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