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: www.phylosoft.org/forester
25 package org.forester.archaeopteryx;
27 import java.awt.Component;
28 import java.awt.Container;
30 import java.awt.event.ActionEvent;
31 import java.awt.event.ActionListener;
32 import java.io.IOException;
33 import java.util.List;
34 import java.util.Locale;
37 import javax.swing.JApplet;
38 import javax.swing.JCheckBoxMenuItem;
39 import javax.swing.JFrame;
40 import javax.swing.JMenu;
41 import javax.swing.JMenuBar;
42 import javax.swing.JMenuItem;
43 import javax.swing.JOptionPane;
44 import javax.swing.JRadioButtonMenuItem;
46 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
47 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.phylogeny.Phylogeny;
50 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
51 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
52 import org.forester.util.ForesterConstants;
53 import org.forester.util.ForesterUtil;
55 public abstract class MainFrame extends JFrame implements ActionListener {
57 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
58 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
59 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
60 private static final long serialVersionUID = 3655000897845508358L;
61 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
64 static final String TYPE_MENU_HEADER = "Type";
65 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
66 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
67 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
68 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
69 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
70 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
71 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
72 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
73 static final String OPTIONS_HEADER = "Options";
74 static final String SEARCH_SUBHEADER = "Search:";
75 static final String DISPLAY_SUBHEADER = "Display:";
76 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
77 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
78 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
79 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
80 static final String DISPLAY_SCALE_LABEL = "Display Scale";
81 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
82 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
83 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
84 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
85 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
86 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
87 static final String BG_GRAD_LABEL = "Background Color Gradient";
88 static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Shapes";
89 static final String SHOW_OVERVIEW_LABEL = "Show Overview";
90 static final String FONT_SIZE_MENU_LABEL = "Font Size";
91 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
92 static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
93 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";
94 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
95 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
96 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
97 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
98 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
103 JMenu _options_jmenu;
104 JMenu _font_size_menu;
106 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
108 JMenuItem _open_item;
109 JMenuItem _open_url_item;
110 JMenuItem _save_item;
111 JMenuItem _save_all_item;
112 JMenuItem _close_item;
113 JMenuItem _exit_item;
116 JMenuItem _midpoint_root_item;
117 JMenuItem _taxcolor_item;
118 JMenuItem _confcolor_item;
119 JMenuItem _color_rank_jmi;
120 JMenuItem _infer_common_sn_names_item;
121 JMenuItem _collapse_species_specific_subtrees;
122 JMenuItem _collapse_below_threshold; //TODO implememt me
123 JMenuItem _obtain_detailed_taxonomic_information_jmi;
124 JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
125 JMenuItem _obtain_uniprot_seq_information_jmi;
126 JMenuItem _move_node_names_to_tax_sn_jmi;
127 JMenuItem _move_node_names_to_seq_names_jmi;
128 JMenuItem _extract_tax_code_from_node_names_jmi;
130 JMenuItem _super_tiny_fonts_item;
131 JMenuItem _tiny_fonts_item;
132 JMenuItem _small_fonts_item;
133 JMenuItem _medium_fonts_item;
134 JMenuItem _large_fonts_item;
136 // _ screen and print
137 JMenuItem _choose_font_mi;
138 JMenuItem _switch_colors_mi;
139 JCheckBoxMenuItem _label_direction_cbmi;
141 JCheckBoxMenuItem _screen_antialias_cbmi;
142 JCheckBoxMenuItem _background_gradient_cbmi;
143 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
144 JRadioButtonMenuItem _uniform_cladograms_rbmi;
145 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
146 JCheckBoxMenuItem _show_branch_length_values_cbmi;
147 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
148 JCheckBoxMenuItem _show_overview_cbmi;
149 JCheckBoxMenuItem _show_domain_labels;
150 JCheckBoxMenuItem _abbreviate_scientific_names;
151 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
152 JMenuItem _overview_placment_mi;
153 JMenuItem _choose_minimal_confidence_mi;
154 JCheckBoxMenuItem _show_default_node_shapes_cbmi;
155 JMenuItem _cycle_node_shape_mi;
156 JMenuItem _cycle_node_fill_mi;
157 JMenuItem _choose_node_size_mi;
158 JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
160 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
161 JCheckBoxMenuItem _antialias_print_cbmi;
162 JCheckBoxMenuItem _print_black_and_white_cbmi;
163 JCheckBoxMenuItem _print_using_actual_size_cbmi;
164 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
165 JMenuItem _print_size_mi;
166 JMenuItem _choose_pdf_width_mi;
168 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
169 JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
170 JCheckBoxMenuItem _replace_underscores_cbmi;
172 JCheckBoxMenuItem _search_case_senstive_cbmi;
173 JCheckBoxMenuItem _search_whole_words_only_cbmi;
174 JCheckBoxMenuItem _inverse_search_result_cbmi;
177 JCheckBoxMenuItem _rectangular_type_cbmi;
178 JCheckBoxMenuItem _triangular_type_cbmi;
179 JCheckBoxMenuItem _curved_type_cbmi;
180 JCheckBoxMenuItem _convex_type_cbmi;
181 JCheckBoxMenuItem _euro_type_cbmi;
182 JCheckBoxMenuItem _rounded_type_cbmi;
183 JCheckBoxMenuItem _unrooted_type_cbmi;
184 JCheckBoxMenuItem _circular_type_cbmi;
185 // view as text menu:
186 JMenuItem _view_as_NH_item;
187 JMenuItem _view_as_NHX_item;
188 JMenuItem _view_as_XML_item;
189 JMenuItem _view_as_nexus_item;
190 JMenuItem _display_basic_information_item;
192 JMenuItem _about_item;
193 JMenuItem _help_item;
194 JMenuItem _website_item;
195 JMenuItem _phyloxml_website_item;
196 JMenuItem _phyloxml_ref_item;
197 JMenuItem _aptx_ref_item;
198 // Handy pointers to child components:
199 MainPanel _mainpanel;
200 Container _contentpane;
201 TextFrame _textframe;
202 Configuration _configuration;
203 JMenuItem _remove_branch_color_item;
207 // Empty constructor.
213 public void actionPerformed( final ActionEvent e ) {
214 final Object o = e.getSource();
215 boolean is_applet = false;
216 JApplet applet = null;
217 if ( getCurrentTreePanel() != null ) {
218 is_applet = getCurrentTreePanel().isApplet();
220 applet = getCurrentTreePanel().obtainApplet();
223 if ( o == _open_url_item ) {
224 readPhylogeniesFromURL();
226 else if ( o == _exit_item ) {
229 else if ( o == _taxcolor_item ) {
232 else if ( o == _confcolor_item ) {
235 else if ( o == _color_rank_jmi ) {
238 else if ( o == _infer_common_sn_names_item ) {
239 if ( isSubtreeDisplayed() ) {
242 if ( getCurrentTreePanel() != null ) {
243 getCurrentTreePanel().inferCommonPartOfScientificNames();
246 else if ( o == _collapse_species_specific_subtrees ) {
247 if ( isSubtreeDisplayed() ) {
250 if ( getCurrentTreePanel() != null ) {
251 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
254 else if ( o == _remove_branch_color_item ) {
255 if ( isSubtreeDisplayed() ) {
258 removeBranchColors();
260 else if ( o == _midpoint_root_item ) {
261 if ( isSubtreeDisplayed() ) {
266 else if ( o == _switch_colors_mi ) {
269 else if ( o == _display_basic_information_item ) {
270 displayBasicInformation();
272 else if ( o == _view_as_NH_item ) {
275 else if ( o == _view_as_NHX_item ) {
278 else if ( o == _view_as_XML_item ) {
281 else if ( o == _view_as_nexus_item ) {
284 else if ( o == _super_tiny_fonts_item ) {
285 if ( getCurrentTreePanel() != null ) {
286 getCurrentTreePanel().setSuperTinyFonts();
287 getCurrentTreePanel().repaint();
290 else if ( o == _tiny_fonts_item ) {
291 if ( getCurrentTreePanel() != null ) {
292 getCurrentTreePanel().setTinyFonts();
293 getCurrentTreePanel().repaint();
296 else if ( o == _small_fonts_item ) {
297 if ( getCurrentTreePanel() != null ) {
298 getCurrentTreePanel().setSmallFonts();
299 getCurrentTreePanel().repaint();
302 else if ( o == _medium_fonts_item ) {
303 if ( getCurrentTreePanel() != null ) {
304 getCurrentTreePanel().setMediumFonts();
305 getCurrentTreePanel().repaint();
308 else if ( o == _large_fonts_item ) {
309 if ( getCurrentTreePanel() != null ) {
310 getCurrentTreePanel().setLargeFonts();
311 getCurrentTreePanel().repaint();
314 else if ( o == _choose_font_mi ) {
317 else if ( o == _choose_minimal_confidence_mi ) {
318 chooseMinimalConfidence();
320 else if ( o == _choose_node_size_mi ) {
321 chooseNodeSize( getOptions(), this );
323 else if ( o == _overview_placment_mi ) {
324 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
326 else if ( o == _cycle_node_fill_mi ) {
327 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
329 else if ( o == _cycle_node_shape_mi ) {
330 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
332 else if ( o == _screen_antialias_cbmi ) {
333 updateOptions( getOptions() );
334 updateScreenTextAntialias( getMainPanel().getTreePanels() );
336 else if ( o == _background_gradient_cbmi ) {
337 updateOptions( getOptions() );
339 else if ( o == _show_domain_labels ) {
340 updateOptions( getOptions() );
342 else if ( o == _abbreviate_scientific_names ) {
343 updateOptions( getOptions() );
345 else if ( o == _color_labels_same_as_parent_branch ) {
346 updateOptions( getOptions() );
348 else if ( o == _show_default_node_shapes_cbmi ) {
349 updateOptions( getOptions() );
351 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
352 updateOptions( getOptions() );
354 else if ( o == _non_lined_up_cladograms_rbmi ) {
355 updateOptions( getOptions() );
358 else if ( o == _uniform_cladograms_rbmi ) {
359 updateOptions( getOptions() );
362 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
363 updateOptions( getOptions() );
366 else if ( o == _search_case_senstive_cbmi ) {
367 updateOptions( getOptions() );
368 getMainPanel().getControlPanel().search();
370 else if ( o == _search_whole_words_only_cbmi ) {
371 updateOptions( getOptions() );
372 getMainPanel().getControlPanel().search();
374 else if ( o == _inverse_search_result_cbmi ) {
375 updateOptions( getOptions() );
376 getMainPanel().getControlPanel().search();
378 else if ( o == _show_scale_cbmi ) {
379 updateOptions( getOptions() );
381 else if ( o == _show_branch_length_values_cbmi ) {
382 updateOptions( getOptions() );
384 else if ( o == _label_direction_cbmi ) {
385 updateOptions( getOptions() );
387 else if ( o == _show_overview_cbmi ) {
388 updateOptions( getOptions() );
389 if ( getCurrentTreePanel() != null ) {
390 getCurrentTreePanel().updateOvSizes();
393 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
394 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
395 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
398 else if ( o == _about_item ) {
401 else if ( o == _help_item ) {
402 help( getConfiguration().getWebLinks() );
404 else if ( o == _website_item ) {
406 Util.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
408 catch ( final IOException e1 ) {
409 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
412 else if ( o == _phyloxml_website_item ) {
414 Util.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
416 catch ( final IOException e1 ) {
417 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
420 else if ( o == _aptx_ref_item ) {
422 Util.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
424 catch ( final IOException e1 ) {
425 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
428 else if ( o == _phyloxml_ref_item ) {
430 Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
432 catch ( final IOException e1 ) {
433 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
437 if ( _load_phylogeny_from_webservice_menu_items != null ) {
438 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
439 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
440 readPhylogeniesFromWebservice( i );
445 _contentpane.repaint();
448 boolean isSubtreeDisplayed() {
449 if ( getCurrentTreePanel() != null ) {
450 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
452 .showMessageDialog( this,
453 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
454 "Operation can not be exectuted on a sub-tree",
455 JOptionPane.WARNING_MESSAGE );
462 void activateSaveAllIfNeeded() {
463 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
464 _save_all_item.setEnabled( true );
467 _save_all_item.setEnabled( false );
471 void buildFileMenu() {
472 _file_jmenu = createMenu( "File", getConfiguration() );
473 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
474 _file_jmenu.addSeparator();
475 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
476 customizeJMenuItem( _open_url_item );
477 customizeJMenuItem( _exit_item );
478 _jmenubar.add( _file_jmenu );
481 void buildFontSizeMenu() {
482 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
483 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
484 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
485 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
486 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
487 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
488 customizeJMenuItem( _super_tiny_fonts_item );
489 customizeJMenuItem( _tiny_fonts_item );
490 customizeJMenuItem( _small_fonts_item );
491 customizeJMenuItem( _medium_fonts_item );
492 customizeJMenuItem( _large_fonts_item );
493 _jmenubar.add( _font_size_menu );
496 void buildHelpMenu() {
497 _help_jmenu = createMenu( "Help", getConfiguration() );
498 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
499 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
500 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
501 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
502 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
503 _help_jmenu.addSeparator();
504 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
505 customizeJMenuItem( _help_item );
506 customizeJMenuItem( _website_item );
507 customizeJMenuItem( _phyloxml_website_item );
508 customizeJMenuItem( _aptx_ref_item );
509 customizeJMenuItem( _phyloxml_ref_item );
510 customizeJMenuItem( _about_item );
511 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
512 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
513 _jmenubar.add( _help_jmenu );
516 void buildTypeMenu() {
517 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
518 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
519 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
520 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
521 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
522 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
523 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
524 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
525 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
526 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
527 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
528 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
529 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
530 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
531 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
532 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
533 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
534 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
535 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
536 initializeTypeMenu( getOptions() );
537 _jmenubar.add( _type_menu );
540 void buildViewMenu() {
541 _view_jmenu = createMenu( "View", getConfiguration() );
542 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
543 _view_jmenu.addSeparator();
544 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
545 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
546 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
547 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
548 customizeJMenuItem( _display_basic_information_item );
549 customizeJMenuItem( _view_as_NH_item );
550 customizeJMenuItem( _view_as_NHX_item );
551 customizeJMenuItem( _view_as_XML_item );
552 customizeJMenuItem( _view_as_nexus_item );
553 _jmenubar.add( _view_jmenu );
556 private void chooseFont() {
557 final FontChooser fc = new FontChooser();
558 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
559 fc.showDialog( this, "Select the Base Font" );
560 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
563 private void chooseMinimalConfidence() {
564 final String s = ( String ) JOptionPane
565 .showInputDialog( this,
566 "Please enter the minimum for confidence values to be displayed.\n"
567 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
568 "Minimal Confidence Value",
569 JOptionPane.QUESTION_MESSAGE,
572 getOptions().getMinConfidenceValue() );
573 if ( !ForesterUtil.isEmpty( s ) ) {
574 boolean success = true;
576 final String m_str = s.trim();
577 if ( !ForesterUtil.isEmpty( m_str ) ) {
579 m = Double.parseDouble( m_str );
581 catch ( final Exception ex ) {
588 if ( success && ( m >= 0.0 ) ) {
589 getOptions().setMinConfidenceValue( m );
594 static void chooseNodeSize( final Options options, final Component parent ) {
595 final String s = ( String ) JOptionPane.showInputDialog( parent,
596 "Please enter the default size for node shapes.\n"
598 + options.getDefaultNodeShapeSize() + "]\n",
600 JOptionPane.QUESTION_MESSAGE,
603 options.getDefaultNodeShapeSize() );
604 if ( !ForesterUtil.isEmpty( s ) ) {
605 boolean success = true;
607 final String m_str = s.trim();
608 if ( !ForesterUtil.isEmpty( m_str ) ) {
610 m = Double.parseDouble( m_str );
612 catch ( final Exception ex ) {
619 if ( success && ( m >= 0.0 ) ) {
620 final short size = ForesterUtil.roundToShort( m );
622 options.setDefaultNodeShapeSize( size );
630 if ( _mainpanel != null ) {
631 _mainpanel.terminate();
633 if ( _contentpane != null ) {
634 _contentpane.removeAll();
641 if ( _mainpanel.getCurrentTreePanel() != null ) {
642 _mainpanel.getCurrentTreePanel().confColor();
647 if ( _mainpanel.getCurrentTreePanel() != null ) {
648 final String[] ranks = Util.getAllPossibleRanks();
649 final String rank = ( String ) JOptionPane
650 .showInputDialog( this,
651 "What rank should the colorization be based on",
653 JOptionPane.QUESTION_MESSAGE,
657 if ( !ForesterUtil.isEmpty( rank ) ) {
658 _mainpanel.getCurrentTreePanel().colorRank( rank );
663 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
664 if ( item != null ) {
665 item.setFont( MainFrame.menu_font );
666 if ( !getConfiguration().isUseNativeUI() ) {
667 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
668 item.setForeground( getConfiguration().getGuiMenuTextColor() );
670 item.setSelected( is_selected );
671 item.addActionListener( this );
675 void customizeJMenuItem( final JMenuItem jmi ) {
677 jmi.setFont( MainFrame.menu_font );
678 if ( !getConfiguration().isUseNativeUI() ) {
679 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
680 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
682 jmi.addActionListener( this );
686 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
687 if ( item != null ) {
688 item.setFont( MainFrame.menu_font );
689 if ( !getConfiguration().isUseNativeUI() ) {
690 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
691 item.setForeground( getConfiguration().getGuiMenuTextColor() );
693 item.setSelected( is_selected );
694 item.addActionListener( this );
698 void exceptionOccuredDuringOpenFile( final Exception e ) {
700 _mainpanel.getCurrentTreePanel().setArrowCursor();
702 catch ( final Exception ex ) {
705 JOptionPane.showMessageDialog( this,
706 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
707 "Error during File|Open",
708 JOptionPane.ERROR_MESSAGE );
711 void exceptionOccuredDuringSaveAs( final Exception e ) {
713 _mainpanel.getCurrentTreePanel().setArrowCursor();
715 catch ( final Exception ex ) {
718 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
721 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
722 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
723 JOptionPane.showMessageDialog( this,
724 "Gene tree and species tree have no species in common.",
726 JOptionPane.ERROR_MESSAGE );
729 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
730 JOptionPane.showMessageDialog( this,
731 "Gene tree and species tree have only one species in common.",
733 JOptionPane.ERROR_MESSAGE );
741 public Configuration getConfiguration() {
742 return _configuration;
745 TreePanel getCurrentTreePanel() {
746 return getMainPanel().getCurrentTreePanel();
749 JMenu getHelpMenu() {
753 JCheckBoxMenuItem getlabelDirectionCbmi() {
754 return _label_direction_cbmi;
757 MainPanel getMainPanel() {
761 JMenuBar getMenuBarOfMainFrame() {
765 Options getOptions() {
769 void initializeTypeMenu( final Options options ) {
770 setTypeMenuToAllUnselected();
771 switch ( options.getPhylogenyGraphicsType() ) {
773 _convex_type_cbmi.setSelected( true );
776 _curved_type_cbmi.setSelected( true );
779 _euro_type_cbmi.setSelected( true );
782 _rounded_type_cbmi.setSelected( true );
785 _triangular_type_cbmi.setSelected( true );
788 _unrooted_type_cbmi.setSelected( true );
791 _circular_type_cbmi.setSelected( true );
794 _rectangular_type_cbmi.setSelected( true );
799 void midpointRoot() {
800 if ( _mainpanel.getCurrentTreePanel() != null ) {
801 _mainpanel.getCurrentTreePanel().midpointRoot();
805 abstract void readPhylogeniesFromURL();
807 void readPhylogeniesFromWebservice( final int i ) {
808 final UrlTreeReader reader = new UrlTreeReader( this, i );
809 new Thread( reader ).start();
812 private void removeBranchColors() {
813 if ( getMainPanel().getCurrentPhylogeny() != null ) {
814 Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
818 void removeTextFrame() {
819 if ( _textframe != null ) {
825 void setConfiguration( final Configuration configuration ) {
826 _configuration = configuration;
829 void setOptions( final Options options ) {
833 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
834 setTypeMenuToAllUnselected();
837 _circular_type_cbmi.setSelected( true );
840 _convex_type_cbmi.setSelected( true );
843 _curved_type_cbmi.setSelected( true );
846 _euro_type_cbmi.setSelected( true );
849 _rounded_type_cbmi.setSelected( true );
852 _rectangular_type_cbmi.setSelected( true );
855 _triangular_type_cbmi.setSelected( true );
858 _unrooted_type_cbmi.setSelected( true );
861 throw new IllegalArgumentException( "unknown type: " + type );
865 void setTypeMenuToAllUnselected() {
866 _convex_type_cbmi.setSelected( false );
867 _curved_type_cbmi.setSelected( false );
868 _euro_type_cbmi.setSelected( false );
869 _rounded_type_cbmi.setSelected( false );
870 _triangular_type_cbmi.setSelected( false );
871 _rectangular_type_cbmi.setSelected( false );
872 _unrooted_type_cbmi.setSelected( false );
873 _circular_type_cbmi.setSelected( false );
876 public void showWhole() {
877 _mainpanel.getControlPanel().showWhole();
880 void switchColors() {
881 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
882 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
883 csc.setVisible( true );
887 if ( _mainpanel.getCurrentTreePanel() != null ) {
888 _mainpanel.getCurrentTreePanel().taxColor();
892 void typeChanged( final Object o ) {
893 updateTypeCheckboxes( getOptions(), o );
894 updateOptions( getOptions() );
895 if ( getCurrentTreePanel() != null ) {
896 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
897 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
898 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
899 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
900 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
901 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
902 getCurrentTreePanel().getControlPanel().showWhole();
904 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
905 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
908 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
910 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
911 updateScreenTextAntialias( getMainPanel().getTreePanels() );
912 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
913 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
914 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
917 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
923 void updateOptions( final Options options ) {
924 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
925 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
926 && _background_gradient_cbmi.isSelected() );
927 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
928 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
929 && _abbreviate_scientific_names.isSelected() );
930 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
931 && _color_labels_same_as_parent_branch.isSelected() );
932 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
933 && _show_default_node_shapes_cbmi.isSelected() );
934 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
935 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
936 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
937 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
939 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
940 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
942 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
943 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
945 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
946 && _search_case_senstive_cbmi.isSelected() );
947 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
948 options.setShowScale( _show_scale_cbmi.isSelected() );
950 if ( _label_direction_cbmi != null ) {
951 if ( _label_direction_cbmi.isSelected() ) {
952 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
955 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
958 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
959 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
960 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
962 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
963 && ( _print_using_actual_size_cbmi.isSelected() ) );
964 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
965 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
966 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
967 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
968 && _print_black_and_white_cbmi.isSelected() );
969 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
970 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
971 options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
972 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
973 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
974 && _replace_underscores_cbmi.isSelected() );
975 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
976 && _search_whole_words_only_cbmi.isSelected() );
977 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
978 && _inverse_search_result_cbmi.isSelected() );
979 if ( _graphics_export_visible_only_cbmi != null ) {
980 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
981 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
982 _graphics_export_using_actual_size_cbmi.setSelected( true );
983 _graphics_export_using_actual_size_cbmi.setEnabled( false );
986 _graphics_export_using_actual_size_cbmi.setEnabled( true );
989 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
990 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
992 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
993 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
995 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
996 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
998 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
999 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1001 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1002 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1004 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1005 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1007 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1008 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1010 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1011 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1015 void updateTypeCheckboxes( final Options options, final Object o ) {
1016 setTypeMenuToAllUnselected();
1017 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1020 void displayBasicInformation() {
1021 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1024 _textframe = TextFrame.instantiate( Util.crateBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
1027 void viewAsNexus() {
1029 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1030 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1033 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus() );
1038 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1039 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1042 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshire( false ) );
1047 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1048 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1051 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
1056 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
1057 && ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
1058 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
1063 * Display the about box.
1065 static void about() {
1066 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1067 about.append( "Copyright (C) 2007-2011 Christian Zmasek\n" );
1068 about.append( "All Rights Reserved\n" );
1069 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1070 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1071 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1072 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1073 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1074 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1076 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1077 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1078 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1079 + ForesterUtil.OS_VERSION + "]\n" );
1081 final Runtime rt = java.lang.Runtime.getRuntime();
1082 final long free_memory = rt.freeMemory() / 1000000;
1083 final long total_memory = rt.totalMemory() / 1000000;
1084 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1085 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1086 about.append( "References:\n" );
1087 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1088 about.append( "For more information & download:\n" );
1089 about.append( Constants.APTX_WEB_SITE + "\n" );
1090 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1091 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1094 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1095 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1098 static JMenu createMenu( final String title, final Configuration conf ) {
1099 final JMenu jmenu = new JMenu( title );
1100 if ( !conf.isUseNativeUI() ) {
1101 jmenu.setFont( MainFrame.menu_font );
1102 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1103 jmenu.setForeground( conf.getGuiMenuTextColor() );
1108 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1109 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1110 if ( !configuration.isUseNativeUI() ) {
1111 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1112 label.setForeground( configuration.getGuiMenuTextColor() );
1113 label.setOpaque( true );
1115 label.setSelected( false );
1116 label.setEnabled( false );
1120 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1121 switch ( op.getOvPlacement() ) {
1123 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1126 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1129 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1132 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1135 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1137 if ( tree_panel != null ) {
1138 tree_panel.updateOvSettings();
1142 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1143 switch ( op.getDefaultNodeFill() ) {
1145 op.setDefaultNodeFill( NodeFill.SOLID );
1148 op.setDefaultNodeFill( NodeFill.GRADIENT );
1151 op.setDefaultNodeFill( NodeFill.NONE );
1154 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1158 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1159 switch ( op.getDefaultNodeShape() ) {
1161 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1164 op.setDefaultNodeShape( NodeShape.CIRCLE );
1167 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1171 static void help( final Map<String, WebLink> weblinks ) {
1172 final StringBuilder sb = new StringBuilder();
1173 sb.append( "Display options\n" );
1174 sb.append( "-------------------\n" );
1175 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1176 sb.append( "Clickable tree nodes\n" );
1177 sb.append( "--------------------\n" );
1178 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1179 sb.append( "or by right clicking:\n" );
1180 sb.append( "o Display Node Data -- display information for a node\n" );
1181 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1182 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1183 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1184 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1185 sb.append( "o Colorize Subtree -- color a subtree\n" );
1186 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1187 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1188 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1189 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1190 sb.append( "Zooming\n" );
1191 sb.append( "---------\n" );
1192 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1193 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1194 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1195 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1196 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1197 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1198 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1199 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1200 sb.append( "Quick tree manipulation:\n" );
1201 sb.append( "------------------------\n" );
1202 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1203 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1204 sb.append( "Memory problems (Java heap space error)\n" );
1205 sb.append( "---------------------------------------\n" );
1206 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1207 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1208 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1209 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1210 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1211 sb.append( "Active web links\n" );
1212 sb.append( "--------------------\n" );
1213 for( final String key : weblinks.keySet() ) {
1214 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1217 // + "General remarks\n"
1218 // + "---------------\n"
1220 // "o The application version permits copying to the clipboard \n"
1222 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1224 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1225 // + " but not any of its parent tree(s).\n"
1227 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1229 // " are likely to be bootstrap values instead of branch length values.\n\n"
1231 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1233 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1235 // " a species: either directly through the \"Species\" field, or the species\n"
1237 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1239 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1241 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1243 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1245 // "o !External nodes of the gene tree associated with species not present in\n"
1247 // " the species tree are REMOVED prior to SDI execution!\n"
1249 // "o Both the gene tree and the species tree must be completely binary.\n"
1251 // "o Duplications and speciations are a function of the position of the root.\n"
1253 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1254 // + " incorrect and need to be inferred again\n"
1256 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1258 sb.append( "phyloXML\n" );
1259 sb.append( "-------------------\n" );
1260 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1261 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1262 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1264 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1265 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1266 TextFrame.instantiate( sb.toString() );
1269 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1270 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1271 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1274 mi.setText( "Cycle Overview Placement..." );
1278 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1279 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1280 mi.setText( "Cycle Node Shape Fill Type... (current: "
1281 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1284 mi.setText( "Cycle Node Shape Fill Type..." );
1288 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1289 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1290 mi.setText( "Cycle Node Shape Fill Type... (current: "
1291 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1294 mi.setText( "Cycle Node Shape Fill Type..." );
1298 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1299 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1300 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1303 mi.setText( "Select Colors..." );
1307 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1308 mi.setText( "Select Font... (current: " + font_desc + ")" );
1311 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1312 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1313 mi.setEnabled( true );
1315 else if ( Util.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1316 mi.setEnabled( true );
1319 mi.setEnabled( false );
1321 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1324 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1325 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1328 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1329 final JCheckBoxMenuItem scale,
1330 final JCheckBoxMenuItem branch_lengths,
1331 final JRadioButtonMenuItem non_lined_up,
1332 final JRadioButtonMenuItem uniform_clado,
1333 final JRadioButtonMenuItem nonuniform_clado,
1334 final JCheckBoxMenuItem label_direction_cbmi ) {
1335 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1336 final ControlPanel control = main_panel.getControlPanel();
1337 final Options options = main_panel.getOptions();
1338 scale.setSelected( options.isShowScale() );
1339 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1340 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1341 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1342 scale.setSelected( false );
1343 scale.setEnabled( false );
1344 branch_lengths.setSelected( false );
1345 branch_lengths.setEnabled( false );
1347 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1348 scale.setSelected( false );
1349 scale.setEnabled( false );
1350 branch_lengths.setEnabled( true );
1353 scale.setEnabled( true );
1354 branch_lengths.setEnabled( true );
1356 if ( ( tree_panel != null )
1357 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1358 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1359 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1360 branch_lengths.setSelected( false );
1361 branch_lengths.setEnabled( false );
1363 if ( tree_panel != null ) {
1364 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1365 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1366 non_lined_up.setEnabled( false );
1367 uniform_clado.setEnabled( false );
1368 nonuniform_clado.setEnabled( false );
1371 non_lined_up.setEnabled( true );
1372 uniform_clado.setEnabled( true );
1373 nonuniform_clado.setEnabled( true );
1377 if ( ( tree_panel != null )
1378 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1379 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1380 branch_lengths.setSelected( false );
1381 branch_lengths.setEnabled( false );
1383 if ( ( tree_panel != null )
1384 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1385 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1386 non_lined_up.setEnabled( false );
1389 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1390 non_lined_up.setEnabled( true );
1393 label_direction_cbmi.setEnabled( true );
1394 if ( tree_panel != null ) {
1395 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1396 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1397 label_direction_cbmi.setEnabled( false );
1399 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1400 scale.setSelected( false );
1401 scale.setEnabled( false );
1406 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1407 for( final TreePanel tree_panel : treepanels ) {
1408 tree_panel.setTextAntialias();