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