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.ByteArrayOutputStream;
  11 import java.io.File;
  12 import java.io.IOException;
  13 import java.net.URL;
  14 import java.util.List;
  15
  16 import javax.swing.ButtonGroup;
  17 import javax.swing.JApplet;
  18 import javax.swing.JCheckBoxMenuItem;
  19 import javax.swing.JMenu;
  20 import javax.swing.JMenuBar;
  21 import javax.swing.JMenuItem;
  22 import javax.swing.JOptionPane;
  23 import javax.swing.JRadioButtonMenuItem;
  24 import javax.swing.UIManager;
  25 import javax.swing.UnsupportedLookAndFeelException;
  26 import javax.swing.event.ChangeEvent;
  27 import javax.swing.event.ChangeListener;
  28
  29 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  30 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  31 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  32 import org.forester.archaeopteryx.Util.GraphicsExportType;
  33 import org.forester.phylogeny.Phylogeny;
  34 import org.forester.phylogeny.data.SequenceRelation;
  35 import org.forester.util.ForesterConstants;
  36 import org.forester.util.ForesterUtil;
  37 import org.apache.commons.codec.binary.Base64;
  38
  39 // Use like this:
  40 // <applet archive="forester.jar"
  41 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  42 // codebase="http://www.myserver.org/path/to/forester"
  43 // width="600"
  44 // height="500"
  45 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  46 // <param name="url_of_tree_to_load"
  47 // value="http://www.myserver.org/examples/data/apaf.xml">
  48 // <param name="config_file"
  49 // value="http://www.myserver.org/examples/config/config_file.txt">
  50 // </applet>
  51 public class ArchaeopteryxE extends JApplet implements ActionListener {
  52
  53     private final static String  NAME             = "ArchaeopteryxE";
  54     private static final long    serialVersionUID = -1220055577935759443L;
  55     private Configuration        _configuration;
  56     private MainPanelApplets     _main_panel;
  57     private JMenuBar             _jmenubar;
  58     private JMenu                _options_jmenu;
  59     private JMenu                _font_size_menu;
  60     private JMenuItem            _super_tiny_fonts_mi;
  61     private JMenuItem            _tiny_fonts_mi;
  62     private JMenuItem            _small_fonts_mi;
  63     private JMenuItem            _medium_fonts_mi;
  64     private JMenuItem            _large_fonts_mi;
  65     private TextFrame            _textframe;
  66     private JMenu                _tools_menu;
  67     private JMenuItem            _taxcolor_item;
  68     private JMenuItem            _confcolor_item;
  69     private JMenuItem            _midpoint_root_item;
  70     private JMenu                _view_jmenu;
  71     private JMenuItem            _view_as_XML_item;
  72     private JMenuItem            _view_as_NH_item;
  73     private JMenuItem            _view_as_NHX_item;
  74     private JMenuItem            _view_as_nexus_item;
  75     private JMenu                _type_menu;
  76     private JCheckBoxMenuItem    _rectangular_type_cbmi;
  77     private JCheckBoxMenuItem    _triangular_type_cbmi;
  78     private JCheckBoxMenuItem    _curved_type_cbmi;
  79     private JCheckBoxMenuItem    _convex_type_cbmi;
  80     private JCheckBoxMenuItem    _euro_type_cbmi;
  81     private JCheckBoxMenuItem    _rounded_type_cbmi;
  82     private JCheckBoxMenuItem    _unrooted_type_cbmi;
  83     private JCheckBoxMenuItem    _circular_type_cbmi;
  84     private JMenuItem            _help_item;
  85     private JMenuItem            _about_item;
  86     private JMenu                _help_jmenu;
  87     private JMenuItem            _website_item;
  88     private JMenuItem            _phyloxml_website_item;
  89     private JMenuItem            _phyloxml_ref_item;
  90     private JMenuItem            _aptx_ref_item;
  91     private JMenuItem            _remove_branch_color_item;
  92     private JMenuItem            _infer_common_sn_names_item;
  93     private JCheckBoxMenuItem    _show_domain_labels;
  94     private JCheckBoxMenuItem    _color_labels_same_as_parent_branch;
  95     private JCheckBoxMenuItem    _abbreviate_scientific_names;
  96     private JCheckBoxMenuItem    _screen_antialias_cbmi;
  97     private JCheckBoxMenuItem    _background_gradient_cbmi;
  98     private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
  99     private JRadioButtonMenuItem _uniform_cladograms_rbmi;
 100     private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
 101     private Options              _options;
 102     private JMenuItem            _choose_font_mi;
 103     private JMenuItem            _switch_colors_mi;
 104     JCheckBoxMenuItem            _label_direction_cbmi;
 105     private JCheckBoxMenuItem    _show_scale_cbmi;
 106     private JCheckBoxMenuItem    _search_case_senstive_cbmi;
 107     private JCheckBoxMenuItem    _search_whole_words_only_cbmi;
 108     private JCheckBoxMenuItem    _inverse_search_result_cbmi;
 109     private JCheckBoxMenuItem    _show_overview_cbmi;
 110     private JMenuItem            _choose_minimal_confidence_mi;
 111     private JCheckBoxMenuItem    _show_branch_length_values_cbmi;
 112     private JMenuItem            _collapse_species_specific_subtrees;
 113     private JMenuItem            _overview_placment_mi;
 114     private ButtonGroup          _radio_group_1;
 115     private JCheckBoxMenuItem    _show_default_node_shapes_cbmi;
 116     private JMenuItem            _cycle_node_shape_mi;
 117     private JMenuItem            _cycle_node_fill_mi;
 118     private JMenuItem            _choose_node_size_mi;
 119     private JCheckBoxMenuItem    _taxonomy_colorize_node_shapes_cbmi;
 120
 121     @Override
 122     public void actionPerformed( final ActionEvent e ) {
 123         final Object o = e.getSource();
 124         if ( o == _midpoint_root_item ) {
 125             getMainPanel().getCurrentTreePanel().midpointRoot();
 126         }
 127         else if ( o == _taxcolor_item ) {
 128             getMainPanel().getCurrentTreePanel().taxColor();
 129         }
 130         else if ( o == _confcolor_item ) {
 131             getMainPanel().getCurrentTreePanel().confColor();
 132         }
 133         else if ( o == _infer_common_sn_names_item ) {
 134             if ( getCurrentTreePanel() != null ) {
 135                 getCurrentTreePanel().inferCommonPartOfScientificNames();
 136             }
 137         }
 138         else if ( o == _collapse_species_specific_subtrees ) {
 139             if ( getCurrentTreePanel() != null ) {
 140                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 141             }
 142         }
 143         else if ( o == _remove_branch_color_item ) {
 144             removeBranchColors();
 145         }
 146         else if ( o == _switch_colors_mi ) {
 147             switchColors();
 148         }
 149         else if ( o == _view_as_NH_item ) {
 150             viewAsNH();
 151         }
 152         else if ( o == _view_as_NHX_item ) {
 153             viewAsNHX();
 154         }
 155         else if ( o == _view_as_XML_item ) {
 156             viewAsXML();
 157         }
 158         else if ( o == _view_as_nexus_item ) {
 159             viewAsNexus();
 160         }
 161         else if ( o == _super_tiny_fonts_mi ) {
 162             if ( getCurrentTreePanel() != null ) {
 163                 getCurrentTreePanel().setSuperTinyFonts();
 164                 getCurrentTreePanel().repaint();
 165             }
 166         }
 167         else if ( o == _tiny_fonts_mi ) {
 168             if ( getCurrentTreePanel() != null ) {
 169                 getCurrentTreePanel().setTinyFonts();
 170                 getCurrentTreePanel().repaint();
 171             }
 172         }
 173         else if ( o == _small_fonts_mi ) {
 174             if ( getCurrentTreePanel() != null ) {
 175                 getCurrentTreePanel().setSmallFonts();
 176                 getCurrentTreePanel().repaint();
 177             }
 178         }
 179         else if ( o == _medium_fonts_mi ) {
 180             if ( getCurrentTreePanel() != null ) {
 181                 getCurrentTreePanel().setMediumFonts();
 182                 getCurrentTreePanel().repaint();
 183             }
 184         }
 185         else if ( o == _large_fonts_mi ) {
 186             if ( getCurrentTreePanel() != null ) {
 187                 getCurrentTreePanel().setLargeFonts();
 188                 getCurrentTreePanel().repaint();
 189             }
 190         }
 191         else if ( o == _choose_font_mi ) {
 192             chooseFont();
 193         }
 194         else if ( o == _choose_minimal_confidence_mi ) {
 195             chooseMinimalConfidence();
 196         }
 197         else if ( o == _choose_node_size_mi ) {
 198             MainFrame.chooseNodeSize( getOptions(), this );
 199         }
 200         else if ( o == _overview_placment_mi ) {
 201             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 202         }
 203         else if ( o == _cycle_node_fill_mi ) {
 204             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 205         }
 206         else if ( o == _cycle_node_shape_mi ) {
 207             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 208         }
 209         else if ( o == _non_lined_up_cladograms_rbmi ) {
 210             updateOptions( getOptions() );
 211             _main_panel.getControlPanel().showWhole();
 212         }
 213         else if ( o == _uniform_cladograms_rbmi ) {
 214             updateOptions( getOptions() );
 215             _main_panel.getControlPanel().showWhole();
 216         }
 217         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 218             updateOptions( getOptions() );
 219             _main_panel.getControlPanel().showWhole();
 220         }
 221         else if ( o == _search_case_senstive_cbmi ) {
 222             updateOptions( getOptions() );
 223             getMainPanel().getControlPanel().search();
 224         }
 225         else if ( o == _search_whole_words_only_cbmi ) {
 226             updateOptions( getOptions() );
 227             getMainPanel().getControlPanel().search();
 228         }
 229         else if ( o == _inverse_search_result_cbmi ) {
 230             updateOptions( getOptions() );
 231             getMainPanel().getControlPanel().search();
 232         }
 233         else if ( o == _show_scale_cbmi ) {
 234             updateOptions( getOptions() );
 235         }
 236         else if ( o == _show_branch_length_values_cbmi ) {
 237             updateOptions( getOptions() );
 238         }
 239         else if ( o == _label_direction_cbmi ) {
 240             updateOptions( getOptions() );
 241         }
 242         else if ( o == _show_overview_cbmi ) {
 243             updateOptions( getOptions() );
 244             if ( getCurrentTreePanel() != null ) {
 245                 getCurrentTreePanel().updateOvSizes();
 246             }
 247         }
 248         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 249                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 250                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 251             typeChanged( o );
 252         }
 253         else if ( o == _screen_antialias_cbmi ) {
 254             updateOptions( getOptions() );
 255             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 256         }
 257         else if ( o == _background_gradient_cbmi ) {
 258             updateOptions( getOptions() );
 259         }
 260         else if ( o == _show_domain_labels ) {
 261             updateOptions( getOptions() );
 262         }
 263         else if ( o == _color_labels_same_as_parent_branch ) {
 264             updateOptions( getOptions() );
 265         }
 266         else if ( o == _show_default_node_shapes_cbmi ) {
 267             updateOptions( getOptions() );
 268         }
 269         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 270             updateOptions( getOptions() );
 271         }
 272         else if ( o == _about_item ) {
 273             MainFrame.about();
 274         }
 275         else if ( o == _help_item ) {
 276             MainFrame.help( getConfiguration().getWebLinks() );
 277         }
 278         else if ( o == _website_item ) {
 279             try {
 280                 Util.openWebsite( Constants.APTX_WEB_SITE, true, this );
 281             }
 282             catch ( final IOException e1 ) {
 283                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 284             }
 285         }
 286         else if ( o == _phyloxml_website_item ) {
 287             try {
 288                 Util.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 289             }
 290             catch ( final IOException e1 ) {
 291                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 292             }
 293         }
 294         else if ( o == _aptx_ref_item ) {
 295             try {
 296                 Util.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 297             }
 298             catch ( final IOException e1 ) {
 299                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 300             }
 301         }
 302         else if ( o == _phyloxml_ref_item ) {
 303             try {
 304                 Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 305             }
 306             catch ( final IOException e1 ) {
 307                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 308             }
 309         }
 310         repaint();
 311     }
 312
 313     /**
 314      * This method returns the current phylogeny as a string in the chosen format
 315      *
 316      * @param format must be NH, NHX, NEXUS or PHYLOXML
 317      * @return the phylogeny string
 318      * @author Herve Menager
 319      */
 320     public String getCurrentPhylogeny( final String format ) {
 321         removeTextFrame();
 322         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 323                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 324             return new String();
 325         }
 326         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 327             case NH:
 328                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 329             case NHX:
 330                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 331             case NEXUS:
 332                 return getMainPanel().getCurrentPhylogeny().toNexus();
 333             case PHYLOXML:
 334                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 335             default:
 336                 break;
 337         }
 338         return new String();
 339     }
 340
 341     /**
 342      * This method returns a view of the current phylogeny in a chosen
 343      * graphics format, base64-encoded in a string so that in can be used
 344      * from javascript.
 345      *
 346      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 347      * @return the phylogeny string
 348      * @author Herve Menager
 349      */
 350     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 351         ByteArrayOutputStream baos = new ByteArrayOutputStream();
 352         try{
 353             Util.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 354                                                                 _main_panel.getWidth(),
 355                                                                 _main_panel.getHeight(),
 356                                                                 this.getCurrentTreePanel(),
 357                                                                 getCurrentTreePanel().getControlPanel(),
 358                                                                 GraphicsExportType.valueOf(format),
 359                                                                 getOptions());
 360         }catch(IOException ioe){
 361             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 362             ioe.printStackTrace();
 363             JOptionPane.showMessageDialog( this,
 364                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 365                                            "Failed to generate graphics",
 366                                            JOptionPane.ERROR_MESSAGE );
 367             return null;
 368         }
 369         byte[] bytes = baos.toByteArray();
 370         String dataImg = Base64.encodeBase64String(bytes);
 371         return dataImg;
 372     }
 373
 374     void buildFontSizeMenu() {
 375         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 376         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 377         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 378         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 379         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 380         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 381         customizeJMenuItem( _super_tiny_fonts_mi );
 382         customizeJMenuItem( _tiny_fonts_mi );
 383         customizeJMenuItem( _small_fonts_mi );
 384         customizeJMenuItem( _medium_fonts_mi );
 385         customizeJMenuItem( _large_fonts_mi );
 386         _jmenubar.add( _font_size_menu );
 387     }
 388
 389     void buildHelpMenu() {
 390         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 391         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 392         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 393         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 394         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 395         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 396         _help_jmenu.addSeparator();
 397         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 398         customizeJMenuItem( _help_item );
 399         customizeJMenuItem( _website_item );
 400         customizeJMenuItem( _phyloxml_website_item );
 401         customizeJMenuItem( _aptx_ref_item );
 402         customizeJMenuItem( _phyloxml_ref_item );
 403         customizeJMenuItem( _about_item );
 404         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 405         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 406         _jmenubar.add( _help_jmenu );
 407     }
 408
 409     void buildOptionsMenu() {
 410         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 411         _options_jmenu.addChangeListener( new ChangeListener() {
 412
 413             @Override
 414             public void stateChanged( final ChangeEvent e ) {
 415                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 416                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 417                 MainFrame
 418                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 419                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 420                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 421                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 422                                                                      _show_scale_cbmi,
 423                                                                      _show_branch_length_values_cbmi,
 424                                                                      _non_lined_up_cladograms_rbmi,
 425                                                                      _uniform_cladograms_rbmi,
 426                                                                      _ext_node_dependent_cladogram_rbmi,
 427                                                                      _label_direction_cbmi );
 428                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 429                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 430                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 431             }
 432         } );
 433         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 434                                                                 getConfiguration() ) );
 435         _options_jmenu
 436                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 437         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 438         _options_jmenu
 439                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 440         _radio_group_1 = new ButtonGroup();
 441         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 442         _radio_group_1.add( _uniform_cladograms_rbmi );
 443         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 444         //
 445         _options_jmenu
 446                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 447         _options_jmenu
 448                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 449         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 450         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 451         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 452         //
 453         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 454         _options_jmenu
 455                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 456         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 457         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 458         _options_jmenu
 459                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 460         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 461         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 462         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 463         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 464         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 465         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 466             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 467         }
 468         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 469         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 470         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 471         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 472         _options_jmenu.addSeparator();
 473         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 474                                                                 getConfiguration() ) );
 475         _options_jmenu
 476                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 477         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 478         _options_jmenu
 479                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 480         customizeJMenuItem( _choose_font_mi );
 481         customizeJMenuItem( _choose_minimal_confidence_mi );
 482         customizeJMenuItem( _switch_colors_mi );
 483         customizeJMenuItem( _overview_placment_mi );
 484         customizeCheckBoxMenuItem( _label_direction_cbmi,
 485                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 486         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 487         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 488         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 489         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 490         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 491         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 492         customizeJMenuItem( _cycle_node_shape_mi );
 493         customizeJMenuItem( _cycle_node_fill_mi );
 494         customizeJMenuItem( _choose_node_size_mi );
 495         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 496         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 497         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 498         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 499                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 500         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 501                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 502         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 503                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 504         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 505         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 506         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 507         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 508         _jmenubar.add( _options_jmenu );
 509     }
 510
 511     void buildToolsMenu() {
 512         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 513         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 514         customizeJMenuItem( _confcolor_item );
 515         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 516         customizeJMenuItem( _taxcolor_item );
 517         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 518         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 519         customizeJMenuItem( _remove_branch_color_item );
 520         _tools_menu.addSeparator();
 521         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 522         customizeJMenuItem( _midpoint_root_item );
 523         _tools_menu.addSeparator();
 524         _tools_menu
 525                 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 526         customizeJMenuItem( _infer_common_sn_names_item );
 527         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 528         customizeJMenuItem( _collapse_species_specific_subtrees );
 529         _jmenubar.add( _tools_menu );
 530     }
 531
 532     void buildTypeMenu() {
 533         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 534         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 535         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 536         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 537         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 538         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 539         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 540         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 541         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 542         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 543         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 544         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 545         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 546         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 547         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 548         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 549         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 550         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 551         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 552         initializeTypeMenu( getOptions() );
 553         _jmenubar.add( _type_menu );
 554     }
 555
 556     void buildViewMenu() {
 557         _view_jmenu = MainFrame.createMenu( "View as Text", getConfiguration() );
 558         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 559         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 560         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 561         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 562         customizeJMenuItem( _view_as_NH_item );
 563         customizeJMenuItem( _view_as_NHX_item );
 564         customizeJMenuItem( _view_as_XML_item );
 565         customizeJMenuItem( _view_as_nexus_item );
 566         _jmenubar.add( _view_jmenu );
 567     }
 568
 569     private void chooseFont() {
 570         final FontChooser fc = new FontChooser();
 571         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
 572         fc.showDialog( this, "Select the Base Font" );
 573         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
 574     }
 575
 576     private void chooseMinimalConfidence() {
 577         final String s = ( String ) JOptionPane
 578                 .showInputDialog( this,
 579                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
 580                                           + getOptions().getMinConfidenceValue() + "]\n",
 581                                   "Minimal Confidence Value",
 582                                   JOptionPane.QUESTION_MESSAGE,
 583                                   null,
 584                                   null,
 585                                   getOptions().getMinConfidenceValue() );
 586         if ( !ForesterUtil.isEmpty( s ) ) {
 587             boolean success = true;
 588             double m = 0.0;
 589             final String m_str = s.trim();
 590             if ( !ForesterUtil.isEmpty( m_str ) ) {
 591                 try {
 592                     m = Double.parseDouble( m_str );
 593                 }
 594                 catch ( final Exception ex ) {
 595                     success = false;
 596                 }
 597             }
 598             else {
 599                 success = false;
 600             }
 601             if ( success && ( m >= 0.0 ) ) {
 602                 getOptions().setMinConfidenceValue( m );
 603             }
 604         }
 605     }
 606
 607     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 608         if ( item != null ) {
 609             item.setFont( MainFrame.menu_font );
 610             if ( !getConfiguration().isUseNativeUI() ) {
 611                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 612                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 613             }
 614             item.setSelected( is_selected );
 615             item.addActionListener( this );
 616         }
 617     }
 618
 619     void customizeJMenuItem( final JMenuItem jmi ) {
 620         jmi.setFont( MainFrame.menu_font );
 621         if ( !getConfiguration().isUseNativeUI() ) {
 622             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 623             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 624         }
 625         jmi.addActionListener( this );
 626     }
 627
 628     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 629         if ( item != null ) {
 630             item.setFont( MainFrame.menu_font );
 631             if ( !getConfiguration().isUseNativeUI() ) {
 632                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 633                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 634             }
 635             item.setSelected( is_selected );
 636             item.addActionListener( this );
 637         }
 638     }
 639
 640     @Override
 641     public void destroy() {
 642         Util.printAppletMessage( NAME, "going to be destroyed " );
 643         removeTextFrame();
 644         if ( getMainPanel() != null ) {
 645             getMainPanel().terminate();
 646         }
 647     }
 648
 649     Configuration getConfiguration() {
 650         return _configuration;
 651     }
 652
 653     TreePanel getCurrentTreePanel() {
 654         return getMainPanel().getCurrentTreePanel();
 655     }
 656
 657     JCheckBoxMenuItem getlabelDirectionCbmi() {
 658         return _label_direction_cbmi;
 659     }
 660
 661     private MainPanel getMainPanel() {
 662         return _main_panel;
 663     }
 664
 665     public Options getOptions() {
 666         return _options;
 667     }
 668
 669     Options getOtions() {
 670         return _options;
 671     }
 672
 673     @Override
 674     public void init() {
 675         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 676         Util.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 677         final Configuration configuration = new Configuration( config_filename, true, true );
 678         setConfiguration( configuration );
 679         setOptions( Options.createInstance( configuration ) );
 680         setupUI();
 681         URL phys_url = null;
 682         Phylogeny[] phys = null;
 683         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 684         Util.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 685         // Get URL to tree file
 686         if ( phys_url_string != null ) {
 687             try {
 688                 phys_url = new URL( phys_url_string );
 689             }
 690             catch ( final Exception e ) {
 691                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 692                 e.printStackTrace();
 693                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 694                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 695             }
 696         }
 697         // Load the tree from URL
 698         if ( phys_url != null ) {
 699             try {
 700                 phys = Util.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
 701             }
 702             catch ( final Exception e ) {
 703                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 704                 e.printStackTrace();
 705                 JOptionPane.showMessageDialog( this,
 706                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 707                                                "Failed to read phylogenies",
 708                                                JOptionPane.ERROR_MESSAGE );
 709             }
 710         }
 711         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 712             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 713             JOptionPane.showMessageDialog( this,
 714                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 715                                            "Failed to read phylogenies",
 716                                            JOptionPane.ERROR_MESSAGE );
 717             return;
 718         }
 719         else {
 720             Util.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 721         }
 722         setVisible( false );
 723         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 724         _jmenubar = new JMenuBar();
 725         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 726             if ( !getConfiguration().isUseNativeUI() ) {
 727                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 728             }
 729             buildToolsMenu();
 730             buildViewMenu();
 731             buildFontSizeMenu();
 732             buildOptionsMenu();
 733             buildTypeMenu();
 734             buildHelpMenu();
 735             setJMenuBar( _jmenubar );
 736         }
 737         final Container contentpane = getContentPane();
 738         contentpane.setLayout( new BorderLayout() );
 739         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 740         addComponentListener( new ComponentAdapter() {
 741
 742             @Override
 743             public void componentResized( final ComponentEvent e ) {
 744                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 745                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 746                                                                                            .getWidth(),
 747                                                                                    getMainPanel().getCurrentTreePanel()
 748                                                                                            .getHeight(),
 749                                                                                    false );
 750                 }
 751             }
 752         } );
 753         if ( getConfiguration().isUseTabbedDisplay() ) {
 754             Util.printAppletMessage( NAME, "using tabbed display" );
 755             Util.addPhylogeniesToTabs( phys,
 756                                        new File( phys_url.getFile() ).getName(),
 757                                        phys_url.toString(),
 758                                        getConfiguration(),
 759                                        getMainPanel() );
 760         }
 761         else {
 762             Util.printAppletMessage( NAME, "not using tabbed display" );
 763             Util.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 764         }
 765         validate();
 766         setName( NAME );
 767         getMainPanel().getControlPanel().showWholeAll();
 768         getMainPanel().getControlPanel().showWhole();
 769         System.gc();
 770         Util.printAppletMessage( NAME, "successfully initialized" );
 771         /* GUILHEM_BEG */
 772         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 773         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 774                 .getRelevantSequenceRelationTypes() ) {
 775             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 776         }
 777         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 778         if ( default_relation != null ) {
 779             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 780         }
 781         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 782         if ( default_sequence != null ) {
 783             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 784             /* GUILHEM_END */
 785         }
 786         setVisible( true );
 787     }
 788
 789     void initializeTypeMenu( final Options options ) {
 790         setTypeMenuToAllUnselected();
 791         try {
 792             switch ( options.getPhylogenyGraphicsType() ) {
 793                 case CONVEX:
 794                     _convex_type_cbmi.setSelected( true );
 795                     break;
 796                 case CURVED:
 797                     _curved_type_cbmi.setSelected( true );
 798                     break;
 799                 case EURO_STYLE:
 800                     _euro_type_cbmi.setSelected( true );
 801                     break;
 802                 case ROUNDED:
 803                     _rounded_type_cbmi.setSelected( true );
 804                     break;
 805                 case TRIANGULAR:
 806                     _triangular_type_cbmi.setSelected( true );
 807                     break;
 808                 case UNROOTED:
 809                     _unrooted_type_cbmi.setSelected( true );
 810                     break;
 811                 case CIRCULAR:
 812                     _circular_type_cbmi.setSelected( true );
 813                     break;
 814                 default:
 815                     _rectangular_type_cbmi.setSelected( true );
 816                     break;
 817             }
 818         }
 819         catch ( final NullPointerException np ) {
 820             // In all likelihood, this is caused by menu-less display.
 821         }
 822     }
 823
 824     private boolean isScreenAntialias() {
 825         return true;
 826     }
 827
 828     private void removeBranchColors() {
 829         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 830             Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
 831         }
 832     }
 833
 834     void removeTextFrame() {
 835         if ( _textframe != null ) {
 836             _textframe.close();
 837             _textframe = null;
 838         }
 839     }
 840
 841     void setConfiguration( final Configuration configuration ) {
 842         _configuration = configuration;
 843     }
 844
 845     private void setMainPanel( final MainPanelApplets main_panel ) {
 846         _main_panel = main_panel;
 847     }
 848
 849     void setOptions( final Options options ) {
 850         _options = options;
 851     }
 852
 853     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 854         setTypeMenuToAllUnselected();
 855         try {
 856             switch ( type ) {
 857                 case CIRCULAR:
 858                     _circular_type_cbmi.setSelected( true );
 859                     break;
 860                 case CONVEX:
 861                     _convex_type_cbmi.setSelected( true );
 862                     break;
 863                 case CURVED:
 864                     _curved_type_cbmi.setSelected( true );
 865                     break;
 866                 case EURO_STYLE:
 867                     _euro_type_cbmi.setSelected( true );
 868                     break;
 869                 case ROUNDED:
 870                     _rounded_type_cbmi.setSelected( true );
 871                     break;
 872                 case RECTANGULAR:
 873                     _rectangular_type_cbmi.setSelected( true );
 874                     break;
 875                 case TRIANGULAR:
 876                     _triangular_type_cbmi.setSelected( true );
 877                     break;
 878                 case UNROOTED:
 879                     _unrooted_type_cbmi.setSelected( true );
 880                     break;
 881                 default:
 882                     throw new IllegalArgumentException( "unknown type: " + type );
 883             }
 884         }
 885         catch ( final NullPointerException np ) {
 886             // In all likelihood, this is caused by menu-less display.
 887         }
 888     }
 889
 890     void setTypeMenuToAllUnselected() {
 891         if ( _convex_type_cbmi != null ) {
 892             _convex_type_cbmi.setSelected( false );
 893         }
 894         if ( _curved_type_cbmi != null ) {
 895             _curved_type_cbmi.setSelected( false );
 896         }
 897         if ( _euro_type_cbmi != null ) {
 898             _euro_type_cbmi.setSelected( false );
 899         }
 900         if ( _rounded_type_cbmi != null ) {
 901             _rounded_type_cbmi.setSelected( false );
 902         }
 903         if ( _triangular_type_cbmi != null ) {
 904             _triangular_type_cbmi.setSelected( false );
 905         }
 906         if ( _rectangular_type_cbmi != null ) {
 907             _rectangular_type_cbmi.setSelected( false );
 908         }
 909         if ( _unrooted_type_cbmi != null ) {
 910             _unrooted_type_cbmi.setSelected( false );
 911         }
 912         if ( _circular_type_cbmi != null ) {
 913             _circular_type_cbmi.setSelected( false );
 914         }
 915     }
 916
 917     private void setupUI() {
 918         try {
 919             if ( getConfiguration().isUseNativeUI() ) {
 920                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 921             }
 922             else {
 923                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 924             }
 925         }
 926         catch ( final UnsupportedLookAndFeelException e ) {
 927             Util.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
 928         }
 929         catch ( final ClassNotFoundException e ) {
 930             Util.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
 931         }
 932         catch ( final InstantiationException e ) {
 933             Util.dieWithSystemError( "InstantiationException: " + e.toString() );
 934         }
 935         catch ( final IllegalAccessException e ) {
 936             Util.dieWithSystemError( "IllegalAccessException: " + e.toString() );
 937         }
 938         catch ( final Exception e ) {
 939             Util.dieWithSystemError( e.toString() );
 940         }
 941     }
 942
 943     @Override
 944     public void start() {
 945         if ( getMainPanel() != null ) {
 946             getMainPanel().validate();
 947         }
 948         requestFocus();
 949         requestFocusInWindow();
 950         requestFocus();
 951         Util.printAppletMessage( NAME, "started" );
 952     }
 953
 954     void switchColors() {
 955         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 956         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 957         csc.setVisible( true );
 958         getMainPanel().setTreeColorSet( colorset );
 959     }
 960
 961     void typeChanged( final Object o ) {
 962         updateTypeCheckboxes( getOptions(), o );
 963         updateOptions( getOptions() );
 964         if ( getCurrentTreePanel() != null ) {
 965             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
 966             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
 967             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 968                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
 969                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 970                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
 971                 getCurrentTreePanel().getControlPanel().showWhole();
 972             }
 973             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
 974                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
 975             }
 976             else {
 977                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
 978             }
 979             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
 980             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
 981         }
 982     }
 983
 984     void updateOptions( final Options options ) {
 985         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
 986         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
 987                 && _background_gradient_cbmi.isSelected() );
 988         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
 989         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
 990                 && _abbreviate_scientific_names.isSelected() );
 991         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
 992                 && _color_labels_same_as_parent_branch.isSelected() );
 993         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
 994                 && _show_default_node_shapes_cbmi.isSelected() );
 995         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
 996                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
 997         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
 998             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
 999         }
1000         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1001             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1002         }
1003         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1004             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1005         }
1006         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1007                 && _search_case_senstive_cbmi.isSelected() );
1008         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1009             options.setShowScale( _show_scale_cbmi.isSelected() );
1010         }
1011         if ( _label_direction_cbmi != null ) {
1012             if ( _label_direction_cbmi.isSelected() ) {
1013                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1014             }
1015             else {
1016                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1017             }
1018         }
1019         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1020         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1021             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1022         }
1023         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1024                 && _search_whole_words_only_cbmi.isSelected() );
1025         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1026                 && _inverse_search_result_cbmi.isSelected() );
1027         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1028             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1029         }
1030         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1031             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1032         }
1033         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1034             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1035         }
1036         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1037             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1038         }
1039         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1040             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1041         }
1042         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1043             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1044         }
1045         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1046             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1047         }
1048         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1049             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1050         }
1051     }
1052
1053     void updateTypeCheckboxes( final Options options, final Object o ) {
1054         setTypeMenuToAllUnselected();
1055         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1056     }
1057
1058     void viewAsNexus() {
1059         removeTextFrame();
1060         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1061                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1062             return;
1063         }
1064         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus() );
1065     }
1066
1067     void viewAsNH() {
1068         removeTextFrame();
1069         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1070                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1071             return;
1072         }
1073         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire( false ) );
1074     }
1075
1076     void viewAsNHX() {
1077         removeTextFrame();
1078         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1079                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1080             return;
1081         }
1082         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() );
1083     }
1084
1085     void viewAsXML() {
1086         removeTextFrame();
1087         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
1088                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1089             return;
1090         }
1091         _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) );
1092     }
1093
1094     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1095         for( final TreePanel tree_panel : treepanels ) {
1096             tree_panel.setTextAntialias();
1097         }
1098     }
1099 }