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.List;
  15
  16 import javax.swing.ButtonGroup;
  17 import javax.swing.JApplet;
  18 import javax.swing.JCheckBoxMenuItem;
  19 import javax.swing.JMenu;
  20 import javax.swing.JMenuBar;
  21 import javax.swing.JMenuItem;
  22 import javax.swing.JOptionPane;
  23 import javax.swing.JRadioButtonMenuItem;
  24 import javax.swing.UIManager;
  25 import javax.swing.UnsupportedLookAndFeelException;
  26 import javax.swing.event.ChangeEvent;
  27 import javax.swing.event.ChangeListener;
  28
  29 import org.apache.commons.codec.binary.Base64;
  30 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  31 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  32 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  33 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  34 import org.forester.phylogeny.Phylogeny;
  35 import org.forester.phylogeny.data.SequenceRelation;
  36 import org.forester.util.ForesterConstants;
  37 import org.forester.util.ForesterUtil;
  38
  39 // Use like this:
  40 // <applet archive="forester.jar"
  41 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  42 // codebase="http://www.myserver.org/path/to/forester"
  43 // width="600"
  44 // height="500"
  45 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  46 // <param name="url_of_tree_to_load"
  47 // value="http://www.myserver.org/examples/data/apaf.xml">
  48 // <param name="config_file"
  49 // value="http://www.myserver.org/examples/config/config_file.txt">
  50 // </applet>
  51 public class ArchaeopteryxE extends JApplet implements ActionListener {
  52
  53     private final static String  NAME             = "ArchaeopteryxE";
  54     private static final long    serialVersionUID = -1220055577935759443L;
  55     private Configuration        _configuration;
  56     private MainPanelApplets     _main_panel;
  57     private JMenuBar             _jmenubar;
  58     private JMenu                _options_jmenu;
  59     private JMenu                _font_size_menu;
  60     private JMenuItem            _super_tiny_fonts_mi;
  61     private JMenuItem            _tiny_fonts_mi;
  62     private JMenuItem            _small_fonts_mi;
  63     private JMenuItem            _medium_fonts_mi;
  64     private JMenuItem            _large_fonts_mi;
  65     private TextFrame            _textframe;
  66     private JMenu                _tools_menu;
  67     private JMenuItem            _taxcolor_item;
  68     private JMenuItem            _confcolor_item;
  69     private JMenuItem            _midpoint_root_item;
  70     private JMenu                _view_jmenu;
  71     private JMenuItem            _view_as_XML_item;
  72     private JMenuItem            _view_as_NH_item;
  73     private JMenuItem            _view_as_NHX_item;
  74     private JMenuItem            _view_as_nexus_item;
  75     private JMenuItem            _display_basic_information_item;
  76     private JMenu                _type_menu;
  77     private JCheckBoxMenuItem    _rectangular_type_cbmi;
  78     private JCheckBoxMenuItem    _triangular_type_cbmi;
  79     private JCheckBoxMenuItem    _curved_type_cbmi;
  80     private JCheckBoxMenuItem    _convex_type_cbmi;
  81     private JCheckBoxMenuItem    _euro_type_cbmi;
  82     private JCheckBoxMenuItem    _rounded_type_cbmi;
  83     private JCheckBoxMenuItem    _unrooted_type_cbmi;
  84     private JCheckBoxMenuItem    _circular_type_cbmi;
  85     private JMenuItem            _help_item;
  86     private JMenuItem            _about_item;
  87     private JMenu                _help_jmenu;
  88     private JMenuItem            _website_item;
  89     private JMenuItem            _phyloxml_website_item;
  90     private JMenuItem            _phyloxml_ref_item;
  91     private JMenuItem            _aptx_ref_item;
  92     private JMenuItem            _remove_branch_color_item;
  93     private JMenuItem            _infer_common_sn_names_item;
  94     private JCheckBoxMenuItem    _show_domain_labels;
  95     private JCheckBoxMenuItem    _color_labels_same_as_parent_branch;
  96     private JCheckBoxMenuItem    _abbreviate_scientific_names;
  97     private JCheckBoxMenuItem    _screen_antialias_cbmi;
  98     private JCheckBoxMenuItem    _background_gradient_cbmi;
  99     private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
 100     private JRadioButtonMenuItem _uniform_cladograms_rbmi;
 101     private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
 102     private Options              _options;
 103     private JMenuItem            _choose_font_mi;
 104     private JMenuItem            _switch_colors_mi;
 105     JCheckBoxMenuItem            _label_direction_cbmi;
 106     private JCheckBoxMenuItem    _show_scale_cbmi;
 107     private JCheckBoxMenuItem    _search_case_senstive_cbmi;
 108     private JCheckBoxMenuItem    _search_whole_words_only_cbmi;
 109     private JCheckBoxMenuItem    _inverse_search_result_cbmi;
 110     private JCheckBoxMenuItem    _show_overview_cbmi;
 111     private JMenuItem            _choose_minimal_confidence_mi;
 112     private JCheckBoxMenuItem    _show_branch_length_values_cbmi;
 113     private JMenuItem            _collapse_species_specific_subtrees;
 114     private JMenuItem            _overview_placment_mi;
 115     private ButtonGroup          _radio_group_1;
 116     private JCheckBoxMenuItem    _show_default_node_shapes_cbmi;
 117     private JMenuItem            _cycle_node_shape_mi;
 118     private JMenuItem            _cycle_node_fill_mi;
 119     private JMenuItem            _choose_node_size_mi;
 120     private JCheckBoxMenuItem    _taxonomy_colorize_node_shapes_cbmi;
 121     private JCheckBoxMenuItem    _show_confidence_stddev_cbmi;
 122
 123     @Override
 124     public void actionPerformed( final ActionEvent e ) {
 125         final Object o = e.getSource();
 126         if ( o == _midpoint_root_item ) {
 127             getMainPanel().getCurrentTreePanel().midpointRoot();
 128         }
 129         else if ( o == _taxcolor_item ) {
 130             getMainPanel().getCurrentTreePanel().taxColor();
 131         }
 132         else if ( o == _confcolor_item ) {
 133             getMainPanel().getCurrentTreePanel().confColor();
 134         }
 135         else if ( o == _infer_common_sn_names_item ) {
 136             if ( getCurrentTreePanel() != null ) {
 137                 getCurrentTreePanel().inferCommonPartOfScientificNames();
 138             }
 139         }
 140         else if ( o == _collapse_species_specific_subtrees ) {
 141             if ( getCurrentTreePanel() != null ) {
 142                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 143             }
 144         }
 145         else if ( o == _remove_branch_color_item ) {
 146             removeBranchColors();
 147         }
 148         else if ( o == _switch_colors_mi ) {
 149             switchColors();
 150         }
 151         else if ( o == _display_basic_information_item ) {
 152             displayBasicInformation();
 153         }
 154         else if ( o == _view_as_NH_item ) {
 155             viewAsNH();
 156         }
 157         else if ( o == _view_as_NHX_item ) {
 158             viewAsNHX();
 159         }
 160         else if ( o == _view_as_XML_item ) {
 161             viewAsXML();
 162         }
 163         else if ( o == _view_as_nexus_item ) {
 164             viewAsNexus();
 165         }
 166         else if ( o == _super_tiny_fonts_mi ) {
 167             if ( getCurrentTreePanel() != null ) {
 168                 getCurrentTreePanel().setSuperTinyFonts();
 169                 getCurrentTreePanel().repaint();
 170             }
 171         }
 172         else if ( o == _tiny_fonts_mi ) {
 173             if ( getCurrentTreePanel() != null ) {
 174                 getCurrentTreePanel().setTinyFonts();
 175                 getCurrentTreePanel().repaint();
 176             }
 177         }
 178         else if ( o == _small_fonts_mi ) {
 179             if ( getCurrentTreePanel() != null ) {
 180                 getCurrentTreePanel().setSmallFonts();
 181                 getCurrentTreePanel().repaint();
 182             }
 183         }
 184         else if ( o == _medium_fonts_mi ) {
 185             if ( getCurrentTreePanel() != null ) {
 186                 getCurrentTreePanel().setMediumFonts();
 187                 getCurrentTreePanel().repaint();
 188             }
 189         }
 190         else if ( o == _large_fonts_mi ) {
 191             if ( getCurrentTreePanel() != null ) {
 192                 getCurrentTreePanel().setLargeFonts();
 193                 getCurrentTreePanel().repaint();
 194             }
 195         }
 196         else if ( o == _choose_font_mi ) {
 197             chooseFont();
 198         }
 199         else if ( o == _choose_minimal_confidence_mi ) {
 200             chooseMinimalConfidence();
 201         }
 202         else if ( o == _choose_node_size_mi ) {
 203             MainFrame.chooseNodeSize( getOptions(), this );
 204         }
 205         else if ( o == _overview_placment_mi ) {
 206             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 207         }
 208         else if ( o == _cycle_node_fill_mi ) {
 209             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 210         }
 211         else if ( o == _cycle_node_shape_mi ) {
 212             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 213         }
 214         else if ( o == _non_lined_up_cladograms_rbmi ) {
 215             updateOptions( getOptions() );
 216             _main_panel.getControlPanel().showWhole();
 217         }
 218         else if ( o == _uniform_cladograms_rbmi ) {
 219             updateOptions( getOptions() );
 220             _main_panel.getControlPanel().showWhole();
 221         }
 222         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 223             updateOptions( getOptions() );
 224             _main_panel.getControlPanel().showWhole();
 225         }
 226         else if ( o == _search_case_senstive_cbmi ) {
 227             updateOptions( getOptions() );
 228             getMainPanel().getControlPanel().search();
 229         }
 230         else if ( o == _search_whole_words_only_cbmi ) {
 231             updateOptions( getOptions() );
 232             getMainPanel().getControlPanel().search();
 233         }
 234         else if ( o == _inverse_search_result_cbmi ) {
 235             updateOptions( getOptions() );
 236             getMainPanel().getControlPanel().search();
 237         }
 238         else if ( o == _show_scale_cbmi ) {
 239             updateOptions( getOptions() );
 240         }
 241         else if ( o == _show_branch_length_values_cbmi ) {
 242             updateOptions( getOptions() );
 243         }
 244         else if ( o == _show_confidence_stddev_cbmi ) {
 245             updateOptions( getOptions() );
 246         }
 247         else if ( o == _label_direction_cbmi ) {
 248             updateOptions( getOptions() );
 249         }
 250         else if ( o == _show_overview_cbmi ) {
 251             updateOptions( getOptions() );
 252             if ( getCurrentTreePanel() != null ) {
 253                 getCurrentTreePanel().updateOvSizes();
 254             }
 255         }
 256         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 257                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 258                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 259             typeChanged( o );
 260         }
 261         else if ( o == _screen_antialias_cbmi ) {
 262             updateOptions( getOptions() );
 263             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 264         }
 265         else if ( o == _background_gradient_cbmi ) {
 266             updateOptions( getOptions() );
 267         }
 268         else if ( o == _show_domain_labels ) {
 269             updateOptions( getOptions() );
 270         }
 271         else if ( o == _color_labels_same_as_parent_branch ) {
 272             updateOptions( getOptions() );
 273         }
 274         else if ( o == _show_default_node_shapes_cbmi ) {
 275             updateOptions( getOptions() );
 276         }
 277         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 278             updateOptions( getOptions() );
 279         }
 280         else if ( o == _about_item ) {
 281             MainFrame.about();
 282         }
 283         else if ( o == _help_item ) {
 284             MainFrame.help( getConfiguration().getWebLinks() );
 285         }
 286         else if ( o == _website_item ) {
 287             try {
 288                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 289             }
 290             catch ( final IOException e1 ) {
 291                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 292             }
 293         }
 294         else if ( o == _phyloxml_website_item ) {
 295             try {
 296                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 297             }
 298             catch ( final IOException e1 ) {
 299                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 300             }
 301         }
 302         else if ( o == _aptx_ref_item ) {
 303             try {
 304                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 305             }
 306             catch ( final IOException e1 ) {
 307                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 308             }
 309         }
 310         else if ( o == _phyloxml_ref_item ) {
 311             try {
 312                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 313             }
 314             catch ( final IOException e1 ) {
 315                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 316             }
 317         }
 318         repaint();
 319     }
 320
 321     /**
 322      * This method returns the current phylogeny as a string in the chosen format
 323      *
 324      * @param format must be NH, NHX, NEXUS or PHYLOXML
 325      * @return the phylogeny string
 326      * @author Herve Menager
 327      */
 328     public String getCurrentPhylogeny( final String format ) {
 329         removeTextFrame();
 330         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 331                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 332             return new String();
 333         }
 334         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 335             case NH:
 336                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 337             case NHX:
 338                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 339             case NEXUS:
 340                 return getMainPanel().getCurrentPhylogeny().toNexus();
 341             case PHYLOXML:
 342                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 343             default:
 344                 break;
 345         }
 346         return new String();
 347     }
 348
 349     /**
 350      * This method returns a view of the current phylogeny in a chosen
 351      * graphics format, base64-encoded in a string so that in can be used
 352      * from javascript.
 353      *
 354      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 355      * @return the phylogeny string
 356      * @author Herve Menager
 357      */
 358     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 359         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 360         try {
 361             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 362                                                                     _main_panel.getWidth(),
 363                                                                     _main_panel.getHeight(),
 364                                                                     getCurrentTreePanel(),
 365                                                                     getCurrentTreePanel().getControlPanel(),
 366                                                                     GraphicsExportType.valueOf( format ),
 367                                                                     getOptions() );
 368         }
 369         catch ( final IOException ioe ) {
 370             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 371             ioe.printStackTrace();
 372             JOptionPane.showMessageDialog( this,
 373                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 374                                            "Failed to generate graphics",
 375                                            JOptionPane.ERROR_MESSAGE );
 376             return null;
 377         }
 378         final byte[] bytes = baos.toByteArray();
 379         final String dataImg = Base64.encodeBase64String( bytes );
 380         return dataImg;
 381     }
 382
 383     void buildFontSizeMenu() {
 384         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 385         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 386         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 387         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 388         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 389         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 390         customizeJMenuItem( _super_tiny_fonts_mi );
 391         customizeJMenuItem( _tiny_fonts_mi );
 392         customizeJMenuItem( _small_fonts_mi );
 393         customizeJMenuItem( _medium_fonts_mi );
 394         customizeJMenuItem( _large_fonts_mi );
 395         _jmenubar.add( _font_size_menu );
 396     }
 397
 398     void buildHelpMenu() {
 399         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 400         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 401         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 402         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 403         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 404         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 405         _help_jmenu.addSeparator();
 406         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 407         customizeJMenuItem( _help_item );
 408         customizeJMenuItem( _website_item );
 409         customizeJMenuItem( _phyloxml_website_item );
 410         customizeJMenuItem( _aptx_ref_item );
 411         customizeJMenuItem( _phyloxml_ref_item );
 412         customizeJMenuItem( _about_item );
 413         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 414         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 415         _jmenubar.add( _help_jmenu );
 416     }
 417
 418     void buildOptionsMenu() {
 419         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 420         _options_jmenu.addChangeListener( new ChangeListener() {
 421
 422             @Override
 423             public void stateChanged( final ChangeEvent e ) {
 424                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 425                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 426                 MainFrame
 427                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 428                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 429                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 430                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 431                                                                      _show_scale_cbmi,
 432                                                                      _show_branch_length_values_cbmi,
 433                                                                      _non_lined_up_cladograms_rbmi,
 434                                                                      _uniform_cladograms_rbmi,
 435                                                                      _ext_node_dependent_cladogram_rbmi,
 436                                                                      _label_direction_cbmi );
 437                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 438                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 439                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 440             }
 441         } );
 442         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 443                                                                 getConfiguration() ) );
 444         _options_jmenu
 445                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 446         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 447         _options_jmenu
 448                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 449         _radio_group_1 = new ButtonGroup();
 450         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 451         _radio_group_1.add( _uniform_cladograms_rbmi );
 452         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 453         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 454         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 455         _options_jmenu
 456                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 457         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 458         _options_jmenu
 459                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
 460         _options_jmenu
 461                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 462         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 463         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 464         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 465         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 466         _options_jmenu
 467                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 468         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 469         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 470         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 471         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 472         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 473         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 474             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 475         }
 476         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 477         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 478         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 479         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 480         _options_jmenu.addSeparator();
 481         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 482                                                                 getConfiguration() ) );
 483         _options_jmenu
 484                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 485         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 486         _options_jmenu
 487                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 488         customizeJMenuItem( _choose_font_mi );
 489         customizeJMenuItem( _choose_minimal_confidence_mi );
 490         customizeJMenuItem( _switch_colors_mi );
 491         customizeJMenuItem( _overview_placment_mi );
 492         customizeCheckBoxMenuItem( _label_direction_cbmi,
 493                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 494         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 495         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 496         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 497         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 498         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
 499         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 500         customizeJMenuItem( _cycle_node_shape_mi );
 501         customizeJMenuItem( _cycle_node_fill_mi );
 502         customizeJMenuItem( _choose_node_size_mi );
 503         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 504         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 505         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 506         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 507                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 508         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 509                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 510         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 511                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 512         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 513         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 514         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 515         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 516         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 517         _jmenubar.add( _options_jmenu );
 518     }
 519
 520     void buildToolsMenu() {
 521         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 522         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 523         customizeJMenuItem( _confcolor_item );
 524         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 525         customizeJMenuItem( _taxcolor_item );
 526         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
 527         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
 528         customizeJMenuItem( _remove_branch_color_item );
 529         _tools_menu.addSeparator();
 530         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 531         customizeJMenuItem( _midpoint_root_item );
 532         _tools_menu.addSeparator();
 533         _tools_menu
 534                 .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 535         customizeJMenuItem( _infer_common_sn_names_item );
 536         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 537         customizeJMenuItem( _collapse_species_specific_subtrees );
 538         _jmenubar.add( _tools_menu );
 539     }
 540
 541     void buildTypeMenu() {
 542         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 543         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 544         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 545         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 546         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 547         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 548         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 549         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 550         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 551         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 552         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 553         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 554         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 555         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 556         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 557         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 558         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 559         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 560         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 561         initializeTypeMenu( getOptions() );
 562         _jmenubar.add( _type_menu );
 563     }
 564
 565     void buildViewMenu() {
 566         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 567         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 568         _view_jmenu.addSeparator();
 569         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 570         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 571         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 572         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 573         customizeJMenuItem( _display_basic_information_item );
 574         customizeJMenuItem( _view_as_NH_item );
 575         customizeJMenuItem( _view_as_NHX_item );
 576         customizeJMenuItem( _view_as_XML_item );
 577         customizeJMenuItem( _view_as_nexus_item );
 578         _jmenubar.add( _view_jmenu );
 579     }
 580
 581     private void chooseFont() {
 582         final FontChooser fc = new FontChooser();
 583         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
 584         fc.showDialog( this, "Select the Base Font" );
 585         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
 586     }
 587
 588     private void chooseMinimalConfidence() {
 589         final String s = ( String ) JOptionPane
 590                 .showInputDialog( this,
 591                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
 592                                           + getOptions().getMinConfidenceValue() + "]\n",
 593                                   "Minimal Confidence Value",
 594                                   JOptionPane.QUESTION_MESSAGE,
 595                                   null,
 596                                   null,
 597                                   getOptions().getMinConfidenceValue() );
 598         if ( !ForesterUtil.isEmpty( s ) ) {
 599             boolean success = true;
 600             double m = 0.0;
 601             final String m_str = s.trim();
 602             if ( !ForesterUtil.isEmpty( m_str ) ) {
 603                 try {
 604                     m = Double.parseDouble( m_str );
 605                 }
 606                 catch ( final Exception ex ) {
 607                     success = false;
 608                 }
 609             }
 610             else {
 611                 success = false;
 612             }
 613             if ( success && ( m >= 0.0 ) ) {
 614                 getOptions().setMinConfidenceValue( m );
 615             }
 616         }
 617     }
 618
 619     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 620         if ( item != null ) {
 621             item.setFont( MainFrame.menu_font );
 622             if ( !getConfiguration().isUseNativeUI() ) {
 623                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 624                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 625             }
 626             item.setSelected( is_selected );
 627             item.addActionListener( this );
 628         }
 629     }
 630
 631     void customizeJMenuItem( final JMenuItem jmi ) {
 632         jmi.setFont( MainFrame.menu_font );
 633         if ( !getConfiguration().isUseNativeUI() ) {
 634             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 635             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 636         }
 637         jmi.addActionListener( this );
 638     }
 639
 640     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 641         if ( item != null ) {
 642             item.setFont( MainFrame.menu_font );
 643             if ( !getConfiguration().isUseNativeUI() ) {
 644                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 645                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 646             }
 647             item.setSelected( is_selected );
 648             item.addActionListener( this );
 649         }
 650     }
 651
 652     @Override
 653     public void destroy() {
 654         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 655         removeTextFrame();
 656         if ( getMainPanel() != null ) {
 657             getMainPanel().terminate();
 658         }
 659     }
 660
 661     Configuration getConfiguration() {
 662         return _configuration;
 663     }
 664
 665     TreePanel getCurrentTreePanel() {
 666         return getMainPanel().getCurrentTreePanel();
 667     }
 668
 669     JCheckBoxMenuItem getlabelDirectionCbmi() {
 670         return _label_direction_cbmi;
 671     }
 672
 673     private MainPanel getMainPanel() {
 674         return _main_panel;
 675     }
 676
 677     public Options getOptions() {
 678         return _options;
 679     }
 680
 681     Options getOtions() {
 682         return _options;
 683     }
 684
 685     @Override
 686     public void init() {
 687         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 688         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 689         final Configuration configuration = new Configuration( config_filename, true, true, true );
 690         setConfiguration( configuration );
 691         setOptions( Options.createInstance( configuration ) );
 692         setupUI();
 693         URL phys_url = null;
 694         Phylogeny[] phys = null;
 695         final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 696         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
 697         // Get URL to tree file
 698         if ( phys_url_string != null ) {
 699             try {
 700                 phys_url = new URL( phys_url_string );
 701             }
 702             catch ( final Exception e ) {
 703                 ForesterUtil.printErrorMessage( NAME, "error: " + e );
 704                 e.printStackTrace();
 705                 JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
 706                         + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 707             }
 708         }
 709         // Load the tree from URL
 710         if ( phys_url != null ) {
 711             try {
 712                 phys = AptxUtil.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
 713             }
 714             catch ( final Exception e ) {
 715                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 716                 e.printStackTrace();
 717                 JOptionPane.showMessageDialog( this,
 718                                                NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 719                                                "Failed to read phylogenies",
 720                                                JOptionPane.ERROR_MESSAGE );
 721             }
 722         }
 723         if ( ( phys == null ) || ( phys.length < 1 ) ) {
 724             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
 725             JOptionPane.showMessageDialog( this,
 726                                            NAME + ": phylogenies from [" + phys_url + "] are null or empty",
 727                                            "Failed to read phylogenies",
 728                                            JOptionPane.ERROR_MESSAGE );
 729             return;
 730         }
 731         else {
 732             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 733         }
 734         setVisible( false );
 735         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 736         _jmenubar = new JMenuBar();
 737         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 738             if ( !getConfiguration().isUseNativeUI() ) {
 739                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 740             }
 741             buildToolsMenu();
 742             buildViewMenu();
 743             buildFontSizeMenu();
 744             buildOptionsMenu();
 745             buildTypeMenu();
 746             buildHelpMenu();
 747             setJMenuBar( _jmenubar );
 748         }
 749         final Container contentpane = getContentPane();
 750         contentpane.setLayout( new BorderLayout() );
 751         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 752         addComponentListener( new ComponentAdapter() {
 753
 754             @Override
 755             public void componentResized( final ComponentEvent e ) {
 756                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 757                     getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
 758                                                                                            .getWidth(),
 759                                                                                    getMainPanel().getCurrentTreePanel()
 760                                                                                            .getHeight(),
 761                                                                                    false );
 762                 }
 763             }
 764         } );
 765         if ( getConfiguration().isUseTabbedDisplay() ) {
 766             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 767             AptxUtil.addPhylogeniesToTabs( phys,
 768                                            new File( phys_url.getFile() ).getName(),
 769                                            phys_url.toString(),
 770                                            getConfiguration(),
 771                                            getMainPanel() );
 772         }
 773         else {
 774             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 775             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 776         }
 777         validate();
 778         setName( NAME );
 779         getMainPanel().getControlPanel().showWholeAll();
 780         getMainPanel().getControlPanel().showWhole();
 781         System.gc();
 782         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 783         /* GUILHEM_BEG */
 784         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 785         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 786                 .getRelevantSequenceRelationTypes() ) {
 787             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 788         }
 789         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 790         if ( default_relation != null ) {
 791             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 792         }
 793         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 794         if ( default_sequence != null ) {
 795             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 796             /* GUILHEM_END */
 797         }
 798         setVisible( true );
 799     }
 800
 801     void initializeTypeMenu( final Options options ) {
 802         setTypeMenuToAllUnselected();
 803         try {
 804             switch ( options.getPhylogenyGraphicsType() ) {
 805                 case CONVEX:
 806                     _convex_type_cbmi.setSelected( true );
 807                     break;
 808                 case CURVED:
 809                     _curved_type_cbmi.setSelected( true );
 810                     break;
 811                 case EURO_STYLE:
 812                     _euro_type_cbmi.setSelected( true );
 813                     break;
 814                 case ROUNDED:
 815                     _rounded_type_cbmi.setSelected( true );
 816                     break;
 817                 case TRIANGULAR:
 818                     _triangular_type_cbmi.setSelected( true );
 819                     break;
 820                 case UNROOTED:
 821                     _unrooted_type_cbmi.setSelected( true );
 822                     break;
 823                 case CIRCULAR:
 824                     _circular_type_cbmi.setSelected( true );
 825                     break;
 826                 default:
 827                     _rectangular_type_cbmi.setSelected( true );
 828                     break;
 829             }
 830         }
 831         catch ( final NullPointerException np ) {
 832             // In all likelihood, this is caused by menu-less display.
 833         }
 834     }
 835
 836     private boolean isScreenAntialias() {
 837         return true;
 838     }
 839
 840     private void removeBranchColors() {
 841         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 842             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
 843         }
 844     }
 845
 846     void removeTextFrame() {
 847         if ( _textframe != null ) {
 848             _textframe.close();
 849             _textframe = null;
 850         }
 851     }
 852
 853     void setConfiguration( final Configuration configuration ) {
 854         _configuration = configuration;
 855     }
 856
 857     private void setMainPanel( final MainPanelApplets main_panel ) {
 858         _main_panel = main_panel;
 859     }
 860
 861     void setOptions( final Options options ) {
 862         _options = options;
 863     }
 864
 865     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 866         setTypeMenuToAllUnselected();
 867         try {
 868             switch ( type ) {
 869                 case CIRCULAR:
 870                     _circular_type_cbmi.setSelected( true );
 871                     break;
 872                 case CONVEX:
 873                     _convex_type_cbmi.setSelected( true );
 874                     break;
 875                 case CURVED:
 876                     _curved_type_cbmi.setSelected( true );
 877                     break;
 878                 case EURO_STYLE:
 879                     _euro_type_cbmi.setSelected( true );
 880                     break;
 881                 case ROUNDED:
 882                     _rounded_type_cbmi.setSelected( true );
 883                     break;
 884                 case RECTANGULAR:
 885                     _rectangular_type_cbmi.setSelected( true );
 886                     break;
 887                 case TRIANGULAR:
 888                     _triangular_type_cbmi.setSelected( true );
 889                     break;
 890                 case UNROOTED:
 891                     _unrooted_type_cbmi.setSelected( true );
 892                     break;
 893                 default:
 894                     throw new IllegalArgumentException( "unknown type: " + type );
 895             }
 896         }
 897         catch ( final NullPointerException np ) {
 898             // In all likelihood, this is caused by menu-less display.
 899         }
 900     }
 901
 902     void setTypeMenuToAllUnselected() {
 903         if ( _convex_type_cbmi != null ) {
 904             _convex_type_cbmi.setSelected( false );
 905         }
 906         if ( _curved_type_cbmi != null ) {
 907             _curved_type_cbmi.setSelected( false );
 908         }
 909         if ( _euro_type_cbmi != null ) {
 910             _euro_type_cbmi.setSelected( false );
 911         }
 912         if ( _rounded_type_cbmi != null ) {
 913             _rounded_type_cbmi.setSelected( false );
 914         }
 915         if ( _triangular_type_cbmi != null ) {
 916             _triangular_type_cbmi.setSelected( false );
 917         }
 918         if ( _rectangular_type_cbmi != null ) {
 919             _rectangular_type_cbmi.setSelected( false );
 920         }
 921         if ( _unrooted_type_cbmi != null ) {
 922             _unrooted_type_cbmi.setSelected( false );
 923         }
 924         if ( _circular_type_cbmi != null ) {
 925             _circular_type_cbmi.setSelected( false );
 926         }
 927     }
 928
 929     private void setupUI() {
 930         try {
 931             if ( getConfiguration().isUseNativeUI() ) {
 932                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 933             }
 934             else {
 935                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 936             }
 937         }
 938         catch ( final UnsupportedLookAndFeelException e ) {
 939             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
 940         }
 941         catch ( final ClassNotFoundException e ) {
 942             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
 943         }
 944         catch ( final InstantiationException e ) {
 945             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
 946         }
 947         catch ( final IllegalAccessException e ) {
 948             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
 949         }
 950         catch ( final Exception e ) {
 951             AptxUtil.dieWithSystemError( e.toString() );
 952         }
 953     }
 954
 955     @Override
 956     public void start() {
 957         if ( getMainPanel() != null ) {
 958             getMainPanel().validate();
 959         }
 960         requestFocus();
 961         requestFocusInWindow();
 962         requestFocus();
 963         AptxUtil.printAppletMessage( NAME, "started" );
 964     }
 965
 966     void switchColors() {
 967         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
 968         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 969         csc.setVisible( true );
 970         getMainPanel().setTreeColorSet( colorset );
 971     }
 972
 973     void typeChanged( final Object o ) {
 974         updateTypeCheckboxes( getOptions(), o );
 975         updateOptions( getOptions() );
 976         if ( getCurrentTreePanel() != null ) {
 977             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
 978             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
 979             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 980                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
 981                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
 982                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
 983                 getCurrentTreePanel().getControlPanel().showWhole();
 984             }
 985             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
 986                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
 987             }
 988             else {
 989                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
 990             }
 991             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
 992             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
 993         }
 994     }
 995
 996     void updateOptions( final Options options ) {
 997         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
 998         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
 999                 && _background_gradient_cbmi.isSelected() );
1000         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1001         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1002                 && _abbreviate_scientific_names.isSelected() );
1003         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1004                 && _color_labels_same_as_parent_branch.isSelected() );
1005         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1006                 && _show_default_node_shapes_cbmi.isSelected() );
1007         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1008                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1009         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1010             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1011         }
1012         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1013             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1014         }
1015         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1016             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1017         }
1018         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1019                 && _search_case_senstive_cbmi.isSelected() );
1020         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1021             options.setShowScale( _show_scale_cbmi.isSelected() );
1022         }
1023         if ( _label_direction_cbmi != null ) {
1024             if ( _label_direction_cbmi.isSelected() ) {
1025                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1026             }
1027             else {
1028                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1029             }
1030         }
1031         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1032         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1033                 && _show_confidence_stddev_cbmi.isSelected() );
1034         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1035             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1036         }
1037         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1038                 && _search_whole_words_only_cbmi.isSelected() );
1039         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1040                 && _inverse_search_result_cbmi.isSelected() );
1041         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1042             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1043         }
1044         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1045             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1046         }
1047         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1048             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1049         }
1050         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1051             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1052         }
1053         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1054             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1055         }
1056         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1057             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1058         }
1059         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1060             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1061         }
1062         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1063             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1064         }
1065     }
1066
1067     void updateTypeCheckboxes( final Options options, final Object o ) {
1068         setTypeMenuToAllUnselected();
1069         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1070     }
1071
1072     void viewAsNexus() {
1073         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1074             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1075                     .getNhConversionSupportValueStyle() ) );
1076         }
1077     }
1078
1079     void viewAsNH() {
1080         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1081             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire() );
1082         }
1083     }
1084
1085     void viewAsNHX() {
1086         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1087             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX() );
1088         }
1089     }
1090
1091     void viewAsXML() {
1092         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1093             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) );
1094         }
1095     }
1096
1097     void displayBasicInformation() {
1098         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1099             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ) );
1100         }
1101     }
1102
1103     public void showTextFrame( final String s ) {
1104         removeTextFrame();
1105         _textframe = TextFrame.instantiate( s );
1106     }
1107
1108     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1109         for( final TreePanel tree_panel : treepanels ) {
1110             tree_panel.setTextAntialias();
1111         }
1112     }
1113 }