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_internal_cbmi;
 117     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 118     private JMenuItem                   _cycle_node_shape_mi;
 119     private JMenuItem                   _cycle_node_fill_mi;
 120     private JMenuItem                   _choose_node_size_mi;
 121     private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 122     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 123     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 124
 125     // private String                      _ext_node_data_buffer                = "";
 126     // private int                         _ext_node_data_buffer_change_counter = 0;
 127     @Override
 128     public void actionPerformed( final ActionEvent e ) {
 129         final Object o = e.getSource();
 130         if ( o == _midpoint_root_item ) {
 131             getMainPanel().getCurrentTreePanel().midpointRoot();
 132         }
 133         else if ( o == _taxcolor_item ) {
 134             getMainPanel().getCurrentTreePanel().taxColor();
 135         }
 136         else if ( o == _confcolor_item ) {
 137             getMainPanel().getCurrentTreePanel().confColor();
 138         }
 139         else if ( o == _collapse_species_specific_subtrees ) {
 140             if ( getCurrentTreePanel() != null ) {
 141                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 142             }
 143         }
 144         else if ( o == _remove_branch_color_item ) {
 145             removeBranchColors();
 146         }
 147         else if ( o == _switch_colors_mi ) {
 148             switchColors();
 149         }
 150         else if ( o == _display_basic_information_item ) {
 151             displayBasicInformation();
 152         }
 153         else if ( o == _view_as_NH_item ) {
 154             viewAsNH();
 155         }
 156         else if ( o == _view_as_XML_item ) {
 157             viewAsXML();
 158         }
 159         else if ( o == _view_as_nexus_item ) {
 160             viewAsNexus();
 161         }
 162         else if ( o == _super_tiny_fonts_mi ) {
 163             if ( getCurrentTreePanel() != null ) {
 164                 getCurrentTreePanel().setSuperTinyFonts();
 165                 getCurrentTreePanel().repaint();
 166             }
 167         }
 168         else if ( o == _tiny_fonts_mi ) {
 169             if ( getCurrentTreePanel() != null ) {
 170                 getCurrentTreePanel().setTinyFonts();
 171                 getCurrentTreePanel().repaint();
 172             }
 173         }
 174         else if ( o == _small_fonts_mi ) {
 175             if ( getCurrentTreePanel() != null ) {
 176                 getCurrentTreePanel().setSmallFonts();
 177                 getCurrentTreePanel().repaint();
 178             }
 179         }
 180         else if ( o == _medium_fonts_mi ) {
 181             if ( getCurrentTreePanel() != null ) {
 182                 getCurrentTreePanel().setMediumFonts();
 183                 getCurrentTreePanel().repaint();
 184             }
 185         }
 186         else if ( o == _large_fonts_mi ) {
 187             if ( getCurrentTreePanel() != null ) {
 188                 getCurrentTreePanel().setLargeFonts();
 189                 getCurrentTreePanel().repaint();
 190             }
 191         }
 192         else if ( o == _choose_font_mi ) {
 193             chooseFont();
 194         }
 195         else if ( o == _choose_minimal_confidence_mi ) {
 196             chooseMinimalConfidence();
 197         }
 198         else if ( o == _choose_node_size_mi ) {
 199             MainFrame.chooseNodeSize( getOptions(), this );
 200         }
 201         else if ( o == _overview_placment_mi ) {
 202             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 203         }
 204         else if ( o == _cycle_node_fill_mi ) {
 205             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 206         }
 207         else if ( o == _cycle_node_shape_mi ) {
 208             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 209         }
 210         else if ( o == _non_lined_up_cladograms_rbmi ) {
 211             updateOptions( getOptions() );
 212             _main_panel.getControlPanel().showWhole();
 213         }
 214         else if ( o == _uniform_cladograms_rbmi ) {
 215             updateOptions( getOptions() );
 216             _main_panel.getControlPanel().showWhole();
 217         }
 218         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 219             updateOptions( getOptions() );
 220             _main_panel.getControlPanel().showWhole();
 221         }
 222         else if ( o == _search_case_senstive_cbmi ) {
 223             updateOptions( getOptions() );
 224             getMainPanel().getControlPanel().search();
 225         }
 226         else if ( o == _search_whole_words_only_cbmi ) {
 227             updateOptions( getOptions() );
 228             getMainPanel().getControlPanel().search();
 229         }
 230         else if ( o == _inverse_search_result_cbmi ) {
 231             updateOptions( getOptions() );
 232             getMainPanel().getControlPanel().search();
 233         }
 234         else if ( o == _show_scale_cbmi ) {
 235             updateOptions( getOptions() );
 236         }
 237         else if ( o == _show_branch_length_values_cbmi ) {
 238             updateOptions( getOptions() );
 239         }
 240         else if ( o == _show_confidence_stddev_cbmi ) {
 241             updateOptions( getOptions() );
 242         }
 243         else if ( o == _label_direction_cbmi ) {
 244             updateOptions( getOptions() );
 245         }
 246         else if ( o == _show_overview_cbmi ) {
 247             updateOptions( getOptions() );
 248             if ( getCurrentTreePanel() != null ) {
 249                 getCurrentTreePanel().updateOvSizes();
 250             }
 251         }
 252         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 253                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 254                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 255             typeChanged( o );
 256         }
 257         else if ( o == _screen_antialias_cbmi ) {
 258             updateOptions( getOptions() );
 259             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 260         }
 261         else if ( o == _background_gradient_cbmi ) {
 262             updateOptions( getOptions() );
 263         }
 264         else if ( o == _show_domain_labels ) {
 265             updateOptions( getOptions() );
 266         }
 267         else if ( o == _color_labels_same_as_parent_branch ) {
 268             updateOptions( getOptions() );
 269         }
 270         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 271             updateOptions( getOptions() );
 272         }
 273         else if ( o == _show_default_node_shapes_external_cbmi ) {
 274             updateOptions( getOptions() );
 275         }
 276         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 277             updateOptions( getOptions() );
 278         }
 279         else if ( o == _about_item ) {
 280             MainFrame.about();
 281         }
 282         else if ( o == _help_item ) {
 283             help( getConfiguration().getWebLinks() );
 284         }
 285         else if ( o == _website_item ) {
 286             try {
 287                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 288             }
 289             catch ( final IOException e1 ) {
 290                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 291             }
 292         }
 293         else if ( o == _phyloxml_website_item ) {
 294             try {
 295                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 296             }
 297             catch ( final IOException e1 ) {
 298                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 299             }
 300         }
 301         else if ( o == _aptx_ref_item ) {
 302             try {
 303                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 304             }
 305             catch ( final IOException e1 ) {
 306                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 307             }
 308         }
 309         else if ( o == _phyloxml_ref_item ) {
 310             try {
 311                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 312             }
 313             catch ( final IOException e1 ) {
 314                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 315             }
 316         }
 317         repaint();
 318     }
 319
 320     @Override
 321     public void destroy() {
 322         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 323         removeAllTextFrames();
 324         if ( getMainPanel() != null ) {
 325             getMainPanel().terminate();
 326         }
 327     }
 328
 329     /**
 330      * This method returns the current external node data which
 331      * has been selected by the user by clicking the "Return ..."
 332      * menu item. This method is expected to be called from Javascript or
 333      * something like it.
 334      *
 335      * @return current external node data as String
 336      */
 337     public String getCurrentExternalNodesDataBuffer() {
 338         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 339     }
 340
 341     public int getCurrentExternalNodesDataBufferChangeCounter() {
 342         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 343     }
 344
 345     public int getCurrentExternalNodesDataBufferLength() {
 346         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 347     }
 348
 349     /**
 350      * This method returns the current phylogeny as a string in the chosen format
 351      *
 352      * @param format must be NH, NHX, NEXUS or PHYLOXML
 353      * @return the phylogeny string
 354      * @author Herve Menager
 355      */
 356     public String getCurrentPhylogeny( final String format ) {
 357         removeAllTextFrames();
 358         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 359                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 360             return new String();
 361         }
 362         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 363             case NH:
 364                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 365             case NHX:
 366                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 367             case NEXUS:
 368                 return getMainPanel().getCurrentPhylogeny().toNexus();
 369             case PHYLOXML:
 370                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 371             default:
 372                 break;
 373         }
 374         return new String();
 375     }
 376
 377     /**
 378      * This method returns a view of the current phylogeny in a chosen
 379      * graphics format, base64-encoded in a string so that in can be used
 380      * from javascript.
 381      *
 382      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 383      * @return the phylogeny string
 384      * @author Herve Menager
 385      */
 386     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 387         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 388         try {
 389             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 390                                                                     _main_panel.getWidth(),
 391                                                                     _main_panel.getHeight(),
 392                                                                     getCurrentTreePanel(),
 393                                                                     getCurrentTreePanel().getControlPanel(),
 394                                                                     GraphicsExportType.valueOf( format ),
 395                                                                     getOptions() );
 396         }
 397         catch ( final IOException ioe ) {
 398             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 399             ioe.printStackTrace();
 400             JOptionPane.showMessageDialog( this,
 401                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 402                                            "Failed to generate graphics",
 403                                            JOptionPane.ERROR_MESSAGE );
 404             return null;
 405         }
 406         final byte[] bytes = baos.toByteArray();
 407         final String dataImg = Base64.encodeBase64String( bytes );
 408         return dataImg;
 409     }
 410
 411     public Options getOptions() {
 412         return _options;
 413     }
 414
 415     @Override
 416     public void init() {
 417         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 418         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 419         final Configuration configuration = new Configuration( config_filename, true, true, true );
 420         setConfiguration( configuration );
 421         setOptions( Options.createInstance( configuration ) );
 422         setupUI();
 423         URL phys_url = null;
 424         Phylogeny[] phys = null;
 425         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 426         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 427         // Get URL to tree file
 428         if ( phys_url_string != null ) {
 429             try {
 430                 phys_url = new URL( phys_url_string );
 431             }
 432             catch ( final Exception e ) {
 433                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 434                 e.printStackTrace();
 435                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 436                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 437             }
 438         }
 439         // Load the tree from URL
 440         if ( phys_url != null ) {
 441             try {
 442                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 443                                                         getConfiguration().isValidatePhyloXmlAgainstSchema(),
 444                                                         getConfiguration().isReplaceUnderscoresInNhParsing(),
 445                                                         getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 446                                                         getConfiguration().getTaxonomyExtraction() );
 447             }
 448             catch ( final Exception e ) {
 449                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 450                 e.printStackTrace();
 451                 JOptionPane.showMessageDialog( this,
 452                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 453                                                "Failed to read phylogenies",
 454                                                JOptionPane.ERROR_MESSAGE );
 455             }
 456         }
 457         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 458             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 459             JOptionPane.showMessageDialog( this,
 460                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 461                                            "Failed to read phylogenies",
 462                                            JOptionPane.ERROR_MESSAGE );
 463             return;
 464         }
 465         else {
 466             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 467         }
 468         setVisible( false );
 469         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 470         _jmenubar = new JMenuBar();
 471         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 472             if ( !getConfiguration().isUseNativeUI() ) {
 473                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 474             }
 475             buildToolsMenu();
 476             buildViewMenu();
 477             buildFontSizeMenu();
 478             buildOptionsMenu();
 479             buildTypeMenu();
 480             buildHelpMenu();
 481             setJMenuBar( _jmenubar );
 482         }
 483         final Container contentpane = getContentPane();
 484         contentpane.setLayout( new BorderLayout() );
 485         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 486         addComponentListener( new ComponentAdapter() {
 487
 488             @Override
 489             public void componentResized( final ComponentEvent e ) {
 490                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 491                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 492                                                                                            .getWidth(),
 493                                                                                    getMainPanel().getCurrentTreePanel()
 494                                                                                            .getHeight(),
 495                                                                                    false );
 496                 }
 497             }
 498         } );
 499         if ( getConfiguration().isUseTabbedDisplay() ) {
 500             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 501             AptxUtil.addPhylogeniesToTabs( phys,
 502                                            new File( phys_url.getFile() ).getName(),
 503                                            phys_url.toString(),
 504                                            getConfiguration(),
 505                                            getMainPanel() );
 506         }
 507         else {
 508             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 509             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 510         }
 511         validate();
 512         setName( NAME );
 513         getMainPanel().getControlPanel().showWholeAll();
 514         getMainPanel().getControlPanel().showWhole();
 515         System.gc();
 516         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 517         /* GUILHEM_BEG */
 518         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 519         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 520                 .getRelevantSequenceRelationTypes() ) {
 521             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 522         }
 523         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 524         if ( default_relation != null ) {
 525             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 526         }
 527         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 528         if ( default_sequence != null ) {
 529             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 530             /* GUILHEM_END */
 531         }
 532         setVisible( true );
 533     }
 534
 535     public void showTextFrame( final String s, final String title ) {
 536         checkTextFrames();
 537         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 538     }
 539
 540     @Override
 541     public void start() {
 542         if ( getMainPanel() != null ) {
 543             getMainPanel().validate();
 544         }
 545         requestFocus();
 546         requestFocusInWindow();
 547         requestFocus();
 548         AptxUtil.printAppletMessage( NAME, "started" );
 549     }
 550
 551     void buildFontSizeMenu() {
 552         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 553         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 554         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 555         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 556         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 557         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 558         customizeJMenuItem( _super_tiny_fonts_mi );
 559         customizeJMenuItem( _tiny_fonts_mi );
 560         customizeJMenuItem( _small_fonts_mi );
 561         customizeJMenuItem( _medium_fonts_mi );
 562         customizeJMenuItem( _large_fonts_mi );
 563         _jmenubar.add( _font_size_menu );
 564     }
 565
 566     void buildHelpMenu() {
 567         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 568         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 569         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 570         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 571         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 572         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 573         _help_jmenu.addSeparator();
 574         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 575         customizeJMenuItem( _help_item );
 576         customizeJMenuItem( _website_item );
 577         customizeJMenuItem( _phyloxml_website_item );
 578         customizeJMenuItem( _aptx_ref_item );
 579         customizeJMenuItem( _phyloxml_ref_item );
 580         customizeJMenuItem( _about_item );
 581         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 582         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 583         _jmenubar.add( _help_jmenu );
 584     }
 585
 586     void buildOptionsMenu() {
 587         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 588         _options_jmenu.addChangeListener( new ChangeListener() {
 589
 590             @Override
 591             public void stateChanged( final ChangeEvent e ) {
 592                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 593                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 594                 MainFrame
 595                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 596                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 597                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 598                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 599                                                                      _show_scale_cbmi,
 600                                                                      _show_branch_length_values_cbmi,
 601                                                                      _non_lined_up_cladograms_rbmi,
 602                                                                      _uniform_cladograms_rbmi,
 603                                                                      _ext_node_dependent_cladogram_rbmi,
 604                                                                      _label_direction_cbmi );
 605                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 606                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 607                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 608             }
 609         } );
 610         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 611                                                                 getConfiguration() ) );
 612         _options_jmenu
 613                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 614         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 615         _options_jmenu
 616                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 617         _radio_group_1 = new ButtonGroup();
 618         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 619         _radio_group_1.add( _uniform_cladograms_rbmi );
 620         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 621         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 622         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 623         _options_jmenu
 624                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 625         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 626         _options_jmenu
 627                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 628         _options_jmenu
 629                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 630         _options_jmenu
 631                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 632         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 633         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 634         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 635         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 636         _options_jmenu
 637                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 638         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 639         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 640         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 641         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 642         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 643         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 644             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 645         }
 646         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 647         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 648         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 649         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 650         _options_jmenu.addSeparator();
 651         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 652                                                                 getConfiguration() ) );
 653         _options_jmenu
 654                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 655         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 656         _options_jmenu
 657                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 658         customizeJMenuItem( _choose_font_mi );
 659         customizeJMenuItem( _choose_minimal_confidence_mi );
 660         customizeJMenuItem( _switch_colors_mi );
 661         customizeJMenuItem( _overview_placment_mi );
 662         customizeCheckBoxMenuItem( _label_direction_cbmi,
 663                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 664         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 665         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 666         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 667         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 668         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 669                 .isShowDefaultNodeShapesExternal() );
 670         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 671                 .isShowDefaultNodeShapesInternal() );
 672         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 673         customizeJMenuItem( _cycle_node_shape_mi );
 674         customizeJMenuItem( _cycle_node_fill_mi );
 675         customizeJMenuItem( _choose_node_size_mi );
 676         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 677         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 678         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 679         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 680                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 681         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 682                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 683         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 684                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 685         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 686         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 687         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 688         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 689         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 690         _jmenubar.add( _options_jmenu );
 691     }
 692
 693     void buildToolsMenu() {
 694         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 695         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 696         customizeJMenuItem( _confcolor_item );
 697         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 698         customizeJMenuItem( _taxcolor_item );
 699         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 700         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 701         customizeJMenuItem( _remove_branch_color_item );
 702         _tools_menu.addSeparator();
 703         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 704         customizeJMenuItem( _midpoint_root_item );
 705         _tools_menu.addSeparator();
 706         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 707         customizeJMenuItem( _collapse_species_specific_subtrees );
 708         _jmenubar.add( _tools_menu );
 709     }
 710
 711     void buildTypeMenu() {
 712         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 713         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 714         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 715         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 716         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 717         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 718         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 719         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 720         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 721         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 722         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 723         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 724         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 725         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 726         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 727         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 728         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 729         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 730         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 731         initializeTypeMenu( getOptions() );
 732         _jmenubar.add( _type_menu );
 733     }
 734
 735     void buildViewMenu() {
 736         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 737         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 738         _view_jmenu.addSeparator();
 739         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 740         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 741         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 742         customizeJMenuItem( _display_basic_information_item );
 743         customizeJMenuItem( _view_as_NH_item );
 744         customizeJMenuItem( _view_as_XML_item );
 745         customizeJMenuItem( _view_as_nexus_item );
 746         _jmenubar.add( _view_jmenu );
 747     }
 748
 749     void checkTextFrames() {
 750         if ( _textframes.size() > 5 ) {
 751             try {
 752                 if ( _textframes.getFirst() != null ) {
 753                     _textframes.getFirst().removeMe();
 754                 }
 755                 else {
 756                     _textframes.removeFirst();
 757                 }
 758             }
 759             catch ( final NoSuchElementException e ) {
 760                 // Ignore.
 761             }
 762         }
 763     }
 764
 765     void clearCurrentExternalNodesDataBuffer() {
 766         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 767     }
 768
 769     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 770         if ( item != null ) {
 771             item.setFont( MainFrame.menu_font );
 772             if ( !getConfiguration().isUseNativeUI() ) {
 773                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 774                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 775             }
 776             item.setSelected( is_selected );
 777             item.addActionListener( this );
 778         }
 779     }
 780
 781     void customizeJMenuItem( final JMenuItem jmi ) {
 782         jmi.setFont( MainFrame.menu_font );
 783         if ( !getConfiguration().isUseNativeUI() ) {
 784             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 785             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 786         }
 787         jmi.addActionListener( this );
 788     }
 789
 790     void displayBasicInformation() {
 791         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 792             String title = "Basic Information";
 793             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 794                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
 795             }
 796             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
 797         }
 798     }
 799
 800     Configuration getConfiguration() {
 801         return _configuration;
 802     }
 803
 804     TreePanel getCurrentTreePanel() {
 805         return getMainPanel().getCurrentTreePanel();
 806     }
 807
 808     JCheckBoxMenuItem getlabelDirectionCbmi() {
 809         return _label_direction_cbmi;
 810     }
 811
 812     Options getOtions() {
 813         return _options;
 814     }
 815
 816     void help( final Map<String, WebLink> weblinks ) {
 817         final StringBuilder sb = new StringBuilder();
 818         sb.append( "Display options\n" );
 819         sb.append( "-------------------\n" );
 820         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 821         sb.append( "Clickable tree nodes\n" );
 822         sb.append( "--------------------\n" );
 823         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 824         sb.append( "or by right clicking:\n" );
 825         sb.append( "o  Display Node Data -- display information for a node\n" );
 826         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 827         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 828         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 829         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 830         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 831         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 832         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 833         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 834         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 835         sb.append( "Zooming\n" );
 836         sb.append( "---------\n" );
 837         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 838         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 839         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 840         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 841         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 842         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 843         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 844         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 845         sb.append( "Quick tree manipulation:\n" );
 846         sb.append( "------------------------\n" );
 847         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 848         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 849         sb.append( "Memory problems (Java heap space error)\n" );
 850         sb.append( "---------------------------------------\n" );
 851         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 852         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 853         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 854         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 855         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 856             sb.append( "Active web links\n" );
 857             sb.append( "--------------------\n" );
 858             for( final String key : weblinks.keySet() ) {
 859                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 860             }
 861         }
 862         sb.append( "\n" );
 863         sb.append( "phyloXML\n" );
 864         sb.append( "-------------------\n" );
 865         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 866         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 867         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 868         sb.append( "\n" );
 869         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 870         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 871         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 872     }
 873
 874     void initializeTypeMenu( final Options options ) {
 875         setTypeMenuToAllUnselected();
 876         try {
 877             switch ( options.getPhylogenyGraphicsType() ) {
 878                 case CONVEX:
 879                     _convex_type_cbmi.setSelected( true );
 880                     break;
 881                 case CURVED:
 882                     _curved_type_cbmi.setSelected( true );
 883                     break;
 884                 case EURO_STYLE:
 885                     _euro_type_cbmi.setSelected( true );
 886                     break;
 887                 case ROUNDED:
 888                     _rounded_type_cbmi.setSelected( true );
 889                     break;
 890                 case TRIANGULAR:
 891                     _triangular_type_cbmi.setSelected( true );
 892                     break;
 893                 case UNROOTED:
 894                     _unrooted_type_cbmi.setSelected( true );
 895                     break;
 896                 case CIRCULAR:
 897                     _circular_type_cbmi.setSelected( true );
 898                     break;
 899                 default:
 900                     _rectangular_type_cbmi.setSelected( true );
 901                     break;
 902             }
 903         }
 904         catch ( final NullPointerException np ) {
 905             // In all likelihood, this is caused by menu-less display.
 906         }
 907     }
 908
 909     void removeAllTextFrames() {
 910         for( final TextFrame tf : _textframes ) {
 911             if ( tf != null ) {
 912                 tf.close();
 913             }
 914         }
 915         _textframes.clear();
 916     }
 917
 918     void setConfiguration( final Configuration configuration ) {
 919         _configuration = configuration;
 920     }
 921
 922     void setOptions( final Options options ) {
 923         _options = options;
 924     }
 925
 926     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 927         setTypeMenuToAllUnselected();
 928         try {
 929             switch ( type ) {
 930                 case CIRCULAR:
 931                     _circular_type_cbmi.setSelected( true );
 932                     break;
 933                 case CONVEX:
 934                     _convex_type_cbmi.setSelected( true );
 935                     break;
 936                 case CURVED:
 937                     _curved_type_cbmi.setSelected( true );
 938                     break;
 939                 case EURO_STYLE:
 940                     _euro_type_cbmi.setSelected( true );
 941                     break;
 942                 case ROUNDED:
 943                     _rounded_type_cbmi.setSelected( true );
 944                     break;
 945                 case RECTANGULAR:
 946                     _rectangular_type_cbmi.setSelected( true );
 947                     break;
 948                 case TRIANGULAR:
 949                     _triangular_type_cbmi.setSelected( true );
 950                     break;
 951                 case UNROOTED:
 952                     _unrooted_type_cbmi.setSelected( true );
 953                     break;
 954                 default:
 955                     throw new IllegalArgumentException( "unknown type: " + type );
 956             }
 957         }
 958         catch ( final NullPointerException np ) {
 959             // In all likelihood, this is caused by menu-less display.
 960         }
 961     }
 962
 963     void setTypeMenuToAllUnselected() {
 964         if ( _convex_type_cbmi != null ) {
 965             _convex_type_cbmi.setSelected( false );
 966         }
 967         if ( _curved_type_cbmi != null ) {
 968             _curved_type_cbmi.setSelected( false );
 969         }
 970         if ( _euro_type_cbmi != null ) {
 971             _euro_type_cbmi.setSelected( false );
 972         }
 973         if ( _rounded_type_cbmi != null ) {
 974             _rounded_type_cbmi.setSelected( false );
 975         }
 976         if ( _triangular_type_cbmi != null ) {
 977             _triangular_type_cbmi.setSelected( false );
 978         }
 979         if ( _rectangular_type_cbmi != null ) {
 980             _rectangular_type_cbmi.setSelected( false );
 981         }
 982         if ( _unrooted_type_cbmi != null ) {
 983             _unrooted_type_cbmi.setSelected( false );
 984         }
 985         if ( _circular_type_cbmi != null ) {
 986             _circular_type_cbmi.setSelected( false );
 987         }
 988     }
 989
 990     void switchColors() {
 991         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 992         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 993         csc.setVisible( true );
 994         getMainPanel().setTreeColorSet( colorset );
 995     }
 996
 997     void typeChanged( final Object o ) {
 998         updateTypeCheckboxes( getOptions(), o );
 999         updateOptions( getOptions() );
1000         if ( getCurrentTreePanel() != null ) {
1001             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1002             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1003             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1004                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1005                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1006                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1007                 getCurrentTreePanel().getControlPanel().showWhole();
1008             }
1009             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1010                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1011             }
1012             else {
1013                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1014             }
1015             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1016             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1017         }
1018     }
1019
1020     void updateOptions( final Options options ) {
1021         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1022         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1023                 && _background_gradient_cbmi.isSelected() );
1024         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1025         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1026                 && _abbreviate_scientific_names.isSelected() );
1027         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1028                 && _color_labels_same_as_parent_branch.isSelected() );
1029         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1030                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1031         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1032                 && _show_default_node_shapes_external_cbmi.isSelected() );
1033         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1034                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1035         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1036             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1037         }
1038         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1039             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1040         }
1041         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1042             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1043         }
1044         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1045                 && _search_case_senstive_cbmi.isSelected() );
1046         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1047             options.setShowScale( _show_scale_cbmi.isSelected() );
1048         }
1049         if ( _label_direction_cbmi != null ) {
1050             if ( _label_direction_cbmi.isSelected() ) {
1051                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1052             }
1053             else {
1054                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1055             }
1056         }
1057         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1058         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1059                 && _show_confidence_stddev_cbmi.isSelected() );
1060         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1061             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1062         }
1063         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1064                 && _search_whole_words_only_cbmi.isSelected() );
1065         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1066                 && _inverse_search_result_cbmi.isSelected() );
1067         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1068             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1069         }
1070         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1071             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1072         }
1073         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1074             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1075         }
1076         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1077             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1078         }
1079         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1080             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1081         }
1082         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1083             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1084         }
1085         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1086             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1087         }
1088         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1089             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1090         }
1091     }
1092
1093     void updateTypeCheckboxes( final Options options, final Object o ) {
1094         setTypeMenuToAllUnselected();
1095         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1096     }
1097
1098     void viewAsNexus() {
1099         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1100             String title = "Nexus";
1101             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1102                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1103             }
1104             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1105                                    .getNhConversionSupportValueStyle() ),
1106                            title );
1107         }
1108     }
1109
1110     void viewAsNH() {
1111         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1112             String title = "New Hampshire";
1113             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1114                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1115             }
1116             showTextFrame( getMainPanel().getCurrentPhylogeny()
1117                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1118                            title );
1119         }
1120     }
1121
1122     void viewAsXML() {
1123         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1124             String title = "phyloXML";
1125             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1126                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1127             }
1128             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1129         }
1130     }
1131
1132     private void chooseFont() {
1133         final FontChooser fc = new FontChooser();
1134         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1135         fc.showDialog( this, "Select the Base Font" );
1136         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1137     }
1138
1139     private void chooseMinimalConfidence() {
1140         final String s = ( String ) JOptionPane
1141                 .showInputDialog( this,
1142                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1143                                           + getOptions().getMinConfidenceValue() + "]\n",
1144                                   "Minimal Confidence Value",
1145                                   JOptionPane.QUESTION_MESSAGE,
1146                                   null,
1147                                   null,
1148                                   getOptions().getMinConfidenceValue() );
1149         if ( !ForesterUtil.isEmpty( s ) ) {
1150             boolean success = true;
1151             double m = 0.0;
1152             final String m_str = s.trim();
1153             if ( !ForesterUtil.isEmpty( m_str ) ) {
1154                 try {
1155                     m = Double.parseDouble( m_str );
1156                 }
1157                 catch ( final Exception ex ) {
1158                     success = false;
1159                 }
1160             }
1161             else {
1162                 success = false;
1163             }
1164             if ( success && ( m >= 0.0 ) ) {
1165                 getOptions().setMinConfidenceValue( m );
1166             }
1167         }
1168     }
1169
1170     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1171         if ( item != null ) {
1172             item.setFont( MainFrame.menu_font );
1173             if ( !getConfiguration().isUseNativeUI() ) {
1174                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1175                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1176             }
1177             item.setSelected( is_selected );
1178             item.addActionListener( this );
1179         }
1180     }
1181
1182     private MainPanel getMainPanel() {
1183         return _main_panel;
1184     }
1185
1186     private boolean isScreenAntialias() {
1187         return true;
1188     }
1189
1190     private void removeBranchColors() {
1191         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1192             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1193         }
1194     }
1195
1196     private void setMainPanel( final MainPanelApplets main_panel ) {
1197         _main_panel = main_panel;
1198     }
1199
1200     private void setupUI() {
1201         try {
1202             if ( getConfiguration().isUseNativeUI() ) {
1203                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1204             }
1205             else {
1206                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1207             }
1208         }
1209         catch ( final UnsupportedLookAndFeelException e ) {
1210             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1211         }
1212         catch ( final ClassNotFoundException e ) {
1213             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1214         }
1215         catch ( final InstantiationException e ) {
1216             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1217         }
1218         catch ( final IllegalAccessException e ) {
1219             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1220         }
1221         catch ( final Exception e ) {
1222             AptxUtil.dieWithSystemError( e.toString() );
1223         }
1224     }
1225
1226     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1227         for( final TreePanel tree_panel : treepanels ) {
1228             tree_panel.setTextAntialias();
1229         }
1230     }
1231 }