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_NHX_item;
  76     private JMenuItem                   _view_as_nexus_item;
  77     private JMenuItem                   _display_basic_information_item;
  78     private JMenu                       _type_menu;
  79     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  80     private JCheckBoxMenuItem           _triangular_type_cbmi;
  81     private JCheckBoxMenuItem           _curved_type_cbmi;
  82     private JCheckBoxMenuItem           _convex_type_cbmi;
  83     private JCheckBoxMenuItem           _euro_type_cbmi;
  84     private JCheckBoxMenuItem           _rounded_type_cbmi;
  85     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  86     private JCheckBoxMenuItem           _circular_type_cbmi;
  87     private JMenuItem                   _help_item;
  88     private JMenuItem                   _about_item;
  89     private JMenu                       _help_jmenu;
  90     private JMenuItem                   _website_item;
  91     private JMenuItem                   _phyloxml_website_item;
  92     private JMenuItem                   _phyloxml_ref_item;
  93     private JMenuItem                   _aptx_ref_item;
  94     private JMenuItem                   _remove_branch_color_item;
  95     private JMenuItem                   _infer_common_sn_names_item;
  96     private JCheckBoxMenuItem           _show_domain_labels;
  97     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
  98     private JCheckBoxMenuItem           _abbreviate_scientific_names;
  99     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 100     private JCheckBoxMenuItem           _background_gradient_cbmi;
 101     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 102     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 103     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 104     private Options                     _options;
 105     private JMenuItem                   _choose_font_mi;
 106     private JMenuItem                   _switch_colors_mi;
 107     JCheckBoxMenuItem                   _label_direction_cbmi;
 108     private JCheckBoxMenuItem           _show_scale_cbmi;
 109     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 110     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 111     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 112     private JCheckBoxMenuItem           _show_overview_cbmi;
 113     private JMenuItem                   _choose_minimal_confidence_mi;
 114     private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 115     private JMenuItem                   _collapse_species_specific_subtrees;
 116     private JMenuItem                   _overview_placment_mi;
 117     private ButtonGroup                 _radio_group_1;
 118     private JCheckBoxMenuItem           _show_default_node_shapes_cbmi;
 119     private JMenuItem                   _cycle_node_shape_mi;
 120     private JMenuItem                   _cycle_node_fill_mi;
 121     private JMenuItem                   _choose_node_size_mi;
 122     private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 123     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 124     private final LinkedList<TextFrame> _textframes                          = new LinkedList<TextFrame>();
 125     private String                      _ext_node_data_buffer                = "";
 126     private int                         _ext_node_data_buffer_change_counter = 0;
 127
 128     @Override
 129     public void actionPerformed( final ActionEvent e ) {
 130         final Object o = e.getSource();
 131         if ( o == _midpoint_root_item ) {
 132             getMainPanel().getCurrentTreePanel().midpointRoot();
 133         }
 134         else if ( o == _taxcolor_item ) {
 135             getMainPanel().getCurrentTreePanel().taxColor();
 136         }
 137         else if ( o == _confcolor_item ) {
 138             getMainPanel().getCurrentTreePanel().confColor();
 139         }
 140         else if ( o == _collapse_species_specific_subtrees ) {
 141             if ( getCurrentTreePanel() != null ) {
 142                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 143             }
 144         }
 145         else if ( o == _remove_branch_color_item ) {
 146             removeBranchColors();
 147         }
 148         else if ( o == _switch_colors_mi ) {
 149             switchColors();
 150         }
 151         else if ( o == _display_basic_information_item ) {
 152             displayBasicInformation();
 153         }
 154         else if ( o == _view_as_NH_item ) {
 155             viewAsNH();
 156         }
 157         else if ( o == _view_as_NHX_item ) {
 158             viewAsNHX();
 159         }
 160         else if ( o == _view_as_XML_item ) {
 161             viewAsXML();
 162         }
 163         else if ( o == _view_as_nexus_item ) {
 164             viewAsNexus();
 165         }
 166         else if ( o == _super_tiny_fonts_mi ) {
 167             if ( getCurrentTreePanel() != null ) {
 168                 getCurrentTreePanel().setSuperTinyFonts();
 169                 getCurrentTreePanel().repaint();
 170             }
 171         }
 172         else if ( o == _tiny_fonts_mi ) {
 173             if ( getCurrentTreePanel() != null ) {
 174                 getCurrentTreePanel().setTinyFonts();
 175                 getCurrentTreePanel().repaint();
 176             }
 177         }
 178         else if ( o == _small_fonts_mi ) {
 179             if ( getCurrentTreePanel() != null ) {
 180                 getCurrentTreePanel().setSmallFonts();
 181                 getCurrentTreePanel().repaint();
 182             }
 183         }
 184         else if ( o == _medium_fonts_mi ) {
 185             if ( getCurrentTreePanel() != null ) {
 186                 getCurrentTreePanel().setMediumFonts();
 187                 getCurrentTreePanel().repaint();
 188             }
 189         }
 190         else if ( o == _large_fonts_mi ) {
 191             if ( getCurrentTreePanel() != null ) {
 192                 getCurrentTreePanel().setLargeFonts();
 193                 getCurrentTreePanel().repaint();
 194             }
 195         }
 196         else if ( o == _choose_font_mi ) {
 197             chooseFont();
 198         }
 199         else if ( o == _choose_minimal_confidence_mi ) {
 200             chooseMinimalConfidence();
 201         }
 202         else if ( o == _choose_node_size_mi ) {
 203             MainFrame.chooseNodeSize( getOptions(), this );
 204         }
 205         else if ( o == _overview_placment_mi ) {
 206             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 207         }
 208         else if ( o == _cycle_node_fill_mi ) {
 209             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 210         }
 211         else if ( o == _cycle_node_shape_mi ) {
 212             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 213         }
 214         else if ( o == _non_lined_up_cladograms_rbmi ) {
 215             updateOptions( getOptions() );
 216             _main_panel.getControlPanel().showWhole();
 217         }
 218         else if ( o == _uniform_cladograms_rbmi ) {
 219             updateOptions( getOptions() );
 220             _main_panel.getControlPanel().showWhole();
 221         }
 222         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 223             updateOptions( getOptions() );
 224             _main_panel.getControlPanel().showWhole();
 225         }
 226         else if ( o == _search_case_senstive_cbmi ) {
 227             updateOptions( getOptions() );
 228             getMainPanel().getControlPanel().search();
 229         }
 230         else if ( o == _search_whole_words_only_cbmi ) {
 231             updateOptions( getOptions() );
 232             getMainPanel().getControlPanel().search();
 233         }
 234         else if ( o == _inverse_search_result_cbmi ) {
 235             updateOptions( getOptions() );
 236             getMainPanel().getControlPanel().search();
 237         }
 238         else if ( o == _show_scale_cbmi ) {
 239             updateOptions( getOptions() );
 240         }
 241         else if ( o == _show_branch_length_values_cbmi ) {
 242             updateOptions( getOptions() );
 243         }
 244         else if ( o == _show_confidence_stddev_cbmi ) {
 245             updateOptions( getOptions() );
 246         }
 247         else if ( o == _label_direction_cbmi ) {
 248             updateOptions( getOptions() );
 249         }
 250         else if ( o == _show_overview_cbmi ) {
 251             updateOptions( getOptions() );
 252             if ( getCurrentTreePanel() != null ) {
 253                 getCurrentTreePanel().updateOvSizes();
 254             }
 255         }
 256         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 257                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 258                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 259             typeChanged( o );
 260         }
 261         else if ( o == _screen_antialias_cbmi ) {
 262             updateOptions( getOptions() );
 263             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 264         }
 265         else if ( o == _background_gradient_cbmi ) {
 266             updateOptions( getOptions() );
 267         }
 268         else if ( o == _show_domain_labels ) {
 269             updateOptions( getOptions() );
 270         }
 271         else if ( o == _color_labels_same_as_parent_branch ) {
 272             updateOptions( getOptions() );
 273         }
 274         else if ( o == _show_default_node_shapes_cbmi ) {
 275             updateOptions( getOptions() );
 276         }
 277         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 278             updateOptions( getOptions() );
 279         }
 280         else if ( o == _about_item ) {
 281             MainFrame.about();
 282         }
 283         else if ( o == _help_item ) {
 284             help( getConfiguration().getWebLinks() );
 285         }
 286         else if ( o == _website_item ) {
 287             try {
 288                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 289             }
 290             catch ( final IOException e1 ) {
 291                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 292             }
 293         }
 294         else if ( o == _phyloxml_website_item ) {
 295             try {
 296                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 297             }
 298             catch ( final IOException e1 ) {
 299                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 300             }
 301         }
 302         else if ( o == _aptx_ref_item ) {
 303             try {
 304                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 305             }
 306             catch ( final IOException e1 ) {
 307                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 308             }
 309         }
 310         else if ( o == _phyloxml_ref_item ) {
 311             try {
 312                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 313             }
 314             catch ( final IOException e1 ) {
 315                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 316             }
 317         }
 318         repaint();
 319     }
 320
 321     @Override
 322     public void destroy() {
 323         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 324         removeAllTextFrames();
 325         if ( getMainPanel() != null ) {
 326             getMainPanel().terminate();
 327         }
 328     }
 329
 330     /**
 331      * This method returns the current external node data which
 332      * has been selected by the user by clicking the "Return ..."
 333      * menu item. This method is expected to be called from Javascript or
 334      * something like it.
 335      *
 336      * @return current external node data as String
 337      */
 338     public String getCurrentExternalNodesDataBuffer() {
 339         return _ext_node_data_buffer;
 340     }
 341
 342     /**
 343      * This method returns the current phylogeny as a string in the chosen format
 344      *
 345      * @param format must be NH, NHX, NEXUS or PHYLOXML
 346      * @return the phylogeny string
 347      * @author Herve Menager
 348      */
 349     public String getCurrentPhylogeny( final String format ) {
 350         removeAllTextFrames();
 351         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 352                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 353             return new String();
 354         }
 355         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 356             case NH:
 357                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 358             case NHX:
 359                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 360             case NEXUS:
 361                 return getMainPanel().getCurrentPhylogeny().toNexus();
 362             case PHYLOXML:
 363                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 364             default:
 365                 break;
 366         }
 367         return new String();
 368     }
 369
 370     /**
 371      * This method returns a view of the current phylogeny in a chosen
 372      * graphics format, base64-encoded in a string so that in can be used
 373      * from javascript.
 374      *
 375      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 376      * @return the phylogeny string
 377      * @author Herve Menager
 378      */
 379     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 380         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 381         try {
 382             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 383                                                                     _main_panel.getWidth(),
 384                                                                     _main_panel.getHeight(),
 385                                                                     getCurrentTreePanel(),
 386                                                                     getCurrentTreePanel().getControlPanel(),
 387                                                                     GraphicsExportType.valueOf( format ),
 388                                                                     getOptions() );
 389         }
 390         catch ( final IOException ioe ) {
 391             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 392             ioe.printStackTrace();
 393             JOptionPane.showMessageDialog( this,
 394                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 395                                            "Failed to generate graphics",
 396                                            JOptionPane.ERROR_MESSAGE );
 397             return null;
 398         }
 399         final byte[] bytes = baos.toByteArray();
 400         final String dataImg = Base64.encodeBase64String( bytes );
 401         return dataImg;
 402     }
 403
 404     public int getExtNodeDataBufferChangeCounter() {
 405         return _ext_node_data_buffer_change_counter;
 406     }
 407
 408     public Options getOptions() {
 409         return _options;
 410     }
 411
 412     public void increaseExtNodeDataBufferChangeCounter() {
 413         _ext_node_data_buffer_change_counter++;
 414     }
 415
 416     @Override
 417     public void init() {
 418         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 419         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 420         final Configuration configuration = new Configuration( config_filename, true, true, true );
 421         setConfiguration( configuration );
 422         setOptions( Options.createInstance( configuration ) );
 423         setupUI();
 424         URL phys_url = null;
 425         Phylogeny[] phys = null;
 426         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 427         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 428         // Get URL to tree file
 429         if ( phys_url_string != null ) {
 430             try {
 431                 phys_url = new URL( phys_url_string );
 432             }
 433             catch ( final Exception e ) {
 434                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 435                 e.printStackTrace();
 436                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 437                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 438             }
 439         }
 440         // Load the tree from URL
 441         if ( phys_url != null ) {
 442             try {
 443                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 444                                                         getConfiguration().isValidatePhyloXmlAgainstSchema(),
 445                                                         getConfiguration().isReplaceUnderscoresInNhParsing(),
 446                                                         getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 447                                                         getConfiguration().getTaxonomyExtraction() );
 448             }
 449             catch ( final Exception e ) {
 450                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 451                 e.printStackTrace();
 452                 JOptionPane.showMessageDialog( this,
 453                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 454                                                "Failed to read phylogenies",
 455                                                JOptionPane.ERROR_MESSAGE );
 456             }
 457         }
 458         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 459             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 460             JOptionPane.showMessageDialog( this,
 461                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 462                                            "Failed to read phylogenies",
 463                                            JOptionPane.ERROR_MESSAGE );
 464             return;
 465         }
 466         else {
 467             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 468         }
 469         setVisible( false );
 470         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 471         _jmenubar = new JMenuBar();
 472         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 473             if ( !getConfiguration().isUseNativeUI() ) {
 474                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 475             }
 476             buildToolsMenu();
 477             buildViewMenu();
 478             buildFontSizeMenu();
 479             buildOptionsMenu();
 480             buildTypeMenu();
 481             buildHelpMenu();
 482             setJMenuBar( _jmenubar );
 483         }
 484         final Container contentpane = getContentPane();
 485         contentpane.setLayout( new BorderLayout() );
 486         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 487         addComponentListener( new ComponentAdapter() {
 488
 489             @Override
 490             public void componentResized( final ComponentEvent e ) {
 491                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 492                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 493                                                                                            .getWidth(),
 494                                                                                    getMainPanel().getCurrentTreePanel()
 495                                                                                            .getHeight(),
 496                                                                                    false );
 497                 }
 498             }
 499         } );
 500         if ( getConfiguration().isUseTabbedDisplay() ) {
 501             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 502             AptxUtil.addPhylogeniesToTabs( phys,
 503                                            new File( phys_url.getFile() ).getName(),
 504                                            phys_url.toString(),
 505                                            getConfiguration(),
 506                                            getMainPanel() );
 507         }
 508         else {
 509             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 510             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 511         }
 512         validate();
 513         setName( NAME );
 514         getMainPanel().getControlPanel().showWholeAll();
 515         getMainPanel().getControlPanel().showWhole();
 516         System.gc();
 517         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 518         /* GUILHEM_BEG */
 519         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 520         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 521                 .getRelevantSequenceRelationTypes() ) {
 522             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 523         }
 524         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 525         if ( default_relation != null ) {
 526             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 527         }
 528         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 529         if ( default_sequence != null ) {
 530             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 531             /* GUILHEM_END */
 532         }
 533         setVisible( true );
 534     }
 535
 536     public void showTextFrame( final String s, final String title ) {
 537         checkTextFrames();
 538         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 539     }
 540
 541     @Override
 542     public void start() {
 543         if ( getMainPanel() != null ) {
 544             getMainPanel().validate();
 545         }
 546         requestFocus();
 547         requestFocusInWindow();
 548         requestFocus();
 549         AptxUtil.printAppletMessage( NAME, "started" );
 550     }
 551
 552     void buildFontSizeMenu() {
 553         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 554         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 555         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 556         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 557         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 558         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 559         customizeJMenuItem( _super_tiny_fonts_mi );
 560         customizeJMenuItem( _tiny_fonts_mi );
 561         customizeJMenuItem( _small_fonts_mi );
 562         customizeJMenuItem( _medium_fonts_mi );
 563         customizeJMenuItem( _large_fonts_mi );
 564         _jmenubar.add( _font_size_menu );
 565     }
 566
 567     void buildHelpMenu() {
 568         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 569         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 570         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 571         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 572         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 573         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 574         _help_jmenu.addSeparator();
 575         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 576         customizeJMenuItem( _help_item );
 577         customizeJMenuItem( _website_item );
 578         customizeJMenuItem( _phyloxml_website_item );
 579         customizeJMenuItem( _aptx_ref_item );
 580         customizeJMenuItem( _phyloxml_ref_item );
 581         customizeJMenuItem( _about_item );
 582         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 583         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 584         _jmenubar.add( _help_jmenu );
 585     }
 586
 587     void buildOptionsMenu() {
 588         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 589         _options_jmenu.addChangeListener( new ChangeListener() {
 590
 591             @Override
 592             public void stateChanged( final ChangeEvent e ) {
 593                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 594                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 595                 MainFrame
 596                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 597                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 598                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 599                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 600                                                                      _show_scale_cbmi,
 601                                                                      _show_branch_length_values_cbmi,
 602                                                                      _non_lined_up_cladograms_rbmi,
 603                                                                      _uniform_cladograms_rbmi,
 604                                                                      _ext_node_dependent_cladogram_rbmi,
 605                                                                      _label_direction_cbmi );
 606                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 607                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 608                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 609             }
 610         } );
 611         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 612                                                                 getConfiguration() ) );
 613         _options_jmenu
 614                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 615         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 616         _options_jmenu
 617                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 618         _radio_group_1 = new ButtonGroup();
 619         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 620         _radio_group_1.add( _uniform_cladograms_rbmi );
 621         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 622         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 623         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 624         _options_jmenu
 625                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 626         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 627         _options_jmenu
 628                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 629         _options_jmenu
 630                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 631         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 632         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 633         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 634         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 635         _options_jmenu
 636                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 637         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 638         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 639         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 640         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 641         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 642         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 643             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 644         }
 645         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 646         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 647         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 648         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 649         _options_jmenu.addSeparator();
 650         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 651                                                                 getConfiguration() ) );
 652         _options_jmenu
 653                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 654         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 655         _options_jmenu
 656                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 657         customizeJMenuItem( _choose_font_mi );
 658         customizeJMenuItem( _choose_minimal_confidence_mi );
 659         customizeJMenuItem( _switch_colors_mi );
 660         customizeJMenuItem( _overview_placment_mi );
 661         customizeCheckBoxMenuItem( _label_direction_cbmi,
 662                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 663         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 664         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 665         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 666         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 667         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 668         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 669         customizeJMenuItem( _cycle_node_shape_mi );
 670         customizeJMenuItem( _cycle_node_fill_mi );
 671         customizeJMenuItem( _choose_node_size_mi );
 672         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 673         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 674         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 675         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 676                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 677         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 678                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 679         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 680                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 681         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 682         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 683         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 684         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 685         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 686         _jmenubar.add( _options_jmenu );
 687     }
 688
 689     void buildToolsMenu() {
 690         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 691         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 692         customizeJMenuItem( _confcolor_item );
 693         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 694         customizeJMenuItem( _taxcolor_item );
 695         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 696         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 697         customizeJMenuItem( _remove_branch_color_item );
 698         _tools_menu.addSeparator();
 699         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 700         customizeJMenuItem( _midpoint_root_item );
 701         _tools_menu.addSeparator();
 702         _tools_menu
 703                 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 704         customizeJMenuItem( _infer_common_sn_names_item );
 705         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 706         customizeJMenuItem( _collapse_species_specific_subtrees );
 707         _jmenubar.add( _tools_menu );
 708     }
 709
 710     void buildTypeMenu() {
 711         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 712         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 713         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 714         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 715         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 716         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 717         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 718         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 719         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 720         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 721         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 722         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 723         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 724         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 725         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 726         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 727         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 728         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 729         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 730         initializeTypeMenu( getOptions() );
 731         _jmenubar.add( _type_menu );
 732     }
 733
 734     void buildViewMenu() {
 735         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 736         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 737         _view_jmenu.addSeparator();
 738         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 739         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 740         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 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_NHX_item );
 745         customizeJMenuItem( _view_as_XML_item );
 746         customizeJMenuItem( _view_as_nexus_item );
 747         _jmenubar.add( _view_jmenu );
 748     }
 749
 750     void checkTextFrames() {
 751         if ( _textframes.size() > 5 ) {
 752             try {
 753                 if ( _textframes.getFirst() != null ) {
 754                     _textframes.getFirst().removeMe();
 755                 }
 756                 else {
 757                     _textframes.removeFirst();
 758                 }
 759             }
 760             catch ( final NoSuchElementException e ) {
 761                 // Ignore.
 762             }
 763         }
 764     }
 765
 766     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 767         if ( item != null ) {
 768             item.setFont( MainFrame.menu_font );
 769             if ( !getConfiguration().isUseNativeUI() ) {
 770                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 771                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 772             }
 773             item.setSelected( is_selected );
 774             item.addActionListener( this );
 775         }
 776     }
 777
 778     void customizeJMenuItem( final JMenuItem jmi ) {
 779         jmi.setFont( MainFrame.menu_font );
 780         if ( !getConfiguration().isUseNativeUI() ) {
 781             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 782             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 783         }
 784         jmi.addActionListener( this );
 785     }
 786
 787     void displayBasicInformation() {
 788         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 789             String title = "Basic Information";
 790             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 791                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
 792             }
 793             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
 794         }
 795     }
 796
 797     Configuration getConfiguration() {
 798         return _configuration;
 799     }
 800
 801     TreePanel getCurrentTreePanel() {
 802         return getMainPanel().getCurrentTreePanel();
 803     }
 804
 805     JCheckBoxMenuItem getlabelDirectionCbmi() {
 806         return _label_direction_cbmi;
 807     }
 808
 809     Options getOtions() {
 810         return _options;
 811     }
 812
 813     void help( final Map<String, WebLink> weblinks ) {
 814         final StringBuilder sb = new StringBuilder();
 815         sb.append( "Display options\n" );
 816         sb.append( "-------------------\n" );
 817         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 818         sb.append( "Clickable tree nodes\n" );
 819         sb.append( "--------------------\n" );
 820         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 821         sb.append( "or by right clicking:\n" );
 822         sb.append( "o  Display Node Data -- display information for a node\n" );
 823         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 824         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 825         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 826         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 827         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 828         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 829         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 830         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 831         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 832         sb.append( "Zooming\n" );
 833         sb.append( "---------\n" );
 834         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 835         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 836         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 837         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 838         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 839         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 840         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 841         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 842         sb.append( "Quick tree manipulation:\n" );
 843         sb.append( "------------------------\n" );
 844         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 845         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 846         sb.append( "Memory problems (Java heap space error)\n" );
 847         sb.append( "---------------------------------------\n" );
 848         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 849         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 850         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 851         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 852         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 853             sb.append( "Active web links\n" );
 854             sb.append( "--------------------\n" );
 855             for( final String key : weblinks.keySet() ) {
 856                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 857             }
 858         }
 859         sb.append( "\n" );
 860         sb.append( "phyloXML\n" );
 861         sb.append( "-------------------\n" );
 862         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 863         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 864         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 865         sb.append( "\n" );
 866         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 867         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 868         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 869     }
 870
 871     void initializeTypeMenu( final Options options ) {
 872         setTypeMenuToAllUnselected();
 873         try {
 874             switch ( options.getPhylogenyGraphicsType() ) {
 875                 case CONVEX:
 876                     _convex_type_cbmi.setSelected( true );
 877                     break;
 878                 case CURVED:
 879                     _curved_type_cbmi.setSelected( true );
 880                     break;
 881                 case EURO_STYLE:
 882                     _euro_type_cbmi.setSelected( true );
 883                     break;
 884                 case ROUNDED:
 885                     _rounded_type_cbmi.setSelected( true );
 886                     break;
 887                 case TRIANGULAR:
 888                     _triangular_type_cbmi.setSelected( true );
 889                     break;
 890                 case UNROOTED:
 891                     _unrooted_type_cbmi.setSelected( true );
 892                     break;
 893                 case CIRCULAR:
 894                     _circular_type_cbmi.setSelected( true );
 895                     break;
 896                 default:
 897                     _rectangular_type_cbmi.setSelected( true );
 898                     break;
 899             }
 900         }
 901         catch ( final NullPointerException np ) {
 902             // In all likelihood, this is caused by menu-less display.
 903         }
 904     }
 905
 906     void removeAllTextFrames() {
 907         for( final TextFrame tf : _textframes ) {
 908             if ( tf != null ) {
 909                 tf.close();
 910             }
 911         }
 912         _textframes.clear();
 913     }
 914
 915     void setConfiguration( final Configuration configuration ) {
 916         _configuration = configuration;
 917     }
 918
 919     void setCurrentExternalNodesDataBuffer( final String s ) {
 920         increaseExtNodeDataBufferChangeCounter();
 921         if ( !ForesterUtil.isEmpty( s ) ) {
 922             _ext_node_data_buffer = s.trim();
 923         }
 924         else {
 925             _ext_node_data_buffer = "";
 926         }
 927     }
 928
 929     void setOptions( final Options options ) {
 930         _options = options;
 931     }
 932
 933     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 934         setTypeMenuToAllUnselected();
 935         try {
 936             switch ( type ) {
 937                 case CIRCULAR:
 938                     _circular_type_cbmi.setSelected( true );
 939                     break;
 940                 case CONVEX:
 941                     _convex_type_cbmi.setSelected( true );
 942                     break;
 943                 case CURVED:
 944                     _curved_type_cbmi.setSelected( true );
 945                     break;
 946                 case EURO_STYLE:
 947                     _euro_type_cbmi.setSelected( true );
 948                     break;
 949                 case ROUNDED:
 950                     _rounded_type_cbmi.setSelected( true );
 951                     break;
 952                 case RECTANGULAR:
 953                     _rectangular_type_cbmi.setSelected( true );
 954                     break;
 955                 case TRIANGULAR:
 956                     _triangular_type_cbmi.setSelected( true );
 957                     break;
 958                 case UNROOTED:
 959                     _unrooted_type_cbmi.setSelected( true );
 960                     break;
 961                 default:
 962                     throw new IllegalArgumentException( "unknown type: " + type );
 963             }
 964         }
 965         catch ( final NullPointerException np ) {
 966             // In all likelihood, this is caused by menu-less display.
 967         }
 968     }
 969
 970     void setTypeMenuToAllUnselected() {
 971         if ( _convex_type_cbmi != null ) {
 972             _convex_type_cbmi.setSelected( false );
 973         }
 974         if ( _curved_type_cbmi != null ) {
 975             _curved_type_cbmi.setSelected( false );
 976         }
 977         if ( _euro_type_cbmi != null ) {
 978             _euro_type_cbmi.setSelected( false );
 979         }
 980         if ( _rounded_type_cbmi != null ) {
 981             _rounded_type_cbmi.setSelected( false );
 982         }
 983         if ( _triangular_type_cbmi != null ) {
 984             _triangular_type_cbmi.setSelected( false );
 985         }
 986         if ( _rectangular_type_cbmi != null ) {
 987             _rectangular_type_cbmi.setSelected( false );
 988         }
 989         if ( _unrooted_type_cbmi != null ) {
 990             _unrooted_type_cbmi.setSelected( false );
 991         }
 992         if ( _circular_type_cbmi != null ) {
 993             _circular_type_cbmi.setSelected( false );
 994         }
 995     }
 996
 997     void switchColors() {
 998         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 999         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1000         csc.setVisible( true );
1001         getMainPanel().setTreeColorSet( colorset );
1002     }
1003
1004     void typeChanged( final Object o ) {
1005         updateTypeCheckboxes( getOptions(), o );
1006         updateOptions( getOptions() );
1007         if ( getCurrentTreePanel() != null ) {
1008             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1009             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1010             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1011                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1012                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1013                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1014                 getCurrentTreePanel().getControlPanel().showWhole();
1015             }
1016             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1017                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1018             }
1019             else {
1020                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1021             }
1022             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1023             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1024         }
1025     }
1026
1027     void updateOptions( final Options options ) {
1028         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1029         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1030                 && _background_gradient_cbmi.isSelected() );
1031         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1032         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1033                 && _abbreviate_scientific_names.isSelected() );
1034         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1035                 && _color_labels_same_as_parent_branch.isSelected() );
1036         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1037                 && _show_default_node_shapes_cbmi.isSelected() );
1038         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1039                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1040         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1041             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1042         }
1043         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1044             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1045         }
1046         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1047             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1048         }
1049         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1050                 && _search_case_senstive_cbmi.isSelected() );
1051         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1052             options.setShowScale( _show_scale_cbmi.isSelected() );
1053         }
1054         if ( _label_direction_cbmi != null ) {
1055             if ( _label_direction_cbmi.isSelected() ) {
1056                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1057             }
1058             else {
1059                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1060             }
1061         }
1062         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1063         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1064                 && _show_confidence_stddev_cbmi.isSelected() );
1065         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1066             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1067         }
1068         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1069                 && _search_whole_words_only_cbmi.isSelected() );
1070         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1071                 && _inverse_search_result_cbmi.isSelected() );
1072         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1073             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1074         }
1075         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1076             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1077         }
1078         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1079             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1080         }
1081         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1082             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1083         }
1084         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1085             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1086         }
1087         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1088             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1089         }
1090         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1091             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1092         }
1093         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1094             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1095         }
1096     }
1097
1098     void updateTypeCheckboxes( final Options options, final Object o ) {
1099         setTypeMenuToAllUnselected();
1100         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1101     }
1102
1103     void viewAsNexus() {
1104         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1105             String title = "Nexus";
1106             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1107                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1108             }
1109             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1110                                    .getNhConversionSupportValueStyle() ),
1111                            title );
1112         }
1113     }
1114
1115     void viewAsNH() {
1116         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1117             String title = "New Hampshire";
1118             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1119                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1120             }
1121             showTextFrame( getMainPanel().getCurrentPhylogeny()
1122                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1123                            title );
1124         }
1125     }
1126
1127     void viewAsNHX() {
1128         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1129             String title = "NHX";
1130             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1131                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1132             }
1133             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title );
1134         }
1135     }
1136
1137     void viewAsXML() {
1138         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1139             String title = "phyloXML";
1140             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1141                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1142             }
1143             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1144         }
1145     }
1146
1147     private void chooseFont() {
1148         final FontChooser fc = new FontChooser();
1149         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1150         fc.showDialog( this, "Select the Base Font" );
1151         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1152     }
1153
1154     private void chooseMinimalConfidence() {
1155         final String s = ( String ) JOptionPane
1156                 .showInputDialog( this,
1157                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1158                                           + getOptions().getMinConfidenceValue() + "]\n",
1159                                   "Minimal Confidence Value",
1160                                   JOptionPane.QUESTION_MESSAGE,
1161                                   null,
1162                                   null,
1163                                   getOptions().getMinConfidenceValue() );
1164         if ( !ForesterUtil.isEmpty( s ) ) {
1165             boolean success = true;
1166             double m = 0.0;
1167             final String m_str = s.trim();
1168             if ( !ForesterUtil.isEmpty( m_str ) ) {
1169                 try {
1170                     m = Double.parseDouble( m_str );
1171                 }
1172                 catch ( final Exception ex ) {
1173                     success = false;
1174                 }
1175             }
1176             else {
1177                 success = false;
1178             }
1179             if ( success && ( m >= 0.0 ) ) {
1180                 getOptions().setMinConfidenceValue( m );
1181             }
1182         }
1183     }
1184
1185     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1186         if ( item != null ) {
1187             item.setFont( MainFrame.menu_font );
1188             if ( !getConfiguration().isUseNativeUI() ) {
1189                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1190                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1191             }
1192             item.setSelected( is_selected );
1193             item.addActionListener( this );
1194         }
1195     }
1196
1197     private MainPanel getMainPanel() {
1198         return _main_panel;
1199     }
1200
1201     private boolean isScreenAntialias() {
1202         return true;
1203     }
1204
1205     private void removeBranchColors() {
1206         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1207             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1208         }
1209     }
1210
1211     private void setMainPanel( final MainPanelApplets main_panel ) {
1212         _main_panel = main_panel;
1213     }
1214
1215     private void setupUI() {
1216         try {
1217             if ( getConfiguration().isUseNativeUI() ) {
1218                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1219             }
1220             else {
1221                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1222             }
1223         }
1224         catch ( final UnsupportedLookAndFeelException e ) {
1225             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1226         }
1227         catch ( final ClassNotFoundException e ) {
1228             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1229         }
1230         catch ( final InstantiationException e ) {
1231             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1232         }
1233         catch ( final IllegalAccessException e ) {
1234             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1235         }
1236         catch ( final Exception e ) {
1237             AptxUtil.dieWithSystemError( e.toString() );
1238         }
1239     }
1240
1241     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1242         for( final TreePanel tree_panel : treepanels ) {
1243             tree_panel.setTextAntialias();
1244         }
1245     }
1246 }