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.JFileChooser;
  22 import javax.swing.JMenu;
  23 import javax.swing.JMenuBar;
  24 import javax.swing.JMenuItem;
  25 import javax.swing.JOptionPane;
  26 import javax.swing.JRadioButtonMenuItem;
  27 import javax.swing.UIManager;
  28 import javax.swing.UnsupportedLookAndFeelException;
  29 import javax.swing.event.ChangeEvent;
  30 import javax.swing.event.ChangeListener;
  31
  32 import org.apache.commons.codec.binary.Base64;
  33 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  34 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  35 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  36 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  37 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  38 import org.forester.phylogeny.Phylogeny;
  39 import org.forester.phylogeny.PhylogenyMethods;
  40 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  41 import org.forester.phylogeny.data.SequenceRelation;
  42 import org.forester.sdi.GSDI;
  43 import org.forester.sdi.GSDIR;
  44 import org.forester.sdi.SDIException;
  45 import org.forester.util.ForesterConstants;
  46 import org.forester.util.ForesterUtil;
  47 import org.forester.util.WindowsUtils;
  48
  49 // Use like this:
  50 // <applet archive="forester.jar"
  51 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  52 // codebase="http://www.myserver.org/path/to/forester"
  53 // width="600"
  54 // height="500"
  55 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  56 // <param name="url_of_tree_to_load"
  57 // value="http://www.myserver.org/examples/data/apaf.xml">
  58 // <param name="config_file"
  59 // value="http://www.myserver.org/examples/config/config_file.txt">
  60 // </applet>
  61 public class ArchaeopteryxE extends JApplet implements ActionListener {
  62
  63     private final static String         NAME             = "ArchaeopteryxE";
  64     private static final long           serialVersionUID = -1220055577935759443L;
  65     private Configuration               _configuration;
  66     private MainPanel                   _mainpanel;
  67     private JMenuBar                    _jmenubar;
  68     private JMenu                       _options_jmenu;
  69     private JMenu                       _font_size_menu;
  70     private JMenuItem                   _super_tiny_fonts_mi;
  71     private JMenuItem                   _tiny_fonts_mi;
  72     private JMenuItem                   _small_fonts_mi;
  73     private JMenuItem                   _medium_fonts_mi;
  74     private JMenuItem                   _large_fonts_mi;
  75     private JMenu                       _tools_menu;
  76     private JMenuItem                   _taxcolor_item;
  77     private JMenuItem                   _confcolor_item;
  78     private JMenuItem                   _midpoint_root_item;
  79     private JMenu                       _view_jmenu;
  80     private JMenuItem                   _view_as_XML_item;
  81     private JMenuItem                   _view_as_NH_item;
  82     private JMenuItem                   _view_as_nexus_item;
  83     private JMenuItem                   _display_basic_information_item;
  84     private JMenu                       _type_menu;
  85     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  86     private JCheckBoxMenuItem           _triangular_type_cbmi;
  87     private JCheckBoxMenuItem           _curved_type_cbmi;
  88     private JCheckBoxMenuItem           _convex_type_cbmi;
  89     private JCheckBoxMenuItem           _euro_type_cbmi;
  90     private JCheckBoxMenuItem           _rounded_type_cbmi;
  91     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  92     private JCheckBoxMenuItem           _circular_type_cbmi;
  93     private JMenuItem                   _help_item;
  94     private JMenuItem                   _about_item;
  95     private JMenu                       _help_jmenu;
  96     private JMenuItem                   _website_item;
  97     private JMenuItem                   _phyloxml_website_item;
  98     private JMenuItem                   _phyloxml_ref_item;
  99     private JMenuItem                   _aptx_ref_item;
 100     private JMenuItem                   _remove_branch_color_item;
 101     private JMenuItem                   _remove_visual_styles_item;
 102     private JCheckBoxMenuItem           _show_domain_labels;
 103     private JCheckBoxMenuItem           _show_annotation_ref_source;
 104     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 105     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 106     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 107     private JCheckBoxMenuItem           _background_gradient_cbmi;
 108     private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 109     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 110     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 111     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 112     private Options                     _options;
 113     private JMenuItem                   _choose_font_mi;
 114     private JMenuItem                   _switch_colors_mi;
 115     JCheckBoxMenuItem                   _label_direction_cbmi;
 116     private JCheckBoxMenuItem           _show_scale_cbmi;
 117     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 118     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 119     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 120     private JCheckBoxMenuItem           _search_with_regex_cbmi;
 121     private JCheckBoxMenuItem           _show_overview_cbmi;
 122     private JMenuItem                   _choose_minimal_confidence_mi;
 123     private JMenuItem                   _collapse_species_specific_subtrees;
 124     private JMenuItem                   _overview_placment_mi;
 125     private ButtonGroup                 _radio_group_1;
 126     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 127     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 128     private JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;
 129     private JMenuItem                   _cycle_node_shape_mi;
 130     private JMenuItem                   _cycle_node_fill_mi;
 131     private JMenuItem                   _choose_node_size_mi;
 132     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 133     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 134     private JMenu                       _analysis_menu;
 135     private JMenuItem                   _gsdi_item;
 136     private JMenuItem                   _gsdir_item;
 137     private Phylogeny                   _species_tree;
 138     private JCheckBoxMenuItem           _right_line_up_domains_cbmi;
 139     private JCheckBoxMenuItem           _line_up_renderable_data_cbmi;
 140     // file menu:
 141     private JMenuItem                   _save_item;
 142     private JMenuItem                   _print_item;
 143     private JMenuItem                   _write_to_pdf_item;
 144     private JMenuItem                   _write_to_jpg_item;
 145     private JMenuItem                   _write_to_gif_item;
 146     private JMenuItem                   _write_to_tif_item;
 147     private JMenuItem                   _write_to_png_item;
 148     private JMenuItem                   _write_to_bmp_item;
 149     private JMenu                       _file_jmenu;
 150     private JFileChooser                _writetopdf_filechooser;
 151     private File                        _current_dir;
 152     private JFileChooser                _save_filechooser;
 153     private JFileChooser                _writetographics_filechooser;
 154     private JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
 155     private JCheckBoxMenuItem           _antialias_print_cbmi;
 156     private JCheckBoxMenuItem           _print_black_and_white_cbmi;
 157     private JCheckBoxMenuItem           _print_using_actual_size_cbmi;
 158     private JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
 159     private JMenuItem                   _print_size_mi;
 160     private JMenuItem                   _choose_pdf_width_mi;
 161
 162     @Override
 163     public void actionPerformed( final ActionEvent e ) {
 164         final Object o = e.getSource();
 165         if ( o == _midpoint_root_item ) {
 166             getMainPanel().getCurrentTreePanel().midpointRoot();
 167         }
 168         else if ( o == _gsdi_item ) {
 169             if ( isSubtreeDisplayed() ) {
 170                 return;
 171             }
 172             executeGSDI();
 173         }
 174         else if ( o == _gsdir_item ) {
 175             if ( isSubtreeDisplayed() ) {
 176                 return;
 177             }
 178             executeGSDIR();
 179         }
 180         else if ( o == _taxcolor_item ) {
 181             getMainPanel().getCurrentTreePanel().taxColor();
 182         }
 183         else if ( o == _confcolor_item ) {
 184             getMainPanel().getCurrentTreePanel().confColor();
 185         }
 186         else if ( o == _collapse_species_specific_subtrees ) {
 187             if ( getCurrentTreePanel() != null ) {
 188                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 189             }
 190         }
 191         else if ( o == _remove_branch_color_item ) {
 192             removeBranchColors();
 193         }
 194         else if ( o == _remove_visual_styles_item ) {
 195             removeVisualStyles();
 196         }
 197         else if ( o == _switch_colors_mi ) {
 198             switchColors();
 199         }
 200         else if ( o == _display_basic_information_item ) {
 201             displayBasicInformation();
 202         }
 203         else if ( o == _view_as_NH_item ) {
 204             viewAsNH();
 205         }
 206         else if ( o == _view_as_XML_item ) {
 207             viewAsXML();
 208         }
 209         else if ( o == _view_as_nexus_item ) {
 210             viewAsNexus();
 211         }
 212         else if ( o == _super_tiny_fonts_mi ) {
 213             if ( getCurrentTreePanel() != null ) {
 214                 getCurrentTreePanel().setSuperTinyFonts();
 215                 getCurrentTreePanel().repaint();
 216             }
 217         }
 218         else if ( o == _tiny_fonts_mi ) {
 219             if ( getCurrentTreePanel() != null ) {
 220                 getCurrentTreePanel().setTinyFonts();
 221                 getCurrentTreePanel().repaint();
 222             }
 223         }
 224         else if ( o == _small_fonts_mi ) {
 225             if ( getCurrentTreePanel() != null ) {
 226                 getCurrentTreePanel().setSmallFonts();
 227                 getCurrentTreePanel().repaint();
 228             }
 229         }
 230         else if ( o == _medium_fonts_mi ) {
 231             if ( getCurrentTreePanel() != null ) {
 232                 getCurrentTreePanel().setMediumFonts();
 233                 getCurrentTreePanel().repaint();
 234             }
 235         }
 236         else if ( o == _large_fonts_mi ) {
 237             if ( getCurrentTreePanel() != null ) {
 238                 getCurrentTreePanel().setLargeFonts();
 239                 getCurrentTreePanel().repaint();
 240             }
 241         }
 242         else if ( o == _choose_font_mi ) {
 243             chooseFont();
 244         }
 245         else if ( o == _choose_minimal_confidence_mi ) {
 246             chooseMinimalConfidence();
 247         }
 248         else if ( o == _choose_node_size_mi ) {
 249             MainFrame.chooseNodeSize( getOptions(), this );
 250         }
 251         else if ( o == _overview_placment_mi ) {
 252             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 253         }
 254         else if ( o == _cycle_node_fill_mi ) {
 255             MainFrame.cycleNodeFill( getOptions() );
 256         }
 257         else if ( o == _cycle_node_shape_mi ) {
 258             MainFrame.cycleNodeShape( getOptions() );
 259         }
 260         else if ( o == _non_lined_up_cladograms_rbmi ) {
 261             updateOptions( getOptions() );
 262             _mainpanel.getControlPanel().showWhole();
 263         }
 264         else if ( o == _uniform_cladograms_rbmi ) {
 265             updateOptions( getOptions() );
 266             _mainpanel.getControlPanel().showWhole();
 267         }
 268         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 269             updateOptions( getOptions() );
 270             _mainpanel.getControlPanel().showWhole();
 271         }
 272         else if ( o == _search_case_senstive_cbmi ) {
 273             updateOptions( getOptions() );
 274             getMainPanel().getControlPanel().search0();
 275             getMainPanel().getControlPanel().search1();
 276         }
 277         else if ( o == _search_whole_words_only_cbmi ) {
 278             if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
 279                 _search_with_regex_cbmi.setSelected( false );
 280             }
 281             updateOptions( getOptions() );
 282             getMainPanel().getControlPanel().search0();
 283             getMainPanel().getControlPanel().search1();
 284         }
 285         else if ( o == _inverse_search_result_cbmi ) {
 286             updateOptions( getOptions() );
 287             getMainPanel().getControlPanel().search0();
 288             getMainPanel().getControlPanel().search1();
 289         }
 290         else if ( o == _search_with_regex_cbmi ) {
 291             if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
 292                 _search_whole_words_only_cbmi.setSelected( false );
 293             }
 294             if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
 295                 _search_case_senstive_cbmi.setSelected( true );
 296             }
 297             updateOptions( getOptions() );
 298             getMainPanel().getControlPanel().search0();
 299             getMainPanel().getControlPanel().search1();
 300         }
 301         else if ( o == _show_scale_cbmi ) {
 302             updateOptions( getOptions() );
 303         }
 304         else if ( o == _show_confidence_stddev_cbmi ) {
 305             updateOptions( getOptions() );
 306         }
 307         else if ( o == _label_direction_cbmi ) {
 308             updateOptions( getOptions() );
 309         }
 310         else if ( o == _abbreviate_scientific_names ) {
 311             updateOptions( getOptions() );
 312         }
 313         else if ( o == _show_overview_cbmi ) {
 314             updateOptions( getOptions() );
 315             if ( getCurrentTreePanel() != null ) {
 316                 getCurrentTreePanel().updateOvSizes();
 317             }
 318         }
 319         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 320                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 321                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 322             typeChanged( o );
 323         }
 324         else if ( o == _screen_antialias_cbmi ) {
 325             updateOptions( getOptions() );
 326             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 327         }
 328         else if ( o == _background_gradient_cbmi ) {
 329             updateOptions( getOptions() );
 330         }
 331         else if ( o == _show_domain_labels ) {
 332             updateOptions( getOptions() );
 333         }
 334         else if ( o == _color_labels_same_as_parent_branch ) {
 335             updateOptions( getOptions() );
 336         }
 337         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 338             updateOptions( getOptions() );
 339         }
 340         else if ( o == _show_default_node_shapes_external_cbmi ) {
 341             updateOptions( getOptions() );
 342         }
 343         else if ( o == _about_item ) {
 344             MainFrame.about();
 345         }
 346         else if ( o == _help_item ) {
 347             try {
 348                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
 349             }
 350             catch ( final IOException e1 ) {
 351                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 352             }
 353         }
 354         else if ( o == _website_item ) {
 355             try {
 356                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 357             }
 358             catch ( final IOException e1 ) {
 359                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 360             }
 361         }
 362         else if ( o == _phyloxml_website_item ) {
 363             try {
 364                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 365             }
 366             catch ( final IOException e1 ) {
 367                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 368             }
 369         }
 370         else if ( o == _aptx_ref_item ) {
 371             try {
 372                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 373             }
 374             catch ( final IOException e1 ) {
 375                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 376             }
 377         }
 378         else if ( o == _phyloxml_ref_item ) {
 379             try {
 380                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 381             }
 382             catch ( final IOException e1 ) {
 383                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 384             }
 385         }
 386         else if ( o == _color_by_taxonomic_group_cbmi ) {
 387             updateOptions( getOptions() );
 388         }
 389         else if ( o == _line_up_renderable_data_cbmi ) {
 390             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
 391                 _right_line_up_domains_cbmi.setSelected( false );
 392             }
 393             updateOptions( getOptions() );
 394         }
 395         else if ( o == _right_line_up_domains_cbmi ) {
 396             if ( _right_line_up_domains_cbmi.isSelected() ) {
 397                 _line_up_renderable_data_cbmi.setSelected( true );
 398             }
 399             updateOptions( getOptions() );
 400         }
 401         else if ( o == _write_to_pdf_item ) {
 402             final File curr_dir = MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(),
 403                                                         getMainPanel(),
 404                                                         _writetopdf_filechooser,
 405                                                         _current_dir,
 406                                                         getContentPane(),
 407                                                         this );
 408             if ( curr_dir != null ) {
 409                 setCurrentDir( curr_dir );
 410             }
 411         }
 412         else if ( o == _write_to_jpg_item ) {
 413             final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
 414                                                                  GraphicsExportType.JPG,
 415                                                                  _mainpanel,
 416                                                                  _writetographics_filechooser,
 417                                                                  this,
 418                                                                  getContentPane(),
 419                                                                  _current_dir );
 420             if ( curr_dir != null ) {
 421                 setCurrentDir( curr_dir );
 422             }
 423         }
 424         else if ( o == _write_to_gif_item ) {
 425             final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
 426                                                                  GraphicsExportType.GIF,
 427                                                                  _mainpanel,
 428                                                                  _writetographics_filechooser,
 429                                                                  this,
 430                                                                  getContentPane(),
 431                                                                  _current_dir );
 432             if ( curr_dir != null ) {
 433                 setCurrentDir( curr_dir );
 434             }
 435         }
 436         else if ( o == _write_to_tif_item ) {
 437             final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
 438                                                                  GraphicsExportType.TIFF,
 439                                                                  _mainpanel,
 440                                                                  _writetographics_filechooser,
 441                                                                  this,
 442                                                                  getContentPane(),
 443                                                                  _current_dir );
 444             if ( curr_dir != null ) {
 445                 setCurrentDir( curr_dir );
 446             }
 447         }
 448         else if ( o == _write_to_bmp_item ) {
 449             final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
 450                                                                  GraphicsExportType.BMP,
 451                                                                  _mainpanel,
 452                                                                  _writetographics_filechooser,
 453                                                                  this,
 454                                                                  getContentPane(),
 455                                                                  _current_dir );
 456             if ( curr_dir != null ) {
 457                 setCurrentDir( curr_dir );
 458             }
 459         }
 460         else if ( o == _write_to_png_item ) {
 461             final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
 462                                                                  GraphicsExportType.PNG,
 463                                                                  _mainpanel,
 464                                                                  _writetographics_filechooser,
 465                                                                  this,
 466                                                                  getContentPane(),
 467                                                                  _current_dir );
 468             if ( curr_dir != null ) {
 469                 setCurrentDir( curr_dir );
 470             }
 471         }
 472         else if ( o == _print_item ) {
 473             MainFrame.print( getCurrentTreePanel(), getOptions(), this );
 474         }
 475         else if ( o == _save_item ) {
 476             final File new_dir = MainFrame.writeToFile( _mainpanel.getCurrentPhylogeny(),
 477                                                         getMainPanel(),
 478                                                         _save_filechooser,
 479                                                         _current_dir,
 480                                                         getContentPane(),
 481                                                         this );
 482             if ( new_dir != null ) {
 483                 setCurrentDir( new_dir );
 484             }
 485         }
 486         else if ( o == _graphics_export_visible_only_cbmi ) {
 487             updateOptions( getOptions() );
 488         }
 489         else if ( o == _antialias_print_cbmi ) {
 490             updateOptions( getOptions() );
 491         }
 492         else if ( o == _print_black_and_white_cbmi ) {
 493             updateOptions( getOptions() );
 494         }
 495         else if ( o == _print_using_actual_size_cbmi ) {
 496             updateOptions( getOptions() );
 497         }
 498         else if ( o == _graphics_export_using_actual_size_cbmi ) {
 499             updateOptions( getOptions() );
 500         }
 501         else if ( o == _print_size_mi ) {
 502             choosePrintSize();
 503         }
 504         else if ( o == _choose_pdf_width_mi ) {
 505             choosePdfWidth();
 506         }
 507         repaint();
 508     }
 509
 510     @Override
 511     public void destroy() {
 512         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 513         removeAllTextFrames();
 514         if ( getMainPanel() != null ) {
 515             getMainPanel().terminate();
 516         }
 517     }
 518
 519     /**
 520      * This method returns the current external node data which
 521      * has been selected by the user by clicking the "Return ..."
 522      * menu item. This method is expected to be called from Javascript or
 523      * something like it.
 524      *
 525      * @return current external node data as String
 526      */
 527     public String getCurrentExternalNodesDataBuffer() {
 528         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 529     }
 530
 531     public int getCurrentExternalNodesDataBufferChangeCounter() {
 532         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 533     }
 534
 535     public int getCurrentExternalNodesDataBufferLength() {
 536         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 537     }
 538
 539     /**
 540      * This method returns the current phylogeny as a string in the chosen format
 541      *
 542      * @param format must be NH, NHX, NEXUS or PHYLOXML
 543      * @return the phylogeny string
 544      * @author Herve Menager
 545      */
 546     public String getCurrentPhylogeny( final String format ) {
 547         removeAllTextFrames();
 548         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 549                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 550             return new String();
 551         }
 552         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 553             case NH:
 554                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 555             case NHX:
 556                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 557             case NEXUS:
 558                 return getMainPanel().getCurrentPhylogeny().toNexus();
 559             case PHYLOXML:
 560                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 561             default:
 562                 break;
 563         }
 564         return new String();
 565     }
 566
 567     /**
 568      * This method returns a view of the current phylogeny in a chosen
 569      * graphics format, base64-encoded in a string so that in can be used
 570      * from javascript.
 571      *
 572      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 573      * @return the phylogeny string
 574      * @author Herve Menager
 575      */
 576     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 577         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 578         try {
 579             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 580                                                                     _mainpanel.getWidth(),
 581                                                                     _mainpanel.getHeight(),
 582                                                                     getCurrentTreePanel(),
 583                                                                     getCurrentTreePanel().getControlPanel(),
 584                                                                     GraphicsExportType.valueOf( format ),
 585                                                                     getOptions() );
 586         }
 587         catch ( final IOException ioe ) {
 588             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 589             ioe.printStackTrace();
 590             JOptionPane.showMessageDialog( this,
 591                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 592                                            "Failed to generate graphics",
 593                                            JOptionPane.ERROR_MESSAGE );
 594             return null;
 595         }
 596         final byte[] bytes = baos.toByteArray();
 597         final String dataImg = Base64.encodeBase64String( bytes );
 598         return dataImg;
 599     }
 600
 601     public Options getOptions() {
 602         return _options;
 603     }
 604
 605     @Override
 606     public void init() {
 607         _writetopdf_filechooser = new JFileChooser();
 608         _writetopdf_filechooser.setMultiSelectionEnabled( false );
 609         _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter );
 610         _writetographics_filechooser = new JFileChooser();
 611         _writetographics_filechooser.setMultiSelectionEnabled( false );
 612         _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );
 613         _save_filechooser = new JFileChooser();
 614         _save_filechooser.setMultiSelectionEnabled( false );
 615         _save_filechooser.setFileFilter( MainFrame.xmlfilter );
 616         _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
 617         _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
 618         _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
 619         try {
 620             final String home_dir = System.getProperty( "user.home" );
 621             _save_filechooser.setCurrentDirectory( new File( home_dir ) );
 622             _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
 623             _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
 624         }
 625         catch ( final Exception e ) {
 626             e.printStackTrace();
 627             // Do nothing. Not important.
 628         }
 629         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 630         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 631         final Configuration configuration = new Configuration( config_filename, true, true, true );
 632         setConfiguration( configuration );
 633         setOptions( Options.createInstance( configuration ) );
 634         setupUI();
 635         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 636         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 637             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 638                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 639             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 640                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 641             return;
 642         }
 643         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 644         // Get URL to tree file
 645         URL phys_url = null;
 646         try {
 647             phys_url = new URL( tree_url_str );
 648         }
 649         catch ( final Exception e ) {
 650             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 651             e.printStackTrace();
 652             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 653                                            + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 654         }
 655         if ( phys_url == null ) {
 656             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 657                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 658             JOptionPane.showMessageDialog( this,
 659                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 660                                            "Failed to create URL",
 661                                            JOptionPane.ERROR_MESSAGE );
 662             return;
 663         }
 664         // Load the tree from URL
 665         Phylogeny[] phys = null;
 666         try {
 667             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 668                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 669                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 670                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 671                                                     getConfiguration().getTaxonomyExtraction(),
 672                                                     getConfiguration().isMidpointReroot() );
 673         }
 674         catch ( final Exception e ) {
 675             ForesterUtil.printErrorMessage( NAME, e.toString() );
 676             e.printStackTrace();
 677             JOptionPane.showMessageDialog( this,
 678                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 679                                            "Failed to read phylogenies",
 680                                            JOptionPane.ERROR_MESSAGE );
 681         }
 682         if ( phys == null ) {
 683             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 684             JOptionPane.showMessageDialog( this,
 685                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 686                                            "Failed to read phylogenies",
 687                                            JOptionPane.ERROR_MESSAGE );
 688             return;
 689         }
 690         else if ( phys.length < 1 ) {
 691             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 692             JOptionPane.showMessageDialog( this,
 693                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 694                                            "Failed to read phylogenies",
 695                                            JOptionPane.ERROR_MESSAGE );
 696             return;
 697         }
 698         else {
 699             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 700         }
 701         //
 702         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 703         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 704             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 705             Phylogeny[] species_trees = null;
 706             try {
 707                 final URL species_tree_url = new URL( species_tree_url_str );
 708                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 709                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 710                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 711                                                                  false,
 712                                                                  TAXONOMY_EXTRACTION.NO,
 713                                                                  false );
 714             }
 715             catch ( final IOException e ) {
 716                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 717                                                 + "]" );
 718                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 719                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 720             }
 721             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 722                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 723                 if ( species_trees[ 0 ].isEmpty() ) {
 724                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 725                 }
 726                 else if ( !species_trees[ 0 ].isRooted() ) {
 727                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 728                 }
 729                 else {
 730                     setSpeciesTree( species_trees[ 0 ] );
 731                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 732                 }
 733             }
 734         }
 735         //
 736         try {
 737             setVisible( false );
 738             setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 739             _jmenubar = new JMenuBar();
 740             if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 741                 buildFileMenu();
 742                 if ( !getConfiguration().isUseNativeUI() ) {
 743                     _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 744                 }
 745                 if ( getSpeciesTree() != null ) {
 746                     buildAnalysisMenu();
 747                 }
 748                 buildToolsMenu();
 749                 buildViewMenu();
 750                 buildFontSizeMenu();
 751                 buildOptionsMenu();
 752                 buildTypeMenu();
 753                 buildHelpMenu();
 754                 setJMenuBar( _jmenubar );
 755             }
 756             final Container contentpane = getContentPane();
 757             contentpane.setLayout( new BorderLayout() );
 758             contentpane.add( getMainPanel(), BorderLayout.CENTER );
 759             addComponentListener( new ComponentAdapter() {
 760
 761                 @Override
 762                 public void componentResized( final ComponentEvent e ) {
 763                     if ( getMainPanel().getCurrentTreePanel() != null ) {
 764                         getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 765                                                                                         .getCurrentTreePanel()
 766                                                                                         .getWidth(),
 767                                                                                         getMainPanel()
 768                                                                                         .getCurrentTreePanel()
 769                                                                                         .getHeight() );
 770                     }
 771                 }
 772             } );
 773             if ( getConfiguration().isUseTabbedDisplay() ) {
 774                 try {
 775                     AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 776                     AptxUtil.addPhylogeniesToTabs( phys,
 777                                                    new File( phys_url.getFile() ).getName(),
 778                                                    phys_url.toString(),
 779                                                    getConfiguration(),
 780                                                    getMainPanel() );
 781                 }
 782                 catch ( final Exception e ) {
 783                     ForesterUtil.printErrorMessage( NAME, e.toString() );
 784                     e.printStackTrace();
 785                 }
 786             }
 787             else {
 788                 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 789                 if ( getSpeciesTree() != null ) {
 790                     AptxUtil.printAppletMessage( NAME,
 791                             "Warning: gsdi (gene duplication inference) only available tabbed display" );
 792                 }
 793                 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 794             }
 795             validate();
 796             setName( NAME );
 797             getMainPanel().getControlPanel().showWholeAll();
 798             getMainPanel().getControlPanel().showWhole();
 799             /* GUILHEM_BEG */
 800             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 801             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 802                     .getRelevantSequenceRelationTypes() ) {
 803                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 804             }
 805             final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 806             if ( default_relation != null ) {
 807                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 808             }
 809             final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 810             if ( default_sequence != null ) {
 811                 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 812             }
 813             /* GUILHEM_END */
 814             System.gc();
 815             AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 816             setVisible( true );
 817         }
 818         catch ( final Exception e ) {
 819             ForesterUtil.printErrorMessage( NAME, e.toString() );
 820             e.printStackTrace();
 821         }
 822     }
 823
 824     public void showTextFrame( final String s, final String title ) {
 825         checkTextFrames();
 826         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 827     }
 828
 829     @Override
 830     public void start() {
 831         if ( getMainPanel() != null ) {
 832             getMainPanel().validate();
 833         }
 834         requestFocus();
 835         requestFocusInWindow();
 836         requestFocus();
 837         AptxUtil.printAppletMessage( NAME, "started" );
 838     }
 839
 840     private void chooseFont() {
 841         final FontChooser fc = new FontChooser();
 842         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
 843         fc.showDialog( this, "Select the Base Font" );
 844         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
 845     }
 846
 847     private void chooseMinimalConfidence() {
 848         final String s = ( String ) JOptionPane
 849                 .showInputDialog( this,
 850                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
 851                                           + getOptions().getMinConfidenceValue() + "]\n",
 852                                           "Minimal Confidence Value",
 853                                           JOptionPane.QUESTION_MESSAGE,
 854                                           null,
 855                                           null,
 856                                           getOptions().getMinConfidenceValue() );
 857         if ( !ForesterUtil.isEmpty( s ) ) {
 858             boolean success = true;
 859             double m = 0.0;
 860             final String m_str = s.trim();
 861             if ( !ForesterUtil.isEmpty( m_str ) ) {
 862                 try {
 863                     m = Double.parseDouble( m_str );
 864                 }
 865                 catch ( final Exception ex ) {
 866                     success = false;
 867                 }
 868             }
 869             else {
 870                 success = false;
 871             }
 872             if ( success && ( m >= 0.0 ) ) {
 873                 getOptions().setMinConfidenceValue( m );
 874             }
 875         }
 876     }
 877
 878     private void choosePdfWidth() {
 879         final String s = ( String ) JOptionPane.showInputDialog( this,
 880                                                                  "Please enter the default line width for PDF export.\n"
 881                                                                          + "[current value: "
 882                                                                          + getOptions().getPrintLineWidth() + "]\n",
 883                                                                  "Line Width for PDF Export",
 884                                                                  JOptionPane.QUESTION_MESSAGE,
 885                                                                  null,
 886                                                                  null,
 887                                                                  getOptions().getPrintLineWidth() );
 888         if ( !ForesterUtil.isEmpty( s ) ) {
 889             boolean success = true;
 890             float f = 0.0f;
 891             final String m_str = s.trim();
 892             if ( !ForesterUtil.isEmpty( m_str ) ) {
 893                 try {
 894                     f = Float.parseFloat( m_str );
 895                 }
 896                 catch ( final Exception ex ) {
 897                     success = false;
 898                 }
 899             }
 900             else {
 901                 success = false;
 902             }
 903             if ( success && ( f > 0.0 ) ) {
 904                 getOptions().setPrintLineWidth( f );
 905             }
 906         }
 907     }
 908
 909     private void choosePrintSize() {
 910         final String s = ( String ) JOptionPane.showInputDialog( this,
 911                                                                  "Please enter values for width and height,\nseparated by a comma.\n"
 912                                                                          + "[current values: "
 913                                                                          + getOptions().getPrintSizeX() + ", "
 914                                                                          + getOptions().getPrintSizeY() + "]\n"
 915                                                                          + "[A4: " + Constants.A4_SIZE_X + ", "
 916                                                                          + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
 917                                                                          + Constants.US_LETTER_SIZE_X + ", "
 918                                                                          + Constants.US_LETTER_SIZE_Y + "]",
 919                                                                  "Default Size for Graphics Export",
 920                                                                  JOptionPane.QUESTION_MESSAGE,
 921                                                                  null,
 922                                                                  null,
 923                                                                  getOptions().getPrintSizeX() + ", "
 924                                                                          + getOptions().getPrintSizeY() );
 925         if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
 926             boolean success = true;
 927             int x = 0;
 928             int y = 0;
 929             final String[] str_ary = s.split( "," );
 930             if ( str_ary.length == 2 ) {
 931                 final String x_str = str_ary[ 0 ].trim();
 932                 final String y_str = str_ary[ 1 ].trim();
 933                 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
 934                     try {
 935                         x = Integer.parseInt( x_str );
 936                         y = Integer.parseInt( y_str );
 937                     }
 938                     catch ( final Exception ex ) {
 939                         success = false;
 940                     }
 941                 }
 942                 else {
 943                     success = false;
 944                 }
 945             }
 946             else {
 947                 success = false;
 948             }
 949             if ( success && ( x > 1 ) && ( y > 1 ) ) {
 950                 getOptions().setPrintSizeX( x );
 951                 getOptions().setPrintSizeY( y );
 952             }
 953         }
 954     }
 955
 956     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 957         if ( item != null ) {
 958             item.setFont( MainFrame.menu_font );
 959             if ( !getConfiguration().isUseNativeUI() ) {
 960                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 961                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 962             }
 963             item.setSelected( is_selected );
 964             item.addActionListener( this );
 965         }
 966     }
 967
 968     private Phylogeny getSpeciesTree() {
 969         return _species_tree;
 970     }
 971
 972     private boolean isScreenAntialias() {
 973         return true;
 974     }
 975
 976     private void removeBranchColors() {
 977         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 978             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
 979         }
 980     }
 981
 982     private void removeVisualStyles() {
 983         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 984             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
 985         }
 986     }
 987
 988     private void setMainPanel( final MainPanelApplets main_panel ) {
 989         _mainpanel = main_panel;
 990     }
 991
 992     private void setSpeciesTree( final Phylogeny species_tree ) {
 993         _species_tree = species_tree;
 994     }
 995
 996     private void setupUI() {
 997         try {
 998             if ( getConfiguration().isUseNativeUI() ) {
 999                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1000             }
1001             else {
1002                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1003             }
1004         }
1005         catch ( final UnsupportedLookAndFeelException e ) {
1006             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1007         }
1008         catch ( final ClassNotFoundException e ) {
1009             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1010         }
1011         catch ( final InstantiationException e ) {
1012             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1013         }
1014         catch ( final IllegalAccessException e ) {
1015             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1016         }
1017         catch ( final Exception e ) {
1018             AptxUtil.dieWithSystemError( e.toString() );
1019         }
1020     }
1021
1022     void buildAnalysisMenu() {
1023         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
1024         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
1025         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
1026         customizeJMenuItem( _gsdi_item );
1027         customizeJMenuItem( _gsdir_item );
1028         //  _analysis_menu.addSeparator();
1029         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
1030         //  customizeJMenuItem( _lineage_inference );
1031         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
1032         _jmenubar.add( _analysis_menu );
1033     }
1034
1035     void buildFileMenu() {
1036         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
1037         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
1038         _file_jmenu.addSeparator();
1039         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
1040         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
1041             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
1042         }
1043         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
1044         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
1045         if ( AptxUtil.canWriteFormat( "gif" ) ) {
1046             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
1047         }
1048         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
1049             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
1050         }
1051         _file_jmenu.addSeparator();
1052         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
1053         customizeJMenuItem( _save_item );
1054         customizeJMenuItem( _write_to_pdf_item );
1055         customizeJMenuItem( _write_to_png_item );
1056         customizeJMenuItem( _write_to_jpg_item );
1057         customizeJMenuItem( _write_to_gif_item );
1058         customizeJMenuItem( _write_to_tif_item );
1059         customizeJMenuItem( _write_to_bmp_item );
1060         customizeJMenuItem( _print_item );
1061         _jmenubar.add( _file_jmenu );
1062     }
1063
1064     void buildFontSizeMenu() {
1065         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
1066         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
1067         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
1068         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
1069         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
1070         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
1071         customizeJMenuItem( _super_tiny_fonts_mi );
1072         customizeJMenuItem( _tiny_fonts_mi );
1073         customizeJMenuItem( _small_fonts_mi );
1074         customizeJMenuItem( _medium_fonts_mi );
1075         customizeJMenuItem( _large_fonts_mi );
1076         _jmenubar.add( _font_size_menu );
1077     }
1078
1079     void buildHelpMenu() {
1080         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
1081         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
1082         _help_jmenu.addSeparator();
1083         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
1084         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
1085         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
1086         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
1087         _help_jmenu.addSeparator();
1088         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
1089         customizeJMenuItem( _help_item );
1090         customizeJMenuItem( _website_item );
1091         customizeJMenuItem( _phyloxml_website_item );
1092         customizeJMenuItem( _aptx_ref_item );
1093         customizeJMenuItem( _phyloxml_ref_item );
1094         customizeJMenuItem( _about_item );
1095         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
1096         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
1097         _jmenubar.add( _help_jmenu );
1098     }
1099
1100     void buildOptionsMenu() {
1101         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
1102         _options_jmenu.addChangeListener( new ChangeListener() {
1103
1104             @Override
1105             public void stateChanged( final ChangeEvent e ) {
1106                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
1107                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
1108                 MainFrame
1109                 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
1110                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
1111                                                          .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
1112                 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
1113                 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
1114                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
1115                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
1116                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
1117                 try {
1118                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
1119                     getMainPanel().getControlPanel().setVisibilityOfX();
1120                 }
1121                 catch ( final Exception ignore ) {
1122                     // do nothing, not important.
1123                 }
1124             }
1125         } );
1126         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
1127                                                                 getConfiguration() ) );
1128         _options_jmenu
1129         .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
1130         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
1131         _options_jmenu
1132         .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
1133         _radio_group_1 = new ButtonGroup();
1134         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
1135         _radio_group_1.add( _uniform_cladograms_rbmi );
1136         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
1137         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
1138         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
1139         _options_jmenu
1140         .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
1141         _options_jmenu
1142         .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
1143         _options_jmenu
1144         .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
1145         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
1146         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
1147             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
1148             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
1149         }
1150         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
1151         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
1152         _options_jmenu
1153         .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
1154         _options_jmenu
1155         .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
1156         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
1157         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
1158         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
1159         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
1160         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
1161         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
1162         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
1163         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
1164         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
1165         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
1166         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
1167         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
1168         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
1169         _options_jmenu.addSeparator();
1170         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
1171                                                                 getConfiguration() ) );
1172         _options_jmenu
1173         .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
1174         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
1175         _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
1176         _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
1177         _options_jmenu
1178         .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
1179         //
1180         _options_jmenu.addSeparator();
1181         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
1182                                                                 getConfiguration() ) );
1183         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
1184         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
1185         _options_jmenu
1186         .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
1187         _options_jmenu
1188         .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
1189         _options_jmenu
1190         .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
1191         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
1192         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
1193         //
1194         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1195         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1196         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1197         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1198         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1199                                    .isGraphicsExportUsingActualSize() );
1200         customizeJMenuItem( _print_size_mi );
1201         customizeJMenuItem( _choose_pdf_width_mi );
1202         //
1203         customizeJMenuItem( _choose_font_mi );
1204         customizeJMenuItem( _choose_minimal_confidence_mi );
1205         customizeJMenuItem( _switch_colors_mi );
1206         customizeJMenuItem( _overview_placment_mi );
1207         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
1208         customizeCheckBoxMenuItem( _label_direction_cbmi,
1209                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1210         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
1211         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
1212         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
1213         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
1214         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
1215         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
1216                                    .isShowDefaultNodeShapesExternal() );
1217         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
1218                                    .isShowDefaultNodeShapesInternal() );
1219         customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
1220                                    .isShowDefaultNodeShapesForMarkedNodes() );
1221         customizeJMenuItem( _cycle_node_shape_mi );
1222         customizeJMenuItem( _cycle_node_fill_mi );
1223         customizeJMenuItem( _choose_node_size_mi );
1224         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
1225         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
1226         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
1227         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
1228                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
1229         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
1230                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1231         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
1232                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1233         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1234         customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
1235         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1236         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1237         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1238         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
1239         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
1240         _jmenubar.add( _options_jmenu );
1241     }
1242
1243     void buildToolsMenu() {
1244         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
1245         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1246         customizeJMenuItem( _confcolor_item );
1247         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1248         customizeJMenuItem( _taxcolor_item );
1249         _tools_menu.addSeparator();
1250         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
1251         _remove_visual_styles_item
1252         .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
1253         customizeJMenuItem( _remove_visual_styles_item );
1254         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
1255         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
1256         customizeJMenuItem( _remove_branch_color_item );
1257         _tools_menu.addSeparator();
1258         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1259         customizeJMenuItem( _midpoint_root_item );
1260         _tools_menu.addSeparator();
1261         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1262         customizeJMenuItem( _collapse_species_specific_subtrees );
1263         _jmenubar.add( _tools_menu );
1264     }
1265
1266     void buildTypeMenu() {
1267         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
1268         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
1269         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
1270         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
1271         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
1272         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
1273         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
1274         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
1275         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
1276         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
1277         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
1278         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
1279         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
1280         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
1281         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
1282         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
1283         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
1284         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1285         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1286         initializeTypeMenu( getOptions() );
1287         _jmenubar.add( _type_menu );
1288     }
1289
1290     void buildViewMenu() {
1291         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
1292         _view_jmenu
1293         .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
1294         _view_jmenu.addSeparator();
1295         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
1296         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
1297         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
1298         customizeJMenuItem( _display_basic_information_item );
1299         customizeJMenuItem( _view_as_NH_item );
1300         customizeJMenuItem( _view_as_XML_item );
1301         customizeJMenuItem( _view_as_nexus_item );
1302         _jmenubar.add( _view_jmenu );
1303     }
1304
1305     void checkTextFrames() {
1306         if ( _textframes.size() > 5 ) {
1307             try {
1308                 if ( _textframes.getFirst() != null ) {
1309                     _textframes.getFirst().removeMe();
1310                 }
1311                 else {
1312                     _textframes.removeFirst();
1313                 }
1314             }
1315             catch ( final NoSuchElementException e ) {
1316                 // Ignore.
1317             }
1318         }
1319     }
1320
1321     void clearCurrentExternalNodesDataBuffer() {
1322         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
1323     }
1324
1325     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
1326         if ( item != null ) {
1327             item.setFont( MainFrame.menu_font );
1328             if ( !getConfiguration().isUseNativeUI() ) {
1329                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1330                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1331             }
1332             item.setSelected( is_selected );
1333             item.addActionListener( this );
1334         }
1335     }
1336
1337     void customizeJMenuItem( final JMenuItem jmi ) {
1338         if ( jmi != null ) {
1339             jmi.setFont( MainFrame.menu_font );
1340             if ( !getConfiguration().isUseNativeUI() ) {
1341                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1342                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
1343             }
1344             jmi.addActionListener( this );
1345         }
1346     }
1347
1348     void displayBasicInformation() {
1349         if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
1350                 && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1351             String title = "Basic Information";
1352             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1353                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
1354             }
1355             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
1356         }
1357     }
1358
1359     void executeGSDI() {
1360         if ( !isOKforSDI( false, true ) ) {
1361             return;
1362         }
1363         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1364             JOptionPane.showMessageDialog( this,
1365                                            "Gene tree is not rooted.",
1366                                            "Cannot execute GSDI",
1367                                            JOptionPane.ERROR_MESSAGE );
1368             return;
1369         }
1370         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1371         gene_tree.setAllNodesToNotCollapse();
1372         gene_tree.recalculateNumberOfExternalDescendants( false );
1373         GSDI gsdi = null;
1374         final Phylogeny species_tree = _species_tree.copy();
1375         try {
1376             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
1377         }
1378         catch ( final SDIException e ) {
1379             JOptionPane.showMessageDialog( this,
1380                                            e.getLocalizedMessage(),
1381                                            "Error during GSDI",
1382                                            JOptionPane.ERROR_MESSAGE );
1383             return;
1384         }
1385         catch ( final Exception e ) {
1386             AptxUtil.unexpectedException( e );
1387             return;
1388         }
1389         gene_tree.setRerootable( false );
1390         gene_tree.clearHashIdToNodeMap();
1391         gene_tree.recalculateNumberOfExternalDescendants( true );
1392         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
1393         getMainPanel().getControlPanel().setShowEvents( true );
1394         showWhole();
1395         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1396         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1397         showWhole();
1398         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1399         showWhole();
1400         _mainpanel.getCurrentTreePanel().setEdited( true );
1401         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1402         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1403             JOptionPane.showMessageDialog( this,
1404                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1405                                                    + "Potential duplications: "
1406                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1407                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1408                                                    + "Stripped gene tree nodes: "
1409                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1410                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1411                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1412                                                    "GSDI successfully completed",
1413                                                    JOptionPane.WARNING_MESSAGE );
1414         }
1415         else {
1416             JOptionPane.showMessageDialog( this,
1417                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1418                                                    + "Potential duplications: "
1419                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1420                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1421                                                    + "Stripped gene tree nodes: "
1422                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1423                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1424                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1425                                                    "GSDI successfully completed",
1426                                                    JOptionPane.INFORMATION_MESSAGE );
1427         }
1428     }
1429
1430     void executeGSDIR() {
1431         if ( !isOKforSDI( false, false ) ) {
1432             return;
1433         }
1434         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1435         if ( ( p > 0 )
1436                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1437             JOptionPane.showMessageDialog( this,
1438                                            "Gene tree is not completely binary",
1439                                            "Cannot execute GSDI",
1440                                            JOptionPane.ERROR_MESSAGE );
1441             return;
1442         }
1443         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1444         gene_tree.setAllNodesToNotCollapse();
1445         gene_tree.recalculateNumberOfExternalDescendants( false );
1446         GSDIR gsdir = null;
1447         final Phylogeny species_tree = _species_tree.copy();
1448         try {
1449             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1450         }
1451         catch ( final SDIException e ) {
1452             JOptionPane.showMessageDialog( this,
1453                                            e.getLocalizedMessage(),
1454                                            "Error during GSDIR",
1455                                            JOptionPane.ERROR_MESSAGE );
1456             return;
1457         }
1458         catch ( final Exception e ) {
1459             AptxUtil.unexpectedException( e );
1460             return;
1461         }
1462         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1463         result_gene_tree.setRerootable( false );
1464         result_gene_tree.clearHashIdToNodeMap();
1465         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1466         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1467         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1468         getMainPanel().getControlPanel().setShowEvents( true );
1469         showWhole();
1470         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1471         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1472         showWhole();
1473         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1474         showWhole();
1475         _mainpanel.getCurrentTreePanel().setEdited( true );
1476         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1477         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1478             JOptionPane.showMessageDialog( this,
1479                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1480                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1481                                                    + "Stripped gene tree nodes: "
1482                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1483                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1484                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1485                                                    "GSDIR successfully completed",
1486                                                    JOptionPane.WARNING_MESSAGE );
1487         }
1488         else {
1489             JOptionPane.showMessageDialog( this,
1490                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1491                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1492                                                    + "Stripped gene tree nodes: "
1493                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1494                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1495                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1496                                                    "GSDIR successfully completed",
1497                                                    JOptionPane.INFORMATION_MESSAGE );
1498         }
1499     }
1500
1501     Configuration getConfiguration() {
1502         return _configuration;
1503     }
1504
1505     File getCurrentDir() {
1506         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1507             if ( ForesterUtil.isWindows() ) {
1508                 try {
1509                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1510                 }
1511                 catch ( final Exception e ) {
1512                     _current_dir = null;
1513                 }
1514             }
1515         }
1516         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1517             if ( System.getProperty( "user.home" ) != null ) {
1518                 _current_dir = new File( System.getProperty( "user.home" ) );
1519             }
1520             else if ( System.getProperty( "user.dir" ) != null ) {
1521                 _current_dir = new File( System.getProperty( "user.dir" ) );
1522             }
1523         }
1524         return _current_dir;
1525     }
1526
1527     TreePanel getCurrentTreePanel() {
1528         return getMainPanel().getCurrentTreePanel();
1529     }
1530
1531     JCheckBoxMenuItem getlabelDirectionCbmi() {
1532         return _label_direction_cbmi;
1533     }
1534
1535     MainPanel getMainPanel() {
1536         return _mainpanel;
1537     }
1538
1539     Options getOtions() {
1540         return _options;
1541     }
1542
1543     void initializeTypeMenu( final Options options ) {
1544         setTypeMenuToAllUnselected();
1545         try {
1546             switch ( options.getPhylogenyGraphicsType() ) {
1547                 case CONVEX:
1548                     _convex_type_cbmi.setSelected( true );
1549                     break;
1550                 case CURVED:
1551                     _curved_type_cbmi.setSelected( true );
1552                     break;
1553                 case EURO_STYLE:
1554                     _euro_type_cbmi.setSelected( true );
1555                     break;
1556                 case ROUNDED:
1557                     _rounded_type_cbmi.setSelected( true );
1558                     break;
1559                 case TRIANGULAR:
1560                     _triangular_type_cbmi.setSelected( true );
1561                     break;
1562                 case UNROOTED:
1563                     _unrooted_type_cbmi.setSelected( true );
1564                     break;
1565                 case CIRCULAR:
1566                     _circular_type_cbmi.setSelected( true );
1567                     break;
1568                 default:
1569                     _rectangular_type_cbmi.setSelected( true );
1570                     break;
1571             }
1572         }
1573         catch ( final NullPointerException np ) {
1574             // In all likelihood, this is caused by menu-less display.
1575         }
1576     }
1577
1578     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1579         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1580             return false;
1581         }
1582         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1583             JOptionPane.showMessageDialog( this,
1584                                            "No species tree loaded",
1585                                            "Cannot execute GSDI",
1586                                            JOptionPane.ERROR_MESSAGE );
1587             return false;
1588         }
1589         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1590             JOptionPane.showMessageDialog( this,
1591                                            "Species tree is not completely binary",
1592                                            "Cannot execute GSDI",
1593                                            JOptionPane.ERROR_MESSAGE );
1594             return false;
1595         }
1596         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1597             JOptionPane.showMessageDialog( this,
1598                                            "Gene tree is not completely binary",
1599                                            "Cannot execute GSDI",
1600                                            JOptionPane.ERROR_MESSAGE );
1601             return false;
1602         }
1603         else {
1604             return true;
1605         }
1606     }
1607
1608     boolean isSubtreeDisplayed() {
1609         if ( getCurrentTreePanel() != null ) {
1610             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1611                 JOptionPane
1612                 .showMessageDialog( this,
1613                                     "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1614                                     "Operation can not be exectuted on a sub-tree",
1615                                     JOptionPane.WARNING_MESSAGE );
1616                 return true;
1617             }
1618         }
1619         return false;
1620     }
1621
1622     void removeAllTextFrames() {
1623         for( final TextFrame tf : _textframes ) {
1624             if ( tf != null ) {
1625                 tf.close();
1626             }
1627         }
1628         _textframes.clear();
1629     }
1630
1631     void setConfiguration( final Configuration configuration ) {
1632         _configuration = configuration;
1633     }
1634
1635     void setCurrentDir( final File current_dir ) {
1636         _current_dir = current_dir;
1637     }
1638
1639     void setOptions( final Options options ) {
1640         _options = options;
1641     }
1642
1643     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1644         setTypeMenuToAllUnselected();
1645         try {
1646             switch ( type ) {
1647                 case CIRCULAR:
1648                     _circular_type_cbmi.setSelected( true );
1649                     break;
1650                 case CONVEX:
1651                     _convex_type_cbmi.setSelected( true );
1652                     break;
1653                 case CURVED:
1654                     _curved_type_cbmi.setSelected( true );
1655                     break;
1656                 case EURO_STYLE:
1657                     _euro_type_cbmi.setSelected( true );
1658                     break;
1659                 case ROUNDED:
1660                     _rounded_type_cbmi.setSelected( true );
1661                     break;
1662                 case RECTANGULAR:
1663                     _rectangular_type_cbmi.setSelected( true );
1664                     break;
1665                 case TRIANGULAR:
1666                     _triangular_type_cbmi.setSelected( true );
1667                     break;
1668                 case UNROOTED:
1669                     _unrooted_type_cbmi.setSelected( true );
1670                     break;
1671                 default:
1672                     throw new IllegalArgumentException( "unknown type: " + type );
1673             }
1674         }
1675         catch ( final NullPointerException np ) {
1676             // In all likelihood, this is caused by menu-less display.
1677         }
1678     }
1679
1680     void setTypeMenuToAllUnselected() {
1681         if ( _convex_type_cbmi != null ) {
1682             _convex_type_cbmi.setSelected( false );
1683         }
1684         if ( _curved_type_cbmi != null ) {
1685             _curved_type_cbmi.setSelected( false );
1686         }
1687         if ( _euro_type_cbmi != null ) {
1688             _euro_type_cbmi.setSelected( false );
1689         }
1690         if ( _rounded_type_cbmi != null ) {
1691             _rounded_type_cbmi.setSelected( false );
1692         }
1693         if ( _triangular_type_cbmi != null ) {
1694             _triangular_type_cbmi.setSelected( false );
1695         }
1696         if ( _rectangular_type_cbmi != null ) {
1697             _rectangular_type_cbmi.setSelected( false );
1698         }
1699         if ( _unrooted_type_cbmi != null ) {
1700             _unrooted_type_cbmi.setSelected( false );
1701         }
1702         if ( _circular_type_cbmi != null ) {
1703             _circular_type_cbmi.setSelected( false );
1704         }
1705     }
1706
1707     void showWhole() {
1708         _mainpanel.getControlPanel().showWhole();
1709     }
1710
1711     void switchColors() {
1712         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1713         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1714         csc.setVisible( true );
1715         getMainPanel().setTreeColorSet( colorset );
1716     }
1717
1718     void typeChanged( final Object o ) {
1719         updateTypeCheckboxes( getOptions(), o );
1720         updateOptions( getOptions() );
1721         if ( getCurrentTreePanel() != null ) {
1722             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1723             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1724             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1725                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1726                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1727                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1728                 getCurrentTreePanel().getControlPanel().showWhole();
1729             }
1730             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1731                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1732             }
1733             else {
1734                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1735             }
1736             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1737             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1738         }
1739     }
1740
1741     void updateOptions( final Options options ) {
1742         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1743         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1744                                             && _background_gradient_cbmi.isSelected() );
1745         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1746         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1747                                             && _show_annotation_ref_source.isSelected() );
1748         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1749                                                    && _abbreviate_scientific_names.isSelected() );
1750         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1751                                                   && _color_labels_same_as_parent_branch.isSelected() );
1752         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1753                                                   && _show_default_node_shapes_internal_cbmi.isSelected() );
1754         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1755                                                   && _show_default_node_shapes_external_cbmi.isSelected() );
1756         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1757                                                         && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1758         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1759             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1760         }
1761         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1762             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1763         }
1764         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1765             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1766         }
1767         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1768                                         && _search_case_senstive_cbmi.isSelected() );
1769         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1770             options.setShowScale( _show_scale_cbmi.isSelected() );
1771         }
1772         if ( _label_direction_cbmi != null ) {
1773             if ( _label_direction_cbmi.isSelected() ) {
1774                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1775             }
1776             else {
1777                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1778             }
1779         }
1780         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1781         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1782                                          && _show_confidence_stddev_cbmi.isSelected() );
1783         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1784                                         && _search_whole_words_only_cbmi.isSelected() );
1785         options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
1786         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1787                                         && _inverse_search_result_cbmi.isSelected() );
1788         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1789                 && ( _print_using_actual_size_cbmi.isSelected() ) );
1790         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1791                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1792         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1793         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1794                 && _print_black_and_white_cbmi.isSelected() );
1795         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1796             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1797         }
1798         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1799             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1800         }
1801         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1802             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1803         }
1804         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1805             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1806         }
1807         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1808             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1809         }
1810         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1811             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1812         }
1813         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1814             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1815         }
1816         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1817             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1818         }
1819         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1820             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1821         }
1822         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1823             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1824         }
1825         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1826             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1827         }
1828         if ( _graphics_export_visible_only_cbmi != null ) {
1829             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1830             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1831                 _graphics_export_using_actual_size_cbmi.setSelected( true );
1832                 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1833             }
1834             else {
1835                 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1836             }
1837         }
1838     }
1839
1840     void updateTypeCheckboxes( final Options options, final Object o ) {
1841         setTypeMenuToAllUnselected();
1842         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1843     }
1844
1845     void viewAsNexus() {
1846         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1847             String title = "Nexus";
1848             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1849                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1850             }
1851             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1852                                                                          .getNhConversionSupportValueStyle() ),
1853                                                                          title );
1854         }
1855     }
1856
1857     void viewAsNH() {
1858         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1859             String title = "New Hampshire";
1860             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1861                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1862             }
1863             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1864                                                                                 .getNhConversionSupportValueStyle() ),
1865                                                                                 title );
1866         }
1867     }
1868
1869     void viewAsXML() {
1870         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1871             String title = "phyloXML";
1872             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1873                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1874             }
1875             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1876         }
1877     }
1878
1879     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
1880         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
1881                 + o.getPrintSizeY() + ")" );
1882     }
1883
1884     static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
1885         mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
1886     }
1887
1888     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1889         for( final TreePanel tree_panel : treepanels ) {
1890             tree_panel.setTextAntialias();
1891         }
1892     }
1893 }