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