forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java

   1
   2 package org.forester.archaeopteryx;
   3
   4 import java.awt.BorderLayout;
   5 import java.awt.Container;
   6 import java.awt.event.ActionEvent;
   7 import java.awt.event.ActionListener;
   8 import java.awt.event.ComponentAdapter;
   9 import java.awt.event.ComponentEvent;
  10 import java.io.ByteArrayOutputStream;
  11 import java.io.File;
  12 import java.io.IOException;
  13 import java.net.URL;
  14 import java.util.LinkedList;
  15 import java.util.List;
  16 import java.util.NoSuchElementException;
  17
  18 import javax.swing.ButtonGroup;
  19 import javax.swing.JApplet;
  20 import javax.swing.JCheckBoxMenuItem;
  21 import javax.swing.JMenu;
  22 import javax.swing.JMenuBar;
  23 import javax.swing.JMenuItem;
  24 import javax.swing.JOptionPane;
  25 import javax.swing.JRadioButtonMenuItem;
  26 import javax.swing.UIManager;
  27 import javax.swing.UnsupportedLookAndFeelException;
  28 import javax.swing.event.ChangeEvent;
  29 import javax.swing.event.ChangeListener;
  30
  31 import org.apache.commons.codec.binary.Base64;
  32 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  33 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  34 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  35 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  36 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.PhylogenyMethods;
  39 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  40 import org.forester.phylogeny.data.SequenceRelation;
  41 import org.forester.sdi.GSDI;
  42 import org.forester.sdi.GSDIR;
  43 import org.forester.sdi.SDIException;
  44 import org.forester.util.ForesterConstants;
  45 import org.forester.util.ForesterUtil;
  46
  47 // Use like this:
  48 // <applet archive="forester.jar"
  49 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  50 // codebase="http://www.myserver.org/path/to/forester"
  51 // width="600"
  52 // height="500"
  53 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  54 // <param name="url_of_tree_to_load"
  55 // value="http://www.myserver.org/examples/data/apaf.xml">
  56 // <param name="config_file"
  57 // value="http://www.myserver.org/examples/config/config_file.txt">
  58 // </applet>
  59 public class ArchaeopteryxE extends JApplet implements ActionListener {
  60
  61     private final static String         NAME             = "ArchaeopteryxE";
  62     private static final long           serialVersionUID = -1220055577935759443L;
  63     private Configuration               _configuration;
  64     private MainPanelApplets            _mainpanel;
  65     private JMenuBar                    _jmenubar;
  66     private JMenu                       _options_jmenu;
  67     private JMenu                       _font_size_menu;
  68     private JMenuItem                   _super_tiny_fonts_mi;
  69     private JMenuItem                   _tiny_fonts_mi;
  70     private JMenuItem                   _small_fonts_mi;
  71     private JMenuItem                   _medium_fonts_mi;
  72     private JMenuItem                   _large_fonts_mi;
  73     private JMenu                       _tools_menu;
  74     private JMenuItem                   _taxcolor_item;
  75     private JMenuItem                   _confcolor_item;
  76     private JMenuItem                   _midpoint_root_item;
  77     private JMenu                       _view_jmenu;
  78     private JMenuItem                   _view_as_XML_item;
  79     private JMenuItem                   _view_as_NH_item;
  80     private JMenuItem                   _view_as_nexus_item;
  81     private JMenuItem                   _display_basic_information_item;
  82     private JMenu                       _type_menu;
  83     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  84     private JCheckBoxMenuItem           _triangular_type_cbmi;
  85     private JCheckBoxMenuItem           _curved_type_cbmi;
  86     private JCheckBoxMenuItem           _convex_type_cbmi;
  87     private JCheckBoxMenuItem           _euro_type_cbmi;
  88     private JCheckBoxMenuItem           _rounded_type_cbmi;
  89     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  90     private JCheckBoxMenuItem           _circular_type_cbmi;
  91     private JMenuItem                   _help_item;
  92     private JMenuItem                   _about_item;
  93     private JMenu                       _help_jmenu;
  94     private JMenuItem                   _website_item;
  95     private JMenuItem                   _phyloxml_website_item;
  96     private JMenuItem                   _phyloxml_ref_item;
  97     private JMenuItem                   _aptx_ref_item;
  98     private JMenuItem                   _remove_branch_color_item;
  99     private JCheckBoxMenuItem           _show_domain_labels;
 100     private JCheckBoxMenuItem           _show_annotation_ref_source;
 101     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 102     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 103     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 104     private JCheckBoxMenuItem           _background_gradient_cbmi;
 105     private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 106     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 107     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 108     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 109     private Options                     _options;
 110     private JMenuItem                   _choose_font_mi;
 111     private JMenuItem                   _switch_colors_mi;
 112     JCheckBoxMenuItem                   _label_direction_cbmi;
 113     private JCheckBoxMenuItem           _show_scale_cbmi;
 114     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 115     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 116     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 117     private JCheckBoxMenuItem           _show_overview_cbmi;
 118     private JMenuItem                   _choose_minimal_confidence_mi;
 119     private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 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 JMenuItem                   _cycle_node_shape_mi;
 126     private JMenuItem                   _cycle_node_fill_mi;
 127     private JMenuItem                   _choose_node_size_mi;
 128     private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 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
 136     @Override
 137     public void actionPerformed( final ActionEvent e ) {
 138         final Object o = e.getSource();
 139         if ( o == _midpoint_root_item ) {
 140             getMainPanel().getCurrentTreePanel().midpointRoot();
 141         }
 142         else if ( o == _gsdi_item ) {
 143             if ( isSubtreeDisplayed() ) {
 144                 return;
 145             }
 146             executeGSDI();
 147         }
 148         else if ( o == _gsdir_item ) {
 149             if ( isSubtreeDisplayed() ) {
 150                 return;
 151             }
 152             executeGSDIR();
 153         }
 154         else if ( o == _taxcolor_item ) {
 155             getMainPanel().getCurrentTreePanel().taxColor();
 156         }
 157         else if ( o == _confcolor_item ) {
 158             getMainPanel().getCurrentTreePanel().confColor();
 159         }
 160         else if ( o == _collapse_species_specific_subtrees ) {
 161             if ( getCurrentTreePanel() != null ) {
 162                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 163             }
 164         }
 165         else if ( o == _remove_branch_color_item ) {
 166             removeBranchColors();
 167         }
 168         else if ( o == _switch_colors_mi ) {
 169             switchColors();
 170         }
 171         else if ( o == _display_basic_information_item ) {
 172             displayBasicInformation();
 173         }
 174         else if ( o == _view_as_NH_item ) {
 175             viewAsNH();
 176         }
 177         else if ( o == _view_as_XML_item ) {
 178             viewAsXML();
 179         }
 180         else if ( o == _view_as_nexus_item ) {
 181             viewAsNexus();
 182         }
 183         else if ( o == _super_tiny_fonts_mi ) {
 184             if ( getCurrentTreePanel() != null ) {
 185                 getCurrentTreePanel().setSuperTinyFonts();
 186                 getCurrentTreePanel().repaint();
 187             }
 188         }
 189         else if ( o == _tiny_fonts_mi ) {
 190             if ( getCurrentTreePanel() != null ) {
 191                 getCurrentTreePanel().setTinyFonts();
 192                 getCurrentTreePanel().repaint();
 193             }
 194         }
 195         else if ( o == _small_fonts_mi ) {
 196             if ( getCurrentTreePanel() != null ) {
 197                 getCurrentTreePanel().setSmallFonts();
 198                 getCurrentTreePanel().repaint();
 199             }
 200         }
 201         else if ( o == _medium_fonts_mi ) {
 202             if ( getCurrentTreePanel() != null ) {
 203                 getCurrentTreePanel().setMediumFonts();
 204                 getCurrentTreePanel().repaint();
 205             }
 206         }
 207         else if ( o == _large_fonts_mi ) {
 208             if ( getCurrentTreePanel() != null ) {
 209                 getCurrentTreePanel().setLargeFonts();
 210                 getCurrentTreePanel().repaint();
 211             }
 212         }
 213         else if ( o == _choose_font_mi ) {
 214             chooseFont();
 215         }
 216         else if ( o == _choose_minimal_confidence_mi ) {
 217             chooseMinimalConfidence();
 218         }
 219         else if ( o == _choose_node_size_mi ) {
 220             MainFrame.chooseNodeSize( getOptions(), this );
 221         }
 222         else if ( o == _overview_placment_mi ) {
 223             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 224         }
 225         else if ( o == _cycle_node_fill_mi ) {
 226             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 227         }
 228         else if ( o == _cycle_node_shape_mi ) {
 229             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 230         }
 231         else if ( o == _non_lined_up_cladograms_rbmi ) {
 232             updateOptions( getOptions() );
 233             _mainpanel.getControlPanel().showWhole();
 234         }
 235         else if ( o == _uniform_cladograms_rbmi ) {
 236             updateOptions( getOptions() );
 237             _mainpanel.getControlPanel().showWhole();
 238         }
 239         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 240             updateOptions( getOptions() );
 241             _mainpanel.getControlPanel().showWhole();
 242         }
 243         else if ( o == _search_case_senstive_cbmi ) {
 244             updateOptions( getOptions() );
 245             getMainPanel().getControlPanel().search();
 246         }
 247         else if ( o == _search_whole_words_only_cbmi ) {
 248             updateOptions( getOptions() );
 249             getMainPanel().getControlPanel().search();
 250         }
 251         else if ( o == _inverse_search_result_cbmi ) {
 252             updateOptions( getOptions() );
 253             getMainPanel().getControlPanel().search();
 254         }
 255         else if ( o == _show_scale_cbmi ) {
 256             updateOptions( getOptions() );
 257         }
 258         else if ( o == _show_branch_length_values_cbmi ) {
 259             updateOptions( getOptions() );
 260         }
 261         else if ( o == _show_confidence_stddev_cbmi ) {
 262             updateOptions( getOptions() );
 263         }
 264         else if ( o == _label_direction_cbmi ) {
 265             updateOptions( getOptions() );
 266         }
 267         else if ( o == _abbreviate_scientific_names ) {
 268             updateOptions( getOptions() );
 269         }
 270         else if ( o == _show_overview_cbmi ) {
 271             updateOptions( getOptions() );
 272             if ( getCurrentTreePanel() != null ) {
 273                 getCurrentTreePanel().updateOvSizes();
 274             }
 275         }
 276         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 277                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 278                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 279             typeChanged( o );
 280         }
 281         else if ( o == _screen_antialias_cbmi ) {
 282             updateOptions( getOptions() );
 283             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 284         }
 285         else if ( o == _background_gradient_cbmi ) {
 286             updateOptions( getOptions() );
 287         }
 288         else if ( o == _show_domain_labels ) {
 289             updateOptions( getOptions() );
 290         }
 291         else if ( o == _color_labels_same_as_parent_branch ) {
 292             updateOptions( getOptions() );
 293         }
 294         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 295             updateOptions( getOptions() );
 296         }
 297         else if ( o == _show_default_node_shapes_external_cbmi ) {
 298             updateOptions( getOptions() );
 299         }
 300         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 301             updateOptions( getOptions() );
 302         }
 303         else if ( o == _about_item ) {
 304             MainFrame.about();
 305         }
 306         else if ( o == _help_item ) {
 307             help();
 308         }
 309         else if ( o == _website_item ) {
 310             try {
 311                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 312             }
 313             catch ( final IOException e1 ) {
 314                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 315             }
 316         }
 317         else if ( o == _phyloxml_website_item ) {
 318             try {
 319                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 320             }
 321             catch ( final IOException e1 ) {
 322                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 323             }
 324         }
 325         else if ( o == _aptx_ref_item ) {
 326             try {
 327                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 328             }
 329             catch ( final IOException e1 ) {
 330                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 331             }
 332         }
 333         else if ( o == _phyloxml_ref_item ) {
 334             try {
 335                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 336             }
 337             catch ( final IOException e1 ) {
 338                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 339             }
 340         }
 341         else if ( o == _color_by_taxonomic_group_cbmi ) {
 342             updateOptions( getOptions() );
 343         }
 344         repaint();
 345     }
 346
 347     @Override
 348     public void destroy() {
 349         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 350         removeAllTextFrames();
 351         if ( getMainPanel() != null ) {
 352             getMainPanel().terminate();
 353         }
 354     }
 355
 356     /**
 357      * This method returns the current external node data which
 358      * has been selected by the user by clicking the "Return ..."
 359      * menu item. This method is expected to be called from Javascript or
 360      * something like it.
 361      *
 362      * @return current external node data as String
 363      */
 364     public String getCurrentExternalNodesDataBuffer() {
 365         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 366     }
 367
 368     public int getCurrentExternalNodesDataBufferChangeCounter() {
 369         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 370     }
 371
 372     public int getCurrentExternalNodesDataBufferLength() {
 373         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 374     }
 375
 376     /**
 377      * This method returns the current phylogeny as a string in the chosen format
 378      *
 379      * @param format must be NH, NHX, NEXUS or PHYLOXML
 380      * @return the phylogeny string
 381      * @author Herve Menager
 382      */
 383     public String getCurrentPhylogeny( final String format ) {
 384         removeAllTextFrames();
 385         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 386                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 387             return new String();
 388         }
 389         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 390             case NH:
 391                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 392             case NHX:
 393                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 394             case NEXUS:
 395                 return getMainPanel().getCurrentPhylogeny().toNexus();
 396             case PHYLOXML:
 397                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 398             default:
 399                 break;
 400         }
 401         return new String();
 402     }
 403
 404     /**
 405      * This method returns a view of the current phylogeny in a chosen
 406      * graphics format, base64-encoded in a string so that in can be used
 407      * from javascript.
 408      *
 409      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 410      * @return the phylogeny string
 411      * @author Herve Menager
 412      */
 413     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 414         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 415         try {
 416             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 417                                                                     _mainpanel.getWidth(),
 418                                                                     _mainpanel.getHeight(),
 419                                                                     getCurrentTreePanel(),
 420                                                                     getCurrentTreePanel().getControlPanel(),
 421                                                                     GraphicsExportType.valueOf( format ),
 422                                                                     getOptions() );
 423         }
 424         catch ( final IOException ioe ) {
 425             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 426             ioe.printStackTrace();
 427             JOptionPane.showMessageDialog( this,
 428                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 429                                            "Failed to generate graphics",
 430                                            JOptionPane.ERROR_MESSAGE );
 431             return null;
 432         }
 433         final byte[] bytes = baos.toByteArray();
 434         final String dataImg = Base64.encodeBase64String( bytes );
 435         return dataImg;
 436     }
 437
 438     public Options getOptions() {
 439         return _options;
 440     }
 441
 442     @Override
 443     public void init() {
 444         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 445         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 446         final Configuration configuration = new Configuration( config_filename, true, true, true );
 447         setConfiguration( configuration );
 448         setOptions( Options.createInstance( configuration ) );
 449         setupUI();
 450         URL phys_url = null;
 451         Phylogeny[] phys = null;
 452         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 453         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 454         // Get URL to tree file
 455         if ( tree_url_str != null ) {
 456             try {
 457                 phys_url = new URL( tree_url_str );
 458             }
 459             catch ( final Exception e ) {
 460                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 461                 e.printStackTrace();
 462                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 463                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 464             }
 465         }
 466         // Load the tree from URL
 467         if ( phys_url != null ) {
 468             try {
 469                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 470                                                         getConfiguration().isValidatePhyloXmlAgainstSchema(),
 471                                                         getConfiguration().isReplaceUnderscoresInNhParsing(),
 472                                                         getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 473                                                         getConfiguration().getTaxonomyExtraction(),
 474                                                         getConfiguration().isMidpointReroot() );
 475             }
 476             catch ( final Exception e ) {
 477                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 478                 e.printStackTrace();
 479                 JOptionPane.showMessageDialog( this,
 480                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 481                                                "Failed to read phylogenies",
 482                                                JOptionPane.ERROR_MESSAGE );
 483             }
 484         }
 485         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 486             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 487             JOptionPane.showMessageDialog( this,
 488                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 489                                            "Failed to read phylogenies",
 490                                            JOptionPane.ERROR_MESSAGE );
 491             return;
 492         }
 493         else {
 494             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 495         }
 496         //
 497         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 498         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 499             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 500             Phylogeny[] species_trees = null;
 501             try {
 502                 final URL species_tree_url = new URL( species_tree_url_str );
 503                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 504                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 505                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 506                                                                  false,
 507                                                                  TAXONOMY_EXTRACTION.NO,
 508                                                                  false );
 509             }
 510             catch ( final IOException e ) {
 511                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 512                         + "]" );
 513                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 514                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 515             }
 516             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 517                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 518                 if ( species_trees[ 0 ].isEmpty() ) {
 519                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 520                 }
 521                 else if ( !species_trees[ 0 ].isRooted() ) {
 522                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 523                 }
 524                 else {
 525                     setSpeciesTree( species_trees[ 0 ] );
 526                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 527                 }
 528             }
 529         }
 530         //
 531         setVisible( false );
 532         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 533         _jmenubar = new JMenuBar();
 534         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 535             if ( !getConfiguration().isUseNativeUI() ) {
 536                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 537             }
 538             if ( getSpeciesTree() != null ) {
 539                 buildAnalysisMenu();
 540             }
 541             buildToolsMenu();
 542             buildViewMenu();
 543             buildFontSizeMenu();
 544             buildOptionsMenu();
 545             buildTypeMenu();
 546             buildHelpMenu();
 547             setJMenuBar( _jmenubar );
 548         }
 549         final Container contentpane = getContentPane();
 550         contentpane.setLayout( new BorderLayout() );
 551         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 552         addComponentListener( new ComponentAdapter() {
 553
 554             @Override
 555             public void componentResized( final ComponentEvent e ) {
 556                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 557                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 558                                                                                             .getCurrentTreePanel()
 559                                                                                             .getWidth(),
 560                                                                                     getMainPanel()
 561                                                                                             .getCurrentTreePanel()
 562                                                                                             .getHeight(),
 563                                                                                     getOptions()
 564                                                                                             .isAllowFontSizeChange() );
 565                 }
 566             }
 567         } );
 568         if ( getConfiguration().isUseTabbedDisplay() ) {
 569             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 570             AptxUtil.addPhylogeniesToTabs( phys,
 571                                            new File( phys_url.getFile() ).getName(),
 572                                            phys_url.toString(),
 573                                            getConfiguration(),
 574                                            getMainPanel() );
 575         }
 576         else {
 577             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 578             if ( getSpeciesTree() != null ) {
 579                 AptxUtil.printAppletMessage( NAME,
 580                                              "Warning: gsdi (gene duplication inference) only available tabbed display" );
 581             }
 582             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 583         }
 584         validate();
 585         setName( NAME );
 586         getMainPanel().getControlPanel().showWholeAll();
 587         getMainPanel().getControlPanel().showWhole();
 588         System.gc();
 589         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 590         /* GUILHEM_BEG */
 591         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 592         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 593                 .getRelevantSequenceRelationTypes() ) {
 594             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 595         }
 596         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 597         if ( default_relation != null ) {
 598             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 599         }
 600         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 601         if ( default_sequence != null ) {
 602             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 603         }
 604         /* GUILHEM_END */
 605         setVisible( true );
 606     }
 607
 608     public void showTextFrame( final String s, final String title ) {
 609         checkTextFrames();
 610         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 611     }
 612
 613     @Override
 614     public void start() {
 615         if ( getMainPanel() != null ) {
 616             getMainPanel().validate();
 617         }
 618         requestFocus();
 619         requestFocusInWindow();
 620         requestFocus();
 621         AptxUtil.printAppletMessage( NAME, "started" );
 622     }
 623
 624     void buildAnalysisMenu() {
 625         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 626         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 627         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 628         customizeJMenuItem( _gsdi_item );
 629         customizeJMenuItem( _gsdir_item );
 630         //  _analysis_menu.addSeparator();
 631         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 632         //  customizeJMenuItem( _lineage_inference );
 633         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 634         _jmenubar.add( _analysis_menu );
 635     }
 636
 637     void buildFontSizeMenu() {
 638         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 639         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 640         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 641         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 642         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 643         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 644         customizeJMenuItem( _super_tiny_fonts_mi );
 645         customizeJMenuItem( _tiny_fonts_mi );
 646         customizeJMenuItem( _small_fonts_mi );
 647         customizeJMenuItem( _medium_fonts_mi );
 648         customizeJMenuItem( _large_fonts_mi );
 649         _jmenubar.add( _font_size_menu );
 650     }
 651
 652     void buildHelpMenu() {
 653         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 654         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 655         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 656         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 657         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 658         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 659         _help_jmenu.addSeparator();
 660         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 661         customizeJMenuItem( _help_item );
 662         customizeJMenuItem( _website_item );
 663         customizeJMenuItem( _phyloxml_website_item );
 664         customizeJMenuItem( _aptx_ref_item );
 665         customizeJMenuItem( _phyloxml_ref_item );
 666         customizeJMenuItem( _about_item );
 667         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 668         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 669         _jmenubar.add( _help_jmenu );
 670     }
 671
 672     void buildOptionsMenu() {
 673         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 674         _options_jmenu.addChangeListener( new ChangeListener() {
 675
 676             @Override
 677             public void stateChanged( final ChangeEvent e ) {
 678                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 679                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 680                 MainFrame
 681                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 682                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 683                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 684                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 685                                                                      _show_scale_cbmi,
 686                                                                      _show_branch_length_values_cbmi,
 687                                                                      _non_lined_up_cladograms_rbmi,
 688                                                                      _uniform_cladograms_rbmi,
 689                                                                      _ext_node_dependent_cladogram_rbmi,
 690                                                                      _label_direction_cbmi );
 691                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 692                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 693                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 694             }
 695         } );
 696         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 697                                                                 getConfiguration() ) );
 698         _options_jmenu
 699                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 700         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 701         _options_jmenu
 702                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 703         _radio_group_1 = new ButtonGroup();
 704         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 705         _radio_group_1.add( _uniform_cladograms_rbmi );
 706         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 707         /////
 708         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 709         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 710         _options_jmenu
 711                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 712         _options_jmenu
 713                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 714         _options_jmenu
 715                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 716         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 717             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 718         }
 719         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 720         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 721         _options_jmenu
 722                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 723         _options_jmenu
 724                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 725         _options_jmenu
 726                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 727         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 728         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 729         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 730         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 731         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 732         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 733         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 734         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 735         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 736         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 737         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 738         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 739         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 740         /////
 741         _options_jmenu.addSeparator();
 742         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 743                                                                 getConfiguration() ) );
 744         _options_jmenu
 745                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 746         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 747         _options_jmenu
 748                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 749         customizeJMenuItem( _choose_font_mi );
 750         customizeJMenuItem( _choose_minimal_confidence_mi );
 751         customizeJMenuItem( _switch_colors_mi );
 752         customizeJMenuItem( _overview_placment_mi );
 753         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 754         customizeCheckBoxMenuItem( _label_direction_cbmi,
 755                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 756         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 757         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 758         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 759         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 760         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 761         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 762                 .isShowDefaultNodeShapesExternal() );
 763         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 764                 .isShowDefaultNodeShapesInternal() );
 765         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 766         customizeJMenuItem( _cycle_node_shape_mi );
 767         customizeJMenuItem( _cycle_node_fill_mi );
 768         customizeJMenuItem( _choose_node_size_mi );
 769         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 770         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 771         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 772         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 773                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 774         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 775                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 776         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 777                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 778         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 779         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 780         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 781         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 782         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 783         _jmenubar.add( _options_jmenu );
 784     }
 785
 786     void buildToolsMenu() {
 787         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 788         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 789         customizeJMenuItem( _confcolor_item );
 790         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 791         customizeJMenuItem( _taxcolor_item );
 792         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 793         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 794         customizeJMenuItem( _remove_branch_color_item );
 795         _tools_menu.addSeparator();
 796         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 797         customizeJMenuItem( _midpoint_root_item );
 798         _tools_menu.addSeparator();
 799         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 800         customizeJMenuItem( _collapse_species_specific_subtrees );
 801         _jmenubar.add( _tools_menu );
 802     }
 803
 804     void buildTypeMenu() {
 805         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 806         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 807         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 808         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 809         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 810         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 811         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 812         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 813         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 814         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 815         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 816         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 817         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 818         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 819         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 820         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 821         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 822         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 823         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 824         initializeTypeMenu( getOptions() );
 825         _jmenubar.add( _type_menu );
 826     }
 827
 828     void buildViewMenu() {
 829         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 830         _view_jmenu
 831                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 832         _view_jmenu.addSeparator();
 833         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 834         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 835         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 836         customizeJMenuItem( _display_basic_information_item );
 837         customizeJMenuItem( _view_as_NH_item );
 838         customizeJMenuItem( _view_as_XML_item );
 839         customizeJMenuItem( _view_as_nexus_item );
 840         _jmenubar.add( _view_jmenu );
 841     }
 842
 843     void checkTextFrames() {
 844         if ( _textframes.size() > 5 ) {
 845             try {
 846                 if ( _textframes.getFirst() != null ) {
 847                     _textframes.getFirst().removeMe();
 848                 }
 849                 else {
 850                     _textframes.removeFirst();
 851                 }
 852             }
 853             catch ( final NoSuchElementException e ) {
 854                 // Ignore.
 855             }
 856         }
 857     }
 858
 859     void clearCurrentExternalNodesDataBuffer() {
 860         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 861     }
 862
 863     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 864         if ( item != null ) {
 865             item.setFont( MainFrame.menu_font );
 866             if ( !getConfiguration().isUseNativeUI() ) {
 867                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 868                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 869             }
 870             item.setSelected( is_selected );
 871             item.addActionListener( this );
 872         }
 873     }
 874
 875     void customizeJMenuItem( final JMenuItem jmi ) {
 876         jmi.setFont( MainFrame.menu_font );
 877         if ( !getConfiguration().isUseNativeUI() ) {
 878             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 879             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 880         }
 881         jmi.addActionListener( this );
 882     }
 883
 884     void displayBasicInformation() {
 885         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 886             String title = "Basic Information";
 887             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 888                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 889             }
 890             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 891         }
 892     }
 893
 894     void executeGSDI() {
 895         if ( !isOKforSDI( false, true ) ) {
 896             return;
 897         }
 898         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 899             JOptionPane.showMessageDialog( this,
 900                                            "Gene tree is not rooted.",
 901                                            "Cannot execute GSDI",
 902                                            JOptionPane.ERROR_MESSAGE );
 903             return;
 904         }
 905         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 906         gene_tree.setAllNodesToNotCollapse();
 907         gene_tree.recalculateNumberOfExternalDescendants( false );
 908         GSDI gsdi = null;
 909         final Phylogeny species_tree = _species_tree.copy();
 910         try {
 911             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 912         }
 913         catch ( final SDIException e ) {
 914             JOptionPane.showMessageDialog( this,
 915                                            e.getLocalizedMessage(),
 916                                            "Error during GSDI",
 917                                            JOptionPane.ERROR_MESSAGE );
 918             return;
 919         }
 920         catch ( final Exception e ) {
 921             AptxUtil.unexpectedException( e );
 922             return;
 923         }
 924         gene_tree.setRerootable( false );
 925         gene_tree.clearHashIdToNodeMap();
 926         gene_tree.recalculateNumberOfExternalDescendants( true );
 927         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 928         getMainPanel().getControlPanel().setShowEvents( true );
 929         showWhole();
 930         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 931         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 932         showWhole();
 933         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 934         showWhole();
 935         _mainpanel.getCurrentTreePanel().setEdited( true );
 936         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 937         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 938             JOptionPane.showMessageDialog( this,
 939                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 940                                                    + "Potential duplications: "
 941                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 942                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 943                                                    + "Stripped gene tree nodes: "
 944                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 945                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 946                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 947                                            "GSDI successfully completed",
 948                                            JOptionPane.WARNING_MESSAGE );
 949         }
 950         else {
 951             JOptionPane.showMessageDialog( this,
 952                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 953                                                    + "Potential duplications: "
 954                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 955                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 956                                                    + "Stripped gene tree nodes: "
 957                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 958                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 959                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 960                                            "GSDI successfully completed",
 961                                            JOptionPane.INFORMATION_MESSAGE );
 962         }
 963     }
 964
 965     void executeGSDIR() {
 966         if ( !isOKforSDI( false, false ) ) {
 967             return;
 968         }
 969         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
 970         if ( ( p > 0 )
 971                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
 972             JOptionPane.showMessageDialog( this,
 973                                            "Gene tree is not completely binary",
 974                                            "Cannot execute GSDI",
 975                                            JOptionPane.ERROR_MESSAGE );
 976             return;
 977         }
 978         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 979         gene_tree.setAllNodesToNotCollapse();
 980         gene_tree.recalculateNumberOfExternalDescendants( false );
 981         GSDIR gsdir = null;
 982         final Phylogeny species_tree = _species_tree.copy();
 983         try {
 984             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
 985         }
 986         catch ( final SDIException e ) {
 987             JOptionPane.showMessageDialog( this,
 988                                            e.getLocalizedMessage(),
 989                                            "Error during GSDIR",
 990                                            JOptionPane.ERROR_MESSAGE );
 991             return;
 992         }
 993         catch ( final Exception e ) {
 994             AptxUtil.unexpectedException( e );
 995             return;
 996         }
 997         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
 998         result_gene_tree.setRerootable( false );
 999         result_gene_tree.clearHashIdToNodeMap();
1000         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1001         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1002         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1003         getMainPanel().getControlPanel().setShowEvents( true );
1004         showWhole();
1005         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1006         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1007         showWhole();
1008         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1009         showWhole();
1010         _mainpanel.getCurrentTreePanel().setEdited( true );
1011         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1012         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1013             JOptionPane.showMessageDialog( this,
1014                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1015                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1016                                                    + "Stripped gene tree nodes: "
1017                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1018                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1019                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1020                                            "GSDIR successfully completed",
1021                                            JOptionPane.WARNING_MESSAGE );
1022         }
1023         else {
1024             JOptionPane.showMessageDialog( this,
1025                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1026                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1027                                                    + "Stripped gene tree nodes: "
1028                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1029                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1030                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1031                                            "GSDIR successfully completed",
1032                                            JOptionPane.INFORMATION_MESSAGE );
1033         }
1034     }
1035
1036     Configuration getConfiguration() {
1037         return _configuration;
1038     }
1039
1040     TreePanel getCurrentTreePanel() {
1041         return getMainPanel().getCurrentTreePanel();
1042     }
1043
1044     JCheckBoxMenuItem getlabelDirectionCbmi() {
1045         return _label_direction_cbmi;
1046     }
1047
1048     Options getOtions() {
1049         return _options;
1050     }
1051
1052     void help() {
1053         final StringBuilder sb = new StringBuilder();
1054         sb.append( "Display options\n" );
1055         sb.append( "-------------------\n" );
1056         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1057         sb.append( "Clickable tree nodes\n" );
1058         sb.append( "--------------------\n" );
1059         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1060         sb.append( "or by right clicking:\n" );
1061         sb.append( "o  Display Node Data -- display information for a node\n" );
1062         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1063         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
1064         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1065         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
1066         sb.append( "o  Colorize Subtree -- color a subtree\n" );
1067         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
1068         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1069         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
1070         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1071         sb.append( "Zooming\n" );
1072         sb.append( "---------\n" );
1073         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1074         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1075         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1076         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1077         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1078         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1079         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1080         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1081         sb.append( "Quick tree manipulation:\n" );
1082         sb.append( "------------------------\n" );
1083         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1084         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1085         sb.append( "phyloXML\n" );
1086         sb.append( "-------------------\n" );
1087         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1088         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1089         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1090         sb.append( "\n" );
1091         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1092         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1093         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1094     }
1095
1096     void initializeTypeMenu( final Options options ) {
1097         setTypeMenuToAllUnselected();
1098         try {
1099             switch ( options.getPhylogenyGraphicsType() ) {
1100                 case CONVEX:
1101                     _convex_type_cbmi.setSelected( true );
1102                     break;
1103                 case CURVED:
1104                     _curved_type_cbmi.setSelected( true );
1105                     break;
1106                 case EURO_STYLE:
1107                     _euro_type_cbmi.setSelected( true );
1108                     break;
1109                 case ROUNDED:
1110                     _rounded_type_cbmi.setSelected( true );
1111                     break;
1112                 case TRIANGULAR:
1113                     _triangular_type_cbmi.setSelected( true );
1114                     break;
1115                 case UNROOTED:
1116                     _unrooted_type_cbmi.setSelected( true );
1117                     break;
1118                 case CIRCULAR:
1119                     _circular_type_cbmi.setSelected( true );
1120                     break;
1121                 default:
1122                     _rectangular_type_cbmi.setSelected( true );
1123                     break;
1124             }
1125         }
1126         catch ( final NullPointerException np ) {
1127             // In all likelihood, this is caused by menu-less display.
1128         }
1129     }
1130
1131     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1132         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1133             return false;
1134         }
1135         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1136             JOptionPane.showMessageDialog( this,
1137                                            "No species tree loaded",
1138                                            "Cannot execute GSDI",
1139                                            JOptionPane.ERROR_MESSAGE );
1140             return false;
1141         }
1142         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1143             JOptionPane.showMessageDialog( this,
1144                                            "Species tree is not completely binary",
1145                                            "Cannot execute GSDI",
1146                                            JOptionPane.ERROR_MESSAGE );
1147             return false;
1148         }
1149         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1150             JOptionPane.showMessageDialog( this,
1151                                            "Gene tree is not completely binary",
1152                                            "Cannot execute GSDI",
1153                                            JOptionPane.ERROR_MESSAGE );
1154             return false;
1155         }
1156         else {
1157             return true;
1158         }
1159     }
1160
1161     boolean isSubtreeDisplayed() {
1162         if ( getCurrentTreePanel() != null ) {
1163             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1164                 JOptionPane
1165                         .showMessageDialog( this,
1166                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1167                                             "Operation can not be exectuted on a sub-tree",
1168                                             JOptionPane.WARNING_MESSAGE );
1169                 return true;
1170             }
1171         }
1172         return false;
1173     }
1174
1175     void removeAllTextFrames() {
1176         for( final TextFrame tf : _textframes ) {
1177             if ( tf != null ) {
1178                 tf.close();
1179             }
1180         }
1181         _textframes.clear();
1182     }
1183
1184     void setConfiguration( final Configuration configuration ) {
1185         _configuration = configuration;
1186     }
1187
1188     void setOptions( final Options options ) {
1189         _options = options;
1190     }
1191
1192     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1193         setTypeMenuToAllUnselected();
1194         try {
1195             switch ( type ) {
1196                 case CIRCULAR:
1197                     _circular_type_cbmi.setSelected( true );
1198                     break;
1199                 case CONVEX:
1200                     _convex_type_cbmi.setSelected( true );
1201                     break;
1202                 case CURVED:
1203                     _curved_type_cbmi.setSelected( true );
1204                     break;
1205                 case EURO_STYLE:
1206                     _euro_type_cbmi.setSelected( true );
1207                     break;
1208                 case ROUNDED:
1209                     _rounded_type_cbmi.setSelected( true );
1210                     break;
1211                 case RECTANGULAR:
1212                     _rectangular_type_cbmi.setSelected( true );
1213                     break;
1214                 case TRIANGULAR:
1215                     _triangular_type_cbmi.setSelected( true );
1216                     break;
1217                 case UNROOTED:
1218                     _unrooted_type_cbmi.setSelected( true );
1219                     break;
1220                 default:
1221                     throw new IllegalArgumentException( "unknown type: " + type );
1222             }
1223         }
1224         catch ( final NullPointerException np ) {
1225             // In all likelihood, this is caused by menu-less display.
1226         }
1227     }
1228
1229     void setTypeMenuToAllUnselected() {
1230         if ( _convex_type_cbmi != null ) {
1231             _convex_type_cbmi.setSelected( false );
1232         }
1233         if ( _curved_type_cbmi != null ) {
1234             _curved_type_cbmi.setSelected( false );
1235         }
1236         if ( _euro_type_cbmi != null ) {
1237             _euro_type_cbmi.setSelected( false );
1238         }
1239         if ( _rounded_type_cbmi != null ) {
1240             _rounded_type_cbmi.setSelected( false );
1241         }
1242         if ( _triangular_type_cbmi != null ) {
1243             _triangular_type_cbmi.setSelected( false );
1244         }
1245         if ( _rectangular_type_cbmi != null ) {
1246             _rectangular_type_cbmi.setSelected( false );
1247         }
1248         if ( _unrooted_type_cbmi != null ) {
1249             _unrooted_type_cbmi.setSelected( false );
1250         }
1251         if ( _circular_type_cbmi != null ) {
1252             _circular_type_cbmi.setSelected( false );
1253         }
1254     }
1255
1256     void showWhole() {
1257         _mainpanel.getControlPanel().showWhole();
1258     }
1259
1260     void switchColors() {
1261         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1262         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1263         csc.setVisible( true );
1264         getMainPanel().setTreeColorSet( colorset );
1265     }
1266
1267     void typeChanged( final Object o ) {
1268         updateTypeCheckboxes( getOptions(), o );
1269         updateOptions( getOptions() );
1270         if ( getCurrentTreePanel() != null ) {
1271             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1272             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1273             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1274                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1275                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1276                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1277                 getCurrentTreePanel().getControlPanel().showWhole();
1278             }
1279             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1280                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1281             }
1282             else {
1283                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1284             }
1285             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1286             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1287         }
1288     }
1289
1290     void updateOptions( final Options options ) {
1291         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1292         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1293                 && _background_gradient_cbmi.isSelected() );
1294         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1295         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1296                 && _show_annotation_ref_source.isSelected() );
1297         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1298                 && _abbreviate_scientific_names.isSelected() );
1299         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1300                 && _color_labels_same_as_parent_branch.isSelected() );
1301         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1302                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1303         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1304                 && _show_default_node_shapes_external_cbmi.isSelected() );
1305         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1306                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1307         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1308             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1309         }
1310         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1311             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1312         }
1313         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1314             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1315         }
1316         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1317                 && _search_case_senstive_cbmi.isSelected() );
1318         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1319             options.setShowScale( _show_scale_cbmi.isSelected() );
1320         }
1321         if ( _label_direction_cbmi != null ) {
1322             if ( _label_direction_cbmi.isSelected() ) {
1323                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1324             }
1325             else {
1326                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1327             }
1328         }
1329         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1330         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1331                 && _show_confidence_stddev_cbmi.isSelected() );
1332         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1333             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1334         }
1335         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1336                 && _search_whole_words_only_cbmi.isSelected() );
1337         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1338                 && _inverse_search_result_cbmi.isSelected() );
1339         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1340             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1341         }
1342         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1343             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1344         }
1345         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1346             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1347         }
1348         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1349             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1350         }
1351         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1352             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1353         }
1354         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1355             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1356         }
1357         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1358             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1359         }
1360         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1361             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1362         }
1363         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1364             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1365         }
1366     }
1367
1368     void updateTypeCheckboxes( final Options options, final Object o ) {
1369         setTypeMenuToAllUnselected();
1370         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1371     }
1372
1373     void viewAsNexus() {
1374         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1375             String title = "Nexus";
1376             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1377                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1378             }
1379             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1380                                    .getNhConversionSupportValueStyle() ),
1381                            title );
1382         }
1383     }
1384
1385     void viewAsNH() {
1386         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1387             String title = "New Hampshire";
1388             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1389                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1390             }
1391             showTextFrame( getMainPanel().getCurrentPhylogeny()
1392                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1393                            title );
1394         }
1395     }
1396
1397     void viewAsXML() {
1398         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1399             String title = "phyloXML";
1400             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1401                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1402             }
1403             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1404         }
1405     }
1406
1407     private void chooseFont() {
1408         final FontChooser fc = new FontChooser();
1409         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1410         fc.showDialog( this, "Select the Base Font" );
1411         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1412     }
1413
1414     private void chooseMinimalConfidence() {
1415         final String s = ( String ) JOptionPane
1416                 .showInputDialog( this,
1417                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1418                                           + getOptions().getMinConfidenceValue() + "]\n",
1419                                   "Minimal Confidence Value",
1420                                   JOptionPane.QUESTION_MESSAGE,
1421                                   null,
1422                                   null,
1423                                   getOptions().getMinConfidenceValue() );
1424         if ( !ForesterUtil.isEmpty( s ) ) {
1425             boolean success = true;
1426             double m = 0.0;
1427             final String m_str = s.trim();
1428             if ( !ForesterUtil.isEmpty( m_str ) ) {
1429                 try {
1430                     m = Double.parseDouble( m_str );
1431                 }
1432                 catch ( final Exception ex ) {
1433                     success = false;
1434                 }
1435             }
1436             else {
1437                 success = false;
1438             }
1439             if ( success && ( m >= 0.0 ) ) {
1440                 getOptions().setMinConfidenceValue( m );
1441             }
1442         }
1443     }
1444
1445     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1446         if ( item != null ) {
1447             item.setFont( MainFrame.menu_font );
1448             if ( !getConfiguration().isUseNativeUI() ) {
1449                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1450                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1451             }
1452             item.setSelected( is_selected );
1453             item.addActionListener( this );
1454         }
1455     }
1456
1457     private MainPanel getMainPanel() {
1458         return _mainpanel;
1459     }
1460
1461     private Phylogeny getSpeciesTree() {
1462         return _species_tree;
1463     }
1464
1465     private boolean isScreenAntialias() {
1466         return true;
1467     }
1468
1469     private void removeBranchColors() {
1470         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1471             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1472         }
1473     }
1474
1475     private void setMainPanel( final MainPanelApplets main_panel ) {
1476         _mainpanel = main_panel;
1477     }
1478
1479     private void setSpeciesTree( final Phylogeny species_tree ) {
1480         _species_tree = species_tree;
1481     }
1482
1483     private void setupUI() {
1484         try {
1485             if ( getConfiguration().isUseNativeUI() ) {
1486                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1487             }
1488             else {
1489                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1490             }
1491         }
1492         catch ( final UnsupportedLookAndFeelException e ) {
1493             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1494         }
1495         catch ( final ClassNotFoundException e ) {
1496             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1497         }
1498         catch ( final InstantiationException e ) {
1499             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1500         }
1501         catch ( final IllegalAccessException e ) {
1502             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1503         }
1504         catch ( final Exception e ) {
1505             AptxUtil.dieWithSystemError( e.toString() );
1506         }
1507     }
1508
1509     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1510         for( final TreePanel tree_panel : treepanels ) {
1511             tree_panel.setTextAntialias();
1512         }
1513     }
1514 }