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     final LinkedList<TextFrame>  _textframes      = new LinkedList<TextFrame>(); ;
 125
 126     @Override
 127     public void actionPerformed( final ActionEvent e ) {
 128         final Object o = e.getSource();
 129         if ( o == _midpoint_root_item ) {
 130             getMainPanel().getCurrentTreePanel().midpointRoot();
 131         }
 132         else if ( o == _taxcolor_item ) {
 133             getMainPanel().getCurrentTreePanel().taxColor();
 134         }
 135         else if ( o == _confcolor_item ) {
 136             getMainPanel().getCurrentTreePanel().confColor();
 137         }
 138         else if ( o == _infer_common_sn_names_item ) {
 139             if ( getCurrentTreePanel() != null ) {
 140                 getCurrentTreePanel().inferCommonPartOfScientificNames();
 141             }
 142         }
 143         else if ( o == _collapse_species_specific_subtrees ) {
 144             if ( getCurrentTreePanel() != null ) {
 145                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 146             }
 147         }
 148         else if ( o == _remove_branch_color_item ) {
 149             removeBranchColors();
 150         }
 151         else if ( o == _switch_colors_mi ) {
 152             switchColors();
 153         }
 154         else if ( o == _display_basic_information_item ) {
 155             displayBasicInformation();
 156         }
 157         else if ( o == _view_as_NH_item ) {
 158             viewAsNH();
 159         }
 160         else if ( o == _view_as_NHX_item ) {
 161             viewAsNHX();
 162         }
 163         else if ( o == _view_as_XML_item ) {
 164             viewAsXML();
 165         }
 166         else if ( o == _view_as_nexus_item ) {
 167             viewAsNexus();
 168         }
 169         else if ( o == _super_tiny_fonts_mi ) {
 170             if ( getCurrentTreePanel() != null ) {
 171                 getCurrentTreePanel().setSuperTinyFonts();
 172                 getCurrentTreePanel().repaint();
 173             }
 174         }
 175         else if ( o == _tiny_fonts_mi ) {
 176             if ( getCurrentTreePanel() != null ) {
 177                 getCurrentTreePanel().setTinyFonts();
 178                 getCurrentTreePanel().repaint();
 179             }
 180         }
 181         else if ( o == _small_fonts_mi ) {
 182             if ( getCurrentTreePanel() != null ) {
 183                 getCurrentTreePanel().setSmallFonts();
 184                 getCurrentTreePanel().repaint();
 185             }
 186         }
 187         else if ( o == _medium_fonts_mi ) {
 188             if ( getCurrentTreePanel() != null ) {
 189                 getCurrentTreePanel().setMediumFonts();
 190                 getCurrentTreePanel().repaint();
 191             }
 192         }
 193         else if ( o == _large_fonts_mi ) {
 194             if ( getCurrentTreePanel() != null ) {
 195                 getCurrentTreePanel().setLargeFonts();
 196                 getCurrentTreePanel().repaint();
 197             }
 198         }
 199         else if ( o == _choose_font_mi ) {
 200             chooseFont();
 201         }
 202         else if ( o == _choose_minimal_confidence_mi ) {
 203             chooseMinimalConfidence();
 204         }
 205         else if ( o == _choose_node_size_mi ) {
 206             MainFrame.chooseNodeSize( getOptions(), this );
 207         }
 208         else if ( o == _overview_placment_mi ) {
 209             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 210         }
 211         else if ( o == _cycle_node_fill_mi ) {
 212             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 213         }
 214         else if ( o == _cycle_node_shape_mi ) {
 215             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 216         }
 217         else if ( o == _non_lined_up_cladograms_rbmi ) {
 218             updateOptions( getOptions() );
 219             _main_panel.getControlPanel().showWhole();
 220         }
 221         else if ( o == _uniform_cladograms_rbmi ) {
 222             updateOptions( getOptions() );
 223             _main_panel.getControlPanel().showWhole();
 224         }
 225         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 226             updateOptions( getOptions() );
 227             _main_panel.getControlPanel().showWhole();
 228         }
 229         else if ( o == _search_case_senstive_cbmi ) {
 230             updateOptions( getOptions() );
 231             getMainPanel().getControlPanel().search();
 232         }
 233         else if ( o == _search_whole_words_only_cbmi ) {
 234             updateOptions( getOptions() );
 235             getMainPanel().getControlPanel().search();
 236         }
 237         else if ( o == _inverse_search_result_cbmi ) {
 238             updateOptions( getOptions() );
 239             getMainPanel().getControlPanel().search();
 240         }
 241         else if ( o == _show_scale_cbmi ) {
 242             updateOptions( getOptions() );
 243         }
 244         else if ( o == _show_branch_length_values_cbmi ) {
 245             updateOptions( getOptions() );
 246         }
 247         else if ( o == _show_confidence_stddev_cbmi ) {
 248             updateOptions( getOptions() );
 249         }
 250         else if ( o == _label_direction_cbmi ) {
 251             updateOptions( getOptions() );
 252         }
 253         else if ( o == _show_overview_cbmi ) {
 254             updateOptions( getOptions() );
 255             if ( getCurrentTreePanel() != null ) {
 256                 getCurrentTreePanel().updateOvSizes();
 257             }
 258         }
 259         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 260                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 261                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 262             typeChanged( o );
 263         }
 264         else if ( o == _screen_antialias_cbmi ) {
 265             updateOptions( getOptions() );
 266             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 267         }
 268         else if ( o == _background_gradient_cbmi ) {
 269             updateOptions( getOptions() );
 270         }
 271         else if ( o == _show_domain_labels ) {
 272             updateOptions( getOptions() );
 273         }
 274         else if ( o == _color_labels_same_as_parent_branch ) {
 275             updateOptions( getOptions() );
 276         }
 277         else if ( o == _show_default_node_shapes_cbmi ) {
 278             updateOptions( getOptions() );
 279         }
 280         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 281             updateOptions( getOptions() );
 282         }
 283         else if ( o == _about_item ) {
 284             MainFrame.about();
 285         }
 286         else if ( o == _help_item ) {
 287             help( getConfiguration().getWebLinks() );
 288         }
 289         else if ( o == _website_item ) {
 290             try {
 291                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 292             }
 293             catch ( final IOException e1 ) {
 294                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 295             }
 296         }
 297         else if ( o == _phyloxml_website_item ) {
 298             try {
 299                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 300             }
 301             catch ( final IOException e1 ) {
 302                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 303             }
 304         }
 305         else if ( o == _aptx_ref_item ) {
 306             try {
 307                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 308             }
 309             catch ( final IOException e1 ) {
 310                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 311             }
 312         }
 313         else if ( o == _phyloxml_ref_item ) {
 314             try {
 315                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 316             }
 317             catch ( final IOException e1 ) {
 318                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 319             }
 320         }
 321         repaint();
 322     }
 323
 324     void help( final Map<String, WebLink> weblinks ) {
 325         final StringBuilder sb = new StringBuilder();
 326         sb.append( "Display options\n" );
 327         sb.append( "-------------------\n" );
 328         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 329         sb.append( "Clickable tree nodes\n" );
 330         sb.append( "--------------------\n" );
 331         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 332         sb.append( "or by right clicking:\n" );
 333         sb.append( "o  Display Node Data -- display information for a node\n" );
 334         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 335         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 336         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 337         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 338         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 339         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 340         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 341         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 342         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 343         sb.append( "Zooming\n" );
 344         sb.append( "---------\n" );
 345         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 346         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 347         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 348         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 349         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 350         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 351         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 352         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 353         sb.append( "Quick tree manipulation:\n" );
 354         sb.append( "------------------------\n" );
 355         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 356         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 357         sb.append( "Memory problems (Java heap space error)\n" );
 358         sb.append( "---------------------------------------\n" );
 359         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 360         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 361         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 362         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 363         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 364             sb.append( "Active web links\n" );
 365             sb.append( "--------------------\n" );
 366             for( final String key : weblinks.keySet() ) {
 367                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 368             }
 369         }
 370         sb.append( "\n" );
 371         sb.append( "phyloXML\n" );
 372         sb.append( "-------------------\n" );
 373         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 374         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 375         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 376         sb.append( "\n" );
 377         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 378         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 379         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 380     }
 381
 382     /**
 383      * This method returns the current phylogeny as a string in the chosen format
 384      *
 385      * @param format must be NH, NHX, NEXUS or PHYLOXML
 386      * @return the phylogeny string
 387      * @author Herve Menager
 388      */
 389     public String getCurrentPhylogeny( final String format ) {
 390         removeAllTextFrames();
 391         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 392                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 393             return new String();
 394         }
 395         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 396             case NH:
 397                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 398             case NHX:
 399                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 400             case NEXUS:
 401                 return getMainPanel().getCurrentPhylogeny().toNexus();
 402             case PHYLOXML:
 403                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 404             default:
 405                 break;
 406         }
 407         return new String();
 408     }
 409
 410     /**
 411      * This method returns a view of the current phylogeny in a chosen
 412      * graphics format, base64-encoded in a string so that in can be used
 413      * from javascript.
 414      *
 415      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 416      * @return the phylogeny string
 417      * @author Herve Menager
 418      */
 419     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 420         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 421         try {
 422             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 423                                                                     _main_panel.getWidth(),
 424                                                                     _main_panel.getHeight(),
 425                                                                     getCurrentTreePanel(),
 426                                                                     getCurrentTreePanel().getControlPanel(),
 427                                                                     GraphicsExportType.valueOf( format ),
 428                                                                     getOptions() );
 429         }
 430         catch ( final IOException ioe ) {
 431             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 432             ioe.printStackTrace();
 433             JOptionPane.showMessageDialog( this,
 434                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 435                                            "Failed to generate graphics",
 436                                            JOptionPane.ERROR_MESSAGE );
 437             return null;
 438         }
 439         final byte[] bytes = baos.toByteArray();
 440         final String dataImg = Base64.encodeBase64String( bytes );
 441         return dataImg;
 442     }
 443
 444     void buildFontSizeMenu() {
 445         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 446         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 447         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 448         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 449         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 450         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 451         customizeJMenuItem( _super_tiny_fonts_mi );
 452         customizeJMenuItem( _tiny_fonts_mi );
 453         customizeJMenuItem( _small_fonts_mi );
 454         customizeJMenuItem( _medium_fonts_mi );
 455         customizeJMenuItem( _large_fonts_mi );
 456         _jmenubar.add( _font_size_menu );
 457     }
 458
 459     void buildHelpMenu() {
 460         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 461         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 462         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 463         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 464         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 465         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 466         _help_jmenu.addSeparator();
 467         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 468         customizeJMenuItem( _help_item );
 469         customizeJMenuItem( _website_item );
 470         customizeJMenuItem( _phyloxml_website_item );
 471         customizeJMenuItem( _aptx_ref_item );
 472         customizeJMenuItem( _phyloxml_ref_item );
 473         customizeJMenuItem( _about_item );
 474         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 475         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 476         _jmenubar.add( _help_jmenu );
 477     }
 478
 479     void buildOptionsMenu() {
 480         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 481         _options_jmenu.addChangeListener( new ChangeListener() {
 482
 483             @Override
 484             public void stateChanged( final ChangeEvent e ) {
 485                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 486                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 487                 MainFrame
 488                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 489                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 490                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 491                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 492                                                                      _show_scale_cbmi,
 493                                                                      _show_branch_length_values_cbmi,
 494                                                                      _non_lined_up_cladograms_rbmi,
 495                                                                      _uniform_cladograms_rbmi,
 496                                                                      _ext_node_dependent_cladogram_rbmi,
 497                                                                      _label_direction_cbmi );
 498                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 499                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 500                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 501             }
 502         } );
 503         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 504                                                                 getConfiguration() ) );
 505         _options_jmenu
 506                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 507         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 508         _options_jmenu
 509                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 510         _radio_group_1 = new ButtonGroup();
 511         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 512         _radio_group_1.add( _uniform_cladograms_rbmi );
 513         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 514         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 515         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 516         _options_jmenu
 517                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 518         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 519         _options_jmenu
 520                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 521         _options_jmenu
 522                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 523         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 524         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 525         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 526         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 527         _options_jmenu
 528                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 529         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 530         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 531         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 532         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 533         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 534         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 535             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 536         }
 537         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 538         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 539         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 540         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 541         _options_jmenu.addSeparator();
 542         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 543                                                                 getConfiguration() ) );
 544         _options_jmenu
 545                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 546         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 547         _options_jmenu
 548                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 549         customizeJMenuItem( _choose_font_mi );
 550         customizeJMenuItem( _choose_minimal_confidence_mi );
 551         customizeJMenuItem( _switch_colors_mi );
 552         customizeJMenuItem( _overview_placment_mi );
 553         customizeCheckBoxMenuItem( _label_direction_cbmi,
 554                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 555         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 556         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 557         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 558         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 559         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 560         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 561         customizeJMenuItem( _cycle_node_shape_mi );
 562         customizeJMenuItem( _cycle_node_fill_mi );
 563         customizeJMenuItem( _choose_node_size_mi );
 564         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 565         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 566         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 567         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 568                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 569         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 570                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 571         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 572                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 573         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 574         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 575         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 576         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 577         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 578         _jmenubar.add( _options_jmenu );
 579     }
 580
 581     void buildToolsMenu() {
 582         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 583         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 584         customizeJMenuItem( _confcolor_item );
 585         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 586         customizeJMenuItem( _taxcolor_item );
 587         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 588         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 589         customizeJMenuItem( _remove_branch_color_item );
 590         _tools_menu.addSeparator();
 591         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 592         customizeJMenuItem( _midpoint_root_item );
 593         _tools_menu.addSeparator();
 594         _tools_menu
 595                 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 596         customizeJMenuItem( _infer_common_sn_names_item );
 597         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 598         customizeJMenuItem( _collapse_species_specific_subtrees );
 599         _jmenubar.add( _tools_menu );
 600     }
 601
 602     void buildTypeMenu() {
 603         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 604         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 605         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 606         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 607         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 608         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 609         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 610         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 611         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 612         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 613         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 614         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 615         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 616         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 617         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 618         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 619         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 620         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 621         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 622         initializeTypeMenu( getOptions() );
 623         _jmenubar.add( _type_menu );
 624     }
 625
 626     void buildViewMenu() {
 627         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 628         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 629         _view_jmenu.addSeparator();
 630         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 631         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 632         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 633         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 634         customizeJMenuItem( _display_basic_information_item );
 635         customizeJMenuItem( _view_as_NH_item );
 636         customizeJMenuItem( _view_as_NHX_item );
 637         customizeJMenuItem( _view_as_XML_item );
 638         customizeJMenuItem( _view_as_nexus_item );
 639         _jmenubar.add( _view_jmenu );
 640     }
 641
 642     private void chooseFont() {
 643         final FontChooser fc = new FontChooser();
 644         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
 645         fc.showDialog( this, "Select the Base Font" );
 646         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
 647     }
 648
 649     private void chooseMinimalConfidence() {
 650         final String s = ( String ) JOptionPane
 651                 .showInputDialog( this,
 652                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
 653                                           + getOptions().getMinConfidenceValue() + "]\n",
 654                                   "Minimal Confidence Value",
 655                                   JOptionPane.QUESTION_MESSAGE,
 656                                   null,
 657                                   null,
 658                                   getOptions().getMinConfidenceValue() );
 659         if ( !ForesterUtil.isEmpty( s ) ) {
 660             boolean success = true;
 661             double m = 0.0;
 662             final String m_str = s.trim();
 663             if ( !ForesterUtil.isEmpty( m_str ) ) {
 664                 try {
 665                     m = Double.parseDouble( m_str );
 666                 }
 667                 catch ( final Exception ex ) {
 668                     success = false;
 669                 }
 670             }
 671             else {
 672                 success = false;
 673             }
 674             if ( success && ( m >= 0.0 ) ) {
 675                 getOptions().setMinConfidenceValue( m );
 676             }
 677         }
 678     }
 679
 680     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 681         if ( item != null ) {
 682             item.setFont( MainFrame.menu_font );
 683             if ( !getConfiguration().isUseNativeUI() ) {
 684                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 685                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 686             }
 687             item.setSelected( is_selected );
 688             item.addActionListener( this );
 689         }
 690     }
 691
 692     void customizeJMenuItem( final JMenuItem jmi ) {
 693         jmi.setFont( MainFrame.menu_font );
 694         if ( !getConfiguration().isUseNativeUI() ) {
 695             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 696             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 697         }
 698         jmi.addActionListener( this );
 699     }
 700
 701     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 702         if ( item != null ) {
 703             item.setFont( MainFrame.menu_font );
 704             if ( !getConfiguration().isUseNativeUI() ) {
 705                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 706                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 707             }
 708             item.setSelected( is_selected );
 709             item.addActionListener( this );
 710         }
 711     }
 712
 713     @Override
 714     public void destroy() {
 715         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 716         removeAllTextFrames();
 717         if ( getMainPanel() != null ) {
 718             getMainPanel().terminate();
 719         }
 720     }
 721
 722     Configuration getConfiguration() {
 723         return _configuration;
 724     }
 725
 726     TreePanel getCurrentTreePanel() {
 727         return getMainPanel().getCurrentTreePanel();
 728     }
 729
 730     JCheckBoxMenuItem getlabelDirectionCbmi() {
 731         return _label_direction_cbmi;
 732     }
 733
 734     private MainPanel getMainPanel() {
 735         return _main_panel;
 736     }
 737
 738     public Options getOptions() {
 739         return _options;
 740     }
 741
 742     Options getOtions() {
 743         return _options;
 744     }
 745
 746     @Override
 747     public void init() {
 748         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 749         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 750         final Configuration configuration = new Configuration( config_filename, true, true, true );
 751         setConfiguration( configuration );
 752         setOptions( Options.createInstance( configuration ) );
 753         setupUI();
 754         URL phys_url = null;
 755         Phylogeny[] phys = null;
 756         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 757         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 758         // Get URL to tree file
 759         if ( phys_url_string != null ) {
 760             try {
 761                 phys_url = new URL( phys_url_string );
 762             }
 763             catch ( final Exception e ) {
 764                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 765                 e.printStackTrace();
 766                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 767                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 768             }
 769         }
 770         // Load the tree from URL
 771         if ( phys_url != null ) {
 772             try {
 773                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
 774             }
 775             catch ( final Exception e ) {
 776                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 777                 e.printStackTrace();
 778                 JOptionPane.showMessageDialog( this,
 779                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 780                                                "Failed to read phylogenies",
 781                                                JOptionPane.ERROR_MESSAGE );
 782             }
 783         }
 784         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 785             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 786             JOptionPane.showMessageDialog( this,
 787                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 788                                            "Failed to read phylogenies",
 789                                            JOptionPane.ERROR_MESSAGE );
 790             return;
 791         }
 792         else {
 793             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 794         }
 795         setVisible( false );
 796         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 797         _jmenubar = new JMenuBar();
 798         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 799             if ( !getConfiguration().isUseNativeUI() ) {
 800                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 801             }
 802             buildToolsMenu();
 803             buildViewMenu();
 804             buildFontSizeMenu();
 805             buildOptionsMenu();
 806             buildTypeMenu();
 807             buildHelpMenu();
 808             setJMenuBar( _jmenubar );
 809         }
 810         final Container contentpane = getContentPane();
 811         contentpane.setLayout( new BorderLayout() );
 812         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 813         addComponentListener( new ComponentAdapter() {
 814
 815             @Override
 816             public void componentResized( final ComponentEvent e ) {
 817                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 818                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 819                                                                                            .getWidth(),
 820                                                                                    getMainPanel().getCurrentTreePanel()
 821                                                                                            .getHeight(),
 822                                                                                    false );
 823                 }
 824             }
 825         } );
 826         if ( getConfiguration().isUseTabbedDisplay() ) {
 827             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 828             AptxUtil.addPhylogeniesToTabs( phys,
 829                                            new File( phys_url.getFile() ).getName(),
 830                                            phys_url.toString(),
 831                                            getConfiguration(),
 832                                            getMainPanel() );
 833         }
 834         else {
 835             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 836             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 837         }
 838         validate();
 839         setName( NAME );
 840         getMainPanel().getControlPanel().showWholeAll();
 841         getMainPanel().getControlPanel().showWhole();
 842         System.gc();
 843         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 844         /* GUILHEM_BEG */
 845         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 846         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 847                 .getRelevantSequenceRelationTypes() ) {
 848             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 849         }
 850         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 851         if ( default_relation != null ) {
 852             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 853         }
 854         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 855         if ( default_sequence != null ) {
 856             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 857             /* GUILHEM_END */
 858         }
 859         setVisible( true );
 860     }
 861
 862     void initializeTypeMenu( final Options options ) {
 863         setTypeMenuToAllUnselected();
 864         try {
 865             switch ( options.getPhylogenyGraphicsType() ) {
 866                 case CONVEX:
 867                     _convex_type_cbmi.setSelected( true );
 868                     break;
 869                 case CURVED:
 870                     _curved_type_cbmi.setSelected( true );
 871                     break;
 872                 case EURO_STYLE:
 873                     _euro_type_cbmi.setSelected( true );
 874                     break;
 875                 case ROUNDED:
 876                     _rounded_type_cbmi.setSelected( true );
 877                     break;
 878                 case TRIANGULAR:
 879                     _triangular_type_cbmi.setSelected( true );
 880                     break;
 881                 case UNROOTED:
 882                     _unrooted_type_cbmi.setSelected( true );
 883                     break;
 884                 case CIRCULAR:
 885                     _circular_type_cbmi.setSelected( true );
 886                     break;
 887                 default:
 888                     _rectangular_type_cbmi.setSelected( true );
 889                     break;
 890             }
 891         }
 892         catch ( final NullPointerException np ) {
 893             // In all likelihood, this is caused by menu-less display.
 894         }
 895     }
 896
 897     private boolean isScreenAntialias() {
 898         return true;
 899     }
 900
 901     private void removeBranchColors() {
 902         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 903             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
 904         }
 905     }
 906
 907     void setConfiguration( final Configuration configuration ) {
 908         _configuration = configuration;
 909     }
 910
 911     private void setMainPanel( final MainPanelApplets main_panel ) {
 912         _main_panel = main_panel;
 913     }
 914
 915     void setOptions( final Options options ) {
 916         _options = options;
 917     }
 918
 919     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 920         setTypeMenuToAllUnselected();
 921         try {
 922             switch ( type ) {
 923                 case CIRCULAR:
 924                     _circular_type_cbmi.setSelected( true );
 925                     break;
 926                 case CONVEX:
 927                     _convex_type_cbmi.setSelected( true );
 928                     break;
 929                 case CURVED:
 930                     _curved_type_cbmi.setSelected( true );
 931                     break;
 932                 case EURO_STYLE:
 933                     _euro_type_cbmi.setSelected( true );
 934                     break;
 935                 case ROUNDED:
 936                     _rounded_type_cbmi.setSelected( true );
 937                     break;
 938                 case RECTANGULAR:
 939                     _rectangular_type_cbmi.setSelected( true );
 940                     break;
 941                 case TRIANGULAR:
 942                     _triangular_type_cbmi.setSelected( true );
 943                     break;
 944                 case UNROOTED:
 945                     _unrooted_type_cbmi.setSelected( true );
 946                     break;
 947                 default:
 948                     throw new IllegalArgumentException( "unknown type: " + type );
 949             }
 950         }
 951         catch ( final NullPointerException np ) {
 952             // In all likelihood, this is caused by menu-less display.
 953         }
 954     }
 955
 956     void setTypeMenuToAllUnselected() {
 957         if ( _convex_type_cbmi != null ) {
 958             _convex_type_cbmi.setSelected( false );
 959         }
 960         if ( _curved_type_cbmi != null ) {
 961             _curved_type_cbmi.setSelected( false );
 962         }
 963         if ( _euro_type_cbmi != null ) {
 964             _euro_type_cbmi.setSelected( false );
 965         }
 966         if ( _rounded_type_cbmi != null ) {
 967             _rounded_type_cbmi.setSelected( false );
 968         }
 969         if ( _triangular_type_cbmi != null ) {
 970             _triangular_type_cbmi.setSelected( false );
 971         }
 972         if ( _rectangular_type_cbmi != null ) {
 973             _rectangular_type_cbmi.setSelected( false );
 974         }
 975         if ( _unrooted_type_cbmi != null ) {
 976             _unrooted_type_cbmi.setSelected( false );
 977         }
 978         if ( _circular_type_cbmi != null ) {
 979             _circular_type_cbmi.setSelected( false );
 980         }
 981     }
 982
 983     private void setupUI() {
 984         try {
 985             if ( getConfiguration().isUseNativeUI() ) {
 986                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 987             }
 988             else {
 989                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 990             }
 991         }
 992         catch ( final UnsupportedLookAndFeelException e ) {
 993             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
 994         }
 995         catch ( final ClassNotFoundException e ) {
 996             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
 997         }
 998         catch ( final InstantiationException e ) {
 999             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1000         }
1001         catch ( final IllegalAccessException e ) {
1002             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1003         }
1004         catch ( final Exception e ) {
1005             AptxUtil.dieWithSystemError( e.toString() );
1006         }
1007     }
1008
1009     @Override
1010     public void start() {
1011         if ( getMainPanel() != null ) {
1012             getMainPanel().validate();
1013         }
1014         requestFocus();
1015         requestFocusInWindow();
1016         requestFocus();
1017         AptxUtil.printAppletMessage( NAME, "started" );
1018     }
1019
1020     void switchColors() {
1021         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1022         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1023         csc.setVisible( true );
1024         getMainPanel().setTreeColorSet( colorset );
1025     }
1026
1027     void typeChanged( final Object o ) {
1028         updateTypeCheckboxes( getOptions(), o );
1029         updateOptions( getOptions() );
1030         if ( getCurrentTreePanel() != null ) {
1031             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1032             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1033             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1034                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1035                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1036                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1037                 getCurrentTreePanel().getControlPanel().showWhole();
1038             }
1039             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1040                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1041             }
1042             else {
1043                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1044             }
1045             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1046             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1047         }
1048     }
1049
1050     void updateOptions( final Options options ) {
1051         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1052         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1053                 && _background_gradient_cbmi.isSelected() );
1054         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1055         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1056                 && _abbreviate_scientific_names.isSelected() );
1057         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1058                 && _color_labels_same_as_parent_branch.isSelected() );
1059         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1060                 && _show_default_node_shapes_cbmi.isSelected() );
1061         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1062                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1063         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1064             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1065         }
1066         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1067             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1068         }
1069         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1070             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1071         }
1072         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1073                 && _search_case_senstive_cbmi.isSelected() );
1074         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1075             options.setShowScale( _show_scale_cbmi.isSelected() );
1076         }
1077         if ( _label_direction_cbmi != null ) {
1078             if ( _label_direction_cbmi.isSelected() ) {
1079                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1080             }
1081             else {
1082                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1083             }
1084         }
1085         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1086         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1087                 && _show_confidence_stddev_cbmi.isSelected() );
1088         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1089             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1090         }
1091         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1092                 && _search_whole_words_only_cbmi.isSelected() );
1093         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1094                 && _inverse_search_result_cbmi.isSelected() );
1095         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1096             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1097         }
1098         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1099             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1100         }
1101         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1102             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1103         }
1104         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1105             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1106         }
1107         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1108             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1109         }
1110         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1111             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1112         }
1113         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1114             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1115         }
1116         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1117             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1118         }
1119     }
1120
1121     void updateTypeCheckboxes( final Options options, final Object o ) {
1122         setTypeMenuToAllUnselected();
1123         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1124     }
1125
1126     void displayBasicInformation() {
1127         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1128             String title = "Basic Information";
1129             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1130                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1131             }
1132             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
1133         }
1134     }
1135
1136     void viewAsNexus() {
1137         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1138             String title = "Nexus";
1139             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1140                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1141             }
1142             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1143                                    .getNhConversionSupportValueStyle() ),
1144                            title );
1145         }
1146     }
1147
1148     void viewAsNH() {
1149         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1150             String title = "New Hampshire";
1151             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1152                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1153             }
1154             showTextFrame( getMainPanel().getCurrentPhylogeny()
1155                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1156                            title );
1157         }
1158     }
1159
1160     void viewAsNHX() {
1161         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1162             String title = "NHX";
1163             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1164                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1165             }
1166             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title );
1167         }
1168     }
1169
1170     void viewAsXML() {
1171         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1172             String title = "phyloXML";
1173             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1174                 title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
1175             }
1176             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1177         }
1178     }
1179
1180     public void showTextFrame( final String s, final String title ) {
1181         checkTextFrames();
1182         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
1183     }
1184
1185     void checkTextFrames() {
1186         if ( _textframes.size() > 5 ) {
1187             try {
1188                 if ( _textframes.getFirst() != null ) {
1189                     _textframes.getFirst().removeMe();
1190                 }
1191                 else {
1192                     _textframes.removeFirst();
1193                 }
1194             }
1195             catch ( final NoSuchElementException e ) {
1196                 // Ignore.
1197             }
1198         }
1199     }
1200
1201     void removeAllTextFrames() {
1202         for( final TextFrame tf : _textframes ) {
1203             if ( tf != null ) {
1204                 tf.close();
1205             }
1206         }
1207         _textframes.clear();
1208     }
1209
1210     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1211         for( final TreePanel tree_panel : treepanels ) {
1212             tree_panel.setTextAntialias();
1213         }
1214     }
1215 }