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
 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 == _remove_visual_styles_item ) {
 169             removeVisualStyles();
 170         }
 171         else if ( o == _switch_colors_mi ) {
 172             switchColors();
 173         }
 174         else if ( o == _display_basic_information_item ) {
 175             displayBasicInformation();
 176         }
 177         else if ( o == _view_as_NH_item ) {
 178             viewAsNH();
 179         }
 180         else if ( o == _view_as_XML_item ) {
 181             viewAsXML();
 182         }
 183         else if ( o == _view_as_nexus_item ) {
 184             viewAsNexus();
 185         }
 186         else if ( o == _super_tiny_fonts_mi ) {
 187             if ( getCurrentTreePanel() != null ) {
 188                 getCurrentTreePanel().setSuperTinyFonts();
 189                 getCurrentTreePanel().repaint();
 190             }
 191         }
 192         else if ( o == _tiny_fonts_mi ) {
 193             if ( getCurrentTreePanel() != null ) {
 194                 getCurrentTreePanel().setTinyFonts();
 195                 getCurrentTreePanel().repaint();
 196             }
 197         }
 198         else if ( o == _small_fonts_mi ) {
 199             if ( getCurrentTreePanel() != null ) {
 200                 getCurrentTreePanel().setSmallFonts();
 201                 getCurrentTreePanel().repaint();
 202             }
 203         }
 204         else if ( o == _medium_fonts_mi ) {
 205             if ( getCurrentTreePanel() != null ) {
 206                 getCurrentTreePanel().setMediumFonts();
 207                 getCurrentTreePanel().repaint();
 208             }
 209         }
 210         else if ( o == _large_fonts_mi ) {
 211             if ( getCurrentTreePanel() != null ) {
 212                 getCurrentTreePanel().setLargeFonts();
 213                 getCurrentTreePanel().repaint();
 214             }
 215         }
 216         else if ( o == _choose_font_mi ) {
 217             chooseFont();
 218         }
 219         else if ( o == _choose_minimal_confidence_mi ) {
 220             chooseMinimalConfidence();
 221         }
 222         else if ( o == _choose_node_size_mi ) {
 223             MainFrame.chooseNodeSize( getOptions(), this );
 224         }
 225         else if ( o == _overview_placment_mi ) {
 226             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 227         }
 228         else if ( o == _cycle_node_fill_mi ) {
 229             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 230         }
 231         else if ( o == _cycle_node_shape_mi ) {
 232             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 233         }
 234         else if ( o == _non_lined_up_cladograms_rbmi ) {
 235             updateOptions( getOptions() );
 236             _mainpanel.getControlPanel().showWhole();
 237         }
 238         else if ( o == _uniform_cladograms_rbmi ) {
 239             updateOptions( getOptions() );
 240             _mainpanel.getControlPanel().showWhole();
 241         }
 242         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 243             updateOptions( getOptions() );
 244             _mainpanel.getControlPanel().showWhole();
 245         }
 246         else if ( o == _search_case_senstive_cbmi ) {
 247             updateOptions( getOptions() );
 248             getMainPanel().getControlPanel().search0();
 249             getMainPanel().getControlPanel().search1();
 250         }
 251         else if ( o == _search_whole_words_only_cbmi ) {
 252             updateOptions( getOptions() );
 253             getMainPanel().getControlPanel().search0();
 254             getMainPanel().getControlPanel().search1();
 255         }
 256         else if ( o == _inverse_search_result_cbmi ) {
 257             updateOptions( getOptions() );
 258             getMainPanel().getControlPanel().search0();
 259             getMainPanel().getControlPanel().search1();
 260         }
 261         else if ( o == _show_scale_cbmi ) {
 262             updateOptions( getOptions() );
 263         }
 264         else if ( o == _show_branch_length_values_cbmi ) {
 265             updateOptions( getOptions() );
 266         }
 267         else if ( o == _show_confidence_stddev_cbmi ) {
 268             updateOptions( getOptions() );
 269         }
 270         else if ( o == _label_direction_cbmi ) {
 271             updateOptions( getOptions() );
 272         }
 273         else if ( o == _abbreviate_scientific_names ) {
 274             updateOptions( getOptions() );
 275         }
 276         else if ( o == _show_overview_cbmi ) {
 277             updateOptions( getOptions() );
 278             if ( getCurrentTreePanel() != null ) {
 279                 getCurrentTreePanel().updateOvSizes();
 280             }
 281         }
 282         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 283                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 284                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 285             typeChanged( o );
 286         }
 287         else if ( o == _screen_antialias_cbmi ) {
 288             updateOptions( getOptions() );
 289             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 290         }
 291         else if ( o == _background_gradient_cbmi ) {
 292             updateOptions( getOptions() );
 293         }
 294         else if ( o == _show_domain_labels ) {
 295             updateOptions( getOptions() );
 296         }
 297         else if ( o == _color_labels_same_as_parent_branch ) {
 298             updateOptions( getOptions() );
 299         }
 300         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 301             updateOptions( getOptions() );
 302         }
 303         else if ( o == _show_default_node_shapes_external_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         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 454         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 455             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 456                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 457             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 458                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 459             return;
 460         }
 461         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 462         // Get URL to tree file
 463         URL phys_url = null;
 464         try {
 465             phys_url = new URL( tree_url_str );
 466         }
 467         catch ( final Exception e ) {
 468             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 469             e.printStackTrace();
 470             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 471                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 472         }
 473         if ( phys_url == null ) {
 474             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 475                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 476             JOptionPane.showMessageDialog( this,
 477                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 478                                            "Failed to create URL",
 479                                            JOptionPane.ERROR_MESSAGE );
 480             return;
 481         }
 482         // Load the tree from URL
 483         Phylogeny[] phys = null;
 484         try {
 485             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 486                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 487                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 488                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 489                                                     getConfiguration().getTaxonomyExtraction(),
 490                                                     getConfiguration().isMidpointReroot() );
 491         }
 492         catch ( final Exception e ) {
 493             ForesterUtil.printErrorMessage( NAME, e.toString() );
 494             e.printStackTrace();
 495             JOptionPane.showMessageDialog( this,
 496                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 497                                            "Failed to read phylogenies",
 498                                            JOptionPane.ERROR_MESSAGE );
 499         }
 500         if ( phys == null ) {
 501             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 502             JOptionPane.showMessageDialog( this,
 503                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 504                                            "Failed to read phylogenies",
 505                                            JOptionPane.ERROR_MESSAGE );
 506             return;
 507         }
 508         else if ( phys.length < 1 ) {
 509             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 510             JOptionPane.showMessageDialog( this,
 511                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 512                                            "Failed to read phylogenies",
 513                                            JOptionPane.ERROR_MESSAGE );
 514             return;
 515         }
 516         else {
 517             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 518         }
 519         //
 520         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 521         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 522             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 523             Phylogeny[] species_trees = null;
 524             try {
 525                 final URL species_tree_url = new URL( species_tree_url_str );
 526                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 527                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 528                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 529                                                                  false,
 530                                                                  TAXONOMY_EXTRACTION.NO,
 531                                                                  false );
 532             }
 533             catch ( final IOException e ) {
 534                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 535                         + "]" );
 536                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 537                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 538             }
 539             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 540                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 541                 if ( species_trees[ 0 ].isEmpty() ) {
 542                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 543                 }
 544                 else if ( !species_trees[ 0 ].isRooted() ) {
 545                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 546                 }
 547                 else {
 548                     setSpeciesTree( species_trees[ 0 ] );
 549                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 550                 }
 551             }
 552         }
 553         //
 554         setVisible( false );
 555         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 556         _jmenubar = new JMenuBar();
 557         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 558             if ( !getConfiguration().isUseNativeUI() ) {
 559                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 560             }
 561             if ( getSpeciesTree() != null ) {
 562                 buildAnalysisMenu();
 563             }
 564             buildToolsMenu();
 565             buildViewMenu();
 566             buildFontSizeMenu();
 567             buildOptionsMenu();
 568             buildTypeMenu();
 569             buildHelpMenu();
 570             setJMenuBar( _jmenubar );
 571         }
 572         final Container contentpane = getContentPane();
 573         contentpane.setLayout( new BorderLayout() );
 574         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 575         addComponentListener( new ComponentAdapter() {
 576
 577             @Override
 578             public void componentResized( final ComponentEvent e ) {
 579                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 580                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 581                                                                                             .getCurrentTreePanel()
 582                                                                                             .getWidth(),
 583                                                                                     getMainPanel()
 584                                                                                             .getCurrentTreePanel()
 585                                                                                             .getHeight(),
 586                                                                                     getOptions()
 587                                                                                             .isAllowFontSizeChange() );
 588                 }
 589             }
 590         } );
 591         if ( getConfiguration().isUseTabbedDisplay() ) {
 592             AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 593             AptxUtil.addPhylogeniesToTabs( phys,
 594                                            new File( phys_url.getFile() ).getName(),
 595                                            phys_url.toString(),
 596                                            getConfiguration(),
 597                                            getMainPanel() );
 598         }
 599         else {
 600             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 601             if ( getSpeciesTree() != null ) {
 602                 AptxUtil.printAppletMessage( NAME,
 603                                              "Warning: gsdi (gene duplication inference) only available tabbed display" );
 604             }
 605             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 606         }
 607         validate();
 608         setName( NAME );
 609         getMainPanel().getControlPanel().showWholeAll();
 610         getMainPanel().getControlPanel().showWhole();
 611         /* GUILHEM_BEG */
 612         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 613         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 614                 .getRelevantSequenceRelationTypes() ) {
 615             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 616         }
 617         final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 618         if ( default_relation != null ) {
 619             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 620         }
 621         final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 622         if ( default_sequence != null ) {
 623             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 624         }
 625         /* GUILHEM_END */
 626         System.gc();
 627         AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 628         setVisible( true );
 629     }
 630
 631     public void showTextFrame( final String s, final String title ) {
 632         checkTextFrames();
 633         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 634     }
 635
 636     @Override
 637     public void start() {
 638         if ( getMainPanel() != null ) {
 639             getMainPanel().validate();
 640         }
 641         requestFocus();
 642         requestFocusInWindow();
 643         requestFocus();
 644         AptxUtil.printAppletMessage( NAME, "started" );
 645     }
 646
 647     void buildAnalysisMenu() {
 648         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 649         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 650         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 651         customizeJMenuItem( _gsdi_item );
 652         customizeJMenuItem( _gsdir_item );
 653         //  _analysis_menu.addSeparator();
 654         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 655         //  customizeJMenuItem( _lineage_inference );
 656         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 657         _jmenubar.add( _analysis_menu );
 658     }
 659
 660     void buildFontSizeMenu() {
 661         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 662         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 663         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 664         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 665         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 666         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 667         customizeJMenuItem( _super_tiny_fonts_mi );
 668         customizeJMenuItem( _tiny_fonts_mi );
 669         customizeJMenuItem( _small_fonts_mi );
 670         customizeJMenuItem( _medium_fonts_mi );
 671         customizeJMenuItem( _large_fonts_mi );
 672         _jmenubar.add( _font_size_menu );
 673     }
 674
 675     void buildHelpMenu() {
 676         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 677         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 678         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 679         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 680         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 681         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 682         _help_jmenu.addSeparator();
 683         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 684         customizeJMenuItem( _help_item );
 685         customizeJMenuItem( _website_item );
 686         customizeJMenuItem( _phyloxml_website_item );
 687         customizeJMenuItem( _aptx_ref_item );
 688         customizeJMenuItem( _phyloxml_ref_item );
 689         customizeJMenuItem( _about_item );
 690         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 691         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 692         _jmenubar.add( _help_jmenu );
 693     }
 694
 695     void buildOptionsMenu() {
 696         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 697         _options_jmenu.addChangeListener( new ChangeListener() {
 698
 699             @Override
 700             public void stateChanged( final ChangeEvent e ) {
 701                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 702                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 703                 MainFrame
 704                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 705                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 706                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 707                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 708                                                                      _show_scale_cbmi,
 709                                                                      _show_branch_length_values_cbmi,
 710                                                                      _non_lined_up_cladograms_rbmi,
 711                                                                      _uniform_cladograms_rbmi,
 712                                                                      _ext_node_dependent_cladogram_rbmi,
 713                                                                      _label_direction_cbmi );
 714                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 715                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 716                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 717             }
 718         } );
 719         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 720                                                                 getConfiguration() ) );
 721         _options_jmenu
 722                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 723         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 724         _options_jmenu
 725                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 726         _radio_group_1 = new ButtonGroup();
 727         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 728         _radio_group_1.add( _uniform_cladograms_rbmi );
 729         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 730         /////
 731         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 732         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 733         _options_jmenu
 734                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 735         _options_jmenu
 736                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 737         _options_jmenu
 738                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 739         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 740             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 741         }
 742         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 743         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 744         _options_jmenu
 745                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 746         _options_jmenu
 747                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 748         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 749         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 750         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 751         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 752         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 753         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 754         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 755         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 756         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 757         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 758         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 759         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 760         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 761         /////
 762         _options_jmenu.addSeparator();
 763         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 764                                                                 getConfiguration() ) );
 765         _options_jmenu
 766                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 767         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 768         _options_jmenu
 769                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 770         customizeJMenuItem( _choose_font_mi );
 771         customizeJMenuItem( _choose_minimal_confidence_mi );
 772         customizeJMenuItem( _switch_colors_mi );
 773         customizeJMenuItem( _overview_placment_mi );
 774         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 775         customizeCheckBoxMenuItem( _label_direction_cbmi,
 776                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 777         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 778         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 779         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 780         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 781         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 782         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 783                 .isShowDefaultNodeShapesExternal() );
 784         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 785                 .isShowDefaultNodeShapesInternal() );
 786         customizeJMenuItem( _cycle_node_shape_mi );
 787         customizeJMenuItem( _cycle_node_fill_mi );
 788         customizeJMenuItem( _choose_node_size_mi );
 789         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 790         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 791         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 792         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 793                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 794         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 795                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 796         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 797                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 798         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 799         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 800         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 801         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 802         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 803         _jmenubar.add( _options_jmenu );
 804     }
 805
 806     void buildToolsMenu() {
 807         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 808         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 809         customizeJMenuItem( _confcolor_item );
 810         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 811         customizeJMenuItem( _taxcolor_item );
 812         _tools_menu.addSeparator();
 813         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 814         _remove_visual_styles_item
 815                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 816         customizeJMenuItem( _remove_visual_styles_item );
 817         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 818         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 819         customizeJMenuItem( _remove_branch_color_item );
 820         _tools_menu.addSeparator();
 821         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 822         customizeJMenuItem( _midpoint_root_item );
 823         _tools_menu.addSeparator();
 824         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 825         customizeJMenuItem( _collapse_species_specific_subtrees );
 826         _jmenubar.add( _tools_menu );
 827     }
 828
 829     void buildTypeMenu() {
 830         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 831         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 832         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 833         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 834         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 835         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 836         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 837         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 838         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 839         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 840         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 841         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 842         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 843         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 844         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 845         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 846         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 847         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 848         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 849         initializeTypeMenu( getOptions() );
 850         _jmenubar.add( _type_menu );
 851     }
 852
 853     void buildViewMenu() {
 854         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 855         _view_jmenu
 856                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 857         _view_jmenu.addSeparator();
 858         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 859         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 860         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 861         customizeJMenuItem( _display_basic_information_item );
 862         customizeJMenuItem( _view_as_NH_item );
 863         customizeJMenuItem( _view_as_XML_item );
 864         customizeJMenuItem( _view_as_nexus_item );
 865         _jmenubar.add( _view_jmenu );
 866     }
 867
 868     void checkTextFrames() {
 869         if ( _textframes.size() > 5 ) {
 870             try {
 871                 if ( _textframes.getFirst() != null ) {
 872                     _textframes.getFirst().removeMe();
 873                 }
 874                 else {
 875                     _textframes.removeFirst();
 876                 }
 877             }
 878             catch ( final NoSuchElementException e ) {
 879                 // Ignore.
 880             }
 881         }
 882     }
 883
 884     void clearCurrentExternalNodesDataBuffer() {
 885         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 886     }
 887
 888     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 889         if ( item != null ) {
 890             item.setFont( MainFrame.menu_font );
 891             if ( !getConfiguration().isUseNativeUI() ) {
 892                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 893                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 894             }
 895             item.setSelected( is_selected );
 896             item.addActionListener( this );
 897         }
 898     }
 899
 900     void customizeJMenuItem( final JMenuItem jmi ) {
 901         jmi.setFont( MainFrame.menu_font );
 902         if ( !getConfiguration().isUseNativeUI() ) {
 903             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 904             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 905         }
 906         jmi.addActionListener( this );
 907     }
 908
 909     void displayBasicInformation() {
 910         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 911             String title = "Basic Information";
 912             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 913                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 914             }
 915             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 916         }
 917     }
 918
 919     void executeGSDI() {
 920         if ( !isOKforSDI( false, true ) ) {
 921             return;
 922         }
 923         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 924             JOptionPane.showMessageDialog( this,
 925                                            "Gene tree is not rooted.",
 926                                            "Cannot execute GSDI",
 927                                            JOptionPane.ERROR_MESSAGE );
 928             return;
 929         }
 930         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 931         gene_tree.setAllNodesToNotCollapse();
 932         gene_tree.recalculateNumberOfExternalDescendants( false );
 933         GSDI gsdi = null;
 934         final Phylogeny species_tree = _species_tree.copy();
 935         try {
 936             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 937         }
 938         catch ( final SDIException e ) {
 939             JOptionPane.showMessageDialog( this,
 940                                            e.getLocalizedMessage(),
 941                                            "Error during GSDI",
 942                                            JOptionPane.ERROR_MESSAGE );
 943             return;
 944         }
 945         catch ( final Exception e ) {
 946             AptxUtil.unexpectedException( e );
 947             return;
 948         }
 949         gene_tree.setRerootable( false );
 950         gene_tree.clearHashIdToNodeMap();
 951         gene_tree.recalculateNumberOfExternalDescendants( true );
 952         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 953         getMainPanel().getControlPanel().setShowEvents( true );
 954         showWhole();
 955         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 956         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 957         showWhole();
 958         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 959         showWhole();
 960         _mainpanel.getCurrentTreePanel().setEdited( true );
 961         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 962         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 963             JOptionPane.showMessageDialog( this,
 964                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 965                                                    + "Potential duplications: "
 966                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 967                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 968                                                    + "Stripped gene tree nodes: "
 969                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 970                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 971                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 972                                            "GSDI successfully completed",
 973                                            JOptionPane.WARNING_MESSAGE );
 974         }
 975         else {
 976             JOptionPane.showMessageDialog( this,
 977                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 978                                                    + "Potential duplications: "
 979                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 980                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 981                                                    + "Stripped gene tree nodes: "
 982                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 983                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 984                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 985                                            "GSDI successfully completed",
 986                                            JOptionPane.INFORMATION_MESSAGE );
 987         }
 988     }
 989
 990     void executeGSDIR() {
 991         if ( !isOKforSDI( false, false ) ) {
 992             return;
 993         }
 994         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
 995         if ( ( p > 0 )
 996                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
 997             JOptionPane.showMessageDialog( this,
 998                                            "Gene tree is not completely binary",
 999                                            "Cannot execute GSDI",
1000                                            JOptionPane.ERROR_MESSAGE );
1001             return;
1002         }
1003         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1004         gene_tree.setAllNodesToNotCollapse();
1005         gene_tree.recalculateNumberOfExternalDescendants( false );
1006         GSDIR gsdir = null;
1007         final Phylogeny species_tree = _species_tree.copy();
1008         try {
1009             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1010         }
1011         catch ( final SDIException e ) {
1012             JOptionPane.showMessageDialog( this,
1013                                            e.getLocalizedMessage(),
1014                                            "Error during GSDIR",
1015                                            JOptionPane.ERROR_MESSAGE );
1016             return;
1017         }
1018         catch ( final Exception e ) {
1019             AptxUtil.unexpectedException( e );
1020             return;
1021         }
1022         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1023         result_gene_tree.setRerootable( false );
1024         result_gene_tree.clearHashIdToNodeMap();
1025         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1026         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1027         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1028         getMainPanel().getControlPanel().setShowEvents( true );
1029         showWhole();
1030         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1031         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1032         showWhole();
1033         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1034         showWhole();
1035         _mainpanel.getCurrentTreePanel().setEdited( true );
1036         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1037         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1038             JOptionPane.showMessageDialog( this,
1039                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1040                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1041                                                    + "Stripped gene tree nodes: "
1042                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1043                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1044                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1045                                            "GSDIR successfully completed",
1046                                            JOptionPane.WARNING_MESSAGE );
1047         }
1048         else {
1049             JOptionPane.showMessageDialog( this,
1050                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1051                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1052                                                    + "Stripped gene tree nodes: "
1053                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1054                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1055                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1056                                            "GSDIR successfully completed",
1057                                            JOptionPane.INFORMATION_MESSAGE );
1058         }
1059     }
1060
1061     Configuration getConfiguration() {
1062         return _configuration;
1063     }
1064
1065     TreePanel getCurrentTreePanel() {
1066         return getMainPanel().getCurrentTreePanel();
1067     }
1068
1069     JCheckBoxMenuItem getlabelDirectionCbmi() {
1070         return _label_direction_cbmi;
1071     }
1072
1073     Options getOtions() {
1074         return _options;
1075     }
1076
1077     void help() {
1078         final StringBuilder sb = new StringBuilder();
1079         sb.append( "Display options\n" );
1080         sb.append( "-------------------\n" );
1081         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1082         sb.append( "Clickable tree nodes\n" );
1083         sb.append( "--------------------\n" );
1084         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1085         sb.append( "or by right clicking:\n" );
1086         sb.append( "o  Display Node Data -- display information for a node\n" );
1087         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1088         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
1089         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1090         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
1091         sb.append( "o  Colorize Subtree -- color a subtree\n" );
1092         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
1093         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1094         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
1095         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1096         sb.append( "Zooming\n" );
1097         sb.append( "---------\n" );
1098         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1099         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1100         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1101         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1102         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1103         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1104         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1105         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1106         sb.append( "Quick tree manipulation:\n" );
1107         sb.append( "------------------------\n" );
1108         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1109         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1110         sb.append( "phyloXML\n" );
1111         sb.append( "-------------------\n" );
1112         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1113         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1114         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1115         sb.append( "\n" );
1116         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1117         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1118         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1119     }
1120
1121     void initializeTypeMenu( final Options options ) {
1122         setTypeMenuToAllUnselected();
1123         try {
1124             switch ( options.getPhylogenyGraphicsType() ) {
1125                 case CONVEX:
1126                     _convex_type_cbmi.setSelected( true );
1127                     break;
1128                 case CURVED:
1129                     _curved_type_cbmi.setSelected( true );
1130                     break;
1131                 case EURO_STYLE:
1132                     _euro_type_cbmi.setSelected( true );
1133                     break;
1134                 case ROUNDED:
1135                     _rounded_type_cbmi.setSelected( true );
1136                     break;
1137                 case TRIANGULAR:
1138                     _triangular_type_cbmi.setSelected( true );
1139                     break;
1140                 case UNROOTED:
1141                     _unrooted_type_cbmi.setSelected( true );
1142                     break;
1143                 case CIRCULAR:
1144                     _circular_type_cbmi.setSelected( true );
1145                     break;
1146                 default:
1147                     _rectangular_type_cbmi.setSelected( true );
1148                     break;
1149             }
1150         }
1151         catch ( final NullPointerException np ) {
1152             // In all likelihood, this is caused by menu-less display.
1153         }
1154     }
1155
1156     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1157         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1158             return false;
1159         }
1160         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1161             JOptionPane.showMessageDialog( this,
1162                                            "No species tree loaded",
1163                                            "Cannot execute GSDI",
1164                                            JOptionPane.ERROR_MESSAGE );
1165             return false;
1166         }
1167         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1168             JOptionPane.showMessageDialog( this,
1169                                            "Species tree is not completely binary",
1170                                            "Cannot execute GSDI",
1171                                            JOptionPane.ERROR_MESSAGE );
1172             return false;
1173         }
1174         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1175             JOptionPane.showMessageDialog( this,
1176                                            "Gene tree is not completely binary",
1177                                            "Cannot execute GSDI",
1178                                            JOptionPane.ERROR_MESSAGE );
1179             return false;
1180         }
1181         else {
1182             return true;
1183         }
1184     }
1185
1186     boolean isSubtreeDisplayed() {
1187         if ( getCurrentTreePanel() != null ) {
1188             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1189                 JOptionPane
1190                         .showMessageDialog( this,
1191                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1192                                             "Operation can not be exectuted on a sub-tree",
1193                                             JOptionPane.WARNING_MESSAGE );
1194                 return true;
1195             }
1196         }
1197         return false;
1198     }
1199
1200     void removeAllTextFrames() {
1201         for( final TextFrame tf : _textframes ) {
1202             if ( tf != null ) {
1203                 tf.close();
1204             }
1205         }
1206         _textframes.clear();
1207     }
1208
1209     void setConfiguration( final Configuration configuration ) {
1210         _configuration = configuration;
1211     }
1212
1213     void setOptions( final Options options ) {
1214         _options = options;
1215     }
1216
1217     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1218         setTypeMenuToAllUnselected();
1219         try {
1220             switch ( type ) {
1221                 case CIRCULAR:
1222                     _circular_type_cbmi.setSelected( true );
1223                     break;
1224                 case CONVEX:
1225                     _convex_type_cbmi.setSelected( true );
1226                     break;
1227                 case CURVED:
1228                     _curved_type_cbmi.setSelected( true );
1229                     break;
1230                 case EURO_STYLE:
1231                     _euro_type_cbmi.setSelected( true );
1232                     break;
1233                 case ROUNDED:
1234                     _rounded_type_cbmi.setSelected( true );
1235                     break;
1236                 case RECTANGULAR:
1237                     _rectangular_type_cbmi.setSelected( true );
1238                     break;
1239                 case TRIANGULAR:
1240                     _triangular_type_cbmi.setSelected( true );
1241                     break;
1242                 case UNROOTED:
1243                     _unrooted_type_cbmi.setSelected( true );
1244                     break;
1245                 default:
1246                     throw new IllegalArgumentException( "unknown type: " + type );
1247             }
1248         }
1249         catch ( final NullPointerException np ) {
1250             // In all likelihood, this is caused by menu-less display.
1251         }
1252     }
1253
1254     void setTypeMenuToAllUnselected() {
1255         if ( _convex_type_cbmi != null ) {
1256             _convex_type_cbmi.setSelected( false );
1257         }
1258         if ( _curved_type_cbmi != null ) {
1259             _curved_type_cbmi.setSelected( false );
1260         }
1261         if ( _euro_type_cbmi != null ) {
1262             _euro_type_cbmi.setSelected( false );
1263         }
1264         if ( _rounded_type_cbmi != null ) {
1265             _rounded_type_cbmi.setSelected( false );
1266         }
1267         if ( _triangular_type_cbmi != null ) {
1268             _triangular_type_cbmi.setSelected( false );
1269         }
1270         if ( _rectangular_type_cbmi != null ) {
1271             _rectangular_type_cbmi.setSelected( false );
1272         }
1273         if ( _unrooted_type_cbmi != null ) {
1274             _unrooted_type_cbmi.setSelected( false );
1275         }
1276         if ( _circular_type_cbmi != null ) {
1277             _circular_type_cbmi.setSelected( false );
1278         }
1279     }
1280
1281     void showWhole() {
1282         _mainpanel.getControlPanel().showWhole();
1283     }
1284
1285     void switchColors() {
1286         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1287         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1288         csc.setVisible( true );
1289         getMainPanel().setTreeColorSet( colorset );
1290     }
1291
1292     void typeChanged( final Object o ) {
1293         updateTypeCheckboxes( getOptions(), o );
1294         updateOptions( getOptions() );
1295         if ( getCurrentTreePanel() != null ) {
1296             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1297             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1298             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1299                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1300                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1301                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1302                 getCurrentTreePanel().getControlPanel().showWhole();
1303             }
1304             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1305                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1306             }
1307             else {
1308                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1309             }
1310             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1311             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1312         }
1313     }
1314
1315     void updateOptions( final Options options ) {
1316         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1317         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1318                 && _background_gradient_cbmi.isSelected() );
1319         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1320         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1321                 && _show_annotation_ref_source.isSelected() );
1322         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1323                 && _abbreviate_scientific_names.isSelected() );
1324         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1325                 && _color_labels_same_as_parent_branch.isSelected() );
1326         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1327                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1328         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1329                 && _show_default_node_shapes_external_cbmi.isSelected() );
1330         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1331             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1332         }
1333         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1334             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1335         }
1336         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1337             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1338         }
1339         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1340                 && _search_case_senstive_cbmi.isSelected() );
1341         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1342             options.setShowScale( _show_scale_cbmi.isSelected() );
1343         }
1344         if ( _label_direction_cbmi != null ) {
1345             if ( _label_direction_cbmi.isSelected() ) {
1346                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1347             }
1348             else {
1349                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1350             }
1351         }
1352         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1353         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1354                 && _show_confidence_stddev_cbmi.isSelected() );
1355         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1356             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1357         }
1358         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1359                 && _search_whole_words_only_cbmi.isSelected() );
1360         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1361                 && _inverse_search_result_cbmi.isSelected() );
1362         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1363             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1364         }
1365         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1366             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1367         }
1368         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1369             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1370         }
1371         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1372             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1373         }
1374         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1375             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1376         }
1377         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1378             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1379         }
1380         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1381             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1382         }
1383         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1384             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1385         }
1386         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1387             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1388         }
1389     }
1390
1391     void updateTypeCheckboxes( final Options options, final Object o ) {
1392         setTypeMenuToAllUnselected();
1393         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1394     }
1395
1396     void viewAsNexus() {
1397         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1398             String title = "Nexus";
1399             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1400                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1401             }
1402             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1403                                    .getNhConversionSupportValueStyle() ),
1404                            title );
1405         }
1406     }
1407
1408     void viewAsNH() {
1409         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1410             String title = "New Hampshire";
1411             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1412                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1413             }
1414             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1415                                    .getNhConversionSupportValueStyle() ),
1416                            title );
1417         }
1418     }
1419
1420     void viewAsXML() {
1421         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1422             String title = "phyloXML";
1423             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1424                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1425             }
1426             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1427         }
1428     }
1429
1430     private void chooseFont() {
1431         final FontChooser fc = new FontChooser();
1432         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1433         fc.showDialog( this, "Select the Base Font" );
1434         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1435     }
1436
1437     private void chooseMinimalConfidence() {
1438         final String s = ( String ) JOptionPane
1439                 .showInputDialog( this,
1440                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1441                                           + getOptions().getMinConfidenceValue() + "]\n",
1442                                   "Minimal Confidence Value",
1443                                   JOptionPane.QUESTION_MESSAGE,
1444                                   null,
1445                                   null,
1446                                   getOptions().getMinConfidenceValue() );
1447         if ( !ForesterUtil.isEmpty( s ) ) {
1448             boolean success = true;
1449             double m = 0.0;
1450             final String m_str = s.trim();
1451             if ( !ForesterUtil.isEmpty( m_str ) ) {
1452                 try {
1453                     m = Double.parseDouble( m_str );
1454                 }
1455                 catch ( final Exception ex ) {
1456                     success = false;
1457                 }
1458             }
1459             else {
1460                 success = false;
1461             }
1462             if ( success && ( m >= 0.0 ) ) {
1463                 getOptions().setMinConfidenceValue( m );
1464             }
1465         }
1466     }
1467
1468     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1469         if ( item != null ) {
1470             item.setFont( MainFrame.menu_font );
1471             if ( !getConfiguration().isUseNativeUI() ) {
1472                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1473                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1474             }
1475             item.setSelected( is_selected );
1476             item.addActionListener( this );
1477         }
1478     }
1479
1480     private MainPanel getMainPanel() {
1481         return _mainpanel;
1482     }
1483
1484     private Phylogeny getSpeciesTree() {
1485         return _species_tree;
1486     }
1487
1488     private boolean isScreenAntialias() {
1489         return true;
1490     }
1491
1492     private void removeBranchColors() {
1493         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1494             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1495         }
1496     }
1497
1498     private void removeVisualStyles() {
1499         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1500             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1501         }
1502     }
1503
1504     private void setMainPanel( final MainPanelApplets main_panel ) {
1505         _mainpanel = main_panel;
1506     }
1507
1508     private void setSpeciesTree( final Phylogeny species_tree ) {
1509         _species_tree = species_tree;
1510     }
1511
1512     private void setupUI() {
1513         try {
1514             if ( getConfiguration().isUseNativeUI() ) {
1515                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1516             }
1517             else {
1518                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1519             }
1520         }
1521         catch ( final UnsupportedLookAndFeelException e ) {
1522             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1523         }
1524         catch ( final ClassNotFoundException e ) {
1525             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1526         }
1527         catch ( final InstantiationException e ) {
1528             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1529         }
1530         catch ( final IllegalAccessException e ) {
1531             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1532         }
1533         catch ( final Exception e ) {
1534             AptxUtil.dieWithSystemError( e.toString() );
1535         }
1536     }
1537
1538     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1539         for( final TreePanel tree_panel : treepanels ) {
1540             tree_panel.setTextAntialias();
1541         }
1542     }
1543 }