forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java

   1
   2 package org.forester.archaeopteryx;
   3
   4 import java.awt.BorderLayout;
   5 import java.awt.Container;
   6 import java.awt.event.ActionEvent;
   7 import java.awt.event.ActionListener;
   8 import java.awt.event.ComponentAdapter;
   9 import java.awt.event.ComponentEvent;
  10 import java.io.ByteArrayOutputStream;
  11 import java.io.File;
  12 import java.io.IOException;
  13 import java.net.URL;
  14 import java.util.LinkedList;
  15 import java.util.List;
  16 import java.util.NoSuchElementException;
  17
  18 import javax.swing.ButtonGroup;
  19 import javax.swing.JApplet;
  20 import javax.swing.JCheckBoxMenuItem;
  21 import javax.swing.JMenu;
  22 import javax.swing.JMenuBar;
  23 import javax.swing.JMenuItem;
  24 import javax.swing.JOptionPane;
  25 import javax.swing.JRadioButtonMenuItem;
  26 import javax.swing.UIManager;
  27 import javax.swing.UnsupportedLookAndFeelException;
  28 import javax.swing.event.ChangeEvent;
  29 import javax.swing.event.ChangeListener;
  30
  31 import org.apache.commons.codec.binary.Base64;
  32 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  33 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  34 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  35 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  36 import org.forester.phylogeny.Phylogeny;
  37 import org.forester.phylogeny.data.SequenceRelation;
  38 import org.forester.util.ForesterConstants;
  39 import org.forester.util.ForesterUtil;
  40
  41 // Use like this:
  42 // <applet archive="forester.jar"
  43 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  44 // codebase="http://www.myserver.org/path/to/forester"
  45 // width="600"
  46 // height="500"
  47 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  48 // <param name="url_of_tree_to_load"
  49 // value="http://www.myserver.org/examples/data/apaf.xml">
  50 // <param name="config_file"
  51 // value="http://www.myserver.org/examples/config/config_file.txt">
  52 // </applet>
  53 public class ArchaeopteryxE extends JApplet implements ActionListener {
  54
  55     private final static String         NAME             = "ArchaeopteryxE";
  56     private static final long           serialVersionUID = -1220055577935759443L;
  57     private Configuration               _configuration;
  58     private MainPanelApplets            _main_panel;
  59     private JMenuBar                    _jmenubar;
  60     private JMenu                       _options_jmenu;
  61     private JMenu                       _font_size_menu;
  62     private JMenuItem                   _super_tiny_fonts_mi;
  63     private JMenuItem                   _tiny_fonts_mi;
  64     private JMenuItem                   _small_fonts_mi;
  65     private JMenuItem                   _medium_fonts_mi;
  66     private JMenuItem                   _large_fonts_mi;
  67     private JMenu                       _tools_menu;
  68     private JMenuItem                   _taxcolor_item;
  69     private JMenuItem                   _confcolor_item;
  70     private JMenuItem                   _midpoint_root_item;
  71     private JMenu                       _view_jmenu;
  72     private JMenuItem                   _view_as_XML_item;
  73     private JMenuItem                   _view_as_NH_item;
  74     private JMenuItem                   _view_as_nexus_item;
  75     private JMenuItem                   _display_basic_information_item;
  76     private JMenu                       _type_menu;
  77     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  78     private JCheckBoxMenuItem           _triangular_type_cbmi;
  79     private JCheckBoxMenuItem           _curved_type_cbmi;
  80     private JCheckBoxMenuItem           _convex_type_cbmi;
  81     private JCheckBoxMenuItem           _euro_type_cbmi;
  82     private JCheckBoxMenuItem           _rounded_type_cbmi;
  83     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  84     private JCheckBoxMenuItem           _circular_type_cbmi;
  85     private JMenuItem                   _help_item;
  86     private JMenuItem                   _about_item;
  87     private JMenu                       _help_jmenu;
  88     private JMenuItem                   _website_item;
  89     private JMenuItem                   _phyloxml_website_item;
  90     private JMenuItem                   _phyloxml_ref_item;
  91     private JMenuItem                   _aptx_ref_item;
  92     private JMenuItem                   _remove_branch_color_item;
  93     private JCheckBoxMenuItem           _show_domain_labels;
  94     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
  95     private JCheckBoxMenuItem           _abbreviate_scientific_names;
  96     private JCheckBoxMenuItem           _screen_antialias_cbmi;
  97     private JCheckBoxMenuItem           _background_gradient_cbmi;
  98     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
  99     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 100     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 101     private Options                     _options;
 102     private JMenuItem                   _choose_font_mi;
 103     private JMenuItem                   _switch_colors_mi;
 104     JCheckBoxMenuItem                   _label_direction_cbmi;
 105     private JCheckBoxMenuItem           _show_scale_cbmi;
 106     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 107     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 108     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 109     private JCheckBoxMenuItem           _show_overview_cbmi;
 110     private JMenuItem                   _choose_minimal_confidence_mi;
 111     private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 112     private JMenuItem                   _collapse_species_specific_subtrees;
 113     private JMenuItem                   _overview_placment_mi;
 114     private ButtonGroup                 _radio_group_1;
 115     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 116     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 117     private JMenuItem                   _cycle_node_shape_mi;
 118     private JMenuItem                   _cycle_node_fill_mi;
 119     private JMenuItem                   _choose_node_size_mi;
 120     private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 121     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 122     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 123
 124     // private String                      _ext_node_data_buffer                = "";
 125     // private int                         _ext_node_data_buffer_change_counter = 0;
 126     @Override
 127     public void actionPerformed( final ActionEvent e ) {
 128         final Object o = e.getSource();
 129         if ( o == _midpoint_root_item ) {
 130             getMainPanel().getCurrentTreePanel().midpointRoot();
 131         }
 132         else if ( o == _taxcolor_item ) {
 133             getMainPanel().getCurrentTreePanel().taxColor();
 134         }
 135         else if ( o == _confcolor_item ) {
 136             getMainPanel().getCurrentTreePanel().confColor();
 137         }
 138         else if ( o == _collapse_species_specific_subtrees ) {
 139             if ( getCurrentTreePanel() != null ) {
 140                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 141             }
 142         }
 143         else if ( o == _remove_branch_color_item ) {
 144             removeBranchColors();
 145         }
 146         else if ( o == _switch_colors_mi ) {
 147             switchColors();
 148         }
 149         else if ( o == _display_basic_information_item ) {
 150             displayBasicInformation();
 151         }
 152         else if ( o == _view_as_NH_item ) {
 153             viewAsNH();
 154         }
 155         else if ( o == _view_as_XML_item ) {
 156             viewAsXML();
 157         }
 158         else if ( o == _view_as_nexus_item ) {
 159             viewAsNexus();
 160         }
 161         else if ( o == _super_tiny_fonts_mi ) {
 162             if ( getCurrentTreePanel() != null ) {
 163                 getCurrentTreePanel().setSuperTinyFonts();
 164                 getCurrentTreePanel().repaint();
 165             }
 166         }
 167         else if ( o == _tiny_fonts_mi ) {
 168             if ( getCurrentTreePanel() != null ) {
 169                 getCurrentTreePanel().setTinyFonts();
 170                 getCurrentTreePanel().repaint();
 171             }
 172         }
 173         else if ( o == _small_fonts_mi ) {
 174             if ( getCurrentTreePanel() != null ) {
 175                 getCurrentTreePanel().setSmallFonts();
 176                 getCurrentTreePanel().repaint();
 177             }
 178         }
 179         else if ( o == _medium_fonts_mi ) {
 180             if ( getCurrentTreePanel() != null ) {
 181                 getCurrentTreePanel().setMediumFonts();
 182                 getCurrentTreePanel().repaint();
 183             }
 184         }
 185         else if ( o == _large_fonts_mi ) {
 186             if ( getCurrentTreePanel() != null ) {
 187                 getCurrentTreePanel().setLargeFonts();
 188                 getCurrentTreePanel().repaint();
 189             }
 190         }
 191         else if ( o == _choose_font_mi ) {
 192             chooseFont();
 193         }
 194         else if ( o == _choose_minimal_confidence_mi ) {
 195             chooseMinimalConfidence();
 196         }
 197         else if ( o == _choose_node_size_mi ) {
 198             MainFrame.chooseNodeSize( getOptions(), this );
 199         }
 200         else if ( o == _overview_placment_mi ) {
 201             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 202         }
 203         else if ( o == _cycle_node_fill_mi ) {
 204             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 205         }
 206         else if ( o == _cycle_node_shape_mi ) {
 207             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 208         }
 209         else if ( o == _non_lined_up_cladograms_rbmi ) {
 210             updateOptions( getOptions() );
 211             _main_panel.getControlPanel().showWhole();
 212         }
 213         else if ( o == _uniform_cladograms_rbmi ) {
 214             updateOptions( getOptions() );
 215             _main_panel.getControlPanel().showWhole();
 216         }
 217         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 218             updateOptions( getOptions() );
 219             _main_panel.getControlPanel().showWhole();
 220         }
 221         else if ( o == _search_case_senstive_cbmi ) {
 222             updateOptions( getOptions() );
 223             getMainPanel().getControlPanel().search();
 224         }
 225         else if ( o == _search_whole_words_only_cbmi ) {
 226             updateOptions( getOptions() );
 227             getMainPanel().getControlPanel().search();
 228         }
 229         else if ( o == _inverse_search_result_cbmi ) {
 230             updateOptions( getOptions() );
 231             getMainPanel().getControlPanel().search();
 232         }
 233         else if ( o == _show_scale_cbmi ) {
 234             updateOptions( getOptions() );
 235         }
 236         else if ( o == _show_branch_length_values_cbmi ) {
 237             updateOptions( getOptions() );
 238         }
 239         else if ( o == _show_confidence_stddev_cbmi ) {
 240             updateOptions( getOptions() );
 241         }
 242         else if ( o == _label_direction_cbmi ) {
 243             updateOptions( getOptions() );
 244         }
 245         else if ( o == _show_overview_cbmi ) {
 246             updateOptions( getOptions() );
 247             if ( getCurrentTreePanel() != null ) {
 248                 getCurrentTreePanel().updateOvSizes();
 249             }
 250         }
 251         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 252                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 253                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 254             typeChanged( o );
 255         }
 256         else if ( o == _screen_antialias_cbmi ) {
 257             updateOptions( getOptions() );
 258             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 259         }
 260         else if ( o == _background_gradient_cbmi ) {
 261             updateOptions( getOptions() );
 262         }
 263         else if ( o == _show_domain_labels ) {
 264             updateOptions( getOptions() );
 265         }
 266         else if ( o == _color_labels_same_as_parent_branch ) {
 267             updateOptions( getOptions() );
 268         }
 269         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 270             updateOptions( getOptions() );
 271         }
 272         else if ( o == _show_default_node_shapes_external_cbmi ) {
 273             updateOptions( getOptions() );
 274         }
 275         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 276             updateOptions( getOptions() );
 277         }
 278         else if ( o == _about_item ) {
 279             MainFrame.about();
 280         }
 281         else if ( o == _help_item ) {
 282             help();
 283         }
 284         else if ( o == _website_item ) {
 285             try {
 286                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 287             }
 288             catch ( final IOException e1 ) {
 289                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 290             }
 291         }
 292         else if ( o == _phyloxml_website_item ) {
 293             try {
 294                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 295             }
 296             catch ( final IOException e1 ) {
 297                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 298             }
 299         }
 300         else if ( o == _aptx_ref_item ) {
 301             try {
 302                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 303             }
 304             catch ( final IOException e1 ) {
 305                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 306             }
 307         }
 308         else if ( o == _phyloxml_ref_item ) {
 309             try {
 310                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 311             }
 312             catch ( final IOException e1 ) {
 313                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 314             }
 315         }
 316         repaint();
 317     }
 318
 319     @Override
 320     public void destroy() {
 321         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 322         removeAllTextFrames();
 323         if ( getMainPanel() != null ) {
 324             getMainPanel().terminate();
 325         }
 326     }
 327
 328     /**
 329      * This method returns the current external node data which
 330      * has been selected by the user by clicking the "Return ..."
 331      * menu item. This method is expected to be called from Javascript or
 332      * something like it.
 333      *
 334      * @return current external node data as String
 335      */
 336     public String getCurrentExternalNodesDataBuffer() {
 337         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 338     }
 339
 340     public int getCurrentExternalNodesDataBufferChangeCounter() {
 341         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 342     }
 343
 344     public int getCurrentExternalNodesDataBufferLength() {
 345         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 346     }
 347
 348     /**
 349      * This method returns the current phylogeny as a string in the chosen format
 350      *
 351      * @param format must be NH, NHX, NEXUS or PHYLOXML
 352      * @return the phylogeny string
 353      * @author Herve Menager
 354      */
 355     public String getCurrentPhylogeny( final String format ) {
 356         removeAllTextFrames();
 357         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 358                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 359             return new String();
 360         }
 361         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 362             case NH:
 363                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 364             case NHX:
 365                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 366             case NEXUS:
 367                 return getMainPanel().getCurrentPhylogeny().toNexus();
 368             case PHYLOXML:
 369                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 370             default:
 371                 break;
 372         }
 373         return new String();
 374     }
 375
 376     /**
 377      * This method returns a view of the current phylogeny in a chosen
 378      * graphics format, base64-encoded in a string so that in can be used
 379      * from javascript.
 380      *
 381      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 382      * @return the phylogeny string
 383      * @author Herve Menager
 384      */
 385     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 386         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 387         try {
 388             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 389                                                                     _main_panel.getWidth(),
 390                                                                     _main_panel.getHeight(),
 391                                                                     getCurrentTreePanel(),
 392                                                                     getCurrentTreePanel().getControlPanel(),
 393                                                                     GraphicsExportType.valueOf( format ),
 394                                                                     getOptions() );
 395         }
 396         catch ( final IOException ioe ) {
 397             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 398             ioe.printStackTrace();
 399             JOptionPane.showMessageDialog( this,
 400                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 401                                            "Failed to generate graphics",
 402                                            JOptionPane.ERROR_MESSAGE );
 403             return null;
 404         }
 405         final byte[] bytes = baos.toByteArray();
 406         final String dataImg = Base64.encodeBase64String( bytes );
 407         return dataImg;
 408     }
 409
 410     public Options getOptions() {
 411         return _options;
 412     }
 413
 414     @Override
 415     public void init() {
 416         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 417         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 418         final Configuration configuration = new Configuration( config_filename, true, true, true );
 419         setConfiguration( configuration );
 420         setOptions( Options.createInstance( configuration ) );
 421         setupUI();
 422         URL phys_url = null;
 423         Phylogeny[] phys = null;
 424         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 425         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 426         // Get URL to tree file
 427         if ( tree_url_str != null ) {
 428             try {
 429                 phys_url = new URL( tree_url_str );
 430             }
 431             catch ( final Exception e ) {
 432                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 433                 e.printStackTrace();
 434                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 435                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 436             }
 437         }
 438         // Load the tree from URL
 439         if ( phys_url != null ) {
 440             try {
 441                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 442                                                         getConfiguration().isValidatePhyloXmlAgainstSchema(),
 443                                                         getConfiguration().isReplaceUnderscoresInNhParsing(),
 444                                                         getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 445                                                         getConfiguration().getTaxonomyExtraction() );
 446             }
 447             catch ( final Exception e ) {
 448                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 449                 e.printStackTrace();
 450                 JOptionPane.showMessageDialog( this,
 451                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 452                                                "Failed to read phylogenies",
 453                                                JOptionPane.ERROR_MESSAGE );
 454             }
 455         }
 456         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 457             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 458             JOptionPane.showMessageDialog( this,
 459                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 460                                            "Failed to read phylogenies",
 461                                            JOptionPane.ERROR_MESSAGE );
 462             return;
 463         }
 464         else {
 465             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 466         }
 467         setVisible( false );
 468         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 469         _jmenubar = new JMenuBar();
 470         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 471             if ( !getConfiguration().isUseNativeUI() ) {
 472                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 473             }
 474             buildToolsMenu();
 475             buildViewMenu();
 476             buildFontSizeMenu();
 477             buildOptionsMenu();
 478             buildTypeMenu();
 479             buildHelpMenu();
 480             setJMenuBar( _jmenubar );
 481         }
 482         final Container contentpane = getContentPane();
 483         contentpane.setLayout( new BorderLayout() );
 484         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 485         addComponentListener( new ComponentAdapter() {
 486
 487             @Override
 488             public void componentResized( final ComponentEvent e ) {
 489                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 490                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 491                                                                                             .getCurrentTreePanel()
 492                                                                                             .getWidth(),
 493                                                                                     getMainPanel()
 494                                                                                             .getCurrentTreePanel()
 495                                                                                             .getHeight(),
 496                                                                                     getOptions()
 497                                                                                             .isAllowFontSizeChange() );
 498                 }
 499             }
 500         } );
 501         if ( getConfiguration().isUseTabbedDisplay() ) {
 502             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 503             AptxUtil.addPhylogeniesToTabs( phys,
 504                                            new File( phys_url.getFile() ).getName(),
 505                                            phys_url.toString(),
 506                                            getConfiguration(),
 507                                            getMainPanel() );
 508         }
 509         else {
 510             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 511             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 512         }
 513         validate();
 514         setName( NAME );
 515         getMainPanel().getControlPanel().showWholeAll();
 516         getMainPanel().getControlPanel().showWhole();
 517         System.gc();
 518         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 519         /* GUILHEM_BEG */
 520         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 521         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 522                 .getRelevantSequenceRelationTypes() ) {
 523             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 524         }
 525         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 526         if ( default_relation != null ) {
 527             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 528         }
 529         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 530         if ( default_sequence != null ) {
 531             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 532             /* GUILHEM_END */
 533         }
 534         setVisible( true );
 535     }
 536
 537     public void showTextFrame( final String s, final String title ) {
 538         checkTextFrames();
 539         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 540     }
 541
 542     @Override
 543     public void start() {
 544         if ( getMainPanel() != null ) {
 545             getMainPanel().validate();
 546         }
 547         requestFocus();
 548         requestFocusInWindow();
 549         requestFocus();
 550         AptxUtil.printAppletMessage( NAME, "started" );
 551     }
 552
 553     void buildFontSizeMenu() {
 554         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 555         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 556         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 557         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 558         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 559         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 560         customizeJMenuItem( _super_tiny_fonts_mi );
 561         customizeJMenuItem( _tiny_fonts_mi );
 562         customizeJMenuItem( _small_fonts_mi );
 563         customizeJMenuItem( _medium_fonts_mi );
 564         customizeJMenuItem( _large_fonts_mi );
 565         _jmenubar.add( _font_size_menu );
 566     }
 567
 568     void buildHelpMenu() {
 569         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 570         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 571         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 572         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 573         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 574         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 575         _help_jmenu.addSeparator();
 576         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 577         customizeJMenuItem( _help_item );
 578         customizeJMenuItem( _website_item );
 579         customizeJMenuItem( _phyloxml_website_item );
 580         customizeJMenuItem( _aptx_ref_item );
 581         customizeJMenuItem( _phyloxml_ref_item );
 582         customizeJMenuItem( _about_item );
 583         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 584         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 585         _jmenubar.add( _help_jmenu );
 586     }
 587
 588     void buildOptionsMenu() {
 589         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 590         _options_jmenu.addChangeListener( new ChangeListener() {
 591
 592             @Override
 593             public void stateChanged( final ChangeEvent e ) {
 594                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 595                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 596                 MainFrame
 597                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 598                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 599                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 600                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 601                                                                      _show_scale_cbmi,
 602                                                                      _show_branch_length_values_cbmi,
 603                                                                      _non_lined_up_cladograms_rbmi,
 604                                                                      _uniform_cladograms_rbmi,
 605                                                                      _ext_node_dependent_cladogram_rbmi,
 606                                                                      _label_direction_cbmi );
 607                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 608                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 609                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 610             }
 611         } );
 612         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 613                                                                 getConfiguration() ) );
 614         _options_jmenu
 615                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 616         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 617         _options_jmenu
 618                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 619         _radio_group_1 = new ButtonGroup();
 620         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 621         _radio_group_1.add( _uniform_cladograms_rbmi );
 622         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 623         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 624         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 625         _options_jmenu
 626                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 627         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 628         _options_jmenu
 629                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 630         _options_jmenu
 631                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 632         _options_jmenu
 633                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 634         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 635         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 636         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 637         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 638         _options_jmenu
 639                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 640         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 641         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 642         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 643         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 644         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 645         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 646             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 647         }
 648         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 649         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 650         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 651         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 652         _options_jmenu.addSeparator();
 653         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 654                                                                 getConfiguration() ) );
 655         _options_jmenu
 656                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 657         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 658         _options_jmenu
 659                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 660         customizeJMenuItem( _choose_font_mi );
 661         customizeJMenuItem( _choose_minimal_confidence_mi );
 662         customizeJMenuItem( _switch_colors_mi );
 663         customizeJMenuItem( _overview_placment_mi );
 664         customizeCheckBoxMenuItem( _label_direction_cbmi,
 665                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 666         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 667         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 668         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 669         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 670         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 671                 .isShowDefaultNodeShapesExternal() );
 672         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 673                 .isShowDefaultNodeShapesInternal() );
 674         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 675         customizeJMenuItem( _cycle_node_shape_mi );
 676         customizeJMenuItem( _cycle_node_fill_mi );
 677         customizeJMenuItem( _choose_node_size_mi );
 678         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 679         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 680         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 681         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 682                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 683         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 684                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 685         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 686                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 687         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 688         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 689         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 690         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 691         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 692         _jmenubar.add( _options_jmenu );
 693     }
 694
 695     void buildToolsMenu() {
 696         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 697         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 698         customizeJMenuItem( _confcolor_item );
 699         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 700         customizeJMenuItem( _taxcolor_item );
 701         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 702         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 703         customizeJMenuItem( _remove_branch_color_item );
 704         _tools_menu.addSeparator();
 705         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 706         customizeJMenuItem( _midpoint_root_item );
 707         _tools_menu.addSeparator();
 708         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 709         customizeJMenuItem( _collapse_species_specific_subtrees );
 710         _jmenubar.add( _tools_menu );
 711     }
 712
 713     void buildTypeMenu() {
 714         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 715         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 716         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 717         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 718         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 719         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 720         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 721         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 722         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 723         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 724         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 725         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 726         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 727         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 728         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 729         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 730         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 731         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 732         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 733         initializeTypeMenu( getOptions() );
 734         _jmenubar.add( _type_menu );
 735     }
 736
 737     void buildViewMenu() {
 738         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 739         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 740         _view_jmenu.addSeparator();
 741         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 742         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 743         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 744         customizeJMenuItem( _display_basic_information_item );
 745         customizeJMenuItem( _view_as_NH_item );
 746         customizeJMenuItem( _view_as_XML_item );
 747         customizeJMenuItem( _view_as_nexus_item );
 748         _jmenubar.add( _view_jmenu );
 749     }
 750
 751     void checkTextFrames() {
 752         if ( _textframes.size() > 5 ) {
 753             try {
 754                 if ( _textframes.getFirst() != null ) {
 755                     _textframes.getFirst().removeMe();
 756                 }
 757                 else {
 758                     _textframes.removeFirst();
 759                 }
 760             }
 761             catch ( final NoSuchElementException e ) {
 762                 // Ignore.
 763             }
 764         }
 765     }
 766
 767     void clearCurrentExternalNodesDataBuffer() {
 768         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 769     }
 770
 771     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 772         if ( item != null ) {
 773             item.setFont( MainFrame.menu_font );
 774             if ( !getConfiguration().isUseNativeUI() ) {
 775                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 776                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 777             }
 778             item.setSelected( is_selected );
 779             item.addActionListener( this );
 780         }
 781     }
 782
 783     void customizeJMenuItem( final JMenuItem jmi ) {
 784         jmi.setFont( MainFrame.menu_font );
 785         if ( !getConfiguration().isUseNativeUI() ) {
 786             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 787             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 788         }
 789         jmi.addActionListener( this );
 790     }
 791
 792     void displayBasicInformation() {
 793         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 794             String title = "Basic Information";
 795             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 796                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
 797             }
 798             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
 799         }
 800     }
 801
 802     Configuration getConfiguration() {
 803         return _configuration;
 804     }
 805
 806     TreePanel getCurrentTreePanel() {
 807         return getMainPanel().getCurrentTreePanel();
 808     }
 809
 810     JCheckBoxMenuItem getlabelDirectionCbmi() {
 811         return _label_direction_cbmi;
 812     }
 813
 814     Options getOtions() {
 815         return _options;
 816     }
 817
 818     void help() {
 819         final StringBuilder sb = new StringBuilder();
 820         sb.append( "Display options\n" );
 821         sb.append( "-------------------\n" );
 822         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 823         sb.append( "Clickable tree nodes\n" );
 824         sb.append( "--------------------\n" );
 825         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 826         sb.append( "or by right clicking:\n" );
 827         sb.append( "o  Display Node Data -- display information for a node\n" );
 828         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 829         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 830         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 831         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 832         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 833         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 834         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 835         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 836         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 837         sb.append( "Zooming\n" );
 838         sb.append( "---------\n" );
 839         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 840         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 841         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 842         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 843         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 844         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 845         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 846         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 847         sb.append( "Quick tree manipulation:\n" );
 848         sb.append( "------------------------\n" );
 849         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 850         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 851         sb.append( "Memory problems (Java heap space error)\n" );
 852         sb.append( "---------------------------------------\n" );
 853         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 854         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 855         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 856         sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 857         sb.append( "phyloXML\n" );
 858         sb.append( "-------------------\n" );
 859         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 860         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 861         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 862         sb.append( "\n" );
 863         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 864         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 865         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 866     }
 867
 868     void initializeTypeMenu( final Options options ) {
 869         setTypeMenuToAllUnselected();
 870         try {
 871             switch ( options.getPhylogenyGraphicsType() ) {
 872                 case CONVEX:
 873                     _convex_type_cbmi.setSelected( true );
 874                     break;
 875                 case CURVED:
 876                     _curved_type_cbmi.setSelected( true );
 877                     break;
 878                 case EURO_STYLE:
 879                     _euro_type_cbmi.setSelected( true );
 880                     break;
 881                 case ROUNDED:
 882                     _rounded_type_cbmi.setSelected( true );
 883                     break;
 884                 case TRIANGULAR:
 885                     _triangular_type_cbmi.setSelected( true );
 886                     break;
 887                 case UNROOTED:
 888                     _unrooted_type_cbmi.setSelected( true );
 889                     break;
 890                 case CIRCULAR:
 891                     _circular_type_cbmi.setSelected( true );
 892                     break;
 893                 default:
 894                     _rectangular_type_cbmi.setSelected( true );
 895                     break;
 896             }
 897         }
 898         catch ( final NullPointerException np ) {
 899             // In all likelihood, this is caused by menu-less display.
 900         }
 901     }
 902
 903     void removeAllTextFrames() {
 904         for( final TextFrame tf : _textframes ) {
 905             if ( tf != null ) {
 906                 tf.close();
 907             }
 908         }
 909         _textframes.clear();
 910     }
 911
 912     void setConfiguration( final Configuration configuration ) {
 913         _configuration = configuration;
 914     }
 915
 916     void setOptions( final Options options ) {
 917         _options = options;
 918     }
 919
 920     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 921         setTypeMenuToAllUnselected();
 922         try {
 923             switch ( type ) {
 924                 case CIRCULAR:
 925                     _circular_type_cbmi.setSelected( true );
 926                     break;
 927                 case CONVEX:
 928                     _convex_type_cbmi.setSelected( true );
 929                     break;
 930                 case CURVED:
 931                     _curved_type_cbmi.setSelected( true );
 932                     break;
 933                 case EURO_STYLE:
 934                     _euro_type_cbmi.setSelected( true );
 935                     break;
 936                 case ROUNDED:
 937                     _rounded_type_cbmi.setSelected( true );
 938                     break;
 939                 case RECTANGULAR:
 940                     _rectangular_type_cbmi.setSelected( true );
 941                     break;
 942                 case TRIANGULAR:
 943                     _triangular_type_cbmi.setSelected( true );
 944                     break;
 945                 case UNROOTED:
 946                     _unrooted_type_cbmi.setSelected( true );
 947                     break;
 948                 default:
 949                     throw new IllegalArgumentException( "unknown type: " + type );
 950             }
 951         }
 952         catch ( final NullPointerException np ) {
 953             // In all likelihood, this is caused by menu-less display.
 954         }
 955     }
 956
 957     void setTypeMenuToAllUnselected() {
 958         if ( _convex_type_cbmi != null ) {
 959             _convex_type_cbmi.setSelected( false );
 960         }
 961         if ( _curved_type_cbmi != null ) {
 962             _curved_type_cbmi.setSelected( false );
 963         }
 964         if ( _euro_type_cbmi != null ) {
 965             _euro_type_cbmi.setSelected( false );
 966         }
 967         if ( _rounded_type_cbmi != null ) {
 968             _rounded_type_cbmi.setSelected( false );
 969         }
 970         if ( _triangular_type_cbmi != null ) {
 971             _triangular_type_cbmi.setSelected( false );
 972         }
 973         if ( _rectangular_type_cbmi != null ) {
 974             _rectangular_type_cbmi.setSelected( false );
 975         }
 976         if ( _unrooted_type_cbmi != null ) {
 977             _unrooted_type_cbmi.setSelected( false );
 978         }
 979         if ( _circular_type_cbmi != null ) {
 980             _circular_type_cbmi.setSelected( false );
 981         }
 982     }
 983
 984     void switchColors() {
 985         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 986         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 987         csc.setVisible( true );
 988         getMainPanel().setTreeColorSet( colorset );
 989     }
 990
 991     void typeChanged( final Object o ) {
 992         updateTypeCheckboxes( getOptions(), o );
 993         updateOptions( getOptions() );
 994         if ( getCurrentTreePanel() != null ) {
 995             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
 996             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
 997             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 998                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
 999                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1000                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1001                 getCurrentTreePanel().getControlPanel().showWhole();
1002             }
1003             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1004                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1005             }
1006             else {
1007                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1008             }
1009             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1010             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1011         }
1012     }
1013
1014     void updateOptions( final Options options ) {
1015         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1016         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1017                 && _background_gradient_cbmi.isSelected() );
1018         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1019         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1020                 && _abbreviate_scientific_names.isSelected() );
1021         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1022                 && _color_labels_same_as_parent_branch.isSelected() );
1023         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1024                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1025         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1026                 && _show_default_node_shapes_external_cbmi.isSelected() );
1027         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1028                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1029         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1030             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1031         }
1032         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1033             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1034         }
1035         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1036             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1037         }
1038         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1039                 && _search_case_senstive_cbmi.isSelected() );
1040         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1041             options.setShowScale( _show_scale_cbmi.isSelected() );
1042         }
1043         if ( _label_direction_cbmi != null ) {
1044             if ( _label_direction_cbmi.isSelected() ) {
1045                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1046             }
1047             else {
1048                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1049             }
1050         }
1051         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1052         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1053                 && _show_confidence_stddev_cbmi.isSelected() );
1054         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1055             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1056         }
1057         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1058                 && _search_whole_words_only_cbmi.isSelected() );
1059         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1060                 && _inverse_search_result_cbmi.isSelected() );
1061         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1062             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1063         }
1064         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1065             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1066         }
1067         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1068             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1069         }
1070         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1071             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1072         }
1073         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1074             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1075         }
1076         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1077             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1078         }
1079         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1080             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1081         }
1082         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1083             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1084         }
1085     }
1086
1087     void updateTypeCheckboxes( final Options options, final Object o ) {
1088         setTypeMenuToAllUnselected();
1089         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1090     }
1091
1092     void viewAsNexus() {
1093         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1094             String title = "Nexus";
1095             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1096                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1097             }
1098             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1099                                    .getNhConversionSupportValueStyle() ),
1100                            title );
1101         }
1102     }
1103
1104     void viewAsNH() {
1105         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1106             String title = "New Hampshire";
1107             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1108                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1109             }
1110             showTextFrame( getMainPanel().getCurrentPhylogeny()
1111                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1112                            title );
1113         }
1114     }
1115
1116     void viewAsXML() {
1117         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1118             String title = "phyloXML";
1119             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1120                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1121             }
1122             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1123         }
1124     }
1125
1126     private void chooseFont() {
1127         final FontChooser fc = new FontChooser();
1128         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1129         fc.showDialog( this, "Select the Base Font" );
1130         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1131     }
1132
1133     private void chooseMinimalConfidence() {
1134         final String s = ( String ) JOptionPane
1135                 .showInputDialog( this,
1136                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1137                                           + getOptions().getMinConfidenceValue() + "]\n",
1138                                   "Minimal Confidence Value",
1139                                   JOptionPane.QUESTION_MESSAGE,
1140                                   null,
1141                                   null,
1142                                   getOptions().getMinConfidenceValue() );
1143         if ( !ForesterUtil.isEmpty( s ) ) {
1144             boolean success = true;
1145             double m = 0.0;
1146             final String m_str = s.trim();
1147             if ( !ForesterUtil.isEmpty( m_str ) ) {
1148                 try {
1149                     m = Double.parseDouble( m_str );
1150                 }
1151                 catch ( final Exception ex ) {
1152                     success = false;
1153                 }
1154             }
1155             else {
1156                 success = false;
1157             }
1158             if ( success && ( m >= 0.0 ) ) {
1159                 getOptions().setMinConfidenceValue( m );
1160             }
1161         }
1162     }
1163
1164     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1165         if ( item != null ) {
1166             item.setFont( MainFrame.menu_font );
1167             if ( !getConfiguration().isUseNativeUI() ) {
1168                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1169                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1170             }
1171             item.setSelected( is_selected );
1172             item.addActionListener( this );
1173         }
1174     }
1175
1176     private MainPanel getMainPanel() {
1177         return _main_panel;
1178     }
1179
1180     private boolean isScreenAntialias() {
1181         return true;
1182     }
1183
1184     private void removeBranchColors() {
1185         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1186             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1187         }
1188     }
1189
1190     private void setMainPanel( final MainPanelApplets main_panel ) {
1191         _main_panel = main_panel;
1192     }
1193
1194     private void setupUI() {
1195         try {
1196             if ( getConfiguration().isUseNativeUI() ) {
1197                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1198             }
1199             else {
1200                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1201             }
1202         }
1203         catch ( final UnsupportedLookAndFeelException e ) {
1204             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1205         }
1206         catch ( final ClassNotFoundException e ) {
1207             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1208         }
1209         catch ( final InstantiationException e ) {
1210             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1211         }
1212         catch ( final IllegalAccessException e ) {
1213             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1214         }
1215         catch ( final Exception e ) {
1216             AptxUtil.dieWithSystemError( e.toString() );
1217         }
1218     }
1219
1220     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1221         for( final TreePanel tree_panel : treepanels ) {
1222             tree_panel.setTextAntialias();
1223         }
1224     }
1225 }