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

   1
   2 package org.forester.archaeopteryx;
   3
   4 import java.awt.BorderLayout;
   5 import java.awt.Container;
   6 import java.awt.event.ActionEvent;
   7 import java.awt.event.ActionListener;
   8 import java.awt.event.ComponentAdapter;
   9 import java.awt.event.ComponentEvent;
  10 import java.io.ByteArrayOutputStream;
  11 import java.io.File;
  12 import java.io.IOException;
  13 import java.net.URL;
  14 import java.util.LinkedList;
  15 import java.util.List;
  16 import java.util.NoSuchElementException;
  17
  18 import javax.swing.ButtonGroup;
  19 import javax.swing.JApplet;
  20 import javax.swing.JCheckBoxMenuItem;
  21 import javax.swing.JMenu;
  22 import javax.swing.JMenuBar;
  23 import javax.swing.JMenuItem;
  24 import javax.swing.JOptionPane;
  25 import javax.swing.JRadioButtonMenuItem;
  26 import javax.swing.UIManager;
  27 import javax.swing.UnsupportedLookAndFeelException;
  28 import javax.swing.event.ChangeEvent;
  29 import javax.swing.event.ChangeListener;
  30
  31 import org.apache.commons.codec.binary.Base64;
  32 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  33 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  34 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  35 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  36 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.PhylogenyMethods;
  39 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  40 import org.forester.phylogeny.data.SequenceRelation;
  41 import org.forester.sdi.GSDI;
  42 import org.forester.sdi.GSDIR;
  43 import org.forester.sdi.SDIException;
  44 import org.forester.util.ForesterConstants;
  45 import org.forester.util.ForesterUtil;
  46
  47 // Use like this:
  48 // <applet archive="forester.jar"
  49 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  50 // codebase="http://www.myserver.org/path/to/forester"
  51 // width="600"
  52 // height="500"
  53 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  54 // <param name="url_of_tree_to_load"
  55 // value="http://www.myserver.org/examples/data/apaf.xml">
  56 // <param name="config_file"
  57 // value="http://www.myserver.org/examples/config/config_file.txt">
  58 // </applet>
  59 public class ArchaeopteryxE extends JApplet implements ActionListener {
  60
  61     private final static String         NAME             = "ArchaeopteryxE";
  62     private static final long           serialVersionUID = -1220055577935759443L;
  63     private Configuration               _configuration;
  64     private MainPanelApplets            _mainpanel;
  65     private JMenuBar                    _jmenubar;
  66     private JMenu                       _options_jmenu;
  67     private JMenu                       _font_size_menu;
  68     private JMenuItem                   _super_tiny_fonts_mi;
  69     private JMenuItem                   _tiny_fonts_mi;
  70     private JMenuItem                   _small_fonts_mi;
  71     private JMenuItem                   _medium_fonts_mi;
  72     private JMenuItem                   _large_fonts_mi;
  73     private JMenu                       _tools_menu;
  74     private JMenuItem                   _taxcolor_item;
  75     private JMenuItem                   _confcolor_item;
  76     private JMenuItem                   _midpoint_root_item;
  77     private JMenu                       _view_jmenu;
  78     private JMenuItem                   _view_as_XML_item;
  79     private JMenuItem                   _view_as_NH_item;
  80     private JMenuItem                   _view_as_nexus_item;
  81     private JMenuItem                   _display_basic_information_item;
  82     private JMenu                       _type_menu;
  83     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  84     private JCheckBoxMenuItem           _triangular_type_cbmi;
  85     private JCheckBoxMenuItem           _curved_type_cbmi;
  86     private JCheckBoxMenuItem           _convex_type_cbmi;
  87     private JCheckBoxMenuItem           _euro_type_cbmi;
  88     private JCheckBoxMenuItem           _rounded_type_cbmi;
  89     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  90     private JCheckBoxMenuItem           _circular_type_cbmi;
  91     private JMenuItem                   _help_item;
  92     private JMenuItem                   _about_item;
  93     private JMenu                       _help_jmenu;
  94     private JMenuItem                   _website_item;
  95     private JMenuItem                   _phyloxml_website_item;
  96     private JMenuItem                   _phyloxml_ref_item;
  97     private JMenuItem                   _aptx_ref_item;
  98     private JMenuItem                   _remove_branch_color_item;
  99     private JCheckBoxMenuItem           _show_domain_labels;
 100     private JCheckBoxMenuItem           _show_annotation_ref_source;
 101     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 102     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 103     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 104     private JCheckBoxMenuItem           _background_gradient_cbmi;
 105     private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 106     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 107     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 108     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 109     private Options                     _options;
 110     private JMenuItem                   _choose_font_mi;
 111     private JMenuItem                   _switch_colors_mi;
 112     JCheckBoxMenuItem                   _label_direction_cbmi;
 113     private JCheckBoxMenuItem           _show_scale_cbmi;
 114     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 115     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 116     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 117     private JCheckBoxMenuItem           _show_overview_cbmi;
 118     private JMenuItem                   _choose_minimal_confidence_mi;
 119     private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 120     private JMenuItem                   _collapse_species_specific_subtrees;
 121     private JMenuItem                   _overview_placment_mi;
 122     private ButtonGroup                 _radio_group_1;
 123     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 124     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 125     private JMenuItem                   _cycle_node_shape_mi;
 126     private JMenuItem                   _cycle_node_fill_mi;
 127     private JMenuItem                   _choose_node_size_mi;
 128     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 129     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 130     private JMenu                       _analysis_menu;
 131     private JMenuItem                   _gsdi_item;
 132     private JMenuItem                   _gsdir_item;
 133     private Phylogeny                   _species_tree;
 134
 135     @Override
 136     public void actionPerformed( final ActionEvent e ) {
 137         final Object o = e.getSource();
 138         if ( o == _midpoint_root_item ) {
 139             getMainPanel().getCurrentTreePanel().midpointRoot();
 140         }
 141         else if ( o == _gsdi_item ) {
 142             if ( isSubtreeDisplayed() ) {
 143                 return;
 144             }
 145             executeGSDI();
 146         }
 147         else if ( o == _gsdir_item ) {
 148             if ( isSubtreeDisplayed() ) {
 149                 return;
 150             }
 151             executeGSDIR();
 152         }
 153         else if ( o == _taxcolor_item ) {
 154             getMainPanel().getCurrentTreePanel().taxColor();
 155         }
 156         else if ( o == _confcolor_item ) {
 157             getMainPanel().getCurrentTreePanel().confColor();
 158         }
 159         else if ( o == _collapse_species_specific_subtrees ) {
 160             if ( getCurrentTreePanel() != null ) {
 161                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 162             }
 163         }
 164         else if ( o == _remove_branch_color_item ) {
 165             removeBranchColors();
 166         }
 167         else if ( o == _switch_colors_mi ) {
 168             switchColors();
 169         }
 170         else if ( o == _display_basic_information_item ) {
 171             displayBasicInformation();
 172         }
 173         else if ( o == _view_as_NH_item ) {
 174             viewAsNH();
 175         }
 176         else if ( o == _view_as_XML_item ) {
 177             viewAsXML();
 178         }
 179         else if ( o == _view_as_nexus_item ) {
 180             viewAsNexus();
 181         }
 182         else if ( o == _super_tiny_fonts_mi ) {
 183             if ( getCurrentTreePanel() != null ) {
 184                 getCurrentTreePanel().setSuperTinyFonts();
 185                 getCurrentTreePanel().repaint();
 186             }
 187         }
 188         else if ( o == _tiny_fonts_mi ) {
 189             if ( getCurrentTreePanel() != null ) {
 190                 getCurrentTreePanel().setTinyFonts();
 191                 getCurrentTreePanel().repaint();
 192             }
 193         }
 194         else if ( o == _small_fonts_mi ) {
 195             if ( getCurrentTreePanel() != null ) {
 196                 getCurrentTreePanel().setSmallFonts();
 197                 getCurrentTreePanel().repaint();
 198             }
 199         }
 200         else if ( o == _medium_fonts_mi ) {
 201             if ( getCurrentTreePanel() != null ) {
 202                 getCurrentTreePanel().setMediumFonts();
 203                 getCurrentTreePanel().repaint();
 204             }
 205         }
 206         else if ( o == _large_fonts_mi ) {
 207             if ( getCurrentTreePanel() != null ) {
 208                 getCurrentTreePanel().setLargeFonts();
 209                 getCurrentTreePanel().repaint();
 210             }
 211         }
 212         else if ( o == _choose_font_mi ) {
 213             chooseFont();
 214         }
 215         else if ( o == _choose_minimal_confidence_mi ) {
 216             chooseMinimalConfidence();
 217         }
 218         else if ( o == _choose_node_size_mi ) {
 219             MainFrame.chooseNodeSize( getOptions(), this );
 220         }
 221         else if ( o == _overview_placment_mi ) {
 222             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 223         }
 224         else if ( o == _cycle_node_fill_mi ) {
 225             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 226         }
 227         else if ( o == _cycle_node_shape_mi ) {
 228             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 229         }
 230         else if ( o == _non_lined_up_cladograms_rbmi ) {
 231             updateOptions( getOptions() );
 232             _mainpanel.getControlPanel().showWhole();
 233         }
 234         else if ( o == _uniform_cladograms_rbmi ) {
 235             updateOptions( getOptions() );
 236             _mainpanel.getControlPanel().showWhole();
 237         }
 238         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 239             updateOptions( getOptions() );
 240             _mainpanel.getControlPanel().showWhole();
 241         }
 242         else if ( o == _search_case_senstive_cbmi ) {
 243             updateOptions( getOptions() );
 244             getMainPanel().getControlPanel().search0();
 245             getMainPanel().getControlPanel().search1();
 246         }
 247         else if ( o == _search_whole_words_only_cbmi ) {
 248             updateOptions( getOptions() );
 249             getMainPanel().getControlPanel().search0();
 250             getMainPanel().getControlPanel().search1();
 251         }
 252         else if ( o == _inverse_search_result_cbmi ) {
 253             updateOptions( getOptions() );
 254             getMainPanel().getControlPanel().search0();
 255             getMainPanel().getControlPanel().search1();
 256         }
 257         else if ( o == _show_scale_cbmi ) {
 258             updateOptions( getOptions() );
 259         }
 260         else if ( o == _show_branch_length_values_cbmi ) {
 261             updateOptions( getOptions() );
 262         }
 263         else if ( o == _show_confidence_stddev_cbmi ) {
 264             updateOptions( getOptions() );
 265         }
 266         else if ( o == _label_direction_cbmi ) {
 267             updateOptions( getOptions() );
 268         }
 269         else if ( o == _abbreviate_scientific_names ) {
 270             updateOptions( getOptions() );
 271         }
 272         else if ( o == _show_overview_cbmi ) {
 273             updateOptions( getOptions() );
 274             if ( getCurrentTreePanel() != null ) {
 275                 getCurrentTreePanel().updateOvSizes();
 276             }
 277         }
 278         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 279                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 280                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 281             typeChanged( o );
 282         }
 283         else if ( o == _screen_antialias_cbmi ) {
 284             updateOptions( getOptions() );
 285             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 286         }
 287         else if ( o == _background_gradient_cbmi ) {
 288             updateOptions( getOptions() );
 289         }
 290         else if ( o == _show_domain_labels ) {
 291             updateOptions( getOptions() );
 292         }
 293         else if ( o == _color_labels_same_as_parent_branch ) {
 294             updateOptions( getOptions() );
 295         }
 296         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 297             updateOptions( getOptions() );
 298         }
 299         else if ( o == _show_default_node_shapes_external_cbmi ) {
 300             updateOptions( getOptions() );
 301         }
 302         else if ( o == _about_item ) {
 303             MainFrame.about();
 304         }
 305         else if ( o == _help_item ) {
 306             help();
 307         }
 308         else if ( o == _website_item ) {
 309             try {
 310                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 311             }
 312             catch ( final IOException e1 ) {
 313                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 314             }
 315         }
 316         else if ( o == _phyloxml_website_item ) {
 317             try {
 318                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 319             }
 320             catch ( final IOException e1 ) {
 321                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 322             }
 323         }
 324         else if ( o == _aptx_ref_item ) {
 325             try {
 326                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 327             }
 328             catch ( final IOException e1 ) {
 329                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 330             }
 331         }
 332         else if ( o == _phyloxml_ref_item ) {
 333             try {
 334                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 335             }
 336             catch ( final IOException e1 ) {
 337                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 338             }
 339         }
 340         else if ( o == _color_by_taxonomic_group_cbmi ) {
 341             updateOptions( getOptions() );
 342         }
 343         repaint();
 344     }
 345
 346     @Override
 347     public void destroy() {
 348         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 349         removeAllTextFrames();
 350         if ( getMainPanel() != null ) {
 351             getMainPanel().terminate();
 352         }
 353     }
 354
 355     /**
 356      * This method returns the current external node data which
 357      * has been selected by the user by clicking the "Return ..."
 358      * menu item. This method is expected to be called from Javascript or
 359      * something like it.
 360      *
 361      * @return current external node data as String
 362      */
 363     public String getCurrentExternalNodesDataBuffer() {
 364         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 365     }
 366
 367     public int getCurrentExternalNodesDataBufferChangeCounter() {
 368         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 369     }
 370
 371     public int getCurrentExternalNodesDataBufferLength() {
 372         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 373     }
 374
 375     /**
 376      * This method returns the current phylogeny as a string in the chosen format
 377      *
 378      * @param format must be NH, NHX, NEXUS or PHYLOXML
 379      * @return the phylogeny string
 380      * @author Herve Menager
 381      */
 382     public String getCurrentPhylogeny( final String format ) {
 383         removeAllTextFrames();
 384         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 385                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 386             return new String();
 387         }
 388         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 389             case NH:
 390                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 391             case NHX:
 392                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 393             case NEXUS:
 394                 return getMainPanel().getCurrentPhylogeny().toNexus();
 395             case PHYLOXML:
 396                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 397             default:
 398                 break;
 399         }
 400         return new String();
 401     }
 402
 403     /**
 404      * This method returns a view of the current phylogeny in a chosen
 405      * graphics format, base64-encoded in a string so that in can be used
 406      * from javascript.
 407      *
 408      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 409      * @return the phylogeny string
 410      * @author Herve Menager
 411      */
 412     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 413         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 414         try {
 415             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 416                                                                     _mainpanel.getWidth(),
 417                                                                     _mainpanel.getHeight(),
 418                                                                     getCurrentTreePanel(),
 419                                                                     getCurrentTreePanel().getControlPanel(),
 420                                                                     GraphicsExportType.valueOf( format ),
 421                                                                     getOptions() );
 422         }
 423         catch ( final IOException ioe ) {
 424             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 425             ioe.printStackTrace();
 426             JOptionPane.showMessageDialog( this,
 427                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 428                                            "Failed to generate graphics",
 429                                            JOptionPane.ERROR_MESSAGE );
 430             return null;
 431         }
 432         final byte[] bytes = baos.toByteArray();
 433         final String dataImg = Base64.encodeBase64String( bytes );
 434         return dataImg;
 435     }
 436
 437     public Options getOptions() {
 438         return _options;
 439     }
 440
 441     @Override
 442     public void init() {
 443         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 444         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 445         final Configuration configuration = new Configuration( config_filename, true, true, true );
 446         setConfiguration( configuration );
 447         setOptions( Options.createInstance( configuration ) );
 448         setupUI();
 449         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 450         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 451             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 452                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 453             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 454                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 455             return;
 456         }
 457         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 458         // Get URL to tree file
 459         URL phys_url = null;
 460         try {
 461             phys_url = new URL( tree_url_str );
 462         }
 463         catch ( final Exception e ) {
 464             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 465             e.printStackTrace();
 466             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 467                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 468         }
 469         if ( phys_url == null ) {
 470             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 471                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 472             JOptionPane.showMessageDialog( this,
 473                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 474                                            "Failed to create URL",
 475                                            JOptionPane.ERROR_MESSAGE );
 476             return;
 477         }
 478         // Load the tree from URL
 479         Phylogeny[] phys = null;
 480         try {
 481             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 482                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 483                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 484                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 485                                                     getConfiguration().getTaxonomyExtraction(),
 486                                                     getConfiguration().isMidpointReroot() );
 487         }
 488         catch ( final Exception e ) {
 489             ForesterUtil.printErrorMessage( NAME, e.toString() );
 490             e.printStackTrace();
 491             JOptionPane.showMessageDialog( this,
 492                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 493                                            "Failed to read phylogenies",
 494                                            JOptionPane.ERROR_MESSAGE );
 495         }
 496         if ( phys == null ) {
 497             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 498             JOptionPane.showMessageDialog( this,
 499                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 500                                            "Failed to read phylogenies",
 501                                            JOptionPane.ERROR_MESSAGE );
 502             return;
 503         }
 504         else if ( phys.length < 1 ) {
 505             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 506             JOptionPane.showMessageDialog( this,
 507                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 508                                            "Failed to read phylogenies",
 509                                            JOptionPane.ERROR_MESSAGE );
 510             return;
 511         }
 512         else {
 513             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 514         }
 515         //
 516         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 517         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 518             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 519             Phylogeny[] species_trees = null;
 520             try {
 521                 final URL species_tree_url = new URL( species_tree_url_str );
 522                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 523                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 524                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 525                                                                  false,
 526                                                                  TAXONOMY_EXTRACTION.NO,
 527                                                                  false );
 528             }
 529             catch ( final IOException e ) {
 530                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 531                         + "]" );
 532                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 533                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 534             }
 535             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 536                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 537                 if ( species_trees[ 0 ].isEmpty() ) {
 538                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 539                 }
 540                 else if ( !species_trees[ 0 ].isRooted() ) {
 541                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 542                 }
 543                 else {
 544                     setSpeciesTree( species_trees[ 0 ] );
 545                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 546                 }
 547             }
 548         }
 549         //
 550         setVisible( false );
 551         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 552         _jmenubar = new JMenuBar();
 553         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 554             if ( !getConfiguration().isUseNativeUI() ) {
 555                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 556             }
 557             if ( getSpeciesTree() != null ) {
 558                 buildAnalysisMenu();
 559             }
 560             buildToolsMenu();
 561             buildViewMenu();
 562             buildFontSizeMenu();
 563             buildOptionsMenu();
 564             buildTypeMenu();
 565             buildHelpMenu();
 566             setJMenuBar( _jmenubar );
 567         }
 568         final Container contentpane = getContentPane();
 569         contentpane.setLayout( new BorderLayout() );
 570         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 571         addComponentListener( new ComponentAdapter() {
 572
 573             @Override
 574             public void componentResized( final ComponentEvent e ) {
 575                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 576                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 577                                                                                             .getCurrentTreePanel()
 578                                                                                             .getWidth(),
 579                                                                                     getMainPanel()
 580                                                                                             .getCurrentTreePanel()
 581                                                                                             .getHeight(),
 582                                                                                     getOptions()
 583                                                                                             .isAllowFontSizeChange() );
 584                 }
 585             }
 586         } );
 587         if ( getConfiguration().isUseTabbedDisplay() ) {
 588             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 589             AptxUtil.addPhylogeniesToTabs( phys,
 590                                            new File( phys_url.getFile() ).getName(),
 591                                            phys_url.toString(),
 592                                            getConfiguration(),
 593                                            getMainPanel() );
 594         }
 595         else {
 596             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 597             if ( getSpeciesTree() != null ) {
 598                 AptxUtil.printAppletMessage( NAME,
 599                                              "Warning: gsdi (gene duplication inference) only available tabbed display" );
 600             }
 601             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 602         }
 603         validate();
 604         setName( NAME );
 605         getMainPanel().getControlPanel().showWholeAll();
 606         getMainPanel().getControlPanel().showWhole();
 607         /* GUILHEM_BEG */
 608         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 609         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 610                 .getRelevantSequenceRelationTypes() ) {
 611             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 612         }
 613         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 614         if ( default_relation != null ) {
 615             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 616         }
 617         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 618         if ( default_sequence != null ) {
 619             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 620         }
 621         /* GUILHEM_END */
 622         System.gc();
 623         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 624         setVisible( true );
 625     }
 626
 627     public void showTextFrame( final String s, final String title ) {
 628         checkTextFrames();
 629         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 630     }
 631
 632     @Override
 633     public void start() {
 634         if ( getMainPanel() != null ) {
 635             getMainPanel().validate();
 636         }
 637         requestFocus();
 638         requestFocusInWindow();
 639         requestFocus();
 640         AptxUtil.printAppletMessage( NAME, "started" );
 641     }
 642
 643     void buildAnalysisMenu() {
 644         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 645         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 646         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 647         customizeJMenuItem( _gsdi_item );
 648         customizeJMenuItem( _gsdir_item );
 649         //  _analysis_menu.addSeparator();
 650         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 651         //  customizeJMenuItem( _lineage_inference );
 652         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 653         _jmenubar.add( _analysis_menu );
 654     }
 655
 656     void buildFontSizeMenu() {
 657         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 658         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 659         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 660         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 661         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 662         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 663         customizeJMenuItem( _super_tiny_fonts_mi );
 664         customizeJMenuItem( _tiny_fonts_mi );
 665         customizeJMenuItem( _small_fonts_mi );
 666         customizeJMenuItem( _medium_fonts_mi );
 667         customizeJMenuItem( _large_fonts_mi );
 668         _jmenubar.add( _font_size_menu );
 669     }
 670
 671     void buildHelpMenu() {
 672         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 673         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 674         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 675         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 676         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 677         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 678         _help_jmenu.addSeparator();
 679         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 680         customizeJMenuItem( _help_item );
 681         customizeJMenuItem( _website_item );
 682         customizeJMenuItem( _phyloxml_website_item );
 683         customizeJMenuItem( _aptx_ref_item );
 684         customizeJMenuItem( _phyloxml_ref_item );
 685         customizeJMenuItem( _about_item );
 686         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 687         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 688         _jmenubar.add( _help_jmenu );
 689     }
 690
 691     void buildOptionsMenu() {
 692         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 693         _options_jmenu.addChangeListener( new ChangeListener() {
 694
 695             @Override
 696             public void stateChanged( final ChangeEvent e ) {
 697                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 698                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 699                 MainFrame
 700                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 701                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 702                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 703                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 704                                                                      _show_scale_cbmi,
 705                                                                      _show_branch_length_values_cbmi,
 706                                                                      _non_lined_up_cladograms_rbmi,
 707                                                                      _uniform_cladograms_rbmi,
 708                                                                      _ext_node_dependent_cladogram_rbmi,
 709                                                                      _label_direction_cbmi );
 710                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 711                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 712                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 713             }
 714         } );
 715         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 716                                                                 getConfiguration() ) );
 717         _options_jmenu
 718                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 719         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 720         _options_jmenu
 721                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 722         _radio_group_1 = new ButtonGroup();
 723         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 724         _radio_group_1.add( _uniform_cladograms_rbmi );
 725         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 726         /////
 727         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 728         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 729         _options_jmenu
 730                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 731         _options_jmenu
 732                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 733         _options_jmenu
 734                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 735         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 736             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 737         }
 738         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 739         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 740         _options_jmenu
 741                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 742         _options_jmenu
 743                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 744         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 745         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 746         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 747         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 748         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 749         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 750         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 751         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 752         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 753         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 754         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 755         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 756         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 757         /////
 758         _options_jmenu.addSeparator();
 759         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 760                                                                 getConfiguration() ) );
 761         _options_jmenu
 762                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 763         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 764         _options_jmenu
 765                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 766         customizeJMenuItem( _choose_font_mi );
 767         customizeJMenuItem( _choose_minimal_confidence_mi );
 768         customizeJMenuItem( _switch_colors_mi );
 769         customizeJMenuItem( _overview_placment_mi );
 770         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 771         customizeCheckBoxMenuItem( _label_direction_cbmi,
 772                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 773         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 774         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 775         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 776         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 777         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 778         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 779                 .isShowDefaultNodeShapesExternal() );
 780         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 781                 .isShowDefaultNodeShapesInternal() );
 782         customizeJMenuItem( _cycle_node_shape_mi );
 783         customizeJMenuItem( _cycle_node_fill_mi );
 784         customizeJMenuItem( _choose_node_size_mi );
 785         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 786         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 787         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 788         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 789                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 790         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 791                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 792         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 793                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 794         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 795         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 796         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 797         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 798         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 799         _jmenubar.add( _options_jmenu );
 800     }
 801
 802     void buildToolsMenu() {
 803         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 804         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 805         customizeJMenuItem( _confcolor_item );
 806         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 807         customizeJMenuItem( _taxcolor_item );
 808         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 809         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 810         customizeJMenuItem( _remove_branch_color_item );
 811         _tools_menu.addSeparator();
 812         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 813         customizeJMenuItem( _midpoint_root_item );
 814         _tools_menu.addSeparator();
 815         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 816         customizeJMenuItem( _collapse_species_specific_subtrees );
 817         _jmenubar.add( _tools_menu );
 818     }
 819
 820     void buildTypeMenu() {
 821         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 822         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 823         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 824         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 825         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 826         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 827         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 828         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 829         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 830         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 831         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 832         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 833         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 834         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 835         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 836         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 837         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 838         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 839         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 840         initializeTypeMenu( getOptions() );
 841         _jmenubar.add( _type_menu );
 842     }
 843
 844     void buildViewMenu() {
 845         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 846         _view_jmenu
 847                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 848         _view_jmenu.addSeparator();
 849         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 850         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 851         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 852         customizeJMenuItem( _display_basic_information_item );
 853         customizeJMenuItem( _view_as_NH_item );
 854         customizeJMenuItem( _view_as_XML_item );
 855         customizeJMenuItem( _view_as_nexus_item );
 856         _jmenubar.add( _view_jmenu );
 857     }
 858
 859     void checkTextFrames() {
 860         if ( _textframes.size() > 5 ) {
 861             try {
 862                 if ( _textframes.getFirst() != null ) {
 863                     _textframes.getFirst().removeMe();
 864                 }
 865                 else {
 866                     _textframes.removeFirst();
 867                 }
 868             }
 869             catch ( final NoSuchElementException e ) {
 870                 // Ignore.
 871             }
 872         }
 873     }
 874
 875     void clearCurrentExternalNodesDataBuffer() {
 876         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 877     }
 878
 879     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 880         if ( item != null ) {
 881             item.setFont( MainFrame.menu_font );
 882             if ( !getConfiguration().isUseNativeUI() ) {
 883                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 884                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 885             }
 886             item.setSelected( is_selected );
 887             item.addActionListener( this );
 888         }
 889     }
 890
 891     void customizeJMenuItem( final JMenuItem jmi ) {
 892         jmi.setFont( MainFrame.menu_font );
 893         if ( !getConfiguration().isUseNativeUI() ) {
 894             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 895             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 896         }
 897         jmi.addActionListener( this );
 898     }
 899
 900     void displayBasicInformation() {
 901         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 902             String title = "Basic Information";
 903             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 904                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 905             }
 906             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 907         }
 908     }
 909
 910     void executeGSDI() {
 911         if ( !isOKforSDI( false, true ) ) {
 912             return;
 913         }
 914         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 915             JOptionPane.showMessageDialog( this,
 916                                            "Gene tree is not rooted.",
 917                                            "Cannot execute GSDI",
 918                                            JOptionPane.ERROR_MESSAGE );
 919             return;
 920         }
 921         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 922         gene_tree.setAllNodesToNotCollapse();
 923         gene_tree.recalculateNumberOfExternalDescendants( false );
 924         GSDI gsdi = null;
 925         final Phylogeny species_tree = _species_tree.copy();
 926         try {
 927             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 928         }
 929         catch ( final SDIException e ) {
 930             JOptionPane.showMessageDialog( this,
 931                                            e.getLocalizedMessage(),
 932                                            "Error during GSDI",
 933                                            JOptionPane.ERROR_MESSAGE );
 934             return;
 935         }
 936         catch ( final Exception e ) {
 937             AptxUtil.unexpectedException( e );
 938             return;
 939         }
 940         gene_tree.setRerootable( false );
 941         gene_tree.clearHashIdToNodeMap();
 942         gene_tree.recalculateNumberOfExternalDescendants( true );
 943         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 944         getMainPanel().getControlPanel().setShowEvents( true );
 945         showWhole();
 946         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 947         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 948         showWhole();
 949         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 950         showWhole();
 951         _mainpanel.getCurrentTreePanel().setEdited( true );
 952         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 953         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 954             JOptionPane.showMessageDialog( this,
 955                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 956                                                    + "Potential duplications: "
 957                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 958                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 959                                                    + "Stripped gene tree nodes: "
 960                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 961                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 962                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 963                                            "GSDI successfully completed",
 964                                            JOptionPane.WARNING_MESSAGE );
 965         }
 966         else {
 967             JOptionPane.showMessageDialog( this,
 968                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 969                                                    + "Potential duplications: "
 970                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 971                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 972                                                    + "Stripped gene tree nodes: "
 973                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 974                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 975                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 976                                            "GSDI successfully completed",
 977                                            JOptionPane.INFORMATION_MESSAGE );
 978         }
 979     }
 980
 981     void executeGSDIR() {
 982         if ( !isOKforSDI( false, false ) ) {
 983             return;
 984         }
 985         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
 986         if ( ( p > 0 )
 987                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
 988             JOptionPane.showMessageDialog( this,
 989                                            "Gene tree is not completely binary",
 990                                            "Cannot execute GSDI",
 991                                            JOptionPane.ERROR_MESSAGE );
 992             return;
 993         }
 994         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 995         gene_tree.setAllNodesToNotCollapse();
 996         gene_tree.recalculateNumberOfExternalDescendants( false );
 997         GSDIR gsdir = null;
 998         final Phylogeny species_tree = _species_tree.copy();
 999         try {
1000             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1001         }
1002         catch ( final SDIException e ) {
1003             JOptionPane.showMessageDialog( this,
1004                                            e.getLocalizedMessage(),
1005                                            "Error during GSDIR",
1006                                            JOptionPane.ERROR_MESSAGE );
1007             return;
1008         }
1009         catch ( final Exception e ) {
1010             AptxUtil.unexpectedException( e );
1011             return;
1012         }
1013         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1014         result_gene_tree.setRerootable( false );
1015         result_gene_tree.clearHashIdToNodeMap();
1016         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1017         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1018         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1019         getMainPanel().getControlPanel().setShowEvents( true );
1020         showWhole();
1021         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1022         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1023         showWhole();
1024         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1025         showWhole();
1026         _mainpanel.getCurrentTreePanel().setEdited( true );
1027         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1028         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1029             JOptionPane.showMessageDialog( this,
1030                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1031                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1032                                                    + "Stripped gene tree nodes: "
1033                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1034                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1035                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1036                                            "GSDIR successfully completed",
1037                                            JOptionPane.WARNING_MESSAGE );
1038         }
1039         else {
1040             JOptionPane.showMessageDialog( this,
1041                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1042                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1043                                                    + "Stripped gene tree nodes: "
1044                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1045                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1046                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1047                                            "GSDIR successfully completed",
1048                                            JOptionPane.INFORMATION_MESSAGE );
1049         }
1050     }
1051
1052     Configuration getConfiguration() {
1053         return _configuration;
1054     }
1055
1056     TreePanel getCurrentTreePanel() {
1057         return getMainPanel().getCurrentTreePanel();
1058     }
1059
1060     JCheckBoxMenuItem getlabelDirectionCbmi() {
1061         return _label_direction_cbmi;
1062     }
1063
1064     Options getOtions() {
1065         return _options;
1066     }
1067
1068     void help() {
1069         final StringBuilder sb = new StringBuilder();
1070         sb.append( "Display options\n" );
1071         sb.append( "-------------------\n" );
1072         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1073         sb.append( "Clickable tree nodes\n" );
1074         sb.append( "--------------------\n" );
1075         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1076         sb.append( "or by right clicking:\n" );
1077         sb.append( "o  Display Node Data -- display information for a node\n" );
1078         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1079         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
1080         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1081         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
1082         sb.append( "o  Colorize Subtree -- color a subtree\n" );
1083         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
1084         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1085         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
1086         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1087         sb.append( "Zooming\n" );
1088         sb.append( "---------\n" );
1089         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1090         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1091         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1092         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1093         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1094         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1095         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1096         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1097         sb.append( "Quick tree manipulation:\n" );
1098         sb.append( "------------------------\n" );
1099         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1100         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1101         sb.append( "phyloXML\n" );
1102         sb.append( "-------------------\n" );
1103         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1104         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1105         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1106         sb.append( "\n" );
1107         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1108         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1109         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1110     }
1111
1112     void initializeTypeMenu( final Options options ) {
1113         setTypeMenuToAllUnselected();
1114         try {
1115             switch ( options.getPhylogenyGraphicsType() ) {
1116                 case CONVEX:
1117                     _convex_type_cbmi.setSelected( true );
1118                     break;
1119                 case CURVED:
1120                     _curved_type_cbmi.setSelected( true );
1121                     break;
1122                 case EURO_STYLE:
1123                     _euro_type_cbmi.setSelected( true );
1124                     break;
1125                 case ROUNDED:
1126                     _rounded_type_cbmi.setSelected( true );
1127                     break;
1128                 case TRIANGULAR:
1129                     _triangular_type_cbmi.setSelected( true );
1130                     break;
1131                 case UNROOTED:
1132                     _unrooted_type_cbmi.setSelected( true );
1133                     break;
1134                 case CIRCULAR:
1135                     _circular_type_cbmi.setSelected( true );
1136                     break;
1137                 default:
1138                     _rectangular_type_cbmi.setSelected( true );
1139                     break;
1140             }
1141         }
1142         catch ( final NullPointerException np ) {
1143             // In all likelihood, this is caused by menu-less display.
1144         }
1145     }
1146
1147     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1148         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1149             return false;
1150         }
1151         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1152             JOptionPane.showMessageDialog( this,
1153                                            "No species tree loaded",
1154                                            "Cannot execute GSDI",
1155                                            JOptionPane.ERROR_MESSAGE );
1156             return false;
1157         }
1158         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1159             JOptionPane.showMessageDialog( this,
1160                                            "Species tree is not completely binary",
1161                                            "Cannot execute GSDI",
1162                                            JOptionPane.ERROR_MESSAGE );
1163             return false;
1164         }
1165         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1166             JOptionPane.showMessageDialog( this,
1167                                            "Gene tree is not completely binary",
1168                                            "Cannot execute GSDI",
1169                                            JOptionPane.ERROR_MESSAGE );
1170             return false;
1171         }
1172         else {
1173             return true;
1174         }
1175     }
1176
1177     boolean isSubtreeDisplayed() {
1178         if ( getCurrentTreePanel() != null ) {
1179             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1180                 JOptionPane
1181                         .showMessageDialog( this,
1182                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1183                                             "Operation can not be exectuted on a sub-tree",
1184                                             JOptionPane.WARNING_MESSAGE );
1185                 return true;
1186             }
1187         }
1188         return false;
1189     }
1190
1191     void removeAllTextFrames() {
1192         for( final TextFrame tf : _textframes ) {
1193             if ( tf != null ) {
1194                 tf.close();
1195             }
1196         }
1197         _textframes.clear();
1198     }
1199
1200     void setConfiguration( final Configuration configuration ) {
1201         _configuration = configuration;
1202     }
1203
1204     void setOptions( final Options options ) {
1205         _options = options;
1206     }
1207
1208     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1209         setTypeMenuToAllUnselected();
1210         try {
1211             switch ( type ) {
1212                 case CIRCULAR:
1213                     _circular_type_cbmi.setSelected( true );
1214                     break;
1215                 case CONVEX:
1216                     _convex_type_cbmi.setSelected( true );
1217                     break;
1218                 case CURVED:
1219                     _curved_type_cbmi.setSelected( true );
1220                     break;
1221                 case EURO_STYLE:
1222                     _euro_type_cbmi.setSelected( true );
1223                     break;
1224                 case ROUNDED:
1225                     _rounded_type_cbmi.setSelected( true );
1226                     break;
1227                 case RECTANGULAR:
1228                     _rectangular_type_cbmi.setSelected( true );
1229                     break;
1230                 case TRIANGULAR:
1231                     _triangular_type_cbmi.setSelected( true );
1232                     break;
1233                 case UNROOTED:
1234                     _unrooted_type_cbmi.setSelected( true );
1235                     break;
1236                 default:
1237                     throw new IllegalArgumentException( "unknown type: " + type );
1238             }
1239         }
1240         catch ( final NullPointerException np ) {
1241             // In all likelihood, this is caused by menu-less display.
1242         }
1243     }
1244
1245     void setTypeMenuToAllUnselected() {
1246         if ( _convex_type_cbmi != null ) {
1247             _convex_type_cbmi.setSelected( false );
1248         }
1249         if ( _curved_type_cbmi != null ) {
1250             _curved_type_cbmi.setSelected( false );
1251         }
1252         if ( _euro_type_cbmi != null ) {
1253             _euro_type_cbmi.setSelected( false );
1254         }
1255         if ( _rounded_type_cbmi != null ) {
1256             _rounded_type_cbmi.setSelected( false );
1257         }
1258         if ( _triangular_type_cbmi != null ) {
1259             _triangular_type_cbmi.setSelected( false );
1260         }
1261         if ( _rectangular_type_cbmi != null ) {
1262             _rectangular_type_cbmi.setSelected( false );
1263         }
1264         if ( _unrooted_type_cbmi != null ) {
1265             _unrooted_type_cbmi.setSelected( false );
1266         }
1267         if ( _circular_type_cbmi != null ) {
1268             _circular_type_cbmi.setSelected( false );
1269         }
1270     }
1271
1272     void showWhole() {
1273         _mainpanel.getControlPanel().showWhole();
1274     }
1275
1276     void switchColors() {
1277         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1278         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1279         csc.setVisible( true );
1280         getMainPanel().setTreeColorSet( colorset );
1281     }
1282
1283     void typeChanged( final Object o ) {
1284         updateTypeCheckboxes( getOptions(), o );
1285         updateOptions( getOptions() );
1286         if ( getCurrentTreePanel() != null ) {
1287             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1288             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1289             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1290                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1291                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1292                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1293                 getCurrentTreePanel().getControlPanel().showWhole();
1294             }
1295             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1296                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1297             }
1298             else {
1299                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1300             }
1301             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1302             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1303         }
1304     }
1305
1306     void updateOptions( final Options options ) {
1307         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1308         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1309                 && _background_gradient_cbmi.isSelected() );
1310         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1311         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1312                 && _show_annotation_ref_source.isSelected() );
1313         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1314                 && _abbreviate_scientific_names.isSelected() );
1315         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1316                 && _color_labels_same_as_parent_branch.isSelected() );
1317         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1318                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1319         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1320                 && _show_default_node_shapes_external_cbmi.isSelected() );
1321         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1322             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1323         }
1324         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1325             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1326         }
1327         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1328             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1329         }
1330         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1331                 && _search_case_senstive_cbmi.isSelected() );
1332         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1333             options.setShowScale( _show_scale_cbmi.isSelected() );
1334         }
1335         if ( _label_direction_cbmi != null ) {
1336             if ( _label_direction_cbmi.isSelected() ) {
1337                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1338             }
1339             else {
1340                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1341             }
1342         }
1343         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1344         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1345                 && _show_confidence_stddev_cbmi.isSelected() );
1346         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1347             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1348         }
1349         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1350                 && _search_whole_words_only_cbmi.isSelected() );
1351         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1352                 && _inverse_search_result_cbmi.isSelected() );
1353         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1354             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1355         }
1356         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1357             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1358         }
1359         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1360             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1361         }
1362         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1363             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1364         }
1365         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1366             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1367         }
1368         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1369             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1370         }
1371         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1372             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1373         }
1374         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1375             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1376         }
1377         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1378             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1379         }
1380     }
1381
1382     void updateTypeCheckboxes( final Options options, final Object o ) {
1383         setTypeMenuToAllUnselected();
1384         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1385     }
1386
1387     void viewAsNexus() {
1388         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1389             String title = "Nexus";
1390             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1391                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1392             }
1393             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1394                                    .getNhConversionSupportValueStyle() ),
1395                            title );
1396         }
1397     }
1398
1399     void viewAsNH() {
1400         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1401             String title = "New Hampshire";
1402             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1403                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1404             }
1405             showTextFrame( getMainPanel().getCurrentPhylogeny()
1406                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1407                            title );
1408         }
1409     }
1410
1411     void viewAsXML() {
1412         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1413             String title = "phyloXML";
1414             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1415                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1416             }
1417             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1418         }
1419     }
1420
1421     private void chooseFont() {
1422         final FontChooser fc = new FontChooser();
1423         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1424         fc.showDialog( this, "Select the Base Font" );
1425         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1426     }
1427
1428     private void chooseMinimalConfidence() {
1429         final String s = ( String ) JOptionPane
1430                 .showInputDialog( this,
1431                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1432                                           + getOptions().getMinConfidenceValue() + "]\n",
1433                                   "Minimal Confidence Value",
1434                                   JOptionPane.QUESTION_MESSAGE,
1435                                   null,
1436                                   null,
1437                                   getOptions().getMinConfidenceValue() );
1438         if ( !ForesterUtil.isEmpty( s ) ) {
1439             boolean success = true;
1440             double m = 0.0;
1441             final String m_str = s.trim();
1442             if ( !ForesterUtil.isEmpty( m_str ) ) {
1443                 try {
1444                     m = Double.parseDouble( m_str );
1445                 }
1446                 catch ( final Exception ex ) {
1447                     success = false;
1448                 }
1449             }
1450             else {
1451                 success = false;
1452             }
1453             if ( success && ( m >= 0.0 ) ) {
1454                 getOptions().setMinConfidenceValue( m );
1455             }
1456         }
1457     }
1458
1459     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1460         if ( item != null ) {
1461             item.setFont( MainFrame.menu_font );
1462             if ( !getConfiguration().isUseNativeUI() ) {
1463                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1464                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1465             }
1466             item.setSelected( is_selected );
1467             item.addActionListener( this );
1468         }
1469     }
1470
1471     private MainPanel getMainPanel() {
1472         return _mainpanel;
1473     }
1474
1475     private Phylogeny getSpeciesTree() {
1476         return _species_tree;
1477     }
1478
1479     private boolean isScreenAntialias() {
1480         return true;
1481     }
1482
1483     private void removeBranchColors() {
1484         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1485             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1486         }
1487     }
1488
1489     private void setMainPanel( final MainPanelApplets main_panel ) {
1490         _mainpanel = main_panel;
1491     }
1492
1493     private void setSpeciesTree( final Phylogeny species_tree ) {
1494         _species_tree = species_tree;
1495     }
1496
1497     private void setupUI() {
1498         try {
1499             if ( getConfiguration().isUseNativeUI() ) {
1500                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1501             }
1502             else {
1503                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1504             }
1505         }
1506         catch ( final UnsupportedLookAndFeelException e ) {
1507             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1508         }
1509         catch ( final ClassNotFoundException e ) {
1510             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1511         }
1512         catch ( final InstantiationException e ) {
1513             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1514         }
1515         catch ( final IllegalAccessException e ) {
1516             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1517         }
1518         catch ( final Exception e ) {
1519             AptxUtil.dieWithSystemError( e.toString() );
1520         }
1521     }
1522
1523     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1524         for( final TreePanel tree_panel : treepanels ) {
1525             tree_panel.setTextAntialias();
1526         }
1527     }
1528 }