forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java

   1
   2 package org.forester.archaeopteryx;
   3
   4 import java.awt.BorderLayout;
   5 import java.awt.Container;
   6 import java.awt.event.ActionEvent;
   7 import java.awt.event.ActionListener;
   8 import java.awt.event.ComponentAdapter;
   9 import java.awt.event.ComponentEvent;
  10 import java.io.ByteArrayOutputStream;
  11 import java.io.File;
  12 import java.io.IOException;
  13 import java.net.URL;
  14 import java.util.LinkedList;
  15 import java.util.List;
  16 import java.util.NoSuchElementException;
  17
  18 import javax.swing.ButtonGroup;
  19 import javax.swing.JApplet;
  20 import javax.swing.JCheckBoxMenuItem;
  21 import javax.swing.JMenu;
  22 import javax.swing.JMenuBar;
  23 import javax.swing.JMenuItem;
  24 import javax.swing.JOptionPane;
  25 import javax.swing.JRadioButtonMenuItem;
  26 import javax.swing.UIManager;
  27 import javax.swing.UnsupportedLookAndFeelException;
  28 import javax.swing.event.ChangeEvent;
  29 import javax.swing.event.ChangeListener;
  30
  31 import org.apache.commons.codec.binary.Base64;
  32 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  33 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  34 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  35 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  36 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.PhylogenyMethods;
  39 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  40 import org.forester.phylogeny.data.SequenceRelation;
  41 import org.forester.sdi.GSDI;
  42 import org.forester.sdi.GSDIR;
  43 import org.forester.sdi.SDIException;
  44 import org.forester.util.ForesterConstants;
  45 import org.forester.util.ForesterUtil;
  46
  47 // Use like this:
  48 // <applet archive="forester.jar"
  49 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  50 // codebase="http://www.myserver.org/path/to/forester"
  51 // width="600"
  52 // height="500"
  53 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  54 // <param name="url_of_tree_to_load"
  55 // value="http://www.myserver.org/examples/data/apaf.xml">
  56 // <param name="config_file"
  57 // value="http://www.myserver.org/examples/config/config_file.txt">
  58 // </applet>
  59 public class ArchaeopteryxE extends JApplet implements ActionListener {
  60
  61     private final static String         NAME             = "ArchaeopteryxE";
  62     private static final long           serialVersionUID = -1220055577935759443L;
  63     private Configuration               _configuration;
  64     private MainPanelApplets            _mainpanel;
  65     private JMenuBar                    _jmenubar;
  66     private JMenu                       _options_jmenu;
  67     private JMenu                       _font_size_menu;
  68     private JMenuItem                   _super_tiny_fonts_mi;
  69     private JMenuItem                   _tiny_fonts_mi;
  70     private JMenuItem                   _small_fonts_mi;
  71     private JMenuItem                   _medium_fonts_mi;
  72     private JMenuItem                   _large_fonts_mi;
  73     private JMenu                       _tools_menu;
  74     private JMenuItem                   _taxcolor_item;
  75     private JMenuItem                   _confcolor_item;
  76     private JMenuItem                   _midpoint_root_item;
  77     private JMenu                       _view_jmenu;
  78     private JMenuItem                   _view_as_XML_item;
  79     private JMenuItem                   _view_as_NH_item;
  80     private JMenuItem                   _view_as_nexus_item;
  81     private JMenuItem                   _display_basic_information_item;
  82     private JMenu                       _type_menu;
  83     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  84     private JCheckBoxMenuItem           _triangular_type_cbmi;
  85     private JCheckBoxMenuItem           _curved_type_cbmi;
  86     private JCheckBoxMenuItem           _convex_type_cbmi;
  87     private JCheckBoxMenuItem           _euro_type_cbmi;
  88     private JCheckBoxMenuItem           _rounded_type_cbmi;
  89     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  90     private JCheckBoxMenuItem           _circular_type_cbmi;
  91     private JMenuItem                   _help_item;
  92     private JMenuItem                   _about_item;
  93     private JMenu                       _help_jmenu;
  94     private JMenuItem                   _website_item;
  95     private JMenuItem                   _phyloxml_website_item;
  96     private JMenuItem                   _phyloxml_ref_item;
  97     private JMenuItem                   _aptx_ref_item;
  98     private JMenuItem                   _remove_branch_color_item;
  99     private JMenuItem                   _remove_visual_styles_item;
 100     private JCheckBoxMenuItem           _show_domain_labels;
 101     private JCheckBoxMenuItem           _show_annotation_ref_source;
 102     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 103     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 104     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 105     private JCheckBoxMenuItem           _background_gradient_cbmi;
 106     private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 107     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 108     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 109     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 110     private Options                     _options;
 111     private JMenuItem                   _choose_font_mi;
 112     private JMenuItem                   _switch_colors_mi;
 113     JCheckBoxMenuItem                   _label_direction_cbmi;
 114     private JCheckBoxMenuItem           _show_scale_cbmi;
 115     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 116     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 117     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 118     private JCheckBoxMenuItem           _search_with_regex_cbmi;
 119     private JCheckBoxMenuItem           _show_overview_cbmi;
 120     private JMenuItem                   _choose_minimal_confidence_mi;
 121     private JMenuItem                   _collapse_species_specific_subtrees;
 122     private JMenuItem                   _overview_placment_mi;
 123     private ButtonGroup                 _radio_group_1;
 124     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 125     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 126     private JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;
 127     private JMenuItem                   _cycle_node_shape_mi;
 128     private JMenuItem                   _cycle_node_fill_mi;
 129     private JMenuItem                   _choose_node_size_mi;
 130     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 131     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 132     private JMenu                       _analysis_menu;
 133     private JMenuItem                   _gsdi_item;
 134     private JMenuItem                   _gsdir_item;
 135     private Phylogeny                   _species_tree;
 136     private JCheckBoxMenuItem           _right_line_up_domains_cbmi;
 137     private JCheckBoxMenuItem           _line_up_renderable_data_cbmi;
 138
 139     @Override
 140     public void actionPerformed( final ActionEvent e ) {
 141         final Object o = e.getSource();
 142         if ( o == _midpoint_root_item ) {
 143             getMainPanel().getCurrentTreePanel().midpointRoot();
 144         }
 145         else if ( o == _gsdi_item ) {
 146             if ( isSubtreeDisplayed() ) {
 147                 return;
 148             }
 149             executeGSDI();
 150         }
 151         else if ( o == _gsdir_item ) {
 152             if ( isSubtreeDisplayed() ) {
 153                 return;
 154             }
 155             executeGSDIR();
 156         }
 157         else if ( o == _taxcolor_item ) {
 158             getMainPanel().getCurrentTreePanel().taxColor();
 159         }
 160         else if ( o == _confcolor_item ) {
 161             getMainPanel().getCurrentTreePanel().confColor();
 162         }
 163         else if ( o == _collapse_species_specific_subtrees ) {
 164             if ( getCurrentTreePanel() != null ) {
 165                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 166             }
 167         }
 168         else if ( o == _remove_branch_color_item ) {
 169             removeBranchColors();
 170         }
 171         else if ( o == _remove_visual_styles_item ) {
 172             removeVisualStyles();
 173         }
 174         else if ( o == _switch_colors_mi ) {
 175             switchColors();
 176         }
 177         else if ( o == _display_basic_information_item ) {
 178             displayBasicInformation();
 179         }
 180         else if ( o == _view_as_NH_item ) {
 181             viewAsNH();
 182         }
 183         else if ( o == _view_as_XML_item ) {
 184             viewAsXML();
 185         }
 186         else if ( o == _view_as_nexus_item ) {
 187             viewAsNexus();
 188         }
 189         else if ( o == _super_tiny_fonts_mi ) {
 190             if ( getCurrentTreePanel() != null ) {
 191                 getCurrentTreePanel().setSuperTinyFonts();
 192                 getCurrentTreePanel().repaint();
 193             }
 194         }
 195         else if ( o == _tiny_fonts_mi ) {
 196             if ( getCurrentTreePanel() != null ) {
 197                 getCurrentTreePanel().setTinyFonts();
 198                 getCurrentTreePanel().repaint();
 199             }
 200         }
 201         else if ( o == _small_fonts_mi ) {
 202             if ( getCurrentTreePanel() != null ) {
 203                 getCurrentTreePanel().setSmallFonts();
 204                 getCurrentTreePanel().repaint();
 205             }
 206         }
 207         else if ( o == _medium_fonts_mi ) {
 208             if ( getCurrentTreePanel() != null ) {
 209                 getCurrentTreePanel().setMediumFonts();
 210                 getCurrentTreePanel().repaint();
 211             }
 212         }
 213         else if ( o == _large_fonts_mi ) {
 214             if ( getCurrentTreePanel() != null ) {
 215                 getCurrentTreePanel().setLargeFonts();
 216                 getCurrentTreePanel().repaint();
 217             }
 218         }
 219         else if ( o == _choose_font_mi ) {
 220             chooseFont();
 221         }
 222         else if ( o == _choose_minimal_confidence_mi ) {
 223             chooseMinimalConfidence();
 224         }
 225         else if ( o == _choose_node_size_mi ) {
 226             MainFrame.chooseNodeSize( getOptions(), this );
 227         }
 228         else if ( o == _overview_placment_mi ) {
 229             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 230         }
 231         else if ( o == _cycle_node_fill_mi ) {
 232             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 233         }
 234         else if ( o == _cycle_node_shape_mi ) {
 235             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 236         }
 237         else if ( o == _non_lined_up_cladograms_rbmi ) {
 238             updateOptions( getOptions() );
 239             _mainpanel.getControlPanel().showWhole();
 240         }
 241         else if ( o == _uniform_cladograms_rbmi ) {
 242             updateOptions( getOptions() );
 243             _mainpanel.getControlPanel().showWhole();
 244         }
 245         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 246             updateOptions( getOptions() );
 247             _mainpanel.getControlPanel().showWhole();
 248         }
 249         else if ( o == _search_case_senstive_cbmi ) {
 250             updateOptions( getOptions() );
 251             getMainPanel().getControlPanel().search0();
 252             getMainPanel().getControlPanel().search1();
 253         }
 254         else if ( o == _search_whole_words_only_cbmi ) {
 255             if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
 256                 _search_with_regex_cbmi.setSelected( false );
 257             }
 258             updateOptions( getOptions() );
 259             getMainPanel().getControlPanel().search0();
 260             getMainPanel().getControlPanel().search1();
 261         }
 262         else if ( o == _inverse_search_result_cbmi ) {
 263             updateOptions( getOptions() );
 264             getMainPanel().getControlPanel().search0();
 265             getMainPanel().getControlPanel().search1();
 266         }
 267         else if ( o == _search_with_regex_cbmi ) {
 268             if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
 269                 _search_whole_words_only_cbmi.setSelected( false );
 270             }
 271             if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
 272                 _search_case_senstive_cbmi.setSelected( true );
 273             }
 274             updateOptions( getOptions() );
 275             getMainPanel().getControlPanel().search0();
 276             getMainPanel().getControlPanel().search1();
 277         }
 278         else if ( o == _show_scale_cbmi ) {
 279             updateOptions( getOptions() );
 280         }
 281         else if ( o == _show_confidence_stddev_cbmi ) {
 282             updateOptions( getOptions() );
 283         }
 284         else if ( o == _label_direction_cbmi ) {
 285             updateOptions( getOptions() );
 286         }
 287         else if ( o == _abbreviate_scientific_names ) {
 288             updateOptions( getOptions() );
 289         }
 290         else if ( o == _show_overview_cbmi ) {
 291             updateOptions( getOptions() );
 292             if ( getCurrentTreePanel() != null ) {
 293                 getCurrentTreePanel().updateOvSizes();
 294             }
 295         }
 296         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 297                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 298                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 299             typeChanged( o );
 300         }
 301         else if ( o == _screen_antialias_cbmi ) {
 302             updateOptions( getOptions() );
 303             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 304         }
 305         else if ( o == _background_gradient_cbmi ) {
 306             updateOptions( getOptions() );
 307         }
 308         else if ( o == _show_domain_labels ) {
 309             updateOptions( getOptions() );
 310         }
 311         else if ( o == _color_labels_same_as_parent_branch ) {
 312             updateOptions( getOptions() );
 313         }
 314         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 315             updateOptions( getOptions() );
 316         }
 317         else if ( o == _show_default_node_shapes_external_cbmi ) {
 318             updateOptions( getOptions() );
 319         }
 320         else if ( o == _about_item ) {
 321             MainFrame.about();
 322         }
 323         else if ( o == _help_item ) {
 324             try {
 325                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
 326             }
 327             catch ( final IOException e1 ) {
 328                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 329             }
 330         }
 331         else if ( o == _website_item ) {
 332             try {
 333                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 334             }
 335             catch ( final IOException e1 ) {
 336                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 337             }
 338         }
 339         else if ( o == _phyloxml_website_item ) {
 340             try {
 341                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 342             }
 343             catch ( final IOException e1 ) {
 344                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 345             }
 346         }
 347         else if ( o == _aptx_ref_item ) {
 348             try {
 349                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 350             }
 351             catch ( final IOException e1 ) {
 352                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 353             }
 354         }
 355         else if ( o == _phyloxml_ref_item ) {
 356             try {
 357                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 358             }
 359             catch ( final IOException e1 ) {
 360                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 361             }
 362         }
 363         else if ( o == _color_by_taxonomic_group_cbmi ) {
 364             updateOptions( getOptions() );
 365         }
 366         else if ( o == _line_up_renderable_data_cbmi ) {
 367             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
 368                 _right_line_up_domains_cbmi.setSelected( false );
 369             }
 370             updateOptions( getOptions() );
 371         }
 372         else if ( o == _right_line_up_domains_cbmi ) {
 373             if ( _right_line_up_domains_cbmi.isSelected() ) {
 374                 _line_up_renderable_data_cbmi.setSelected( true );
 375             }
 376             updateOptions( getOptions() );
 377         }
 378         repaint();
 379     }
 380
 381     @Override
 382     public void destroy() {
 383         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 384         removeAllTextFrames();
 385         if ( getMainPanel() != null ) {
 386             getMainPanel().terminate();
 387         }
 388     }
 389
 390     /**
 391      * This method returns the current external node data which
 392      * has been selected by the user by clicking the "Return ..."
 393      * menu item. This method is expected to be called from Javascript or
 394      * something like it.
 395      *
 396      * @return current external node data as String
 397      */
 398     public String getCurrentExternalNodesDataBuffer() {
 399         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 400     }
 401
 402     public int getCurrentExternalNodesDataBufferChangeCounter() {
 403         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 404     }
 405
 406     public int getCurrentExternalNodesDataBufferLength() {
 407         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 408     }
 409
 410     /**
 411      * This method returns the current phylogeny as a string in the chosen format
 412      *
 413      * @param format must be NH, NHX, NEXUS or PHYLOXML
 414      * @return the phylogeny string
 415      * @author Herve Menager
 416      */
 417     public String getCurrentPhylogeny( final String format ) {
 418         removeAllTextFrames();
 419         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 420                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 421             return new String();
 422         }
 423         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 424             case NH:
 425                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 426             case NHX:
 427                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 428             case NEXUS:
 429                 return getMainPanel().getCurrentPhylogeny().toNexus();
 430             case PHYLOXML:
 431                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 432             default:
 433                 break;
 434         }
 435         return new String();
 436     }
 437
 438     /**
 439      * This method returns a view of the current phylogeny in a chosen
 440      * graphics format, base64-encoded in a string so that in can be used
 441      * from javascript.
 442      *
 443      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 444      * @return the phylogeny string
 445      * @author Herve Menager
 446      */
 447     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 448         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 449         try {
 450             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 451                                                                     _mainpanel.getWidth(),
 452                                                                     _mainpanel.getHeight(),
 453                                                                     getCurrentTreePanel(),
 454                                                                     getCurrentTreePanel().getControlPanel(),
 455                                                                     GraphicsExportType.valueOf( format ),
 456                                                                     getOptions() );
 457         }
 458         catch ( final IOException ioe ) {
 459             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 460             ioe.printStackTrace();
 461             JOptionPane.showMessageDialog( this,
 462                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 463                                            "Failed to generate graphics",
 464                                            JOptionPane.ERROR_MESSAGE );
 465             return null;
 466         }
 467         final byte[] bytes = baos.toByteArray();
 468         final String dataImg = Base64.encodeBase64String( bytes );
 469         return dataImg;
 470     }
 471
 472     public Options getOptions() {
 473         return _options;
 474     }
 475
 476     @Override
 477     public void init() {
 478         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 479         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 480         final Configuration configuration = new Configuration( config_filename, true, true, true );
 481         setConfiguration( configuration );
 482         setOptions( Options.createInstance( configuration ) );
 483         setupUI();
 484         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 485         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 486             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 487                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 488             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 489                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 490             return;
 491         }
 492         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 493         // Get URL to tree file
 494         URL phys_url = null;
 495         try {
 496             phys_url = new URL( tree_url_str );
 497         }
 498         catch ( final Exception e ) {
 499             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 500             e.printStackTrace();
 501             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 502                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 503         }
 504         if ( phys_url == null ) {
 505             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 506                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 507             JOptionPane.showMessageDialog( this,
 508                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 509                                            "Failed to create URL",
 510                                            JOptionPane.ERROR_MESSAGE );
 511             return;
 512         }
 513         // Load the tree from URL
 514         Phylogeny[] phys = null;
 515         try {
 516             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 517                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 518                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 519                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 520                                                     getConfiguration().getTaxonomyExtraction(),
 521                                                     getConfiguration().isMidpointReroot() );
 522         }
 523         catch ( final Exception e ) {
 524             ForesterUtil.printErrorMessage( NAME, e.toString() );
 525             e.printStackTrace();
 526             JOptionPane.showMessageDialog( this,
 527                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 528                                            "Failed to read phylogenies",
 529                                            JOptionPane.ERROR_MESSAGE );
 530         }
 531         if ( phys == null ) {
 532             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 533             JOptionPane.showMessageDialog( this,
 534                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 535                                            "Failed to read phylogenies",
 536                                            JOptionPane.ERROR_MESSAGE );
 537             return;
 538         }
 539         else if ( phys.length < 1 ) {
 540             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 541             JOptionPane.showMessageDialog( this,
 542                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 543                                            "Failed to read phylogenies",
 544                                            JOptionPane.ERROR_MESSAGE );
 545             return;
 546         }
 547         else {
 548             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 549         }
 550         //
 551         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 552         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 553             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 554             Phylogeny[] species_trees = null;
 555             try {
 556                 final URL species_tree_url = new URL( species_tree_url_str );
 557                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 558                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 559                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 560                                                                  false,
 561                                                                  TAXONOMY_EXTRACTION.NO,
 562                                                                  false );
 563             }
 564             catch ( final IOException e ) {
 565                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 566                         + "]" );
 567                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 568                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 569             }
 570             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 571                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 572                 if ( species_trees[ 0 ].isEmpty() ) {
 573                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 574                 }
 575                 else if ( !species_trees[ 0 ].isRooted() ) {
 576                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 577                 }
 578                 else {
 579                     setSpeciesTree( species_trees[ 0 ] );
 580                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 581                 }
 582             }
 583         }
 584         //
 585         try {
 586             setVisible( false );
 587             setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 588             _jmenubar = new JMenuBar();
 589             if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 590                 if ( !getConfiguration().isUseNativeUI() ) {
 591                     _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 592                 }
 593                 if ( getSpeciesTree() != null ) {
 594                     buildAnalysisMenu();
 595                 }
 596                 buildToolsMenu();
 597                 buildViewMenu();
 598                 buildFontSizeMenu();
 599                 buildOptionsMenu();
 600                 buildTypeMenu();
 601                 buildHelpMenu();
 602                 setJMenuBar( _jmenubar );
 603             }
 604             final Container contentpane = getContentPane();
 605             contentpane.setLayout( new BorderLayout() );
 606             contentpane.add( getMainPanel(), BorderLayout.CENTER );
 607             addComponentListener( new ComponentAdapter() {
 608
 609                 @Override
 610                 public void componentResized( final ComponentEvent e ) {
 611                     if ( getMainPanel().getCurrentTreePanel() != null ) {
 612                         getMainPanel().getCurrentTreePanel()
 613                                 .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
 614                                                             getMainPanel().getCurrentTreePanel().getHeight(),
 615                                                             getOptions().isAllowFontSizeChange() );
 616                     }
 617                 }
 618             } );
 619             if ( getConfiguration().isUseTabbedDisplay() ) {
 620                 try {
 621                     AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 622                     AptxUtil.addPhylogeniesToTabs( phys,
 623                                                    new File( phys_url.getFile() ).getName(),
 624                                                    phys_url.toString(),
 625                                                    getConfiguration(),
 626                                                    getMainPanel() );
 627                 }
 628                 catch ( final Exception e ) {
 629                     ForesterUtil.printErrorMessage( NAME, e.toString() );
 630                     e.printStackTrace();
 631                 }
 632             }
 633             else {
 634                 AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 635                 if ( getSpeciesTree() != null ) {
 636                     AptxUtil.printAppletMessage( NAME,
 637                                                  "Warning: gsdi (gene duplication inference) only available tabbed display" );
 638                 }
 639                 AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 640             }
 641             validate();
 642             setName( NAME );
 643             getMainPanel().getControlPanel().showWholeAll();
 644             getMainPanel().getControlPanel().showWhole();
 645             /* GUILHEM_BEG */
 646             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 647             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 648                     .getRelevantSequenceRelationTypes() ) {
 649                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 650             }
 651             final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 652             if ( default_relation != null ) {
 653                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 654             }
 655             final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 656             if ( default_sequence != null ) {
 657                 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 658             }
 659             /* GUILHEM_END */
 660             System.gc();
 661             AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 662             setVisible( true );
 663         }
 664         catch ( final Exception e ) {
 665             ForesterUtil.printErrorMessage( NAME, e.toString() );
 666             e.printStackTrace();
 667         }
 668     }
 669
 670     public void showTextFrame( final String s, final String title ) {
 671         checkTextFrames();
 672         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 673     }
 674
 675     @Override
 676     public void start() {
 677         if ( getMainPanel() != null ) {
 678             getMainPanel().validate();
 679         }
 680         requestFocus();
 681         requestFocusInWindow();
 682         requestFocus();
 683         AptxUtil.printAppletMessage( NAME, "started" );
 684     }
 685
 686     void buildAnalysisMenu() {
 687         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 688         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 689         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 690         customizeJMenuItem( _gsdi_item );
 691         customizeJMenuItem( _gsdir_item );
 692         //  _analysis_menu.addSeparator();
 693         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 694         //  customizeJMenuItem( _lineage_inference );
 695         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 696         _jmenubar.add( _analysis_menu );
 697     }
 698
 699     void buildFontSizeMenu() {
 700         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 701         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 702         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 703         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 704         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 705         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 706         customizeJMenuItem( _super_tiny_fonts_mi );
 707         customizeJMenuItem( _tiny_fonts_mi );
 708         customizeJMenuItem( _small_fonts_mi );
 709         customizeJMenuItem( _medium_fonts_mi );
 710         customizeJMenuItem( _large_fonts_mi );
 711         _jmenubar.add( _font_size_menu );
 712     }
 713
 714     void buildHelpMenu() {
 715         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 716         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
 717         _help_jmenu.addSeparator();
 718         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 719         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 720         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 721         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 722         _help_jmenu.addSeparator();
 723         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 724         customizeJMenuItem( _help_item );
 725         customizeJMenuItem( _website_item );
 726         customizeJMenuItem( _phyloxml_website_item );
 727         customizeJMenuItem( _aptx_ref_item );
 728         customizeJMenuItem( _phyloxml_ref_item );
 729         customizeJMenuItem( _about_item );
 730         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 731         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 732         _jmenubar.add( _help_jmenu );
 733     }
 734
 735     void buildOptionsMenu() {
 736         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 737         _options_jmenu.addChangeListener( new ChangeListener() {
 738
 739             @Override
 740             public void stateChanged( final ChangeEvent e ) {
 741                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 742                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 743                 MainFrame
 744                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 745                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 746                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 747                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 748                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 749                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 750                 try {
 751                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
 752                     getMainPanel().getControlPanel().setVisibilityOfX();
 753                 }
 754                 catch ( final Exception ignore ) {
 755                     // do nothing, not important.
 756                 }
 757             }
 758         } );
 759         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 760                                                                 getConfiguration() ) );
 761         _options_jmenu
 762                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 763         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 764         _options_jmenu
 765                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 766         _radio_group_1 = new ButtonGroup();
 767         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 768         _radio_group_1.add( _uniform_cladograms_rbmi );
 769         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 770         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 771         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 772         _options_jmenu
 773                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 774         _options_jmenu
 775                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 776         _options_jmenu
 777                 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
 778         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 779         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 780             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 781             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 782         }
 783         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 784         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 785         _options_jmenu
 786                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 787         _options_jmenu
 788                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 789         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 790         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 791         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 792         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 793         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 794         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 795         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 796         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 797         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 798         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 799         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 800         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 801         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 802         _options_jmenu.addSeparator();
 803         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 804                                                                 getConfiguration() ) );
 805         _options_jmenu
 806                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 807         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 808         _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
 809         _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
 810         _options_jmenu
 811                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 812         customizeJMenuItem( _choose_font_mi );
 813         customizeJMenuItem( _choose_minimal_confidence_mi );
 814         customizeJMenuItem( _switch_colors_mi );
 815         customizeJMenuItem( _overview_placment_mi );
 816         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 817         customizeCheckBoxMenuItem( _label_direction_cbmi,
 818                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 819         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 820         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 821         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 822         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 823         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 824         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 825                 .isShowDefaultNodeShapesExternal() );
 826         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 827                 .isShowDefaultNodeShapesInternal() );
 828         customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
 829                 .isShowDefaultNodeShapesForMarkedNodes() );
 830         customizeJMenuItem( _cycle_node_shape_mi );
 831         customizeJMenuItem( _cycle_node_fill_mi );
 832         customizeJMenuItem( _choose_node_size_mi );
 833         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 834         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 835         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 836         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 837                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 838         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 839                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 840         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 841                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 842         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 843         customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
 844         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 845         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 846         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 847         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
 848         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
 849         _jmenubar.add( _options_jmenu );
 850     }
 851
 852     void buildToolsMenu() {
 853         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 854         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 855         customizeJMenuItem( _confcolor_item );
 856         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 857         customizeJMenuItem( _taxcolor_item );
 858         _tools_menu.addSeparator();
 859         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 860         _remove_visual_styles_item
 861                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 862         customizeJMenuItem( _remove_visual_styles_item );
 863         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 864         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 865         customizeJMenuItem( _remove_branch_color_item );
 866         _tools_menu.addSeparator();
 867         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 868         customizeJMenuItem( _midpoint_root_item );
 869         _tools_menu.addSeparator();
 870         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 871         customizeJMenuItem( _collapse_species_specific_subtrees );
 872         _jmenubar.add( _tools_menu );
 873     }
 874
 875     void buildTypeMenu() {
 876         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 877         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 878         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 879         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 880         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 881         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 882         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 883         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 884         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 885         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 886         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 887         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 888         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 889         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 890         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 891         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 892         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 893         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 894         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 895         initializeTypeMenu( getOptions() );
 896         _jmenubar.add( _type_menu );
 897     }
 898
 899     void buildViewMenu() {
 900         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 901         _view_jmenu
 902                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 903         _view_jmenu.addSeparator();
 904         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 905         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 906         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 907         customizeJMenuItem( _display_basic_information_item );
 908         customizeJMenuItem( _view_as_NH_item );
 909         customizeJMenuItem( _view_as_XML_item );
 910         customizeJMenuItem( _view_as_nexus_item );
 911         _jmenubar.add( _view_jmenu );
 912     }
 913
 914     void checkTextFrames() {
 915         if ( _textframes.size() > 5 ) {
 916             try {
 917                 if ( _textframes.getFirst() != null ) {
 918                     _textframes.getFirst().removeMe();
 919                 }
 920                 else {
 921                     _textframes.removeFirst();
 922                 }
 923             }
 924             catch ( final NoSuchElementException e ) {
 925                 // Ignore.
 926             }
 927         }
 928     }
 929
 930     void clearCurrentExternalNodesDataBuffer() {
 931         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 932     }
 933
 934     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 935         if ( item != null ) {
 936             item.setFont( MainFrame.menu_font );
 937             if ( !getConfiguration().isUseNativeUI() ) {
 938                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 939                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 940             }
 941             item.setSelected( is_selected );
 942             item.addActionListener( this );
 943         }
 944     }
 945
 946     void customizeJMenuItem( final JMenuItem jmi ) {
 947         jmi.setFont( MainFrame.menu_font );
 948         if ( !getConfiguration().isUseNativeUI() ) {
 949             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 950             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 951         }
 952         jmi.addActionListener( this );
 953     }
 954
 955     void displayBasicInformation() {
 956         if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
 957                 && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 958             String title = "Basic Information";
 959             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 960                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 961             }
 962             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 963         }
 964     }
 965
 966     void executeGSDI() {
 967         if ( !isOKforSDI( false, true ) ) {
 968             return;
 969         }
 970         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 971             JOptionPane.showMessageDialog( this,
 972                                            "Gene tree is not rooted.",
 973                                            "Cannot execute GSDI",
 974                                            JOptionPane.ERROR_MESSAGE );
 975             return;
 976         }
 977         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 978         gene_tree.setAllNodesToNotCollapse();
 979         gene_tree.recalculateNumberOfExternalDescendants( false );
 980         GSDI gsdi = null;
 981         final Phylogeny species_tree = _species_tree.copy();
 982         try {
 983             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 984         }
 985         catch ( final SDIException e ) {
 986             JOptionPane.showMessageDialog( this,
 987                                            e.getLocalizedMessage(),
 988                                            "Error during GSDI",
 989                                            JOptionPane.ERROR_MESSAGE );
 990             return;
 991         }
 992         catch ( final Exception e ) {
 993             AptxUtil.unexpectedException( e );
 994             return;
 995         }
 996         gene_tree.setRerootable( false );
 997         gene_tree.clearHashIdToNodeMap();
 998         gene_tree.recalculateNumberOfExternalDescendants( true );
 999         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
1000         getMainPanel().getControlPanel().setShowEvents( true );
1001         showWhole();
1002         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1003         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1004         showWhole();
1005         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1006         showWhole();
1007         _mainpanel.getCurrentTreePanel().setEdited( true );
1008         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1009         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1010             JOptionPane.showMessageDialog( this,
1011                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1012                                                    + "Potential duplications: "
1013                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1014                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1015                                                    + "Stripped gene tree nodes: "
1016                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1017                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1018                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1019                                            "GSDI successfully completed",
1020                                            JOptionPane.WARNING_MESSAGE );
1021         }
1022         else {
1023             JOptionPane.showMessageDialog( this,
1024                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1025                                                    + "Potential duplications: "
1026                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1027                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1028                                                    + "Stripped gene tree nodes: "
1029                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1030                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1031                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1032                                            "GSDI successfully completed",
1033                                            JOptionPane.INFORMATION_MESSAGE );
1034         }
1035     }
1036
1037     void executeGSDIR() {
1038         if ( !isOKforSDI( false, false ) ) {
1039             return;
1040         }
1041         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1042         if ( ( p > 0 )
1043                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1044             JOptionPane.showMessageDialog( this,
1045                                            "Gene tree is not completely binary",
1046                                            "Cannot execute GSDI",
1047                                            JOptionPane.ERROR_MESSAGE );
1048             return;
1049         }
1050         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1051         gene_tree.setAllNodesToNotCollapse();
1052         gene_tree.recalculateNumberOfExternalDescendants( false );
1053         GSDIR gsdir = null;
1054         final Phylogeny species_tree = _species_tree.copy();
1055         try {
1056             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1057         }
1058         catch ( final SDIException e ) {
1059             JOptionPane.showMessageDialog( this,
1060                                            e.getLocalizedMessage(),
1061                                            "Error during GSDIR",
1062                                            JOptionPane.ERROR_MESSAGE );
1063             return;
1064         }
1065         catch ( final Exception e ) {
1066             AptxUtil.unexpectedException( e );
1067             return;
1068         }
1069         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1070         result_gene_tree.setRerootable( false );
1071         result_gene_tree.clearHashIdToNodeMap();
1072         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1073         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1074         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1075         getMainPanel().getControlPanel().setShowEvents( true );
1076         showWhole();
1077         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1078         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1079         showWhole();
1080         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1081         showWhole();
1082         _mainpanel.getCurrentTreePanel().setEdited( true );
1083         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1084         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1085             JOptionPane.showMessageDialog( this,
1086                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1087                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1088                                                    + "Stripped gene tree nodes: "
1089                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1090                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1091                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1092                                            "GSDIR successfully completed",
1093                                            JOptionPane.WARNING_MESSAGE );
1094         }
1095         else {
1096             JOptionPane.showMessageDialog( this,
1097                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1098                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1099                                                    + "Stripped gene tree nodes: "
1100                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1101                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1102                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1103                                            "GSDIR successfully completed",
1104                                            JOptionPane.INFORMATION_MESSAGE );
1105         }
1106     }
1107
1108     Configuration getConfiguration() {
1109         return _configuration;
1110     }
1111
1112     TreePanel getCurrentTreePanel() {
1113         return getMainPanel().getCurrentTreePanel();
1114     }
1115
1116     JCheckBoxMenuItem getlabelDirectionCbmi() {
1117         return _label_direction_cbmi;
1118     }
1119
1120     Options getOtions() {
1121         return _options;
1122     }
1123
1124     void initializeTypeMenu( final Options options ) {
1125         setTypeMenuToAllUnselected();
1126         try {
1127             switch ( options.getPhylogenyGraphicsType() ) {
1128                 case CONVEX:
1129                     _convex_type_cbmi.setSelected( true );
1130                     break;
1131                 case CURVED:
1132                     _curved_type_cbmi.setSelected( true );
1133                     break;
1134                 case EURO_STYLE:
1135                     _euro_type_cbmi.setSelected( true );
1136                     break;
1137                 case ROUNDED:
1138                     _rounded_type_cbmi.setSelected( true );
1139                     break;
1140                 case TRIANGULAR:
1141                     _triangular_type_cbmi.setSelected( true );
1142                     break;
1143                 case UNROOTED:
1144                     _unrooted_type_cbmi.setSelected( true );
1145                     break;
1146                 case CIRCULAR:
1147                     _circular_type_cbmi.setSelected( true );
1148                     break;
1149                 default:
1150                     _rectangular_type_cbmi.setSelected( true );
1151                     break;
1152             }
1153         }
1154         catch ( final NullPointerException np ) {
1155             // In all likelihood, this is caused by menu-less display.
1156         }
1157     }
1158
1159     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1160         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1161             return false;
1162         }
1163         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1164             JOptionPane.showMessageDialog( this,
1165                                            "No species tree loaded",
1166                                            "Cannot execute GSDI",
1167                                            JOptionPane.ERROR_MESSAGE );
1168             return false;
1169         }
1170         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1171             JOptionPane.showMessageDialog( this,
1172                                            "Species tree is not completely binary",
1173                                            "Cannot execute GSDI",
1174                                            JOptionPane.ERROR_MESSAGE );
1175             return false;
1176         }
1177         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1178             JOptionPane.showMessageDialog( this,
1179                                            "Gene tree is not completely binary",
1180                                            "Cannot execute GSDI",
1181                                            JOptionPane.ERROR_MESSAGE );
1182             return false;
1183         }
1184         else {
1185             return true;
1186         }
1187     }
1188
1189     boolean isSubtreeDisplayed() {
1190         if ( getCurrentTreePanel() != null ) {
1191             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1192                 JOptionPane
1193                         .showMessageDialog( this,
1194                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1195                                             "Operation can not be exectuted on a sub-tree",
1196                                             JOptionPane.WARNING_MESSAGE );
1197                 return true;
1198             }
1199         }
1200         return false;
1201     }
1202
1203     void removeAllTextFrames() {
1204         for( final TextFrame tf : _textframes ) {
1205             if ( tf != null ) {
1206                 tf.close();
1207             }
1208         }
1209         _textframes.clear();
1210     }
1211
1212     void setConfiguration( final Configuration configuration ) {
1213         _configuration = configuration;
1214     }
1215
1216     void setOptions( final Options options ) {
1217         _options = options;
1218     }
1219
1220     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1221         setTypeMenuToAllUnselected();
1222         try {
1223             switch ( type ) {
1224                 case CIRCULAR:
1225                     _circular_type_cbmi.setSelected( true );
1226                     break;
1227                 case CONVEX:
1228                     _convex_type_cbmi.setSelected( true );
1229                     break;
1230                 case CURVED:
1231                     _curved_type_cbmi.setSelected( true );
1232                     break;
1233                 case EURO_STYLE:
1234                     _euro_type_cbmi.setSelected( true );
1235                     break;
1236                 case ROUNDED:
1237                     _rounded_type_cbmi.setSelected( true );
1238                     break;
1239                 case RECTANGULAR:
1240                     _rectangular_type_cbmi.setSelected( true );
1241                     break;
1242                 case TRIANGULAR:
1243                     _triangular_type_cbmi.setSelected( true );
1244                     break;
1245                 case UNROOTED:
1246                     _unrooted_type_cbmi.setSelected( true );
1247                     break;
1248                 default:
1249                     throw new IllegalArgumentException( "unknown type: " + type );
1250             }
1251         }
1252         catch ( final NullPointerException np ) {
1253             // In all likelihood, this is caused by menu-less display.
1254         }
1255     }
1256
1257     void setTypeMenuToAllUnselected() {
1258         if ( _convex_type_cbmi != null ) {
1259             _convex_type_cbmi.setSelected( false );
1260         }
1261         if ( _curved_type_cbmi != null ) {
1262             _curved_type_cbmi.setSelected( false );
1263         }
1264         if ( _euro_type_cbmi != null ) {
1265             _euro_type_cbmi.setSelected( false );
1266         }
1267         if ( _rounded_type_cbmi != null ) {
1268             _rounded_type_cbmi.setSelected( false );
1269         }
1270         if ( _triangular_type_cbmi != null ) {
1271             _triangular_type_cbmi.setSelected( false );
1272         }
1273         if ( _rectangular_type_cbmi != null ) {
1274             _rectangular_type_cbmi.setSelected( false );
1275         }
1276         if ( _unrooted_type_cbmi != null ) {
1277             _unrooted_type_cbmi.setSelected( false );
1278         }
1279         if ( _circular_type_cbmi != null ) {
1280             _circular_type_cbmi.setSelected( false );
1281         }
1282     }
1283
1284     void showWhole() {
1285         _mainpanel.getControlPanel().showWhole();
1286     }
1287
1288     void switchColors() {
1289         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1290         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1291         csc.setVisible( true );
1292         getMainPanel().setTreeColorSet( colorset );
1293     }
1294
1295     void typeChanged( final Object o ) {
1296         updateTypeCheckboxes( getOptions(), o );
1297         updateOptions( getOptions() );
1298         if ( getCurrentTreePanel() != null ) {
1299             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1300             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1301             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1302                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1303                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1304                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1305                 getCurrentTreePanel().getControlPanel().showWhole();
1306             }
1307             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1308                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1309             }
1310             else {
1311                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1312             }
1313             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1314             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1315         }
1316     }
1317
1318     void updateOptions( final Options options ) {
1319         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1320         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1321                 && _background_gradient_cbmi.isSelected() );
1322         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1323         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1324                 && _show_annotation_ref_source.isSelected() );
1325         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1326                 && _abbreviate_scientific_names.isSelected() );
1327         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1328                 && _color_labels_same_as_parent_branch.isSelected() );
1329         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1330                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1331         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1332                 && _show_default_node_shapes_external_cbmi.isSelected() );
1333         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
1334                 && _show_default_node_shapes_for_marked_cbmi.isSelected() );
1335         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1336             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1337         }
1338         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1339             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1340         }
1341         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1342             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1343         }
1344         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1345                 && _search_case_senstive_cbmi.isSelected() );
1346         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1347             options.setShowScale( _show_scale_cbmi.isSelected() );
1348         }
1349         if ( _label_direction_cbmi != null ) {
1350             if ( _label_direction_cbmi.isSelected() ) {
1351                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1352             }
1353             else {
1354                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1355             }
1356         }
1357         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1358         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1359                 && _show_confidence_stddev_cbmi.isSelected() );
1360         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1361                 && _search_whole_words_only_cbmi.isSelected() );
1362         options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
1363         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1364                 && _inverse_search_result_cbmi.isSelected() );
1365         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1366             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1367         }
1368         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1369             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1370         }
1371         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1372             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1373         }
1374         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1375             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1376         }
1377         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1378             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1379         }
1380         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1381             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1382         }
1383         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1384             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1385         }
1386         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1387             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1388         }
1389         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1390             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1391         }
1392         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1393             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1394         }
1395         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1396             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1397         }
1398     }
1399
1400     void updateTypeCheckboxes( final Options options, final Object o ) {
1401         setTypeMenuToAllUnselected();
1402         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1403     }
1404
1405     void viewAsNexus() {
1406         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1407             String title = "Nexus";
1408             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1409                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1410             }
1411             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1412                                    .getNhConversionSupportValueStyle() ),
1413                            title );
1414         }
1415     }
1416
1417     void viewAsNH() {
1418         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1419             String title = "New Hampshire";
1420             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1421                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1422             }
1423             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1424                                    .getNhConversionSupportValueStyle() ),
1425                            title );
1426         }
1427     }
1428
1429     void viewAsXML() {
1430         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1431             String title = "phyloXML";
1432             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1433                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1434             }
1435             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1436         }
1437     }
1438
1439     private void chooseFont() {
1440         final FontChooser fc = new FontChooser();
1441         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1442         fc.showDialog( this, "Select the Base Font" );
1443         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1444     }
1445
1446     private void chooseMinimalConfidence() {
1447         final String s = ( String ) JOptionPane
1448                 .showInputDialog( this,
1449                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1450                                           + getOptions().getMinConfidenceValue() + "]\n",
1451                                   "Minimal Confidence Value",
1452                                   JOptionPane.QUESTION_MESSAGE,
1453                                   null,
1454                                   null,
1455                                   getOptions().getMinConfidenceValue() );
1456         if ( !ForesterUtil.isEmpty( s ) ) {
1457             boolean success = true;
1458             double m = 0.0;
1459             final String m_str = s.trim();
1460             if ( !ForesterUtil.isEmpty( m_str ) ) {
1461                 try {
1462                     m = Double.parseDouble( m_str );
1463                 }
1464                 catch ( final Exception ex ) {
1465                     success = false;
1466                 }
1467             }
1468             else {
1469                 success = false;
1470             }
1471             if ( success && ( m >= 0.0 ) ) {
1472                 getOptions().setMinConfidenceValue( m );
1473             }
1474         }
1475     }
1476
1477     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1478         if ( item != null ) {
1479             item.setFont( MainFrame.menu_font );
1480             if ( !getConfiguration().isUseNativeUI() ) {
1481                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1482                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1483             }
1484             item.setSelected( is_selected );
1485             item.addActionListener( this );
1486         }
1487     }
1488
1489     MainPanel getMainPanel() {
1490         return _mainpanel;
1491     }
1492
1493     private Phylogeny getSpeciesTree() {
1494         return _species_tree;
1495     }
1496
1497     private boolean isScreenAntialias() {
1498         return true;
1499     }
1500
1501     private void removeBranchColors() {
1502         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1503             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1504         }
1505     }
1506
1507     private void removeVisualStyles() {
1508         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1509             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1510         }
1511     }
1512
1513     private void setMainPanel( final MainPanelApplets main_panel ) {
1514         _mainpanel = main_panel;
1515     }
1516
1517     private void setSpeciesTree( final Phylogeny species_tree ) {
1518         _species_tree = species_tree;
1519     }
1520
1521     private void setupUI() {
1522         try {
1523             if ( getConfiguration().isUseNativeUI() ) {
1524                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1525             }
1526             else {
1527                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1528             }
1529         }
1530         catch ( final UnsupportedLookAndFeelException e ) {
1531             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1532         }
1533         catch ( final ClassNotFoundException e ) {
1534             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1535         }
1536         catch ( final InstantiationException e ) {
1537             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1538         }
1539         catch ( final IllegalAccessException e ) {
1540             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1541         }
1542         catch ( final Exception e ) {
1543             AptxUtil.dieWithSystemError( e.toString() );
1544         }
1545     }
1546
1547     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1548         for( final TreePanel tree_panel : treepanels ) {
1549             tree_panel.setTextAntialias();
1550         }
1551     }
1552 }