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