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