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