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.Font;
   7 import java.awt.event.ActionEvent;
   8 import java.awt.event.ActionListener;
   9 import java.awt.event.ComponentAdapter;
  10 import java.awt.event.ComponentEvent;
  11 import java.io.ByteArrayOutputStream;
  12 import java.io.File;
  13 import java.io.IOException;
  14 import java.net.URL;
  15 import java.util.LinkedList;
  16 import java.util.List;
  17 import java.util.NoSuchElementException;
  18
  19 import javax.swing.ButtonGroup;
  20 import javax.swing.JApplet;
  21 import javax.swing.JCheckBoxMenuItem;
  22 import javax.swing.JFileChooser;
  23 import javax.swing.JMenu;
  24 import javax.swing.JMenuBar;
  25 import javax.swing.JMenuItem;
  26 import javax.swing.JOptionPane;
  27 import javax.swing.JRadioButtonMenuItem;
  28 import javax.swing.UIManager;
  29 import javax.swing.UnsupportedLookAndFeelException;
  30 import javax.swing.event.ChangeEvent;
  31 import javax.swing.event.ChangeListener;
  32
  33 import org.apache.commons.codec.binary.Base64;
  34 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  35 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  36 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  37 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  38 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  39 import org.forester.archaeopteryx.webservices.WebservicesManager;
  40 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  41 import org.forester.phylogeny.Phylogeny;
  42 import org.forester.phylogeny.PhylogenyMethods;
  43 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  44 import org.forester.phylogeny.data.SequenceRelation;
  45 import org.forester.sdi.GSDI;
  46 import org.forester.sdi.GSDIR;
  47 import org.forester.sdi.SDIException;
  48 import org.forester.util.ForesterConstants;
  49 import org.forester.util.ForesterUtil;
  50 import org.forester.util.WindowsUtils;
  51
  52 // Use like this:
  53 // <applet archive="forester.jar"
  54 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  55 // codebase="http://www.myserver.org/path/to/forester"
  56 // width="600"
  57 // height="500"
  58 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  59 // <param name="url_of_tree_to_load"
  60 // value="http://www.myserver.org/examples/data/apaf.xml">
  61 // <param name="config_file"
  62 // value="http://www.myserver.org/examples/config/config_file.txt">
  63 // </applet>
  64 public class ArchaeopteryxE extends JApplet implements ActionListener {
  65
  66     private final static String         NAME             = "ArchaeopteryxE";
  67     private static final long           serialVersionUID = -1220055577935759443L;
  68     private Configuration               _configuration;
  69     private MainPanelApplets            _mainpanel;
  70     private JMenuBar                    _jmenubar;
  71     private JMenu                       _options_jmenu;
  72     private JMenu                       _font_size_menu;
  73     private JMenuItem                   _super_tiny_fonts_mi;
  74     private JMenuItem                   _tiny_fonts_mi;
  75     private JMenuItem                   _small_fonts_mi;
  76     private JMenuItem                   _medium_fonts_mi;
  77     private JMenuItem                   _large_fonts_mi;
  78     private JMenu                       _tools_menu;
  79     private JMenuItem                   _taxcolor_item;
  80     private JMenuItem                   _confcolor_item;
  81     private JMenuItem                   _midpoint_root_item;
  82     private JMenu                       _view_jmenu;
  83     private JMenuItem                   _view_as_XML_item;
  84     private JMenuItem                   _view_as_NH_item;
  85     private JMenuItem                   _view_as_nexus_item;
  86     private JMenuItem                   _display_basic_information_item;
  87     private JMenu                       _type_menu;
  88     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  89     private JCheckBoxMenuItem           _triangular_type_cbmi;
  90     private JCheckBoxMenuItem           _curved_type_cbmi;
  91     private JCheckBoxMenuItem           _convex_type_cbmi;
  92     private JCheckBoxMenuItem           _euro_type_cbmi;
  93     private JCheckBoxMenuItem           _rounded_type_cbmi;
  94     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  95     private JCheckBoxMenuItem           _circular_type_cbmi;
  96     private JMenuItem                   _help_item;
  97     private JMenuItem                   _about_item;
  98     private JMenu                       _help_jmenu;
  99     private JMenuItem                   _website_item;
 100     private JMenuItem                   _phyloxml_website_item;
 101     private JMenuItem                   _phyloxml_ref_item;
 102     private JMenuItem                   _aptx_ref_item;
 103     private JMenuItem                   _remove_branch_color_item;
 104     private JMenuItem                   _remove_visual_styles_item;
 105     private JCheckBoxMenuItem           _show_domain_labels;
 106     private JCheckBoxMenuItem           _show_annotation_ref_source;
 107     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 108     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 109     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 110     private JCheckBoxMenuItem           _background_gradient_cbmi;
 111     private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 112     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 113     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 114     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 115     private Options                     _options;
 116     private JMenuItem                   _choose_font_mi;
 117     private JMenuItem                   _switch_colors_mi;
 118     JCheckBoxMenuItem                   _label_direction_cbmi;
 119     private JCheckBoxMenuItem           _show_scale_cbmi;
 120     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 121     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 122     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 123     private JCheckBoxMenuItem           _search_with_regex_cbmi;
 124     private JCheckBoxMenuItem           _show_overview_cbmi;
 125     private JMenuItem                   _choose_minimal_confidence_mi;
 126     private JMenuItem                   _collapse_species_specific_subtrees;
 127     private JMenuItem                   _overview_placment_mi;
 128     private ButtonGroup                 _radio_group_1;
 129     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 130     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 131     private JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;
 132     private JMenuItem                   _cycle_node_shape_mi;
 133     private JMenuItem                   _cycle_node_fill_mi;
 134     private JMenuItem                   _choose_node_size_mi;
 135     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 136     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 137     private JMenu                       _analysis_menu;
 138     private JMenuItem                   _gsdi_item;
 139     private JMenuItem                   _gsdir_item;
 140     private Phylogeny                   _species_tree;
 141     private JCheckBoxMenuItem           _right_line_up_domains_cbmi;
 142     private JCheckBoxMenuItem           _line_up_renderable_data_cbmi;
 143     // file menu:
 144     private JMenuItem                        _open_item;
 145     private JMenuItem                        _open_url_item;
 146     private JMenuItem                        _save_item;
 147     private JMenuItem                        _save_all_item;
 148     private JMenuItem                        _close_item;
 149     private  JMenuItem                        _exit_item;
 150     private JMenuItem                        _new_item;
 151     private JMenuItem                        _print_item;
 152     private JMenuItem                        _write_to_pdf_item;
 153     private JMenuItem                        _write_to_jpg_item;
 154     private JMenuItem                        _write_to_gif_item;
 155     private JMenuItem                        _write_to_tif_item;
 156     private JMenuItem                        _write_to_png_item;
 157     private JMenuItem                        _write_to_bmp_item;
 158     private JMenu                            _file_jmenu;
 159     private JFileChooser                     _writetopdf_filechooser;
 160     private File                             _current_dir;
 161     private JFileChooser                     _save_filechooser;
 162     private JFileChooser                     _writetographics_filechooser;
 163
 164
 165     void setCurrentDir( final File current_dir ) {
 166         _current_dir = current_dir;
 167     }
 168
 169     File getCurrentDir() {
 170         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
 171             if ( ForesterUtil.isWindows() ) {
 172                 try {
 173                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
 174                 }
 175                 catch ( final Exception e ) {
 176                     _current_dir = null;
 177                 }
 178             }
 179         }
 180         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
 181             if ( System.getProperty( "user.home" ) != null ) {
 182                 _current_dir = new File( System.getProperty( "user.home" ) );
 183             }
 184             else if ( System.getProperty( "user.dir" ) != null ) {
 185                 _current_dir = new File( System.getProperty( "user.dir" ) );
 186             }
 187         }
 188         return _current_dir;
 189     }
 190
 191
 192
 193
 194     void buildFileMenu() {
 195         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
 196         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
 197         _file_jmenu.addSeparator();
 198         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
 199         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
 200             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
 201         }
 202         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
 203         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
 204         if ( AptxUtil.canWriteFormat( "gif" ) ) {
 205             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
 206         }
 207         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
 208             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
 209         }
 210         _file_jmenu.addSeparator();
 211         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
 212         _file_jmenu.addSeparator();
 213         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 214         customizeJMenuItem( _save_item );
 215         customizeJMenuItem( _write_to_pdf_item );
 216         customizeJMenuItem( _write_to_png_item );
 217         customizeJMenuItem( _write_to_jpg_item );
 218         customizeJMenuItem( _write_to_gif_item );
 219         customizeJMenuItem( _write_to_tif_item );
 220         customizeJMenuItem( _write_to_bmp_item );
 221         customizeJMenuItem( _print_item );
 222         customizeJMenuItem( _exit_item );
 223         _jmenubar.add( _file_jmenu );
 224     }
 225
 226     @Override
 227     public void actionPerformed( final ActionEvent e ) {
 228         final Object o = e.getSource();
 229         if ( o == _midpoint_root_item ) {
 230             getMainPanel().getCurrentTreePanel().midpointRoot();
 231         }
 232         else if ( o == _gsdi_item ) {
 233             if ( isSubtreeDisplayed() ) {
 234                 return;
 235             }
 236             executeGSDI();
 237         }
 238         else if ( o == _gsdir_item ) {
 239             if ( isSubtreeDisplayed() ) {
 240                 return;
 241             }
 242             executeGSDIR();
 243         }
 244         else if ( o == _taxcolor_item ) {
 245             getMainPanel().getCurrentTreePanel().taxColor();
 246         }
 247         else if ( o == _confcolor_item ) {
 248             getMainPanel().getCurrentTreePanel().confColor();
 249         }
 250         else if ( o == _collapse_species_specific_subtrees ) {
 251             if ( getCurrentTreePanel() != null ) {
 252                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 253             }
 254         }
 255         else if ( o == _remove_branch_color_item ) {
 256             removeBranchColors();
 257         }
 258         else if ( o == _remove_visual_styles_item ) {
 259             removeVisualStyles();
 260         }
 261         else if ( o == _switch_colors_mi ) {
 262             switchColors();
 263         }
 264         else if ( o == _display_basic_information_item ) {
 265             displayBasicInformation();
 266         }
 267         else if ( o == _view_as_NH_item ) {
 268             viewAsNH();
 269         }
 270         else if ( o == _view_as_XML_item ) {
 271             viewAsXML();
 272         }
 273         else if ( o == _view_as_nexus_item ) {
 274             viewAsNexus();
 275         }
 276         else if ( o == _super_tiny_fonts_mi ) {
 277             if ( getCurrentTreePanel() != null ) {
 278                 getCurrentTreePanel().setSuperTinyFonts();
 279                 getCurrentTreePanel().repaint();
 280             }
 281         }
 282         else if ( o == _tiny_fonts_mi ) {
 283             if ( getCurrentTreePanel() != null ) {
 284                 getCurrentTreePanel().setTinyFonts();
 285                 getCurrentTreePanel().repaint();
 286             }
 287         }
 288         else if ( o == _small_fonts_mi ) {
 289             if ( getCurrentTreePanel() != null ) {
 290                 getCurrentTreePanel().setSmallFonts();
 291                 getCurrentTreePanel().repaint();
 292             }
 293         }
 294         else if ( o == _medium_fonts_mi ) {
 295             if ( getCurrentTreePanel() != null ) {
 296                 getCurrentTreePanel().setMediumFonts();
 297                 getCurrentTreePanel().repaint();
 298             }
 299         }
 300         else if ( o == _large_fonts_mi ) {
 301             if ( getCurrentTreePanel() != null ) {
 302                 getCurrentTreePanel().setLargeFonts();
 303                 getCurrentTreePanel().repaint();
 304             }
 305         }
 306         else if ( o == _choose_font_mi ) {
 307             chooseFont();
 308         }
 309         else if ( o == _choose_minimal_confidence_mi ) {
 310             chooseMinimalConfidence();
 311         }
 312         else if ( o == _choose_node_size_mi ) {
 313             MainFrame.chooseNodeSize( getOptions(), this );
 314         }
 315         else if ( o == _overview_placment_mi ) {
 316             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 317         }
 318         else if ( o == _cycle_node_fill_mi ) {
 319             MainFrame.cycleNodeFill( getOptions() );
 320         }
 321         else if ( o == _cycle_node_shape_mi ) {
 322             MainFrame.cycleNodeShape( getOptions() );
 323         }
 324         else if ( o == _non_lined_up_cladograms_rbmi ) {
 325             updateOptions( getOptions() );
 326             _mainpanel.getControlPanel().showWhole();
 327         }
 328         else if ( o == _uniform_cladograms_rbmi ) {
 329             updateOptions( getOptions() );
 330             _mainpanel.getControlPanel().showWhole();
 331         }
 332         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 333             updateOptions( getOptions() );
 334             _mainpanel.getControlPanel().showWhole();
 335         }
 336         else if ( o == _search_case_senstive_cbmi ) {
 337             updateOptions( getOptions() );
 338             getMainPanel().getControlPanel().search0();
 339             getMainPanel().getControlPanel().search1();
 340         }
 341         else if ( o == _search_whole_words_only_cbmi ) {
 342             if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
 343                 _search_with_regex_cbmi.setSelected( false );
 344             }
 345             updateOptions( getOptions() );
 346             getMainPanel().getControlPanel().search0();
 347             getMainPanel().getControlPanel().search1();
 348         }
 349         else if ( o == _inverse_search_result_cbmi ) {
 350             updateOptions( getOptions() );
 351             getMainPanel().getControlPanel().search0();
 352             getMainPanel().getControlPanel().search1();
 353         }
 354         else if ( o == _search_with_regex_cbmi ) {
 355             if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
 356                 _search_whole_words_only_cbmi.setSelected( false );
 357             }
 358             if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
 359                 _search_case_senstive_cbmi.setSelected( true );
 360             }
 361             updateOptions( getOptions() );
 362             getMainPanel().getControlPanel().search0();
 363             getMainPanel().getControlPanel().search1();
 364         }
 365         else if ( o == _show_scale_cbmi ) {
 366             updateOptions( getOptions() );
 367         }
 368         else if ( o == _show_confidence_stddev_cbmi ) {
 369             updateOptions( getOptions() );
 370         }
 371         else if ( o == _label_direction_cbmi ) {
 372             updateOptions( getOptions() );
 373         }
 374         else if ( o == _abbreviate_scientific_names ) {
 375             updateOptions( getOptions() );
 376         }
 377         else if ( o == _show_overview_cbmi ) {
 378             updateOptions( getOptions() );
 379             if ( getCurrentTreePanel() != null ) {
 380                 getCurrentTreePanel().updateOvSizes();
 381             }
 382         }
 383         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 384                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 385                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 386             typeChanged( o );
 387         }
 388         else if ( o == _screen_antialias_cbmi ) {
 389             updateOptions( getOptions() );
 390             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 391         }
 392         else if ( o == _background_gradient_cbmi ) {
 393             updateOptions( getOptions() );
 394         }
 395         else if ( o == _show_domain_labels ) {
 396             updateOptions( getOptions() );
 397         }
 398         else if ( o == _color_labels_same_as_parent_branch ) {
 399             updateOptions( getOptions() );
 400         }
 401         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 402             updateOptions( getOptions() );
 403         }
 404         else if ( o == _show_default_node_shapes_external_cbmi ) {
 405             updateOptions( getOptions() );
 406         }
 407         else if ( o == _about_item ) {
 408             MainFrame.about();
 409         }
 410         else if ( o == _help_item ) {
 411             try {
 412                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
 413             }
 414             catch ( final IOException e1 ) {
 415                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 416             }
 417         }
 418         else if ( o == _website_item ) {
 419             try {
 420                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 421             }
 422             catch ( final IOException e1 ) {
 423                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 424             }
 425         }
 426         else if ( o == _phyloxml_website_item ) {
 427             try {
 428                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 429             }
 430             catch ( final IOException e1 ) {
 431                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 432             }
 433         }
 434         else if ( o == _aptx_ref_item ) {
 435             try {
 436                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 437             }
 438             catch ( final IOException e1 ) {
 439                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 440             }
 441         }
 442         else if ( o == _phyloxml_ref_item ) {
 443             try {
 444                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 445             }
 446             catch ( final IOException e1 ) {
 447                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 448             }
 449         }
 450         else if ( o == _color_by_taxonomic_group_cbmi ) {
 451             updateOptions( getOptions() );
 452         }
 453         else if ( o == _line_up_renderable_data_cbmi ) {
 454             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
 455                 _right_line_up_domains_cbmi.setSelected( false );
 456             }
 457             updateOptions( getOptions() );
 458         }
 459         else if ( o == _right_line_up_domains_cbmi ) {
 460             if ( _right_line_up_domains_cbmi.isSelected() ) {
 461                 _line_up_renderable_data_cbmi.setSelected( true );
 462             }
 463             updateOptions( getOptions() );
 464         }
 465         //
 466         else if ( o == _write_to_pdf_item ) {
 467            // writeToPdf( _mainpanel.getCurrentPhylogeny() );
 468             final File curr_dir =MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(),
 469                                   getMainPanel(),
 470                                   _writetopdf_filechooser,
 471                                   _current_dir,
 472                                   getContentPane(),
 473                                   this );
 474
 475
 476             if ( curr_dir != null ) {
 477                 setCurrentDir( curr_dir );
 478             }
 479
 480         }
 481
 482         else if ( o == _write_to_jpg_item ) {
 483
 484             writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
 485         }
 486         else if ( o == _write_to_gif_item ) {
 487             writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
 488         }
 489         else if ( o == _write_to_tif_item ) {
 490             writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
 491         }
 492         else if ( o == _write_to_bmp_item ) {
 493             writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
 494         }
 495         else if ( o == _write_to_png_item ) {
 496             writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
 497         }
 498         else if ( o == _print_item ) {
 499             MainFrame.print( getCurrentTreePanel(),
 500                              getOptions(),
 501
 502                              this );
 503
 504         }
 505         else if ( o == _save_item ) {
 506             writeToFile( _mainpanel.getCurrentPhylogeny() );
 507         }
 508
 509 //        else if ( o == _graphics_export_visible_only_cbmi ) {
 510 //            updateOptions( getOptions() );
 511 //        }
 512 //        else if ( o == _antialias_print_cbmi ) {
 513 //            updateOptions( getOptions() );
 514 //        }
 515 //        else if ( o == _print_black_and_white_cbmi ) {
 516 //            updateOptions( getOptions() );
 517 //        }
 518 //        else if ( o == _print_using_actual_size_cbmi ) {
 519 //            updateOptions( getOptions() );
 520 //        }
 521 //        else if ( o == _graphics_export_using_actual_size_cbmi ) {
 522 //            updateOptions( getOptions() );
 523 //        }
 524 //        else if ( o == _print_size_mi ) {
 525 //            choosePrintSize();
 526 //        }
 527 //        else if ( o == _choose_pdf_width_mi ) {
 528 //            choosePdfWidth();
 529 //        }
 530
 531         repaint();
 532     }
 533
 534     @Override
 535     public void destroy() {
 536         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 537         removeAllTextFrames();
 538         if ( getMainPanel() != null ) {
 539             getMainPanel().terminate();
 540         }
 541     }
 542
 543     /**
 544      * This method returns the current external node data which
 545      * has been selected by the user by clicking the "Return ..."
 546      * menu item. This method is expected to be called from Javascript or
 547      * something like it.
 548      *
 549      * @return current external node data as String
 550      */
 551     public String getCurrentExternalNodesDataBuffer() {
 552         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 553     }
 554
 555     public int getCurrentExternalNodesDataBufferChangeCounter() {
 556         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 557     }
 558
 559     public int getCurrentExternalNodesDataBufferLength() {
 560         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 561     }
 562
 563     /**
 564      * This method returns the current phylogeny as a string in the chosen format
 565      *
 566      * @param format must be NH, NHX, NEXUS or PHYLOXML
 567      * @return the phylogeny string
 568      * @author Herve Menager
 569      */
 570     public String getCurrentPhylogeny( final String format ) {
 571         removeAllTextFrames();
 572         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 573                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 574             return new String();
 575         }
 576         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 577             case NH:
 578                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 579             case NHX:
 580                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 581             case NEXUS:
 582                 return getMainPanel().getCurrentPhylogeny().toNexus();
 583             case PHYLOXML:
 584                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 585             default:
 586                 break;
 587         }
 588         return new String();
 589     }
 590
 591     /**
 592      * This method returns a view of the current phylogeny in a chosen
 593      * graphics format, base64-encoded in a string so that in can be used
 594      * from javascript.
 595      *
 596      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 597      * @return the phylogeny string
 598      * @author Herve Menager
 599      */
 600     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 601         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 602         try {
 603             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 604                                                                     _mainpanel.getWidth(),
 605                                                                     _mainpanel.getHeight(),
 606                                                                     getCurrentTreePanel(),
 607                                                                     getCurrentTreePanel().getControlPanel(),
 608                                                                     GraphicsExportType.valueOf( format ),
 609                                                                     getOptions() );
 610         }
 611         catch ( final IOException ioe ) {
 612             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 613             ioe.printStackTrace();
 614             JOptionPane.showMessageDialog( this,
 615                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 616                                            "Failed to generate graphics",
 617                                            JOptionPane.ERROR_MESSAGE );
 618             return null;
 619         }
 620         final byte[] bytes = baos.toByteArray();
 621         final String dataImg = Base64.encodeBase64String( bytes );
 622         return dataImg;
 623     }
 624
 625     public Options getOptions() {
 626         return _options;
 627     }
 628
 629     @Override
 630     public void init() {
 631         _writetopdf_filechooser = new JFileChooser();
 632         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 633         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 634         final Configuration configuration = new Configuration( config_filename, true, true, true );
 635         setConfiguration( configuration );
 636         setOptions( Options.createInstance( configuration ) );
 637         setupUI();
 638         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 639         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 640             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 641                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 642             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 643                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 644             return;
 645         }
 646         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 647         // Get URL to tree file
 648         URL phys_url = null;
 649         try {
 650             phys_url = new URL( tree_url_str );
 651         }
 652         catch ( final Exception e ) {
 653             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 654             e.printStackTrace();
 655             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 656                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 657         }
 658         if ( phys_url == null ) {
 659             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 660                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 661             JOptionPane.showMessageDialog( this,
 662                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 663                                            "Failed to create URL",
 664                                            JOptionPane.ERROR_MESSAGE );
 665             return;
 666         }
 667         // Load the tree from URL
 668         Phylogeny[] phys = null;
 669         try {
 670             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 671                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 672                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 673                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 674                                                     getConfiguration().getTaxonomyExtraction(),
 675                                                     getConfiguration().isMidpointReroot() );
 676         }
 677         catch ( final Exception e ) {
 678             ForesterUtil.printErrorMessage( NAME, e.toString() );
 679             e.printStackTrace();
 680             JOptionPane.showMessageDialog( this,
 681                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 682                                            "Failed to read phylogenies",
 683                                            JOptionPane.ERROR_MESSAGE );
 684         }
 685         if ( phys == null ) {
 686             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 687             JOptionPane.showMessageDialog( this,
 688                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 689                                            "Failed to read phylogenies",
 690                                            JOptionPane.ERROR_MESSAGE );
 691             return;
 692         }
 693         else if ( phys.length < 1 ) {
 694             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 695             JOptionPane.showMessageDialog( this,
 696                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 697                                            "Failed to read phylogenies",
 698                                            JOptionPane.ERROR_MESSAGE );
 699             return;
 700         }
 701         else {
 702             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 703         }
 704         //
 705         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 706         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 707             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 708             Phylogeny[] species_trees = null;
 709             try {
 710                 final URL species_tree_url = new URL( species_tree_url_str );
 711                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 712                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 713                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 714                                                                  false,
 715                                                                  TAXONOMY_EXTRACTION.NO,
 716                                                                  false );
 717             }
 718             catch ( final IOException e ) {
 719                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 720                         + "]" );
 721                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 722                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 723             }
 724             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 725                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 726                 if ( species_trees[ 0 ].isEmpty() ) {
 727                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 728                 }
 729                 else if ( !species_trees[ 0 ].isRooted() ) {
 730                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 731                 }
 732                 else {
 733                     setSpeciesTree( species_trees[ 0 ] );
 734                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 735                 }
 736             }
 737         }
 738         //
 739         try {
 740             setVisible( false );
 741             setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 742             _jmenubar = new JMenuBar();
 743             if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 744                 buildFileMenu();
 745                 if ( !getConfiguration().isUseNativeUI() ) {
 746                     _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 747                 }
 748                 if ( getSpeciesTree() != null ) {
 749                     buildAnalysisMenu();
 750                 }
 751                 buildToolsMenu();
 752                 buildViewMenu();
 753                 buildFontSizeMenu();
 754                 buildOptionsMenu();
 755                 buildTypeMenu();
 756                 buildHelpMenu();
 757                 setJMenuBar( _jmenubar );
 758             }
 759             final Container contentpane = getContentPane();
 760             contentpane.setLayout( new BorderLayout() );
 761             contentpane.add( getMainPanel(), BorderLayout.CENTER );
 762             addComponentListener( new ComponentAdapter() {
 763
 764                 @Override
 765                 public void componentResized( final ComponentEvent e ) {
 766                     if ( getMainPanel().getCurrentTreePanel() != null ) {
 767                         getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 768                                                                                         .getCurrentTreePanel()
 769                                                                                         .getWidth(),
 770                                                                                         getMainPanel()
 771                                                                                         .getCurrentTreePanel()
 772                                                                                         .getHeight() );
 773                     }
 774                 }
 775             } );
 776             if ( getConfiguration().isUseTabbedDisplay() ) {
 777                 try {
 778                     AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 779                     AptxUtil.addPhylogeniesToTabs( phys,
 780                                                    new File( phys_url.getFile() ).getName(),
 781                                                    phys_url.toString(),
 782                                                    getConfiguration(),
 783                                                    getMainPanel() );
 784                 }
 785                 catch ( final Exception e ) {
 786                     ForesterUtil.printErrorMessage( NAME, e.toString() );
 787                     e.printStackTrace();
 788                 }
 789             }
 790             else {
 791                 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 792                 if ( getSpeciesTree() != null ) {
 793                     AptxUtil.printAppletMessage( NAME,
 794                                                  "Warning: gsdi (gene duplication inference) only available tabbed display" );
 795                 }
 796                 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 797             }
 798             validate();
 799             setName( NAME );
 800             getMainPanel().getControlPanel().showWholeAll();
 801             getMainPanel().getControlPanel().showWhole();
 802             /* GUILHEM_BEG */
 803             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 804             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 805                     .getRelevantSequenceRelationTypes() ) {
 806                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 807             }
 808             final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 809             if ( default_relation != null ) {
 810                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 811             }
 812             final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 813             if ( default_sequence != null ) {
 814                 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 815             }
 816             /* GUILHEM_END */
 817             System.gc();
 818             AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 819             setVisible( true );
 820         }
 821         catch ( final Exception e ) {
 822             ForesterUtil.printErrorMessage( NAME, e.toString() );
 823             e.printStackTrace();
 824         }
 825     }
 826
 827     public void showTextFrame( final String s, final String title ) {
 828         checkTextFrames();
 829         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 830     }
 831
 832     @Override
 833     public void start() {
 834         if ( getMainPanel() != null ) {
 835             getMainPanel().validate();
 836         }
 837         requestFocus();
 838         requestFocusInWindow();
 839         requestFocus();
 840         AptxUtil.printAppletMessage( NAME, "started" );
 841     }
 842
 843     void buildAnalysisMenu() {
 844         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 845         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 846         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 847         customizeJMenuItem( _gsdi_item );
 848         customizeJMenuItem( _gsdir_item );
 849         //  _analysis_menu.addSeparator();
 850         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 851         //  customizeJMenuItem( _lineage_inference );
 852         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 853         _jmenubar.add( _analysis_menu );
 854     }
 855
 856     void buildFontSizeMenu() {
 857         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 858         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 859         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 860         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 861         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 862         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 863         customizeJMenuItem( _super_tiny_fonts_mi );
 864         customizeJMenuItem( _tiny_fonts_mi );
 865         customizeJMenuItem( _small_fonts_mi );
 866         customizeJMenuItem( _medium_fonts_mi );
 867         customizeJMenuItem( _large_fonts_mi );
 868         _jmenubar.add( _font_size_menu );
 869     }
 870
 871     void buildHelpMenu() {
 872         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 873         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
 874         _help_jmenu.addSeparator();
 875         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 876         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 877         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 878         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 879         _help_jmenu.addSeparator();
 880         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 881         customizeJMenuItem( _help_item );
 882         customizeJMenuItem( _website_item );
 883         customizeJMenuItem( _phyloxml_website_item );
 884         customizeJMenuItem( _aptx_ref_item );
 885         customizeJMenuItem( _phyloxml_ref_item );
 886         customizeJMenuItem( _about_item );
 887         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 888         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 889         _jmenubar.add( _help_jmenu );
 890     }
 891
 892     void buildOptionsMenu() {
 893         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 894         _options_jmenu.addChangeListener( new ChangeListener() {
 895
 896             @Override
 897             public void stateChanged( final ChangeEvent e ) {
 898                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 899                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 900                 MainFrame
 901                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 902                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 903                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 904                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 905                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 906                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 907                 try {
 908                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
 909                     getMainPanel().getControlPanel().setVisibilityOfX();
 910                 }
 911                 catch ( final Exception ignore ) {
 912                     // do nothing, not important.
 913                 }
 914             }
 915         } );
 916         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 917                                                                 getConfiguration() ) );
 918         _options_jmenu
 919                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 920         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 921         _options_jmenu
 922                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 923         _radio_group_1 = new ButtonGroup();
 924         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 925         _radio_group_1.add( _uniform_cladograms_rbmi );
 926         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 927         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 928         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 929         _options_jmenu
 930                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 931         _options_jmenu
 932                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 933         _options_jmenu
 934                 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
 935         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 936         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 937             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 938             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 939         }
 940         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 941         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 942         _options_jmenu
 943                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 944         _options_jmenu
 945                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 946         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 947         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 948         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 949         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 950         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 951         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 952         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 953         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 954         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 955         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 956         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 957         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 958         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 959         _options_jmenu.addSeparator();
 960         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 961                                                                 getConfiguration() ) );
 962         _options_jmenu
 963                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 964         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 965         _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
 966         _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
 967         _options_jmenu
 968                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 969         customizeJMenuItem( _choose_font_mi );
 970         customizeJMenuItem( _choose_minimal_confidence_mi );
 971         customizeJMenuItem( _switch_colors_mi );
 972         customizeJMenuItem( _overview_placment_mi );
 973         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 974         customizeCheckBoxMenuItem( _label_direction_cbmi,
 975                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 976         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 977         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 978         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 979         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 980         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 981         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 982                 .isShowDefaultNodeShapesExternal() );
 983         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 984                 .isShowDefaultNodeShapesInternal() );
 985         customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
 986                 .isShowDefaultNodeShapesForMarkedNodes() );
 987         customizeJMenuItem( _cycle_node_shape_mi );
 988         customizeJMenuItem( _cycle_node_fill_mi );
 989         customizeJMenuItem( _choose_node_size_mi );
 990         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 991         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 992         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 993         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 994                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 995         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 996                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 997         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 998                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 999         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1000         customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
1001         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1002         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1003         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1004         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
1005         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
1006         _jmenubar.add( _options_jmenu );
1007     }
1008
1009     void buildToolsMenu() {
1010         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
1011         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1012         customizeJMenuItem( _confcolor_item );
1013         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1014         customizeJMenuItem( _taxcolor_item );
1015         _tools_menu.addSeparator();
1016         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
1017         _remove_visual_styles_item
1018                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
1019         customizeJMenuItem( _remove_visual_styles_item );
1020         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
1021         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
1022         customizeJMenuItem( _remove_branch_color_item );
1023         _tools_menu.addSeparator();
1024         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1025         customizeJMenuItem( _midpoint_root_item );
1026         _tools_menu.addSeparator();
1027         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1028         customizeJMenuItem( _collapse_species_specific_subtrees );
1029         _jmenubar.add( _tools_menu );
1030     }
1031
1032     void buildTypeMenu() {
1033         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
1034         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
1035         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
1036         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
1037         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
1038         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
1039         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
1040         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
1041         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
1042         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
1043         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
1044         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
1045         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
1046         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
1047         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
1048         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
1049         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
1050         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1051         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
1052         initializeTypeMenu( getOptions() );
1053         _jmenubar.add( _type_menu );
1054     }
1055
1056     void buildViewMenu() {
1057         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
1058         _view_jmenu
1059                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
1060         _view_jmenu.addSeparator();
1061         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
1062         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
1063         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
1064         customizeJMenuItem( _display_basic_information_item );
1065         customizeJMenuItem( _view_as_NH_item );
1066         customizeJMenuItem( _view_as_XML_item );
1067         customizeJMenuItem( _view_as_nexus_item );
1068         _jmenubar.add( _view_jmenu );
1069     }
1070
1071     void checkTextFrames() {
1072         if ( _textframes.size() > 5 ) {
1073             try {
1074                 if ( _textframes.getFirst() != null ) {
1075                     _textframes.getFirst().removeMe();
1076                 }
1077                 else {
1078                     _textframes.removeFirst();
1079                 }
1080             }
1081             catch ( final NoSuchElementException e ) {
1082                 // Ignore.
1083             }
1084         }
1085     }
1086
1087     void clearCurrentExternalNodesDataBuffer() {
1088         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
1089     }
1090
1091     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
1092         if ( item != null ) {
1093             item.setFont( MainFrame.menu_font );
1094             if ( !getConfiguration().isUseNativeUI() ) {
1095                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1096                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1097             }
1098             item.setSelected( is_selected );
1099             item.addActionListener( this );
1100         }
1101     }
1102
1103     void customizeJMenuItem( final JMenuItem jmi ) {
1104         if ( jmi != null ) {
1105         jmi.setFont( MainFrame.menu_font );
1106         if ( !getConfiguration().isUseNativeUI() ) {
1107             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1108             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
1109         }
1110         jmi.addActionListener( this );
1111         }
1112     }
1113
1114     void displayBasicInformation() {
1115         if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
1116                 && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1117             String title = "Basic Information";
1118             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1119                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
1120             }
1121             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
1122         }
1123     }
1124
1125     void executeGSDI() {
1126         if ( !isOKforSDI( false, true ) ) {
1127             return;
1128         }
1129         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1130             JOptionPane.showMessageDialog( this,
1131                                            "Gene tree is not rooted.",
1132                                            "Cannot execute GSDI",
1133                                            JOptionPane.ERROR_MESSAGE );
1134             return;
1135         }
1136         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1137         gene_tree.setAllNodesToNotCollapse();
1138         gene_tree.recalculateNumberOfExternalDescendants( false );
1139         GSDI gsdi = null;
1140         final Phylogeny species_tree = _species_tree.copy();
1141         try {
1142             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
1143         }
1144         catch ( final SDIException e ) {
1145             JOptionPane.showMessageDialog( this,
1146                                            e.getLocalizedMessage(),
1147                                            "Error during GSDI",
1148                                            JOptionPane.ERROR_MESSAGE );
1149             return;
1150         }
1151         catch ( final Exception e ) {
1152             AptxUtil.unexpectedException( e );
1153             return;
1154         }
1155         gene_tree.setRerootable( false );
1156         gene_tree.clearHashIdToNodeMap();
1157         gene_tree.recalculateNumberOfExternalDescendants( true );
1158         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
1159         getMainPanel().getControlPanel().setShowEvents( true );
1160         showWhole();
1161         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1162         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1163         showWhole();
1164         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1165         showWhole();
1166         _mainpanel.getCurrentTreePanel().setEdited( true );
1167         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1168         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1169             JOptionPane.showMessageDialog( this,
1170                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1171                                                    + "Potential duplications: "
1172                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1173                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1174                                                    + "Stripped gene tree nodes: "
1175                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1176                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1177                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1178                                            "GSDI successfully completed",
1179                                            JOptionPane.WARNING_MESSAGE );
1180         }
1181         else {
1182             JOptionPane.showMessageDialog( this,
1183                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1184                                                    + "Potential duplications: "
1185                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1186                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1187                                                    + "Stripped gene tree nodes: "
1188                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1189                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1190                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1191                                            "GSDI successfully completed",
1192                                            JOptionPane.INFORMATION_MESSAGE );
1193         }
1194     }
1195
1196     void executeGSDIR() {
1197         if ( !isOKforSDI( false, false ) ) {
1198             return;
1199         }
1200         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1201         if ( ( p > 0 )
1202                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1203             JOptionPane.showMessageDialog( this,
1204                                            "Gene tree is not completely binary",
1205                                            "Cannot execute GSDI",
1206                                            JOptionPane.ERROR_MESSAGE );
1207             return;
1208         }
1209         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1210         gene_tree.setAllNodesToNotCollapse();
1211         gene_tree.recalculateNumberOfExternalDescendants( false );
1212         GSDIR gsdir = null;
1213         final Phylogeny species_tree = _species_tree.copy();
1214         try {
1215             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1216         }
1217         catch ( final SDIException e ) {
1218             JOptionPane.showMessageDialog( this,
1219                                            e.getLocalizedMessage(),
1220                                            "Error during GSDIR",
1221                                            JOptionPane.ERROR_MESSAGE );
1222             return;
1223         }
1224         catch ( final Exception e ) {
1225             AptxUtil.unexpectedException( e );
1226             return;
1227         }
1228         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1229         result_gene_tree.setRerootable( false );
1230         result_gene_tree.clearHashIdToNodeMap();
1231         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1232         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1233         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1234         getMainPanel().getControlPanel().setShowEvents( true );
1235         showWhole();
1236         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1237         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1238         showWhole();
1239         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1240         showWhole();
1241         _mainpanel.getCurrentTreePanel().setEdited( true );
1242         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1243         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1244             JOptionPane.showMessageDialog( this,
1245                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1246                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1247                                                    + "Stripped gene tree nodes: "
1248                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1249                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1250                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1251                                            "GSDIR successfully completed",
1252                                            JOptionPane.WARNING_MESSAGE );
1253         }
1254         else {
1255             JOptionPane.showMessageDialog( this,
1256                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1257                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1258                                                    + "Stripped gene tree nodes: "
1259                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1260                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1261                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1262                                            "GSDIR successfully completed",
1263                                            JOptionPane.INFORMATION_MESSAGE );
1264         }
1265     }
1266
1267     Configuration getConfiguration() {
1268         return _configuration;
1269     }
1270
1271     TreePanel getCurrentTreePanel() {
1272         return getMainPanel().getCurrentTreePanel();
1273     }
1274
1275     JCheckBoxMenuItem getlabelDirectionCbmi() {
1276         return _label_direction_cbmi;
1277     }
1278
1279     Options getOtions() {
1280         return _options;
1281     }
1282
1283     void initializeTypeMenu( final Options options ) {
1284         setTypeMenuToAllUnselected();
1285         try {
1286             switch ( options.getPhylogenyGraphicsType() ) {
1287                 case CONVEX:
1288                     _convex_type_cbmi.setSelected( true );
1289                     break;
1290                 case CURVED:
1291                     _curved_type_cbmi.setSelected( true );
1292                     break;
1293                 case EURO_STYLE:
1294                     _euro_type_cbmi.setSelected( true );
1295                     break;
1296                 case ROUNDED:
1297                     _rounded_type_cbmi.setSelected( true );
1298                     break;
1299                 case TRIANGULAR:
1300                     _triangular_type_cbmi.setSelected( true );
1301                     break;
1302                 case UNROOTED:
1303                     _unrooted_type_cbmi.setSelected( true );
1304                     break;
1305                 case CIRCULAR:
1306                     _circular_type_cbmi.setSelected( true );
1307                     break;
1308                 default:
1309                     _rectangular_type_cbmi.setSelected( true );
1310                     break;
1311             }
1312         }
1313         catch ( final NullPointerException np ) {
1314             // In all likelihood, this is caused by menu-less display.
1315         }
1316     }
1317
1318     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1319         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1320             return false;
1321         }
1322         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1323             JOptionPane.showMessageDialog( this,
1324                                            "No species tree loaded",
1325                                            "Cannot execute GSDI",
1326                                            JOptionPane.ERROR_MESSAGE );
1327             return false;
1328         }
1329         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1330             JOptionPane.showMessageDialog( this,
1331                                            "Species tree is not completely binary",
1332                                            "Cannot execute GSDI",
1333                                            JOptionPane.ERROR_MESSAGE );
1334             return false;
1335         }
1336         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1337             JOptionPane.showMessageDialog( this,
1338                                            "Gene tree is not completely binary",
1339                                            "Cannot execute GSDI",
1340                                            JOptionPane.ERROR_MESSAGE );
1341             return false;
1342         }
1343         else {
1344             return true;
1345         }
1346     }
1347
1348     boolean isSubtreeDisplayed() {
1349         if ( getCurrentTreePanel() != null ) {
1350             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1351                 JOptionPane
1352                         .showMessageDialog( this,
1353                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1354                                             "Operation can not be exectuted on a sub-tree",
1355                                             JOptionPane.WARNING_MESSAGE );
1356                 return true;
1357             }
1358         }
1359         return false;
1360     }
1361
1362     void removeAllTextFrames() {
1363         for( final TextFrame tf : _textframes ) {
1364             if ( tf != null ) {
1365                 tf.close();
1366             }
1367         }
1368         _textframes.clear();
1369     }
1370
1371     void setConfiguration( final Configuration configuration ) {
1372         _configuration = configuration;
1373     }
1374
1375     void setOptions( final Options options ) {
1376         _options = options;
1377     }
1378
1379     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1380         setTypeMenuToAllUnselected();
1381         try {
1382             switch ( type ) {
1383                 case CIRCULAR:
1384                     _circular_type_cbmi.setSelected( true );
1385                     break;
1386                 case CONVEX:
1387                     _convex_type_cbmi.setSelected( true );
1388                     break;
1389                 case CURVED:
1390                     _curved_type_cbmi.setSelected( true );
1391                     break;
1392                 case EURO_STYLE:
1393                     _euro_type_cbmi.setSelected( true );
1394                     break;
1395                 case ROUNDED:
1396                     _rounded_type_cbmi.setSelected( true );
1397                     break;
1398                 case RECTANGULAR:
1399                     _rectangular_type_cbmi.setSelected( true );
1400                     break;
1401                 case TRIANGULAR:
1402                     _triangular_type_cbmi.setSelected( true );
1403                     break;
1404                 case UNROOTED:
1405                     _unrooted_type_cbmi.setSelected( true );
1406                     break;
1407                 default:
1408                     throw new IllegalArgumentException( "unknown type: " + type );
1409             }
1410         }
1411         catch ( final NullPointerException np ) {
1412             // In all likelihood, this is caused by menu-less display.
1413         }
1414     }
1415
1416     void setTypeMenuToAllUnselected() {
1417         if ( _convex_type_cbmi != null ) {
1418             _convex_type_cbmi.setSelected( false );
1419         }
1420         if ( _curved_type_cbmi != null ) {
1421             _curved_type_cbmi.setSelected( false );
1422         }
1423         if ( _euro_type_cbmi != null ) {
1424             _euro_type_cbmi.setSelected( false );
1425         }
1426         if ( _rounded_type_cbmi != null ) {
1427             _rounded_type_cbmi.setSelected( false );
1428         }
1429         if ( _triangular_type_cbmi != null ) {
1430             _triangular_type_cbmi.setSelected( false );
1431         }
1432         if ( _rectangular_type_cbmi != null ) {
1433             _rectangular_type_cbmi.setSelected( false );
1434         }
1435         if ( _unrooted_type_cbmi != null ) {
1436             _unrooted_type_cbmi.setSelected( false );
1437         }
1438         if ( _circular_type_cbmi != null ) {
1439             _circular_type_cbmi.setSelected( false );
1440         }
1441     }
1442
1443     void showWhole() {
1444         _mainpanel.getControlPanel().showWhole();
1445     }
1446
1447     void switchColors() {
1448         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1449         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1450         csc.setVisible( true );
1451         getMainPanel().setTreeColorSet( colorset );
1452     }
1453
1454     void typeChanged( final Object o ) {
1455         updateTypeCheckboxes( getOptions(), o );
1456         updateOptions( getOptions() );
1457         if ( getCurrentTreePanel() != null ) {
1458             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1459             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1460             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1461                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1462                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1463                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1464                 getCurrentTreePanel().getControlPanel().showWhole();
1465             }
1466             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1467                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1468             }
1469             else {
1470                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1471             }
1472             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1473             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1474         }
1475     }
1476
1477     void updateOptions( final Options options ) {
1478         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1479         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1480                 && _background_gradient_cbmi.isSelected() );
1481         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1482         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1483                 && _show_annotation_ref_source.isSelected() );
1484         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1485                 && _abbreviate_scientific_names.isSelected() );
1486         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1487                 && _color_labels_same_as_parent_branch.isSelected() );
1488         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1489                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1490         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1491                 && _show_default_node_shapes_external_cbmi.isSelected() );
1492         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1493                 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1494         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1495             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1496         }
1497         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1498             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1499         }
1500         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1501             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1502         }
1503         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1504                 && _search_case_senstive_cbmi.isSelected() );
1505         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1506             options.setShowScale( _show_scale_cbmi.isSelected() );
1507         }
1508         if ( _label_direction_cbmi != null ) {
1509             if ( _label_direction_cbmi.isSelected() ) {
1510                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1511             }
1512             else {
1513                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1514             }
1515         }
1516         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1517         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1518                 && _show_confidence_stddev_cbmi.isSelected() );
1519         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1520                 && _search_whole_words_only_cbmi.isSelected() );
1521         options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
1522         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1523                 && _inverse_search_result_cbmi.isSelected() );
1524         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1525             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1526         }
1527         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1528             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1529         }
1530         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1531             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1532         }
1533         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1534             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1535         }
1536         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1537             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1538         }
1539         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1540             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1541         }
1542         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1543             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1544         }
1545         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1546             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1547         }
1548         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1549             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1550         }
1551         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1552             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1553         }
1554         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1555             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1556         }
1557     }
1558
1559     void updateTypeCheckboxes( final Options options, final Object o ) {
1560         setTypeMenuToAllUnselected();
1561         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1562     }
1563
1564     void viewAsNexus() {
1565         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1566             String title = "Nexus";
1567             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1568                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1569             }
1570             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1571                                    .getNhConversionSupportValueStyle() ),
1572                            title );
1573         }
1574     }
1575
1576     void viewAsNH() {
1577         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1578             String title = "New Hampshire";
1579             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1580                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1581             }
1582             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1583                                    .getNhConversionSupportValueStyle() ),
1584                            title );
1585         }
1586     }
1587
1588     void viewAsXML() {
1589         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1590             String title = "phyloXML";
1591             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1592                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1593             }
1594             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1595         }
1596     }
1597
1598     private void chooseFont() {
1599         final FontChooser fc = new FontChooser();
1600         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1601         fc.showDialog( this, "Select the Base Font" );
1602         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1603     }
1604
1605     private void chooseMinimalConfidence() {
1606         final String s = ( String ) JOptionPane
1607                 .showInputDialog( this,
1608                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1609                                           + getOptions().getMinConfidenceValue() + "]\n",
1610                                   "Minimal Confidence Value",
1611                                   JOptionPane.QUESTION_MESSAGE,
1612                                   null,
1613                                   null,
1614                                   getOptions().getMinConfidenceValue() );
1615         if ( !ForesterUtil.isEmpty( s ) ) {
1616             boolean success = true;
1617             double m = 0.0;
1618             final String m_str = s.trim();
1619             if ( !ForesterUtil.isEmpty( m_str ) ) {
1620                 try {
1621                     m = Double.parseDouble( m_str );
1622                 }
1623                 catch ( final Exception ex ) {
1624                     success = false;
1625                 }
1626             }
1627             else {
1628                 success = false;
1629             }
1630             if ( success && ( m >= 0.0 ) ) {
1631                 getOptions().setMinConfidenceValue( m );
1632             }
1633         }
1634     }
1635
1636     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1637         if ( item != null ) {
1638             item.setFont( MainFrame.menu_font );
1639             if ( !getConfiguration().isUseNativeUI() ) {
1640                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1641                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1642             }
1643             item.setSelected( is_selected );
1644             item.addActionListener( this );
1645         }
1646     }
1647
1648     MainPanel getMainPanel() {
1649         return _mainpanel;
1650     }
1651
1652     private Phylogeny getSpeciesTree() {
1653         return _species_tree;
1654     }
1655
1656     private boolean isScreenAntialias() {
1657         return true;
1658     }
1659
1660     private void removeBranchColors() {
1661         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1662             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1663         }
1664     }
1665
1666     private void removeVisualStyles() {
1667         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1668             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1669         }
1670     }
1671
1672     private void setMainPanel( final MainPanelApplets main_panel ) {
1673         _mainpanel = main_panel;
1674     }
1675
1676     private void setSpeciesTree( final Phylogeny species_tree ) {
1677         _species_tree = species_tree;
1678     }
1679
1680     private void setupUI() {
1681         try {
1682             if ( getConfiguration().isUseNativeUI() ) {
1683                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1684             }
1685             else {
1686                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1687             }
1688         }
1689         catch ( final UnsupportedLookAndFeelException e ) {
1690             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1691         }
1692         catch ( final ClassNotFoundException e ) {
1693             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1694         }
1695         catch ( final InstantiationException e ) {
1696             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1697         }
1698         catch ( final IllegalAccessException e ) {
1699             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1700         }
1701         catch ( final Exception e ) {
1702             AptxUtil.dieWithSystemError( e.toString() );
1703         }
1704     }
1705
1706     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1707         for( final TreePanel tree_panel : treepanels ) {
1708             tree_panel.setTextAntialias();
1709         }
1710     }
1711 }