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