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