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