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 == _infer_common_sn_names_item ) {
 140             if ( getCurrentTreePanel() != null ) {
 141                 getCurrentTreePanel().inferCommonPartOfScientificNames();
 142             }
 143         }
 144         else if ( o == _collapse_species_specific_subtrees ) {
 145             if ( getCurrentTreePanel() != null ) {
 146                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 147             }
 148         }
 149         else if ( o == _remove_branch_color_item ) {
 150             removeBranchColors();
 151         }
 152         else if ( o == _switch_colors_mi ) {
 153             switchColors();
 154         }
 155         else if ( o == _display_basic_information_item ) {
 156             displayBasicInformation();
 157         }
 158         else if ( o == _view_as_NH_item ) {
 159             viewAsNH();
 160         }
 161         else if ( o == _view_as_NHX_item ) {
 162             viewAsNHX();
 163         }
 164         else if ( o == _view_as_XML_item ) {
 165             viewAsXML();
 166         }
 167         else if ( o == _view_as_nexus_item ) {
 168             viewAsNexus();
 169         }
 170         else if ( o == _super_tiny_fonts_mi ) {
 171             if ( getCurrentTreePanel() != null ) {
 172                 getCurrentTreePanel().setSuperTinyFonts();
 173                 getCurrentTreePanel().repaint();
 174             }
 175         }
 176         else if ( o == _tiny_fonts_mi ) {
 177             if ( getCurrentTreePanel() != null ) {
 178                 getCurrentTreePanel().setTinyFonts();
 179                 getCurrentTreePanel().repaint();
 180             }
 181         }
 182         else if ( o == _small_fonts_mi ) {
 183             if ( getCurrentTreePanel() != null ) {
 184                 getCurrentTreePanel().setSmallFonts();
 185                 getCurrentTreePanel().repaint();
 186             }
 187         }
 188         else if ( o == _medium_fonts_mi ) {
 189             if ( getCurrentTreePanel() != null ) {
 190                 getCurrentTreePanel().setMediumFonts();
 191                 getCurrentTreePanel().repaint();
 192             }
 193         }
 194         else if ( o == _large_fonts_mi ) {
 195             if ( getCurrentTreePanel() != null ) {
 196                 getCurrentTreePanel().setLargeFonts();
 197                 getCurrentTreePanel().repaint();
 198             }
 199         }
 200         else if ( o == _choose_font_mi ) {
 201             chooseFont();
 202         }
 203         else if ( o == _choose_minimal_confidence_mi ) {
 204             chooseMinimalConfidence();
 205         }
 206         else if ( o == _choose_node_size_mi ) {
 207             MainFrame.chooseNodeSize( getOptions(), this );
 208         }
 209         else if ( o == _overview_placment_mi ) {
 210             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 211         }
 212         else if ( o == _cycle_node_fill_mi ) {
 213             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 214         }
 215         else if ( o == _cycle_node_shape_mi ) {
 216             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 217         }
 218         else if ( o == _non_lined_up_cladograms_rbmi ) {
 219             updateOptions( getOptions() );
 220             _main_panel.getControlPanel().showWhole();
 221         }
 222         else if ( o == _uniform_cladograms_rbmi ) {
 223             updateOptions( getOptions() );
 224             _main_panel.getControlPanel().showWhole();
 225         }
 226         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 227             updateOptions( getOptions() );
 228             _main_panel.getControlPanel().showWhole();
 229         }
 230         else if ( o == _search_case_senstive_cbmi ) {
 231             updateOptions( getOptions() );
 232             getMainPanel().getControlPanel().search();
 233         }
 234         else if ( o == _search_whole_words_only_cbmi ) {
 235             updateOptions( getOptions() );
 236             getMainPanel().getControlPanel().search();
 237         }
 238         else if ( o == _inverse_search_result_cbmi ) {
 239             updateOptions( getOptions() );
 240             getMainPanel().getControlPanel().search();
 241         }
 242         else if ( o == _show_scale_cbmi ) {
 243             updateOptions( getOptions() );
 244         }
 245         else if ( o == _show_branch_length_values_cbmi ) {
 246             updateOptions( getOptions() );
 247         }
 248         else if ( o == _show_confidence_stddev_cbmi ) {
 249             updateOptions( getOptions() );
 250         }
 251         else if ( o == _label_direction_cbmi ) {
 252             updateOptions( getOptions() );
 253         }
 254         else if ( o == _show_overview_cbmi ) {
 255             updateOptions( getOptions() );
 256             if ( getCurrentTreePanel() != null ) {
 257                 getCurrentTreePanel().updateOvSizes();
 258             }
 259         }
 260         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 261                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 262                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 263             typeChanged( o );
 264         }
 265         else if ( o == _screen_antialias_cbmi ) {
 266             updateOptions( getOptions() );
 267             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 268         }
 269         else if ( o == _background_gradient_cbmi ) {
 270             updateOptions( getOptions() );
 271         }
 272         else if ( o == _show_domain_labels ) {
 273             updateOptions( getOptions() );
 274         }
 275         else if ( o == _color_labels_same_as_parent_branch ) {
 276             updateOptions( getOptions() );
 277         }
 278         else if ( o == _show_default_node_shapes_cbmi ) {
 279             updateOptions( getOptions() );
 280         }
 281         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 282             updateOptions( getOptions() );
 283         }
 284         else if ( o == _about_item ) {
 285             MainFrame.about();
 286         }
 287         else if ( o == _help_item ) {
 288             help( getConfiguration().getWebLinks() );
 289         }
 290         else if ( o == _website_item ) {
 291             try {
 292                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 293             }
 294             catch ( final IOException e1 ) {
 295                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 296             }
 297         }
 298         else if ( o == _phyloxml_website_item ) {
 299             try {
 300                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 301             }
 302             catch ( final IOException e1 ) {
 303                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 304             }
 305         }
 306         else if ( o == _aptx_ref_item ) {
 307             try {
 308                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 309             }
 310             catch ( final IOException e1 ) {
 311                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 312             }
 313         }
 314         else if ( o == _phyloxml_ref_item ) {
 315             try {
 316                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 317             }
 318             catch ( final IOException e1 ) {
 319                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 320             }
 321         }
 322         repaint();
 323     }
 324
 325     void help( final Map<String, WebLink> weblinks ) {
 326         final StringBuilder sb = new StringBuilder();
 327         sb.append( "Display options\n" );
 328         sb.append( "-------------------\n" );
 329         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 330         sb.append( "Clickable tree nodes\n" );
 331         sb.append( "--------------------\n" );
 332         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 333         sb.append( "or by right clicking:\n" );
 334         sb.append( "o  Display Node Data -- display information for a node\n" );
 335         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 336         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 337         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 338         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 339         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 340         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 341         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 342         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 343         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 344         sb.append( "Zooming\n" );
 345         sb.append( "---------\n" );
 346         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 347         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 348         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 349         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 350         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 351         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 352         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 353         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 354         sb.append( "Quick tree manipulation:\n" );
 355         sb.append( "------------------------\n" );
 356         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 357         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 358         sb.append( "Memory problems (Java heap space error)\n" );
 359         sb.append( "---------------------------------------\n" );
 360         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 361         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 362         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 363         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 364         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 365             sb.append( "Active web links\n" );
 366             sb.append( "--------------------\n" );
 367             for( final String key : weblinks.keySet() ) {
 368                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 369             }
 370         }
 371         sb.append( "\n" );
 372         sb.append( "phyloXML\n" );
 373         sb.append( "-------------------\n" );
 374         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 375         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 376         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 377         sb.append( "\n" );
 378         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 379         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 380         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 381     }
 382
 383     void setCurrentExternalNodesDataBuffer( final String s ) {
 384         if ( !ForesterUtil.isEmpty( s ) ) {
 385             _ext_node_data_buffer = s.trim();
 386         }
 387         else {
 388             _ext_node_data_buffer = "";
 389         }
 390     }
 391
 392     /**
 393      * This method returns the current external node data which
 394      * has been selected by the user by clicking the "Return ..."
 395      * menu item. This method is expected to be called from Javascript or
 396      * something like it.
 397      *
 398      * @return current external node data as String
 399      */
 400     public String getCurrentExternalNodesDataBuffer() {
 401         return _ext_node_data_buffer;
 402     }
 403
 404     /**
 405      * This method returns the current phylogeny as a string in the chosen format
 406      *
 407      * @param format must be NH, NHX, NEXUS or PHYLOXML
 408      * @return the phylogeny string
 409      * @author Herve Menager
 410      */
 411     public String getCurrentPhylogeny( final String format ) {
 412         removeAllTextFrames();
 413         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 414                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 415             return new String();
 416         }
 417         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 418             case NH:
 419                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 420             case NHX:
 421                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 422             case NEXUS:
 423                 return getMainPanel().getCurrentPhylogeny().toNexus();
 424             case PHYLOXML:
 425                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 426             default:
 427                 break;
 428         }
 429         return new String();
 430     }
 431
 432     /**
 433      * This method returns a view of the current phylogeny in a chosen
 434      * graphics format, base64-encoded in a string so that in can be used
 435      * from javascript.
 436      *
 437      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 438      * @return the phylogeny string
 439      * @author Herve Menager
 440      */
 441     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 442         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 443         try {
 444             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 445                                                                     _main_panel.getWidth(),
 446                                                                     _main_panel.getHeight(),
 447                                                                     getCurrentTreePanel(),
 448                                                                     getCurrentTreePanel().getControlPanel(),
 449                                                                     GraphicsExportType.valueOf( format ),
 450                                                                     getOptions() );
 451         }
 452         catch ( final IOException ioe ) {
 453             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 454             ioe.printStackTrace();
 455             JOptionPane.showMessageDialog( this,
 456                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 457                                            "Failed to generate graphics",
 458                                            JOptionPane.ERROR_MESSAGE );
 459             return null;
 460         }
 461         final byte[] bytes = baos.toByteArray();
 462         final String dataImg = Base64.encodeBase64String( bytes );
 463         return dataImg;
 464     }
 465
 466     void buildFontSizeMenu() {
 467         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 468         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 469         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 470         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 471         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 472         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 473         customizeJMenuItem( _super_tiny_fonts_mi );
 474         customizeJMenuItem( _tiny_fonts_mi );
 475         customizeJMenuItem( _small_fonts_mi );
 476         customizeJMenuItem( _medium_fonts_mi );
 477         customizeJMenuItem( _large_fonts_mi );
 478         _jmenubar.add( _font_size_menu );
 479     }
 480
 481     void buildHelpMenu() {
 482         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 483         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 484         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 485         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 486         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 487         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 488         _help_jmenu.addSeparator();
 489         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 490         customizeJMenuItem( _help_item );
 491         customizeJMenuItem( _website_item );
 492         customizeJMenuItem( _phyloxml_website_item );
 493         customizeJMenuItem( _aptx_ref_item );
 494         customizeJMenuItem( _phyloxml_ref_item );
 495         customizeJMenuItem( _about_item );
 496         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 497         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 498         _jmenubar.add( _help_jmenu );
 499     }
 500
 501     void buildOptionsMenu() {
 502         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 503         _options_jmenu.addChangeListener( new ChangeListener() {
 504
 505             @Override
 506             public void stateChanged( final ChangeEvent e ) {
 507                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 508                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 509                 MainFrame
 510                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 511                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 512                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 513                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 514                                                                      _show_scale_cbmi,
 515                                                                      _show_branch_length_values_cbmi,
 516                                                                      _non_lined_up_cladograms_rbmi,
 517                                                                      _uniform_cladograms_rbmi,
 518                                                                      _ext_node_dependent_cladogram_rbmi,
 519                                                                      _label_direction_cbmi );
 520                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 521                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 522                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 523             }
 524         } );
 525         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 526                                                                 getConfiguration() ) );
 527         _options_jmenu
 528                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 529         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 530         _options_jmenu
 531                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 532         _radio_group_1 = new ButtonGroup();
 533         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 534         _radio_group_1.add( _uniform_cladograms_rbmi );
 535         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 536         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 537         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 538         _options_jmenu
 539                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 540         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 541         _options_jmenu
 542                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 543         _options_jmenu
 544                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 545         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 546         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 547         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 548         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 549         _options_jmenu
 550                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 551         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 552         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 553         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 554         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 555         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 556         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 557             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 558         }
 559         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 560         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 561         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 562         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 563         _options_jmenu.addSeparator();
 564         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 565                                                                 getConfiguration() ) );
 566         _options_jmenu
 567                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 568         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 569         _options_jmenu
 570                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 571         customizeJMenuItem( _choose_font_mi );
 572         customizeJMenuItem( _choose_minimal_confidence_mi );
 573         customizeJMenuItem( _switch_colors_mi );
 574         customizeJMenuItem( _overview_placment_mi );
 575         customizeCheckBoxMenuItem( _label_direction_cbmi,
 576                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 577         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 578         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 579         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 580         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 581         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 582         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 583         customizeJMenuItem( _cycle_node_shape_mi );
 584         customizeJMenuItem( _cycle_node_fill_mi );
 585         customizeJMenuItem( _choose_node_size_mi );
 586         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 587         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 588         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 589         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 590                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 591         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 592                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 593         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 594                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 595         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 596         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 597         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 598         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 599         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 600         _jmenubar.add( _options_jmenu );
 601     }
 602
 603     void buildToolsMenu() {
 604         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 605         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 606         customizeJMenuItem( _confcolor_item );
 607         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 608         customizeJMenuItem( _taxcolor_item );
 609         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 610         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 611         customizeJMenuItem( _remove_branch_color_item );
 612         _tools_menu.addSeparator();
 613         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 614         customizeJMenuItem( _midpoint_root_item );
 615         _tools_menu.addSeparator();
 616         _tools_menu
 617                 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 618         customizeJMenuItem( _infer_common_sn_names_item );
 619         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 620         customizeJMenuItem( _collapse_species_specific_subtrees );
 621         _jmenubar.add( _tools_menu );
 622     }
 623
 624     void buildTypeMenu() {
 625         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 626         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 627         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 628         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 629         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 630         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 631         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 632         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 633         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 634         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 635         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 636         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 637         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 638         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 639         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 640         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 641         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 642         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 643         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 644         initializeTypeMenu( getOptions() );
 645         _jmenubar.add( _type_menu );
 646     }
 647
 648     void buildViewMenu() {
 649         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 650         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 651         _view_jmenu.addSeparator();
 652         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 653         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 654         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 655         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 656         customizeJMenuItem( _display_basic_information_item );
 657         customizeJMenuItem( _view_as_NH_item );
 658         customizeJMenuItem( _view_as_NHX_item );
 659         customizeJMenuItem( _view_as_XML_item );
 660         customizeJMenuItem( _view_as_nexus_item );
 661         _jmenubar.add( _view_jmenu );
 662     }
 663
 664     private void chooseFont() {
 665         final FontChooser fc = new FontChooser();
 666         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
 667         fc.showDialog( this, "Select the Base Font" );
 668         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
 669     }
 670
 671     private void chooseMinimalConfidence() {
 672         final String s = ( String ) JOptionPane
 673                 .showInputDialog( this,
 674                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
 675                                           + getOptions().getMinConfidenceValue() + "]\n",
 676                                   "Minimal Confidence Value",
 677                                   JOptionPane.QUESTION_MESSAGE,
 678                                   null,
 679                                   null,
 680                                   getOptions().getMinConfidenceValue() );
 681         if ( !ForesterUtil.isEmpty( s ) ) {
 682             boolean success = true;
 683             double m = 0.0;
 684             final String m_str = s.trim();
 685             if ( !ForesterUtil.isEmpty( m_str ) ) {
 686                 try {
 687                     m = Double.parseDouble( m_str );
 688                 }
 689                 catch ( final Exception ex ) {
 690                     success = false;
 691                 }
 692             }
 693             else {
 694                 success = false;
 695             }
 696             if ( success && ( m >= 0.0 ) ) {
 697                 getOptions().setMinConfidenceValue( m );
 698             }
 699         }
 700     }
 701
 702     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 703         if ( item != null ) {
 704             item.setFont( MainFrame.menu_font );
 705             if ( !getConfiguration().isUseNativeUI() ) {
 706                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 707                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 708             }
 709             item.setSelected( is_selected );
 710             item.addActionListener( this );
 711         }
 712     }
 713
 714     void customizeJMenuItem( final JMenuItem jmi ) {
 715         jmi.setFont( MainFrame.menu_font );
 716         if ( !getConfiguration().isUseNativeUI() ) {
 717             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 718             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 719         }
 720         jmi.addActionListener( this );
 721     }
 722
 723     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 724         if ( item != null ) {
 725             item.setFont( MainFrame.menu_font );
 726             if ( !getConfiguration().isUseNativeUI() ) {
 727                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 728                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 729             }
 730             item.setSelected( is_selected );
 731             item.addActionListener( this );
 732         }
 733     }
 734
 735     @Override
 736     public void destroy() {
 737         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 738         removeAllTextFrames();
 739         if ( getMainPanel() != null ) {
 740             getMainPanel().terminate();
 741         }
 742     }
 743
 744     Configuration getConfiguration() {
 745         return _configuration;
 746     }
 747
 748     TreePanel getCurrentTreePanel() {
 749         return getMainPanel().getCurrentTreePanel();
 750     }
 751
 752     JCheckBoxMenuItem getlabelDirectionCbmi() {
 753         return _label_direction_cbmi;
 754     }
 755
 756     private MainPanel getMainPanel() {
 757         return _main_panel;
 758     }
 759
 760     public Options getOptions() {
 761         return _options;
 762     }
 763
 764     Options getOtions() {
 765         return _options;
 766     }
 767
 768     @Override
 769     public void init() {
 770         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 771         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 772         final Configuration configuration = new Configuration( config_filename, true, true, true );
 773         setConfiguration( configuration );
 774         setOptions( Options.createInstance( configuration ) );
 775         setupUI();
 776         URL phys_url = null;
 777         Phylogeny[] phys = null;
 778         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 779         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 780         // Get URL to tree file
 781         if ( phys_url_string != null ) {
 782             try {
 783                 phys_url = new URL( phys_url_string );
 784             }
 785             catch ( final Exception e ) {
 786                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 787                 e.printStackTrace();
 788                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 789                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 790             }
 791         }
 792         // Load the tree from URL
 793         if ( phys_url != null ) {
 794             try {
 795                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
 796             }
 797             catch ( final Exception e ) {
 798                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 799                 e.printStackTrace();
 800                 JOptionPane.showMessageDialog( this,
 801                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 802                                                "Failed to read phylogenies",
 803                                                JOptionPane.ERROR_MESSAGE );
 804             }
 805         }
 806         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 807             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 808             JOptionPane.showMessageDialog( this,
 809                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 810                                            "Failed to read phylogenies",
 811                                            JOptionPane.ERROR_MESSAGE );
 812             return;
 813         }
 814         else {
 815             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 816         }
 817         setVisible( false );
 818         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 819         _jmenubar = new JMenuBar();
 820         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 821             if ( !getConfiguration().isUseNativeUI() ) {
 822                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 823             }
 824             buildToolsMenu();
 825             buildViewMenu();
 826             buildFontSizeMenu();
 827             buildOptionsMenu();
 828             buildTypeMenu();
 829             buildHelpMenu();
 830             setJMenuBar( _jmenubar );
 831         }
 832         final Container contentpane = getContentPane();
 833         contentpane.setLayout( new BorderLayout() );
 834         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 835         addComponentListener( new ComponentAdapter() {
 836
 837             @Override
 838             public void componentResized( final ComponentEvent e ) {
 839                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 840                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 841                                                                                            .getWidth(),
 842                                                                                    getMainPanel().getCurrentTreePanel()
 843                                                                                            .getHeight(),
 844                                                                                    false );
 845                 }
 846             }
 847         } );
 848         if ( getConfiguration().isUseTabbedDisplay() ) {
 849             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 850             AptxUtil.addPhylogeniesToTabs( phys,
 851                                            new File( phys_url.getFile() ).getName(),
 852                                            phys_url.toString(),
 853                                            getConfiguration(),
 854                                            getMainPanel() );
 855         }
 856         else {
 857             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 858             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 859         }
 860         validate();
 861         setName( NAME );
 862         getMainPanel().getControlPanel().showWholeAll();
 863         getMainPanel().getControlPanel().showWhole();
 864         System.gc();
 865         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 866         /* GUILHEM_BEG */
 867         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 868         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 869                 .getRelevantSequenceRelationTypes() ) {
 870             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 871         }
 872         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 873         if ( default_relation != null ) {
 874             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 875         }
 876         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 877         if ( default_sequence != null ) {
 878             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 879             /* GUILHEM_END */
 880         }
 881         setVisible( true );
 882     }
 883
 884     void initializeTypeMenu( final Options options ) {
 885         setTypeMenuToAllUnselected();
 886         try {
 887             switch ( options.getPhylogenyGraphicsType() ) {
 888                 case CONVEX:
 889                     _convex_type_cbmi.setSelected( true );
 890                     break;
 891                 case CURVED:
 892                     _curved_type_cbmi.setSelected( true );
 893                     break;
 894                 case EURO_STYLE:
 895                     _euro_type_cbmi.setSelected( true );
 896                     break;
 897                 case ROUNDED:
 898                     _rounded_type_cbmi.setSelected( true );
 899                     break;
 900                 case TRIANGULAR:
 901                     _triangular_type_cbmi.setSelected( true );
 902                     break;
 903                 case UNROOTED:
 904                     _unrooted_type_cbmi.setSelected( true );
 905                     break;
 906                 case CIRCULAR:
 907                     _circular_type_cbmi.setSelected( true );
 908                     break;
 909                 default:
 910                     _rectangular_type_cbmi.setSelected( true );
 911                     break;
 912             }
 913         }
 914         catch ( final NullPointerException np ) {
 915             // In all likelihood, this is caused by menu-less display.
 916         }
 917     }
 918
 919     private boolean isScreenAntialias() {
 920         return true;
 921     }
 922
 923     private void removeBranchColors() {
 924         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 925             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
 926         }
 927     }
 928
 929     void setConfiguration( final Configuration configuration ) {
 930         _configuration = configuration;
 931     }
 932
 933     private void setMainPanel( final MainPanelApplets main_panel ) {
 934         _main_panel = main_panel;
 935     }
 936
 937     void setOptions( final Options options ) {
 938         _options = options;
 939     }
 940
 941     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 942         setTypeMenuToAllUnselected();
 943         try {
 944             switch ( type ) {
 945                 case CIRCULAR:
 946                     _circular_type_cbmi.setSelected( true );
 947                     break;
 948                 case CONVEX:
 949                     _convex_type_cbmi.setSelected( true );
 950                     break;
 951                 case CURVED:
 952                     _curved_type_cbmi.setSelected( true );
 953                     break;
 954                 case EURO_STYLE:
 955                     _euro_type_cbmi.setSelected( true );
 956                     break;
 957                 case ROUNDED:
 958                     _rounded_type_cbmi.setSelected( true );
 959                     break;
 960                 case RECTANGULAR:
 961                     _rectangular_type_cbmi.setSelected( true );
 962                     break;
 963                 case TRIANGULAR:
 964                     _triangular_type_cbmi.setSelected( true );
 965                     break;
 966                 case UNROOTED:
 967                     _unrooted_type_cbmi.setSelected( true );
 968                     break;
 969                 default:
 970                     throw new IllegalArgumentException( "unknown type: " + type );
 971             }
 972         }
 973         catch ( final NullPointerException np ) {
 974             // In all likelihood, this is caused by menu-less display.
 975         }
 976     }
 977
 978     void setTypeMenuToAllUnselected() {
 979         if ( _convex_type_cbmi != null ) {
 980             _convex_type_cbmi.setSelected( false );
 981         }
 982         if ( _curved_type_cbmi != null ) {
 983             _curved_type_cbmi.setSelected( false );
 984         }
 985         if ( _euro_type_cbmi != null ) {
 986             _euro_type_cbmi.setSelected( false );
 987         }
 988         if ( _rounded_type_cbmi != null ) {
 989             _rounded_type_cbmi.setSelected( false );
 990         }
 991         if ( _triangular_type_cbmi != null ) {
 992             _triangular_type_cbmi.setSelected( false );
 993         }
 994         if ( _rectangular_type_cbmi != null ) {
 995             _rectangular_type_cbmi.setSelected( false );
 996         }
 997         if ( _unrooted_type_cbmi != null ) {
 998             _unrooted_type_cbmi.setSelected( false );
 999         }
1000         if ( _circular_type_cbmi != null ) {
1001             _circular_type_cbmi.setSelected( false );
1002         }
1003     }
1004
1005     private void setupUI() {
1006         try {
1007             if ( getConfiguration().isUseNativeUI() ) {
1008                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1009             }
1010             else {
1011                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1012             }
1013         }
1014         catch ( final UnsupportedLookAndFeelException e ) {
1015             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1016         }
1017         catch ( final ClassNotFoundException e ) {
1018             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1019         }
1020         catch ( final InstantiationException e ) {
1021             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1022         }
1023         catch ( final IllegalAccessException e ) {
1024             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1025         }
1026         catch ( final Exception e ) {
1027             AptxUtil.dieWithSystemError( e.toString() );
1028         }
1029     }
1030
1031     @Override
1032     public void start() {
1033         if ( getMainPanel() != null ) {
1034             getMainPanel().validate();
1035         }
1036         requestFocus();
1037         requestFocusInWindow();
1038         requestFocus();
1039         AptxUtil.printAppletMessage( NAME, "started" );
1040     }
1041
1042     void switchColors() {
1043         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1044         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1045         csc.setVisible( true );
1046         getMainPanel().setTreeColorSet( colorset );
1047     }
1048
1049     void typeChanged( final Object o ) {
1050         updateTypeCheckboxes( getOptions(), o );
1051         updateOptions( getOptions() );
1052         if ( getCurrentTreePanel() != null ) {
1053             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1054             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1055             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1056                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1057                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1058                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1059                 getCurrentTreePanel().getControlPanel().showWhole();
1060             }
1061             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1062                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1063             }
1064             else {
1065                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1066             }
1067             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1068             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1069         }
1070     }
1071
1072     void updateOptions( final Options options ) {
1073         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1074         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1075                 && _background_gradient_cbmi.isSelected() );
1076         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1077         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1078                 && _abbreviate_scientific_names.isSelected() );
1079         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1080                 && _color_labels_same_as_parent_branch.isSelected() );
1081         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1082                 && _show_default_node_shapes_cbmi.isSelected() );
1083         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1084                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1085         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1086             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1087         }
1088         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1089             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1090         }
1091         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1092             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1093         }
1094         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1095                 && _search_case_senstive_cbmi.isSelected() );
1096         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1097             options.setShowScale( _show_scale_cbmi.isSelected() );
1098         }
1099         if ( _label_direction_cbmi != null ) {
1100             if ( _label_direction_cbmi.isSelected() ) {
1101                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1102             }
1103             else {
1104                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1105             }
1106         }
1107         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1108         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1109                 && _show_confidence_stddev_cbmi.isSelected() );
1110         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1111             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1112         }
1113         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1114                 && _search_whole_words_only_cbmi.isSelected() );
1115         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1116                 && _inverse_search_result_cbmi.isSelected() );
1117         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1118             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1119         }
1120         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1121             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1122         }
1123         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1124             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1125         }
1126         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1127             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1128         }
1129         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1130             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1131         }
1132         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1133             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1134         }
1135         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1136             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1137         }
1138         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1139             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1140         }
1141     }
1142
1143     void updateTypeCheckboxes( final Options options, final Object o ) {
1144         setTypeMenuToAllUnselected();
1145         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1146     }
1147
1148     void displayBasicInformation() {
1149         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1150             String title = "Basic Information";
1151             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1152                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1153             }
1154             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
1155         }
1156     }
1157
1158     void viewAsNexus() {
1159         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1160             String title = "Nexus";
1161             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1162                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1163             }
1164             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1165                                    .getNhConversionSupportValueStyle() ),
1166                            title );
1167         }
1168     }
1169
1170     void viewAsNH() {
1171         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1172             String title = "New Hampshire";
1173             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1174                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1175             }
1176             showTextFrame( getMainPanel().getCurrentPhylogeny()
1177                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1178                            title );
1179         }
1180     }
1181
1182     void viewAsNHX() {
1183         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1184             String title = "NHX";
1185             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1186                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1187             }
1188             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title );
1189         }
1190     }
1191
1192     void viewAsXML() {
1193         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1194             String title = "phyloXML";
1195             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1196                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1197             }
1198             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1199         }
1200     }
1201
1202     public void showTextFrame( final String s, final String title ) {
1203         checkTextFrames();
1204         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
1205     }
1206
1207     void checkTextFrames() {
1208         if ( _textframes.size() > 5 ) {
1209             try {
1210                 if ( _textframes.getFirst() != null ) {
1211                     _textframes.getFirst().removeMe();
1212                 }
1213                 else {
1214                     _textframes.removeFirst();
1215                 }
1216             }
1217             catch ( final NoSuchElementException e ) {
1218                 // Ignore.
1219             }
1220         }
1221     }
1222
1223     void removeAllTextFrames() {
1224         for( final TextFrame tf : _textframes ) {
1225             if ( tf != null ) {
1226                 tf.close();
1227             }
1228         }
1229         _textframes.clear();
1230     }
1231
1232     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1233         for( final TreePanel tree_panel : treepanels ) {
1234             tree_panel.setTextAntialias();
1235         }
1236     }
1237 }