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().calcParametersForPainting( getMainPanel()
 492                                                                                             .getCurrentTreePanel()
 493                                                                                             .getWidth(),
 494                                                                                     getMainPanel()
 495                                                                                             .getCurrentTreePanel()
 496                                                                                             .getHeight(),
 497                                                                                     getOptions()
 498                                                                                             .isAllowFontSizeChange() );
 499                 }
 500             }
 501         } );
 502         if ( getConfiguration().isUseTabbedDisplay() ) {
 503             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 504             AptxUtil.addPhylogeniesToTabs( phys,
 505                                            new File( phys_url.getFile() ).getName(),
 506                                            phys_url.toString(),
 507                                            getConfiguration(),
 508                                            getMainPanel() );
 509         }
 510         else {
 511             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 512             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 513         }
 514         validate();
 515         setName( NAME );
 516         getMainPanel().getControlPanel().showWholeAll();
 517         getMainPanel().getControlPanel().showWhole();
 518         System.gc();
 519         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 520         /* GUILHEM_BEG */
 521         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 522         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 523                 .getRelevantSequenceRelationTypes() ) {
 524             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 525         }
 526         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 527         if ( default_relation != null ) {
 528             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 529         }
 530         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 531         if ( default_sequence != null ) {
 532             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 533             /* GUILHEM_END */
 534         }
 535         setVisible( true );
 536     }
 537
 538     public void showTextFrame( final String s, final String title ) {
 539         checkTextFrames();
 540         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 541     }
 542
 543     @Override
 544     public void start() {
 545         if ( getMainPanel() != null ) {
 546             getMainPanel().validate();
 547         }
 548         requestFocus();
 549         requestFocusInWindow();
 550         requestFocus();
 551         AptxUtil.printAppletMessage( NAME, "started" );
 552     }
 553
 554     void buildFontSizeMenu() {
 555         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 556         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 557         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 558         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 559         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 560         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 561         customizeJMenuItem( _super_tiny_fonts_mi );
 562         customizeJMenuItem( _tiny_fonts_mi );
 563         customizeJMenuItem( _small_fonts_mi );
 564         customizeJMenuItem( _medium_fonts_mi );
 565         customizeJMenuItem( _large_fonts_mi );
 566         _jmenubar.add( _font_size_menu );
 567     }
 568
 569     void buildHelpMenu() {
 570         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 571         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 572         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 573         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 574         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 575         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 576         _help_jmenu.addSeparator();
 577         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 578         customizeJMenuItem( _help_item );
 579         customizeJMenuItem( _website_item );
 580         customizeJMenuItem( _phyloxml_website_item );
 581         customizeJMenuItem( _aptx_ref_item );
 582         customizeJMenuItem( _phyloxml_ref_item );
 583         customizeJMenuItem( _about_item );
 584         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 585         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 586         _jmenubar.add( _help_jmenu );
 587     }
 588
 589     void buildOptionsMenu() {
 590         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 591         _options_jmenu.addChangeListener( new ChangeListener() {
 592
 593             @Override
 594             public void stateChanged( final ChangeEvent e ) {
 595                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 596                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 597                 MainFrame
 598                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 599                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 600                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 601                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 602                                                                      _show_scale_cbmi,
 603                                                                      _show_branch_length_values_cbmi,
 604                                                                      _non_lined_up_cladograms_rbmi,
 605                                                                      _uniform_cladograms_rbmi,
 606                                                                      _ext_node_dependent_cladogram_rbmi,
 607                                                                      _label_direction_cbmi );
 608                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 609                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 610                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 611             }
 612         } );
 613         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 614                                                                 getConfiguration() ) );
 615         _options_jmenu
 616                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 617         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 618         _options_jmenu
 619                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 620         _radio_group_1 = new ButtonGroup();
 621         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 622         _radio_group_1.add( _uniform_cladograms_rbmi );
 623         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 624         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 625         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 626         _options_jmenu
 627                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 628         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 629         _options_jmenu
 630                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 631         _options_jmenu
 632                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 633         _options_jmenu
 634                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 635         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 636         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 637         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 638         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 639         _options_jmenu
 640                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 641         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 642         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 643         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 644         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 645         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 646         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 647             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 648         }
 649         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 650         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 651         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 652         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 653         _options_jmenu.addSeparator();
 654         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 655                                                                 getConfiguration() ) );
 656         _options_jmenu
 657                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 658         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 659         _options_jmenu
 660                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 661         customizeJMenuItem( _choose_font_mi );
 662         customizeJMenuItem( _choose_minimal_confidence_mi );
 663         customizeJMenuItem( _switch_colors_mi );
 664         customizeJMenuItem( _overview_placment_mi );
 665         customizeCheckBoxMenuItem( _label_direction_cbmi,
 666                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 667         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 668         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 669         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 670         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 671         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 672                 .isShowDefaultNodeShapesExternal() );
 673         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 674                 .isShowDefaultNodeShapesInternal() );
 675         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 676         customizeJMenuItem( _cycle_node_shape_mi );
 677         customizeJMenuItem( _cycle_node_fill_mi );
 678         customizeJMenuItem( _choose_node_size_mi );
 679         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 680         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 681         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 682         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 683                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 684         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 685                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 686         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 687                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 688         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 689         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 690         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 691         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 692         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 693         _jmenubar.add( _options_jmenu );
 694     }
 695
 696     void buildToolsMenu() {
 697         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 698         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 699         customizeJMenuItem( _confcolor_item );
 700         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 701         customizeJMenuItem( _taxcolor_item );
 702         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 703         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 704         customizeJMenuItem( _remove_branch_color_item );
 705         _tools_menu.addSeparator();
 706         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 707         customizeJMenuItem( _midpoint_root_item );
 708         _tools_menu.addSeparator();
 709         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 710         customizeJMenuItem( _collapse_species_specific_subtrees );
 711         _jmenubar.add( _tools_menu );
 712     }
 713
 714     void buildTypeMenu() {
 715         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 716         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 717         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 718         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 719         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 720         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 721         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 722         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 723         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 724         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 725         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 726         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 727         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 728         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 729         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 730         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 731         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 732         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 733         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 734         initializeTypeMenu( getOptions() );
 735         _jmenubar.add( _type_menu );
 736     }
 737
 738     void buildViewMenu() {
 739         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 740         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 741         _view_jmenu.addSeparator();
 742         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 743         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 744         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 745         customizeJMenuItem( _display_basic_information_item );
 746         customizeJMenuItem( _view_as_NH_item );
 747         customizeJMenuItem( _view_as_XML_item );
 748         customizeJMenuItem( _view_as_nexus_item );
 749         _jmenubar.add( _view_jmenu );
 750     }
 751
 752     void checkTextFrames() {
 753         if ( _textframes.size() > 5 ) {
 754             try {
 755                 if ( _textframes.getFirst() != null ) {
 756                     _textframes.getFirst().removeMe();
 757                 }
 758                 else {
 759                     _textframes.removeFirst();
 760                 }
 761             }
 762             catch ( final NoSuchElementException e ) {
 763                 // Ignore.
 764             }
 765         }
 766     }
 767
 768     void clearCurrentExternalNodesDataBuffer() {
 769         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 770     }
 771
 772     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 773         if ( item != null ) {
 774             item.setFont( MainFrame.menu_font );
 775             if ( !getConfiguration().isUseNativeUI() ) {
 776                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 777                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 778             }
 779             item.setSelected( is_selected );
 780             item.addActionListener( this );
 781         }
 782     }
 783
 784     void customizeJMenuItem( final JMenuItem jmi ) {
 785         jmi.setFont( MainFrame.menu_font );
 786         if ( !getConfiguration().isUseNativeUI() ) {
 787             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 788             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 789         }
 790         jmi.addActionListener( this );
 791     }
 792
 793     void displayBasicInformation() {
 794         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 795             String title = "Basic Information";
 796             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 797                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
 798             }
 799             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
 800         }
 801     }
 802
 803     Configuration getConfiguration() {
 804         return _configuration;
 805     }
 806
 807     TreePanel getCurrentTreePanel() {
 808         return getMainPanel().getCurrentTreePanel();
 809     }
 810
 811     JCheckBoxMenuItem getlabelDirectionCbmi() {
 812         return _label_direction_cbmi;
 813     }
 814
 815     Options getOtions() {
 816         return _options;
 817     }
 818
 819     void help( final Map<String, WebLink> weblinks ) {
 820         final StringBuilder sb = new StringBuilder();
 821         sb.append( "Display options\n" );
 822         sb.append( "-------------------\n" );
 823         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 824         sb.append( "Clickable tree nodes\n" );
 825         sb.append( "--------------------\n" );
 826         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 827         sb.append( "or by right clicking:\n" );
 828         sb.append( "o  Display Node Data -- display information for a node\n" );
 829         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 830         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 831         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 832         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 833         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 834         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 835         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 836         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 837         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 838         sb.append( "Zooming\n" );
 839         sb.append( "---------\n" );
 840         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 841         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 842         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 843         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 844         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 845         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 846         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 847         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 848         sb.append( "Quick tree manipulation:\n" );
 849         sb.append( "------------------------\n" );
 850         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 851         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 852         sb.append( "Memory problems (Java heap space error)\n" );
 853         sb.append( "---------------------------------------\n" );
 854         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 855         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 856         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 857         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 858         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 859             sb.append( "Active web links\n" );
 860             sb.append( "--------------------\n" );
 861             for( final String key : weblinks.keySet() ) {
 862                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 863             }
 864         }
 865         sb.append( "\n" );
 866         sb.append( "phyloXML\n" );
 867         sb.append( "-------------------\n" );
 868         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 869         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 870         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 871         sb.append( "\n" );
 872         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 873         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 874         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 875     }
 876
 877     void initializeTypeMenu( final Options options ) {
 878         setTypeMenuToAllUnselected();
 879         try {
 880             switch ( options.getPhylogenyGraphicsType() ) {
 881                 case CONVEX:
 882                     _convex_type_cbmi.setSelected( true );
 883                     break;
 884                 case CURVED:
 885                     _curved_type_cbmi.setSelected( true );
 886                     break;
 887                 case EURO_STYLE:
 888                     _euro_type_cbmi.setSelected( true );
 889                     break;
 890                 case ROUNDED:
 891                     _rounded_type_cbmi.setSelected( true );
 892                     break;
 893                 case TRIANGULAR:
 894                     _triangular_type_cbmi.setSelected( true );
 895                     break;
 896                 case UNROOTED:
 897                     _unrooted_type_cbmi.setSelected( true );
 898                     break;
 899                 case CIRCULAR:
 900                     _circular_type_cbmi.setSelected( true );
 901                     break;
 902                 default:
 903                     _rectangular_type_cbmi.setSelected( true );
 904                     break;
 905             }
 906         }
 907         catch ( final NullPointerException np ) {
 908             // In all likelihood, this is caused by menu-less display.
 909         }
 910     }
 911
 912     void removeAllTextFrames() {
 913         for( final TextFrame tf : _textframes ) {
 914             if ( tf != null ) {
 915                 tf.close();
 916             }
 917         }
 918         _textframes.clear();
 919     }
 920
 921     void setConfiguration( final Configuration configuration ) {
 922         _configuration = configuration;
 923     }
 924
 925     void setOptions( final Options options ) {
 926         _options = options;
 927     }
 928
 929     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 930         setTypeMenuToAllUnselected();
 931         try {
 932             switch ( type ) {
 933                 case CIRCULAR:
 934                     _circular_type_cbmi.setSelected( true );
 935                     break;
 936                 case CONVEX:
 937                     _convex_type_cbmi.setSelected( true );
 938                     break;
 939                 case CURVED:
 940                     _curved_type_cbmi.setSelected( true );
 941                     break;
 942                 case EURO_STYLE:
 943                     _euro_type_cbmi.setSelected( true );
 944                     break;
 945                 case ROUNDED:
 946                     _rounded_type_cbmi.setSelected( true );
 947                     break;
 948                 case RECTANGULAR:
 949                     _rectangular_type_cbmi.setSelected( true );
 950                     break;
 951                 case TRIANGULAR:
 952                     _triangular_type_cbmi.setSelected( true );
 953                     break;
 954                 case UNROOTED:
 955                     _unrooted_type_cbmi.setSelected( true );
 956                     break;
 957                 default:
 958                     throw new IllegalArgumentException( "unknown type: " + type );
 959             }
 960         }
 961         catch ( final NullPointerException np ) {
 962             // In all likelihood, this is caused by menu-less display.
 963         }
 964     }
 965
 966     void setTypeMenuToAllUnselected() {
 967         if ( _convex_type_cbmi != null ) {
 968             _convex_type_cbmi.setSelected( false );
 969         }
 970         if ( _curved_type_cbmi != null ) {
 971             _curved_type_cbmi.setSelected( false );
 972         }
 973         if ( _euro_type_cbmi != null ) {
 974             _euro_type_cbmi.setSelected( false );
 975         }
 976         if ( _rounded_type_cbmi != null ) {
 977             _rounded_type_cbmi.setSelected( false );
 978         }
 979         if ( _triangular_type_cbmi != null ) {
 980             _triangular_type_cbmi.setSelected( false );
 981         }
 982         if ( _rectangular_type_cbmi != null ) {
 983             _rectangular_type_cbmi.setSelected( false );
 984         }
 985         if ( _unrooted_type_cbmi != null ) {
 986             _unrooted_type_cbmi.setSelected( false );
 987         }
 988         if ( _circular_type_cbmi != null ) {
 989             _circular_type_cbmi.setSelected( false );
 990         }
 991     }
 992
 993     void switchColors() {
 994         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 995         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 996         csc.setVisible( true );
 997         getMainPanel().setTreeColorSet( colorset );
 998     }
 999
1000     void typeChanged( final Object o ) {
1001         updateTypeCheckboxes( getOptions(), o );
1002         updateOptions( getOptions() );
1003         if ( getCurrentTreePanel() != null ) {
1004             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1005             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1006             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1007                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1008                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1009                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1010                 getCurrentTreePanel().getControlPanel().showWhole();
1011             }
1012             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1013                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1014             }
1015             else {
1016                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1017             }
1018             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1019             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1020         }
1021     }
1022
1023     void updateOptions( final Options options ) {
1024         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1025         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1026                 && _background_gradient_cbmi.isSelected() );
1027         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1028         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1029                 && _abbreviate_scientific_names.isSelected() );
1030         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1031                 && _color_labels_same_as_parent_branch.isSelected() );
1032         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1033                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1034         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1035                 && _show_default_node_shapes_external_cbmi.isSelected() );
1036         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1037                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1038         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1039             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1040         }
1041         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1042             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1043         }
1044         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1045             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1046         }
1047         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1048                 && _search_case_senstive_cbmi.isSelected() );
1049         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1050             options.setShowScale( _show_scale_cbmi.isSelected() );
1051         }
1052         if ( _label_direction_cbmi != null ) {
1053             if ( _label_direction_cbmi.isSelected() ) {
1054                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1055             }
1056             else {
1057                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1058             }
1059         }
1060         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1061         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1062                 && _show_confidence_stddev_cbmi.isSelected() );
1063         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1064             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1065         }
1066         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1067                 && _search_whole_words_only_cbmi.isSelected() );
1068         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1069                 && _inverse_search_result_cbmi.isSelected() );
1070         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1071             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1072         }
1073         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1074             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1075         }
1076         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1077             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1078         }
1079         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1080             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1081         }
1082         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1083             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1084         }
1085         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1086             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1087         }
1088         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1089             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1090         }
1091         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1092             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1093         }
1094     }
1095
1096     void updateTypeCheckboxes( final Options options, final Object o ) {
1097         setTypeMenuToAllUnselected();
1098         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1099     }
1100
1101     void viewAsNexus() {
1102         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1103             String title = "Nexus";
1104             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1105                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1106             }
1107             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1108                                    .getNhConversionSupportValueStyle() ),
1109                            title );
1110         }
1111     }
1112
1113     void viewAsNH() {
1114         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1115             String title = "New Hampshire";
1116             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1117                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1118             }
1119             showTextFrame( getMainPanel().getCurrentPhylogeny()
1120                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1121                            title );
1122         }
1123     }
1124
1125     void viewAsXML() {
1126         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1127             String title = "phyloXML";
1128             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1129                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1130             }
1131             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1132         }
1133     }
1134
1135     private void chooseFont() {
1136         final FontChooser fc = new FontChooser();
1137         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1138         fc.showDialog( this, "Select the Base Font" );
1139         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1140     }
1141
1142     private void chooseMinimalConfidence() {
1143         final String s = ( String ) JOptionPane
1144                 .showInputDialog( this,
1145                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1146                                           + getOptions().getMinConfidenceValue() + "]\n",
1147                                   "Minimal Confidence Value",
1148                                   JOptionPane.QUESTION_MESSAGE,
1149                                   null,
1150                                   null,
1151                                   getOptions().getMinConfidenceValue() );
1152         if ( !ForesterUtil.isEmpty( s ) ) {
1153             boolean success = true;
1154             double m = 0.0;
1155             final String m_str = s.trim();
1156             if ( !ForesterUtil.isEmpty( m_str ) ) {
1157                 try {
1158                     m = Double.parseDouble( m_str );
1159                 }
1160                 catch ( final Exception ex ) {
1161                     success = false;
1162                 }
1163             }
1164             else {
1165                 success = false;
1166             }
1167             if ( success && ( m >= 0.0 ) ) {
1168                 getOptions().setMinConfidenceValue( m );
1169             }
1170         }
1171     }
1172
1173     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1174         if ( item != null ) {
1175             item.setFont( MainFrame.menu_font );
1176             if ( !getConfiguration().isUseNativeUI() ) {
1177                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1178                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1179             }
1180             item.setSelected( is_selected );
1181             item.addActionListener( this );
1182         }
1183     }
1184
1185     private MainPanel getMainPanel() {
1186         return _main_panel;
1187     }
1188
1189     private boolean isScreenAntialias() {
1190         return true;
1191     }
1192
1193     private void removeBranchColors() {
1194         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1195             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1196         }
1197     }
1198
1199     private void setMainPanel( final MainPanelApplets main_panel ) {
1200         _main_panel = main_panel;
1201     }
1202
1203     private void setupUI() {
1204         try {
1205             if ( getConfiguration().isUseNativeUI() ) {
1206                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1207             }
1208             else {
1209                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1210             }
1211         }
1212         catch ( final UnsupportedLookAndFeelException e ) {
1213             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1214         }
1215         catch ( final ClassNotFoundException e ) {
1216             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1217         }
1218         catch ( final InstantiationException e ) {
1219             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1220         }
1221         catch ( final IllegalAccessException e ) {
1222             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1223         }
1224         catch ( final Exception e ) {
1225             AptxUtil.dieWithSystemError( e.toString() );
1226         }
1227     }
1228
1229     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1230         for( final TreePanel tree_panel : treepanels ) {
1231             tree_panel.setTextAntialias();
1232         }
1233     }
1234 }