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             }
 466             catch ( final Exception e ) {
 467                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 468                 e.printStackTrace();
 469                 JOptionPane.showMessageDialog( this,
 470                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 471                                                "Failed to read phylogenies",
 472                                                JOptionPane.ERROR_MESSAGE );
 473             }
 474         }
 475         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 476             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 477             JOptionPane.showMessageDialog( this,
 478                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 479                                            "Failed to read phylogenies",
 480                                            JOptionPane.ERROR_MESSAGE );
 481             return;
 482         }
 483         else {
 484             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 485         }
 486         //
 487         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 488         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 489             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 490             Phylogeny[] species_trees = null;
 491             try {
 492                 final URL species_tree_url = new URL( species_tree_url_str );
 493                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 494                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 495                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 496                                                                  false,
 497                                                                  TAXONOMY_EXTRACTION.NO );
 498             }
 499             catch ( final IOException e ) {
 500                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 501                         + "]" );
 502                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 503                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 504             }
 505             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 506                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 507                 if ( species_trees[ 0 ].isEmpty() ) {
 508                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 509                 }
 510                 else if ( !species_trees[ 0 ].isRooted() ) {
 511                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 512                 }
 513                 else {
 514                     setSpeciesTree( species_trees[ 0 ] );
 515                 }
 516             }
 517         }
 518         //
 519         setVisible( false );
 520         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 521         _jmenubar = new JMenuBar();
 522         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 523             if ( !getConfiguration().isUseNativeUI() ) {
 524                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 525             }
 526             if ( getSpeciesTree() != null ) {
 527                 buildAnalysisMenu();
 528             }
 529             buildToolsMenu();
 530             buildViewMenu();
 531             buildFontSizeMenu();
 532             buildOptionsMenu();
 533             buildTypeMenu();
 534             buildHelpMenu();
 535             setJMenuBar( _jmenubar );
 536         }
 537         final Container contentpane = getContentPane();
 538         contentpane.setLayout( new BorderLayout() );
 539         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 540         addComponentListener( new ComponentAdapter() {
 541
 542             @Override
 543             public void componentResized( final ComponentEvent e ) {
 544                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 545                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 546                                                                                             .getCurrentTreePanel()
 547                                                                                             .getWidth(),
 548                                                                                     getMainPanel()
 549                                                                                             .getCurrentTreePanel()
 550                                                                                             .getHeight(),
 551                                                                                     getOptions()
 552                                                                                             .isAllowFontSizeChange() );
 553                 }
 554             }
 555         } );
 556         if ( getConfiguration().isUseTabbedDisplay() ) {
 557             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 558             AptxUtil.addPhylogeniesToTabs( phys,
 559                                            new File( phys_url.getFile() ).getName(),
 560                                            phys_url.toString(),
 561                                            getConfiguration(),
 562                                            getMainPanel() );
 563         }
 564         else {
 565             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 566             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 567         }
 568         validate();
 569         setName( NAME );
 570         getMainPanel().getControlPanel().showWholeAll();
 571         getMainPanel().getControlPanel().showWhole();
 572         System.gc();
 573         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 574         /* GUILHEM_BEG */
 575         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 576         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 577                 .getRelevantSequenceRelationTypes() ) {
 578             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 579         }
 580         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 581         if ( default_relation != null ) {
 582             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 583         }
 584         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 585         if ( default_sequence != null ) {
 586             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 587         }
 588         /* GUILHEM_END */
 589         setVisible( true );
 590     }
 591
 592     public void showTextFrame( final String s, final String title ) {
 593         checkTextFrames();
 594         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 595     }
 596
 597     @Override
 598     public void start() {
 599         if ( getMainPanel() != null ) {
 600             getMainPanel().validate();
 601         }
 602         requestFocus();
 603         requestFocusInWindow();
 604         requestFocus();
 605         AptxUtil.printAppletMessage( NAME, "started" );
 606     }
 607
 608     void buildAnalysisMenu() {
 609         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 610         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 611         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 612         customizeJMenuItem( _gsdi_item );
 613         customizeJMenuItem( _gsdir_item );
 614         //  _analysis_menu.addSeparator();
 615         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 616         //  customizeJMenuItem( _lineage_inference );
 617         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 618         _jmenubar.add( _analysis_menu );
 619     }
 620
 621     void buildFontSizeMenu() {
 622         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 623         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 624         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 625         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 626         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 627         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 628         customizeJMenuItem( _super_tiny_fonts_mi );
 629         customizeJMenuItem( _tiny_fonts_mi );
 630         customizeJMenuItem( _small_fonts_mi );
 631         customizeJMenuItem( _medium_fonts_mi );
 632         customizeJMenuItem( _large_fonts_mi );
 633         _jmenubar.add( _font_size_menu );
 634     }
 635
 636     void buildHelpMenu() {
 637         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 638         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 639         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 640         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 641         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 642         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 643         _help_jmenu.addSeparator();
 644         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 645         customizeJMenuItem( _help_item );
 646         customizeJMenuItem( _website_item );
 647         customizeJMenuItem( _phyloxml_website_item );
 648         customizeJMenuItem( _aptx_ref_item );
 649         customizeJMenuItem( _phyloxml_ref_item );
 650         customizeJMenuItem( _about_item );
 651         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 652         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 653         _jmenubar.add( _help_jmenu );
 654     }
 655
 656     void buildOptionsMenu() {
 657         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 658         _options_jmenu.addChangeListener( new ChangeListener() {
 659
 660             @Override
 661             public void stateChanged( final ChangeEvent e ) {
 662                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 663                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 664                 MainFrame
 665                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 666                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 667                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 668                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 669                                                                      _show_scale_cbmi,
 670                                                                      _show_branch_length_values_cbmi,
 671                                                                      _non_lined_up_cladograms_rbmi,
 672                                                                      _uniform_cladograms_rbmi,
 673                                                                      _ext_node_dependent_cladogram_rbmi,
 674                                                                      _label_direction_cbmi );
 675                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 676                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 677                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 678             }
 679         } );
 680         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 681                                                                 getConfiguration() ) );
 682         _options_jmenu
 683                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 684         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 685         _options_jmenu
 686                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 687         _radio_group_1 = new ButtonGroup();
 688         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 689         _radio_group_1.add( _uniform_cladograms_rbmi );
 690         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 691         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 692         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 693         _options_jmenu
 694                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 695         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 696         _options_jmenu
 697                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 698         _options_jmenu
 699                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 700         _options_jmenu
 701                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 702         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 703         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 704         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 705         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 706         _options_jmenu
 707                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 708         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 709         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 710         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 711         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 712         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 713         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 714             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 715         }
 716         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 717         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 718         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 719         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 720         _options_jmenu.addSeparator();
 721         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 722                                                                 getConfiguration() ) );
 723         _options_jmenu
 724                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 725         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 726         _options_jmenu
 727                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 728         customizeJMenuItem( _choose_font_mi );
 729         customizeJMenuItem( _choose_minimal_confidence_mi );
 730         customizeJMenuItem( _switch_colors_mi );
 731         customizeJMenuItem( _overview_placment_mi );
 732         customizeCheckBoxMenuItem( _label_direction_cbmi,
 733                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 734         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 735         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 736         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 737         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 738         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 739                 .isShowDefaultNodeShapesExternal() );
 740         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 741                 .isShowDefaultNodeShapesInternal() );
 742         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 743         customizeJMenuItem( _cycle_node_shape_mi );
 744         customizeJMenuItem( _cycle_node_fill_mi );
 745         customizeJMenuItem( _choose_node_size_mi );
 746         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 747         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 748         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 749         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 750                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 751         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 752                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 753         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 754                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 755         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 756         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 757         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 758         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 759         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 760         _jmenubar.add( _options_jmenu );
 761     }
 762
 763     void buildToolsMenu() {
 764         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 765         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 766         customizeJMenuItem( _confcolor_item );
 767         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 768         customizeJMenuItem( _taxcolor_item );
 769         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 770         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 771         customizeJMenuItem( _remove_branch_color_item );
 772         _tools_menu.addSeparator();
 773         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 774         customizeJMenuItem( _midpoint_root_item );
 775         _tools_menu.addSeparator();
 776         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 777         customizeJMenuItem( _collapse_species_specific_subtrees );
 778         _jmenubar.add( _tools_menu );
 779     }
 780
 781     void buildTypeMenu() {
 782         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 783         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 784         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 785         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 786         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 787         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 788         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 789         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 790         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 791         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 792         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 793         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 794         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 795         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 796         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 797         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 798         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 799         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 800         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 801         initializeTypeMenu( getOptions() );
 802         _jmenubar.add( _type_menu );
 803     }
 804
 805     void buildViewMenu() {
 806         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 807         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 808         _view_jmenu.addSeparator();
 809         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 810         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 811         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 812         customizeJMenuItem( _display_basic_information_item );
 813         customizeJMenuItem( _view_as_NH_item );
 814         customizeJMenuItem( _view_as_XML_item );
 815         customizeJMenuItem( _view_as_nexus_item );
 816         _jmenubar.add( _view_jmenu );
 817     }
 818
 819     void checkTextFrames() {
 820         if ( _textframes.size() > 5 ) {
 821             try {
 822                 if ( _textframes.getFirst() != null ) {
 823                     _textframes.getFirst().removeMe();
 824                 }
 825                 else {
 826                     _textframes.removeFirst();
 827                 }
 828             }
 829             catch ( final NoSuchElementException e ) {
 830                 // Ignore.
 831             }
 832         }
 833     }
 834
 835     void clearCurrentExternalNodesDataBuffer() {
 836         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 837     }
 838
 839     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 840         if ( item != null ) {
 841             item.setFont( MainFrame.menu_font );
 842             if ( !getConfiguration().isUseNativeUI() ) {
 843                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 844                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 845             }
 846             item.setSelected( is_selected );
 847             item.addActionListener( this );
 848         }
 849     }
 850
 851     void customizeJMenuItem( final JMenuItem jmi ) {
 852         jmi.setFont( MainFrame.menu_font );
 853         if ( !getConfiguration().isUseNativeUI() ) {
 854             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 855             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 856         }
 857         jmi.addActionListener( this );
 858     }
 859
 860     void displayBasicInformation() {
 861         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 862             String title = "Basic Information";
 863             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 864                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
 865             }
 866             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
 867         }
 868     }
 869
 870     void executeGSDI() {
 871         if ( !isOKforSDI( false, true ) ) {
 872             return;
 873         }
 874         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 875             JOptionPane.showMessageDialog( this,
 876                                            "Gene tree is not rooted.",
 877                                            "Cannot execute GSDI",
 878                                            JOptionPane.ERROR_MESSAGE );
 879             return;
 880         }
 881         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 882         gene_tree.setAllNodesToNotCollapse();
 883         gene_tree.recalculateNumberOfExternalDescendants( false );
 884         GSDI gsdi = null;
 885         final Phylogeny species_tree = _species_tree.copy();
 886         try {
 887             gsdi = new GSDI( gene_tree, species_tree, false, true, true );
 888         }
 889         catch ( final SDIException e ) {
 890             JOptionPane.showMessageDialog( this,
 891                                            e.getLocalizedMessage(),
 892                                            "Error during GSDI",
 893                                            JOptionPane.ERROR_MESSAGE );
 894             return;
 895         }
 896         catch ( final Exception e ) {
 897             AptxUtil.unexpectedException( e );
 898             return;
 899         }
 900         gene_tree.setRerootable( false );
 901         gene_tree.clearHashIdToNodeMap();
 902         gene_tree.recalculateNumberOfExternalDescendants( true );
 903         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 904         getMainPanel().getControlPanel().setShowEvents( true );
 905         showWhole();
 906         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 907         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 908         showWhole();
 909         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 910         showWhole();
 911         _mainpanel.getCurrentTreePanel().setEdited( true );
 912         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 913         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 914             JOptionPane.showMessageDialog( this,
 915                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 916                                                    + "Potential duplications: "
 917                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 918                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 919                                                    + "Stripped gene tree nodes: "
 920                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 921                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 922                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 923                                            "GSDI successfully completed",
 924                                            JOptionPane.WARNING_MESSAGE );
 925         }
 926         else {
 927             JOptionPane.showMessageDialog( this,
 928                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 929                                                    + "Potential duplications: "
 930                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 931                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 932                                                    + "Stripped gene tree nodes: "
 933                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 934                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 935                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 936                                            "GSDI successfully completed",
 937                                            JOptionPane.INFORMATION_MESSAGE );
 938         }
 939     }
 940
 941     void executeGSDIR() {
 942         if ( !isOKforSDI( false, false ) ) {
 943             return;
 944         }
 945         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
 946         if ( ( p > 0 )
 947                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
 948             JOptionPane.showMessageDialog( this,
 949                                            "Gene tree is not completely binary",
 950                                            "Cannot execute GSDI",
 951                                            JOptionPane.ERROR_MESSAGE );
 952             return;
 953         }
 954         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 955         gene_tree.setAllNodesToNotCollapse();
 956         gene_tree.recalculateNumberOfExternalDescendants( false );
 957         GSDIR gsdir = null;
 958         final Phylogeny species_tree = _species_tree.copy();
 959         try {
 960             gsdir = new GSDIR( gene_tree, species_tree, true, true );
 961         }
 962         catch ( final SDIException e ) {
 963             JOptionPane.showMessageDialog( this,
 964                                            e.getLocalizedMessage(),
 965                                            "Error during GSDIR",
 966                                            JOptionPane.ERROR_MESSAGE );
 967             return;
 968         }
 969         catch ( final Exception e ) {
 970             AptxUtil.unexpectedException( e );
 971             return;
 972         }
 973         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
 974         result_gene_tree.setRerootable( false );
 975         result_gene_tree.clearHashIdToNodeMap();
 976         result_gene_tree.recalculateNumberOfExternalDescendants( true );
 977         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
 978         getMainPanel().getControlPanel().setShowEvents( true );
 979         showWhole();
 980         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 981         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 982         showWhole();
 983         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 984         showWhole();
 985         _mainpanel.getCurrentTreePanel().setEdited( true );
 986         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 987         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 988             JOptionPane.showMessageDialog( this,
 989                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
 990                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
 991                                                    + "Stripped gene tree nodes: "
 992                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
 993                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
 994                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 995                                            "GSDIR successfully completed",
 996                                            JOptionPane.WARNING_MESSAGE );
 997         }
 998         else {
 999             JOptionPane.showMessageDialog( this,
1000                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1001                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1002                                                    + "Stripped gene tree nodes: "
1003                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1004                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1005                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1006                                            "GSDIR successfully completed",
1007                                            JOptionPane.INFORMATION_MESSAGE );
1008         }
1009     }
1010
1011     Configuration getConfiguration() {
1012         return _configuration;
1013     }
1014
1015     TreePanel getCurrentTreePanel() {
1016         return getMainPanel().getCurrentTreePanel();
1017     }
1018
1019     JCheckBoxMenuItem getlabelDirectionCbmi() {
1020         return _label_direction_cbmi;
1021     }
1022
1023     Options getOtions() {
1024         return _options;
1025     }
1026
1027     void help() {
1028         final StringBuilder sb = new StringBuilder();
1029         sb.append( "Display options\n" );
1030         sb.append( "-------------------\n" );
1031         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1032         sb.append( "Clickable tree nodes\n" );
1033         sb.append( "--------------------\n" );
1034         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1035         sb.append( "or by right clicking:\n" );
1036         sb.append( "o  Display Node Data -- display information for a node\n" );
1037         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1038         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
1039         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1040         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
1041         sb.append( "o  Colorize Subtree -- color a subtree\n" );
1042         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
1043         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1044         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
1045         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1046         sb.append( "Zooming\n" );
1047         sb.append( "---------\n" );
1048         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1049         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1050         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1051         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1052         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1053         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1054         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1055         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1056         sb.append( "Quick tree manipulation:\n" );
1057         sb.append( "------------------------\n" );
1058         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1059         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1060         sb.append( "phyloXML\n" );
1061         sb.append( "-------------------\n" );
1062         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1063         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1064         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1065         sb.append( "\n" );
1066         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1067         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1068         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1069     }
1070
1071     void initializeTypeMenu( final Options options ) {
1072         setTypeMenuToAllUnselected();
1073         try {
1074             switch ( options.getPhylogenyGraphicsType() ) {
1075                 case CONVEX:
1076                     _convex_type_cbmi.setSelected( true );
1077                     break;
1078                 case CURVED:
1079                     _curved_type_cbmi.setSelected( true );
1080                     break;
1081                 case EURO_STYLE:
1082                     _euro_type_cbmi.setSelected( true );
1083                     break;
1084                 case ROUNDED:
1085                     _rounded_type_cbmi.setSelected( true );
1086                     break;
1087                 case TRIANGULAR:
1088                     _triangular_type_cbmi.setSelected( true );
1089                     break;
1090                 case UNROOTED:
1091                     _unrooted_type_cbmi.setSelected( true );
1092                     break;
1093                 case CIRCULAR:
1094                     _circular_type_cbmi.setSelected( true );
1095                     break;
1096                 default:
1097                     _rectangular_type_cbmi.setSelected( true );
1098                     break;
1099             }
1100         }
1101         catch ( final NullPointerException np ) {
1102             // In all likelihood, this is caused by menu-less display.
1103         }
1104     }
1105
1106     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1107         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1108             return false;
1109         }
1110         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1111             JOptionPane.showMessageDialog( this,
1112                                            "No species tree loaded",
1113                                            "Cannot execute GSDI",
1114                                            JOptionPane.ERROR_MESSAGE );
1115             return false;
1116         }
1117         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1118             JOptionPane.showMessageDialog( this,
1119                                            "Species tree is not completely binary",
1120                                            "Cannot execute GSDI",
1121                                            JOptionPane.ERROR_MESSAGE );
1122             return false;
1123         }
1124         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1125             JOptionPane.showMessageDialog( this,
1126                                            "Gene tree is not completely binary",
1127                                            "Cannot execute GSDI",
1128                                            JOptionPane.ERROR_MESSAGE );
1129             return false;
1130         }
1131         else {
1132             return true;
1133         }
1134     }
1135
1136     boolean isSubtreeDisplayed() {
1137         if ( getCurrentTreePanel() != null ) {
1138             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1139                 JOptionPane
1140                         .showMessageDialog( this,
1141                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1142                                             "Operation can not be exectuted on a sub-tree",
1143                                             JOptionPane.WARNING_MESSAGE );
1144                 return true;
1145             }
1146         }
1147         return false;
1148     }
1149
1150     void removeAllTextFrames() {
1151         for( final TextFrame tf : _textframes ) {
1152             if ( tf != null ) {
1153                 tf.close();
1154             }
1155         }
1156         _textframes.clear();
1157     }
1158
1159     void setConfiguration( final Configuration configuration ) {
1160         _configuration = configuration;
1161     }
1162
1163     void setOptions( final Options options ) {
1164         _options = options;
1165     }
1166
1167     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1168         setTypeMenuToAllUnselected();
1169         try {
1170             switch ( type ) {
1171                 case CIRCULAR:
1172                     _circular_type_cbmi.setSelected( true );
1173                     break;
1174                 case CONVEX:
1175                     _convex_type_cbmi.setSelected( true );
1176                     break;
1177                 case CURVED:
1178                     _curved_type_cbmi.setSelected( true );
1179                     break;
1180                 case EURO_STYLE:
1181                     _euro_type_cbmi.setSelected( true );
1182                     break;
1183                 case ROUNDED:
1184                     _rounded_type_cbmi.setSelected( true );
1185                     break;
1186                 case RECTANGULAR:
1187                     _rectangular_type_cbmi.setSelected( true );
1188                     break;
1189                 case TRIANGULAR:
1190                     _triangular_type_cbmi.setSelected( true );
1191                     break;
1192                 case UNROOTED:
1193                     _unrooted_type_cbmi.setSelected( true );
1194                     break;
1195                 default:
1196                     throw new IllegalArgumentException( "unknown type: " + type );
1197             }
1198         }
1199         catch ( final NullPointerException np ) {
1200             // In all likelihood, this is caused by menu-less display.
1201         }
1202     }
1203
1204     void setTypeMenuToAllUnselected() {
1205         if ( _convex_type_cbmi != null ) {
1206             _convex_type_cbmi.setSelected( false );
1207         }
1208         if ( _curved_type_cbmi != null ) {
1209             _curved_type_cbmi.setSelected( false );
1210         }
1211         if ( _euro_type_cbmi != null ) {
1212             _euro_type_cbmi.setSelected( false );
1213         }
1214         if ( _rounded_type_cbmi != null ) {
1215             _rounded_type_cbmi.setSelected( false );
1216         }
1217         if ( _triangular_type_cbmi != null ) {
1218             _triangular_type_cbmi.setSelected( false );
1219         }
1220         if ( _rectangular_type_cbmi != null ) {
1221             _rectangular_type_cbmi.setSelected( false );
1222         }
1223         if ( _unrooted_type_cbmi != null ) {
1224             _unrooted_type_cbmi.setSelected( false );
1225         }
1226         if ( _circular_type_cbmi != null ) {
1227             _circular_type_cbmi.setSelected( false );
1228         }
1229     }
1230
1231     void showWhole() {
1232         _mainpanel.getControlPanel().showWhole();
1233     }
1234
1235     void switchColors() {
1236         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1237         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1238         csc.setVisible( true );
1239         getMainPanel().setTreeColorSet( colorset );
1240     }
1241
1242     void typeChanged( final Object o ) {
1243         updateTypeCheckboxes( getOptions(), o );
1244         updateOptions( getOptions() );
1245         if ( getCurrentTreePanel() != null ) {
1246             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1247             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1248             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1249                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1250                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1251                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1252                 getCurrentTreePanel().getControlPanel().showWhole();
1253             }
1254             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1255                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1256             }
1257             else {
1258                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1259             }
1260             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1261             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1262         }
1263     }
1264
1265     void updateOptions( final Options options ) {
1266         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1267         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1268                 && _background_gradient_cbmi.isSelected() );
1269         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1270         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1271                 && _abbreviate_scientific_names.isSelected() );
1272         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1273                 && _color_labels_same_as_parent_branch.isSelected() );
1274         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1275                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1276         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1277                 && _show_default_node_shapes_external_cbmi.isSelected() );
1278         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1279                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1280         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1281             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1282         }
1283         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1284             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1285         }
1286         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1287             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1288         }
1289         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1290                 && _search_case_senstive_cbmi.isSelected() );
1291         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1292             options.setShowScale( _show_scale_cbmi.isSelected() );
1293         }
1294         if ( _label_direction_cbmi != null ) {
1295             if ( _label_direction_cbmi.isSelected() ) {
1296                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1297             }
1298             else {
1299                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1300             }
1301         }
1302         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1303         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1304                 && _show_confidence_stddev_cbmi.isSelected() );
1305         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1306             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1307         }
1308         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1309                 && _search_whole_words_only_cbmi.isSelected() );
1310         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1311                 && _inverse_search_result_cbmi.isSelected() );
1312         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1313             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1314         }
1315         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1316             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1317         }
1318         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1319             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1320         }
1321         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1322             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1323         }
1324         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1325             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1326         }
1327         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1328             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1329         }
1330         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1331             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1332         }
1333         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1334             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1335         }
1336     }
1337
1338     void updateTypeCheckboxes( final Options options, final Object o ) {
1339         setTypeMenuToAllUnselected();
1340         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1341     }
1342
1343     void viewAsNexus() {
1344         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1345             String title = "Nexus";
1346             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1347                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1348             }
1349             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1350                                    .getNhConversionSupportValueStyle() ),
1351                            title );
1352         }
1353     }
1354
1355     void viewAsNH() {
1356         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1357             String title = "New Hampshire";
1358             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1359                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1360             }
1361             showTextFrame( getMainPanel().getCurrentPhylogeny()
1362                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1363                            title );
1364         }
1365     }
1366
1367     void viewAsXML() {
1368         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1369             String title = "phyloXML";
1370             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1371                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1372             }
1373             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1374         }
1375     }
1376
1377     private void chooseFont() {
1378         final FontChooser fc = new FontChooser();
1379         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1380         fc.showDialog( this, "Select the Base Font" );
1381         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1382     }
1383
1384     private void chooseMinimalConfidence() {
1385         final String s = ( String ) JOptionPane
1386                 .showInputDialog( this,
1387                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1388                                           + getOptions().getMinConfidenceValue() + "]\n",
1389                                   "Minimal Confidence Value",
1390                                   JOptionPane.QUESTION_MESSAGE,
1391                                   null,
1392                                   null,
1393                                   getOptions().getMinConfidenceValue() );
1394         if ( !ForesterUtil.isEmpty( s ) ) {
1395             boolean success = true;
1396             double m = 0.0;
1397             final String m_str = s.trim();
1398             if ( !ForesterUtil.isEmpty( m_str ) ) {
1399                 try {
1400                     m = Double.parseDouble( m_str );
1401                 }
1402                 catch ( final Exception ex ) {
1403                     success = false;
1404                 }
1405             }
1406             else {
1407                 success = false;
1408             }
1409             if ( success && ( m >= 0.0 ) ) {
1410                 getOptions().setMinConfidenceValue( m );
1411             }
1412         }
1413     }
1414
1415     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1416         if ( item != null ) {
1417             item.setFont( MainFrame.menu_font );
1418             if ( !getConfiguration().isUseNativeUI() ) {
1419                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1420                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1421             }
1422             item.setSelected( is_selected );
1423             item.addActionListener( this );
1424         }
1425     }
1426
1427     private MainPanel getMainPanel() {
1428         return _mainpanel;
1429     }
1430
1431     private Phylogeny getSpeciesTree() {
1432         return _species_tree;
1433     }
1434
1435     private boolean isScreenAntialias() {
1436         return true;
1437     }
1438
1439     private void removeBranchColors() {
1440         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1441             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1442         }
1443     }
1444
1445     private void setMainPanel( final MainPanelApplets main_panel ) {
1446         _mainpanel = main_panel;
1447     }
1448
1449     private void setSpeciesTree( final Phylogeny species_tree ) {
1450         _species_tree = species_tree;
1451     }
1452
1453     private void setupUI() {
1454         try {
1455             if ( getConfiguration().isUseNativeUI() ) {
1456                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1457             }
1458             else {
1459                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1460             }
1461         }
1462         catch ( final UnsupportedLookAndFeelException e ) {
1463             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1464         }
1465         catch ( final ClassNotFoundException e ) {
1466             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1467         }
1468         catch ( final InstantiationException e ) {
1469             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1470         }
1471         catch ( final IllegalAccessException e ) {
1472             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1473         }
1474         catch ( final Exception e ) {
1475             AptxUtil.dieWithSystemError( e.toString() );
1476         }
1477     }
1478
1479     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1480         for( final TreePanel tree_panel : treepanels ) {
1481             tree_panel.setTextAntialias();
1482         }
1483     }
1484 }