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     private JCheckBoxMenuItem _right_line_up_domains_cbmi;
 137     private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
 138
 139
 140     @Override
 141     public void actionPerformed( final ActionEvent e ) {
 142         final Object o = e.getSource();
 143         if ( o == _midpoint_root_item ) {
 144             getMainPanel().getCurrentTreePanel().midpointRoot();
 145         }
 146         else if ( o == _gsdi_item ) {
 147             if ( isSubtreeDisplayed() ) {
 148                 return;
 149             }
 150             executeGSDI();
 151         }
 152         else if ( o == _gsdir_item ) {
 153             if ( isSubtreeDisplayed() ) {
 154                 return;
 155             }
 156             executeGSDIR();
 157         }
 158         else if ( o == _taxcolor_item ) {
 159             getMainPanel().getCurrentTreePanel().taxColor();
 160         }
 161         else if ( o == _confcolor_item ) {
 162             getMainPanel().getCurrentTreePanel().confColor();
 163         }
 164         else if ( o == _collapse_species_specific_subtrees ) {
 165             if ( getCurrentTreePanel() != null ) {
 166                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 167             }
 168         }
 169         else if ( o == _remove_branch_color_item ) {
 170             removeBranchColors();
 171         }
 172         else if ( o == _remove_visual_styles_item ) {
 173             removeVisualStyles();
 174         }
 175         else if ( o == _switch_colors_mi ) {
 176             switchColors();
 177         }
 178         else if ( o == _display_basic_information_item ) {
 179             displayBasicInformation();
 180         }
 181         else if ( o == _view_as_NH_item ) {
 182             viewAsNH();
 183         }
 184         else if ( o == _view_as_XML_item ) {
 185             viewAsXML();
 186         }
 187         else if ( o == _view_as_nexus_item ) {
 188             viewAsNexus();
 189         }
 190         else if ( o == _super_tiny_fonts_mi ) {
 191             if ( getCurrentTreePanel() != null ) {
 192                 getCurrentTreePanel().setSuperTinyFonts();
 193                 getCurrentTreePanel().repaint();
 194             }
 195         }
 196         else if ( o == _tiny_fonts_mi ) {
 197             if ( getCurrentTreePanel() != null ) {
 198                 getCurrentTreePanel().setTinyFonts();
 199                 getCurrentTreePanel().repaint();
 200             }
 201         }
 202         else if ( o == _small_fonts_mi ) {
 203             if ( getCurrentTreePanel() != null ) {
 204                 getCurrentTreePanel().setSmallFonts();
 205                 getCurrentTreePanel().repaint();
 206             }
 207         }
 208         else if ( o == _medium_fonts_mi ) {
 209             if ( getCurrentTreePanel() != null ) {
 210                 getCurrentTreePanel().setMediumFonts();
 211                 getCurrentTreePanel().repaint();
 212             }
 213         }
 214         else if ( o == _large_fonts_mi ) {
 215             if ( getCurrentTreePanel() != null ) {
 216                 getCurrentTreePanel().setLargeFonts();
 217                 getCurrentTreePanel().repaint();
 218             }
 219         }
 220         else if ( o == _choose_font_mi ) {
 221             chooseFont();
 222         }
 223         else if ( o == _choose_minimal_confidence_mi ) {
 224             chooseMinimalConfidence();
 225         }
 226         else if ( o == _choose_node_size_mi ) {
 227             MainFrame.chooseNodeSize( getOptions(), this );
 228         }
 229         else if ( o == _overview_placment_mi ) {
 230             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 231         }
 232         else if ( o == _cycle_node_fill_mi ) {
 233             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 234         }
 235         else if ( o == _cycle_node_shape_mi ) {
 236             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 237         }
 238         else if ( o == _non_lined_up_cladograms_rbmi ) {
 239             updateOptions( getOptions() );
 240             _mainpanel.getControlPanel().showWhole();
 241         }
 242         else if ( o == _uniform_cladograms_rbmi ) {
 243             updateOptions( getOptions() );
 244             _mainpanel.getControlPanel().showWhole();
 245         }
 246         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 247             updateOptions( getOptions() );
 248             _mainpanel.getControlPanel().showWhole();
 249         }
 250         else if ( o == _search_case_senstive_cbmi ) {
 251             updateOptions( getOptions() );
 252             getMainPanel().getControlPanel().search0();
 253             getMainPanel().getControlPanel().search1();
 254         }
 255         else if ( o == _search_whole_words_only_cbmi ) {
 256             updateOptions( getOptions() );
 257             getMainPanel().getControlPanel().search0();
 258             getMainPanel().getControlPanel().search1();
 259         }
 260         else if ( o == _inverse_search_result_cbmi ) {
 261             updateOptions( getOptions() );
 262             getMainPanel().getControlPanel().search0();
 263             getMainPanel().getControlPanel().search1();
 264         }
 265         else if ( o == _show_scale_cbmi ) {
 266             updateOptions( getOptions() );
 267         }
 268         else if ( o == _show_branch_length_values_cbmi ) {
 269             updateOptions( getOptions() );
 270         }
 271         else if ( o == _show_confidence_stddev_cbmi ) {
 272             updateOptions( getOptions() );
 273         }
 274         else if ( o == _label_direction_cbmi ) {
 275             updateOptions( getOptions() );
 276         }
 277         else if ( o == _abbreviate_scientific_names ) {
 278             updateOptions( getOptions() );
 279         }
 280         else if ( o == _show_overview_cbmi ) {
 281             updateOptions( getOptions() );
 282             if ( getCurrentTreePanel() != null ) {
 283                 getCurrentTreePanel().updateOvSizes();
 284             }
 285         }
 286         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 287                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 288                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 289             typeChanged( o );
 290         }
 291         else if ( o == _screen_antialias_cbmi ) {
 292             updateOptions( getOptions() );
 293             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 294         }
 295         else if ( o == _background_gradient_cbmi ) {
 296             updateOptions( getOptions() );
 297         }
 298         else if ( o == _show_domain_labels ) {
 299             updateOptions( getOptions() );
 300         }
 301         else if ( o == _color_labels_same_as_parent_branch ) {
 302             updateOptions( getOptions() );
 303         }
 304         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 305             updateOptions( getOptions() );
 306         }
 307         else if ( o == _show_default_node_shapes_external_cbmi ) {
 308             updateOptions( getOptions() );
 309         }
 310         else if ( o == _about_item ) {
 311             MainFrame.about();
 312         }
 313         else if ( o == _help_item ) {
 314             try {
 315                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
 316             }
 317             catch ( final IOException e1 ) {
 318                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 319             }
 320         }
 321         else if ( o == _website_item ) {
 322             try {
 323                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 324             }
 325             catch ( final IOException e1 ) {
 326                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 327             }
 328         }
 329         else if ( o == _phyloxml_website_item ) {
 330             try {
 331                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 332             }
 333             catch ( final IOException e1 ) {
 334                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 335             }
 336         }
 337         else if ( o == _aptx_ref_item ) {
 338             try {
 339                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 340             }
 341             catch ( final IOException e1 ) {
 342                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 343             }
 344         }
 345         else if ( o == _phyloxml_ref_item ) {
 346             try {
 347                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 348             }
 349             catch ( final IOException e1 ) {
 350                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 351             }
 352         }
 353         else if ( o == _color_by_taxonomic_group_cbmi ) {
 354             updateOptions( getOptions() );
 355         }
 356         else if ( o == _right_line_up_domains_cbmi ) {
 357             updateOptions( getOptions() );
 358         }
 359         else if ( o == _line_up_renderable_data_cbmi ) {
 360             updateOptions( getOptions() );
 361         }
 362
 363
 364         repaint();
 365     }
 366
 367     @Override
 368     public void destroy() {
 369         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 370         removeAllTextFrames();
 371         if ( getMainPanel() != null ) {
 372             getMainPanel().terminate();
 373         }
 374     }
 375
 376     /**
 377      * This method returns the current external node data which
 378      * has been selected by the user by clicking the "Return ..."
 379      * menu item. This method is expected to be called from Javascript or
 380      * something like it.
 381      *
 382      * @return current external node data as String
 383      */
 384     public String getCurrentExternalNodesDataBuffer() {
 385         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 386     }
 387
 388     public int getCurrentExternalNodesDataBufferChangeCounter() {
 389         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 390     }
 391
 392     public int getCurrentExternalNodesDataBufferLength() {
 393         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 394     }
 395
 396     /**
 397      * This method returns the current phylogeny as a string in the chosen format
 398      *
 399      * @param format must be NH, NHX, NEXUS or PHYLOXML
 400      * @return the phylogeny string
 401      * @author Herve Menager
 402      */
 403     public String getCurrentPhylogeny( final String format ) {
 404         removeAllTextFrames();
 405         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 406                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 407             return new String();
 408         }
 409         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 410             case NH:
 411                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 412             case NHX:
 413                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 414             case NEXUS:
 415                 return getMainPanel().getCurrentPhylogeny().toNexus();
 416             case PHYLOXML:
 417                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 418             default:
 419                 break;
 420         }
 421         return new String();
 422     }
 423
 424     /**
 425      * This method returns a view of the current phylogeny in a chosen
 426      * graphics format, base64-encoded in a string so that in can be used
 427      * from javascript.
 428      *
 429      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 430      * @return the phylogeny string
 431      * @author Herve Menager
 432      */
 433     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 434         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 435         try {
 436             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 437                                                                     _mainpanel.getWidth(),
 438                                                                     _mainpanel.getHeight(),
 439                                                                     getCurrentTreePanel(),
 440                                                                     getCurrentTreePanel().getControlPanel(),
 441                                                                     GraphicsExportType.valueOf( format ),
 442                                                                     getOptions() );
 443         }
 444         catch ( final IOException ioe ) {
 445             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 446             ioe.printStackTrace();
 447             JOptionPane.showMessageDialog( this,
 448                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 449                                            "Failed to generate graphics",
 450                                            JOptionPane.ERROR_MESSAGE );
 451             return null;
 452         }
 453         final byte[] bytes = baos.toByteArray();
 454         final String dataImg = Base64.encodeBase64String( bytes );
 455         return dataImg;
 456     }
 457
 458     public Options getOptions() {
 459         return _options;
 460     }
 461
 462     @Override
 463     public void init() {
 464         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 465         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 466         final Configuration configuration = new Configuration( config_filename, true, true, true );
 467         setConfiguration( configuration );
 468         setOptions( Options.createInstance( configuration ) );
 469         setupUI();
 470         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 471         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 472             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 473                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 474             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 475                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 476             return;
 477         }
 478         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 479         // Get URL to tree file
 480         URL phys_url = null;
 481         try {
 482             phys_url = new URL( tree_url_str );
 483         }
 484         catch ( final Exception e ) {
 485             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 486             e.printStackTrace();
 487             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 488                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 489         }
 490         if ( phys_url == null ) {
 491             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 492                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 493             JOptionPane.showMessageDialog( this,
 494                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 495                                            "Failed to create URL",
 496                                            JOptionPane.ERROR_MESSAGE );
 497             return;
 498         }
 499         // Load the tree from URL
 500         Phylogeny[] phys = null;
 501         try {
 502             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 503                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 504                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 505                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 506                                                     getConfiguration().getTaxonomyExtraction(),
 507                                                     getConfiguration().isMidpointReroot() );
 508         }
 509         catch ( final Exception e ) {
 510             ForesterUtil.printErrorMessage( NAME, e.toString() );
 511             e.printStackTrace();
 512             JOptionPane.showMessageDialog( this,
 513                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 514                                            "Failed to read phylogenies",
 515                                            JOptionPane.ERROR_MESSAGE );
 516         }
 517         if ( phys == null ) {
 518             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 519             JOptionPane.showMessageDialog( this,
 520                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 521                                            "Failed to read phylogenies",
 522                                            JOptionPane.ERROR_MESSAGE );
 523             return;
 524         }
 525         else if ( phys.length < 1 ) {
 526             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 527             JOptionPane.showMessageDialog( this,
 528                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 529                                            "Failed to read phylogenies",
 530                                            JOptionPane.ERROR_MESSAGE );
 531             return;
 532         }
 533         else {
 534             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 535         }
 536         //
 537         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 538         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 539             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 540             Phylogeny[] species_trees = null;
 541             try {
 542                 final URL species_tree_url = new URL( species_tree_url_str );
 543                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 544                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 545                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 546                                                                  false,
 547                                                                  TAXONOMY_EXTRACTION.NO,
 548                                                                  false );
 549             }
 550             catch ( final IOException e ) {
 551                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 552                         + "]" );
 553                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 554                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 555             }
 556             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 557                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 558                 if ( species_trees[ 0 ].isEmpty() ) {
 559                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 560                 }
 561                 else if ( !species_trees[ 0 ].isRooted() ) {
 562                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 563                 }
 564                 else {
 565                     setSpeciesTree( species_trees[ 0 ] );
 566                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 567                 }
 568             }
 569         }
 570         //
 571         setVisible( false );
 572         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 573         _jmenubar = new JMenuBar();
 574         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 575             if ( !getConfiguration().isUseNativeUI() ) {
 576                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 577             }
 578             if ( getSpeciesTree() != null ) {
 579                 buildAnalysisMenu();
 580             }
 581             buildToolsMenu();
 582             buildViewMenu();
 583             buildFontSizeMenu();
 584             buildOptionsMenu();
 585             buildTypeMenu();
 586             buildHelpMenu();
 587             setJMenuBar( _jmenubar );
 588         }
 589         final Container contentpane = getContentPane();
 590         contentpane.setLayout( new BorderLayout() );
 591         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 592         addComponentListener( new ComponentAdapter() {
 593
 594             @Override
 595             public void componentResized( final ComponentEvent e ) {
 596                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 597                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 598                                                                                             .getCurrentTreePanel()
 599                                                                                             .getWidth(),
 600                                                                                     getMainPanel()
 601                                                                                             .getCurrentTreePanel()
 602                                                                                             .getHeight(),
 603                                                                                     getOptions()
 604                                                                                             .isAllowFontSizeChange() );
 605                 }
 606             }
 607         } );
 608         if ( getConfiguration().isUseTabbedDisplay() ) {
 609             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 610             AptxUtil.addPhylogeniesToTabs( phys,
 611                                            new File( phys_url.getFile() ).getName(),
 612                                            phys_url.toString(),
 613                                            getConfiguration(),
 614                                            getMainPanel() );
 615         }
 616         else {
 617             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 618             if ( getSpeciesTree() != null ) {
 619                 AptxUtil.printAppletMessage( NAME,
 620                                              "Warning: gsdi (gene duplication inference) only available tabbed display" );
 621             }
 622             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 623         }
 624         validate();
 625         setName( NAME );
 626         getMainPanel().getControlPanel().showWholeAll();
 627         getMainPanel().getControlPanel().showWhole();
 628         /* GUILHEM_BEG */
 629         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 630         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 631                 .getRelevantSequenceRelationTypes() ) {
 632             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 633         }
 634         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 635         if ( default_relation != null ) {
 636             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 637         }
 638         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 639         if ( default_sequence != null ) {
 640             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 641         }
 642         /* GUILHEM_END */
 643         System.gc();
 644         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 645         setVisible( true );
 646     }
 647
 648     public void showTextFrame( final String s, final String title ) {
 649         checkTextFrames();
 650         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 651     }
 652
 653     @Override
 654     public void start() {
 655         if ( getMainPanel() != null ) {
 656             getMainPanel().validate();
 657         }
 658         requestFocus();
 659         requestFocusInWindow();
 660         requestFocus();
 661         AptxUtil.printAppletMessage( NAME, "started" );
 662     }
 663
 664     void buildAnalysisMenu() {
 665         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 666         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 667         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 668         customizeJMenuItem( _gsdi_item );
 669         customizeJMenuItem( _gsdir_item );
 670         //  _analysis_menu.addSeparator();
 671         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 672         //  customizeJMenuItem( _lineage_inference );
 673         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 674         _jmenubar.add( _analysis_menu );
 675     }
 676
 677     void buildFontSizeMenu() {
 678         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 679         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 680         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 681         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 682         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 683         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 684         customizeJMenuItem( _super_tiny_fonts_mi );
 685         customizeJMenuItem( _tiny_fonts_mi );
 686         customizeJMenuItem( _small_fonts_mi );
 687         customizeJMenuItem( _medium_fonts_mi );
 688         customizeJMenuItem( _large_fonts_mi );
 689         _jmenubar.add( _font_size_menu );
 690     }
 691
 692     void buildHelpMenu() {
 693         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 694         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
 695         _help_jmenu.addSeparator();
 696         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 697         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 698         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 699         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 700         _help_jmenu.addSeparator();
 701         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 702         customizeJMenuItem( _help_item );
 703         customizeJMenuItem( _website_item );
 704         customizeJMenuItem( _phyloxml_website_item );
 705         customizeJMenuItem( _aptx_ref_item );
 706         customizeJMenuItem( _phyloxml_ref_item );
 707         customizeJMenuItem( _about_item );
 708         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 709         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 710         _jmenubar.add( _help_jmenu );
 711     }
 712
 713     void buildOptionsMenu() {
 714         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 715         _options_jmenu.addChangeListener( new ChangeListener() {
 716
 717             @Override
 718             public void stateChanged( final ChangeEvent e ) {
 719                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 720                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 721                 MainFrame
 722                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 723                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 724                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 725                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 726                                                                      _show_scale_cbmi,
 727                                                                      _show_branch_length_values_cbmi,
 728                                                                      _non_lined_up_cladograms_rbmi,
 729                                                                      _uniform_cladograms_rbmi,
 730                                                                      _ext_node_dependent_cladogram_rbmi,
 731                                                                      _label_direction_cbmi );
 732                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 733                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 734                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 735             }
 736         } );
 737         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 738                                                                 getConfiguration() ) );
 739         _options_jmenu
 740                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 741         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 742         _options_jmenu
 743                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 744         _radio_group_1 = new ButtonGroup();
 745         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 746         _radio_group_1.add( _uniform_cladograms_rbmi );
 747         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 748         /////
 749         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 750         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 751         _options_jmenu
 752                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 753         _options_jmenu
 754                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 755         _options_jmenu
 756                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 757         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 758             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 759             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 760         }
 761         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 762         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 763         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 764         _options_jmenu
 765                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 766         _options_jmenu
 767                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 768         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 769         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 770         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 771         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 772         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 773         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 774         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 775         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 776         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 777         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 778         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 779         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 780         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 781         /////
 782         _options_jmenu.addSeparator();
 783         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 784                                                                 getConfiguration() ) );
 785         _options_jmenu
 786                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 787         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 788         _options_jmenu
 789                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 790         customizeJMenuItem( _choose_font_mi );
 791         customizeJMenuItem( _choose_minimal_confidence_mi );
 792         customizeJMenuItem( _switch_colors_mi );
 793         customizeJMenuItem( _overview_placment_mi );
 794         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 795         customizeCheckBoxMenuItem( _label_direction_cbmi,
 796                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 797         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 798         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 799         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 800         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 801         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 802         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 803                 .isShowDefaultNodeShapesExternal() );
 804         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 805                 .isShowDefaultNodeShapesInternal() );
 806         customizeJMenuItem( _cycle_node_shape_mi );
 807         customizeJMenuItem( _cycle_node_fill_mi );
 808         customizeJMenuItem( _choose_node_size_mi );
 809         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 810         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 811         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 812         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 813                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 814         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 815                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 816         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 817                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 818         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 819         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 820         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 821         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 822         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 823         _jmenubar.add( _options_jmenu );
 824     }
 825
 826     void buildToolsMenu() {
 827         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 828         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 829         customizeJMenuItem( _confcolor_item );
 830         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 831         customizeJMenuItem( _taxcolor_item );
 832         _tools_menu.addSeparator();
 833         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 834         _remove_visual_styles_item
 835                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 836         customizeJMenuItem( _remove_visual_styles_item );
 837         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 838         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 839         customizeJMenuItem( _remove_branch_color_item );
 840         _tools_menu.addSeparator();
 841         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 842         customizeJMenuItem( _midpoint_root_item );
 843         _tools_menu.addSeparator();
 844         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 845         customizeJMenuItem( _collapse_species_specific_subtrees );
 846         _jmenubar.add( _tools_menu );
 847     }
 848
 849     void buildTypeMenu() {
 850         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 851         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 852         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 853         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 854         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 855         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 856         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 857         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 858         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 859         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 860         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 861         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 862         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 863         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 864         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 865         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 866         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 867         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 868         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 869         initializeTypeMenu( getOptions() );
 870         _jmenubar.add( _type_menu );
 871     }
 872
 873     void buildViewMenu() {
 874         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 875         _view_jmenu
 876                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 877         _view_jmenu.addSeparator();
 878         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 879         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 880         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 881         customizeJMenuItem( _display_basic_information_item );
 882         customizeJMenuItem( _view_as_NH_item );
 883         customizeJMenuItem( _view_as_XML_item );
 884         customizeJMenuItem( _view_as_nexus_item );
 885         _jmenubar.add( _view_jmenu );
 886     }
 887
 888     void checkTextFrames() {
 889         if ( _textframes.size() > 5 ) {
 890             try {
 891                 if ( _textframes.getFirst() != null ) {
 892                     _textframes.getFirst().removeMe();
 893                 }
 894                 else {
 895                     _textframes.removeFirst();
 896                 }
 897             }
 898             catch ( final NoSuchElementException e ) {
 899                 // Ignore.
 900             }
 901         }
 902     }
 903
 904     void clearCurrentExternalNodesDataBuffer() {
 905         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 906     }
 907
 908     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 909         if ( item != null ) {
 910             item.setFont( MainFrame.menu_font );
 911             if ( !getConfiguration().isUseNativeUI() ) {
 912                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 913                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 914             }
 915             item.setSelected( is_selected );
 916             item.addActionListener( this );
 917         }
 918     }
 919
 920     void customizeJMenuItem( final JMenuItem jmi ) {
 921         jmi.setFont( MainFrame.menu_font );
 922         if ( !getConfiguration().isUseNativeUI() ) {
 923             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 924             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 925         }
 926         jmi.addActionListener( this );
 927     }
 928
 929     void displayBasicInformation() {
 930         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 931             String title = "Basic Information";
 932             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 933                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 934             }
 935             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 936         }
 937     }
 938
 939     void executeGSDI() {
 940         if ( !isOKforSDI( false, true ) ) {
 941             return;
 942         }
 943         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 944             JOptionPane.showMessageDialog( this,
 945                                            "Gene tree is not rooted.",
 946                                            "Cannot execute GSDI",
 947                                            JOptionPane.ERROR_MESSAGE );
 948             return;
 949         }
 950         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 951         gene_tree.setAllNodesToNotCollapse();
 952         gene_tree.recalculateNumberOfExternalDescendants( false );
 953         GSDI gsdi = null;
 954         final Phylogeny species_tree = _species_tree.copy();
 955         try {
 956             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 957         }
 958         catch ( final SDIException e ) {
 959             JOptionPane.showMessageDialog( this,
 960                                            e.getLocalizedMessage(),
 961                                            "Error during GSDI",
 962                                            JOptionPane.ERROR_MESSAGE );
 963             return;
 964         }
 965         catch ( final Exception e ) {
 966             AptxUtil.unexpectedException( e );
 967             return;
 968         }
 969         gene_tree.setRerootable( false );
 970         gene_tree.clearHashIdToNodeMap();
 971         gene_tree.recalculateNumberOfExternalDescendants( true );
 972         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 973         getMainPanel().getControlPanel().setShowEvents( true );
 974         showWhole();
 975         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 976         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 977         showWhole();
 978         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 979         showWhole();
 980         _mainpanel.getCurrentTreePanel().setEdited( true );
 981         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 982         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 983             JOptionPane.showMessageDialog( this,
 984                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 985                                                    + "Potential duplications: "
 986                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 987                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 988                                                    + "Stripped gene tree nodes: "
 989                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 990                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 991                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 992                                            "GSDI successfully completed",
 993                                            JOptionPane.WARNING_MESSAGE );
 994         }
 995         else {
 996             JOptionPane.showMessageDialog( this,
 997                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 998                                                    + "Potential duplications: "
 999                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1000                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1001                                                    + "Stripped gene tree nodes: "
1002                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1003                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1004                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1005                                            "GSDI successfully completed",
1006                                            JOptionPane.INFORMATION_MESSAGE );
1007         }
1008     }
1009
1010     void executeGSDIR() {
1011         if ( !isOKforSDI( false, false ) ) {
1012             return;
1013         }
1014         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1015         if ( ( p > 0 )
1016                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1017             JOptionPane.showMessageDialog( this,
1018                                            "Gene tree is not completely binary",
1019                                            "Cannot execute GSDI",
1020                                            JOptionPane.ERROR_MESSAGE );
1021             return;
1022         }
1023         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1024         gene_tree.setAllNodesToNotCollapse();
1025         gene_tree.recalculateNumberOfExternalDescendants( false );
1026         GSDIR gsdir = null;
1027         final Phylogeny species_tree = _species_tree.copy();
1028         try {
1029             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1030         }
1031         catch ( final SDIException e ) {
1032             JOptionPane.showMessageDialog( this,
1033                                            e.getLocalizedMessage(),
1034                                            "Error during GSDIR",
1035                                            JOptionPane.ERROR_MESSAGE );
1036             return;
1037         }
1038         catch ( final Exception e ) {
1039             AptxUtil.unexpectedException( e );
1040             return;
1041         }
1042         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1043         result_gene_tree.setRerootable( false );
1044         result_gene_tree.clearHashIdToNodeMap();
1045         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1046         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1047         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1048         getMainPanel().getControlPanel().setShowEvents( true );
1049         showWhole();
1050         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1051         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1052         showWhole();
1053         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1054         showWhole();
1055         _mainpanel.getCurrentTreePanel().setEdited( true );
1056         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1057         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1058             JOptionPane.showMessageDialog( this,
1059                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1060                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1061                                                    + "Stripped gene tree nodes: "
1062                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1063                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1064                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1065                                            "GSDIR successfully completed",
1066                                            JOptionPane.WARNING_MESSAGE );
1067         }
1068         else {
1069             JOptionPane.showMessageDialog( this,
1070                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1071                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1072                                                    + "Stripped gene tree nodes: "
1073                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1074                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1075                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1076                                            "GSDIR successfully completed",
1077                                            JOptionPane.INFORMATION_MESSAGE );
1078         }
1079     }
1080
1081     Configuration getConfiguration() {
1082         return _configuration;
1083     }
1084
1085     TreePanel getCurrentTreePanel() {
1086         return getMainPanel().getCurrentTreePanel();
1087     }
1088
1089     JCheckBoxMenuItem getlabelDirectionCbmi() {
1090         return _label_direction_cbmi;
1091     }
1092
1093     Options getOtions() {
1094         return _options;
1095     }
1096
1097
1098
1099     void initializeTypeMenu( final Options options ) {
1100         setTypeMenuToAllUnselected();
1101         try {
1102             switch ( options.getPhylogenyGraphicsType() ) {
1103                 case CONVEX:
1104                     _convex_type_cbmi.setSelected( true );
1105                     break;
1106                 case CURVED:
1107                     _curved_type_cbmi.setSelected( true );
1108                     break;
1109                 case EURO_STYLE:
1110                     _euro_type_cbmi.setSelected( true );
1111                     break;
1112                 case ROUNDED:
1113                     _rounded_type_cbmi.setSelected( true );
1114                     break;
1115                 case TRIANGULAR:
1116                     _triangular_type_cbmi.setSelected( true );
1117                     break;
1118                 case UNROOTED:
1119                     _unrooted_type_cbmi.setSelected( true );
1120                     break;
1121                 case CIRCULAR:
1122                     _circular_type_cbmi.setSelected( true );
1123                     break;
1124                 default:
1125                     _rectangular_type_cbmi.setSelected( true );
1126                     break;
1127             }
1128         }
1129         catch ( final NullPointerException np ) {
1130             // In all likelihood, this is caused by menu-less display.
1131         }
1132     }
1133
1134     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1135         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1136             return false;
1137         }
1138         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1139             JOptionPane.showMessageDialog( this,
1140                                            "No species tree loaded",
1141                                            "Cannot execute GSDI",
1142                                            JOptionPane.ERROR_MESSAGE );
1143             return false;
1144         }
1145         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1146             JOptionPane.showMessageDialog( this,
1147                                            "Species tree is not completely binary",
1148                                            "Cannot execute GSDI",
1149                                            JOptionPane.ERROR_MESSAGE );
1150             return false;
1151         }
1152         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1153             JOptionPane.showMessageDialog( this,
1154                                            "Gene tree is not completely binary",
1155                                            "Cannot execute GSDI",
1156                                            JOptionPane.ERROR_MESSAGE );
1157             return false;
1158         }
1159         else {
1160             return true;
1161         }
1162     }
1163
1164     boolean isSubtreeDisplayed() {
1165         if ( getCurrentTreePanel() != null ) {
1166             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1167                 JOptionPane
1168                         .showMessageDialog( this,
1169                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1170                                             "Operation can not be exectuted on a sub-tree",
1171                                             JOptionPane.WARNING_MESSAGE );
1172                 return true;
1173             }
1174         }
1175         return false;
1176     }
1177
1178     void removeAllTextFrames() {
1179         for( final TextFrame tf : _textframes ) {
1180             if ( tf != null ) {
1181                 tf.close();
1182             }
1183         }
1184         _textframes.clear();
1185     }
1186
1187     void setConfiguration( final Configuration configuration ) {
1188         _configuration = configuration;
1189     }
1190
1191     void setOptions( final Options options ) {
1192         _options = options;
1193     }
1194
1195     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1196         setTypeMenuToAllUnselected();
1197         try {
1198             switch ( type ) {
1199                 case CIRCULAR:
1200                     _circular_type_cbmi.setSelected( true );
1201                     break;
1202                 case CONVEX:
1203                     _convex_type_cbmi.setSelected( true );
1204                     break;
1205                 case CURVED:
1206                     _curved_type_cbmi.setSelected( true );
1207                     break;
1208                 case EURO_STYLE:
1209                     _euro_type_cbmi.setSelected( true );
1210                     break;
1211                 case ROUNDED:
1212                     _rounded_type_cbmi.setSelected( true );
1213                     break;
1214                 case RECTANGULAR:
1215                     _rectangular_type_cbmi.setSelected( true );
1216                     break;
1217                 case TRIANGULAR:
1218                     _triangular_type_cbmi.setSelected( true );
1219                     break;
1220                 case UNROOTED:
1221                     _unrooted_type_cbmi.setSelected( true );
1222                     break;
1223                 default:
1224                     throw new IllegalArgumentException( "unknown type: " + type );
1225             }
1226         }
1227         catch ( final NullPointerException np ) {
1228             // In all likelihood, this is caused by menu-less display.
1229         }
1230     }
1231
1232     void setTypeMenuToAllUnselected() {
1233         if ( _convex_type_cbmi != null ) {
1234             _convex_type_cbmi.setSelected( false );
1235         }
1236         if ( _curved_type_cbmi != null ) {
1237             _curved_type_cbmi.setSelected( false );
1238         }
1239         if ( _euro_type_cbmi != null ) {
1240             _euro_type_cbmi.setSelected( false );
1241         }
1242         if ( _rounded_type_cbmi != null ) {
1243             _rounded_type_cbmi.setSelected( false );
1244         }
1245         if ( _triangular_type_cbmi != null ) {
1246             _triangular_type_cbmi.setSelected( false );
1247         }
1248         if ( _rectangular_type_cbmi != null ) {
1249             _rectangular_type_cbmi.setSelected( false );
1250         }
1251         if ( _unrooted_type_cbmi != null ) {
1252             _unrooted_type_cbmi.setSelected( false );
1253         }
1254         if ( _circular_type_cbmi != null ) {
1255             _circular_type_cbmi.setSelected( false );
1256         }
1257     }
1258
1259     void showWhole() {
1260         _mainpanel.getControlPanel().showWhole();
1261     }
1262
1263     void switchColors() {
1264         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1265         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1266         csc.setVisible( true );
1267         getMainPanel().setTreeColorSet( colorset );
1268     }
1269
1270     void typeChanged( final Object o ) {
1271         updateTypeCheckboxes( getOptions(), o );
1272         updateOptions( getOptions() );
1273         if ( getCurrentTreePanel() != null ) {
1274             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1275             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1276             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1277                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1278                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1279                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1280                 getCurrentTreePanel().getControlPanel().showWhole();
1281             }
1282             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1283                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1284             }
1285             else {
1286                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1287             }
1288             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1289             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1290         }
1291     }
1292
1293     void updateOptions( final Options options ) {
1294         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1295         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1296                 && _background_gradient_cbmi.isSelected() );
1297         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1298         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1299                 && _show_annotation_ref_source.isSelected() );
1300         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1301                 && _abbreviate_scientific_names.isSelected() );
1302         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1303                 && _color_labels_same_as_parent_branch.isSelected() );
1304         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1305                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1306         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1307                 && _show_default_node_shapes_external_cbmi.isSelected() );
1308         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1309             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1310         }
1311         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1312             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1313         }
1314         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1315             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1316         }
1317         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1318                 && _search_case_senstive_cbmi.isSelected() );
1319         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1320             options.setShowScale( _show_scale_cbmi.isSelected() );
1321         }
1322         if ( _label_direction_cbmi != null ) {
1323             if ( _label_direction_cbmi.isSelected() ) {
1324                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1325             }
1326             else {
1327                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1328             }
1329         }
1330         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1331         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1332                 && _show_confidence_stddev_cbmi.isSelected() );
1333         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1334             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1335         }
1336         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1337                 && _search_whole_words_only_cbmi.isSelected() );
1338         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1339                 && _inverse_search_result_cbmi.isSelected() );
1340         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1341             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1342         }
1343         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1344             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1345         }
1346         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1347             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1348         }
1349         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1350             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1351         }
1352         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1353             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1354         }
1355         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1356             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1357         }
1358         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1359             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1360         }
1361         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1362             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1363         }
1364         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1365             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1366         }
1367
1368
1369         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1370             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1371         }
1372
1373
1374         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1375             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1376         }
1377
1378     }
1379
1380     void updateTypeCheckboxes( final Options options, final Object o ) {
1381         setTypeMenuToAllUnselected();
1382         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1383     }
1384
1385     void viewAsNexus() {
1386         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1387             String title = "Nexus";
1388             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1389                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1390             }
1391             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1392                                    .getNhConversionSupportValueStyle() ),
1393                            title );
1394         }
1395     }
1396
1397     void viewAsNH() {
1398         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1399             String title = "New Hampshire";
1400             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1401                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1402             }
1403             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1404                                    .getNhConversionSupportValueStyle() ),
1405                            title );
1406         }
1407     }
1408
1409     void viewAsXML() {
1410         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1411             String title = "phyloXML";
1412             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1413                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1414             }
1415             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1416         }
1417     }
1418
1419     private void chooseFont() {
1420         final FontChooser fc = new FontChooser();
1421         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1422         fc.showDialog( this, "Select the Base Font" );
1423         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1424     }
1425
1426     private void chooseMinimalConfidence() {
1427         final String s = ( String ) JOptionPane
1428                 .showInputDialog( this,
1429                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1430                                           + getOptions().getMinConfidenceValue() + "]\n",
1431                                   "Minimal Confidence Value",
1432                                   JOptionPane.QUESTION_MESSAGE,
1433                                   null,
1434                                   null,
1435                                   getOptions().getMinConfidenceValue() );
1436         if ( !ForesterUtil.isEmpty( s ) ) {
1437             boolean success = true;
1438             double m = 0.0;
1439             final String m_str = s.trim();
1440             if ( !ForesterUtil.isEmpty( m_str ) ) {
1441                 try {
1442                     m = Double.parseDouble( m_str );
1443                 }
1444                 catch ( final Exception ex ) {
1445                     success = false;
1446                 }
1447             }
1448             else {
1449                 success = false;
1450             }
1451             if ( success && ( m >= 0.0 ) ) {
1452                 getOptions().setMinConfidenceValue( m );
1453             }
1454         }
1455     }
1456
1457     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1458         if ( item != null ) {
1459             item.setFont( MainFrame.menu_font );
1460             if ( !getConfiguration().isUseNativeUI() ) {
1461                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1462                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1463             }
1464             item.setSelected( is_selected );
1465             item.addActionListener( this );
1466         }
1467     }
1468
1469     private MainPanel getMainPanel() {
1470         return _mainpanel;
1471     }
1472
1473     private Phylogeny getSpeciesTree() {
1474         return _species_tree;
1475     }
1476
1477     private boolean isScreenAntialias() {
1478         return true;
1479     }
1480
1481     private void removeBranchColors() {
1482         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1483             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1484         }
1485     }
1486
1487     private void removeVisualStyles() {
1488         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1489             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1490         }
1491     }
1492
1493     private void setMainPanel( final MainPanelApplets main_panel ) {
1494         _mainpanel = main_panel;
1495     }
1496
1497     private void setSpeciesTree( final Phylogeny species_tree ) {
1498         _species_tree = species_tree;
1499     }
1500
1501     private void setupUI() {
1502         try {
1503             if ( getConfiguration().isUseNativeUI() ) {
1504                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1505             }
1506             else {
1507                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1508             }
1509         }
1510         catch ( final UnsupportedLookAndFeelException e ) {
1511             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1512         }
1513         catch ( final ClassNotFoundException e ) {
1514             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1515         }
1516         catch ( final InstantiationException e ) {
1517             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1518         }
1519         catch ( final IllegalAccessException e ) {
1520             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1521         }
1522         catch ( final Exception e ) {
1523             AptxUtil.dieWithSystemError( e.toString() );
1524         }
1525     }
1526
1527     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1528         for( final TreePanel tree_panel : treepanels ) {
1529             tree_panel.setTextAntialias();
1530         }
1531     }
1532 }