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