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.LinkedList;
  15 import java.util.List;
  16 import java.util.NoSuchElementException;
  17
  18 import javax.swing.ButtonGroup;
  19 import javax.swing.JApplet;
  20 import javax.swing.JCheckBoxMenuItem;
  21 import javax.swing.JMenu;
  22 import javax.swing.JMenuBar;
  23 import javax.swing.JMenuItem;
  24 import javax.swing.JOptionPane;
  25 import javax.swing.JRadioButtonMenuItem;
  26 import javax.swing.UIManager;
  27 import javax.swing.UnsupportedLookAndFeelException;
  28 import javax.swing.event.ChangeEvent;
  29 import javax.swing.event.ChangeListener;
  30
  31 import org.apache.commons.codec.binary.Base64;
  32 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  33 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  34 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  35 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  36 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.PhylogenyMethods;
  39 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  40 import org.forester.phylogeny.data.SequenceRelation;
  41 import org.forester.sdi.GSDI;
  42 import org.forester.sdi.GSDIR;
  43 import org.forester.sdi.SDIException;
  44 import org.forester.util.ForesterConstants;
  45 import org.forester.util.ForesterUtil;
  46
  47 // Use like this:
  48 // <applet archive="forester.jar"
  49 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  50 // codebase="http://www.myserver.org/path/to/forester"
  51 // width="600"
  52 // height="500"
  53 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  54 // <param name="url_of_tree_to_load"
  55 // value="http://www.myserver.org/examples/data/apaf.xml">
  56 // <param name="config_file"
  57 // value="http://www.myserver.org/examples/config/config_file.txt">
  58 // </applet>
  59 public class ArchaeopteryxE extends JApplet implements ActionListener {
  60
  61     private final static String         NAME             = "ArchaeopteryxE";
  62     private static final long           serialVersionUID = -1220055577935759443L;
  63     private Configuration               _configuration;
  64     private MainPanelApplets            _mainpanel;
  65     private JMenuBar                    _jmenubar;
  66     private JMenu                       _options_jmenu;
  67     private JMenu                       _font_size_menu;
  68     private JMenuItem                   _super_tiny_fonts_mi;
  69     private JMenuItem                   _tiny_fonts_mi;
  70     private JMenuItem                   _small_fonts_mi;
  71     private JMenuItem                   _medium_fonts_mi;
  72     private JMenuItem                   _large_fonts_mi;
  73     private JMenu                       _tools_menu;
  74     private JMenuItem                   _taxcolor_item;
  75     private JMenuItem                   _confcolor_item;
  76     private JMenuItem                   _midpoint_root_item;
  77     private JMenu                       _view_jmenu;
  78     private JMenuItem                   _view_as_XML_item;
  79     private JMenuItem                   _view_as_NH_item;
  80     private JMenuItem                   _view_as_nexus_item;
  81     private JMenuItem                   _display_basic_information_item;
  82     private JMenu                       _type_menu;
  83     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  84     private JCheckBoxMenuItem           _triangular_type_cbmi;
  85     private JCheckBoxMenuItem           _curved_type_cbmi;
  86     private JCheckBoxMenuItem           _convex_type_cbmi;
  87     private JCheckBoxMenuItem           _euro_type_cbmi;
  88     private JCheckBoxMenuItem           _rounded_type_cbmi;
  89     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  90     private JCheckBoxMenuItem           _circular_type_cbmi;
  91     private JMenuItem                   _help_item;
  92     private JMenuItem                   _about_item;
  93     private JMenu                       _help_jmenu;
  94     private JMenuItem                   _website_item;
  95     private JMenuItem                   _phyloxml_website_item;
  96     private JMenuItem                   _phyloxml_ref_item;
  97     private JMenuItem                   _aptx_ref_item;
  98     private JMenuItem                   _remove_branch_color_item;
  99     private JCheckBoxMenuItem           _show_domain_labels;
 100     private JCheckBoxMenuItem           _show_annotation_ref_source;
 101     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 102     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 103     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 104     private JCheckBoxMenuItem           _background_gradient_cbmi;
 105     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 106     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 107     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 108     private Options                     _options;
 109     private JMenuItem                   _choose_font_mi;
 110     private JMenuItem                   _switch_colors_mi;
 111     JCheckBoxMenuItem                   _label_direction_cbmi;
 112     private JCheckBoxMenuItem           _show_scale_cbmi;
 113     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 114     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 115     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 116     private JCheckBoxMenuItem           _show_overview_cbmi;
 117     private JMenuItem                   _choose_minimal_confidence_mi;
 118     private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 119     private JMenuItem                   _collapse_species_specific_subtrees;
 120     private JMenuItem                   _overview_placment_mi;
 121     private ButtonGroup                 _radio_group_1;
 122     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 123     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 124     private JMenuItem                   _cycle_node_shape_mi;
 125     private JMenuItem                   _cycle_node_fill_mi;
 126     private JMenuItem                   _choose_node_size_mi;
 127     private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 128     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 129     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 130     private JMenu                       _analysis_menu;
 131     private JMenuItem                   _gsdi_item;
 132     private JMenuItem                   _gsdir_item;
 133     private Phylogeny                   _species_tree;
 134
 135     @Override
 136     public void actionPerformed( final ActionEvent e ) {
 137         final Object o = e.getSource();
 138         if ( o == _midpoint_root_item ) {
 139             getMainPanel().getCurrentTreePanel().midpointRoot();
 140         }
 141         else if ( o == _gsdi_item ) {
 142             if ( isSubtreeDisplayed() ) {
 143                 return;
 144             }
 145             executeGSDI();
 146         }
 147         else if ( o == _gsdir_item ) {
 148             if ( isSubtreeDisplayed() ) {
 149                 return;
 150             }
 151             executeGSDIR();
 152         }
 153         else if ( o == _taxcolor_item ) {
 154             getMainPanel().getCurrentTreePanel().taxColor();
 155         }
 156         else if ( o == _confcolor_item ) {
 157             getMainPanel().getCurrentTreePanel().confColor();
 158         }
 159         else if ( o == _collapse_species_specific_subtrees ) {
 160             if ( getCurrentTreePanel() != null ) {
 161                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 162             }
 163         }
 164         else if ( o == _remove_branch_color_item ) {
 165             removeBranchColors();
 166         }
 167         else if ( o == _switch_colors_mi ) {
 168             switchColors();
 169         }
 170         else if ( o == _display_basic_information_item ) {
 171             displayBasicInformation();
 172         }
 173         else if ( o == _view_as_NH_item ) {
 174             viewAsNH();
 175         }
 176         else if ( o == _view_as_XML_item ) {
 177             viewAsXML();
 178         }
 179         else if ( o == _view_as_nexus_item ) {
 180             viewAsNexus();
 181         }
 182         else if ( o == _super_tiny_fonts_mi ) {
 183             if ( getCurrentTreePanel() != null ) {
 184                 getCurrentTreePanel().setSuperTinyFonts();
 185                 getCurrentTreePanel().repaint();
 186             }
 187         }
 188         else if ( o == _tiny_fonts_mi ) {
 189             if ( getCurrentTreePanel() != null ) {
 190                 getCurrentTreePanel().setTinyFonts();
 191                 getCurrentTreePanel().repaint();
 192             }
 193         }
 194         else if ( o == _small_fonts_mi ) {
 195             if ( getCurrentTreePanel() != null ) {
 196                 getCurrentTreePanel().setSmallFonts();
 197                 getCurrentTreePanel().repaint();
 198             }
 199         }
 200         else if ( o == _medium_fonts_mi ) {
 201             if ( getCurrentTreePanel() != null ) {
 202                 getCurrentTreePanel().setMediumFonts();
 203                 getCurrentTreePanel().repaint();
 204             }
 205         }
 206         else if ( o == _large_fonts_mi ) {
 207             if ( getCurrentTreePanel() != null ) {
 208                 getCurrentTreePanel().setLargeFonts();
 209                 getCurrentTreePanel().repaint();
 210             }
 211         }
 212         else if ( o == _choose_font_mi ) {
 213             chooseFont();
 214         }
 215         else if ( o == _choose_minimal_confidence_mi ) {
 216             chooseMinimalConfidence();
 217         }
 218         else if ( o == _choose_node_size_mi ) {
 219             MainFrame.chooseNodeSize( getOptions(), this );
 220         }
 221         else if ( o == _overview_placment_mi ) {
 222             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 223         }
 224         else if ( o == _cycle_node_fill_mi ) {
 225             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 226         }
 227         else if ( o == _cycle_node_shape_mi ) {
 228             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 229         }
 230         else if ( o == _non_lined_up_cladograms_rbmi ) {
 231             updateOptions( getOptions() );
 232             _mainpanel.getControlPanel().showWhole();
 233         }
 234         else if ( o == _uniform_cladograms_rbmi ) {
 235             updateOptions( getOptions() );
 236             _mainpanel.getControlPanel().showWhole();
 237         }
 238         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 239             updateOptions( getOptions() );
 240             _mainpanel.getControlPanel().showWhole();
 241         }
 242         else if ( o == _search_case_senstive_cbmi ) {
 243             updateOptions( getOptions() );
 244             getMainPanel().getControlPanel().search();
 245         }
 246         else if ( o == _search_whole_words_only_cbmi ) {
 247             updateOptions( getOptions() );
 248             getMainPanel().getControlPanel().search();
 249         }
 250         else if ( o == _inverse_search_result_cbmi ) {
 251             updateOptions( getOptions() );
 252             getMainPanel().getControlPanel().search();
 253         }
 254         else if ( o == _show_scale_cbmi ) {
 255             updateOptions( getOptions() );
 256         }
 257         else if ( o == _show_branch_length_values_cbmi ) {
 258             updateOptions( getOptions() );
 259         }
 260         else if ( o == _show_confidence_stddev_cbmi ) {
 261             updateOptions( getOptions() );
 262         }
 263         else if ( o == _label_direction_cbmi ) {
 264             updateOptions( getOptions() );
 265         }
 266         else if ( o == _abbreviate_scientific_names ) {
 267             updateOptions( getOptions() );
 268         }
 269         else if ( o == _show_overview_cbmi ) {
 270             updateOptions( getOptions() );
 271             if ( getCurrentTreePanel() != null ) {
 272                 getCurrentTreePanel().updateOvSizes();
 273             }
 274         }
 275         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 276                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 277                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 278             typeChanged( o );
 279         }
 280         else if ( o == _screen_antialias_cbmi ) {
 281             updateOptions( getOptions() );
 282             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 283         }
 284         else if ( o == _background_gradient_cbmi ) {
 285             updateOptions( getOptions() );
 286         }
 287         else if ( o == _show_domain_labels ) {
 288             updateOptions( getOptions() );
 289         }
 290         else if ( o == _color_labels_same_as_parent_branch ) {
 291             updateOptions( getOptions() );
 292         }
 293         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 294             updateOptions( getOptions() );
 295         }
 296         else if ( o == _show_default_node_shapes_external_cbmi ) {
 297             updateOptions( getOptions() );
 298         }
 299         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 300             updateOptions( getOptions() );
 301         }
 302         else if ( o == _about_item ) {
 303             MainFrame.about();
 304         }
 305         else if ( o == _help_item ) {
 306             help();
 307         }
 308         else if ( o == _website_item ) {
 309             try {
 310                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 311             }
 312             catch ( final IOException e1 ) {
 313                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 314             }
 315         }
 316         else if ( o == _phyloxml_website_item ) {
 317             try {
 318                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 319             }
 320             catch ( final IOException e1 ) {
 321                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 322             }
 323         }
 324         else if ( o == _aptx_ref_item ) {
 325             try {
 326                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 327             }
 328             catch ( final IOException e1 ) {
 329                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 330             }
 331         }
 332         else if ( o == _phyloxml_ref_item ) {
 333             try {
 334                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 335             }
 336             catch ( final IOException e1 ) {
 337                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 338             }
 339         }
 340         repaint();
 341     }
 342
 343     @Override
 344     public void destroy() {
 345         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 346         removeAllTextFrames();
 347         if ( getMainPanel() != null ) {
 348             getMainPanel().terminate();
 349         }
 350     }
 351
 352     /**
 353      * This method returns the current external node data which
 354      * has been selected by the user by clicking the "Return ..."
 355      * menu item. This method is expected to be called from Javascript or
 356      * something like it.
 357      *
 358      * @return current external node data as String
 359      */
 360     public String getCurrentExternalNodesDataBuffer() {
 361         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 362     }
 363
 364     public int getCurrentExternalNodesDataBufferChangeCounter() {
 365         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 366     }
 367
 368     public int getCurrentExternalNodesDataBufferLength() {
 369         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 370     }
 371
 372     /**
 373      * This method returns the current phylogeny as a string in the chosen format
 374      *
 375      * @param format must be NH, NHX, NEXUS or PHYLOXML
 376      * @return the phylogeny string
 377      * @author Herve Menager
 378      */
 379     public String getCurrentPhylogeny( final String format ) {
 380         removeAllTextFrames();
 381         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 382                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 383             return new String();
 384         }
 385         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 386             case NH:
 387                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 388             case NHX:
 389                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 390             case NEXUS:
 391                 return getMainPanel().getCurrentPhylogeny().toNexus();
 392             case PHYLOXML:
 393                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 394             default:
 395                 break;
 396         }
 397         return new String();
 398     }
 399
 400     /**
 401      * This method returns a view of the current phylogeny in a chosen
 402      * graphics format, base64-encoded in a string so that in can be used
 403      * from javascript.
 404      *
 405      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 406      * @return the phylogeny string
 407      * @author Herve Menager
 408      */
 409     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 410         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 411         try {
 412             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 413                                                                     _mainpanel.getWidth(),
 414                                                                     _mainpanel.getHeight(),
 415                                                                     getCurrentTreePanel(),
 416                                                                     getCurrentTreePanel().getControlPanel(),
 417                                                                     GraphicsExportType.valueOf( format ),
 418                                                                     getOptions() );
 419         }
 420         catch ( final IOException ioe ) {
 421             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 422             ioe.printStackTrace();
 423             JOptionPane.showMessageDialog( this,
 424                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 425                                            "Failed to generate graphics",
 426                                            JOptionPane.ERROR_MESSAGE );
 427             return null;
 428         }
 429         final byte[] bytes = baos.toByteArray();
 430         final String dataImg = Base64.encodeBase64String( bytes );
 431         return dataImg;
 432     }
 433
 434     public Options getOptions() {
 435         return _options;
 436     }
 437
 438     @Override
 439     public void init() {
 440         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 441         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 442         final Configuration configuration = new Configuration( config_filename, true, true, true );
 443         setConfiguration( configuration );
 444         setOptions( Options.createInstance( configuration ) );
 445         setupUI();
 446         URL phys_url = null;
 447         Phylogeny[] phys = null;
 448         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 449         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 450         // Get URL to tree file
 451         if ( tree_url_str != null ) {
 452             try {
 453                 phys_url = new URL( tree_url_str );
 454             }
 455             catch ( final Exception e ) {
 456                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 457                 e.printStackTrace();
 458                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 459                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 460             }
 461         }
 462         // Load the tree from URL
 463         if ( phys_url != null ) {
 464             try {
 465                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 466                                                         getConfiguration().isValidatePhyloXmlAgainstSchema(),
 467                                                         getConfiguration().isReplaceUnderscoresInNhParsing(),
 468                                                         getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 469                                                         getConfiguration().getTaxonomyExtraction(),
 470                                                         getConfiguration().isMidpointReroot() );
 471             }
 472             catch ( final Exception e ) {
 473                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 474                 e.printStackTrace();
 475                 JOptionPane.showMessageDialog( this,
 476                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 477                                                "Failed to read phylogenies",
 478                                                JOptionPane.ERROR_MESSAGE );
 479             }
 480         }
 481         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 482             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 483             JOptionPane.showMessageDialog( this,
 484                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 485                                            "Failed to read phylogenies",
 486                                            JOptionPane.ERROR_MESSAGE );
 487             return;
 488         }
 489         else {
 490             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 491         }
 492         //
 493         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 494         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 495             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 496             Phylogeny[] species_trees = null;
 497             try {
 498                 final URL species_tree_url = new URL( species_tree_url_str );
 499                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 500                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 501                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 502                                                                  false,
 503                                                                  TAXONOMY_EXTRACTION.NO,
 504                                                                  false );
 505             }
 506             catch ( final IOException e ) {
 507                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 508                         + "]" );
 509                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 510                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 511             }
 512             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 513                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 514                 if ( species_trees[ 0 ].isEmpty() ) {
 515                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 516                 }
 517                 else if ( !species_trees[ 0 ].isRooted() ) {
 518                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 519                 }
 520                 else {
 521                     setSpeciesTree( species_trees[ 0 ] );
 522                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 523                 }
 524             }
 525         }
 526         //
 527         setVisible( false );
 528         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 529         _jmenubar = new JMenuBar();
 530         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 531             if ( !getConfiguration().isUseNativeUI() ) {
 532                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 533             }
 534             if ( getSpeciesTree() != null ) {
 535                 buildAnalysisMenu();
 536             }
 537             buildToolsMenu();
 538             buildViewMenu();
 539             buildFontSizeMenu();
 540             buildOptionsMenu();
 541             buildTypeMenu();
 542             buildHelpMenu();
 543             setJMenuBar( _jmenubar );
 544         }
 545         final Container contentpane = getContentPane();
 546         contentpane.setLayout( new BorderLayout() );
 547         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 548         addComponentListener( new ComponentAdapter() {
 549
 550             @Override
 551             public void componentResized( final ComponentEvent e ) {
 552                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 553                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 554                                                                                             .getCurrentTreePanel()
 555                                                                                             .getWidth(),
 556                                                                                     getMainPanel()
 557                                                                                             .getCurrentTreePanel()
 558                                                                                             .getHeight(),
 559                                                                                     getOptions()
 560                                                                                             .isAllowFontSizeChange() );
 561                 }
 562             }
 563         } );
 564         if ( getConfiguration().isUseTabbedDisplay() ) {
 565             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 566             AptxUtil.addPhylogeniesToTabs( phys,
 567                                            new File( phys_url.getFile() ).getName(),
 568                                            phys_url.toString(),
 569                                            getConfiguration(),
 570                                            getMainPanel() );
 571         }
 572         else {
 573             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 574             if ( getSpeciesTree() != null ) {
 575                 AptxUtil.printAppletMessage( NAME,
 576                                              "Warning: gsdi (gene duplication inference) only available tabbed display" );
 577             }
 578             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 579         }
 580         validate();
 581         setName( NAME );
 582         getMainPanel().getControlPanel().showWholeAll();
 583         getMainPanel().getControlPanel().showWhole();
 584         System.gc();
 585         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 586         /* GUILHEM_BEG */
 587         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 588         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 589                 .getRelevantSequenceRelationTypes() ) {
 590             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 591         }
 592         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 593         if ( default_relation != null ) {
 594             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 595         }
 596         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 597         if ( default_sequence != null ) {
 598             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 599         }
 600         /* GUILHEM_END */
 601         setVisible( true );
 602     }
 603
 604     public void showTextFrame( final String s, final String title ) {
 605         checkTextFrames();
 606         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 607     }
 608
 609     @Override
 610     public void start() {
 611         if ( getMainPanel() != null ) {
 612             getMainPanel().validate();
 613         }
 614         requestFocus();
 615         requestFocusInWindow();
 616         requestFocus();
 617         AptxUtil.printAppletMessage( NAME, "started" );
 618     }
 619
 620     void buildAnalysisMenu() {
 621         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 622         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 623         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 624         customizeJMenuItem( _gsdi_item );
 625         customizeJMenuItem( _gsdir_item );
 626         //  _analysis_menu.addSeparator();
 627         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 628         //  customizeJMenuItem( _lineage_inference );
 629         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 630         _jmenubar.add( _analysis_menu );
 631     }
 632
 633     void buildFontSizeMenu() {
 634         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 635         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 636         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 637         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 638         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 639         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 640         customizeJMenuItem( _super_tiny_fonts_mi );
 641         customizeJMenuItem( _tiny_fonts_mi );
 642         customizeJMenuItem( _small_fonts_mi );
 643         customizeJMenuItem( _medium_fonts_mi );
 644         customizeJMenuItem( _large_fonts_mi );
 645         _jmenubar.add( _font_size_menu );
 646     }
 647
 648     void buildHelpMenu() {
 649         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 650         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 651         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 652         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 653         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 654         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 655         _help_jmenu.addSeparator();
 656         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 657         customizeJMenuItem( _help_item );
 658         customizeJMenuItem( _website_item );
 659         customizeJMenuItem( _phyloxml_website_item );
 660         customizeJMenuItem( _aptx_ref_item );
 661         customizeJMenuItem( _phyloxml_ref_item );
 662         customizeJMenuItem( _about_item );
 663         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 664         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 665         _jmenubar.add( _help_jmenu );
 666     }
 667
 668     void buildOptionsMenu() {
 669         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 670         _options_jmenu.addChangeListener( new ChangeListener() {
 671
 672             @Override
 673             public void stateChanged( final ChangeEvent e ) {
 674                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 675                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 676                 MainFrame
 677                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 678                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 679                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 680                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 681                                                                      _show_scale_cbmi,
 682                                                                      _show_branch_length_values_cbmi,
 683                                                                      _non_lined_up_cladograms_rbmi,
 684                                                                      _uniform_cladograms_rbmi,
 685                                                                      _ext_node_dependent_cladogram_rbmi,
 686                                                                      _label_direction_cbmi );
 687                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 688                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 689                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 690             }
 691         } );
 692         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 693                                                                 getConfiguration() ) );
 694         _options_jmenu
 695                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 696         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 697         _options_jmenu
 698                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 699         _radio_group_1 = new ButtonGroup();
 700         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 701         _radio_group_1.add( _uniform_cladograms_rbmi );
 702         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 703         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 704         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 705         _options_jmenu
 706                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 707         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 708         _options_jmenu
 709                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 710         _options_jmenu
 711                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 712         _options_jmenu
 713                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 714         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 715         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 716         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 717         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 718         _options_jmenu
 719                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 720         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 721         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 722         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 723         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 724         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 725         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 726             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 727         }
 728         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 729         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 730         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 731         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 732         _options_jmenu.addSeparator();
 733         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 734                                                                 getConfiguration() ) );
 735         _options_jmenu
 736                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 737         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 738         _options_jmenu
 739                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 740         customizeJMenuItem( _choose_font_mi );
 741         customizeJMenuItem( _choose_minimal_confidence_mi );
 742         customizeJMenuItem( _switch_colors_mi );
 743         customizeJMenuItem( _overview_placment_mi );
 744         customizeCheckBoxMenuItem( _label_direction_cbmi,
 745                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 746         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 747         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 748         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 749         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 750         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 751         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 752                 .isShowDefaultNodeShapesExternal() );
 753         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 754                 .isShowDefaultNodeShapesInternal() );
 755         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 756         customizeJMenuItem( _cycle_node_shape_mi );
 757         customizeJMenuItem( _cycle_node_fill_mi );
 758         customizeJMenuItem( _choose_node_size_mi );
 759         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 760         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 761         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 762         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 763                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 764         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 765                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 766         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 767                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 768         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 769         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 770         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 771         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 772         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 773         _jmenubar.add( _options_jmenu );
 774     }
 775
 776     void buildToolsMenu() {
 777         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 778         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 779         customizeJMenuItem( _confcolor_item );
 780         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 781         customizeJMenuItem( _taxcolor_item );
 782         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 783         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 784         customizeJMenuItem( _remove_branch_color_item );
 785         _tools_menu.addSeparator();
 786         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 787         customizeJMenuItem( _midpoint_root_item );
 788         _tools_menu.addSeparator();
 789         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 790         customizeJMenuItem( _collapse_species_specific_subtrees );
 791         _jmenubar.add( _tools_menu );
 792     }
 793
 794     void buildTypeMenu() {
 795         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 796         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 797         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 798         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 799         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 800         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 801         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 802         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 803         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 804         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 805         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 806         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 807         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 808         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 809         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 810         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 811         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 812         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 813         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 814         initializeTypeMenu( getOptions() );
 815         _jmenubar.add( _type_menu );
 816     }
 817
 818     void buildViewMenu() {
 819         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 820         _view_jmenu
 821                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 822         _view_jmenu.addSeparator();
 823         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 824         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 825         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 826         customizeJMenuItem( _display_basic_information_item );
 827         customizeJMenuItem( _view_as_NH_item );
 828         customizeJMenuItem( _view_as_XML_item );
 829         customizeJMenuItem( _view_as_nexus_item );
 830         _jmenubar.add( _view_jmenu );
 831     }
 832
 833     void checkTextFrames() {
 834         if ( _textframes.size() > 5 ) {
 835             try {
 836                 if ( _textframes.getFirst() != null ) {
 837                     _textframes.getFirst().removeMe();
 838                 }
 839                 else {
 840                     _textframes.removeFirst();
 841                 }
 842             }
 843             catch ( final NoSuchElementException e ) {
 844                 // Ignore.
 845             }
 846         }
 847     }
 848
 849     void clearCurrentExternalNodesDataBuffer() {
 850         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 851     }
 852
 853     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 854         if ( item != null ) {
 855             item.setFont( MainFrame.menu_font );
 856             if ( !getConfiguration().isUseNativeUI() ) {
 857                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 858                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 859             }
 860             item.setSelected( is_selected );
 861             item.addActionListener( this );
 862         }
 863     }
 864
 865     void customizeJMenuItem( final JMenuItem jmi ) {
 866         jmi.setFont( MainFrame.menu_font );
 867         if ( !getConfiguration().isUseNativeUI() ) {
 868             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 869             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 870         }
 871         jmi.addActionListener( this );
 872     }
 873
 874     void displayBasicInformation() {
 875         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 876             String title = "Basic Information";
 877             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 878                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
 879             }
 880             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
 881         }
 882     }
 883
 884     void executeGSDI() {
 885         if ( !isOKforSDI( false, true ) ) {
 886             return;
 887         }
 888         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 889             JOptionPane.showMessageDialog( this,
 890                                            "Gene tree is not rooted.",
 891                                            "Cannot execute GSDI",
 892                                            JOptionPane.ERROR_MESSAGE );
 893             return;
 894         }
 895         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 896         gene_tree.setAllNodesToNotCollapse();
 897         gene_tree.recalculateNumberOfExternalDescendants( false );
 898         GSDI gsdi = null;
 899         final Phylogeny species_tree = _species_tree.copy();
 900         try {
 901             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 902         }
 903         catch ( final SDIException e ) {
 904             JOptionPane.showMessageDialog( this,
 905                                            e.getLocalizedMessage(),
 906                                            "Error during GSDI",
 907                                            JOptionPane.ERROR_MESSAGE );
 908             return;
 909         }
 910         catch ( final Exception e ) {
 911             AptxUtil.unexpectedException( e );
 912             return;
 913         }
 914         gene_tree.setRerootable( false );
 915         gene_tree.clearHashIdToNodeMap();
 916         gene_tree.recalculateNumberOfExternalDescendants( true );
 917         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 918         getMainPanel().getControlPanel().setShowEvents( true );
 919         showWhole();
 920         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 921         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 922         showWhole();
 923         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 924         showWhole();
 925         _mainpanel.getCurrentTreePanel().setEdited( true );
 926         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 927         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 928             JOptionPane.showMessageDialog( this,
 929                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 930                                                    + "Potential duplications: "
 931                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 932                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 933                                                    + "Stripped gene tree nodes: "
 934                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 935                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 936                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 937                                            "GSDI successfully completed",
 938                                            JOptionPane.WARNING_MESSAGE );
 939         }
 940         else {
 941             JOptionPane.showMessageDialog( this,
 942                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 943                                                    + "Potential duplications: "
 944                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 945                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 946                                                    + "Stripped gene tree nodes: "
 947                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 948                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 949                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 950                                            "GSDI successfully completed",
 951                                            JOptionPane.INFORMATION_MESSAGE );
 952         }
 953     }
 954
 955     void executeGSDIR() {
 956         if ( !isOKforSDI( false, false ) ) {
 957             return;
 958         }
 959         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
 960         if ( ( p > 0 )
 961                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
 962             JOptionPane.showMessageDialog( this,
 963                                            "Gene tree is not completely binary",
 964                                            "Cannot execute GSDI",
 965                                            JOptionPane.ERROR_MESSAGE );
 966             return;
 967         }
 968         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 969         gene_tree.setAllNodesToNotCollapse();
 970         gene_tree.recalculateNumberOfExternalDescendants( false );
 971         GSDIR gsdir = null;
 972         final Phylogeny species_tree = _species_tree.copy();
 973         try {
 974             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
 975         }
 976         catch ( final SDIException e ) {
 977             JOptionPane.showMessageDialog( this,
 978                                            e.getLocalizedMessage(),
 979                                            "Error during GSDIR",
 980                                            JOptionPane.ERROR_MESSAGE );
 981             return;
 982         }
 983         catch ( final Exception e ) {
 984             AptxUtil.unexpectedException( e );
 985             return;
 986         }
 987         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
 988         result_gene_tree.setRerootable( false );
 989         result_gene_tree.clearHashIdToNodeMap();
 990         result_gene_tree.recalculateNumberOfExternalDescendants( true );
 991         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
 992         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
 993         getMainPanel().getControlPanel().setShowEvents( true );
 994         showWhole();
 995         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 996         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 997         showWhole();
 998         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 999         showWhole();
1000         _mainpanel.getCurrentTreePanel().setEdited( true );
1001         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1002         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1003             JOptionPane.showMessageDialog( this,
1004                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1005                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1006                                                    + "Stripped gene tree nodes: "
1007                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1008                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1009                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1010                                            "GSDIR successfully completed",
1011                                            JOptionPane.WARNING_MESSAGE );
1012         }
1013         else {
1014             JOptionPane.showMessageDialog( this,
1015                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1016                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1017                                                    + "Stripped gene tree nodes: "
1018                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1019                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1020                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1021                                            "GSDIR successfully completed",
1022                                            JOptionPane.INFORMATION_MESSAGE );
1023         }
1024     }
1025
1026     Configuration getConfiguration() {
1027         return _configuration;
1028     }
1029
1030     TreePanel getCurrentTreePanel() {
1031         return getMainPanel().getCurrentTreePanel();
1032     }
1033
1034     JCheckBoxMenuItem getlabelDirectionCbmi() {
1035         return _label_direction_cbmi;
1036     }
1037
1038     Options getOtions() {
1039         return _options;
1040     }
1041
1042     void help() {
1043         final StringBuilder sb = new StringBuilder();
1044         sb.append( "Display options\n" );
1045         sb.append( "-------------------\n" );
1046         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1047         sb.append( "Clickable tree nodes\n" );
1048         sb.append( "--------------------\n" );
1049         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1050         sb.append( "or by right clicking:\n" );
1051         sb.append( "o  Display Node Data -- display information for a node\n" );
1052         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1053         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
1054         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1055         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
1056         sb.append( "o  Colorize Subtree -- color a subtree\n" );
1057         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
1058         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1059         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
1060         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1061         sb.append( "Zooming\n" );
1062         sb.append( "---------\n" );
1063         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1064         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1065         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1066         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1067         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1068         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1069         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1070         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1071         sb.append( "Quick tree manipulation:\n" );
1072         sb.append( "------------------------\n" );
1073         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1074         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1075         sb.append( "phyloXML\n" );
1076         sb.append( "-------------------\n" );
1077         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1078         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1079         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1080         sb.append( "\n" );
1081         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1082         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1083         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1084     }
1085
1086     void initializeTypeMenu( final Options options ) {
1087         setTypeMenuToAllUnselected();
1088         try {
1089             switch ( options.getPhylogenyGraphicsType() ) {
1090                 case CONVEX:
1091                     _convex_type_cbmi.setSelected( true );
1092                     break;
1093                 case CURVED:
1094                     _curved_type_cbmi.setSelected( true );
1095                     break;
1096                 case EURO_STYLE:
1097                     _euro_type_cbmi.setSelected( true );
1098                     break;
1099                 case ROUNDED:
1100                     _rounded_type_cbmi.setSelected( true );
1101                     break;
1102                 case TRIANGULAR:
1103                     _triangular_type_cbmi.setSelected( true );
1104                     break;
1105                 case UNROOTED:
1106                     _unrooted_type_cbmi.setSelected( true );
1107                     break;
1108                 case CIRCULAR:
1109                     _circular_type_cbmi.setSelected( true );
1110                     break;
1111                 default:
1112                     _rectangular_type_cbmi.setSelected( true );
1113                     break;
1114             }
1115         }
1116         catch ( final NullPointerException np ) {
1117             // In all likelihood, this is caused by menu-less display.
1118         }
1119     }
1120
1121     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1122         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1123             return false;
1124         }
1125         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1126             JOptionPane.showMessageDialog( this,
1127                                            "No species tree loaded",
1128                                            "Cannot execute GSDI",
1129                                            JOptionPane.ERROR_MESSAGE );
1130             return false;
1131         }
1132         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1133             JOptionPane.showMessageDialog( this,
1134                                            "Species tree is not completely binary",
1135                                            "Cannot execute GSDI",
1136                                            JOptionPane.ERROR_MESSAGE );
1137             return false;
1138         }
1139         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1140             JOptionPane.showMessageDialog( this,
1141                                            "Gene tree is not completely binary",
1142                                            "Cannot execute GSDI",
1143                                            JOptionPane.ERROR_MESSAGE );
1144             return false;
1145         }
1146         else {
1147             return true;
1148         }
1149     }
1150
1151     boolean isSubtreeDisplayed() {
1152         if ( getCurrentTreePanel() != null ) {
1153             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1154                 JOptionPane
1155                         .showMessageDialog( this,
1156                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1157                                             "Operation can not be exectuted on a sub-tree",
1158                                             JOptionPane.WARNING_MESSAGE );
1159                 return true;
1160             }
1161         }
1162         return false;
1163     }
1164
1165     void removeAllTextFrames() {
1166         for( final TextFrame tf : _textframes ) {
1167             if ( tf != null ) {
1168                 tf.close();
1169             }
1170         }
1171         _textframes.clear();
1172     }
1173
1174     void setConfiguration( final Configuration configuration ) {
1175         _configuration = configuration;
1176     }
1177
1178     void setOptions( final Options options ) {
1179         _options = options;
1180     }
1181
1182     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1183         setTypeMenuToAllUnselected();
1184         try {
1185             switch ( type ) {
1186                 case CIRCULAR:
1187                     _circular_type_cbmi.setSelected( true );
1188                     break;
1189                 case CONVEX:
1190                     _convex_type_cbmi.setSelected( true );
1191                     break;
1192                 case CURVED:
1193                     _curved_type_cbmi.setSelected( true );
1194                     break;
1195                 case EURO_STYLE:
1196                     _euro_type_cbmi.setSelected( true );
1197                     break;
1198                 case ROUNDED:
1199                     _rounded_type_cbmi.setSelected( true );
1200                     break;
1201                 case RECTANGULAR:
1202                     _rectangular_type_cbmi.setSelected( true );
1203                     break;
1204                 case TRIANGULAR:
1205                     _triangular_type_cbmi.setSelected( true );
1206                     break;
1207                 case UNROOTED:
1208                     _unrooted_type_cbmi.setSelected( true );
1209                     break;
1210                 default:
1211                     throw new IllegalArgumentException( "unknown type: " + type );
1212             }
1213         }
1214         catch ( final NullPointerException np ) {
1215             // In all likelihood, this is caused by menu-less display.
1216         }
1217     }
1218
1219     void setTypeMenuToAllUnselected() {
1220         if ( _convex_type_cbmi != null ) {
1221             _convex_type_cbmi.setSelected( false );
1222         }
1223         if ( _curved_type_cbmi != null ) {
1224             _curved_type_cbmi.setSelected( false );
1225         }
1226         if ( _euro_type_cbmi != null ) {
1227             _euro_type_cbmi.setSelected( false );
1228         }
1229         if ( _rounded_type_cbmi != null ) {
1230             _rounded_type_cbmi.setSelected( false );
1231         }
1232         if ( _triangular_type_cbmi != null ) {
1233             _triangular_type_cbmi.setSelected( false );
1234         }
1235         if ( _rectangular_type_cbmi != null ) {
1236             _rectangular_type_cbmi.setSelected( false );
1237         }
1238         if ( _unrooted_type_cbmi != null ) {
1239             _unrooted_type_cbmi.setSelected( false );
1240         }
1241         if ( _circular_type_cbmi != null ) {
1242             _circular_type_cbmi.setSelected( false );
1243         }
1244     }
1245
1246     void showWhole() {
1247         _mainpanel.getControlPanel().showWhole();
1248     }
1249
1250     void switchColors() {
1251         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1252         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1253         csc.setVisible( true );
1254         getMainPanel().setTreeColorSet( colorset );
1255     }
1256
1257     void typeChanged( final Object o ) {
1258         updateTypeCheckboxes( getOptions(), o );
1259         updateOptions( getOptions() );
1260         if ( getCurrentTreePanel() != null ) {
1261             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1262             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1263             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1264                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1265                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1266                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1267                 getCurrentTreePanel().getControlPanel().showWhole();
1268             }
1269             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1270                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1271             }
1272             else {
1273                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1274             }
1275             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1276             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1277         }
1278     }
1279
1280     void updateOptions( final Options options ) {
1281         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1282         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1283                 && _background_gradient_cbmi.isSelected() );
1284         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1285         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1286                 && _show_annotation_ref_source.isSelected() );
1287         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1288                 && _abbreviate_scientific_names.isSelected() );
1289         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1290                 && _color_labels_same_as_parent_branch.isSelected() );
1291         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1292                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1293         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1294                 && _show_default_node_shapes_external_cbmi.isSelected() );
1295         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1296                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1297         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1298             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1299         }
1300         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1301             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1302         }
1303         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1304             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1305         }
1306         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1307                 && _search_case_senstive_cbmi.isSelected() );
1308         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1309             options.setShowScale( _show_scale_cbmi.isSelected() );
1310         }
1311         if ( _label_direction_cbmi != null ) {
1312             if ( _label_direction_cbmi.isSelected() ) {
1313                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1314             }
1315             else {
1316                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1317             }
1318         }
1319         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1320         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1321                 && _show_confidence_stddev_cbmi.isSelected() );
1322         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1323             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1324         }
1325         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1326                 && _search_whole_words_only_cbmi.isSelected() );
1327         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1328                 && _inverse_search_result_cbmi.isSelected() );
1329         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1330             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1331         }
1332         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1333             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1334         }
1335         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1336             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1337         }
1338         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1339             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1340         }
1341         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1342             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1343         }
1344         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1345             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1346         }
1347         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1348             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1349         }
1350         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1351             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1352         }
1353     }
1354
1355     void updateTypeCheckboxes( final Options options, final Object o ) {
1356         setTypeMenuToAllUnselected();
1357         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1358     }
1359
1360     void viewAsNexus() {
1361         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1362             String title = "Nexus";
1363             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1364                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1365             }
1366             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1367                                    .getNhConversionSupportValueStyle() ),
1368                            title );
1369         }
1370     }
1371
1372     void viewAsNH() {
1373         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1374             String title = "New Hampshire";
1375             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1376                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1377             }
1378             showTextFrame( getMainPanel().getCurrentPhylogeny()
1379                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1380                            title );
1381         }
1382     }
1383
1384     void viewAsXML() {
1385         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1386             String title = "phyloXML";
1387             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1388                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1389             }
1390             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1391         }
1392     }
1393
1394     private void chooseFont() {
1395         final FontChooser fc = new FontChooser();
1396         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1397         fc.showDialog( this, "Select the Base Font" );
1398         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1399     }
1400
1401     private void chooseMinimalConfidence() {
1402         final String s = ( String ) JOptionPane
1403                 .showInputDialog( this,
1404                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1405                                           + getOptions().getMinConfidenceValue() + "]\n",
1406                                   "Minimal Confidence Value",
1407                                   JOptionPane.QUESTION_MESSAGE,
1408                                   null,
1409                                   null,
1410                                   getOptions().getMinConfidenceValue() );
1411         if ( !ForesterUtil.isEmpty( s ) ) {
1412             boolean success = true;
1413             double m = 0.0;
1414             final String m_str = s.trim();
1415             if ( !ForesterUtil.isEmpty( m_str ) ) {
1416                 try {
1417                     m = Double.parseDouble( m_str );
1418                 }
1419                 catch ( final Exception ex ) {
1420                     success = false;
1421                 }
1422             }
1423             else {
1424                 success = false;
1425             }
1426             if ( success && ( m >= 0.0 ) ) {
1427                 getOptions().setMinConfidenceValue( m );
1428             }
1429         }
1430     }
1431
1432     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1433         if ( item != null ) {
1434             item.setFont( MainFrame.menu_font );
1435             if ( !getConfiguration().isUseNativeUI() ) {
1436                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1437                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1438             }
1439             item.setSelected( is_selected );
1440             item.addActionListener( this );
1441         }
1442     }
1443
1444     private MainPanel getMainPanel() {
1445         return _mainpanel;
1446     }
1447
1448     private Phylogeny getSpeciesTree() {
1449         return _species_tree;
1450     }
1451
1452     private boolean isScreenAntialias() {
1453         return true;
1454     }
1455
1456     private void removeBranchColors() {
1457         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1458             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1459         }
1460     }
1461
1462     private void setMainPanel( final MainPanelApplets main_panel ) {
1463         _mainpanel = main_panel;
1464     }
1465
1466     private void setSpeciesTree( final Phylogeny species_tree ) {
1467         _species_tree = species_tree;
1468     }
1469
1470     private void setupUI() {
1471         try {
1472             if ( getConfiguration().isUseNativeUI() ) {
1473                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1474             }
1475             else {
1476                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1477             }
1478         }
1479         catch ( final UnsupportedLookAndFeelException e ) {
1480             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1481         }
1482         catch ( final ClassNotFoundException e ) {
1483             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1484         }
1485         catch ( final InstantiationException e ) {
1486             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1487         }
1488         catch ( final IllegalAccessException e ) {
1489             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1490         }
1491         catch ( final Exception e ) {
1492             AptxUtil.dieWithSystemError( e.toString() );
1493         }
1494     }
1495
1496     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1497         for( final TreePanel tree_panel : treepanels ) {
1498             tree_panel.setTextAntialias();
1499         }
1500     }
1501 }