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