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           _search_with_regex_cbmi;
 119
 120     private JCheckBoxMenuItem           _show_overview_cbmi;
 121     private JMenuItem                   _choose_minimal_confidence_mi;
 122     private JMenuItem                   _collapse_species_specific_subtrees;
 123     private JMenuItem                   _overview_placment_mi;
 124     private ButtonGroup                 _radio_group_1;
 125     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 126     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 127     private JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;
 128     private JMenuItem                   _cycle_node_shape_mi;
 129     private JMenuItem                   _cycle_node_fill_mi;
 130     private JMenuItem                   _choose_node_size_mi;
 131     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 132     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 133     private JMenu                       _analysis_menu;
 134     private JMenuItem                   _gsdi_item;
 135     private JMenuItem                   _gsdir_item;
 136     private Phylogeny                   _species_tree;
 137     private JCheckBoxMenuItem           _right_line_up_domains_cbmi;
 138     private JCheckBoxMenuItem           _line_up_renderable_data_cbmi;
 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 == _search_with_regex_cbmi ) {
 266             updateOptions( getOptions() );
 267             getMainPanel().getControlPanel().search0();
 268             getMainPanel().getControlPanel().search1();
 269         }
 270         else if ( o == _show_scale_cbmi ) {
 271             updateOptions( getOptions() );
 272         }
 273         else if ( o == _show_confidence_stddev_cbmi ) {
 274             updateOptions( getOptions() );
 275         }
 276         else if ( o == _label_direction_cbmi ) {
 277             updateOptions( getOptions() );
 278         }
 279         else if ( o == _abbreviate_scientific_names ) {
 280             updateOptions( getOptions() );
 281         }
 282         else if ( o == _show_overview_cbmi ) {
 283             updateOptions( getOptions() );
 284             if ( getCurrentTreePanel() != null ) {
 285                 getCurrentTreePanel().updateOvSizes();
 286             }
 287         }
 288         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 289                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 290                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 291             typeChanged( o );
 292         }
 293         else if ( o == _screen_antialias_cbmi ) {
 294             updateOptions( getOptions() );
 295             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 296         }
 297         else if ( o == _background_gradient_cbmi ) {
 298             updateOptions( getOptions() );
 299         }
 300         else if ( o == _show_domain_labels ) {
 301             updateOptions( getOptions() );
 302         }
 303         else if ( o == _color_labels_same_as_parent_branch ) {
 304             updateOptions( getOptions() );
 305         }
 306         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 307             updateOptions( getOptions() );
 308         }
 309         else if ( o == _show_default_node_shapes_external_cbmi ) {
 310             updateOptions( getOptions() );
 311         }
 312         else if ( o == _about_item ) {
 313             MainFrame.about();
 314         }
 315         else if ( o == _help_item ) {
 316             try {
 317                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
 318             }
 319             catch ( final IOException e1 ) {
 320                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 321             }
 322         }
 323         else if ( o == _website_item ) {
 324             try {
 325                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 326             }
 327             catch ( final IOException e1 ) {
 328                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 329             }
 330         }
 331         else if ( o == _phyloxml_website_item ) {
 332             try {
 333                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 334             }
 335             catch ( final IOException e1 ) {
 336                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 337             }
 338         }
 339         else if ( o == _aptx_ref_item ) {
 340             try {
 341                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 342             }
 343             catch ( final IOException e1 ) {
 344                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 345             }
 346         }
 347         else if ( o == _phyloxml_ref_item ) {
 348             try {
 349                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 350             }
 351             catch ( final IOException e1 ) {
 352                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 353             }
 354         }
 355         else if ( o == _color_by_taxonomic_group_cbmi ) {
 356             updateOptions( getOptions() );
 357         }
 358         else if ( o == _line_up_renderable_data_cbmi ) {
 359             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
 360                 _right_line_up_domains_cbmi.setSelected( false );
 361             }
 362             updateOptions( getOptions() );
 363         }
 364         else if ( o == _right_line_up_domains_cbmi ) {
 365             if ( _right_line_up_domains_cbmi.isSelected() ) {
 366                 _line_up_renderable_data_cbmi.setSelected( true );
 367             }
 368             updateOptions( getOptions() );
 369         }
 370         repaint();
 371     }
 372
 373     @Override
 374     public void destroy() {
 375         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 376         removeAllTextFrames();
 377         if ( getMainPanel() != null ) {
 378             getMainPanel().terminate();
 379         }
 380     }
 381
 382     /**
 383      * This method returns the current external node data which
 384      * has been selected by the user by clicking the "Return ..."
 385      * menu item. This method is expected to be called from Javascript or
 386      * something like it.
 387      *
 388      * @return current external node data as String
 389      */
 390     public String getCurrentExternalNodesDataBuffer() {
 391         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 392     }
 393
 394     public int getCurrentExternalNodesDataBufferChangeCounter() {
 395         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 396     }
 397
 398     public int getCurrentExternalNodesDataBufferLength() {
 399         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 400     }
 401
 402     /**
 403      * This method returns the current phylogeny as a string in the chosen format
 404      *
 405      * @param format must be NH, NHX, NEXUS or PHYLOXML
 406      * @return the phylogeny string
 407      * @author Herve Menager
 408      */
 409     public String getCurrentPhylogeny( final String format ) {
 410         removeAllTextFrames();
 411         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 412                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 413             return new String();
 414         }
 415         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 416             case NH:
 417                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 418             case NHX:
 419                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 420             case NEXUS:
 421                 return getMainPanel().getCurrentPhylogeny().toNexus();
 422             case PHYLOXML:
 423                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 424             default:
 425                 break;
 426         }
 427         return new String();
 428     }
 429
 430     /**
 431      * This method returns a view of the current phylogeny in a chosen
 432      * graphics format, base64-encoded in a string so that in can be used
 433      * from javascript.
 434      *
 435      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 436      * @return the phylogeny string
 437      * @author Herve Menager
 438      */
 439     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 440         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 441         try {
 442             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 443                                                                     _mainpanel.getWidth(),
 444                                                                     _mainpanel.getHeight(),
 445                                                                     getCurrentTreePanel(),
 446                                                                     getCurrentTreePanel().getControlPanel(),
 447                                                                     GraphicsExportType.valueOf( format ),
 448                                                                     getOptions() );
 449         }
 450         catch ( final IOException ioe ) {
 451             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 452             ioe.printStackTrace();
 453             JOptionPane.showMessageDialog( this,
 454                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 455                                            "Failed to generate graphics",
 456                                            JOptionPane.ERROR_MESSAGE );
 457             return null;
 458         }
 459         final byte[] bytes = baos.toByteArray();
 460         final String dataImg = Base64.encodeBase64String( bytes );
 461         return dataImg;
 462     }
 463
 464     public Options getOptions() {
 465         return _options;
 466     }
 467
 468     @Override
 469     public void init() {
 470         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 471         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 472         final Configuration configuration = new Configuration( config_filename, true, true, true );
 473         setConfiguration( configuration );
 474         setOptions( Options.createInstance( configuration ) );
 475         setupUI();
 476         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 477         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 478             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 479                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 480             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 481                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 482             return;
 483         }
 484         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 485         // Get URL to tree file
 486         URL phys_url = null;
 487         try {
 488             phys_url = new URL( tree_url_str );
 489         }
 490         catch ( final Exception e ) {
 491             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 492             e.printStackTrace();
 493             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 494                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 495         }
 496         if ( phys_url == null ) {
 497             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 498                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 499             JOptionPane.showMessageDialog( this,
 500                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 501                                            "Failed to create URL",
 502                                            JOptionPane.ERROR_MESSAGE );
 503             return;
 504         }
 505         // Load the tree from URL
 506         Phylogeny[] phys = null;
 507         try {
 508             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 509                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 510                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 511                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 512                                                     getConfiguration().getTaxonomyExtraction(),
 513                                                     getConfiguration().isMidpointReroot() );
 514         }
 515         catch ( final Exception e ) {
 516             ForesterUtil.printErrorMessage( NAME, e.toString() );
 517             e.printStackTrace();
 518             JOptionPane.showMessageDialog( this,
 519                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 520                                            "Failed to read phylogenies",
 521                                            JOptionPane.ERROR_MESSAGE );
 522         }
 523         if ( phys == null ) {
 524             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 525             JOptionPane.showMessageDialog( this,
 526                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 527                                            "Failed to read phylogenies",
 528                                            JOptionPane.ERROR_MESSAGE );
 529             return;
 530         }
 531         else if ( phys.length < 1 ) {
 532             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 533             JOptionPane.showMessageDialog( this,
 534                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 535                                            "Failed to read phylogenies",
 536                                            JOptionPane.ERROR_MESSAGE );
 537             return;
 538         }
 539         else {
 540             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 541         }
 542         //
 543         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 544         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 545             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 546             Phylogeny[] species_trees = null;
 547             try {
 548                 final URL species_tree_url = new URL( species_tree_url_str );
 549                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 550                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 551                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 552                                                                  false,
 553                                                                  TAXONOMY_EXTRACTION.NO,
 554                                                                  false );
 555             }
 556             catch ( final IOException e ) {
 557                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 558                         + "]" );
 559                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 560                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 561             }
 562             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 563                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 564                 if ( species_trees[ 0 ].isEmpty() ) {
 565                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 566                 }
 567                 else if ( !species_trees[ 0 ].isRooted() ) {
 568                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 569                 }
 570                 else {
 571                     setSpeciesTree( species_trees[ 0 ] );
 572                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 573                 }
 574             }
 575         }
 576         //
 577         try {
 578             setVisible( false );
 579             setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 580             _jmenubar = new JMenuBar();
 581             if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 582                 if ( !getConfiguration().isUseNativeUI() ) {
 583                     _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 584                 }
 585                 if ( getSpeciesTree() != null ) {
 586                     buildAnalysisMenu();
 587                 }
 588                 buildToolsMenu();
 589                 buildViewMenu();
 590                 buildFontSizeMenu();
 591                 buildOptionsMenu();
 592                 buildTypeMenu();
 593                 buildHelpMenu();
 594                 setJMenuBar( _jmenubar );
 595             }
 596             final Container contentpane = getContentPane();
 597             contentpane.setLayout( new BorderLayout() );
 598             contentpane.add( getMainPanel(), BorderLayout.CENTER );
 599             addComponentListener( new ComponentAdapter() {
 600
 601                 @Override
 602                 public void componentResized( final ComponentEvent e ) {
 603                     if ( getMainPanel().getCurrentTreePanel() != null ) {
 604                         getMainPanel().getCurrentTreePanel()
 605                                 .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
 606                                                             getMainPanel().getCurrentTreePanel().getHeight(),
 607                                                             getOptions().isAllowFontSizeChange() );
 608                     }
 609                 }
 610             } );
 611             if ( getConfiguration().isUseTabbedDisplay() ) {
 612                 try {
 613                     AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 614                     AptxUtil.addPhylogeniesToTabs( phys,
 615                                                    new File( phys_url.getFile() ).getName(),
 616                                                    phys_url.toString(),
 617                                                    getConfiguration(),
 618                                                    getMainPanel() );
 619                 }
 620                 catch ( final Exception e ) {
 621                     ForesterUtil.printErrorMessage( NAME, e.toString() );
 622                     e.printStackTrace();
 623                 }
 624             }
 625             else {
 626                 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 627                 if ( getSpeciesTree() != null ) {
 628                     AptxUtil.printAppletMessage( NAME,
 629                                                  "Warning: gsdi (gene duplication inference) only available tabbed display" );
 630                 }
 631                 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 632             }
 633             validate();
 634             setName( NAME );
 635             getMainPanel().getControlPanel().showWholeAll();
 636             getMainPanel().getControlPanel().showWhole();
 637             /* GUILHEM_BEG */
 638             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 639             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 640                     .getRelevantSequenceRelationTypes() ) {
 641                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 642             }
 643             final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 644             if ( default_relation != null ) {
 645                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 646             }
 647             final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 648             if ( default_sequence != null ) {
 649                 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 650             }
 651             /* GUILHEM_END */
 652             System.gc();
 653             AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 654             setVisible( true );
 655         }
 656         catch ( final Exception e ) {
 657             ForesterUtil.printErrorMessage( NAME, e.toString() );
 658             e.printStackTrace();
 659         }
 660     }
 661
 662     public void showTextFrame( final String s, final String title ) {
 663         checkTextFrames();
 664         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 665     }
 666
 667     @Override
 668     public void start() {
 669         if ( getMainPanel() != null ) {
 670             getMainPanel().validate();
 671         }
 672         requestFocus();
 673         requestFocusInWindow();
 674         requestFocus();
 675         AptxUtil.printAppletMessage( NAME, "started" );
 676     }
 677
 678     void buildAnalysisMenu() {
 679         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 680         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 681         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 682         customizeJMenuItem( _gsdi_item );
 683         customizeJMenuItem( _gsdir_item );
 684         //  _analysis_menu.addSeparator();
 685         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 686         //  customizeJMenuItem( _lineage_inference );
 687         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 688         _jmenubar.add( _analysis_menu );
 689     }
 690
 691     void buildFontSizeMenu() {
 692         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 693         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 694         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 695         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 696         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 697         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 698         customizeJMenuItem( _super_tiny_fonts_mi );
 699         customizeJMenuItem( _tiny_fonts_mi );
 700         customizeJMenuItem( _small_fonts_mi );
 701         customizeJMenuItem( _medium_fonts_mi );
 702         customizeJMenuItem( _large_fonts_mi );
 703         _jmenubar.add( _font_size_menu );
 704     }
 705
 706     void buildHelpMenu() {
 707         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 708         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
 709         _help_jmenu.addSeparator();
 710         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 711         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 712         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 713         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 714         _help_jmenu.addSeparator();
 715         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 716         customizeJMenuItem( _help_item );
 717         customizeJMenuItem( _website_item );
 718         customizeJMenuItem( _phyloxml_website_item );
 719         customizeJMenuItem( _aptx_ref_item );
 720         customizeJMenuItem( _phyloxml_ref_item );
 721         customizeJMenuItem( _about_item );
 722         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 723         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 724         _jmenubar.add( _help_jmenu );
 725     }
 726
 727     void buildOptionsMenu() {
 728         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 729         _options_jmenu.addChangeListener( new ChangeListener() {
 730
 731             @Override
 732             public void stateChanged( final ChangeEvent e ) {
 733                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 734                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 735                 MainFrame
 736                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 737                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 738                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 739                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 740                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 741                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 742                 try {
 743                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
 744                     getMainPanel().getControlPanel().setVisibilityOfX();
 745                 }
 746                 catch ( final Exception ignore ) {
 747                     // do nothing, not important.
 748                 }
 749             }
 750         } );
 751         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 752                                                                 getConfiguration() ) );
 753         _options_jmenu
 754                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 755         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 756         _options_jmenu
 757                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 758         _radio_group_1 = new ButtonGroup();
 759         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 760         _radio_group_1.add( _uniform_cladograms_rbmi );
 761         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 762         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 763         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 764         _options_jmenu
 765                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 766         _options_jmenu
 767                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 768         _options_jmenu
 769                 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 770         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 771         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 772             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 773             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 774         }
 775         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 776         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 777         _options_jmenu
 778                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 779         _options_jmenu
 780                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 781         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 782         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 783         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 784         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 785         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 786         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 787         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 788         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 789         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 790         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 791         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 792         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 793         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 794         _options_jmenu.addSeparator();
 795         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 796                                                                 getConfiguration() ) );
 797         _options_jmenu
 798                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 799         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 800
 801
 802
 803         _options_jmenu
 804         .add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
 805
 806
 807
 808
 809
 810         _options_jmenu
 811                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 812         customizeJMenuItem( _choose_font_mi );
 813         customizeJMenuItem( _choose_minimal_confidence_mi );
 814         customizeJMenuItem( _switch_colors_mi );
 815         customizeJMenuItem( _overview_placment_mi );
 816         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 817         customizeCheckBoxMenuItem( _label_direction_cbmi,
 818                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 819         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 820         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 821         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 822         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 823         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 824         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 825                 .isShowDefaultNodeShapesExternal() );
 826         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 827                 .isShowDefaultNodeShapesInternal() );
 828         customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
 829                 .isShowDefaultNodeShapesForMarkedNodes() );
 830         customizeJMenuItem( _cycle_node_shape_mi );
 831         customizeJMenuItem( _cycle_node_fill_mi );
 832         customizeJMenuItem( _choose_node_size_mi );
 833         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 834         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 835         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 836         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 837                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 838         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 839                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 840         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 841                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 842         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 843
 844
 845         customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
 846
 847
 848
 849         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 850         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 851         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 852         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
 853         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
 854         _jmenubar.add( _options_jmenu );
 855     }
 856
 857     void buildToolsMenu() {
 858         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 859         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 860         customizeJMenuItem( _confcolor_item );
 861         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 862         customizeJMenuItem( _taxcolor_item );
 863         _tools_menu.addSeparator();
 864         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 865         _remove_visual_styles_item
 866                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 867         customizeJMenuItem( _remove_visual_styles_item );
 868         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 869         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 870         customizeJMenuItem( _remove_branch_color_item );
 871         _tools_menu.addSeparator();
 872         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 873         customizeJMenuItem( _midpoint_root_item );
 874         _tools_menu.addSeparator();
 875         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 876         customizeJMenuItem( _collapse_species_specific_subtrees );
 877         _jmenubar.add( _tools_menu );
 878     }
 879
 880     void buildTypeMenu() {
 881         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 882         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 883         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 884         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 885         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 886         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 887         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 888         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 889         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 890         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 891         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 892         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 893         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 894         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 895         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 896         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 897         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 898         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 899         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 900         initializeTypeMenu( getOptions() );
 901         _jmenubar.add( _type_menu );
 902     }
 903
 904     void buildViewMenu() {
 905         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 906         _view_jmenu
 907                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 908         _view_jmenu.addSeparator();
 909         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 910         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 911         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 912         customizeJMenuItem( _display_basic_information_item );
 913         customizeJMenuItem( _view_as_NH_item );
 914         customizeJMenuItem( _view_as_XML_item );
 915         customizeJMenuItem( _view_as_nexus_item );
 916         _jmenubar.add( _view_jmenu );
 917     }
 918
 919     void checkTextFrames() {
 920         if ( _textframes.size() > 5 ) {
 921             try {
 922                 if ( _textframes.getFirst() != null ) {
 923                     _textframes.getFirst().removeMe();
 924                 }
 925                 else {
 926                     _textframes.removeFirst();
 927                 }
 928             }
 929             catch ( final NoSuchElementException e ) {
 930                 // Ignore.
 931             }
 932         }
 933     }
 934
 935     void clearCurrentExternalNodesDataBuffer() {
 936         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 937     }
 938
 939     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 940         if ( item != null ) {
 941             item.setFont( MainFrame.menu_font );
 942             if ( !getConfiguration().isUseNativeUI() ) {
 943                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 944                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 945             }
 946             item.setSelected( is_selected );
 947             item.addActionListener( this );
 948         }
 949     }
 950
 951     void customizeJMenuItem( final JMenuItem jmi ) {
 952         jmi.setFont( MainFrame.menu_font );
 953         if ( !getConfiguration().isUseNativeUI() ) {
 954             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 955             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 956         }
 957         jmi.addActionListener( this );
 958     }
 959
 960     void displayBasicInformation() {
 961         if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
 962                 && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 963             String title = "Basic Information";
 964             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 965                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 966             }
 967             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 968         }
 969     }
 970
 971     void executeGSDI() {
 972         if ( !isOKforSDI( false, true ) ) {
 973             return;
 974         }
 975         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 976             JOptionPane.showMessageDialog( this,
 977                                            "Gene tree is not rooted.",
 978                                            "Cannot execute GSDI",
 979                                            JOptionPane.ERROR_MESSAGE );
 980             return;
 981         }
 982         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 983         gene_tree.setAllNodesToNotCollapse();
 984         gene_tree.recalculateNumberOfExternalDescendants( false );
 985         GSDI gsdi = null;
 986         final Phylogeny species_tree = _species_tree.copy();
 987         try {
 988             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 989         }
 990         catch ( final SDIException e ) {
 991             JOptionPane.showMessageDialog( this,
 992                                            e.getLocalizedMessage(),
 993                                            "Error during GSDI",
 994                                            JOptionPane.ERROR_MESSAGE );
 995             return;
 996         }
 997         catch ( final Exception e ) {
 998             AptxUtil.unexpectedException( e );
 999             return;
1000         }
1001         gene_tree.setRerootable( false );
1002         gene_tree.clearHashIdToNodeMap();
1003         gene_tree.recalculateNumberOfExternalDescendants( true );
1004         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
1005         getMainPanel().getControlPanel().setShowEvents( true );
1006         showWhole();
1007         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1008         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1009         showWhole();
1010         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1011         showWhole();
1012         _mainpanel.getCurrentTreePanel().setEdited( true );
1013         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1014         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1015             JOptionPane.showMessageDialog( this,
1016                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1017                                                    + "Potential duplications: "
1018                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1019                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1020                                                    + "Stripped gene tree nodes: "
1021                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1022                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1023                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1024                                            "GSDI successfully completed",
1025                                            JOptionPane.WARNING_MESSAGE );
1026         }
1027         else {
1028             JOptionPane.showMessageDialog( this,
1029                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1030                                                    + "Potential duplications: "
1031                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1032                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1033                                                    + "Stripped gene tree nodes: "
1034                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1035                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1036                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1037                                            "GSDI successfully completed",
1038                                            JOptionPane.INFORMATION_MESSAGE );
1039         }
1040     }
1041
1042     void executeGSDIR() {
1043         if ( !isOKforSDI( false, false ) ) {
1044             return;
1045         }
1046         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1047         if ( ( p > 0 )
1048                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1049             JOptionPane.showMessageDialog( this,
1050                                            "Gene tree is not completely binary",
1051                                            "Cannot execute GSDI",
1052                                            JOptionPane.ERROR_MESSAGE );
1053             return;
1054         }
1055         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1056         gene_tree.setAllNodesToNotCollapse();
1057         gene_tree.recalculateNumberOfExternalDescendants( false );
1058         GSDIR gsdir = null;
1059         final Phylogeny species_tree = _species_tree.copy();
1060         try {
1061             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1062         }
1063         catch ( final SDIException e ) {
1064             JOptionPane.showMessageDialog( this,
1065                                            e.getLocalizedMessage(),
1066                                            "Error during GSDIR",
1067                                            JOptionPane.ERROR_MESSAGE );
1068             return;
1069         }
1070         catch ( final Exception e ) {
1071             AptxUtil.unexpectedException( e );
1072             return;
1073         }
1074         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1075         result_gene_tree.setRerootable( false );
1076         result_gene_tree.clearHashIdToNodeMap();
1077         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1078         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1079         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1080         getMainPanel().getControlPanel().setShowEvents( true );
1081         showWhole();
1082         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1083         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1084         showWhole();
1085         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1086         showWhole();
1087         _mainpanel.getCurrentTreePanel().setEdited( true );
1088         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1089         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1090             JOptionPane.showMessageDialog( this,
1091                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1092                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1093                                                    + "Stripped gene tree nodes: "
1094                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1095                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1096                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1097                                            "GSDIR successfully completed",
1098                                            JOptionPane.WARNING_MESSAGE );
1099         }
1100         else {
1101             JOptionPane.showMessageDialog( this,
1102                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1103                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1104                                                    + "Stripped gene tree nodes: "
1105                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1106                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1107                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1108                                            "GSDIR successfully completed",
1109                                            JOptionPane.INFORMATION_MESSAGE );
1110         }
1111     }
1112
1113     Configuration getConfiguration() {
1114         return _configuration;
1115     }
1116
1117     TreePanel getCurrentTreePanel() {
1118         return getMainPanel().getCurrentTreePanel();
1119     }
1120
1121     JCheckBoxMenuItem getlabelDirectionCbmi() {
1122         return _label_direction_cbmi;
1123     }
1124
1125     Options getOtions() {
1126         return _options;
1127     }
1128
1129     void initializeTypeMenu( final Options options ) {
1130         setTypeMenuToAllUnselected();
1131         try {
1132             switch ( options.getPhylogenyGraphicsType() ) {
1133                 case CONVEX:
1134                     _convex_type_cbmi.setSelected( true );
1135                     break;
1136                 case CURVED:
1137                     _curved_type_cbmi.setSelected( true );
1138                     break;
1139                 case EURO_STYLE:
1140                     _euro_type_cbmi.setSelected( true );
1141                     break;
1142                 case ROUNDED:
1143                     _rounded_type_cbmi.setSelected( true );
1144                     break;
1145                 case TRIANGULAR:
1146                     _triangular_type_cbmi.setSelected( true );
1147                     break;
1148                 case UNROOTED:
1149                     _unrooted_type_cbmi.setSelected( true );
1150                     break;
1151                 case CIRCULAR:
1152                     _circular_type_cbmi.setSelected( true );
1153                     break;
1154                 default:
1155                     _rectangular_type_cbmi.setSelected( true );
1156                     break;
1157             }
1158         }
1159         catch ( final NullPointerException np ) {
1160             // In all likelihood, this is caused by menu-less display.
1161         }
1162     }
1163
1164     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1165         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1166             return false;
1167         }
1168         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1169             JOptionPane.showMessageDialog( this,
1170                                            "No species tree loaded",
1171                                            "Cannot execute GSDI",
1172                                            JOptionPane.ERROR_MESSAGE );
1173             return false;
1174         }
1175         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1176             JOptionPane.showMessageDialog( this,
1177                                            "Species tree is not completely binary",
1178                                            "Cannot execute GSDI",
1179                                            JOptionPane.ERROR_MESSAGE );
1180             return false;
1181         }
1182         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1183             JOptionPane.showMessageDialog( this,
1184                                            "Gene tree is not completely binary",
1185                                            "Cannot execute GSDI",
1186                                            JOptionPane.ERROR_MESSAGE );
1187             return false;
1188         }
1189         else {
1190             return true;
1191         }
1192     }
1193
1194     boolean isSubtreeDisplayed() {
1195         if ( getCurrentTreePanel() != null ) {
1196             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1197                 JOptionPane
1198                         .showMessageDialog( this,
1199                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1200                                             "Operation can not be exectuted on a sub-tree",
1201                                             JOptionPane.WARNING_MESSAGE );
1202                 return true;
1203             }
1204         }
1205         return false;
1206     }
1207
1208     void removeAllTextFrames() {
1209         for( final TextFrame tf : _textframes ) {
1210             if ( tf != null ) {
1211                 tf.close();
1212             }
1213         }
1214         _textframes.clear();
1215     }
1216
1217     void setConfiguration( final Configuration configuration ) {
1218         _configuration = configuration;
1219     }
1220
1221     void setOptions( final Options options ) {
1222         _options = options;
1223     }
1224
1225     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1226         setTypeMenuToAllUnselected();
1227         try {
1228             switch ( type ) {
1229                 case CIRCULAR:
1230                     _circular_type_cbmi.setSelected( true );
1231                     break;
1232                 case CONVEX:
1233                     _convex_type_cbmi.setSelected( true );
1234                     break;
1235                 case CURVED:
1236                     _curved_type_cbmi.setSelected( true );
1237                     break;
1238                 case EURO_STYLE:
1239                     _euro_type_cbmi.setSelected( true );
1240                     break;
1241                 case ROUNDED:
1242                     _rounded_type_cbmi.setSelected( true );
1243                     break;
1244                 case RECTANGULAR:
1245                     _rectangular_type_cbmi.setSelected( true );
1246                     break;
1247                 case TRIANGULAR:
1248                     _triangular_type_cbmi.setSelected( true );
1249                     break;
1250                 case UNROOTED:
1251                     _unrooted_type_cbmi.setSelected( true );
1252                     break;
1253                 default:
1254                     throw new IllegalArgumentException( "unknown type: " + type );
1255             }
1256         }
1257         catch ( final NullPointerException np ) {
1258             // In all likelihood, this is caused by menu-less display.
1259         }
1260     }
1261
1262     void setTypeMenuToAllUnselected() {
1263         if ( _convex_type_cbmi != null ) {
1264             _convex_type_cbmi.setSelected( false );
1265         }
1266         if ( _curved_type_cbmi != null ) {
1267             _curved_type_cbmi.setSelected( false );
1268         }
1269         if ( _euro_type_cbmi != null ) {
1270             _euro_type_cbmi.setSelected( false );
1271         }
1272         if ( _rounded_type_cbmi != null ) {
1273             _rounded_type_cbmi.setSelected( false );
1274         }
1275         if ( _triangular_type_cbmi != null ) {
1276             _triangular_type_cbmi.setSelected( false );
1277         }
1278         if ( _rectangular_type_cbmi != null ) {
1279             _rectangular_type_cbmi.setSelected( false );
1280         }
1281         if ( _unrooted_type_cbmi != null ) {
1282             _unrooted_type_cbmi.setSelected( false );
1283         }
1284         if ( _circular_type_cbmi != null ) {
1285             _circular_type_cbmi.setSelected( false );
1286         }
1287     }
1288
1289     void showWhole() {
1290         _mainpanel.getControlPanel().showWhole();
1291     }
1292
1293     void switchColors() {
1294         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1295         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1296         csc.setVisible( true );
1297         getMainPanel().setTreeColorSet( colorset );
1298     }
1299
1300     void typeChanged( final Object o ) {
1301         updateTypeCheckboxes( getOptions(), o );
1302         updateOptions( getOptions() );
1303         if ( getCurrentTreePanel() != null ) {
1304             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1305             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1306             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1307                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1308                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1309                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1310                 getCurrentTreePanel().getControlPanel().showWhole();
1311             }
1312             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1313                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1314             }
1315             else {
1316                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1317             }
1318             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1319             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1320         }
1321     }
1322
1323     void updateOptions( final Options options ) {
1324         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1325         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1326                 && _background_gradient_cbmi.isSelected() );
1327         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1328         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1329                 && _show_annotation_ref_source.isSelected() );
1330         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1331                 && _abbreviate_scientific_names.isSelected() );
1332         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1333                 && _color_labels_same_as_parent_branch.isSelected() );
1334         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1335                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1336         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1337                 && _show_default_node_shapes_external_cbmi.isSelected() );
1338         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1339                 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1340         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1341             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1342         }
1343         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1344             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1345         }
1346         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1347             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1348         }
1349         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1350                 && _search_case_senstive_cbmi.isSelected() );
1351         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1352             options.setShowScale( _show_scale_cbmi.isSelected() );
1353         }
1354         if ( _label_direction_cbmi != null ) {
1355             if ( _label_direction_cbmi.isSelected() ) {
1356                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1357             }
1358             else {
1359                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1360             }
1361         }
1362         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1363         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1364                 && _show_confidence_stddev_cbmi.isSelected() );
1365         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1366                 && _search_whole_words_only_cbmi.isSelected() );
1367         options.setSearchWithRegex( ( _search_with_regex_cbmi != null )
1368                                         && _search_with_regex_cbmi.isSelected() );
1369
1370         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1371                 && _inverse_search_result_cbmi.isSelected() );
1372         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1373             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1374         }
1375         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1376             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1377         }
1378         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1379             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1380         }
1381         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1382             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1383         }
1384         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1385             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1386         }
1387         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1388             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1389         }
1390         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1391             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1392         }
1393         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1394             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1395         }
1396         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1397             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1398         }
1399         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1400             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1401         }
1402         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1403             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1404         }
1405     }
1406
1407     void updateTypeCheckboxes( final Options options, final Object o ) {
1408         setTypeMenuToAllUnselected();
1409         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1410     }
1411
1412     void viewAsNexus() {
1413         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1414             String title = "Nexus";
1415             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1416                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1417             }
1418             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1419                                    .getNhConversionSupportValueStyle() ),
1420                            title );
1421         }
1422     }
1423
1424     void viewAsNH() {
1425         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1426             String title = "New Hampshire";
1427             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1428                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1429             }
1430             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1431                                    .getNhConversionSupportValueStyle() ),
1432                            title );
1433         }
1434     }
1435
1436     void viewAsXML() {
1437         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1438             String title = "phyloXML";
1439             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1440                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1441             }
1442             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1443         }
1444     }
1445
1446     private void chooseFont() {
1447         final FontChooser fc = new FontChooser();
1448         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1449         fc.showDialog( this, "Select the Base Font" );
1450         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1451     }
1452
1453     private void chooseMinimalConfidence() {
1454         final String s = ( String ) JOptionPane
1455                 .showInputDialog( this,
1456                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1457                                           + getOptions().getMinConfidenceValue() + "]\n",
1458                                   "Minimal Confidence Value",
1459                                   JOptionPane.QUESTION_MESSAGE,
1460                                   null,
1461                                   null,
1462                                   getOptions().getMinConfidenceValue() );
1463         if ( !ForesterUtil.isEmpty( s ) ) {
1464             boolean success = true;
1465             double m = 0.0;
1466             final String m_str = s.trim();
1467             if ( !ForesterUtil.isEmpty( m_str ) ) {
1468                 try {
1469                     m = Double.parseDouble( m_str );
1470                 }
1471                 catch ( final Exception ex ) {
1472                     success = false;
1473                 }
1474             }
1475             else {
1476                 success = false;
1477             }
1478             if ( success && ( m >= 0.0 ) ) {
1479                 getOptions().setMinConfidenceValue( m );
1480             }
1481         }
1482     }
1483
1484     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1485         if ( item != null ) {
1486             item.setFont( MainFrame.menu_font );
1487             if ( !getConfiguration().isUseNativeUI() ) {
1488                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1489                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1490             }
1491             item.setSelected( is_selected );
1492             item.addActionListener( this );
1493         }
1494     }
1495
1496     MainPanel getMainPanel() {
1497         return _mainpanel;
1498     }
1499
1500     private Phylogeny getSpeciesTree() {
1501         return _species_tree;
1502     }
1503
1504     private boolean isScreenAntialias() {
1505         return true;
1506     }
1507
1508     private void removeBranchColors() {
1509         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1510             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1511         }
1512     }
1513
1514     private void removeVisualStyles() {
1515         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1516             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1517         }
1518     }
1519
1520     private void setMainPanel( final MainPanelApplets main_panel ) {
1521         _mainpanel = main_panel;
1522     }
1523
1524     private void setSpeciesTree( final Phylogeny species_tree ) {
1525         _species_tree = species_tree;
1526     }
1527
1528     private void setupUI() {
1529         try {
1530             if ( getConfiguration().isUseNativeUI() ) {
1531                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1532             }
1533             else {
1534                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1535             }
1536         }
1537         catch ( final UnsupportedLookAndFeelException e ) {
1538             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1539         }
1540         catch ( final ClassNotFoundException e ) {
1541             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1542         }
1543         catch ( final InstantiationException e ) {
1544             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1545         }
1546         catch ( final IllegalAccessException e ) {
1547             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1548         }
1549         catch ( final Exception e ) {
1550             AptxUtil.dieWithSystemError( e.toString() );
1551         }
1552     }
1553
1554     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1555         for( final TreePanel tree_panel : treepanels ) {
1556             tree_panel.setTextAntialias();
1557         }
1558     }
1559 }