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