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