forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java

   1
   2 package org.forester.archaeopteryx;
   3
   4 import java.awt.BorderLayout;
   5 import java.awt.Container;
   6 import java.awt.event.ActionEvent;
   7 import java.awt.event.ActionListener;
   8 import java.awt.event.ComponentAdapter;
   9 import java.awt.event.ComponentEvent;
  10 import java.io.File;
  11 import java.io.IOException;
  12 import java.net.URL;
  13 import java.util.List;
  14
  15 import javax.swing.ButtonGroup;
  16 import javax.swing.JApplet;
  17 import javax.swing.JCheckBoxMenuItem;
  18 import javax.swing.JMenu;
  19 import javax.swing.JMenuBar;
  20 import javax.swing.JMenuItem;
  21 import javax.swing.JOptionPane;
  22 import javax.swing.JRadioButtonMenuItem;
  23 import javax.swing.UIManager;
  24 import javax.swing.UnsupportedLookAndFeelException;
  25 import javax.swing.event.ChangeEvent;
  26 import javax.swing.event.ChangeListener;
  27
  28 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  29 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  30 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  31 import org.forester.phylogeny.Phylogeny;
  32 import org.forester.phylogeny.data.SequenceRelation;
  33 import org.forester.util.ForesterUtil;
  34 import org.forester.util.ForesterConstants;
  35
  36
  37 // Use like this:
  38 // <applet archive="forester.jar"
  39 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  40 // codebase="http://www.myserver.org/path/to/forester"
  41 // width="600"
  42 // height="500"
  43 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  44 // <param name="url_of_tree_to_load"
  45 // value="http://www.myserver.org/examples/data/apaf.xml">
  46 // <param name="config_file"
  47 // value="http://www.myserver.org/examples/config/config_file.txt">
  48 // </applet>
  49 public class ArchaeopteryxE extends JApplet implements ActionListener {
  50
  51     private final static String  NAME             = "ArchaeopteryxE";
  52     private static final long    serialVersionUID = -1220055577935759443L;
  53     private Configuration        _configuration;
  54     private MainPanelApplets     _main_panel;
  55     private JMenuBar             _jmenubar;
  56     private JMenu                _options_jmenu;
  57     private JMenu                _font_size_menu;
  58     private JMenuItem            _super_tiny_fonts_mi;
  59     private JMenuItem            _tiny_fonts_mi;
  60     private JMenuItem            _small_fonts_mi;
  61     private JMenuItem            _medium_fonts_mi;
  62     private JMenuItem            _large_fonts_mi;
  63     private TextFrame            _textframe;
  64     private JMenu                _tools_menu;
  65     private JMenuItem            _taxcolor_item;
  66     private JMenuItem            _confcolor_item;
  67     private JMenuItem            _midpoint_root_item;
  68     private JMenu                _view_jmenu;
  69     private JMenuItem            _view_as_XML_item;
  70     private JMenuItem            _view_as_NH_item;
  71     private JMenuItem            _view_as_NHX_item;
  72     private JMenuItem            _view_as_nexus_item;
  73     private JMenu                _type_menu;
  74     private JCheckBoxMenuItem    _rectangular_type_cbmi;
  75     private JCheckBoxMenuItem    _triangular_type_cbmi;
  76     private JCheckBoxMenuItem    _curved_type_cbmi;
  77     private JCheckBoxMenuItem    _convex_type_cbmi;
  78     private JCheckBoxMenuItem    _euro_type_cbmi;
  79     private JCheckBoxMenuItem    _rounded_type_cbmi;
  80     private JCheckBoxMenuItem    _unrooted_type_cbmi;
  81     private JCheckBoxMenuItem    _circular_type_cbmi;
  82     private JMenuItem            _help_item;
  83     private JMenuItem            _about_item;
  84     private JMenu                _help_jmenu;
  85     private JMenuItem            _website_item;
  86     private JMenuItem            _phyloxml_website_item;
  87     private JMenuItem            _phyloxml_ref_item;
  88     private JMenuItem            _aptx_ref_item;
  89     private JMenuItem            _remove_branch_color_item;
  90     private JMenuItem            _infer_common_sn_names_item;
  91     private JCheckBoxMenuItem    _show_domain_labels;
  92     private JCheckBoxMenuItem    _color_labels_same_as_parent_branch;
  93     private JCheckBoxMenuItem    _abbreviate_scientific_names;
  94     private JCheckBoxMenuItem    _screen_antialias_cbmi;
  95     private JCheckBoxMenuItem    _background_gradient_cbmi;
  96     private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
  97     private JRadioButtonMenuItem _uniform_cladograms_rbmi;
  98     private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
  99     private Options              _options;
 100     private JMenuItem            _choose_font_mi;
 101     private JMenuItem            _switch_colors_mi;
 102     JCheckBoxMenuItem            _label_direction_cbmi;
 103     private JCheckBoxMenuItem    _show_scale_cbmi;
 104     private JCheckBoxMenuItem    _search_case_senstive_cbmi;
 105     private JCheckBoxMenuItem    _search_whole_words_only_cbmi;
 106     private JCheckBoxMenuItem    _inverse_search_result_cbmi;
 107     private JCheckBoxMenuItem    _show_overview_cbmi;
 108     private JMenuItem            _choose_minimal_confidence_mi;
 109     private JCheckBoxMenuItem    _show_branch_length_values_cbmi;
 110     private JMenuItem            _collapse_species_specific_subtrees;
 111     private JMenuItem            _overview_placment_mi;
 112     private ButtonGroup          _radio_group_1;
 113     private JCheckBoxMenuItem    _show_default_node_shapes_cbmi;
 114     private JMenuItem            _cycle_node_shape_mi;
 115     private JMenuItem            _cycle_node_fill_mi;
 116     private JMenuItem            _choose_node_size_mi;
 117     private JCheckBoxMenuItem    _taxonomy_colorize_node_shapes_cbmi;
 118
 119     @Override
 120     public void actionPerformed( final ActionEvent e ) {
 121         final Object o = e.getSource();
 122         if ( o == _midpoint_root_item ) {
 123             getMainPanel().getCurrentTreePanel().midpointRoot();
 124         }
 125         else if ( o == _taxcolor_item ) {
 126             getMainPanel().getCurrentTreePanel().taxColor();
 127         }
 128         else if ( o == _confcolor_item ) {
 129             getMainPanel().getCurrentTreePanel().confColor();
 130         }
 131         else if ( o == _infer_common_sn_names_item ) {
 132             if ( getCurrentTreePanel() != null ) {
 133                 getCurrentTreePanel().inferCommonPartOfScientificNames();
 134             }
 135         }
 136         else if ( o == _collapse_species_specific_subtrees ) {
 137             if ( getCurrentTreePanel() != null ) {
 138                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 139             }
 140         }
 141         else if ( o == _remove_branch_color_item ) {
 142             removeBranchColors();
 143         }
 144         else if ( o == _switch_colors_mi ) {
 145             switchColors();
 146         }
 147         else if ( o == _view_as_NH_item ) {
 148             viewAsNH();
 149         }
 150         else if ( o == _view_as_NHX_item ) {
 151             viewAsNHX();
 152         }
 153         else if ( o == _view_as_XML_item ) {
 154             viewAsXML();
 155         }
 156         else if ( o == _view_as_nexus_item ) {
 157             viewAsNexus();
 158         }
 159         else if ( o == _super_tiny_fonts_mi ) {
 160             if ( getCurrentTreePanel() != null ) {
 161                 getCurrentTreePanel().setSuperTinyFonts();
 162                 getCurrentTreePanel().repaint();
 163             }
 164         }
 165         else if ( o == _tiny_fonts_mi ) {
 166             if ( getCurrentTreePanel() != null ) {
 167                 getCurrentTreePanel().setTinyFonts();
 168                 getCurrentTreePanel().repaint();
 169             }
 170         }
 171         else if ( o == _small_fonts_mi ) {
 172             if ( getCurrentTreePanel() != null ) {
 173                 getCurrentTreePanel().setSmallFonts();
 174                 getCurrentTreePanel().repaint();
 175             }
 176         }
 177         else if ( o == _medium_fonts_mi ) {
 178             if ( getCurrentTreePanel() != null ) {
 179                 getCurrentTreePanel().setMediumFonts();
 180                 getCurrentTreePanel().repaint();
 181             }
 182         }
 183         else if ( o == _large_fonts_mi ) {
 184             if ( getCurrentTreePanel() != null ) {
 185                 getCurrentTreePanel().setLargeFonts();
 186                 getCurrentTreePanel().repaint();
 187             }
 188         }
 189         else if ( o == _choose_font_mi ) {
 190             chooseFont();
 191         }
 192         else if ( o == _choose_minimal_confidence_mi ) {
 193             chooseMinimalConfidence();
 194         }
 195         else if ( o == _choose_node_size_mi ) {
 196             MainFrame.chooseNodeSize( getOptions(), this );
 197         }
 198         else if ( o == _overview_placment_mi ) {
 199             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 200         }
 201         else if ( o == _cycle_node_fill_mi ) {
 202             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 203         }
 204         else if ( o == _cycle_node_shape_mi ) {
 205             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 206         }
 207         else if ( o == _non_lined_up_cladograms_rbmi ) {
 208             updateOptions( getOptions() );
 209             _main_panel.getControlPanel().showWhole();
 210         }
 211         else if ( o == _uniform_cladograms_rbmi ) {
 212             updateOptions( getOptions() );
 213             _main_panel.getControlPanel().showWhole();
 214         }
 215         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 216             updateOptions( getOptions() );
 217             _main_panel.getControlPanel().showWhole();
 218         }
 219         else if ( o == _search_case_senstive_cbmi ) {
 220             updateOptions( getOptions() );
 221             getMainPanel().getControlPanel().search();
 222         }
 223         else if ( o == _search_whole_words_only_cbmi ) {
 224             updateOptions( getOptions() );
 225             getMainPanel().getControlPanel().search();
 226         }
 227         else if ( o == _inverse_search_result_cbmi ) {
 228             updateOptions( getOptions() );
 229             getMainPanel().getControlPanel().search();
 230         }
 231         else if ( o == _show_scale_cbmi ) {
 232             updateOptions( getOptions() );
 233         }
 234         else if ( o == _show_branch_length_values_cbmi ) {
 235             updateOptions( getOptions() );
 236         }
 237         else if ( o == _label_direction_cbmi ) {
 238             updateOptions( getOptions() );
 239         }
 240         else if ( o == _show_overview_cbmi ) {
 241             updateOptions( getOptions() );
 242             if ( getCurrentTreePanel() != null ) {
 243                 getCurrentTreePanel().updateOvSizes();
 244             }
 245         }
 246         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 247                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 248                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 249             typeChanged( o );
 250         }
 251         else if ( o == _screen_antialias_cbmi ) {
 252             updateOptions( getOptions() );
 253             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 254         }
 255         else if ( o == _background_gradient_cbmi ) {
 256             updateOptions( getOptions() );
 257         }
 258         else if ( o == _show_domain_labels ) {
 259             updateOptions( getOptions() );
 260         }
 261         else if ( o == _color_labels_same_as_parent_branch ) {
 262             updateOptions( getOptions() );
 263         }
 264         else if ( o == _show_default_node_shapes_cbmi ) {
 265             updateOptions( getOptions() );
 266         }
 267         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 268             updateOptions( getOptions() );
 269         }
 270         else if ( o == _about_item ) {
 271             MainFrame.about();
 272         }
 273         else if ( o == _help_item ) {
 274             MainFrame.help( getConfiguration().getWebLinks() );
 275         }
 276         else if ( o == _website_item ) {
 277             try {
 278                 Util.openWebsite( Constants.APTX_WEB_SITE, true, this );
 279             }
 280             catch ( final IOException e1 ) {
 281                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 282             }
 283         }
 284         else if ( o == _phyloxml_website_item ) {
 285             try {
 286                 Util.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 287             }
 288             catch ( final IOException e1 ) {
 289                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 290             }
 291         }
 292         else if ( o == _aptx_ref_item ) {
 293             try {
 294                 Util.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 295             }
 296             catch ( final IOException e1 ) {
 297                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 298             }
 299         }
 300         else if ( o == _phyloxml_ref_item ) {
 301             try {
 302                 Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 303             }
 304             catch ( final IOException e1 ) {
 305                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 306             }
 307         }
 308         repaint();
 309     }
 310
 311     /**
 312      * This method returns the current phylogeny as a string in the chosen format
 313      *
 314      * @param format must be NH, NHX, NEXUS or PHYLOXML
 315      * @return the phylogeny string
 316      * @author Hervé Ménager
 317      */
 318     public String getCurrentPhylogeny( final String format ) {
 319         removeTextFrame();
 320         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 321                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 322             return new String();
 323         }
 324         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 325             case NH:
 326                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 327             case NHX:
 328                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 329             case NEXUS:
 330                 return getMainPanel().getCurrentPhylogeny().toNexus();
 331             case PHYLOXML:
 332                 return getMainPanel().getCurrentPhylogeny().toPhyloXML(-1);
 333             default:
 334                 break;
 335         }
 336         return new String();
 337     }
 338
 339
 340     void buildFontSizeMenu() {
 341         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 342         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 343         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 344         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 345         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 346         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 347         customizeJMenuItem( _super_tiny_fonts_mi );
 348         customizeJMenuItem( _tiny_fonts_mi );
 349         customizeJMenuItem( _small_fonts_mi );
 350         customizeJMenuItem( _medium_fonts_mi );
 351         customizeJMenuItem( _large_fonts_mi );
 352         _jmenubar.add( _font_size_menu );
 353     }
 354
 355     void buildHelpMenu() {
 356         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 357         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 358         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 359         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 360         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 361         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 362         _help_jmenu.addSeparator();
 363         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 364         customizeJMenuItem( _help_item );
 365         customizeJMenuItem( _website_item );
 366         customizeJMenuItem( _phyloxml_website_item );
 367         customizeJMenuItem( _aptx_ref_item );
 368         customizeJMenuItem( _phyloxml_ref_item );
 369         customizeJMenuItem( _about_item );
 370         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 371         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 372         _jmenubar.add( _help_jmenu );
 373     }
 374
 375     void buildOptionsMenu() {
 376         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 377         _options_jmenu.addChangeListener( new ChangeListener() {
 378
 379             @Override
 380             public void stateChanged( final ChangeEvent e ) {
 381                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 382                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 383                 MainFrame
 384                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 385                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 386                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 387                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 388                                                                      _show_scale_cbmi,
 389                                                                      _show_branch_length_values_cbmi,
 390                                                                      _non_lined_up_cladograms_rbmi,
 391                                                                      _uniform_cladograms_rbmi,
 392                                                                      _ext_node_dependent_cladogram_rbmi,
 393                                                                      _label_direction_cbmi );
 394                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 395                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 396                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 397             }
 398         } );
 399         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 400                                                                 getConfiguration() ) );
 401         _options_jmenu
 402                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 403         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 404         _options_jmenu
 405                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 406         _radio_group_1 = new ButtonGroup();
 407         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 408         _radio_group_1.add( _uniform_cladograms_rbmi );
 409         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 410         //
 411         _options_jmenu
 412                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 413         _options_jmenu
 414                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 415         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 416         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 417         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 418         //
 419         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 420         _options_jmenu
 421                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 422         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 423         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 424         _options_jmenu
 425                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 426         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 427         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 428         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 429         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 430         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 431         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 432             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 433         }
 434         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 435         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 436         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 437         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 438         _options_jmenu.addSeparator();
 439         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 440                                                                 getConfiguration() ) );
 441         _options_jmenu
 442                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 443         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 444         _options_jmenu
 445                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 446         customizeJMenuItem( _choose_font_mi );
 447         customizeJMenuItem( _choose_minimal_confidence_mi );
 448         customizeJMenuItem( _switch_colors_mi );
 449         customizeJMenuItem( _overview_placment_mi );
 450         customizeCheckBoxMenuItem( _label_direction_cbmi,
 451                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 452         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 453         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 454         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 455         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 456         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 457         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 458         customizeJMenuItem( _cycle_node_shape_mi );
 459         customizeJMenuItem( _cycle_node_fill_mi );
 460         customizeJMenuItem( _choose_node_size_mi );
 461         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 462         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 463         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 464         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 465                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 466         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 467                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 468         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 469                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 470         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 471         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 472         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 473         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 474         _jmenubar.add( _options_jmenu );
 475     }
 476
 477     void buildToolsMenu() {
 478         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 479         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 480         customizeJMenuItem( _confcolor_item );
 481         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 482         customizeJMenuItem( _taxcolor_item );
 483         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 484         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 485         customizeJMenuItem( _remove_branch_color_item );
 486         _tools_menu.addSeparator();
 487         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 488         customizeJMenuItem( _midpoint_root_item );
 489         _tools_menu.addSeparator();
 490         _tools_menu
 491                 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 492         customizeJMenuItem( _infer_common_sn_names_item );
 493         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 494         customizeJMenuItem( _collapse_species_specific_subtrees );
 495         _jmenubar.add( _tools_menu );
 496     }
 497
 498     void buildTypeMenu() {
 499         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 500         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 501         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 502         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 503         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 504         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 505         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 506         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 507         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 508         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 509         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 510         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 511         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 512         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 513         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 514         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 515         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 516         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 517         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 518         initializeTypeMenu( getOptions() );
 519         _jmenubar.add( _type_menu );
 520     }
 521
 522     void buildViewMenu() {
 523         _view_jmenu = MainFrame.createMenu( "View as Text", getConfiguration() );
 524         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 525         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 526         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 527         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 528         customizeJMenuItem( _view_as_NH_item );
 529         customizeJMenuItem( _view_as_NHX_item );
 530         customizeJMenuItem( _view_as_XML_item );
 531         customizeJMenuItem( _view_as_nexus_item );
 532         _jmenubar.add( _view_jmenu );
 533     }
 534
 535     private void chooseFont() {
 536         final FontChooser fc = new FontChooser();
 537         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
 538         fc.showDialog( this, "Select the Base Font" );
 539         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
 540     }
 541
 542     private void chooseMinimalConfidence() {
 543         final String s = ( String ) JOptionPane
 544                 .showInputDialog( this,
 545                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
 546                                           + getOptions().getMinConfidenceValue() + "]\n",
 547                                   "Minimal Confidence Value",
 548                                   JOptionPane.QUESTION_MESSAGE,
 549                                   null,
 550                                   null,
 551                                   getOptions().getMinConfidenceValue() );
 552         if ( !ForesterUtil.isEmpty( s ) ) {
 553             boolean success = true;
 554             double m = 0.0;
 555             final String m_str = s.trim();
 556             if ( !ForesterUtil.isEmpty( m_str ) ) {
 557                 try {
 558                     m = Double.parseDouble( m_str );
 559                 }
 560                 catch ( final Exception ex ) {
 561                     success = false;
 562                 }
 563             }
 564             else {
 565                 success = false;
 566             }
 567             if ( success && ( m >= 0.0 ) ) {
 568                 getOptions().setMinConfidenceValue( m );
 569             }
 570         }
 571     }
 572
 573     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 574         if ( item != null ) {
 575             item.setFont( MainFrame.menu_font );
 576             if ( !getConfiguration().isUseNativeUI() ) {
 577                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 578                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 579             }
 580             item.setSelected( is_selected );
 581             item.addActionListener( this );
 582         }
 583     }
 584
 585     void customizeJMenuItem( final JMenuItem jmi ) {
 586         jmi.setFont( MainFrame.menu_font );
 587         if ( !getConfiguration().isUseNativeUI() ) {
 588             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 589             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 590         }
 591         jmi.addActionListener( this );
 592     }
 593
 594     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 595         if ( item != null ) {
 596             item.setFont( MainFrame.menu_font );
 597             if ( !getConfiguration().isUseNativeUI() ) {
 598                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 599                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 600             }
 601             item.setSelected( is_selected );
 602             item.addActionListener( this );
 603         }
 604     }
 605
 606     @Override
 607     public void destroy() {
 608         Util.printAppletMessage( NAME, "going to be destroyed " );
 609         removeTextFrame();
 610         if ( getMainPanel() != null ) {
 611             getMainPanel().terminate();
 612         }
 613     }
 614
 615     Configuration getConfiguration() {
 616         return _configuration;
 617     }
 618
 619     TreePanel getCurrentTreePanel() {
 620         return getMainPanel().getCurrentTreePanel();
 621     }
 622
 623     JCheckBoxMenuItem getlabelDirectionCbmi() {
 624         return _label_direction_cbmi;
 625     }
 626
 627     private MainPanel getMainPanel() {
 628         return _main_panel;
 629     }
 630
 631     public Options getOptions() {
 632         return _options;
 633     }
 634
 635     Options getOtions() {
 636         return _options;
 637     }
 638
 639     @Override
 640     public void init() {
 641         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 642         Util.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 643         final Configuration configuration = new Configuration( config_filename, true, true );
 644         setConfiguration( configuration );
 645         setOptions( Options.createInstance( configuration ) );
 646         setupUI();
 647         URL phys_url = null;
 648         Phylogeny[] phys = null;
 649         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 650         Util.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 651         // Get URL to tree file
 652         if ( phys_url_string != null ) {
 653             try {
 654                 phys_url = new URL( phys_url_string );
 655             }
 656             catch ( final Exception e ) {
 657                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 658                 e.printStackTrace();
 659                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 660                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 661             }
 662         }
 663         // Load the tree from URL
 664         if ( phys_url != null ) {
 665             try {
 666                 phys = Util.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
 667             }
 668             catch ( final Exception e ) {
 669                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 670                 e.printStackTrace();
 671                 JOptionPane.showMessageDialog( this,
 672                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 673                                                "Failed to read phylogenies",
 674                                                JOptionPane.ERROR_MESSAGE );
 675             }
 676         }
 677         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 678             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 679             JOptionPane.showMessageDialog( this,
 680                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 681                                            "Failed to read phylogenies",
 682                                            JOptionPane.ERROR_MESSAGE );
 683             return;
 684         }
 685         else {
 686             Util.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 687         }
 688         setVisible( false );
 689         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 690         _jmenubar = new JMenuBar();
 691         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 692             if ( !getConfiguration().isUseNativeUI() ) {
 693                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 694             }
 695             buildToolsMenu();
 696             buildViewMenu();
 697             buildFontSizeMenu();
 698             buildOptionsMenu();
 699             buildTypeMenu();
 700             buildHelpMenu();
 701             setJMenuBar( _jmenubar );
 702         }
 703         final Container contentpane = getContentPane();
 704         contentpane.setLayout( new BorderLayout() );
 705         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 706         addComponentListener( new ComponentAdapter() {
 707
 708             @Override
 709             public void componentResized( final ComponentEvent e ) {
 710                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 711                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 712                                                                                            .getWidth(),
 713                                                                                    getMainPanel().getCurrentTreePanel()
 714                                                                                            .getHeight(),
 715                                                                                    false );
 716                 }
 717             }
 718         } );
 719         if ( getConfiguration().isUseTabbedDisplay() ) {
 720             Util.printAppletMessage( NAME, "using tabbed display" );
 721             Util.addPhylogeniesToTabs( phys,
 722                                        new File( phys_url.getFile() ).getName(),
 723                                        phys_url.toString(),
 724                                        getConfiguration(),
 725                                        getMainPanel() );
 726         }
 727         else {
 728             Util.printAppletMessage( NAME, "not using tabbed display" );
 729             Util.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 730         }
 731         validate();
 732         setName( NAME );
 733         getMainPanel().getControlPanel().showWholeAll();
 734         getMainPanel().getControlPanel().showWhole();
 735         System.gc();
 736         Util.printAppletMessage( NAME, "successfully initialized" );
 737         /* GUILHEM_BEG */
 738         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 739         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 740                 .getRelevantSequenceRelationTypes() ) {
 741             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 742         }
 743         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 744         if ( default_relation != null ) {
 745             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 746         }
 747         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 748         if ( default_sequence != null ) {
 749             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 750             /* GUILHEM_END */
 751         }
 752         setVisible( true );
 753     }
 754
 755     void initializeTypeMenu( final Options options ) {
 756         setTypeMenuToAllUnselected();
 757         try {
 758             switch ( options.getPhylogenyGraphicsType() ) {
 759                 case CONVEX:
 760                     _convex_type_cbmi.setSelected( true );
 761                     break;
 762                 case CURVED:
 763                     _curved_type_cbmi.setSelected( true );
 764                     break;
 765                 case EURO_STYLE:
 766                     _euro_type_cbmi.setSelected( true );
 767                     break;
 768                 case ROUNDED:
 769                     _rounded_type_cbmi.setSelected( true );
 770                     break;
 771                 case TRIANGULAR:
 772                     _triangular_type_cbmi.setSelected( true );
 773                     break;
 774                 case UNROOTED:
 775                     _unrooted_type_cbmi.setSelected( true );
 776                     break;
 777                 case CIRCULAR:
 778                     _circular_type_cbmi.setSelected( true );
 779                     break;
 780                 default:
 781                     _rectangular_type_cbmi.setSelected( true );
 782                     break;
 783             }
 784         }
 785         catch ( final NullPointerException np ) {
 786             // In all likelihood, this is caused by menu-less display.
 787         }
 788     }
 789
 790     private boolean isScreenAntialias() {
 791         return true;
 792     }
 793
 794     private void removeBranchColors() {
 795         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 796             Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
 797         }
 798     }
 799
 800     void removeTextFrame() {
 801         if ( _textframe != null ) {
 802             _textframe.close();
 803             _textframe = null;
 804         }
 805     }
 806
 807     void setConfiguration( final Configuration configuration ) {
 808         _configuration = configuration;
 809     }
 810
 811     private void setMainPanel( final MainPanelApplets main_panel ) {
 812         _main_panel = main_panel;
 813     }
 814
 815     void setOptions( final Options options ) {
 816         _options = options;
 817     }
 818
 819     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 820         setTypeMenuToAllUnselected();
 821         try {
 822             switch ( type ) {
 823                 case CIRCULAR:
 824                     _circular_type_cbmi.setSelected( true );
 825                     break;
 826                 case CONVEX:
 827                     _convex_type_cbmi.setSelected( true );
 828                     break;
 829                 case CURVED:
 830                     _curved_type_cbmi.setSelected( true );
 831                     break;
 832                 case EURO_STYLE:
 833                     _euro_type_cbmi.setSelected( true );
 834                     break;
 835                 case ROUNDED:
 836                     _rounded_type_cbmi.setSelected( true );
 837                     break;
 838                 case RECTANGULAR:
 839                     _rectangular_type_cbmi.setSelected( true );
 840                     break;
 841                 case TRIANGULAR:
 842                     _triangular_type_cbmi.setSelected( true );
 843                     break;
 844                 case UNROOTED:
 845                     _unrooted_type_cbmi.setSelected( true );
 846                     break;
 847                 default:
 848                     throw new IllegalArgumentException( "unknown type: " + type );
 849             }
 850         }
 851         catch ( final NullPointerException np ) {
 852             // In all likelihood, this is caused by menu-less display.
 853         }
 854     }
 855
 856     void setTypeMenuToAllUnselected() {
 857         if ( _convex_type_cbmi != null ) {
 858             _convex_type_cbmi.setSelected( false );
 859         }
 860         if ( _curved_type_cbmi != null ) {
 861             _curved_type_cbmi.setSelected( false );
 862         }
 863         if ( _euro_type_cbmi != null ) {
 864             _euro_type_cbmi.setSelected( false );
 865         }
 866         if ( _rounded_type_cbmi != null ) {
 867             _rounded_type_cbmi.setSelected( false );
 868         }
 869         if ( _triangular_type_cbmi != null ) {
 870             _triangular_type_cbmi.setSelected( false );
 871         }
 872         if ( _rectangular_type_cbmi != null ) {
 873             _rectangular_type_cbmi.setSelected( false );
 874         }
 875         if ( _unrooted_type_cbmi != null ) {
 876             _unrooted_type_cbmi.setSelected( false );
 877         }
 878         if ( _circular_type_cbmi != null ) {
 879             _circular_type_cbmi.setSelected( false );
 880         }
 881     }
 882
 883     private void setupUI() {
 884         try {
 885             if ( getConfiguration().isUseNativeUI() ) {
 886                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 887             }
 888             else {
 889                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 890             }
 891         }
 892         catch ( final UnsupportedLookAndFeelException e ) {
 893             Util.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
 894         }
 895         catch ( final ClassNotFoundException e ) {
 896             Util.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
 897         }
 898         catch ( final InstantiationException e ) {
 899             Util.dieWithSystemError( "InstantiationException: " + e.toString() );
 900         }
 901         catch ( final IllegalAccessException e ) {
 902             Util.dieWithSystemError( "IllegalAccessException: " + e.toString() );
 903         }
 904         catch ( final Exception e ) {
 905             Util.dieWithSystemError( e.toString() );
 906         }
 907     }
 908
 909     @Override
 910     public void start() {
 911         if ( getMainPanel() != null ) {
 912             getMainPanel().validate();
 913         }
 914         requestFocus();
 915         requestFocusInWindow();
 916         requestFocus();
 917         Util.printAppletMessage( NAME, "started" );
 918     }
 919
 920     void switchColors() {
 921         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 922         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 923         csc.setVisible( true );
 924         getMainPanel().setTreeColorSet( colorset );
 925     }
 926
 927     void typeChanged( final Object o ) {
 928         updateTypeCheckboxes( getOptions(), o );
 929         updateOptions( getOptions() );
 930         if ( getCurrentTreePanel() != null ) {
 931             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
 932             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
 933             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 934                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
 935                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 936                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
 937                 getCurrentTreePanel().getControlPanel().showWhole();
 938             }
 939             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
 940                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
 941             }
 942             else {
 943                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
 944             }
 945             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
 946             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
 947         }
 948     }
 949
 950     void updateOptions( final Options options ) {
 951         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
 952         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
 953                 && _background_gradient_cbmi.isSelected() );
 954         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
 955         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
 956                 && _abbreviate_scientific_names.isSelected() );
 957         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
 958                 && _color_labels_same_as_parent_branch.isSelected() );
 959         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
 960                 && _show_default_node_shapes_cbmi.isSelected() );
 961         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
 962                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
 963         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
 964             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
 965         }
 966         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
 967             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 968         }
 969         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
 970             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 971         }
 972         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
 973                 && _search_case_senstive_cbmi.isSelected() );
 974         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
 975             options.setShowScale( _show_scale_cbmi.isSelected() );
 976         }
 977         if ( _label_direction_cbmi != null ) {
 978             if ( _label_direction_cbmi.isSelected() ) {
 979                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
 980             }
 981             else {
 982                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
 983             }
 984         }
 985         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
 986         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
 987             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
 988         }
 989         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
 990                 && _search_whole_words_only_cbmi.isSelected() );
 991         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
 992                 && _inverse_search_result_cbmi.isSelected() );
 993         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
 994             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
 995         }
 996         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
 997             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
 998         }
 999         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1000             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1001         }
1002         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1003             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1004         }
1005         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1006             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1007         }
1008         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1009             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1010         }
1011         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1012             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1013         }
1014         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1015             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1016         }
1017     }
1018
1019     void updateTypeCheckboxes( final Options options, final Object o ) {
1020         setTypeMenuToAllUnselected();
1021         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1022     }
1023
1024     void viewAsNexus() {
1025         removeTextFrame();
1026         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1027                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1028             return;
1029         }
1030         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus() );
1031     }
1032
1033     void viewAsNH() {
1034         removeTextFrame();
1035         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1036                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1037             return;
1038         }
1039         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire( false ) );
1040     }
1041
1042     void viewAsNHX() {
1043         removeTextFrame();
1044         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1045                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1046             return;
1047         }
1048         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() );
1049     }
1050
1051     void viewAsXML() {
1052         removeTextFrame();
1053         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1054                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1055             return;
1056         }
1057         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) );
1058     }
1059
1060     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1061         for( final TreePanel tree_panel : treepanels ) {
1062             tree_panel.setTextAntialias();
1063         }
1064     }
1065 }