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