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 JMenuItem                   _remove_visual_styles_item;
 100     private JCheckBoxMenuItem           _show_domain_labels;
 101     private JCheckBoxMenuItem           _show_annotation_ref_source;
 102     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 103     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 104     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 105     private JCheckBoxMenuItem           _background_gradient_cbmi;
 106     private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 107     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 108     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 109     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 110     private Options                     _options;
 111     private JMenuItem                   _choose_font_mi;
 112     private JMenuItem                   _switch_colors_mi;
 113     JCheckBoxMenuItem                   _label_direction_cbmi;
 114     private JCheckBoxMenuItem           _show_scale_cbmi;
 115     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 116     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 117     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 118     private JCheckBoxMenuItem           _show_overview_cbmi;
 119     private JMenuItem                   _choose_minimal_confidence_mi;
 120     private JMenuItem                   _collapse_species_specific_subtrees;
 121     private JMenuItem                   _overview_placment_mi;
 122     private ButtonGroup                 _radio_group_1;
 123     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 124     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 125     private JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;
 126     private JMenuItem                   _cycle_node_shape_mi;
 127     private JMenuItem                   _cycle_node_fill_mi;
 128     private JMenuItem                   _choose_node_size_mi;
 129     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 130     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 131     private JMenu                       _analysis_menu;
 132     private JMenuItem                   _gsdi_item;
 133     private JMenuItem                   _gsdir_item;
 134     private Phylogeny                   _species_tree;
 135     private JCheckBoxMenuItem           _right_line_up_domains_cbmi;
 136     private JCheckBoxMenuItem           _line_up_renderable_data_cbmi;
 137
 138     @Override
 139     public void actionPerformed( final ActionEvent e ) {
 140         final Object o = e.getSource();
 141         if ( o == _midpoint_root_item ) {
 142             getMainPanel().getCurrentTreePanel().midpointRoot();
 143         }
 144         else if ( o == _gsdi_item ) {
 145             if ( isSubtreeDisplayed() ) {
 146                 return;
 147             }
 148             executeGSDI();
 149         }
 150         else if ( o == _gsdir_item ) {
 151             if ( isSubtreeDisplayed() ) {
 152                 return;
 153             }
 154             executeGSDIR();
 155         }
 156         else if ( o == _taxcolor_item ) {
 157             getMainPanel().getCurrentTreePanel().taxColor();
 158         }
 159         else if ( o == _confcolor_item ) {
 160             getMainPanel().getCurrentTreePanel().confColor();
 161         }
 162         else if ( o == _collapse_species_specific_subtrees ) {
 163             if ( getCurrentTreePanel() != null ) {
 164                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 165             }
 166         }
 167         else if ( o == _remove_branch_color_item ) {
 168             removeBranchColors();
 169         }
 170         else if ( o == _remove_visual_styles_item ) {
 171             removeVisualStyles();
 172         }
 173         else if ( o == _switch_colors_mi ) {
 174             switchColors();
 175         }
 176         else if ( o == _display_basic_information_item ) {
 177             displayBasicInformation();
 178         }
 179         else if ( o == _view_as_NH_item ) {
 180             viewAsNH();
 181         }
 182         else if ( o == _view_as_XML_item ) {
 183             viewAsXML();
 184         }
 185         else if ( o == _view_as_nexus_item ) {
 186             viewAsNexus();
 187         }
 188         else if ( o == _super_tiny_fonts_mi ) {
 189             if ( getCurrentTreePanel() != null ) {
 190                 getCurrentTreePanel().setSuperTinyFonts();
 191                 getCurrentTreePanel().repaint();
 192             }
 193         }
 194         else if ( o == _tiny_fonts_mi ) {
 195             if ( getCurrentTreePanel() != null ) {
 196                 getCurrentTreePanel().setTinyFonts();
 197                 getCurrentTreePanel().repaint();
 198             }
 199         }
 200         else if ( o == _small_fonts_mi ) {
 201             if ( getCurrentTreePanel() != null ) {
 202                 getCurrentTreePanel().setSmallFonts();
 203                 getCurrentTreePanel().repaint();
 204             }
 205         }
 206         else if ( o == _medium_fonts_mi ) {
 207             if ( getCurrentTreePanel() != null ) {
 208                 getCurrentTreePanel().setMediumFonts();
 209                 getCurrentTreePanel().repaint();
 210             }
 211         }
 212         else if ( o == _large_fonts_mi ) {
 213             if ( getCurrentTreePanel() != null ) {
 214                 getCurrentTreePanel().setLargeFonts();
 215                 getCurrentTreePanel().repaint();
 216             }
 217         }
 218         else if ( o == _choose_font_mi ) {
 219             chooseFont();
 220         }
 221         else if ( o == _choose_minimal_confidence_mi ) {
 222             chooseMinimalConfidence();
 223         }
 224         else if ( o == _choose_node_size_mi ) {
 225             MainFrame.chooseNodeSize( getOptions(), this );
 226         }
 227         else if ( o == _overview_placment_mi ) {
 228             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 229         }
 230         else if ( o == _cycle_node_fill_mi ) {
 231             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 232         }
 233         else if ( o == _cycle_node_shape_mi ) {
 234             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 235         }
 236         else if ( o == _non_lined_up_cladograms_rbmi ) {
 237             updateOptions( getOptions() );
 238             _mainpanel.getControlPanel().showWhole();
 239         }
 240         else if ( o == _uniform_cladograms_rbmi ) {
 241             updateOptions( getOptions() );
 242             _mainpanel.getControlPanel().showWhole();
 243         }
 244         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 245             updateOptions( getOptions() );
 246             _mainpanel.getControlPanel().showWhole();
 247         }
 248         else if ( o == _search_case_senstive_cbmi ) {
 249             updateOptions( getOptions() );
 250             getMainPanel().getControlPanel().search0();
 251             getMainPanel().getControlPanel().search1();
 252         }
 253         else if ( o == _search_whole_words_only_cbmi ) {
 254             updateOptions( getOptions() );
 255             getMainPanel().getControlPanel().search0();
 256             getMainPanel().getControlPanel().search1();
 257         }
 258         else if ( o == _inverse_search_result_cbmi ) {
 259             updateOptions( getOptions() );
 260             getMainPanel().getControlPanel().search0();
 261             getMainPanel().getControlPanel().search1();
 262         }
 263         else if ( o == _show_scale_cbmi ) {
 264             updateOptions( getOptions() );
 265         }
 266         else if ( o == _show_confidence_stddev_cbmi ) {
 267             updateOptions( getOptions() );
 268         }
 269         else if ( o == _label_direction_cbmi ) {
 270             updateOptions( getOptions() );
 271         }
 272         else if ( o == _abbreviate_scientific_names ) {
 273             updateOptions( getOptions() );
 274         }
 275         else if ( o == _show_overview_cbmi ) {
 276             updateOptions( getOptions() );
 277             if ( getCurrentTreePanel() != null ) {
 278                 getCurrentTreePanel().updateOvSizes();
 279             }
 280         }
 281         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 282                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 283                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 284             typeChanged( o );
 285         }
 286         else if ( o == _screen_antialias_cbmi ) {
 287             updateOptions( getOptions() );
 288             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 289         }
 290         else if ( o == _background_gradient_cbmi ) {
 291             updateOptions( getOptions() );
 292         }
 293         else if ( o == _show_domain_labels ) {
 294             updateOptions( getOptions() );
 295         }
 296         else if ( o == _color_labels_same_as_parent_branch ) {
 297             updateOptions( getOptions() );
 298         }
 299         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 300             updateOptions( getOptions() );
 301         }
 302         else if ( o == _show_default_node_shapes_external_cbmi ) {
 303             updateOptions( getOptions() );
 304         }
 305         else if ( o == _about_item ) {
 306             MainFrame.about();
 307         }
 308         else if ( o == _help_item ) {
 309             try {
 310                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
 311             }
 312             catch ( final IOException e1 ) {
 313                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 314             }
 315         }
 316         else if ( o == _website_item ) {
 317             try {
 318                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 319             }
 320             catch ( final IOException e1 ) {
 321                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 322             }
 323         }
 324         else if ( o == _phyloxml_website_item ) {
 325             try {
 326                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 327             }
 328             catch ( final IOException e1 ) {
 329                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 330             }
 331         }
 332         else if ( o == _aptx_ref_item ) {
 333             try {
 334                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 335             }
 336             catch ( final IOException e1 ) {
 337                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 338             }
 339         }
 340         else if ( o == _phyloxml_ref_item ) {
 341             try {
 342                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 343             }
 344             catch ( final IOException e1 ) {
 345                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 346             }
 347         }
 348         else if ( o == _color_by_taxonomic_group_cbmi ) {
 349             updateOptions( getOptions() );
 350         }
 351         else if ( o == _line_up_renderable_data_cbmi ) {
 352             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
 353                 _right_line_up_domains_cbmi.setSelected( false );
 354             }
 355             updateOptions( getOptions() );
 356         }
 357         else if ( o == _right_line_up_domains_cbmi ) {
 358             if ( _right_line_up_domains_cbmi.isSelected() ) {
 359                 _line_up_renderable_data_cbmi.setSelected( true );
 360             }
 361             updateOptions( getOptions() );
 362         }
 363         repaint();
 364     }
 365
 366     @Override
 367     public void destroy() {
 368         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 369         removeAllTextFrames();
 370         if ( getMainPanel() != null ) {
 371             getMainPanel().terminate();
 372         }
 373     }
 374
 375     /**
 376      * This method returns the current external node data which
 377      * has been selected by the user by clicking the "Return ..."
 378      * menu item. This method is expected to be called from Javascript or
 379      * something like it.
 380      *
 381      * @return current external node data as String
 382      */
 383     public String getCurrentExternalNodesDataBuffer() {
 384         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 385     }
 386
 387     public int getCurrentExternalNodesDataBufferChangeCounter() {
 388         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 389     }
 390
 391     public int getCurrentExternalNodesDataBufferLength() {
 392         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 393     }
 394
 395     /**
 396      * This method returns the current phylogeny as a string in the chosen format
 397      *
 398      * @param format must be NH, NHX, NEXUS or PHYLOXML
 399      * @return the phylogeny string
 400      * @author Herve Menager
 401      */
 402     public String getCurrentPhylogeny( final String format ) {
 403         removeAllTextFrames();
 404         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 405                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 406             return new String();
 407         }
 408         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 409             case NH:
 410                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 411             case NHX:
 412                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 413             case NEXUS:
 414                 return getMainPanel().getCurrentPhylogeny().toNexus();
 415             case PHYLOXML:
 416                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 417             default:
 418                 break;
 419         }
 420         return new String();
 421     }
 422
 423     /**
 424      * This method returns a view of the current phylogeny in a chosen
 425      * graphics format, base64-encoded in a string so that in can be used
 426      * from javascript.
 427      *
 428      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 429      * @return the phylogeny string
 430      * @author Herve Menager
 431      */
 432     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 433         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 434         try {
 435             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 436                                                                     _mainpanel.getWidth(),
 437                                                                     _mainpanel.getHeight(),
 438                                                                     getCurrentTreePanel(),
 439                                                                     getCurrentTreePanel().getControlPanel(),
 440                                                                     GraphicsExportType.valueOf( format ),
 441                                                                     getOptions() );
 442         }
 443         catch ( final IOException ioe ) {
 444             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 445             ioe.printStackTrace();
 446             JOptionPane.showMessageDialog( this,
 447                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 448                                            "Failed to generate graphics",
 449                                            JOptionPane.ERROR_MESSAGE );
 450             return null;
 451         }
 452         final byte[] bytes = baos.toByteArray();
 453         final String dataImg = Base64.encodeBase64String( bytes );
 454         return dataImg;
 455     }
 456
 457     public Options getOptions() {
 458         return _options;
 459     }
 460
 461     @Override
 462     public void init() {
 463         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 464         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 465         final Configuration configuration = new Configuration( config_filename, true, true, true );
 466         setConfiguration( configuration );
 467         setOptions( Options.createInstance( configuration ) );
 468         setupUI();
 469         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 470         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 471             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 472                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 473             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 474                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 475             return;
 476         }
 477         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 478         // Get URL to tree file
 479         URL phys_url = null;
 480         try {
 481             phys_url = new URL( tree_url_str );
 482         }
 483         catch ( final Exception e ) {
 484             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 485             e.printStackTrace();
 486             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 487                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 488         }
 489         if ( phys_url == null ) {
 490             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 491                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 492             JOptionPane.showMessageDialog( this,
 493                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 494                                            "Failed to create URL",
 495                                            JOptionPane.ERROR_MESSAGE );
 496             return;
 497         }
 498         // Load the tree from URL
 499         Phylogeny[] phys = null;
 500         try {
 501             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 502                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 503                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 504                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 505                                                     getConfiguration().getTaxonomyExtraction(),
 506                                                     getConfiguration().isMidpointReroot() );
 507         }
 508         catch ( final Exception e ) {
 509             ForesterUtil.printErrorMessage( NAME, e.toString() );
 510             e.printStackTrace();
 511             JOptionPane.showMessageDialog( this,
 512                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 513                                            "Failed to read phylogenies",
 514                                            JOptionPane.ERROR_MESSAGE );
 515         }
 516         if ( phys == null ) {
 517             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 518             JOptionPane.showMessageDialog( this,
 519                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 520                                            "Failed to read phylogenies",
 521                                            JOptionPane.ERROR_MESSAGE );
 522             return;
 523         }
 524         else if ( phys.length < 1 ) {
 525             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 526             JOptionPane.showMessageDialog( this,
 527                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 528                                            "Failed to read phylogenies",
 529                                            JOptionPane.ERROR_MESSAGE );
 530             return;
 531         }
 532         else {
 533             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 534         }
 535         //
 536         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 537         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 538             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 539             Phylogeny[] species_trees = null;
 540             try {
 541                 final URL species_tree_url = new URL( species_tree_url_str );
 542                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 543                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 544                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 545                                                                  false,
 546                                                                  TAXONOMY_EXTRACTION.NO,
 547                                                                  false );
 548             }
 549             catch ( final IOException e ) {
 550                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 551                         + "]" );
 552                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 553                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 554             }
 555             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 556                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 557                 if ( species_trees[ 0 ].isEmpty() ) {
 558                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 559                 }
 560                 else if ( !species_trees[ 0 ].isRooted() ) {
 561                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 562                 }
 563                 else {
 564                     setSpeciesTree( species_trees[ 0 ] );
 565                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 566                 }
 567             }
 568         }
 569         //
 570         try {
 571             setVisible( false );
 572             setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 573             _jmenubar = new JMenuBar();
 574             if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 575                 if ( !getConfiguration().isUseNativeUI() ) {
 576                     _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 577                 }
 578                 if ( getSpeciesTree() != null ) {
 579                     buildAnalysisMenu();
 580                 }
 581                 buildToolsMenu();
 582                 buildViewMenu();
 583                 buildFontSizeMenu();
 584                 buildOptionsMenu();
 585                 buildTypeMenu();
 586                 buildHelpMenu();
 587                 setJMenuBar( _jmenubar );
 588             }
 589             final Container contentpane = getContentPane();
 590             contentpane.setLayout( new BorderLayout() );
 591             contentpane.add( getMainPanel(), BorderLayout.CENTER );
 592             addComponentListener( new ComponentAdapter() {
 593
 594                 @Override
 595                 public void componentResized( final ComponentEvent e ) {
 596                     if ( getMainPanel().getCurrentTreePanel() != null ) {
 597                         getMainPanel().getCurrentTreePanel()
 598                                 .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
 599                                                             getMainPanel().getCurrentTreePanel().getHeight(),
 600                                                             getOptions().isAllowFontSizeChange() );
 601                     }
 602                 }
 603             } );
 604             if ( getConfiguration().isUseTabbedDisplay() ) {
 605                 try {
 606                     AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 607                     AptxUtil.addPhylogeniesToTabs( phys,
 608                                                    new File( phys_url.getFile() ).getName(),
 609                                                    phys_url.toString(),
 610                                                    getConfiguration(),
 611                                                    getMainPanel() );
 612                 }
 613                 catch ( final Exception e ) {
 614                     ForesterUtil.printErrorMessage( NAME, e.toString() );
 615                     e.printStackTrace();
 616                 }
 617             }
 618             else {
 619                 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 620                 if ( getSpeciesTree() != null ) {
 621                     AptxUtil.printAppletMessage( NAME,
 622                                                  "Warning: gsdi (gene duplication inference) only available tabbed display" );
 623                 }
 624                 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 625             }
 626             validate();
 627             setName( NAME );
 628             getMainPanel().getControlPanel().showWholeAll();
 629             getMainPanel().getControlPanel().showWhole();
 630             /* GUILHEM_BEG */
 631             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 632             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 633                     .getRelevantSequenceRelationTypes() ) {
 634                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 635             }
 636             final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 637             if ( default_relation != null ) {
 638                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 639             }
 640             final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 641             if ( default_sequence != null ) {
 642                 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 643             }
 644             /* GUILHEM_END */
 645             System.gc();
 646             AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 647             setVisible( true );
 648         }
 649         catch ( final Exception e ) {
 650             ForesterUtil.printErrorMessage( NAME, e.toString() );
 651             e.printStackTrace();
 652         }
 653     }
 654
 655     public void showTextFrame( final String s, final String title ) {
 656         checkTextFrames();
 657         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 658     }
 659
 660     @Override
 661     public void start() {
 662         if ( getMainPanel() != null ) {
 663             getMainPanel().validate();
 664         }
 665         requestFocus();
 666         requestFocusInWindow();
 667         requestFocus();
 668         AptxUtil.printAppletMessage( NAME, "started" );
 669     }
 670
 671     void buildAnalysisMenu() {
 672         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 673         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 674         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 675         customizeJMenuItem( _gsdi_item );
 676         customizeJMenuItem( _gsdir_item );
 677         //  _analysis_menu.addSeparator();
 678         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 679         //  customizeJMenuItem( _lineage_inference );
 680         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 681         _jmenubar.add( _analysis_menu );
 682     }
 683
 684     void buildFontSizeMenu() {
 685         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 686         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 687         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 688         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 689         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 690         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 691         customizeJMenuItem( _super_tiny_fonts_mi );
 692         customizeJMenuItem( _tiny_fonts_mi );
 693         customizeJMenuItem( _small_fonts_mi );
 694         customizeJMenuItem( _medium_fonts_mi );
 695         customizeJMenuItem( _large_fonts_mi );
 696         _jmenubar.add( _font_size_menu );
 697     }
 698
 699     void buildHelpMenu() {
 700         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 701         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
 702         _help_jmenu.addSeparator();
 703         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 704         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 705         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 706         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 707         _help_jmenu.addSeparator();
 708         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 709         customizeJMenuItem( _help_item );
 710         customizeJMenuItem( _website_item );
 711         customizeJMenuItem( _phyloxml_website_item );
 712         customizeJMenuItem( _aptx_ref_item );
 713         customizeJMenuItem( _phyloxml_ref_item );
 714         customizeJMenuItem( _about_item );
 715         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 716         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 717         _jmenubar.add( _help_jmenu );
 718     }
 719
 720     void buildOptionsMenu() {
 721         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 722         _options_jmenu.addChangeListener( new ChangeListener() {
 723
 724             @Override
 725             public void stateChanged( final ChangeEvent e ) {
 726                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 727                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 728                 MainFrame
 729                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 730                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 731                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 732                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 733                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 734                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 735                 try {
 736                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
 737                     getMainPanel().getControlPanel().setVisibilityOfX();
 738                 }
 739                 catch ( final Exception ignore ) {
 740                     // do nothing, not important.
 741                 }
 742             }
 743         } );
 744         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 745                                                                 getConfiguration() ) );
 746         _options_jmenu
 747                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 748         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 749         _options_jmenu
 750                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 751         _radio_group_1 = new ButtonGroup();
 752         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 753         _radio_group_1.add( _uniform_cladograms_rbmi );
 754         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 755         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 756         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 757         _options_jmenu
 758                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 759         _options_jmenu
 760                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 761         _options_jmenu
 762                 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 763         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 764         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 765             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 766             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 767         }
 768         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 769         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 770         _options_jmenu
 771                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 772         _options_jmenu
 773                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 774         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 775         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 776         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 777         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 778         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 779         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 780         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 781         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 782         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 783         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 784         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 785         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 786         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 787         _options_jmenu.addSeparator();
 788         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 789                                                                 getConfiguration() ) );
 790         _options_jmenu
 791                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 792         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 793         _options_jmenu
 794                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 795         customizeJMenuItem( _choose_font_mi );
 796         customizeJMenuItem( _choose_minimal_confidence_mi );
 797         customizeJMenuItem( _switch_colors_mi );
 798         customizeJMenuItem( _overview_placment_mi );
 799         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 800         customizeCheckBoxMenuItem( _label_direction_cbmi,
 801                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 802         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 803         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 804         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 805         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 806         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 807         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 808                 .isShowDefaultNodeShapesExternal() );
 809         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 810                 .isShowDefaultNodeShapesInternal() );
 811         customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
 812                 .isShowDefaultNodeShapesForMarkedNodes() );
 813         customizeJMenuItem( _cycle_node_shape_mi );
 814         customizeJMenuItem( _cycle_node_fill_mi );
 815         customizeJMenuItem( _choose_node_size_mi );
 816         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 817         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 818         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 819         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 820                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 821         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 822                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 823         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 824                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 825         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 826         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 827         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 828         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 829         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
 830         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
 831         _jmenubar.add( _options_jmenu );
 832     }
 833
 834     void buildToolsMenu() {
 835         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 836         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 837         customizeJMenuItem( _confcolor_item );
 838         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 839         customizeJMenuItem( _taxcolor_item );
 840         _tools_menu.addSeparator();
 841         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 842         _remove_visual_styles_item
 843                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 844         customizeJMenuItem( _remove_visual_styles_item );
 845         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 846         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 847         customizeJMenuItem( _remove_branch_color_item );
 848         _tools_menu.addSeparator();
 849         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 850         customizeJMenuItem( _midpoint_root_item );
 851         _tools_menu.addSeparator();
 852         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 853         customizeJMenuItem( _collapse_species_specific_subtrees );
 854         _jmenubar.add( _tools_menu );
 855     }
 856
 857     void buildTypeMenu() {
 858         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 859         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 860         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 861         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 862         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 863         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 864         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 865         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 866         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 867         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 868         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 869         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 870         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 871         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 872         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 873         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 874         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 875         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 876         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 877         initializeTypeMenu( getOptions() );
 878         _jmenubar.add( _type_menu );
 879     }
 880
 881     void buildViewMenu() {
 882         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 883         _view_jmenu
 884                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 885         _view_jmenu.addSeparator();
 886         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 887         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 888         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 889         customizeJMenuItem( _display_basic_information_item );
 890         customizeJMenuItem( _view_as_NH_item );
 891         customizeJMenuItem( _view_as_XML_item );
 892         customizeJMenuItem( _view_as_nexus_item );
 893         _jmenubar.add( _view_jmenu );
 894     }
 895
 896     void checkTextFrames() {
 897         if ( _textframes.size() > 5 ) {
 898             try {
 899                 if ( _textframes.getFirst() != null ) {
 900                     _textframes.getFirst().removeMe();
 901                 }
 902                 else {
 903                     _textframes.removeFirst();
 904                 }
 905             }
 906             catch ( final NoSuchElementException e ) {
 907                 // Ignore.
 908             }
 909         }
 910     }
 911
 912     void clearCurrentExternalNodesDataBuffer() {
 913         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 914     }
 915
 916     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 917         if ( item != null ) {
 918             item.setFont( MainFrame.menu_font );
 919             if ( !getConfiguration().isUseNativeUI() ) {
 920                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 921                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 922             }
 923             item.setSelected( is_selected );
 924             item.addActionListener( this );
 925         }
 926     }
 927
 928     void customizeJMenuItem( final JMenuItem jmi ) {
 929         jmi.setFont( MainFrame.menu_font );
 930         if ( !getConfiguration().isUseNativeUI() ) {
 931             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 932             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 933         }
 934         jmi.addActionListener( this );
 935     }
 936
 937     void displayBasicInformation() {
 938         if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
 939                 && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 940             String title = "Basic Information";
 941             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 942                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 943             }
 944             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 945         }
 946     }
 947
 948     void executeGSDI() {
 949         if ( !isOKforSDI( false, true ) ) {
 950             return;
 951         }
 952         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 953             JOptionPane.showMessageDialog( this,
 954                                            "Gene tree is not rooted.",
 955                                            "Cannot execute GSDI",
 956                                            JOptionPane.ERROR_MESSAGE );
 957             return;
 958         }
 959         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 960         gene_tree.setAllNodesToNotCollapse();
 961         gene_tree.recalculateNumberOfExternalDescendants( false );
 962         GSDI gsdi = null;
 963         final Phylogeny species_tree = _species_tree.copy();
 964         try {
 965             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 966         }
 967         catch ( final SDIException e ) {
 968             JOptionPane.showMessageDialog( this,
 969                                            e.getLocalizedMessage(),
 970                                            "Error during GSDI",
 971                                            JOptionPane.ERROR_MESSAGE );
 972             return;
 973         }
 974         catch ( final Exception e ) {
 975             AptxUtil.unexpectedException( e );
 976             return;
 977         }
 978         gene_tree.setRerootable( false );
 979         gene_tree.clearHashIdToNodeMap();
 980         gene_tree.recalculateNumberOfExternalDescendants( true );
 981         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 982         getMainPanel().getControlPanel().setShowEvents( true );
 983         showWhole();
 984         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 985         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 986         showWhole();
 987         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 988         showWhole();
 989         _mainpanel.getCurrentTreePanel().setEdited( true );
 990         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 991         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 992             JOptionPane.showMessageDialog( this,
 993                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 994                                                    + "Potential duplications: "
 995                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 996                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 997                                                    + "Stripped gene tree nodes: "
 998                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 999                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1000                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1001                                            "GSDI successfully completed",
1002                                            JOptionPane.WARNING_MESSAGE );
1003         }
1004         else {
1005             JOptionPane.showMessageDialog( this,
1006                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1007                                                    + "Potential duplications: "
1008                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1009                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1010                                                    + "Stripped gene tree nodes: "
1011                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1012                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1013                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1014                                            "GSDI successfully completed",
1015                                            JOptionPane.INFORMATION_MESSAGE );
1016         }
1017     }
1018
1019     void executeGSDIR() {
1020         if ( !isOKforSDI( false, false ) ) {
1021             return;
1022         }
1023         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1024         if ( ( p > 0 )
1025                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1026             JOptionPane.showMessageDialog( this,
1027                                            "Gene tree is not completely binary",
1028                                            "Cannot execute GSDI",
1029                                            JOptionPane.ERROR_MESSAGE );
1030             return;
1031         }
1032         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1033         gene_tree.setAllNodesToNotCollapse();
1034         gene_tree.recalculateNumberOfExternalDescendants( false );
1035         GSDIR gsdir = null;
1036         final Phylogeny species_tree = _species_tree.copy();
1037         try {
1038             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1039         }
1040         catch ( final SDIException e ) {
1041             JOptionPane.showMessageDialog( this,
1042                                            e.getLocalizedMessage(),
1043                                            "Error during GSDIR",
1044                                            JOptionPane.ERROR_MESSAGE );
1045             return;
1046         }
1047         catch ( final Exception e ) {
1048             AptxUtil.unexpectedException( e );
1049             return;
1050         }
1051         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1052         result_gene_tree.setRerootable( false );
1053         result_gene_tree.clearHashIdToNodeMap();
1054         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1055         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1056         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1057         getMainPanel().getControlPanel().setShowEvents( true );
1058         showWhole();
1059         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1060         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1061         showWhole();
1062         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1063         showWhole();
1064         _mainpanel.getCurrentTreePanel().setEdited( true );
1065         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1066         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1067             JOptionPane.showMessageDialog( this,
1068                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1069                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1070                                                    + "Stripped gene tree nodes: "
1071                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1072                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1073                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1074                                            "GSDIR successfully completed",
1075                                            JOptionPane.WARNING_MESSAGE );
1076         }
1077         else {
1078             JOptionPane.showMessageDialog( this,
1079                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1080                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1081                                                    + "Stripped gene tree nodes: "
1082                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1083                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1084                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1085                                            "GSDIR successfully completed",
1086                                            JOptionPane.INFORMATION_MESSAGE );
1087         }
1088     }
1089
1090     Configuration getConfiguration() {
1091         return _configuration;
1092     }
1093
1094     TreePanel getCurrentTreePanel() {
1095         return getMainPanel().getCurrentTreePanel();
1096     }
1097
1098     JCheckBoxMenuItem getlabelDirectionCbmi() {
1099         return _label_direction_cbmi;
1100     }
1101
1102     Options getOtions() {
1103         return _options;
1104     }
1105
1106     void initializeTypeMenu( final Options options ) {
1107         setTypeMenuToAllUnselected();
1108         try {
1109             switch ( options.getPhylogenyGraphicsType() ) {
1110                 case CONVEX:
1111                     _convex_type_cbmi.setSelected( true );
1112                     break;
1113                 case CURVED:
1114                     _curved_type_cbmi.setSelected( true );
1115                     break;
1116                 case EURO_STYLE:
1117                     _euro_type_cbmi.setSelected( true );
1118                     break;
1119                 case ROUNDED:
1120                     _rounded_type_cbmi.setSelected( true );
1121                     break;
1122                 case TRIANGULAR:
1123                     _triangular_type_cbmi.setSelected( true );
1124                     break;
1125                 case UNROOTED:
1126                     _unrooted_type_cbmi.setSelected( true );
1127                     break;
1128                 case CIRCULAR:
1129                     _circular_type_cbmi.setSelected( true );
1130                     break;
1131                 default:
1132                     _rectangular_type_cbmi.setSelected( true );
1133                     break;
1134             }
1135         }
1136         catch ( final NullPointerException np ) {
1137             // In all likelihood, this is caused by menu-less display.
1138         }
1139     }
1140
1141     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1142         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1143             return false;
1144         }
1145         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1146             JOptionPane.showMessageDialog( this,
1147                                            "No species tree loaded",
1148                                            "Cannot execute GSDI",
1149                                            JOptionPane.ERROR_MESSAGE );
1150             return false;
1151         }
1152         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1153             JOptionPane.showMessageDialog( this,
1154                                            "Species tree is not completely binary",
1155                                            "Cannot execute GSDI",
1156                                            JOptionPane.ERROR_MESSAGE );
1157             return false;
1158         }
1159         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1160             JOptionPane.showMessageDialog( this,
1161                                            "Gene tree is not completely binary",
1162                                            "Cannot execute GSDI",
1163                                            JOptionPane.ERROR_MESSAGE );
1164             return false;
1165         }
1166         else {
1167             return true;
1168         }
1169     }
1170
1171     boolean isSubtreeDisplayed() {
1172         if ( getCurrentTreePanel() != null ) {
1173             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1174                 JOptionPane
1175                         .showMessageDialog( this,
1176                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1177                                             "Operation can not be exectuted on a sub-tree",
1178                                             JOptionPane.WARNING_MESSAGE );
1179                 return true;
1180             }
1181         }
1182         return false;
1183     }
1184
1185     void removeAllTextFrames() {
1186         for( final TextFrame tf : _textframes ) {
1187             if ( tf != null ) {
1188                 tf.close();
1189             }
1190         }
1191         _textframes.clear();
1192     }
1193
1194     void setConfiguration( final Configuration configuration ) {
1195         _configuration = configuration;
1196     }
1197
1198     void setOptions( final Options options ) {
1199         _options = options;
1200     }
1201
1202     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1203         setTypeMenuToAllUnselected();
1204         try {
1205             switch ( type ) {
1206                 case CIRCULAR:
1207                     _circular_type_cbmi.setSelected( true );
1208                     break;
1209                 case CONVEX:
1210                     _convex_type_cbmi.setSelected( true );
1211                     break;
1212                 case CURVED:
1213                     _curved_type_cbmi.setSelected( true );
1214                     break;
1215                 case EURO_STYLE:
1216                     _euro_type_cbmi.setSelected( true );
1217                     break;
1218                 case ROUNDED:
1219                     _rounded_type_cbmi.setSelected( true );
1220                     break;
1221                 case RECTANGULAR:
1222                     _rectangular_type_cbmi.setSelected( true );
1223                     break;
1224                 case TRIANGULAR:
1225                     _triangular_type_cbmi.setSelected( true );
1226                     break;
1227                 case UNROOTED:
1228                     _unrooted_type_cbmi.setSelected( true );
1229                     break;
1230                 default:
1231                     throw new IllegalArgumentException( "unknown type: " + type );
1232             }
1233         }
1234         catch ( final NullPointerException np ) {
1235             // In all likelihood, this is caused by menu-less display.
1236         }
1237     }
1238
1239     void setTypeMenuToAllUnselected() {
1240         if ( _convex_type_cbmi != null ) {
1241             _convex_type_cbmi.setSelected( false );
1242         }
1243         if ( _curved_type_cbmi != null ) {
1244             _curved_type_cbmi.setSelected( false );
1245         }
1246         if ( _euro_type_cbmi != null ) {
1247             _euro_type_cbmi.setSelected( false );
1248         }
1249         if ( _rounded_type_cbmi != null ) {
1250             _rounded_type_cbmi.setSelected( false );
1251         }
1252         if ( _triangular_type_cbmi != null ) {
1253             _triangular_type_cbmi.setSelected( false );
1254         }
1255         if ( _rectangular_type_cbmi != null ) {
1256             _rectangular_type_cbmi.setSelected( false );
1257         }
1258         if ( _unrooted_type_cbmi != null ) {
1259             _unrooted_type_cbmi.setSelected( false );
1260         }
1261         if ( _circular_type_cbmi != null ) {
1262             _circular_type_cbmi.setSelected( false );
1263         }
1264     }
1265
1266     void showWhole() {
1267         _mainpanel.getControlPanel().showWhole();
1268     }
1269
1270     void switchColors() {
1271         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1272         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1273         csc.setVisible( true );
1274         getMainPanel().setTreeColorSet( colorset );
1275     }
1276
1277     void typeChanged( final Object o ) {
1278         updateTypeCheckboxes( getOptions(), o );
1279         updateOptions( getOptions() );
1280         if ( getCurrentTreePanel() != null ) {
1281             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1282             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1283             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1284                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1285                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1286                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1287                 getCurrentTreePanel().getControlPanel().showWhole();
1288             }
1289             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1290                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1291             }
1292             else {
1293                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1294             }
1295             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1296             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1297         }
1298     }
1299
1300     void updateOptions( final Options options ) {
1301         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1302         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1303                 && _background_gradient_cbmi.isSelected() );
1304         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1305         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1306                 && _show_annotation_ref_source.isSelected() );
1307         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1308                 && _abbreviate_scientific_names.isSelected() );
1309         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1310                 && _color_labels_same_as_parent_branch.isSelected() );
1311         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1312                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1313         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1314                 && _show_default_node_shapes_external_cbmi.isSelected() );
1315         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1316                 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1317         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1318             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1319         }
1320         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1321             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1322         }
1323         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1324             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1325         }
1326         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1327                 && _search_case_senstive_cbmi.isSelected() );
1328         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1329             options.setShowScale( _show_scale_cbmi.isSelected() );
1330         }
1331         if ( _label_direction_cbmi != null ) {
1332             if ( _label_direction_cbmi.isSelected() ) {
1333                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1334             }
1335             else {
1336                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1337             }
1338         }
1339         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1340         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1341                 && _show_confidence_stddev_cbmi.isSelected() );
1342         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1343                 && _search_whole_words_only_cbmi.isSelected() );
1344         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1345                 && _inverse_search_result_cbmi.isSelected() );
1346         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1347             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1348         }
1349         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1350             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1351         }
1352         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1353             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1354         }
1355         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1356             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1357         }
1358         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1359             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1360         }
1361         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1362             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1363         }
1364         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1365             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1366         }
1367         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1368             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1369         }
1370         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1371             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1372         }
1373         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1374             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1375         }
1376         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1377             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1378         }
1379     }
1380
1381     void updateTypeCheckboxes( final Options options, final Object o ) {
1382         setTypeMenuToAllUnselected();
1383         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1384     }
1385
1386     void viewAsNexus() {
1387         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1388             String title = "Nexus";
1389             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1390                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1391             }
1392             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1393                                    .getNhConversionSupportValueStyle() ),
1394                            title );
1395         }
1396     }
1397
1398     void viewAsNH() {
1399         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1400             String title = "New Hampshire";
1401             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1402                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1403             }
1404             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1405                                    .getNhConversionSupportValueStyle() ),
1406                            title );
1407         }
1408     }
1409
1410     void viewAsXML() {
1411         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1412             String title = "phyloXML";
1413             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1414                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1415             }
1416             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1417         }
1418     }
1419
1420     private void chooseFont() {
1421         final FontChooser fc = new FontChooser();
1422         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1423         fc.showDialog( this, "Select the Base Font" );
1424         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1425     }
1426
1427     private void chooseMinimalConfidence() {
1428         final String s = ( String ) JOptionPane
1429                 .showInputDialog( this,
1430                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1431                                           + getOptions().getMinConfidenceValue() + "]\n",
1432                                   "Minimal Confidence Value",
1433                                   JOptionPane.QUESTION_MESSAGE,
1434                                   null,
1435                                   null,
1436                                   getOptions().getMinConfidenceValue() );
1437         if ( !ForesterUtil.isEmpty( s ) ) {
1438             boolean success = true;
1439             double m = 0.0;
1440             final String m_str = s.trim();
1441             if ( !ForesterUtil.isEmpty( m_str ) ) {
1442                 try {
1443                     m = Double.parseDouble( m_str );
1444                 }
1445                 catch ( final Exception ex ) {
1446                     success = false;
1447                 }
1448             }
1449             else {
1450                 success = false;
1451             }
1452             if ( success && ( m >= 0.0 ) ) {
1453                 getOptions().setMinConfidenceValue( m );
1454             }
1455         }
1456     }
1457
1458     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1459         if ( item != null ) {
1460             item.setFont( MainFrame.menu_font );
1461             if ( !getConfiguration().isUseNativeUI() ) {
1462                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1463                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1464             }
1465             item.setSelected( is_selected );
1466             item.addActionListener( this );
1467         }
1468     }
1469
1470     MainPanel getMainPanel() {
1471         return _mainpanel;
1472     }
1473
1474     private Phylogeny getSpeciesTree() {
1475         return _species_tree;
1476     }
1477
1478     private boolean isScreenAntialias() {
1479         return true;
1480     }
1481
1482     private void removeBranchColors() {
1483         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1484             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1485         }
1486     }
1487
1488     private void removeVisualStyles() {
1489         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1490             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1491         }
1492     }
1493
1494     private void setMainPanel( final MainPanelApplets main_panel ) {
1495         _mainpanel = main_panel;
1496     }
1497
1498     private void setSpeciesTree( final Phylogeny species_tree ) {
1499         _species_tree = species_tree;
1500     }
1501
1502     private void setupUI() {
1503         try {
1504             if ( getConfiguration().isUseNativeUI() ) {
1505                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1506             }
1507             else {
1508                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1509             }
1510         }
1511         catch ( final UnsupportedLookAndFeelException e ) {
1512             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1513         }
1514         catch ( final ClassNotFoundException e ) {
1515             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1516         }
1517         catch ( final InstantiationException e ) {
1518             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1519         }
1520         catch ( final IllegalAccessException e ) {
1521             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1522         }
1523         catch ( final Exception e ) {
1524             AptxUtil.dieWithSystemError( e.toString() );
1525         }
1526     }
1527
1528     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1529         for( final TreePanel tree_panel : treepanels ) {
1530             tree_panel.setTextAntialias();
1531         }
1532     }
1533 }