( _type_menu );
1235 void buildViewMenu() {
1236 _view_jmenu = createMenu( "View", getConfiguration() );
1237 _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
1238 _view_jmenu.addSeparator();
1239 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
1240 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
1241 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
1242 customizeJMenuItem( _display_basic_information_item );
1243 customizeJMenuItem( _view_as_NH_item );
1244 customizeJMenuItem( _view_as_XML_item );
1245 customizeJMenuItem( _view_as_nexus_item );
1246 _jmenubar.add( _view_jmenu );
1249 void checkTextFrames() {
1250 if ( _textframes.size() > 5 ) {
1252 if ( _textframes.getFirst() != null ) {
1253 _textframes.getFirst().removeMe();
1256 _textframes.removeFirst();
1259 catch ( final NoSuchElementException e ) {
1265 void choosePdfWidth() {
1266 final String s = ( String ) JOptionPane.showInputDialog( this,
1267 "Please enter the default line width for PDF export.\n"
1268 + "[current value: "
1269 + getOptions().getPrintLineWidth() + "]\n",
1270 "Line Width for PDF Export",
1271 JOptionPane.QUESTION_MESSAGE,
1274 getOptions().getPrintLineWidth() );
1275 if ( !ForesterUtil.isEmpty( s ) ) {
1276 boolean success = true;
1278 final String m_str = s.trim();
1279 if ( !ForesterUtil.isEmpty( m_str ) ) {
1281 f = Float.parseFloat( m_str );
1283 catch ( final Exception ex ) {
1290 if ( success && ( f > 0.0 ) ) {
1291 getOptions().setPrintLineWidth( f );
1297 removeAllTextFrames();
1298 if ( _mainpanel != null ) {
1299 _mainpanel.terminate();
1301 if ( _contentpane != null ) {
1302 _contentpane.removeAll();
1304 setVisible( false );
1309 if ( _mainpanel.getCurrentTreePanel() != null ) {
1310 final Map<String, Integer> present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny());
1311 final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks);
1312 String rank = ( String ) JOptionPane
1313 .showInputDialog( this,
1314 "What rank should the colorization be based on",
1316 JOptionPane.QUESTION_MESSAGE,
1320 if ( !ForesterUtil.isEmpty( rank ) ) {
1321 if ( rank.indexOf( '(' ) > 0 ) {
1322 rank = rank.substring( 0, rank.indexOf( '(' ) ).trim();
1324 _mainpanel.getCurrentTreePanel().colorRank( rank );
1330 if ( _mainpanel.getCurrentTreePanel() != null ) {
1331 _mainpanel.getCurrentTreePanel().confColor();
1335 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
1336 if ( item != null ) {
1337 item.setFont( MainFrame.menu_font );
1338 if ( !getConfiguration().isUseNativeUI() ) {
1339 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1340 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1342 item.setSelected( is_selected );
1343 item.addActionListener( this );
1347 JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
1348 if ( jmi != null ) {
1349 jmi.setFont( MainFrame.menu_font );
1350 if ( !getConfiguration().isUseNativeUI() ) {
1351 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1352 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
1354 jmi.addActionListener( this );
1359 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1360 if ( item != null ) {
1361 item.setFont( MainFrame.menu_font );
1362 if ( !getConfiguration().isUseNativeUI() ) {
1363 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1364 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1366 item.setSelected( is_selected );
1367 item.addActionListener( this );
1371 void displayBasicInformation( final File treefile ) {
1372 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1373 String title = "Basic Information";
1374 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1375 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
1377 showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
1381 void exceptionOccuredDuringOpenFile( final Exception e ) {
1383 _mainpanel.getCurrentTreePanel().setArrowCursor();
1385 catch ( final Exception ex ) {
1388 JOptionPane.showMessageDialog( this,
1389 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1390 "Error during File|Open",
1391 JOptionPane.ERROR_MESSAGE );
1394 void executeGSDI() {
1395 if ( !isOKforSDI( false, true ) ) {
1398 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1399 JOptionPane.showMessageDialog( this,
1400 "Gene tree is not rooted.",
1401 "Cannot execute GSDI",
1402 JOptionPane.ERROR_MESSAGE );
1405 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1406 gene_tree.setAllNodesToNotCollapse();
1407 gene_tree.recalculateNumberOfExternalDescendants( false );
1409 final Phylogeny species_tree = getSpeciesTree().copy();
1411 gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
1413 catch ( final SDIException e ) {
1414 JOptionPane.showMessageDialog( this,
1415 e.getLocalizedMessage(),
1416 "Error during GSDI",
1417 JOptionPane.ERROR_MESSAGE );
1420 catch ( final Exception e ) {
1421 AptxUtil.unexpectedException( e );
1424 gene_tree.setRerootable( false );
1425 gene_tree.clearHashIdToNodeMap();
1426 gene_tree.recalculateNumberOfExternalDescendants( true );
1427 _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
1428 getMainPanel().getControlPanel().setShowEvents( true );
1430 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1431 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1433 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1435 _mainpanel.getCurrentTreePanel().setEdited( true );
1436 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1437 if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1438 JOptionPane.showMessageDialog( this,
1439 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1440 + "Potential duplications: "
1441 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1442 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1443 + "Stripped gene tree nodes: "
1444 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1445 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1446 + "Number of polytomies in species tree used: " + poly + "\n",
1447 "GSDI successfully completed",
1448 JOptionPane.WARNING_MESSAGE );
1451 JOptionPane.showMessageDialog( this,
1452 "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1453 + "Potential duplications: "
1454 + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1455 + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1456 + "Stripped gene tree nodes: "
1457 + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1458 + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1459 + "Number of polytomies in species tree used: " + poly + "\n",
1460 "GSDI successfully completed",
1461 JOptionPane.INFORMATION_MESSAGE );
1465 void executeGSDIR() {
1466 if ( !isOKforSDI( false, false ) ) {
1469 final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1471 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1472 JOptionPane.showMessageDialog( this,
1473 "Gene tree is not completely binary",
1474 "Cannot execute GSDI",
1475 JOptionPane.ERROR_MESSAGE );
1478 final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1479 gene_tree.setAllNodesToNotCollapse();
1480 gene_tree.recalculateNumberOfExternalDescendants( false );
1482 final Phylogeny species_tree = getSpeciesTree().copy();
1484 gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1486 catch ( final SDIException e ) {
1487 JOptionPane.showMessageDialog( this,
1488 e.getLocalizedMessage(),
1489 "Error during GSDIR",
1490 JOptionPane.ERROR_MESSAGE );
1493 catch ( final Exception e ) {
1494 AptxUtil.unexpectedException( e );
1497 final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1498 result_gene_tree.setRerootable( false );
1499 result_gene_tree.clearHashIdToNodeMap();
1500 result_gene_tree.recalculateNumberOfExternalDescendants( true );
1501 PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1502 _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1503 getMainPanel().getControlPanel().setShowEvents( true );
1505 final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1506 _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1508 _mainpanel.getTabbedPane().setSelectedIndex( selected );
1510 _mainpanel.getCurrentTreePanel().setEdited( true );
1511 final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1512 if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1513 JOptionPane.showMessageDialog( this,
1514 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1515 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1516 + "Stripped gene tree nodes: "
1517 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1518 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1519 + "Number of polytomies in species tree used: " + poly + "\n",
1520 "GSDIR successfully completed",
1521 JOptionPane.WARNING_MESSAGE );
1524 JOptionPane.showMessageDialog( this,
1525 "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1526 + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1527 + "Stripped gene tree nodes: "
1528 + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1529 + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1530 + "Number of polytomies in species tree used: " + poly + "\n",
1531 "GSDIR successfully completed",
1532 JOptionPane.INFORMATION_MESSAGE );
1536 void executeLineageInference() {
1537 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1540 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1541 JOptionPane.showMessageDialog( this,
1542 "Phylogeny is not rooted.",
1543 "Cannot infer ancestral taxonomies",
1544 JOptionPane.ERROR_MESSAGE );
1547 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1548 _mainpanel.getCurrentTreePanel(),
1549 _mainpanel.getCurrentPhylogeny()
1551 new Thread( inferrer ).start();
1554 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
1555 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
1556 JOptionPane.showMessageDialog( this,
1557 "Gene tree and species tree have no species in common.",
1559 JOptionPane.ERROR_MESSAGE );
1562 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
1563 JOptionPane.showMessageDialog( this,
1564 "Gene tree and species tree have only one species in common.",
1566 JOptionPane.ERROR_MESSAGE );
1574 ControlPanel getControlPanel() {
1575 return getMainPanel().getControlPanel();
1578 File getCurrentDir() {
1579 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1580 if ( ForesterUtil.isWindows() ) {
1582 _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1584 catch ( final Exception e ) {
1585 _current_dir = null;
1589 if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1590 if ( System.getProperty( "user.home" ) != null ) {
1591 _current_dir = new File( System.getProperty( "user.home" ) );
1593 else if ( System.getProperty( "user.dir" ) != null ) {
1594 _current_dir = new File( System.getProperty( "user.dir" ) );
1597 return _current_dir;
1600 TreePanel getCurrentTreePanel() {
1601 return getMainPanel().getCurrentTreePanel();
1604 JMenu getHelpMenu() {
1608 JCheckBoxMenuItem getlabelDirectionCbmi() {
1609 return _label_direction_cbmi;
1612 JMenuBar getMenuBarOfMainFrame() {
1616 final Phylogeny getSpeciesTree() {
1617 return _species_tree;
1620 void initializeTypeMenu( final Options options ) {
1621 setTypeMenuToAllUnselected();
1622 switch ( options.getPhylogenyGraphicsType() ) {
1624 _convex_type_cbmi.setSelected( true );
1627 _curved_type_cbmi.setSelected( true );
1630 _euro_type_cbmi.setSelected( true );
1633 _rounded_type_cbmi.setSelected( true );
1636 _triangular_type_cbmi.setSelected( true );
1639 _unrooted_type_cbmi.setSelected( true );
1642 _circular_type_cbmi.setSelected( true );
1645 _rectangular_type_cbmi.setSelected( true );
1650 boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1651 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1654 else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
1655 JOptionPane.showMessageDialog( this,
1656 "No species tree loaded",
1657 "Cannot execute GSDI",
1658 JOptionPane.ERROR_MESSAGE );
1661 else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
1662 JOptionPane.showMessageDialog( this,
1663 "Species tree is not completely binary",
1664 "Cannot execute GSDI",
1665 JOptionPane.ERROR_MESSAGE );
1668 else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1669 JOptionPane.showMessageDialog( this,
1670 "Gene tree is not completely binary",
1671 "Cannot execute GSDI",
1672 JOptionPane.ERROR_MESSAGE );
1680 boolean isSubtreeDisplayed() {
1681 if ( getCurrentTreePanel() != null ) {
1682 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1684 .showMessageDialog( this,
1685 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1686 "Operation can not be exectuted on a sub-tree",
1687 JOptionPane.WARNING_MESSAGE );
1694 void midpointRoot() {
1695 if ( _mainpanel.getCurrentTreePanel() != null ) {
1696 _mainpanel.getCurrentTreePanel().midpointRoot();
1700 void readPhylogeniesFromWebservice( final int i ) {
1701 final UrlTreeReader reader = new UrlTreeReader( this, i );
1702 new Thread( reader ).start();
1705 void removeAllTextFrames() {
1706 for( final TextFrame tf : _textframes ) {
1711 _textframes.clear();
1714 void resetSearch() {
1715 getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
1716 getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
1717 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
1718 getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
1719 getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
1720 getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
1721 getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
1722 getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
1723 getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
1724 getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
1725 getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
1726 getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
1729 void setConfiguration( final Configuration configuration ) {
1730 _configuration = configuration;
1733 void setCurrentDir( final File current_dir ) {
1734 _current_dir = current_dir;
1737 void setInferenceManager( final InferenceManager i ) {
1738 _inference_manager = i;
1741 void setOptions( final Options options ) {
1745 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1746 setTypeMenuToAllUnselected();
1749 _circular_type_cbmi.setSelected( true );
1752 _convex_type_cbmi.setSelected( true );
1755 _curved_type_cbmi.setSelected( true );
1758 _euro_type_cbmi.setSelected( true );
1761 _rounded_type_cbmi.setSelected( true );
1764 _rectangular_type_cbmi.setSelected( true );
1767 _triangular_type_cbmi.setSelected( true );
1770 _unrooted_type_cbmi.setSelected( true );
1773 throw new IllegalArgumentException( "unknown type: " + type );
1777 final void setSpeciesTree( final Phylogeny species_tree ) {
1778 _species_tree = species_tree;
1781 void setTypeMenuToAllUnselected() {
1782 _convex_type_cbmi.setSelected( false );
1783 _curved_type_cbmi.setSelected( false );
1784 _euro_type_cbmi.setSelected( false );
1785 _rounded_type_cbmi.setSelected( false );
1786 _triangular_type_cbmi.setSelected( false );
1787 _rectangular_type_cbmi.setSelected( false );
1788 _unrooted_type_cbmi.setSelected( false );
1789 _circular_type_cbmi.setSelected( false );
1792 void switchColors() {
1793 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
1794 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1795 csc.setVisible( true );
1799 if ( _mainpanel.getCurrentTreePanel() != null ) {
1800 _mainpanel.getCurrentTreePanel().taxColor();
1804 void typeChanged( final Object o ) {
1805 updateTypeCheckboxes( getOptions(), o );
1806 updateOptions( getOptions() );
1807 if ( getCurrentTreePanel() != null ) {
1808 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1809 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1810 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1811 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1812 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1813 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1814 getCurrentTreePanel().getControlPanel().showWhole();
1816 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1817 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1820 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1822 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1823 updateScreenTextAntialias( getMainPanel().getTreePanels() );
1824 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1825 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1826 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1829 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1835 void updateOptions( final Options options ) {
1836 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1837 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1838 && _background_gradient_cbmi.isSelected() );
1839 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1840 options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1841 && _show_annotation_ref_source.isSelected() );
1842 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1843 && _abbreviate_scientific_names.isSelected() );
1844 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1845 && _color_labels_same_as_parent_branch.isSelected() );
1846 options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1847 && _show_default_node_shapes_internal_cbmi.isSelected() );
1848 options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1849 && _show_default_node_shapes_external_cbmi.isSelected() );
1850 options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1851 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1852 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1853 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1855 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1856 options.setCladogramType( CLADOGRAM_TYPE.LINED_UP );
1858 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1859 && _search_case_senstive_cbmi.isSelected() );
1860 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1861 options.setShowScale( _show_scale_cbmi.isSelected() );
1863 if ( _label_direction_cbmi != null ) {
1864 if ( _label_direction_cbmi.isSelected() ) {
1865 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1868 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1871 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1872 options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1873 && _show_confidence_stddev_cbmi.isSelected() );
1874 if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1875 options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1877 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1878 if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1879 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1880 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1882 else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1883 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1884 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1887 options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1889 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1890 && _print_black_and_white_cbmi.isSelected() );
1891 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1892 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1893 if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
1894 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1896 else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
1897 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1899 else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
1900 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1902 else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
1903 options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1905 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1906 && _replace_underscores_cbmi.isSelected() );
1907 options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
1908 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
1909 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1910 && _search_whole_words_only_cbmi.isSelected() );
1911 options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
1912 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1913 && _inverse_search_result_cbmi.isSelected() );
1914 if ( _graphics_export_visible_only_cbmi != null ) {
1915 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1917 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1918 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1920 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1921 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1923 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1924 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1926 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1927 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1929 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1930 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1932 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1933 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1935 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1936 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1938 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1939 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1941 if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1942 options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1944 if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1945 options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1947 if ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) {
1948 options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_cbmi.isSelected() );
1950 if ( ( _parse_beast_style_extended_nexus_tags_cbmi != null ) && _parse_beast_style_extended_nexus_tags_cbmi.isEnabled() ) {
1951 options.setParseBeastStyleExtendedNexusTags(_parse_beast_style_extended_nexus_tags_cbmi.isSelected() );
1953 if ( ( _collapsed_with_average_height_cbmi != null ) && _collapsed_with_average_height_cbmi.isEnabled() ) {
1954 options.setCollapsedWithAverageHeigh(_collapsed_with_average_height_cbmi.isSelected() );
1956 if ( ( _show_abbreviated_labels_for_collapsed_nodes_cbmi != null ) && _show_abbreviated_labels_for_collapsed_nodes_cbmi.isEnabled() ) {
1957 options.setShowAbbreviatedLabelsForCollapsedNodes(_show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() );
1962 void updateTypeCheckboxes( final Options options, final Object o ) {
1963 setTypeMenuToAllUnselected();
1964 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1967 void viewAsNexus() {
1968 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1969 String title = "Nexus";
1970 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1971 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1973 showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1979 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1980 String title = "New Hampshire";
1981 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1982 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1984 showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
1985 .getNhConversionSupportValueStyle() ),
1991 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1992 String title = "phyloXML";
1993 if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1994 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1996 showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
2000 private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {
2001 switch ( op.getExtDescNodeDataToReturn() ) {
2003 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
2006 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
2008 case DOMAINS_COLLAPSED_PER_PROTEIN:
2009 op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
2011 case SEQ_ANNOTATIONS:
2012 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
2015 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
2017 case SEQUENCE_MOL_SEQ_FASTA:
2018 if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )
2019 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )
2020 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
2021 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )
2022 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )
2023 && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {
2024 op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
2027 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
2031 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
2036 * Display the about box.
2039 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" );
2040 about.append( "Copyright (C) 2016 Christian M Zmasek\n" );
2041 about.append( "All Rights Reserved\n" );
2042 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
2043 about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" );
2044 about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
2046 if ( _configuration.isCouldReadConfigFile() ) {
2047 about.append( "Using configuration file: " + _configuration.config_filename + "\n" );
2050 about.append( "Not using a configuration file\n" );
2053 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
2054 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
2055 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
2056 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
2058 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
2059 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
2060 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
2061 + ForesterUtil.OS_VERSION + "]\n" );
2063 final Runtime rt = java.lang.Runtime.getRuntime();
2064 final long free_memory = rt.freeMemory() / 1000000;
2065 final long total_memory = rt.totalMemory() / 1000000;
2066 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
2067 about.append( "[locale: " + Locale.getDefault() + "]\n" );
2068 about.append( "References:\n" );
2069 about.append( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" );
2070 about.append( "For more information & download:\n" );
2071 about.append( AptxConstants.APTX_WEB_SITE + "\n" );
2072 about.append( "Documentation:\n" );
2073 about.append( AptxConstants.APTX_DOC_SITE + "\n" );
2074 about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL );
2075 JOptionPane.showMessageDialog( null, about, AptxConstants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
2078 static void chooseNodeSize( final Options options, final Component parent ) {
2079 final String s = ( String ) JOptionPane.showInputDialog( parent,
2080 "Please enter the default size for node shapes.\n"
2081 + "[current value: "
2082 + options.getDefaultNodeShapeSize() + "]\n",
2084 JOptionPane.QUESTION_MESSAGE,
2087 options.getDefaultNodeShapeSize() );
2088 if ( !ForesterUtil.isEmpty( s ) ) {
2089 boolean success = true;
2091 final String m_str = s.trim();
2092 if ( !ForesterUtil.isEmpty( m_str ) ) {
2094 m = Double.parseDouble( m_str );
2096 catch ( final Exception ex ) {
2103 if ( success && ( m >= 0.0 ) ) {
2104 final short size = ForesterUtil.roundToShort( m );
2105 if ( size >= 0.0 ) {
2106 options.setDefaultNodeShapeSize( size );
2112 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
2113 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
2116 static JMenu createMenu( final String title, final Configuration conf ) {
2117 final JMenu jmenu = new JMenu( title );
2118 if ( !conf.isUseNativeUI() ) {
2119 jmenu.setFont( MainFrame.menu_font );
2120 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
2121 jmenu.setForeground( conf.getGuiMenuTextColor() );
2126 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
2127 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
2128 if ( !configuration.isUseNativeUI() ) {
2129 label.setBackground( configuration.getGuiMenuBackgroundColor() );
2130 label.setForeground( configuration.getGuiMenuTextColor() );
2131 label.setOpaque( true );
2133 label.setSelected( false );
2134 label.setEnabled( false );
2138 static void cycleNodeFill( final Options op ) {
2139 switch ( op.getDefaultNodeFill() ) {
2141 op.setDefaultNodeFill( NodeFill.SOLID );
2144 op.setDefaultNodeFill( NodeFill.GRADIENT );
2147 op.setDefaultNodeFill( NodeFill.NONE );
2150 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
2154 static void cycleNodeShape( final Options op ) {
2155 switch ( op.getDefaultNodeShape() ) {
2157 op.setDefaultNodeShape( NodeShape.RECTANGLE );
2160 op.setDefaultNodeShape( NodeShape.CIRCLE );
2163 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
2167 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
2168 switch ( op.getOvPlacement() ) {
2170 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
2173 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
2176 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
2179 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
2182 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
2184 if ( tree_panel != null ) {
2185 tree_panel.updateOvSettings();
2189 static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {
2191 tp.setArrowCursor();
2193 catch ( final Exception ex ) {
2196 JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
2199 static void print( final TreePanel tp, final Options op, final Component c ) {
2200 if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {
2203 final String job_name = AptxConstants.PRG_NAME;
2204 boolean error = false;
2205 String printer_name = null;
2207 printer_name = Printer.print( tp, job_name );
2209 catch ( final Exception e ) {
2211 JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2213 if ( !error && ( printer_name != null ) ) {
2214 String msg = "Printing data sent to printer";
2215 if ( printer_name.length() > 1 ) {
2216 msg += " [" + printer_name + "]";
2218 JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2220 if ( !op.isPrintUsingActualSize() ) {
2221 tp.getControlPanel().showWhole();
2225 static void printPhylogenyToPdf( final String file_name,
2228 final Component comp ) {
2230 String pdf_written_to = "";
2231 boolean error = false;
2233 if ( opts.isPrintUsingActualSize() ) {
2234 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() );
2240 catch ( final IOException e ) {
2242 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2245 if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2246 JOptionPane.showMessageDialog( comp,
2247 "Wrote PDF to: " + pdf_written_to,
2249 JOptionPane.INFORMATION_MESSAGE );
2252 JOptionPane.showMessageDialog( comp,
2253 "There was an unknown problem when attempting to write to PDF file: \""
2256 JOptionPane.ERROR_MESSAGE );
2259 if ( !opts.isPrintUsingActualSize() ) {
2260 tp.getControlPanel().showWhole();
2264 static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
2265 if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
2266 mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );
2269 mi.setText( "Cycle Node Return Data..." );
2273 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
2274 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
2275 mi.setText( "Cycle Node Shape Fill Type... (current: "
2276 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
2279 mi.setText( "Cycle Node Shape Fill Type..." );
2283 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
2284 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
2285 mi.setText( "Cycle Node Shape Fill Type... (current: "
2286 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
2289 mi.setText( "Cycle Node Shape Fill Type..." );
2293 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
2294 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
2295 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
2298 mi.setText( "Cycle Overview Placement..." );
2302 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
2303 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
2304 mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
2308 mi.setText( "Select Color Scheme..." );
2312 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
2313 mi.setText( "Select Default Font... (current: " + font_desc + ")" );
2316 static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2317 mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2320 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
2321 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
2322 mi.setEnabled( true );
2324 else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
2325 mi.setEnabled( true );
2328 mi.setEnabled( false );
2330 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
2333 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
2334 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
2337 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
2338 for( final TreePanel tree_panel : treepanels ) {
2339 tree_panel.setTextAntialias();
2343 static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) {
2345 final PhylogenyWriter writer = new PhylogenyWriter();
2346 writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file );
2348 catch ( final Exception e ) {
2350 exceptionOccuredDuringSaveAs( e, tp, tp );
2355 static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) {
2357 final PhylogenyWriter writer = new PhylogenyWriter();
2358 writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() );
2360 catch ( final Exception e ) {
2362 exceptionOccuredDuringSaveAs( e, tp, tp );
2367 static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) {
2369 final PhylogenyWriter writer = new PhylogenyWriter();
2370 writer.toPhyloXML( file, tp.getPhylogeny(), 0 );
2372 catch ( final Exception e ) {
2374 exceptionOccuredDuringSaveAs( e, tp, tp );
2379 static void writePhylogenyToGraphicsFile( final String file_name,
2380 final GraphicsExportType type,
2382 final Component comp,
2383 final Container contentpane ) {
2384 mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),
2385 mp.getCurrentTreePanel().getHeight() );
2386 String file_written_to = "";
2387 boolean error = false;
2389 file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
2390 mp.getCurrentTreePanel().getWidth(),
2391 mp.getCurrentTreePanel().getHeight(),
2392 mp.getCurrentTreePanel(),
2393 mp.getControlPanel(),
2397 catch ( final IOException e ) {
2399 JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2402 if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
2403 JOptionPane.showMessageDialog( comp,
2404 "Wrote image to: " + file_written_to,
2406 JOptionPane.INFORMATION_MESSAGE );
2409 JOptionPane.showMessageDialog( comp,
2410 "There was an unknown problem when attempting to write to an image file: \""
2413 JOptionPane.ERROR_MESSAGE );
2416 contentpane.repaint();
2419 static File writeToFile( final Phylogeny t,
2421 final JFileChooser save_filechooser,
2422 final File current_dir,
2423 final Container contentpane,
2424 final Component comp ) {
2425 File new_file = null;
2429 String initial_filename = null;
2430 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
2432 initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath();
2434 catch ( final IOException e ) {
2435 initial_filename = null;
2438 if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2439 save_filechooser.setSelectedFile( new File( initial_filename ) );
2442 save_filechooser.setSelectedFile( new File( "" ) );
2444 final File my_dir = current_dir;
2445 if ( my_dir != null ) {
2446 save_filechooser.setCurrentDirectory( my_dir );
2448 final int result = save_filechooser.showSaveDialog( contentpane );
2449 final File file = save_filechooser.getSelectedFile();
2450 new_file = save_filechooser.getCurrentDirectory();
2451 boolean exception = false;
2452 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2453 if ( file.exists() ) {
2454 final int i = JOptionPane.showConfirmDialog( comp,
2455 file + " already exists.\nOverwrite?",
2457 JOptionPane.OK_CANCEL_OPTION,
2458 JOptionPane.QUESTION_MESSAGE );
2459 if ( i != JOptionPane.OK_OPTION ) {
2463 final File to = new File( file.getAbsoluteFile().toString() + AptxConstants.BACKUP_FILE_SUFFIX );
2465 ForesterUtil.copyFile( file, to );
2467 catch ( final Exception e ) {
2468 JOptionPane.showMessageDialog( comp,
2469 "Failed to create backup copy " + to,
2470 "Failed to Create Backup Copy",
2471 JOptionPane.WARNING_MESSAGE );
2476 catch ( final Exception e ) {
2477 JOptionPane.showMessageDialog( comp,
2478 "Failed to delete: " + file,
2480 JOptionPane.WARNING_MESSAGE );
2484 if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) {
2485 exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
2487 else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
2488 exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
2490 else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
2491 exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
2495 final String file_name = file.getName().trim().toLowerCase();
2496 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2497 || file_name.endsWith( ".tree" ) ) {
2498 exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
2500 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2501 exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
2505 exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );
2509 mp.setTitleOfSelectedTab( file.getName() );
2510 mp.getCurrentTreePanel().setTreeFile( file );
2511 mp.getCurrentTreePanel().setEdited( false );
2517 static File writeToGraphicsFile( final Phylogeny t,
2518 final GraphicsExportType type,
2520 final JFileChooser writetographics_filechooser,
2521 final Component component,
2522 final Container contentpane,
2523 final File current_dir ) {
2524 File new_dir = null;
2525 if ( ( t == null ) || t.isEmpty() ) {
2528 String initial_filename = "";
2529 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
2530 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
2532 if ( initial_filename.indexOf( '.' ) > 0 ) {
2533 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2535 initial_filename = initial_filename + "." + type;
2536 writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2537 final File my_dir = current_dir;
2538 if ( my_dir != null ) {
2539 writetographics_filechooser.setCurrentDirectory( my_dir );
2541 final int result = writetographics_filechooser.showSaveDialog( contentpane );
2542 File file = writetographics_filechooser.getSelectedFile();
2543 //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );
2544 new_dir = writetographics_filechooser.getCurrentDirectory();
2545 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2546 if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2547 file = new File( file.toString() + "." + type );
2549 if ( file.exists() ) {
2550 final int i = JOptionPane.showConfirmDialog( component,
2551 file + " already exists. Overwrite?",
2553 JOptionPane.OK_CANCEL_OPTION,
2554 JOptionPane.WARNING_MESSAGE );
2555 if ( i != JOptionPane.OK_OPTION ) {
2562 catch ( final Exception e ) {
2563 JOptionPane.showMessageDialog( component,
2564 "Failed to delete: " + file,
2566 JOptionPane.WARNING_MESSAGE );
2570 writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );
2575 static File writeToPdf( final Phylogeny t,
2577 final JFileChooser writetopdf_filechooser,
2578 final File curr_dir,
2579 final Container contentpane,
2580 final Component component ) {
2581 if ( ( t == null ) || t.isEmpty() ) {
2584 String initial_filename = "";
2585 if ( mp.getCurrentTreePanel().getTreeFile() != null ) {
2586 initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();
2588 if ( initial_filename.indexOf( '.' ) > 0 ) {
2589 initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2591 initial_filename = initial_filename + ".pdf";
2592 writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2593 final File my_dir = curr_dir;
2594 if ( my_dir != null ) {
2595 writetopdf_filechooser.setCurrentDirectory( my_dir );
2597 final int result = writetopdf_filechooser.showSaveDialog( contentpane );
2598 File file = writetopdf_filechooser.getSelectedFile();
2599 // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );
2600 final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();
2601 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2602 if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2603 file = new File( file.toString() + ".pdf" );
2605 if ( file.exists() ) {
2606 final int i = JOptionPane.showConfirmDialog( component,
2607 file + " already exists. Overwrite?",
2609 JOptionPane.OK_CANCEL_OPTION,
2610 JOptionPane.WARNING_MESSAGE );
2611 if ( i != JOptionPane.OK_OPTION ) {
2615 printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );
2617 return new_current_dir;
2621 class DefaultFilter extends FileFilter {
2624 public boolean accept( final File f ) {
2625 final String file_name = f.getName().trim().toLowerCase();
2626 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2627 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2628 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2629 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2630 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2631 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2632 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2633 || file_name.endsWith( ".con" ) || f.isDirectory();
2637 public String getDescription() {
2638 return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2642 class GraphicsFileFilter extends FileFilter {
2645 public boolean accept( final File f ) {
2646 final String file_name = f.getName().trim().toLowerCase();
2647 return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2648 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2652 public String getDescription() {
2653 return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2657 class MsaFileFilter extends FileFilter {
2660 public boolean accept( final File f ) {
2661 final String file_name = f.getName().trim().toLowerCase();
2662 return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2663 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2667 public String getDescription() {
2668 return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2672 class NexusFilter extends FileFilter {
2675 public boolean accept( final File f ) {
2676 final String file_name = f.getName().trim().toLowerCase();
2677 return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2678 || file_name.endsWith( ".tre" ) || f.isDirectory();
2682 public String getDescription() {
2683 return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2687 class NHFilter extends FileFilter {
2690 public boolean accept( final File f ) {
2691 final String file_name = f.getName().trim().toLowerCase();
2692 return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2693 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2694 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2699 public String getDescription() {
2700 return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2704 class NHXFilter extends FileFilter {
2707 public boolean accept( final File f ) {
2708 final String file_name = f.getName().trim().toLowerCase();
2709 return file_name.endsWith( ".nhx" ) || f.isDirectory();
2713 public String getDescription() {
2714 return "NHX files (*.nhx) [deprecated]";
2718 class PdfFilter extends FileFilter {
2721 public boolean accept( final File f ) {
2722 return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2726 public String getDescription() {
2727 return "PDF files (*.pdf)";
2731 class SequencesFileFilter extends FileFilter {
2734 public boolean accept( final File f ) {
2735 final String file_name = f.getName().trim().toLowerCase();
2736 return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2737 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2741 public String getDescription() {
2742 return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2746 class TolFilter extends FileFilter {
2749 public boolean accept( final File f ) {
2750 final String file_name = f.getName().trim().toLowerCase();
2751 return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2752 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2756 public String getDescription() {
2757 return "Tree of Life files (*.tol, *.tolxml)";
2761 class XMLFilter extends FileFilter {
2764 public boolean accept( final File f ) {
2765 final String file_name = f.getName().trim().toLowerCase();
2766 return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2767 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2771 public String getDescription() {
2772 return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";