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
 357
 358
 359         else if ( o == _line_up_renderable_data_cbmi ) {
 360             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
 361                 _right_line_up_domains_cbmi.setSelected( false );
 362             }
 363             updateOptions( getOptions() );
 364         }
 365         else if ( o == _right_line_up_domains_cbmi ) {
 366             if ( _right_line_up_domains_cbmi.isSelected() ) {
 367                 _line_up_renderable_data_cbmi.setSelected( true );
 368             }
 369             updateOptions( getOptions() );
 370         }
 371
 372         repaint();
 373     }
 374
 375     @Override
 376     public void destroy() {
 377         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 378         removeAllTextFrames();
 379         if ( getMainPanel() != null ) {
 380             getMainPanel().terminate();
 381         }
 382     }
 383
 384     /**
 385      * This method returns the current external node data which
 386      * has been selected by the user by clicking the "Return ..."
 387      * menu item. This method is expected to be called from Javascript or
 388      * something like it.
 389      *
 390      * @return current external node data as String
 391      */
 392     public String getCurrentExternalNodesDataBuffer() {
 393         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 394     }
 395
 396     public int getCurrentExternalNodesDataBufferChangeCounter() {
 397         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 398     }
 399
 400     public int getCurrentExternalNodesDataBufferLength() {
 401         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 402     }
 403
 404     /**
 405      * This method returns the current phylogeny as a string in the chosen format
 406      *
 407      * @param format must be NH, NHX, NEXUS or PHYLOXML
 408      * @return the phylogeny string
 409      * @author Herve Menager
 410      */
 411     public String getCurrentPhylogeny( final String format ) {
 412         removeAllTextFrames();
 413         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 414                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 415             return new String();
 416         }
 417         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 418             case NH:
 419                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 420             case NHX:
 421                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 422             case NEXUS:
 423                 return getMainPanel().getCurrentPhylogeny().toNexus();
 424             case PHYLOXML:
 425                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 426             default:
 427                 break;
 428         }
 429         return new String();
 430     }
 431
 432     /**
 433      * This method returns a view of the current phylogeny in a chosen
 434      * graphics format, base64-encoded in a string so that in can be used
 435      * from javascript.
 436      *
 437      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 438      * @return the phylogeny string
 439      * @author Herve Menager
 440      */
 441     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 442         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 443         try {
 444             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 445                                                                     _mainpanel.getWidth(),
 446                                                                     _mainpanel.getHeight(),
 447                                                                     getCurrentTreePanel(),
 448                                                                     getCurrentTreePanel().getControlPanel(),
 449                                                                     GraphicsExportType.valueOf( format ),
 450                                                                     getOptions() );
 451         }
 452         catch ( final IOException ioe ) {
 453             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 454             ioe.printStackTrace();
 455             JOptionPane.showMessageDialog( this,
 456                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 457                                            "Failed to generate graphics",
 458                                            JOptionPane.ERROR_MESSAGE );
 459             return null;
 460         }
 461         final byte[] bytes = baos.toByteArray();
 462         final String dataImg = Base64.encodeBase64String( bytes );
 463         return dataImg;
 464     }
 465
 466     public Options getOptions() {
 467         return _options;
 468     }
 469
 470     @Override
 471     public void init() {
 472         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 473         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 474         final Configuration configuration = new Configuration( config_filename, true, true, true );
 475         setConfiguration( configuration );
 476         setOptions( Options.createInstance( configuration ) );
 477         setupUI();
 478         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 479         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 480             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 481                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 482             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 483                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 484             return;
 485         }
 486         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 487         // Get URL to tree file
 488         URL phys_url = null;
 489         try {
 490             phys_url = new URL( tree_url_str );
 491         }
 492         catch ( final Exception e ) {
 493             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 494             e.printStackTrace();
 495             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 496                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 497         }
 498         if ( phys_url == null ) {
 499             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 500                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 501             JOptionPane.showMessageDialog( this,
 502                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 503                                            "Failed to create URL",
 504                                            JOptionPane.ERROR_MESSAGE );
 505             return;
 506         }
 507         // Load the tree from URL
 508         Phylogeny[] phys = null;
 509         try {
 510             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 511                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 512                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 513                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 514                                                     getConfiguration().getTaxonomyExtraction(),
 515                                                     getConfiguration().isMidpointReroot() );
 516         }
 517         catch ( final Exception e ) {
 518             ForesterUtil.printErrorMessage( NAME, e.toString() );
 519             e.printStackTrace();
 520             JOptionPane.showMessageDialog( this,
 521                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 522                                            "Failed to read phylogenies",
 523                                            JOptionPane.ERROR_MESSAGE );
 524         }
 525         if ( phys == null ) {
 526             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 527             JOptionPane.showMessageDialog( this,
 528                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 529                                            "Failed to read phylogenies",
 530                                            JOptionPane.ERROR_MESSAGE );
 531             return;
 532         }
 533         else if ( phys.length < 1 ) {
 534             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 535             JOptionPane.showMessageDialog( this,
 536                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 537                                            "Failed to read phylogenies",
 538                                            JOptionPane.ERROR_MESSAGE );
 539             return;
 540         }
 541         else {
 542             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 543         }
 544         //
 545         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 546         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 547             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 548             Phylogeny[] species_trees = null;
 549             try {
 550                 final URL species_tree_url = new URL( species_tree_url_str );
 551                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 552                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 553                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 554                                                                  false,
 555                                                                  TAXONOMY_EXTRACTION.NO,
 556                                                                  false );
 557             }
 558             catch ( final IOException e ) {
 559                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 560                         + "]" );
 561                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 562                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 563             }
 564             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 565                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 566                 if ( species_trees[ 0 ].isEmpty() ) {
 567                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 568                 }
 569                 else if ( !species_trees[ 0 ].isRooted() ) {
 570                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 571                 }
 572                 else {
 573                     setSpeciesTree( species_trees[ 0 ] );
 574                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 575                 }
 576             }
 577         }
 578         //
 579         setVisible( false );
 580         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 581         _jmenubar = new JMenuBar();
 582         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 583             if ( !getConfiguration().isUseNativeUI() ) {
 584                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 585             }
 586             if ( getSpeciesTree() != null ) {
 587                 buildAnalysisMenu();
 588             }
 589             buildToolsMenu();
 590             buildViewMenu();
 591             buildFontSizeMenu();
 592             buildOptionsMenu();
 593             buildTypeMenu();
 594             buildHelpMenu();
 595             setJMenuBar( _jmenubar );
 596         }
 597         final Container contentpane = getContentPane();
 598         contentpane.setLayout( new BorderLayout() );
 599         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 600         addComponentListener( new ComponentAdapter() {
 601
 602             @Override
 603             public void componentResized( final ComponentEvent e ) {
 604                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 605                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 606                                                                                             .getCurrentTreePanel()
 607                                                                                             .getWidth(),
 608                                                                                     getMainPanel()
 609                                                                                             .getCurrentTreePanel()
 610                                                                                             .getHeight(),
 611                                                                                     getOptions()
 612                                                                                             .isAllowFontSizeChange() );
 613                 }
 614             }
 615         } );
 616         if ( getConfiguration().isUseTabbedDisplay() ) {
 617             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 618             AptxUtil.addPhylogeniesToTabs( phys,
 619                                            new File( phys_url.getFile() ).getName(),
 620                                            phys_url.toString(),
 621                                            getConfiguration(),
 622                                            getMainPanel() );
 623         }
 624         else {
 625             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 626             if ( getSpeciesTree() != null ) {
 627                 AptxUtil.printAppletMessage( NAME,
 628                                              "Warning: gsdi (gene duplication inference) only available tabbed display" );
 629             }
 630             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 631         }
 632         validate();
 633         setName( NAME );
 634         getMainPanel().getControlPanel().showWholeAll();
 635         getMainPanel().getControlPanel().showWhole();
 636         /* GUILHEM_BEG */
 637         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 638         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 639                 .getRelevantSequenceRelationTypes() ) {
 640             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 641         }
 642         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 643         if ( default_relation != null ) {
 644             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 645         }
 646         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 647         if ( default_sequence != null ) {
 648             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 649         }
 650         /* GUILHEM_END */
 651         System.gc();
 652         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 653         setVisible( true );
 654     }
 655
 656     public void showTextFrame( final String s, final String title ) {
 657         checkTextFrames();
 658         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 659     }
 660
 661     @Override
 662     public void start() {
 663         if ( getMainPanel() != null ) {
 664             getMainPanel().validate();
 665         }
 666         requestFocus();
 667         requestFocusInWindow();
 668         requestFocus();
 669         AptxUtil.printAppletMessage( NAME, "started" );
 670     }
 671
 672     void buildAnalysisMenu() {
 673         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 674         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 675         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 676         customizeJMenuItem( _gsdi_item );
 677         customizeJMenuItem( _gsdir_item );
 678         //  _analysis_menu.addSeparator();
 679         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 680         //  customizeJMenuItem( _lineage_inference );
 681         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 682         _jmenubar.add( _analysis_menu );
 683     }
 684
 685     void buildFontSizeMenu() {
 686         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 687         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 688         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 689         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 690         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 691         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 692         customizeJMenuItem( _super_tiny_fonts_mi );
 693         customizeJMenuItem( _tiny_fonts_mi );
 694         customizeJMenuItem( _small_fonts_mi );
 695         customizeJMenuItem( _medium_fonts_mi );
 696         customizeJMenuItem( _large_fonts_mi );
 697         _jmenubar.add( _font_size_menu );
 698     }
 699
 700     void buildHelpMenu() {
 701         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 702         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
 703         _help_jmenu.addSeparator();
 704         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 705         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 706         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 707         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 708         _help_jmenu.addSeparator();
 709         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 710         customizeJMenuItem( _help_item );
 711         customizeJMenuItem( _website_item );
 712         customizeJMenuItem( _phyloxml_website_item );
 713         customizeJMenuItem( _aptx_ref_item );
 714         customizeJMenuItem( _phyloxml_ref_item );
 715         customizeJMenuItem( _about_item );
 716         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 717         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 718         _jmenubar.add( _help_jmenu );
 719     }
 720
 721     void buildOptionsMenu() {
 722         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 723         _options_jmenu.addChangeListener( new ChangeListener() {
 724
 725             @Override
 726             public void stateChanged( final ChangeEvent e ) {
 727                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 728                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 729                 MainFrame
 730                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 731                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 732                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 733                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 734                                                                      _show_scale_cbmi,
 735                                                                      _show_branch_length_values_cbmi,
 736                                                                      _non_lined_up_cladograms_rbmi,
 737                                                                      _uniform_cladograms_rbmi,
 738                                                                      _ext_node_dependent_cladogram_rbmi,
 739                                                                      _label_direction_cbmi );
 740                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 741                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 742                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 743             }
 744         } );
 745         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 746                                                                 getConfiguration() ) );
 747         _options_jmenu
 748                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 749         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 750         _options_jmenu
 751                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 752         _radio_group_1 = new ButtonGroup();
 753         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 754         _radio_group_1.add( _uniform_cladograms_rbmi );
 755         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 756         /////
 757         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 758         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 759         _options_jmenu
 760                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 761         _options_jmenu
 762                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 763         _options_jmenu
 764                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 765         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 766             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 767             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 768         }
 769         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 770         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 771         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 772         _options_jmenu
 773                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 774         _options_jmenu
 775                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 776         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 777         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 778         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 779         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 780         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 781         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 782         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 783         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 784         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 785         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 786         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 787         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 788         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 789         /////
 790         _options_jmenu.addSeparator();
 791         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 792                                                                 getConfiguration() ) );
 793         _options_jmenu
 794                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 795         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 796         _options_jmenu
 797                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 798         customizeJMenuItem( _choose_font_mi );
 799         customizeJMenuItem( _choose_minimal_confidence_mi );
 800         customizeJMenuItem( _switch_colors_mi );
 801         customizeJMenuItem( _overview_placment_mi );
 802         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 803         customizeCheckBoxMenuItem( _label_direction_cbmi,
 804                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 805         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 806         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 807         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 808         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 809         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 810         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 811                 .isShowDefaultNodeShapesExternal() );
 812         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 813                 .isShowDefaultNodeShapesInternal() );
 814         customizeJMenuItem( _cycle_node_shape_mi );
 815         customizeJMenuItem( _cycle_node_fill_mi );
 816         customizeJMenuItem( _choose_node_size_mi );
 817         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 818         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 819         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 820         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 821                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 822         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 823                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 824         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 825                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 826         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 827         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 828         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 829         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 830         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 831         _jmenubar.add( _options_jmenu );
 832     }
 833
 834     void buildToolsMenu() {
 835         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 836         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 837         customizeJMenuItem( _confcolor_item );
 838         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 839         customizeJMenuItem( _taxcolor_item );
 840         _tools_menu.addSeparator();
 841         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 842         _remove_visual_styles_item
 843                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 844         customizeJMenuItem( _remove_visual_styles_item );
 845         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 846         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 847         customizeJMenuItem( _remove_branch_color_item );
 848         _tools_menu.addSeparator();
 849         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 850         customizeJMenuItem( _midpoint_root_item );
 851         _tools_menu.addSeparator();
 852         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 853         customizeJMenuItem( _collapse_species_specific_subtrees );
 854         _jmenubar.add( _tools_menu );
 855     }
 856
 857     void buildTypeMenu() {
 858         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 859         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 860         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 861         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 862         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 863         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 864         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 865         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 866         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 867         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 868         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 869         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 870         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 871         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 872         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 873         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 874         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 875         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 876         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 877         initializeTypeMenu( getOptions() );
 878         _jmenubar.add( _type_menu );
 879     }
 880
 881     void buildViewMenu() {
 882         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 883         _view_jmenu
 884                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 885         _view_jmenu.addSeparator();
 886         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 887         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 888         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 889         customizeJMenuItem( _display_basic_information_item );
 890         customizeJMenuItem( _view_as_NH_item );
 891         customizeJMenuItem( _view_as_XML_item );
 892         customizeJMenuItem( _view_as_nexus_item );
 893         _jmenubar.add( _view_jmenu );
 894     }
 895
 896     void checkTextFrames() {
 897         if ( _textframes.size() > 5 ) {
 898             try {
 899                 if ( _textframes.getFirst() != null ) {
 900                     _textframes.getFirst().removeMe();
 901                 }
 902                 else {
 903                     _textframes.removeFirst();
 904                 }
 905             }
 906             catch ( final NoSuchElementException e ) {
 907                 // Ignore.
 908             }
 909         }
 910     }
 911
 912     void clearCurrentExternalNodesDataBuffer() {
 913         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 914     }
 915
 916     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 917         if ( item != null ) {
 918             item.setFont( MainFrame.menu_font );
 919             if ( !getConfiguration().isUseNativeUI() ) {
 920                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 921                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 922             }
 923             item.setSelected( is_selected );
 924             item.addActionListener( this );
 925         }
 926     }
 927
 928     void customizeJMenuItem( final JMenuItem jmi ) {
 929         jmi.setFont( MainFrame.menu_font );
 930         if ( !getConfiguration().isUseNativeUI() ) {
 931             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 932             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 933         }
 934         jmi.addActionListener( this );
 935     }
 936
 937     void displayBasicInformation() {
 938         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 939             String title = "Basic Information";
 940             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 941                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 942             }
 943             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 944         }
 945     }
 946
 947     void executeGSDI() {
 948         if ( !isOKforSDI( false, true ) ) {
 949             return;
 950         }
 951         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 952             JOptionPane.showMessageDialog( this,
 953                                            "Gene tree is not rooted.",
 954                                            "Cannot execute GSDI",
 955                                            JOptionPane.ERROR_MESSAGE );
 956             return;
 957         }
 958         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 959         gene_tree.setAllNodesToNotCollapse();
 960         gene_tree.recalculateNumberOfExternalDescendants( false );
 961         GSDI gsdi = null;
 962         final Phylogeny species_tree = _species_tree.copy();
 963         try {
 964             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 965         }
 966         catch ( final SDIException e ) {
 967             JOptionPane.showMessageDialog( this,
 968                                            e.getLocalizedMessage(),
 969                                            "Error during GSDI",
 970                                            JOptionPane.ERROR_MESSAGE );
 971             return;
 972         }
 973         catch ( final Exception e ) {
 974             AptxUtil.unexpectedException( e );
 975             return;
 976         }
 977         gene_tree.setRerootable( false );
 978         gene_tree.clearHashIdToNodeMap();
 979         gene_tree.recalculateNumberOfExternalDescendants( true );
 980         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 981         getMainPanel().getControlPanel().setShowEvents( true );
 982         showWhole();
 983         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 984         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 985         showWhole();
 986         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 987         showWhole();
 988         _mainpanel.getCurrentTreePanel().setEdited( true );
 989         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 990         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 991             JOptionPane.showMessageDialog( this,
 992                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 993                                                    + "Potential duplications: "
 994                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 995                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 996                                                    + "Stripped gene tree nodes: "
 997                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 998                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 999                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1000                                            "GSDI successfully completed",
1001                                            JOptionPane.WARNING_MESSAGE );
1002         }
1003         else {
1004             JOptionPane.showMessageDialog( this,
1005                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1006                                                    + "Potential duplications: "
1007                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1008                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1009                                                    + "Stripped gene tree nodes: "
1010                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1011                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1012                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1013                                            "GSDI successfully completed",
1014                                            JOptionPane.INFORMATION_MESSAGE );
1015         }
1016     }
1017
1018     void executeGSDIR() {
1019         if ( !isOKforSDI( false, false ) ) {
1020             return;
1021         }
1022         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1023         if ( ( p > 0 )
1024                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1025             JOptionPane.showMessageDialog( this,
1026                                            "Gene tree is not completely binary",
1027                                            "Cannot execute GSDI",
1028                                            JOptionPane.ERROR_MESSAGE );
1029             return;
1030         }
1031         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1032         gene_tree.setAllNodesToNotCollapse();
1033         gene_tree.recalculateNumberOfExternalDescendants( false );
1034         GSDIR gsdir = null;
1035         final Phylogeny species_tree = _species_tree.copy();
1036         try {
1037             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1038         }
1039         catch ( final SDIException e ) {
1040             JOptionPane.showMessageDialog( this,
1041                                            e.getLocalizedMessage(),
1042                                            "Error during GSDIR",
1043                                            JOptionPane.ERROR_MESSAGE );
1044             return;
1045         }
1046         catch ( final Exception e ) {
1047             AptxUtil.unexpectedException( e );
1048             return;
1049         }
1050         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1051         result_gene_tree.setRerootable( false );
1052         result_gene_tree.clearHashIdToNodeMap();
1053         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1054         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1055         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1056         getMainPanel().getControlPanel().setShowEvents( true );
1057         showWhole();
1058         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1059         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1060         showWhole();
1061         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1062         showWhole();
1063         _mainpanel.getCurrentTreePanel().setEdited( true );
1064         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1065         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1066             JOptionPane.showMessageDialog( this,
1067                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1068                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1069                                                    + "Stripped gene tree nodes: "
1070                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1071                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1072                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1073                                            "GSDIR successfully completed",
1074                                            JOptionPane.WARNING_MESSAGE );
1075         }
1076         else {
1077             JOptionPane.showMessageDialog( this,
1078                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1079                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1080                                                    + "Stripped gene tree nodes: "
1081                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1082                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1083                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1084                                            "GSDIR successfully completed",
1085                                            JOptionPane.INFORMATION_MESSAGE );
1086         }
1087     }
1088
1089     Configuration getConfiguration() {
1090         return _configuration;
1091     }
1092
1093     TreePanel getCurrentTreePanel() {
1094         return getMainPanel().getCurrentTreePanel();
1095     }
1096
1097     JCheckBoxMenuItem getlabelDirectionCbmi() {
1098         return _label_direction_cbmi;
1099     }
1100
1101     Options getOtions() {
1102         return _options;
1103     }
1104
1105
1106
1107     void initializeTypeMenu( final Options options ) {
1108         setTypeMenuToAllUnselected();
1109         try {
1110             switch ( options.getPhylogenyGraphicsType() ) {
1111                 case CONVEX:
1112                     _convex_type_cbmi.setSelected( true );
1113                     break;
1114                 case CURVED:
1115                     _curved_type_cbmi.setSelected( true );
1116                     break;
1117                 case EURO_STYLE:
1118                     _euro_type_cbmi.setSelected( true );
1119                     break;
1120                 case ROUNDED:
1121                     _rounded_type_cbmi.setSelected( true );
1122                     break;
1123                 case TRIANGULAR:
1124                     _triangular_type_cbmi.setSelected( true );
1125                     break;
1126                 case UNROOTED:
1127                     _unrooted_type_cbmi.setSelected( true );
1128                     break;
1129                 case CIRCULAR:
1130                     _circular_type_cbmi.setSelected( true );
1131                     break;
1132                 default:
1133                     _rectangular_type_cbmi.setSelected( true );
1134                     break;
1135             }
1136         }
1137         catch ( final NullPointerException np ) {
1138             // In all likelihood, this is caused by menu-less display.
1139         }
1140     }
1141
1142     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1143         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1144             return false;
1145         }
1146         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1147             JOptionPane.showMessageDialog( this,
1148                                            "No species tree loaded",
1149                                            "Cannot execute GSDI",
1150                                            JOptionPane.ERROR_MESSAGE );
1151             return false;
1152         }
1153         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1154             JOptionPane.showMessageDialog( this,
1155                                            "Species tree is not completely binary",
1156                                            "Cannot execute GSDI",
1157                                            JOptionPane.ERROR_MESSAGE );
1158             return false;
1159         }
1160         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1161             JOptionPane.showMessageDialog( this,
1162                                            "Gene tree is not completely binary",
1163                                            "Cannot execute GSDI",
1164                                            JOptionPane.ERROR_MESSAGE );
1165             return false;
1166         }
1167         else {
1168             return true;
1169         }
1170     }
1171
1172     boolean isSubtreeDisplayed() {
1173         if ( getCurrentTreePanel() != null ) {
1174             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1175                 JOptionPane
1176                         .showMessageDialog( this,
1177                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1178                                             "Operation can not be exectuted on a sub-tree",
1179                                             JOptionPane.WARNING_MESSAGE );
1180                 return true;
1181             }
1182         }
1183         return false;
1184     }
1185
1186     void removeAllTextFrames() {
1187         for( final TextFrame tf : _textframes ) {
1188             if ( tf != null ) {
1189                 tf.close();
1190             }
1191         }
1192         _textframes.clear();
1193     }
1194
1195     void setConfiguration( final Configuration configuration ) {
1196         _configuration = configuration;
1197     }
1198
1199     void setOptions( final Options options ) {
1200         _options = options;
1201     }
1202
1203     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1204         setTypeMenuToAllUnselected();
1205         try {
1206             switch ( type ) {
1207                 case CIRCULAR:
1208                     _circular_type_cbmi.setSelected( true );
1209                     break;
1210                 case CONVEX:
1211                     _convex_type_cbmi.setSelected( true );
1212                     break;
1213                 case CURVED:
1214                     _curved_type_cbmi.setSelected( true );
1215                     break;
1216                 case EURO_STYLE:
1217                     _euro_type_cbmi.setSelected( true );
1218                     break;
1219                 case ROUNDED:
1220                     _rounded_type_cbmi.setSelected( true );
1221                     break;
1222                 case RECTANGULAR:
1223                     _rectangular_type_cbmi.setSelected( true );
1224                     break;
1225                 case TRIANGULAR:
1226                     _triangular_type_cbmi.setSelected( true );
1227                     break;
1228                 case UNROOTED:
1229                     _unrooted_type_cbmi.setSelected( true );
1230                     break;
1231                 default:
1232                     throw new IllegalArgumentException( "unknown type: " + type );
1233             }
1234         }
1235         catch ( final NullPointerException np ) {
1236             // In all likelihood, this is caused by menu-less display.
1237         }
1238     }
1239
1240     void setTypeMenuToAllUnselected() {
1241         if ( _convex_type_cbmi != null ) {
1242             _convex_type_cbmi.setSelected( false );
1243         }
1244         if ( _curved_type_cbmi != null ) {
1245             _curved_type_cbmi.setSelected( false );
1246         }
1247         if ( _euro_type_cbmi != null ) {
1248             _euro_type_cbmi.setSelected( false );
1249         }
1250         if ( _rounded_type_cbmi != null ) {
1251             _rounded_type_cbmi.setSelected( false );
1252         }
1253         if ( _triangular_type_cbmi != null ) {
1254             _triangular_type_cbmi.setSelected( false );
1255         }
1256         if ( _rectangular_type_cbmi != null ) {
1257             _rectangular_type_cbmi.setSelected( false );
1258         }
1259         if ( _unrooted_type_cbmi != null ) {
1260             _unrooted_type_cbmi.setSelected( false );
1261         }
1262         if ( _circular_type_cbmi != null ) {
1263             _circular_type_cbmi.setSelected( false );
1264         }
1265     }
1266
1267     void showWhole() {
1268         _mainpanel.getControlPanel().showWhole();
1269     }
1270
1271     void switchColors() {
1272         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1273         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1274         csc.setVisible( true );
1275         getMainPanel().setTreeColorSet( colorset );
1276     }
1277
1278     void typeChanged( final Object o ) {
1279         updateTypeCheckboxes( getOptions(), o );
1280         updateOptions( getOptions() );
1281         if ( getCurrentTreePanel() != null ) {
1282             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1283             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1284             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1285                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1286                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1287                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1288                 getCurrentTreePanel().getControlPanel().showWhole();
1289             }
1290             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1291                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1292             }
1293             else {
1294                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1295             }
1296             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1297             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1298         }
1299     }
1300
1301     void updateOptions( final Options options ) {
1302         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1303         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1304                 && _background_gradient_cbmi.isSelected() );
1305         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1306         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1307                 && _show_annotation_ref_source.isSelected() );
1308         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1309                 && _abbreviate_scientific_names.isSelected() );
1310         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1311                 && _color_labels_same_as_parent_branch.isSelected() );
1312         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1313                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1314         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1315                 && _show_default_node_shapes_external_cbmi.isSelected() );
1316         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1317             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1318         }
1319         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1320             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1321         }
1322         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1323             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1324         }
1325         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1326                 && _search_case_senstive_cbmi.isSelected() );
1327         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1328             options.setShowScale( _show_scale_cbmi.isSelected() );
1329         }
1330         if ( _label_direction_cbmi != null ) {
1331             if ( _label_direction_cbmi.isSelected() ) {
1332                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1333             }
1334             else {
1335                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1336             }
1337         }
1338         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1339         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1340                 && _show_confidence_stddev_cbmi.isSelected() );
1341         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1342             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1343         }
1344         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1345                 && _search_whole_words_only_cbmi.isSelected() );
1346         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1347                 && _inverse_search_result_cbmi.isSelected() );
1348         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1349             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1350         }
1351         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1352             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1353         }
1354         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1355             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1356         }
1357         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1358             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1359         }
1360         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1361             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1362         }
1363         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1364             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1365         }
1366         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1367             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1368         }
1369         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1370             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1371         }
1372         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1373             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1374         }
1375
1376
1377         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1378             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1379         }
1380
1381
1382         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1383             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1384         }
1385
1386     }
1387
1388     void updateTypeCheckboxes( final Options options, final Object o ) {
1389         setTypeMenuToAllUnselected();
1390         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1391     }
1392
1393     void viewAsNexus() {
1394         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1395             String title = "Nexus";
1396             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1397                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1398             }
1399             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1400                                    .getNhConversionSupportValueStyle() ),
1401                            title );
1402         }
1403     }
1404
1405     void viewAsNH() {
1406         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1407             String title = "New Hampshire";
1408             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1409                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1410             }
1411             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1412                                    .getNhConversionSupportValueStyle() ),
1413                            title );
1414         }
1415     }
1416
1417     void viewAsXML() {
1418         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1419             String title = "phyloXML";
1420             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1421                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1422             }
1423             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1424         }
1425     }
1426
1427     private void chooseFont() {
1428         final FontChooser fc = new FontChooser();
1429         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1430         fc.showDialog( this, "Select the Base Font" );
1431         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1432     }
1433
1434     private void chooseMinimalConfidence() {
1435         final String s = ( String ) JOptionPane
1436                 .showInputDialog( this,
1437                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1438                                           + getOptions().getMinConfidenceValue() + "]\n",
1439                                   "Minimal Confidence Value",
1440                                   JOptionPane.QUESTION_MESSAGE,
1441                                   null,
1442                                   null,
1443                                   getOptions().getMinConfidenceValue() );
1444         if ( !ForesterUtil.isEmpty( s ) ) {
1445             boolean success = true;
1446             double m = 0.0;
1447             final String m_str = s.trim();
1448             if ( !ForesterUtil.isEmpty( m_str ) ) {
1449                 try {
1450                     m = Double.parseDouble( m_str );
1451                 }
1452                 catch ( final Exception ex ) {
1453                     success = false;
1454                 }
1455             }
1456             else {
1457                 success = false;
1458             }
1459             if ( success && ( m >= 0.0 ) ) {
1460                 getOptions().setMinConfidenceValue( m );
1461             }
1462         }
1463     }
1464
1465     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1466         if ( item != null ) {
1467             item.setFont( MainFrame.menu_font );
1468             if ( !getConfiguration().isUseNativeUI() ) {
1469                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1470                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1471             }
1472             item.setSelected( is_selected );
1473             item.addActionListener( this );
1474         }
1475     }
1476
1477     private MainPanel getMainPanel() {
1478         return _mainpanel;
1479     }
1480
1481     private Phylogeny getSpeciesTree() {
1482         return _species_tree;
1483     }
1484
1485     private boolean isScreenAntialias() {
1486         return true;
1487     }
1488
1489     private void removeBranchColors() {
1490         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1491             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1492         }
1493     }
1494
1495     private void removeVisualStyles() {
1496         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1497             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1498         }
1499     }
1500
1501     private void setMainPanel( final MainPanelApplets main_panel ) {
1502         _mainpanel = main_panel;
1503     }
1504
1505     private void setSpeciesTree( final Phylogeny species_tree ) {
1506         _species_tree = species_tree;
1507     }
1508
1509     private void setupUI() {
1510         try {
1511             if ( getConfiguration().isUseNativeUI() ) {
1512                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1513             }
1514             else {
1515                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1516             }
1517         }
1518         catch ( final UnsupportedLookAndFeelException e ) {
1519             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1520         }
1521         catch ( final ClassNotFoundException e ) {
1522             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1523         }
1524         catch ( final InstantiationException e ) {
1525             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1526         }
1527         catch ( final IllegalAccessException e ) {
1528             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1529         }
1530         catch ( final Exception e ) {
1531             AptxUtil.dieWithSystemError( e.toString() );
1532         }
1533     }
1534
1535     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1536         for( final TreePanel tree_panel : treepanels ) {
1537             tree_panel.setTextAntialias();
1538         }
1539     }
1540 }