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