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.Map;
  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.JMenu;
  23 import javax.swing.JMenuBar;
  24 import javax.swing.JMenuItem;
  25 import javax.swing.JOptionPane;
  26 import javax.swing.JRadioButtonMenuItem;
  27 import javax.swing.UIManager;
  28 import javax.swing.UnsupportedLookAndFeelException;
  29 import javax.swing.event.ChangeEvent;
  30 import javax.swing.event.ChangeListener;
  31
  32 import org.apache.commons.codec.binary.Base64;
  33 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  34 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  35 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  36 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.data.SequenceRelation;
  39 import org.forester.util.ForesterConstants;
  40 import org.forester.util.ForesterUtil;
  41
  42 // Use like this:
  43 // <applet archive="forester.jar"
  44 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  45 // codebase="http://www.myserver.org/path/to/forester"
  46 // width="600"
  47 // height="500"
  48 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  49 // <param name="url_of_tree_to_load"
  50 // value="http://www.myserver.org/examples/data/apaf.xml">
  51 // <param name="config_file"
  52 // value="http://www.myserver.org/examples/config/config_file.txt">
  53 // </applet>
  54 public class ArchaeopteryxE extends JApplet implements ActionListener {
  55
  56     private final static String         NAME             = "ArchaeopteryxE";
  57     private static final long           serialVersionUID = -1220055577935759443L;
  58     private Configuration               _configuration;
  59     private MainPanelApplets            _main_panel;
  60     private JMenuBar                    _jmenubar;
  61     private JMenu                       _options_jmenu;
  62     private JMenu                       _font_size_menu;
  63     private JMenuItem                   _super_tiny_fonts_mi;
  64     private JMenuItem                   _tiny_fonts_mi;
  65     private JMenuItem                   _small_fonts_mi;
  66     private JMenuItem                   _medium_fonts_mi;
  67     private JMenuItem                   _large_fonts_mi;
  68     private JMenu                       _tools_menu;
  69     private JMenuItem                   _taxcolor_item;
  70     private JMenuItem                   _confcolor_item;
  71     private JMenuItem                   _midpoint_root_item;
  72     private JMenu                       _view_jmenu;
  73     private JMenuItem                   _view_as_XML_item;
  74     private JMenuItem                   _view_as_NH_item;
  75     private JMenuItem                   _view_as_nexus_item;
  76     private JMenuItem                   _display_basic_information_item;
  77     private JMenu                       _type_menu;
  78     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  79     private JCheckBoxMenuItem           _triangular_type_cbmi;
  80     private JCheckBoxMenuItem           _curved_type_cbmi;
  81     private JCheckBoxMenuItem           _convex_type_cbmi;
  82     private JCheckBoxMenuItem           _euro_type_cbmi;
  83     private JCheckBoxMenuItem           _rounded_type_cbmi;
  84     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  85     private JCheckBoxMenuItem           _circular_type_cbmi;
  86     private JMenuItem                   _help_item;
  87     private JMenuItem                   _about_item;
  88     private JMenu                       _help_jmenu;
  89     private JMenuItem                   _website_item;
  90     private JMenuItem                   _phyloxml_website_item;
  91     private JMenuItem                   _phyloxml_ref_item;
  92     private JMenuItem                   _aptx_ref_item;
  93     private JMenuItem                   _remove_branch_color_item;
  94     private JCheckBoxMenuItem           _show_domain_labels;
  95     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
  96     private JCheckBoxMenuItem           _abbreviate_scientific_names;
  97     private JCheckBoxMenuItem           _screen_antialias_cbmi;
  98     private JCheckBoxMenuItem           _background_gradient_cbmi;
  99     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 100     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 101     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 102     private Options                     _options;
 103     private JMenuItem                   _choose_font_mi;
 104     private JMenuItem                   _switch_colors_mi;
 105     JCheckBoxMenuItem                   _label_direction_cbmi;
 106     private JCheckBoxMenuItem           _show_scale_cbmi;
 107     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 108     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 109     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 110     private JCheckBoxMenuItem           _show_overview_cbmi;
 111     private JMenuItem                   _choose_minimal_confidence_mi;
 112     private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 113     private JMenuItem                   _collapse_species_specific_subtrees;
 114     private JMenuItem                   _overview_placment_mi;
 115     private ButtonGroup                 _radio_group_1;
 116     private JCheckBoxMenuItem           _show_default_node_shapes_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_cbmi ) {
 270             updateOptions( getOptions() );
 271         }
 272         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 273             updateOptions( getOptions() );
 274         }
 275         else if ( o == _about_item ) {
 276             MainFrame.about();
 277         }
 278         else if ( o == _help_item ) {
 279             help( getConfiguration().getWebLinks() );
 280         }
 281         else if ( o == _website_item ) {
 282             try {
 283                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 284             }
 285             catch ( final IOException e1 ) {
 286                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 287             }
 288         }
 289         else if ( o == _phyloxml_website_item ) {
 290             try {
 291                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 292             }
 293             catch ( final IOException e1 ) {
 294                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 295             }
 296         }
 297         else if ( o == _aptx_ref_item ) {
 298             try {
 299                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 300             }
 301             catch ( final IOException e1 ) {
 302                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 303             }
 304         }
 305         else if ( o == _phyloxml_ref_item ) {
 306             try {
 307                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 308             }
 309             catch ( final IOException e1 ) {
 310                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 311             }
 312         }
 313         repaint();
 314     }
 315
 316     @Override
 317     public void destroy() {
 318         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 319         removeAllTextFrames();
 320         if ( getMainPanel() != null ) {
 321             getMainPanel().terminate();
 322         }
 323     }
 324
 325     /**
 326      * This method returns the current external node data which
 327      * has been selected by the user by clicking the "Return ..."
 328      * menu item. This method is expected to be called from Javascript or
 329      * something like it.
 330      *
 331      * @return current external node data as String
 332      */
 333     public String getCurrentExternalNodesDataBuffer() {
 334         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 335     }
 336
 337     public int getCurrentExternalNodesDataBufferChangeCounter() {
 338         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 339     }
 340
 341     public int getCurrentExternalNodesDataBufferLength() {
 342         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 343     }
 344
 345     /**
 346      * This method returns the current phylogeny as a string in the chosen format
 347      *
 348      * @param format must be NH, NHX, NEXUS or PHYLOXML
 349      * @return the phylogeny string
 350      * @author Herve Menager
 351      */
 352     public String getCurrentPhylogeny( final String format ) {
 353         removeAllTextFrames();
 354         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 355                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 356             return new String();
 357         }
 358         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 359             case NH:
 360                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 361             case NHX:
 362                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 363             case NEXUS:
 364                 return getMainPanel().getCurrentPhylogeny().toNexus();
 365             case PHYLOXML:
 366                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 367             default:
 368                 break;
 369         }
 370         return new String();
 371     }
 372
 373     /**
 374      * This method returns a view of the current phylogeny in a chosen
 375      * graphics format, base64-encoded in a string so that in can be used
 376      * from javascript.
 377      *
 378      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 379      * @return the phylogeny string
 380      * @author Herve Menager
 381      */
 382     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 383         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 384         try {
 385             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 386                                                                     _main_panel.getWidth(),
 387                                                                     _main_panel.getHeight(),
 388                                                                     getCurrentTreePanel(),
 389                                                                     getCurrentTreePanel().getControlPanel(),
 390                                                                     GraphicsExportType.valueOf( format ),
 391                                                                     getOptions() );
 392         }
 393         catch ( final IOException ioe ) {
 394             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 395             ioe.printStackTrace();
 396             JOptionPane.showMessageDialog( this,
 397                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 398                                            "Failed to generate graphics",
 399                                            JOptionPane.ERROR_MESSAGE );
 400             return null;
 401         }
 402         final byte[] bytes = baos.toByteArray();
 403         final String dataImg = Base64.encodeBase64String( bytes );
 404         return dataImg;
 405     }
 406
 407     public Options getOptions() {
 408         return _options;
 409     }
 410
 411     @Override
 412     public void init() {
 413         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 414         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 415         final Configuration configuration = new Configuration( config_filename, true, true, true );
 416         setConfiguration( configuration );
 417         setOptions( Options.createInstance( configuration ) );
 418         setupUI();
 419         URL phys_url = null;
 420         Phylogeny[] phys = null;
 421         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 422         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 423         // Get URL to tree file
 424         if ( phys_url_string != null ) {
 425             try {
 426                 phys_url = new URL( phys_url_string );
 427             }
 428             catch ( final Exception e ) {
 429                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 430                 e.printStackTrace();
 431                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 432                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 433             }
 434         }
 435         // Load the tree from URL
 436         if ( phys_url != null ) {
 437             try {
 438                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 439                                                         getConfiguration().isValidatePhyloXmlAgainstSchema(),
 440                                                         getConfiguration().isReplaceUnderscoresInNhParsing(),
 441                                                         getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 442                                                         getConfiguration().getTaxonomyExtraction() );
 443             }
 444             catch ( final Exception e ) {
 445                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 446                 e.printStackTrace();
 447                 JOptionPane.showMessageDialog( this,
 448                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 449                                                "Failed to read phylogenies",
 450                                                JOptionPane.ERROR_MESSAGE );
 451             }
 452         }
 453         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 454             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 455             JOptionPane.showMessageDialog( this,
 456                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 457                                            "Failed to read phylogenies",
 458                                            JOptionPane.ERROR_MESSAGE );
 459             return;
 460         }
 461         else {
 462             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 463         }
 464         setVisible( false );
 465         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 466         _jmenubar = new JMenuBar();
 467         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 468             if ( !getConfiguration().isUseNativeUI() ) {
 469                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 470             }
 471             buildToolsMenu();
 472             buildViewMenu();
 473             buildFontSizeMenu();
 474             buildOptionsMenu();
 475             buildTypeMenu();
 476             buildHelpMenu();
 477             setJMenuBar( _jmenubar );
 478         }
 479         final Container contentpane = getContentPane();
 480         contentpane.setLayout( new BorderLayout() );
 481         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 482         addComponentListener( new ComponentAdapter() {
 483
 484             @Override
 485             public void componentResized( final ComponentEvent e ) {
 486                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 487                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 488                                                                                            .getWidth(),
 489                                                                                    getMainPanel().getCurrentTreePanel()
 490                                                                                            .getHeight(),
 491                                                                                    false );
 492                 }
 493             }
 494         } );
 495         if ( getConfiguration().isUseTabbedDisplay() ) {
 496             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 497             AptxUtil.addPhylogeniesToTabs( phys,
 498                                            new File( phys_url.getFile() ).getName(),
 499                                            phys_url.toString(),
 500                                            getConfiguration(),
 501                                            getMainPanel() );
 502         }
 503         else {
 504             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 505             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 506         }
 507         validate();
 508         setName( NAME );
 509         getMainPanel().getControlPanel().showWholeAll();
 510         getMainPanel().getControlPanel().showWhole();
 511         System.gc();
 512         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 513         /* GUILHEM_BEG */
 514         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 515         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 516                 .getRelevantSequenceRelationTypes() ) {
 517             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 518         }
 519         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 520         if ( default_relation != null ) {
 521             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 522         }
 523         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 524         if ( default_sequence != null ) {
 525             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 526             /* GUILHEM_END */
 527         }
 528         setVisible( true );
 529     }
 530
 531     public void showTextFrame( final String s, final String title ) {
 532         checkTextFrames();
 533         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 534     }
 535
 536     @Override
 537     public void start() {
 538         if ( getMainPanel() != null ) {
 539             getMainPanel().validate();
 540         }
 541         requestFocus();
 542         requestFocusInWindow();
 543         requestFocus();
 544         AptxUtil.printAppletMessage( NAME, "started" );
 545     }
 546
 547     void buildFontSizeMenu() {
 548         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 549         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 550         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 551         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 552         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 553         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 554         customizeJMenuItem( _super_tiny_fonts_mi );
 555         customizeJMenuItem( _tiny_fonts_mi );
 556         customizeJMenuItem( _small_fonts_mi );
 557         customizeJMenuItem( _medium_fonts_mi );
 558         customizeJMenuItem( _large_fonts_mi );
 559         _jmenubar.add( _font_size_menu );
 560     }
 561
 562     void buildHelpMenu() {
 563         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 564         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 565         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 566         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 567         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 568         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 569         _help_jmenu.addSeparator();
 570         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 571         customizeJMenuItem( _help_item );
 572         customizeJMenuItem( _website_item );
 573         customizeJMenuItem( _phyloxml_website_item );
 574         customizeJMenuItem( _aptx_ref_item );
 575         customizeJMenuItem( _phyloxml_ref_item );
 576         customizeJMenuItem( _about_item );
 577         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 578         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 579         _jmenubar.add( _help_jmenu );
 580     }
 581
 582     void buildOptionsMenu() {
 583         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 584         _options_jmenu.addChangeListener( new ChangeListener() {
 585
 586             @Override
 587             public void stateChanged( final ChangeEvent e ) {
 588                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 589                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 590                 MainFrame
 591                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 592                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 593                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 594                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 595                                                                      _show_scale_cbmi,
 596                                                                      _show_branch_length_values_cbmi,
 597                                                                      _non_lined_up_cladograms_rbmi,
 598                                                                      _uniform_cladograms_rbmi,
 599                                                                      _ext_node_dependent_cladogram_rbmi,
 600                                                                      _label_direction_cbmi );
 601                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 602                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 603                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 604             }
 605         } );
 606         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 607                                                                 getConfiguration() ) );
 608         _options_jmenu
 609                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 610         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 611         _options_jmenu
 612                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 613         _radio_group_1 = new ButtonGroup();
 614         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 615         _radio_group_1.add( _uniform_cladograms_rbmi );
 616         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 617         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 618         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 619         _options_jmenu
 620                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 621         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 622         _options_jmenu
 623                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 624         _options_jmenu
 625                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 626         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 627         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 628         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 629         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 630         _options_jmenu
 631                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 632         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 633         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 634         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 635         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 636         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 637         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 638             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 639         }
 640         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 641         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 642         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 643         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 644         _options_jmenu.addSeparator();
 645         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 646                                                                 getConfiguration() ) );
 647         _options_jmenu
 648                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 649         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 650         _options_jmenu
 651                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 652         customizeJMenuItem( _choose_font_mi );
 653         customizeJMenuItem( _choose_minimal_confidence_mi );
 654         customizeJMenuItem( _switch_colors_mi );
 655         customizeJMenuItem( _overview_placment_mi );
 656         customizeCheckBoxMenuItem( _label_direction_cbmi,
 657                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 658         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 659         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 660         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 661         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 662         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 663         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 664         customizeJMenuItem( _cycle_node_shape_mi );
 665         customizeJMenuItem( _cycle_node_fill_mi );
 666         customizeJMenuItem( _choose_node_size_mi );
 667         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 668         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 669         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 670         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 671                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 672         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 673                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 674         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 675                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 676         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 677         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 678         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 679         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 680         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 681         _jmenubar.add( _options_jmenu );
 682     }
 683
 684     void buildToolsMenu() {
 685         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 686         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 687         customizeJMenuItem( _confcolor_item );
 688         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 689         customizeJMenuItem( _taxcolor_item );
 690         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 691         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 692         customizeJMenuItem( _remove_branch_color_item );
 693         _tools_menu.addSeparator();
 694         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 695         customizeJMenuItem( _midpoint_root_item );
 696         _tools_menu.addSeparator();
 697         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 698         customizeJMenuItem( _collapse_species_specific_subtrees );
 699         _jmenubar.add( _tools_menu );
 700     }
 701
 702     void buildTypeMenu() {
 703         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 704         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 705         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 706         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 707         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 708         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 709         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 710         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 711         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 712         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 713         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 714         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 715         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 716         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 717         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 718         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 719         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 720         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 721         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 722         initializeTypeMenu( getOptions() );
 723         _jmenubar.add( _type_menu );
 724     }
 725
 726     void buildViewMenu() {
 727         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 728         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 729         _view_jmenu.addSeparator();
 730         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 731         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 732         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 733         customizeJMenuItem( _display_basic_information_item );
 734         customizeJMenuItem( _view_as_NH_item );
 735         customizeJMenuItem( _view_as_XML_item );
 736         customizeJMenuItem( _view_as_nexus_item );
 737         _jmenubar.add( _view_jmenu );
 738     }
 739
 740     void checkTextFrames() {
 741         if ( _textframes.size() > 5 ) {
 742             try {
 743                 if ( _textframes.getFirst() != null ) {
 744                     _textframes.getFirst().removeMe();
 745                 }
 746                 else {
 747                     _textframes.removeFirst();
 748                 }
 749             }
 750             catch ( final NoSuchElementException e ) {
 751                 // Ignore.
 752             }
 753         }
 754     }
 755
 756     void clearCurrentExternalNodesDataBuffer() {
 757         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 758     }
 759
 760     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 761         if ( item != null ) {
 762             item.setFont( MainFrame.menu_font );
 763             if ( !getConfiguration().isUseNativeUI() ) {
 764                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 765                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 766             }
 767             item.setSelected( is_selected );
 768             item.addActionListener( this );
 769         }
 770     }
 771
 772     void customizeJMenuItem( final JMenuItem jmi ) {
 773         jmi.setFont( MainFrame.menu_font );
 774         if ( !getConfiguration().isUseNativeUI() ) {
 775             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 776             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 777         }
 778         jmi.addActionListener( this );
 779     }
 780
 781     void displayBasicInformation() {
 782         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 783             String title = "Basic Information";
 784             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 785                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
 786             }
 787             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
 788         }
 789     }
 790
 791     Configuration getConfiguration() {
 792         return _configuration;
 793     }
 794
 795     TreePanel getCurrentTreePanel() {
 796         return getMainPanel().getCurrentTreePanel();
 797     }
 798
 799     JCheckBoxMenuItem getlabelDirectionCbmi() {
 800         return _label_direction_cbmi;
 801     }
 802
 803     Options getOtions() {
 804         return _options;
 805     }
 806
 807     void help( final Map<String, WebLink> weblinks ) {
 808         final StringBuilder sb = new StringBuilder();
 809         sb.append( "Display options\n" );
 810         sb.append( "-------------------\n" );
 811         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 812         sb.append( "Clickable tree nodes\n" );
 813         sb.append( "--------------------\n" );
 814         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 815         sb.append( "or by right clicking:\n" );
 816         sb.append( "o  Display Node Data -- display information for a node\n" );
 817         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 818         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 819         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 820         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 821         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 822         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 823         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 824         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 825         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 826         sb.append( "Zooming\n" );
 827         sb.append( "---------\n" );
 828         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 829         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 830         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 831         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 832         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 833         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 834         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 835         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 836         sb.append( "Quick tree manipulation:\n" );
 837         sb.append( "------------------------\n" );
 838         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 839         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 840         sb.append( "Memory problems (Java heap space error)\n" );
 841         sb.append( "---------------------------------------\n" );
 842         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 843         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 844         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 845         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 846         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 847             sb.append( "Active web links\n" );
 848             sb.append( "--------------------\n" );
 849             for( final String key : weblinks.keySet() ) {
 850                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 851             }
 852         }
 853         sb.append( "\n" );
 854         sb.append( "phyloXML\n" );
 855         sb.append( "-------------------\n" );
 856         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 857         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 858         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 859         sb.append( "\n" );
 860         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 861         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 862         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 863     }
 864
 865     void initializeTypeMenu( final Options options ) {
 866         setTypeMenuToAllUnselected();
 867         try {
 868             switch ( options.getPhylogenyGraphicsType() ) {
 869                 case CONVEX:
 870                     _convex_type_cbmi.setSelected( true );
 871                     break;
 872                 case CURVED:
 873                     _curved_type_cbmi.setSelected( true );
 874                     break;
 875                 case EURO_STYLE:
 876                     _euro_type_cbmi.setSelected( true );
 877                     break;
 878                 case ROUNDED:
 879                     _rounded_type_cbmi.setSelected( true );
 880                     break;
 881                 case TRIANGULAR:
 882                     _triangular_type_cbmi.setSelected( true );
 883                     break;
 884                 case UNROOTED:
 885                     _unrooted_type_cbmi.setSelected( true );
 886                     break;
 887                 case CIRCULAR:
 888                     _circular_type_cbmi.setSelected( true );
 889                     break;
 890                 default:
 891                     _rectangular_type_cbmi.setSelected( true );
 892                     break;
 893             }
 894         }
 895         catch ( final NullPointerException np ) {
 896             // In all likelihood, this is caused by menu-less display.
 897         }
 898     }
 899
 900     void removeAllTextFrames() {
 901         for( final TextFrame tf : _textframes ) {
 902             if ( tf != null ) {
 903                 tf.close();
 904             }
 905         }
 906         _textframes.clear();
 907     }
 908
 909     void setConfiguration( final Configuration configuration ) {
 910         _configuration = configuration;
 911     }
 912
 913     void setOptions( final Options options ) {
 914         _options = options;
 915     }
 916
 917     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 918         setTypeMenuToAllUnselected();
 919         try {
 920             switch ( type ) {
 921                 case CIRCULAR:
 922                     _circular_type_cbmi.setSelected( true );
 923                     break;
 924                 case CONVEX:
 925                     _convex_type_cbmi.setSelected( true );
 926                     break;
 927                 case CURVED:
 928                     _curved_type_cbmi.setSelected( true );
 929                     break;
 930                 case EURO_STYLE:
 931                     _euro_type_cbmi.setSelected( true );
 932                     break;
 933                 case ROUNDED:
 934                     _rounded_type_cbmi.setSelected( true );
 935                     break;
 936                 case RECTANGULAR:
 937                     _rectangular_type_cbmi.setSelected( true );
 938                     break;
 939                 case TRIANGULAR:
 940                     _triangular_type_cbmi.setSelected( true );
 941                     break;
 942                 case UNROOTED:
 943                     _unrooted_type_cbmi.setSelected( true );
 944                     break;
 945                 default:
 946                     throw new IllegalArgumentException( "unknown type: " + type );
 947             }
 948         }
 949         catch ( final NullPointerException np ) {
 950             // In all likelihood, this is caused by menu-less display.
 951         }
 952     }
 953
 954     void setTypeMenuToAllUnselected() {
 955         if ( _convex_type_cbmi != null ) {
 956             _convex_type_cbmi.setSelected( false );
 957         }
 958         if ( _curved_type_cbmi != null ) {
 959             _curved_type_cbmi.setSelected( false );
 960         }
 961         if ( _euro_type_cbmi != null ) {
 962             _euro_type_cbmi.setSelected( false );
 963         }
 964         if ( _rounded_type_cbmi != null ) {
 965             _rounded_type_cbmi.setSelected( false );
 966         }
 967         if ( _triangular_type_cbmi != null ) {
 968             _triangular_type_cbmi.setSelected( false );
 969         }
 970         if ( _rectangular_type_cbmi != null ) {
 971             _rectangular_type_cbmi.setSelected( false );
 972         }
 973         if ( _unrooted_type_cbmi != null ) {
 974             _unrooted_type_cbmi.setSelected( false );
 975         }
 976         if ( _circular_type_cbmi != null ) {
 977             _circular_type_cbmi.setSelected( false );
 978         }
 979     }
 980
 981     void switchColors() {
 982         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 983         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 984         csc.setVisible( true );
 985         getMainPanel().setTreeColorSet( colorset );
 986     }
 987
 988     void typeChanged( final Object o ) {
 989         updateTypeCheckboxes( getOptions(), o );
 990         updateOptions( getOptions() );
 991         if ( getCurrentTreePanel() != null ) {
 992             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
 993             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
 994             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 995                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
 996                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 997                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
 998                 getCurrentTreePanel().getControlPanel().showWhole();
 999             }
1000             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1001                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1002             }
1003             else {
1004                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1005             }
1006             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1007             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1008         }
1009     }
1010
1011     void updateOptions( final Options options ) {
1012         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1013         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1014                 && _background_gradient_cbmi.isSelected() );
1015         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1016         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1017                 && _abbreviate_scientific_names.isSelected() );
1018         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1019                 && _color_labels_same_as_parent_branch.isSelected() );
1020         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1021                 && _show_default_node_shapes_cbmi.isSelected() );
1022         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1023                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1024         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1025             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1026         }
1027         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1028             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1029         }
1030         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1031             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1032         }
1033         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1034                 && _search_case_senstive_cbmi.isSelected() );
1035         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1036             options.setShowScale( _show_scale_cbmi.isSelected() );
1037         }
1038         if ( _label_direction_cbmi != null ) {
1039             if ( _label_direction_cbmi.isSelected() ) {
1040                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1041             }
1042             else {
1043                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1044             }
1045         }
1046         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1047         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1048                 && _show_confidence_stddev_cbmi.isSelected() );
1049         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1050             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1051         }
1052         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1053                 && _search_whole_words_only_cbmi.isSelected() );
1054         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1055                 && _inverse_search_result_cbmi.isSelected() );
1056         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1057             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1058         }
1059         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1060             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1061         }
1062         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1063             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1064         }
1065         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1066             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1067         }
1068         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1069             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1070         }
1071         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1072             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1073         }
1074         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1075             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1076         }
1077         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1078             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1079         }
1080     }
1081
1082     void updateTypeCheckboxes( final Options options, final Object o ) {
1083         setTypeMenuToAllUnselected();
1084         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1085     }
1086
1087     void viewAsNexus() {
1088         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1089             String title = "Nexus";
1090             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1091                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1092             }
1093             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1094                                    .getNhConversionSupportValueStyle() ),
1095                            title );
1096         }
1097     }
1098
1099     void viewAsNH() {
1100         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1101             String title = "New Hampshire";
1102             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1103                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1104             }
1105             showTextFrame( getMainPanel().getCurrentPhylogeny()
1106                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1107                            title );
1108         }
1109     }
1110
1111     void viewAsXML() {
1112         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1113             String title = "phyloXML";
1114             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1115                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1116             }
1117             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1118         }
1119     }
1120
1121     private void chooseFont() {
1122         final FontChooser fc = new FontChooser();
1123         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1124         fc.showDialog( this, "Select the Base Font" );
1125         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1126     }
1127
1128     private void chooseMinimalConfidence() {
1129         final String s = ( String ) JOptionPane
1130                 .showInputDialog( this,
1131                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1132                                           + getOptions().getMinConfidenceValue() + "]\n",
1133                                   "Minimal Confidence Value",
1134                                   JOptionPane.QUESTION_MESSAGE,
1135                                   null,
1136                                   null,
1137                                   getOptions().getMinConfidenceValue() );
1138         if ( !ForesterUtil.isEmpty( s ) ) {
1139             boolean success = true;
1140             double m = 0.0;
1141             final String m_str = s.trim();
1142             if ( !ForesterUtil.isEmpty( m_str ) ) {
1143                 try {
1144                     m = Double.parseDouble( m_str );
1145                 }
1146                 catch ( final Exception ex ) {
1147                     success = false;
1148                 }
1149             }
1150             else {
1151                 success = false;
1152             }
1153             if ( success && ( m >= 0.0 ) ) {
1154                 getOptions().setMinConfidenceValue( m );
1155             }
1156         }
1157     }
1158
1159     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1160         if ( item != null ) {
1161             item.setFont( MainFrame.menu_font );
1162             if ( !getConfiguration().isUseNativeUI() ) {
1163                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1164                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1165             }
1166             item.setSelected( is_selected );
1167             item.addActionListener( this );
1168         }
1169     }
1170
1171     private MainPanel getMainPanel() {
1172         return _main_panel;
1173     }
1174
1175     private boolean isScreenAntialias() {
1176         return true;
1177     }
1178
1179     private void removeBranchColors() {
1180         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1181             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1182         }
1183     }
1184
1185     private void setMainPanel( final MainPanelApplets main_panel ) {
1186         _main_panel = main_panel;
1187     }
1188
1189     private void setupUI() {
1190         try {
1191             if ( getConfiguration().isUseNativeUI() ) {
1192                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1193             }
1194             else {
1195                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1196             }
1197         }
1198         catch ( final UnsupportedLookAndFeelException e ) {
1199             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1200         }
1201         catch ( final ClassNotFoundException e ) {
1202             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1203         }
1204         catch ( final InstantiationException e ) {
1205             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1206         }
1207         catch ( final IllegalAccessException e ) {
1208             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1209         }
1210         catch ( final Exception e ) {
1211             AptxUtil.dieWithSystemError( e.toString() );
1212         }
1213     }
1214
1215     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1216         for( final TreePanel tree_panel : treepanels ) {
1217             tree_panel.setTextAntialias();
1218         }
1219     }
1220 }