forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.archaeopteryx;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Font;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ComponentAdapter;
  33 import java.awt.event.ComponentEvent;
  34 import java.awt.event.WindowAdapter;
  35 import java.awt.event.WindowEvent;
  36 import java.io.File;
  37 import java.io.FileInputStream;
  38 import java.io.IOException;
  39 import java.io.InputStream;
  40 import java.net.MalformedURLException;
  41 import java.net.URL;
  42 import java.util.ArrayList;
  43 import java.util.HashSet;
  44 import java.util.List;
  45 import java.util.Set;
  46
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.JCheckBoxMenuItem;
  49 import javax.swing.JFileChooser;
  50 import javax.swing.JMenu;
  51 import javax.swing.JMenuBar;
  52 import javax.swing.JMenuItem;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JRadioButtonMenuItem;
  55 import javax.swing.UIManager;
  56 import javax.swing.UnsupportedLookAndFeelException;
  57 import javax.swing.WindowConstants;
  58 import javax.swing.event.ChangeEvent;
  59 import javax.swing.event.ChangeListener;
  60 import javax.swing.filechooser.FileFilter;
  61 import javax.swing.plaf.synth.SynthLookAndFeel;
  62
  63 import org.forester.analysis.TaxonomyDataManager;
  64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
  69 import org.forester.archaeopteryx.tools.InferenceManager;
  70 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
  71 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
  72 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
  73 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
  74 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  75 import org.forester.archaeopteryx.webservices.WebservicesManager;
  76 import org.forester.io.parsers.FastaParser;
  77 import org.forester.io.parsers.GeneralMsaParser;
  78 import org.forester.io.parsers.PhylogenyParser;
  79 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  80 import org.forester.io.parsers.nhx.NHXParser;
  81 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  82 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  83 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  84 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  85 import org.forester.io.parsers.tol.TolParser;
  86 import org.forester.io.parsers.util.ParserUtils;
  87 import org.forester.io.writers.PhylogenyWriter;
  88 import org.forester.io.writers.SequenceWriter;
  89 import org.forester.msa.Msa;
  90 import org.forester.msa.MsaFormatException;
  91 import org.forester.phylogeny.Phylogeny;
  92 import org.forester.phylogeny.PhylogenyMethods;
  93 import org.forester.phylogeny.PhylogenyNode;
  94 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  95 import org.forester.phylogeny.data.Confidence;
  96 import org.forester.phylogeny.data.Taxonomy;
  97 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  98 import org.forester.phylogeny.factories.PhylogenyFactory;
  99 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 100 import org.forester.sequence.Sequence;
 101 import org.forester.util.BasicDescriptiveStatistics;
 102 import org.forester.util.BasicTable;
 103 import org.forester.util.BasicTableParser;
 104 import org.forester.util.DescriptiveStatistics;
 105 import org.forester.util.ForesterUtil;
 106 import org.forester.util.WindowsUtils;
 107
 108 public final class MainFrameApplication extends MainFrame {
 109
 110     static final String                      INFER_ANCESTOR_TAXONOMIES             = "Infer Ancestor Taxonomies";
 111     static final String                      OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
 112     private final static int                 FRAME_X_SIZE                          = 800;
 113     private final static int                 FRAME_Y_SIZE                          = 800;
 114     // Filters for the file-open dialog (classes defined in this file)
 115     private final static NHFilter            nhfilter                              = new NHFilter();
 116     private final static NHXFilter           nhxfilter                             = new NHXFilter();
 117     private final static XMLFilter           xmlfilter                             = new XMLFilter();
 118     private final static TolFilter           tolfilter                             = new TolFilter();
 119     private final static NexusFilter         nexusfilter                           = new NexusFilter();
 120     private final static PdfFilter           pdffilter                             = new PdfFilter();
 121     private final static GraphicsFileFilter  graphicsfilefilter                    = new GraphicsFileFilter();
 122     private final static MsaFileFilter       msafilter                             = new MsaFileFilter();
 123     private final static SequencesFileFilter seqsfilter                            = new SequencesFileFilter();
 124     private final static DefaultFilter       defaultfilter                         = new DefaultFilter();
 125     private static final long                serialVersionUID                      = -799735726778865234L;
 126     private final JFileChooser               _values_filechooser;
 127     private final JFileChooser               _sequences_filechooser;
 128     private final JFileChooser               _open_filechooser;
 129     private final JFileChooser               _msa_filechooser;
 130     private final JFileChooser               _seqs_pi_filechooser;
 131     private final JFileChooser               _open_filechooser_for_species_tree;
 132     private final JFileChooser               _save_filechooser;
 133     private final JFileChooser               _writetopdf_filechooser;
 134     private final JFileChooser               _writetographics_filechooser;
 135     // Application-only print menu items
 136     private JMenuItem                        _print_item;
 137     private JMenuItem                        _write_to_pdf_item;
 138     private JMenuItem                        _write_to_jpg_item;
 139     private JMenuItem                        _write_to_gif_item;
 140     private JMenuItem                        _write_to_tif_item;
 141     private JMenuItem                        _write_to_png_item;
 142     private JMenuItem                        _write_to_bmp_item;
 143     private File                             _current_dir;
 144     private ButtonGroup                      _radio_group_1;
 145     private ButtonGroup                      _radio_group_2;
 146     // Others:
 147     double                                   _min_not_collapse                     = Constants.MIN_NOT_COLLAPSE_DEFAULT;
 148     // Phylogeny Inference menu
 149     private JMenu                            _inference_menu;
 150     private JMenuItem                        _inference_from_msa_item;
 151     private JMenuItem                        _inference_from_seqs_item;
 152     // Phylogeny Inference
 153     private PhylogeneticInferenceOptions     _phylogenetic_inference_options       = null;
 154     private Msa                              _msa                                  = null;
 155     private File                             _msa_file                             = null;
 156     private List<Sequence>                   _seqs                                 = null;
 157     private File                             _seqs_file                            = null;
 158     JMenuItem                                _read_values_jmi;
 159     JMenuItem                                _read_seqs_jmi;
 160
 161     private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
 162         _configuration = config;
 163         if ( _configuration == null ) {
 164             throw new IllegalArgumentException( "configuration is null" );
 165         }
 166         setVisible( false );
 167         setOptions( Options.createInstance( _configuration ) );
 168         _mainpanel = new MainPanel( _configuration, this );
 169         _open_filechooser = null;
 170         _open_filechooser_for_species_tree = null;
 171         _save_filechooser = null;
 172         _writetopdf_filechooser = null;
 173         _writetographics_filechooser = null;
 174         _msa_filechooser = null;
 175         _seqs_pi_filechooser = null;
 176         _values_filechooser = null;
 177         _sequences_filechooser = null;
 178         _jmenubar = new JMenuBar();
 179         buildFileMenu();
 180         buildTypeMenu();
 181         _contentpane = getContentPane();
 182         _contentpane.setLayout( new BorderLayout() );
 183         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 184         // App is this big
 185         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 186         // The window listener
 187         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 188         addWindowListener( new WindowAdapter() {
 189
 190             @Override
 191             public void windowClosing( final WindowEvent e ) {
 192                 exit();
 193             }
 194         } );
 195         //   setVisible( true );
 196         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 197             AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
 198             validate();
 199             getMainPanel().getControlPanel().showWholeAll();
 200             getMainPanel().getControlPanel().showWhole();
 201         }
 202         //activateSaveAllIfNeeded();
 203         // ...and its children
 204         _contentpane.repaint();
 205     }
 206
 207     private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
 208         this( phys, config, title, null );
 209     }
 210
 211     private MainFrameApplication( final Phylogeny[] phys,
 212                                   final Configuration config,
 213                                   final String title,
 214                                   final File current_dir ) {
 215         super();
 216         _configuration = config;
 217         if ( _configuration == null ) {
 218             throw new IllegalArgumentException( "configuration is null" );
 219         }
 220         try {
 221             boolean synth_exception = false;
 222             if ( Constants.__SYNTH_LF ) {
 223                 try {
 224                     final SynthLookAndFeel synth = new SynthLookAndFeel();
 225                     synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
 226                                 MainFrameApplication.class );
 227                     UIManager.setLookAndFeel( synth );
 228                 }
 229                 catch ( final Exception ex ) {
 230                     synth_exception = true;
 231                     ForesterUtil.printWarningMessage( Constants.PRG_NAME,
 232                                                       "could not create synth look and feel: "
 233                                                               + ex.getLocalizedMessage() );
 234                 }
 235             }
 236             if ( !Constants.__SYNTH_LF || synth_exception ) {
 237                 if ( _configuration.isUseNativeUI() ) {
 238                     UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 239                 }
 240                 else {
 241                     UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 242                 }
 243             }
 244             //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
 245         }
 246         catch ( final UnsupportedLookAndFeelException e ) {
 247             AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
 248         }
 249         catch ( final ClassNotFoundException e ) {
 250             AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
 251         }
 252         catch ( final InstantiationException e ) {
 253             AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
 254         }
 255         catch ( final IllegalAccessException e ) {
 256             AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
 257         }
 258         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
 259             setCurrentDir( current_dir );
 260         }
 261         // hide until everything is ready
 262         setVisible( false );
 263         setOptions( Options.createInstance( _configuration ) );
 264         setInferenceManager( InferenceManager.createInstance( _configuration ) );
 265         setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
 266         //     _textframe = null; #~~~~
 267         // set title
 268         setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
 269         _mainpanel = new MainPanel( _configuration, this );
 270         // The file dialogs
 271         _open_filechooser = new JFileChooser();
 272         _open_filechooser.setCurrentDirectory( new File( "." ) );
 273         _open_filechooser.setMultiSelectionEnabled( false );
 274         _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 275         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
 276         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 277         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 278         _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
 279         _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
 280         _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
 281         _open_filechooser_for_species_tree = new JFileChooser();
 282         _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
 283         _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
 284         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 285         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
 286         _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
 287         _save_filechooser = new JFileChooser();
 288         _save_filechooser.setCurrentDirectory( new File( "." ) );
 289         _save_filechooser.setMultiSelectionEnabled( false );
 290         _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
 291         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 292         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 293         _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
 294         _writetopdf_filechooser = new JFileChooser();
 295         _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
 296         _writetographics_filechooser = new JFileChooser();
 297         _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
 298         // Msa:
 299         _msa_filechooser = new JFileChooser();
 300         _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
 301         _msa_filechooser.setCurrentDirectory( new File( "." ) );
 302         _msa_filechooser.setMultiSelectionEnabled( false );
 303         _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
 304         _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
 305         // Seqs:
 306         _seqs_pi_filechooser = new JFileChooser();
 307         _seqs_pi_filechooser.setName( "Read Sequences File" );
 308         _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
 309         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 310         _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
 311         _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
 312         // Expression
 313         _values_filechooser = new JFileChooser();
 314         _values_filechooser.setCurrentDirectory( new File( "." ) );
 315         _values_filechooser.setMultiSelectionEnabled( false );
 316         // Sequences
 317         _sequences_filechooser = new JFileChooser();
 318         _sequences_filechooser.setCurrentDirectory( new File( "." ) );
 319         _sequences_filechooser.setMultiSelectionEnabled( false );
 320         // build the menu bar
 321         _jmenubar = new JMenuBar();
 322         if ( !_configuration.isUseNativeUI() ) {
 323             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 324         }
 325         buildFileMenu();
 326         if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
 327             buildPhylogeneticInferenceMenu();
 328         }
 329         buildAnalysisMenu();
 330         buildToolsMenu();
 331         buildViewMenu();
 332         buildFontSizeMenu();
 333         buildOptionsMenu();
 334         buildTypeMenu();
 335         buildHelpMenu();
 336         setJMenuBar( _jmenubar );
 337         _jmenubar.add( _help_jmenu );
 338         _contentpane = getContentPane();
 339         _contentpane.setLayout( new BorderLayout() );
 340         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 341         // App is this big
 342         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 343         //        addWindowFocusListener( new WindowAdapter() {
 344         //
 345         //            @Override
 346         //            public void windowGainedFocus( WindowEvent e ) {
 347         //                requestFocusInWindow();
 348         //            }
 349         //        } );
 350         // The window listener
 351         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 352         addWindowListener( new WindowAdapter() {
 353
 354             @Override
 355             public void windowClosing( final WindowEvent e ) {
 356                 if ( isUnsavedDataPresent() ) {
 357                     final int r = JOptionPane.showConfirmDialog( null,
 358                                                                  "Exit despite potentially unsaved changes?",
 359                                                                  "Exit?",
 360                                                                  JOptionPane.YES_NO_OPTION );
 361                     if ( r != JOptionPane.YES_OPTION ) {
 362                         return;
 363                     }
 364                 }
 365                 else {
 366                     final int r = JOptionPane.showConfirmDialog( null,
 367                                                                  "Exit Archaeopteryx?",
 368                                                                  "Exit?",
 369                                                                  JOptionPane.YES_NO_OPTION );
 370                     if ( r != JOptionPane.YES_OPTION ) {
 371                         return;
 372                     }
 373                 }
 374                 exit();
 375             }
 376         } );
 377         // The component listener
 378         addComponentListener( new ComponentAdapter() {
 379
 380             @Override
 381             public void componentResized( final ComponentEvent e ) {
 382                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 383                     _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
 384                                                                                         .getWidth(),
 385                                                                                 _mainpanel.getCurrentTreePanel()
 386                                                                                         .getHeight(),
 387                                                                                 getOptions().isAllowFontSizeChange() );
 388                 }
 389             }
 390         } );
 391         requestFocusInWindow();
 392         // addKeyListener( this );
 393         setVisible( true );
 394         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 395             AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
 396             validate();
 397             getMainPanel().getControlPanel().showWholeAll();
 398             getMainPanel().getControlPanel().showWhole();
 399         }
 400         activateSaveAllIfNeeded();
 401         // ...and its children
 402         _contentpane.repaint();
 403         System.gc();
 404     }
 405
 406     private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
 407         // Reads the config file (false, false => not url, not applet):
 408         this( phys, new Configuration( config_file, false, false, true ), title );
 409     }
 410
 411     @Override
 412     public void actionPerformed( final ActionEvent e ) {
 413         try {
 414             super.actionPerformed( e );
 415             final Object o = e.getSource();
 416             // Handle app-specific actions here:
 417             if ( o == _open_item ) {
 418                 readPhylogeniesFromFile();
 419             }
 420             else if ( o == _save_item ) {
 421                 writeToFile( _mainpanel.getCurrentPhylogeny() );
 422                 // If subtree currently displayed, save it, instead of complete
 423                 // tree.
 424             }
 425             else if ( o == _new_item ) {
 426                 newTree();
 427             }
 428             else if ( o == _save_all_item ) {
 429                 writeAllToFile();
 430             }
 431             else if ( o == _close_item ) {
 432                 closeCurrentPane();
 433             }
 434             else if ( o == _write_to_pdf_item ) {
 435                 writeToPdf( _mainpanel.getCurrentPhylogeny() );
 436             }
 437             else if ( o == _write_to_jpg_item ) {
 438                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
 439             }
 440             else if ( o == _write_to_png_item ) {
 441                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
 442             }
 443             else if ( o == _write_to_gif_item ) {
 444                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
 445             }
 446             else if ( o == _write_to_tif_item ) {
 447                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
 448             }
 449             else if ( o == _write_to_bmp_item ) {
 450                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
 451             }
 452             else if ( o == _print_item ) {
 453                 print();
 454             }
 455             else if ( o == _load_species_tree_item ) {
 456                 readSpeciesTreeFromFile();
 457             }
 458             else if ( o == _lineage_inference ) {
 459                 if ( isSubtreeDisplayed() ) {
 460                     JOptionPane.showMessageDialog( this,
 461                                                    "Subtree is shown.",
 462                                                    "Cannot infer ancestral taxonomies",
 463                                                    JOptionPane.ERROR_MESSAGE );
 464                     return;
 465                 }
 466                 executeLineageInference();
 467             }
 468             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
 469                 if ( isSubtreeDisplayed() ) {
 470                     return;
 471                 }
 472                 obtainDetailedTaxonomicInformation();
 473             }
 474             else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
 475                 if ( isSubtreeDisplayed() ) {
 476                     return;
 477                 }
 478                 obtainDetailedTaxonomicInformationDelete();
 479             }
 480             else if ( o == _obtain_seq_information_jmi ) {
 481                 obtainSequenceInformation();
 482             }
 483             else if ( o == _read_values_jmi ) {
 484                 if ( isSubtreeDisplayed() ) {
 485                     return;
 486                 }
 487                 addExpressionValuesFromFile();
 488             }
 489             else if ( o == _read_seqs_jmi ) {
 490                 if ( isSubtreeDisplayed() ) {
 491                     return;
 492                 }
 493                 addSequencesFromFile();
 494             }
 495             else if ( o == _move_node_names_to_tax_sn_jmi ) {
 496                 moveNodeNamesToTaxSn();
 497             }
 498             else if ( o == _move_node_names_to_seq_names_jmi ) {
 499                 moveNodeNamesToSeqNames();
 500             }
 501             else if ( o == _extract_tax_code_from_node_names_jmi ) {
 502                 extractTaxDataFromNodeNames();
 503             }
 504             else if ( o == _graphics_export_visible_only_cbmi ) {
 505                 updateOptions( getOptions() );
 506             }
 507             else if ( o == _antialias_print_cbmi ) {
 508                 updateOptions( getOptions() );
 509             }
 510             else if ( o == _print_black_and_white_cbmi ) {
 511                 updateOptions( getOptions() );
 512             }
 513             else if ( o == _print_using_actual_size_cbmi ) {
 514                 updateOptions( getOptions() );
 515             }
 516             else if ( o == _graphics_export_using_actual_size_cbmi ) {
 517                 updateOptions( getOptions() );
 518             }
 519             else if ( o == _print_size_mi ) {
 520                 choosePrintSize();
 521             }
 522             else if ( o == _choose_pdf_width_mi ) {
 523                 choosePdfWidth();
 524             }
 525             else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
 526                 updateOptions( getOptions() );
 527             }
 528             else if ( o == _replace_underscores_cbmi ) {
 529                 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
 530                     _extract_taxonomy_no_rbmi.setSelected( true );
 531                 }
 532                 updateOptions( getOptions() );
 533             }
 534             else if ( o == _collapse_below_threshold ) {
 535                 if ( isSubtreeDisplayed() ) {
 536                     return;
 537                 }
 538                 collapseBelowThreshold();
 539             }
 540             else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
 541                     || ( o == _extract_taxonomy_agressive_rbmi ) ) {
 542                 if ( _replace_underscores_cbmi != null ) {
 543                     _replace_underscores_cbmi.setSelected( false );
 544                 }
 545                 updateOptions( getOptions() );
 546             }
 547             else if ( o == _extract_taxonomy_no_rbmi ) {
 548                 updateOptions( getOptions() );
 549             }
 550             else if ( o == _inference_from_msa_item ) {
 551                 executePhyleneticInference( false );
 552             }
 553             else if ( o == _inference_from_seqs_item ) {
 554                 executePhyleneticInference( true );
 555             }
 556             _contentpane.repaint();
 557         }
 558         catch ( final Exception ex ) {
 559             AptxUtil.unexpectedException( ex );
 560         }
 561         catch ( final Error err ) {
 562             AptxUtil.unexpectedError( err );
 563         }
 564     }
 565
 566     public void end() {
 567         _mainpanel.terminate();
 568         _contentpane.removeAll();
 569         setVisible( false );
 570         dispose();
 571     }
 572
 573     @Override
 574     public MainPanel getMainPanel() {
 575         return _mainpanel;
 576     }
 577
 578     public Msa getMsa() {
 579         return _msa;
 580     }
 581
 582     public File getMsaFile() {
 583         return _msa_file;
 584     }
 585
 586     public List<Sequence> getSeqs() {
 587         return _seqs;
 588     }
 589
 590     public File getSeqsFile() {
 591         return _seqs_file;
 592     }
 593
 594     public void readMsaFromFile() {
 595         // Set an initial directory if none set yet
 596         final File my_dir = getCurrentDir();
 597         _msa_filechooser.setMultiSelectionEnabled( false );
 598         // Open file-open dialog and set current directory
 599         if ( my_dir != null ) {
 600             _msa_filechooser.setCurrentDirectory( my_dir );
 601         }
 602         final int result = _msa_filechooser.showOpenDialog( _contentpane );
 603         // All done: get the msa
 604         final File file = _msa_filechooser.getSelectedFile();
 605         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
 606         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 607             setMsaFile( null );
 608             setMsa( null );
 609             Msa msa = null;
 610             try {
 611                 final InputStream is = new FileInputStream( file );
 612                 if ( FastaParser.isLikelyFasta( file ) ) {
 613                     msa = FastaParser.parseMsa( is );
 614                 }
 615                 else {
 616                     msa = GeneralMsaParser.parse( is );
 617                 }
 618             }
 619             catch ( final MsaFormatException e ) {
 620                 setArrowCursor();
 621                 JOptionPane.showMessageDialog( this,
 622                                                e.getLocalizedMessage(),
 623                                                "Multiple sequence alignment format error",
 624                                                JOptionPane.ERROR_MESSAGE );
 625                 return;
 626             }
 627             catch ( final IOException e ) {
 628                 setArrowCursor();
 629                 JOptionPane.showMessageDialog( this,
 630                                                e.getLocalizedMessage(),
 631                                                "Failed to read multiple sequence alignment",
 632                                                JOptionPane.ERROR_MESSAGE );
 633                 return;
 634             }
 635             catch ( final IllegalArgumentException e ) {
 636                 setArrowCursor();
 637                 JOptionPane.showMessageDialog( this,
 638                                                e.getLocalizedMessage(),
 639                                                "Unexpected error during reading of multiple sequence alignment",
 640                                                JOptionPane.ERROR_MESSAGE );
 641                 return;
 642             }
 643             catch ( final Exception e ) {
 644                 setArrowCursor();
 645                 e.printStackTrace();
 646                 JOptionPane.showMessageDialog( this,
 647                                                e.getLocalizedMessage(),
 648                                                "Unexpected error during reading of multiple sequence alignment",
 649                                                JOptionPane.ERROR_MESSAGE );
 650                 return;
 651             }
 652             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
 653                 JOptionPane.showMessageDialog( this,
 654                                                "Multiple sequence alignment is empty",
 655                                                "Illegal Multiple Sequence Alignment",
 656                                                JOptionPane.ERROR_MESSAGE );
 657                 return;
 658             }
 659             if ( msa.getNumberOfSequences() < 4 ) {
 660                 JOptionPane.showMessageDialog( this,
 661                                                "Multiple sequence alignment needs to contain at least 3 sequences",
 662                                                "Illegal multiple sequence alignment",
 663                                                JOptionPane.ERROR_MESSAGE );
 664                 return;
 665             }
 666             if ( msa.getLength() < 2 ) {
 667                 JOptionPane.showMessageDialog( this,
 668                                                "Multiple sequence alignment needs to contain at least 2 residues",
 669                                                "Illegal multiple sequence alignment",
 670                                                JOptionPane.ERROR_MESSAGE );
 671                 return;
 672             }
 673             System.gc();
 674             setMsaFile( _msa_filechooser.getSelectedFile() );
 675             setMsa( msa );
 676         }
 677     }
 678
 679     public void readSeqsFromFileforPI() {
 680         // Set an initial directory if none set yet
 681         final File my_dir = getCurrentDir();
 682         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 683         // Open file-open dialog and set current directory
 684         if ( my_dir != null ) {
 685             _seqs_pi_filechooser.setCurrentDirectory( my_dir );
 686         }
 687         final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
 688         // All done: get the seqs
 689         final File file = _seqs_pi_filechooser.getSelectedFile();
 690         setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
 691         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 692             setSeqsFile( null );
 693             setSeqs( null );
 694             List<Sequence> seqs = null;
 695             try {
 696                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
 697                     seqs = FastaParser.parse( new FileInputStream( file ) );
 698                     for( final Sequence seq : seqs ) {
 699                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
 700                     }
 701                 }
 702                 else {
 703                     //TODO error
 704                 }
 705             }
 706             catch ( final MsaFormatException e ) {
 707                 setArrowCursor();
 708                 JOptionPane.showMessageDialog( this,
 709                                                e.getLocalizedMessage(),
 710                                                "Multiple sequence file format error",
 711                                                JOptionPane.ERROR_MESSAGE );
 712                 return;
 713             }
 714             catch ( final IOException e ) {
 715                 setArrowCursor();
 716                 JOptionPane.showMessageDialog( this,
 717                                                e.getLocalizedMessage(),
 718                                                "Failed to read multiple sequence file",
 719                                                JOptionPane.ERROR_MESSAGE );
 720                 return;
 721             }
 722             catch ( final IllegalArgumentException e ) {
 723                 setArrowCursor();
 724                 JOptionPane.showMessageDialog( this,
 725                                                e.getLocalizedMessage(),
 726                                                "Unexpected error during reading of multiple sequence file",
 727                                                JOptionPane.ERROR_MESSAGE );
 728                 return;
 729             }
 730             catch ( final Exception e ) {
 731                 setArrowCursor();
 732                 e.printStackTrace();
 733                 JOptionPane.showMessageDialog( this,
 734                                                e.getLocalizedMessage(),
 735                                                "Unexpected error during reading of multiple sequence file",
 736                                                JOptionPane.ERROR_MESSAGE );
 737                 return;
 738             }
 739             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 740                 JOptionPane.showMessageDialog( this,
 741                                                "Multiple sequence file is empty",
 742                                                "Illegal multiple sequence file",
 743                                                JOptionPane.ERROR_MESSAGE );
 744                 return;
 745             }
 746             if ( seqs.size() < 4 ) {
 747                 JOptionPane.showMessageDialog( this,
 748                                                "Multiple sequence file needs to contain at least 3 sequences",
 749                                                "Illegal multiple sequence file",
 750                                                JOptionPane.ERROR_MESSAGE );
 751                 return;
 752             }
 753             //  if ( msa.getLength() < 2 ) {
 754             //       JOptionPane.showMessageDialog( this,
 755             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
 756             //                                      "Illegal multiple sequence file",
 757             //                                      JOptionPane.ERROR_MESSAGE );
 758             //       return;
 759             //   }
 760             System.gc();
 761             setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
 762             setSeqs( seqs );
 763         }
 764     }
 765
 766     void buildAnalysisMenu() {
 767         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 768         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 769         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 770         _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
 771         customizeJMenuItem( _gsdi_item );
 772         customizeJMenuItem( _gsdir_item );
 773         customizeJMenuItem( _load_species_tree_item );
 774         _analysis_menu.addSeparator();
 775         _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 776         customizeJMenuItem( _lineage_inference );
 777         _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 778         _jmenubar.add( _analysis_menu );
 779     }
 780
 781     @Override
 782     void buildFileMenu() {
 783         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
 784         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
 785         _file_jmenu.addSeparator();
 786         _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
 787         _file_jmenu.addSeparator();
 788         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
 789         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
 790                 .getAvailablePhylogeniesWebserviceClients().size() ];
 791         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 792             final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
 793             _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
 794             _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
 795         }
 796         if ( getConfiguration().isEditable() ) {
 797             _file_jmenu.addSeparator();
 798             _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
 799             _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
 800         }
 801         _file_jmenu.addSeparator();
 802         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
 803         _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
 804         _save_all_item.setToolTipText( "Write all phylogenies to one file." );
 805         _save_all_item.setEnabled( false );
 806         _file_jmenu.addSeparator();
 807         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
 808         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
 809             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
 810         }
 811         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
 812         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
 813         if ( AptxUtil.canWriteFormat( "gif" ) ) {
 814             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
 815         }
 816         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
 817             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
 818         }
 819         _file_jmenu.addSeparator();
 820         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
 821         _file_jmenu.addSeparator();
 822         _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
 823         _close_item.setToolTipText( "To close the current pane." );
 824         _close_item.setEnabled( true );
 825         _file_jmenu.addSeparator();
 826         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 827         // For print in color option item
 828         customizeJMenuItem( _open_item );
 829         _open_item
 830                 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
 831         customizeJMenuItem( _open_url_item );
 832         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 833             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
 834         }
 835         customizeJMenuItem( _save_item );
 836         if ( getConfiguration().isEditable() ) {
 837             customizeJMenuItem( _new_item );
 838         }
 839         customizeJMenuItem( _close_item );
 840         customizeJMenuItem( _save_all_item );
 841         customizeJMenuItem( _write_to_pdf_item );
 842         customizeJMenuItem( _write_to_png_item );
 843         customizeJMenuItem( _write_to_jpg_item );
 844         customizeJMenuItem( _write_to_gif_item );
 845         customizeJMenuItem( _write_to_tif_item );
 846         customizeJMenuItem( _write_to_bmp_item );
 847         customizeJMenuItem( _print_item );
 848         customizeJMenuItem( _exit_item );
 849         _jmenubar.add( _file_jmenu );
 850     }
 851
 852     void buildOptionsMenu() {
 853         _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
 854         _options_jmenu.addChangeListener( new ChangeListener() {
 855
 856             @Override
 857             public void stateChanged( final ChangeEvent e ) {
 858                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 859                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 860                 MainFrame
 861                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 862                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 863                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 864                 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
 865                 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
 866                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 867                                                                      _show_scale_cbmi,
 868                                                                      _show_branch_length_values_cbmi,
 869                                                                      _non_lined_up_cladograms_rbmi,
 870                                                                      _uniform_cladograms_rbmi,
 871                                                                      _ext_node_dependent_cladogram_rbmi,
 872                                                                      _label_direction_cbmi );
 873                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 874                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 875                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 876             }
 877         } );
 878         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
 879         _options_jmenu
 880                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 881         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 882         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 883         _radio_group_1 = new ButtonGroup();
 884         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 885         _radio_group_1.add( _uniform_cladograms_rbmi );
 886         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 887         ///////
 888         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
 889         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
 890         _options_jmenu
 891                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 892         _options_jmenu
 893                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
 894         _options_jmenu
 895                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
 896         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 897             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 898         }
 899         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
 900         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
 901         _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
 902         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 903         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 904         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
 905         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 906         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 907         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
 908         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
 909         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 910         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 911         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 912         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 913         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 914         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 915         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 916         ///////
 917         _options_jmenu.addSeparator();
 918         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
 919         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
 920         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
 921         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 922         _options_jmenu.addSeparator();
 923         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
 924                                                       getConfiguration() ) );
 925         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
 926         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
 927         _options_jmenu
 928                 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
 929         _options_jmenu
 930                 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
 931         _options_jmenu
 932                 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
 933         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
 934         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
 935         _options_jmenu.addSeparator();
 936         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
 937         _options_jmenu
 938                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
 939         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
 940         //
 941         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
 942         _options_jmenu
 943                 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
 944         _options_jmenu
 945                 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
 946         _options_jmenu
 947                 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
 948         _extract_taxonomy_pfam_strict_rbmi
 949                 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
 950         _extract_taxonomy_pfam_relaxed_rbmi
 951                 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
 952         _extract_taxonomy_agressive_rbmi
 953                 .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
 954         _radio_group_2 = new ButtonGroup();
 955         _radio_group_2.add( _extract_taxonomy_no_rbmi );
 956         _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
 957         _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
 958         _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
 959         //
 960         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
 961         _options_jmenu
 962                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
 963         _use_brackets_for_conf_in_nh_export_cbmi
 964                 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
 965         _options_jmenu
 966                 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
 967         customizeJMenuItem( _choose_font_mi );
 968         customizeJMenuItem( _choose_minimal_confidence_mi );
 969         customizeJMenuItem( _switch_colors_mi );
 970         customizeJMenuItem( _print_size_mi );
 971         customizeJMenuItem( _choose_pdf_width_mi );
 972         customizeJMenuItem( _overview_placment_mi );
 973         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 974                 .isShowDefaultNodeShapesExternal() );
 975         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 976                 .isShowDefaultNodeShapesInternal() );
 977         customizeJMenuItem( _cycle_node_shape_mi );
 978         customizeJMenuItem( _cycle_node_fill_mi );
 979         customizeJMenuItem( _choose_node_size_mi );
 980         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 981         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 982         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 983         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 984         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 985         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 986         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 987         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 988         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 989         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 990                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 991         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 992                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 993         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 994                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 995         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 996         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 997         customizeCheckBoxMenuItem( _label_direction_cbmi,
 998                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 999         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1000         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1001         customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1002                 .isInternalNumberAreConfidenceForNhParsing() );
1003         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1004                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1005         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
1006                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1007         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
1008                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1009         customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
1010                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
1011         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1012         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1013         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1014         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1015         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1016         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1017                 .isGraphicsExportUsingActualSize() );
1018         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1019         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1020                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1021         customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1022                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1023         _jmenubar.add( _options_jmenu );
1024     }
1025
1026     void buildPhylogeneticInferenceMenu() {
1027         final InferenceManager im = getInferenceManager();
1028         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1029         _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1030         customizeJMenuItem( _inference_from_msa_item );
1031         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1032         if ( im.canDoMsa() ) {
1033             _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1034             customizeJMenuItem( _inference_from_seqs_item );
1035             _inference_from_seqs_item
1036                     .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1037         }
1038         else {
1039             _inference_menu
1040                     .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1041             customizeJMenuItem( _inference_from_seqs_item );
1042             _inference_from_seqs_item.setEnabled( false );
1043         }
1044         _jmenubar.add( _inference_menu );
1045     }
1046
1047     void buildToolsMenu() {
1048         _tools_menu = createMenu( "Tools", getConfiguration() );
1049         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1050         customizeJMenuItem( _confcolor_item );
1051         _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1052         customizeJMenuItem( _color_rank_jmi );
1053         _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1054         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1055         customizeJMenuItem( _taxcolor_item );
1056         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1057         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1058         customizeJMenuItem( _remove_branch_color_item );
1059         _tools_menu.addSeparator();
1060         _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1061         customizeJMenuItem( _annotate_item );
1062         _tools_menu.addSeparator();
1063         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1064         customizeJMenuItem( _midpoint_root_item );
1065         _tools_menu.addSeparator();
1066         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1067         customizeJMenuItem( _collapse_species_specific_subtrees );
1068         _tools_menu
1069                 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1070         customizeJMenuItem( _collapse_below_threshold );
1071         _collapse_below_threshold
1072                 .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
1073         _tools_menu.addSeparator();
1074         _tools_menu
1075                 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
1076         customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1077         _extract_tax_code_from_node_names_jmi
1078                 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
1079         _tools_menu
1080                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1081         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1082         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1083         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1084         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1085         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1086         _tools_menu.addSeparator();
1087         _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1088         customizeJMenuItem( _obtain_seq_information_jmi );
1089         _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1090         _tools_menu
1091                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1092         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1093         _obtain_detailed_taxonomic_information_jmi
1094                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1095         _tools_menu
1096                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1097         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1098         _obtain_detailed_taxonomic_information_deleting_jmi
1099                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1100         _tools_menu.addSeparator();
1101         _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
1102         customizeJMenuItem( _read_values_jmi );
1103         _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
1104         _jmenubar.add( _tools_menu );
1105         _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
1106         customizeJMenuItem( _read_seqs_jmi );
1107         _read_seqs_jmi
1108                 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
1109         _jmenubar.add( _tools_menu );
1110     }
1111
1112     @Override
1113     void close() {
1114         if ( isUnsavedDataPresent() ) {
1115             final int r = JOptionPane.showConfirmDialog( this,
1116                                                          "Exit despite potentially unsaved changes?",
1117                                                          "Exit?",
1118                                                          JOptionPane.YES_NO_OPTION );
1119             if ( r != JOptionPane.YES_OPTION ) {
1120                 return;
1121             }
1122         }
1123         exit();
1124     }
1125
1126     void executeLineageInference() {
1127         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1128             return;
1129         }
1130         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1131             JOptionPane.showMessageDialog( this,
1132                                            "Phylogeny is not rooted.",
1133                                            "Cannot infer ancestral taxonomies",
1134                                            JOptionPane.ERROR_MESSAGE );
1135             return;
1136         }
1137         final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1138                                                                                   _mainpanel.getCurrentTreePanel(),
1139                                                                                   _mainpanel.getCurrentPhylogeny()
1140                                                                                           .copy() );
1141         new Thread( inferrer ).start();
1142     }
1143
1144     void exit() {
1145         removeAllTextFrames();
1146         _mainpanel.terminate();
1147         _contentpane.removeAll();
1148         setVisible( false );
1149         dispose();
1150         System.exit( 0 );
1151     }
1152
1153     @Override
1154     void readPhylogeniesFromURL() {
1155         URL url = null;
1156         Phylogeny[] phys = null;
1157         final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1158         final String url_string = JOptionPane.showInputDialog( this,
1159                                                                message,
1160                                                                "Use URL/webservice to obtain a phylogeny",
1161                                                                JOptionPane.QUESTION_MESSAGE );
1162         boolean nhx_or_nexus = false;
1163         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1164             try {
1165                 url = new URL( url_string );
1166                 PhylogenyParser parser = null;
1167                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1168                     parser = new TolParser();
1169                 }
1170                 else {
1171                     parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1172                             .isValidatePhyloXmlAgainstSchema() );
1173                 }
1174                 if ( parser instanceof NexusPhylogeniesParser ) {
1175                     nhx_or_nexus = true;
1176                 }
1177                 else if ( parser instanceof NHXParser ) {
1178                     nhx_or_nexus = true;
1179                 }
1180                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1181                     _mainpanel.getCurrentTreePanel().setWaitCursor();
1182                 }
1183                 else {
1184                     _mainpanel.setWaitCursor();
1185                 }
1186                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1187                 phys = factory.create( url.openStream(), parser );
1188             }
1189             catch ( final MalformedURLException e ) {
1190                 JOptionPane.showMessageDialog( this,
1191                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1192                                                "Malformed URL",
1193                                                JOptionPane.ERROR_MESSAGE );
1194             }
1195             catch ( final IOException e ) {
1196                 JOptionPane.showMessageDialog( this,
1197                                                "Could not read from " + url + "\n"
1198                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1199                                                "Failed to read URL",
1200                                                JOptionPane.ERROR_MESSAGE );
1201             }
1202             catch ( final Exception e ) {
1203                 JOptionPane.showMessageDialog( this,
1204                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1205                                                "Unexpected Exception",
1206                                                JOptionPane.ERROR_MESSAGE );
1207             }
1208             finally {
1209                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1210                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1211                 }
1212                 else {
1213                     _mainpanel.setArrowCursor();
1214                 }
1215             }
1216             if ( ( phys != null ) && ( phys.length > 0 ) ) {
1217                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1218                     for( final Phylogeny phy : phys ) {
1219                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1220                     }
1221                 }
1222                 AptxUtil.addPhylogeniesToTabs( phys,
1223                                                new File( url.getFile() ).getName(),
1224                                                new File( url.getFile() ).toString(),
1225                                                getConfiguration(),
1226                                                getMainPanel() );
1227                 _mainpanel.getControlPanel().showWhole();
1228             }
1229         }
1230         activateSaveAllIfNeeded();
1231         System.gc();
1232     }
1233
1234     void setMsa( final Msa msa ) {
1235         _msa = msa;
1236     }
1237
1238     void setMsaFile( final File msa_file ) {
1239         _msa_file = msa_file;
1240     }
1241
1242     void setSeqs( final List<Sequence> seqs ) {
1243         _seqs = seqs;
1244     }
1245
1246     void setSeqsFile( final File seqs_file ) {
1247         _seqs_file = seqs_file;
1248     }
1249
1250     void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1251         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1252                                                                     _mainpanel.getCurrentTreePanel().getHeight(),
1253                                                                     true );
1254         String file_written_to = "";
1255         boolean error = false;
1256         try {
1257             file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1258                                                                      _mainpanel.getCurrentTreePanel().getWidth(),
1259                                                                      _mainpanel.getCurrentTreePanel().getHeight(),
1260                                                                      _mainpanel.getCurrentTreePanel(),
1261                                                                      _mainpanel.getControlPanel(),
1262                                                                      type,
1263                                                                      getOptions() );
1264         }
1265         catch ( final IOException e ) {
1266             error = true;
1267             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1268         }
1269         if ( !error ) {
1270             if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1271                 JOptionPane.showMessageDialog( this,
1272                                                "Wrote image to: " + file_written_to,
1273                                                "Graphics Export",
1274                                                JOptionPane.INFORMATION_MESSAGE );
1275             }
1276             else {
1277                 JOptionPane.showMessageDialog( this,
1278                                                "There was an unknown problem when attempting to write to an image file: \""
1279                                                        + file_name + "\"",
1280                                                "Error",
1281                                                JOptionPane.ERROR_MESSAGE );
1282             }
1283         }
1284         _contentpane.repaint();
1285     }
1286
1287     private void addExpressionValuesFromFile() {
1288         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1289             JOptionPane.showMessageDialog( this,
1290                                            "Need to load evolutionary tree first",
1291                                            "Can Not Read Expression Values",
1292                                            JOptionPane.WARNING_MESSAGE );
1293             return;
1294         }
1295         final File my_dir = getCurrentDir();
1296         if ( my_dir != null ) {
1297             _values_filechooser.setCurrentDirectory( my_dir );
1298         }
1299         final int result = _values_filechooser.showOpenDialog( _contentpane );
1300         final File file = _values_filechooser.getSelectedFile();
1301         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1302             BasicTable<String> t = null;
1303             try {
1304                 t = BasicTableParser.parse( file, '\t' );
1305                 if ( t.getNumberOfColumns() < 2 ) {
1306                     t = BasicTableParser.parse( file, ',' );
1307                 }
1308                 if ( t.getNumberOfColumns() < 2 ) {
1309                     t = BasicTableParser.parse( file, ' ' );
1310                 }
1311             }
1312             catch ( final IOException e ) {
1313                 JOptionPane.showMessageDialog( this,
1314                                                e.getMessage(),
1315                                                "Could Not Read Expression Value Table",
1316                                                JOptionPane.ERROR_MESSAGE );
1317                 return;
1318             }
1319             if ( t.getNumberOfColumns() < 2 ) {
1320                 JOptionPane.showMessageDialog( this,
1321                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
1322                                                "Problem with Expression Value Table",
1323                                                JOptionPane.ERROR_MESSAGE );
1324                 return;
1325             }
1326             if ( t.getNumberOfRows() < 1 ) {
1327                 JOptionPane.showMessageDialog( this,
1328                                                "Table contains zero rows",
1329                                                "Problem with Expression Value Table",
1330                                                JOptionPane.ERROR_MESSAGE );
1331                 return;
1332             }
1333             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1334             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1335                 JOptionPane.showMessageDialog( this,
1336                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1337                                                        + phy.getNumberOfExternalNodes() + " external nodes",
1338                                                "Warning",
1339                                                JOptionPane.WARNING_MESSAGE );
1340             }
1341             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1342             int not_found = 0;
1343             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1344                 final PhylogenyNode node = iter.next();
1345                 final String node_name = node.getName();
1346                 if ( !ForesterUtil.isEmpty( node_name ) ) {
1347                     int row = -1;
1348                     try {
1349                         row = t.findRow( node_name );
1350                     }
1351                     catch ( final IllegalArgumentException e ) {
1352                         JOptionPane
1353                                 .showMessageDialog( this,
1354                                                     e.getMessage(),
1355                                                     "Error Mapping Node Identifiers to Expression Value Identifiers",
1356                                                     JOptionPane.ERROR_MESSAGE );
1357                         return;
1358                     }
1359                     if ( row < 0 ) {
1360                         if ( node.isExternal() ) {
1361                             not_found++;
1362                         }
1363                         continue;
1364                     }
1365                     final List<Double> l = new ArrayList<Double>();
1366                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1367                         double d = -100;
1368                         try {
1369                             d = Double.parseDouble( t.getValueAsString( col, row ) );
1370                         }
1371                         catch ( final NumberFormatException e ) {
1372                             JOptionPane.showMessageDialog( this,
1373                                                            "Could not parse \"" + t.getValueAsString( col, row )
1374                                                                    + "\" into a decimal value",
1375                                                            "Issue with Expression Value Table",
1376                                                            JOptionPane.ERROR_MESSAGE );
1377                             return;
1378                         }
1379                         stats.addValue( d );
1380                         l.add( d );
1381                     }
1382                     if ( !l.isEmpty() ) {
1383                         if ( node.getNodeData().getProperties() != null ) {
1384                             node.getNodeData().getProperties()
1385                                     .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1386                         }
1387                         node.getNodeData().setVector( l );
1388                     }
1389                 }
1390             }
1391             if ( not_found > 0 ) {
1392                 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1393                         + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1394             }
1395             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1396         }
1397     }
1398
1399     private void addSequencesFromFile() {
1400         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1401             JOptionPane.showMessageDialog( this,
1402                                            "Need to load evolutionary tree first",
1403                                            "Can Not Read Sequences",
1404                                            JOptionPane.WARNING_MESSAGE );
1405             return;
1406         }
1407         final File my_dir = getCurrentDir();
1408         if ( my_dir != null ) {
1409             _sequences_filechooser.setCurrentDirectory( my_dir );
1410         }
1411         final int result = _sequences_filechooser.showOpenDialog( _contentpane );
1412         final File file = _sequences_filechooser.getSelectedFile();
1413         List<Sequence> seqs = null;
1414         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1415             try {
1416                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1417                     seqs = FastaParser.parse( new FileInputStream( file ) );
1418                 }
1419                 else {
1420                     JOptionPane.showMessageDialog( this,
1421                                                    "Format does not appear to be Fasta",
1422                                                    "Multiple sequence file format error",
1423                                                    JOptionPane.ERROR_MESSAGE );
1424                     return;
1425                 }
1426             }
1427             catch ( final MsaFormatException e ) {
1428                 setArrowCursor();
1429                 JOptionPane.showMessageDialog( this,
1430                                                e.getLocalizedMessage(),
1431                                                "Multiple sequence file format error",
1432                                                JOptionPane.ERROR_MESSAGE );
1433                 return;
1434             }
1435             catch ( final IOException e ) {
1436                 setArrowCursor();
1437                 JOptionPane.showMessageDialog( this,
1438                                                e.getLocalizedMessage(),
1439                                                "Failed to read multiple sequence file",
1440                                                JOptionPane.ERROR_MESSAGE );
1441                 return;
1442             }
1443             catch ( final Exception e ) {
1444                 setArrowCursor();
1445                 e.printStackTrace();
1446                 JOptionPane.showMessageDialog( this,
1447                                                e.getLocalizedMessage(),
1448                                                "Unexpected error during reading of multiple sequence file",
1449                                                JOptionPane.ERROR_MESSAGE );
1450                 return;
1451             }
1452             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1453                 JOptionPane.showMessageDialog( this,
1454                                                "Multiple sequence file is empty",
1455                                                "Empty multiple sequence file",
1456                                                JOptionPane.ERROR_MESSAGE );
1457                 setArrowCursor();
1458                 return;
1459             }
1460         }
1461         if ( seqs != null ) {
1462             for( final Sequence seq : seqs ) {
1463                 System.out.println( seq.getIdentifier() );
1464             }
1465             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1466             int total_counter = 0;
1467             int attached_counter = 0;
1468             for( final Sequence seq : seqs ) {
1469                 ++total_counter;
1470                 final String seq_name = seq.getIdentifier();
1471                 if ( !ForesterUtil.isEmpty( seq_name ) ) {
1472                     List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
1473                     if ( nodes.isEmpty() ) {
1474                         nodes = phy.getNodesViaSequenceSymbol( seq_name );
1475                     }
1476                     if ( nodes.isEmpty() ) {
1477                         nodes = phy.getNodesViaGeneName( seq_name );
1478                     }
1479                     if ( nodes.isEmpty() ) {
1480                         nodes = phy.getNodes( seq_name );
1481                     }
1482                     if ( nodes.size() > 1 ) {
1483                         JOptionPane.showMessageDialog( this,
1484                                                        "Sequence name \"" + seq_name + "\" is not unique",
1485                                                        "Sequence name not unique",
1486                                                        JOptionPane.ERROR_MESSAGE );
1487                         setArrowCursor();
1488                         return;
1489                     }
1490                     final String[] a = seq_name.split( "\\s" );
1491                     if ( nodes.isEmpty() && ( a.length > 1 ) ) {
1492                         final String seq_name_split = a[ 0 ];
1493                         nodes = phy.getNodesViaSequenceName( seq_name_split );
1494                         if ( nodes.isEmpty() ) {
1495                             nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
1496                         }
1497                         if ( nodes.isEmpty() ) {
1498                             nodes = phy.getNodes( seq_name_split );
1499                         }
1500                         if ( nodes.size() > 1 ) {
1501                             JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
1502                                     + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
1503                             setArrowCursor();
1504                             return;
1505                         }
1506                     }
1507                     if ( nodes.size() == 1 ) {
1508                         ++attached_counter;
1509                         final PhylogenyNode n = nodes.get( 0 );
1510                         if ( !n.getNodeData().isHasSequence() ) {
1511                             n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
1512                         }
1513                         n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
1514                         if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
1515                             n.getNodeData().getSequence().setName( seq_name );
1516                         }
1517                     }
1518                 }
1519             }
1520             if ( attached_counter > 0 ) {
1521                 int ext_nodes = 0;
1522                 int ext_nodes_with_seq = 0;
1523                 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
1524                     ++ext_nodes;
1525                     final PhylogenyNode n = iter.next();
1526                     if ( n.getNodeData().isHasSequence()
1527                             && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
1528                         ++ext_nodes_with_seq;
1529                     }
1530                 }
1531                 final String s;
1532                 if ( ext_nodes == ext_nodes_with_seq ) {
1533                     s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
1534                 }
1535                 else {
1536                     s = ext_nodes_with_seq + " out of " + ext_nodes
1537                             + " external nodes now have a molecular sequence attached to them.";
1538                 }
1539                 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
1540                     JOptionPane.showMessageDialog( this,
1541                                                    "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
1542                                                    "All sequences attached",
1543                                                    JOptionPane.INFORMATION_MESSAGE );
1544                 }
1545                 else {
1546                     JOptionPane.showMessageDialog( this, "Attached " + attached_counter
1547                             + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
1548                             + " sequences attached", JOptionPane.WARNING_MESSAGE );
1549                 }
1550             }
1551             else {
1552                 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
1553                         + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
1554             }
1555         }
1556     }
1557
1558     private void choosePdfWidth() {
1559         final String s = ( String ) JOptionPane.showInputDialog( this,
1560                                                                  "Please enter the default line width for PDF export.\n"
1561                                                                          + "[current value: "
1562                                                                          + getOptions().getPrintLineWidth() + "]\n",
1563                                                                  "Line Width for PDF Export",
1564                                                                  JOptionPane.QUESTION_MESSAGE,
1565                                                                  null,
1566                                                                  null,
1567                                                                  getOptions().getPrintLineWidth() );
1568         if ( !ForesterUtil.isEmpty( s ) ) {
1569             boolean success = true;
1570             float f = 0.0f;
1571             final String m_str = s.trim();
1572             if ( !ForesterUtil.isEmpty( m_str ) ) {
1573                 try {
1574                     f = Float.parseFloat( m_str );
1575                 }
1576                 catch ( final Exception ex ) {
1577                     success = false;
1578                 }
1579             }
1580             else {
1581                 success = false;
1582             }
1583             if ( success && ( f > 0.0 ) ) {
1584                 getOptions().setPrintLineWidth( f );
1585             }
1586         }
1587     }
1588
1589     private void choosePrintSize() {
1590         final String s = ( String ) JOptionPane.showInputDialog( this,
1591                                                                  "Please enter values for width and height,\nseparated by a comma.\n"
1592                                                                          + "[current values: "
1593                                                                          + getOptions().getPrintSizeX() + ", "
1594                                                                          + getOptions().getPrintSizeY() + "]\n"
1595                                                                          + "[A4: " + Constants.A4_SIZE_X + ", "
1596                                                                          + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1597                                                                          + Constants.US_LETTER_SIZE_X + ", "
1598                                                                          + Constants.US_LETTER_SIZE_Y + "]",
1599                                                                  "Default Size for Graphics Export",
1600                                                                  JOptionPane.QUESTION_MESSAGE,
1601                                                                  null,
1602                                                                  null,
1603                                                                  getOptions().getPrintSizeX() + ", "
1604                                                                          + getOptions().getPrintSizeY() );
1605         if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1606             boolean success = true;
1607             int x = 0;
1608             int y = 0;
1609             final String[] str_ary = s.split( "," );
1610             if ( str_ary.length == 2 ) {
1611                 final String x_str = str_ary[ 0 ].trim();
1612                 final String y_str = str_ary[ 1 ].trim();
1613                 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1614                     try {
1615                         x = Integer.parseInt( x_str );
1616                         y = Integer.parseInt( y_str );
1617                     }
1618                     catch ( final Exception ex ) {
1619                         success = false;
1620                     }
1621                 }
1622                 else {
1623                     success = false;
1624                 }
1625             }
1626             else {
1627                 success = false;
1628             }
1629             if ( success && ( x > 1 ) && ( y > 1 ) ) {
1630                 getOptions().setPrintSizeX( x );
1631                 getOptions().setPrintSizeY( y );
1632             }
1633         }
1634     }
1635
1636     private void closeCurrentPane() {
1637         if ( getMainPanel().getCurrentTreePanel() != null ) {
1638             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1639                 final int r = JOptionPane.showConfirmDialog( this,
1640                                                              "Close tab despite potentially unsaved changes?",
1641                                                              "Close Tab?",
1642                                                              JOptionPane.YES_NO_OPTION );
1643                 if ( r != JOptionPane.YES_OPTION ) {
1644                     return;
1645                 }
1646             }
1647             getMainPanel().closeCurrentPane();
1648             activateSaveAllIfNeeded();
1649         }
1650     }
1651
1652     private void collapse( final Phylogeny phy, final double m ) {
1653         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1654         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1655         double min_support = Double.MAX_VALUE;
1656         boolean conf_present = false;
1657         while ( it.hasNext() ) {
1658             final PhylogenyNode n = it.next();
1659             if ( !n.isExternal() && !n.isRoot() ) {
1660                 final List<Confidence> c = n.getBranchData().getConfidences();
1661                 if ( ( c != null ) && ( c.size() > 0 ) ) {
1662                     conf_present = true;
1663                     double max = 0;
1664                     for( final Confidence confidence : c ) {
1665                         if ( confidence.getValue() > max ) {
1666                             max = confidence.getValue();
1667                         }
1668                     }
1669                     if ( max < getMinNotCollapseConfidenceValue() ) {
1670                         to_be_removed.add( n );
1671                     }
1672                     if ( max < min_support ) {
1673                         min_support = max;
1674                     }
1675                 }
1676             }
1677         }
1678         if ( conf_present ) {
1679             for( final PhylogenyNode node : to_be_removed ) {
1680                 PhylogenyMethods.removeNode( node, phy );
1681             }
1682             if ( to_be_removed.size() > 0 ) {
1683                 phy.externalNodesHaveChanged();
1684                 phy.clearHashIdToNodeMap();
1685                 phy.recalculateNumberOfExternalDescendants( true );
1686                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1687                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1688                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1689                 getCurrentTreePanel().setNodeInPreorderToNull();
1690                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1691                 getCurrentTreePanel().resetPreferredSize();
1692                 getCurrentTreePanel().setEdited( true );
1693                 getCurrentTreePanel().repaint();
1694                 repaint();
1695             }
1696             if ( to_be_removed.size() > 0 ) {
1697                 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1698                         + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1699                         + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1700             }
1701             else {
1702                 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1703                         + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1704             }
1705         }
1706         else {
1707             JOptionPane.showMessageDialog( this,
1708                                            "No branch collapsed because no confidence values present",
1709                                            "No confidence values present",
1710                                            JOptionPane.INFORMATION_MESSAGE );
1711         }
1712     }
1713
1714     private void collapseBelowThreshold() {
1715         if ( getCurrentTreePanel() != null ) {
1716             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1717             if ( ( phy != null ) && !phy.isEmpty() ) {
1718                 final String s = ( String ) JOptionPane.showInputDialog( this,
1719                                                                          "Please enter the minimum confidence value\n",
1720                                                                          "Minimal Confidence Value",
1721                                                                          JOptionPane.QUESTION_MESSAGE,
1722                                                                          null,
1723                                                                          null,
1724                                                                          getMinNotCollapseConfidenceValue() );
1725                 if ( !ForesterUtil.isEmpty( s ) ) {
1726                     boolean success = true;
1727                     double m = 0.0;
1728                     final String m_str = s.trim();
1729                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1730                         try {
1731                             m = Double.parseDouble( m_str );
1732                         }
1733                         catch ( final Exception ex ) {
1734                             success = false;
1735                         }
1736                     }
1737                     else {
1738                         success = false;
1739                     }
1740                     if ( success && ( m >= 0.0 ) ) {
1741                         setMinNotCollapseConfidenceValue( m );
1742                         collapse( phy, m );
1743                     }
1744                 }
1745             }
1746         }
1747     }
1748
1749     private PhyloXmlParser createPhyloXmlParser() {
1750         PhyloXmlParser xml_parser = null;
1751         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1752             try {
1753                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1754             }
1755             catch ( final Exception e ) {
1756                 JOptionPane.showMessageDialog( this,
1757                                                e.getLocalizedMessage(),
1758                                                "failed to create validating XML parser",
1759                                                JOptionPane.WARNING_MESSAGE );
1760             }
1761         }
1762         if ( xml_parser == null ) {
1763             xml_parser = PhyloXmlParser.createPhyloXmlParser();
1764         }
1765         return xml_parser;
1766     }
1767
1768     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1769         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1770                                                                       getPhylogeneticInferenceOptions(),
1771                                                                       from_unaligned_seqs );
1772         dialog.activate();
1773         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1774             if ( !from_unaligned_seqs ) {
1775                 if ( getMsa() != null ) {
1776                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1777                                                                                     getPhylogeneticInferenceOptions()
1778                                                                                             .copy(), this );
1779                     new Thread( inferrer ).start();
1780                 }
1781                 else {
1782                     JOptionPane.showMessageDialog( this,
1783                                                    "No multiple sequence alignment selected",
1784                                                    "Phylogenetic Inference Not Launched",
1785                                                    JOptionPane.WARNING_MESSAGE );
1786                 }
1787             }
1788             else {
1789                 if ( getSeqs() != null ) {
1790                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1791                                                                                     getPhylogeneticInferenceOptions()
1792                                                                                             .copy(), this );
1793                     new Thread( inferrer ).start();
1794                 }
1795                 else {
1796                     JOptionPane.showMessageDialog( this,
1797                                                    "No input sequences selected",
1798                                                    "Phylogenetic Inference Not Launched",
1799                                                    JOptionPane.WARNING_MESSAGE );
1800                 }
1801             }
1802         }
1803     }
1804
1805     private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1806         final StringBuilder sb = new StringBuilder();
1807         final StringBuilder sb_failed = new StringBuilder();
1808         int counter = 0;
1809         int counter_failed = 0;
1810         if ( getCurrentTreePanel() != null ) {
1811             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1812             if ( ( phy != null ) && !phy.isEmpty() ) {
1813                 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1814                 while ( it.hasNext() ) {
1815                     final PhylogenyNode n = it.next();
1816                     final String name = n.getName().trim();
1817                     if ( !ForesterUtil.isEmpty( name ) ) {
1818                         final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
1819                                                                                        TAXONOMY_EXTRACTION.AGGRESSIVE );
1820                         if ( !ForesterUtil.isEmpty( nt ) ) {
1821                             if ( counter < 15 ) {
1822                                 sb.append( name + ": " + nt + "\n" );
1823                             }
1824                             else if ( counter == 15 ) {
1825                                 sb.append( "...\n" );
1826                             }
1827                             counter++;
1828                         }
1829                         else {
1830                             if ( counter_failed < 15 ) {
1831                                 sb_failed.append( name + "\n" );
1832                             }
1833                             else if ( counter_failed == 15 ) {
1834                                 sb_failed.append( "...\n" );
1835                             }
1836                             counter_failed++;
1837                         }
1838                     }
1839                 }
1840                 if ( counter > 0 ) {
1841                     String failed = "";
1842                     String all = "all ";
1843                     if ( counter_failed > 0 ) {
1844                         all = "";
1845                         failed = "\nCould not extract taxonomic data for " + counter_failed
1846                                 + " named external nodes:\n" + sb_failed;
1847                     }
1848                     JOptionPane.showMessageDialog( this,
1849                                                    "Extracted taxonomic data from " + all + counter
1850                                                            + " named external nodes:\n" + sb.toString() + failed,
1851                                                    "Taxonomic Data Extraction Completed",
1852                                                    counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1853                                                            : JOptionPane.INFORMATION_MESSAGE );
1854                 }
1855                 else {
1856                     JOptionPane
1857                             .showMessageDialog( this,
1858                                                 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1859                                                         + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1860                                                         + "or nodes already have taxonomic data?\n",
1861                                                 "No Taxonomic Data Extracted",
1862                                                 JOptionPane.ERROR_MESSAGE );
1863                 }
1864             }
1865         }
1866     }
1867
1868     private ControlPanel getControlPanel() {
1869         return getMainPanel().getControlPanel();
1870     }
1871
1872     private File getCurrentDir() {
1873         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1874             if ( ForesterUtil.isWindows() ) {
1875                 try {
1876                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1877                 }
1878                 catch ( final Exception e ) {
1879                     _current_dir = null;
1880                 }
1881             }
1882         }
1883         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1884             if ( System.getProperty( "user.home" ) != null ) {
1885                 _current_dir = new File( System.getProperty( "user.home" ) );
1886             }
1887             else if ( System.getProperty( "user.dir" ) != null ) {
1888                 _current_dir = new File( System.getProperty( "user.dir" ) );
1889             }
1890         }
1891         return _current_dir;
1892     }
1893
1894     private double getMinNotCollapseConfidenceValue() {
1895         return _min_not_collapse;
1896     }
1897
1898     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1899         if ( _phylogenetic_inference_options == null ) {
1900             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1901         }
1902         return _phylogenetic_inference_options;
1903     }
1904
1905     private boolean isUnsavedDataPresent() {
1906         final List<TreePanel> tps = getMainPanel().getTreePanels();
1907         for( final TreePanel tp : tps ) {
1908             if ( tp.isEdited() ) {
1909                 return true;
1910             }
1911         }
1912         return false;
1913     }
1914
1915     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1916         if ( getCurrentTreePanel() != null ) {
1917             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1918             if ( ( phy != null ) && !phy.isEmpty() ) {
1919                 PhylogenyMethods
1920                         .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1921             }
1922         }
1923     }
1924
1925     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1926         if ( getCurrentTreePanel() != null ) {
1927             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1928             if ( ( phy != null ) && !phy.isEmpty() ) {
1929                 PhylogenyMethods.transferNodeNameToField( phy,
1930                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1931                                                           false );
1932             }
1933         }
1934     }
1935
1936     private void newTree() {
1937         final Phylogeny[] phys = new Phylogeny[ 1 ];
1938         final Phylogeny phy = new Phylogeny();
1939         final PhylogenyNode node = new PhylogenyNode();
1940         phy.setRoot( node );
1941         phy.setRooted( true );
1942         phys[ 0 ] = phy;
1943         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1944         _mainpanel.getControlPanel().showWhole();
1945         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1946         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1947         if ( getMainPanel().getMainFrame() == null ) {
1948             // Must be "E" applet version.
1949             ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1950                     .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1951         }
1952         else {
1953             getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1954         }
1955         activateSaveAllIfNeeded();
1956         System.gc();
1957     }
1958
1959     private void obtainDetailedTaxonomicInformation() {
1960         if ( getCurrentTreePanel() != null ) {
1961             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1962             if ( ( phy != null ) && !phy.isEmpty() ) {
1963                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1964                                                                        _mainpanel.getCurrentTreePanel(),
1965                                                                        phy.copy(),
1966                                                                        false,
1967                                                                        true );
1968                 new Thread( t ).start();
1969             }
1970         }
1971     }
1972
1973     private void obtainDetailedTaxonomicInformationDelete() {
1974         if ( getCurrentTreePanel() != null ) {
1975             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1976             if ( ( phy != null ) && !phy.isEmpty() ) {
1977                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1978                                                                        _mainpanel.getCurrentTreePanel(),
1979                                                                        phy.copy(),
1980                                                                        true,
1981                                                                        true );
1982                 new Thread( t ).start();
1983             }
1984         }
1985     }
1986
1987     private void obtainSequenceInformation() {
1988         if ( getCurrentTreePanel() != null ) {
1989             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1990             if ( ( phy != null ) && !phy.isEmpty() ) {
1991                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1992                                                                          _mainpanel.getCurrentTreePanel(),
1993                                                                          phy.copy() );
1994                 new Thread( u ).start();
1995             }
1996         }
1997     }
1998
1999     private void print() {
2000         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2001                 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2002             return;
2003         }
2004         if ( !getOptions().isPrintUsingActualSize() ) {
2005             getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
2006                                                              getOptions().getPrintSizeY() - 140,
2007                                                              true );
2008             getCurrentTreePanel().resetPreferredSize();
2009             getCurrentTreePanel().repaint();
2010         }
2011         final String job_name = Constants.PRG_NAME;
2012         boolean error = false;
2013         String printer_name = null;
2014         try {
2015             printer_name = Printer.print( getCurrentTreePanel(), job_name );
2016         }
2017         catch ( final Exception e ) {
2018             error = true;
2019             JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2020         }
2021         if ( !error && ( printer_name != null ) ) {
2022             String msg = "Printing data sent to printer";
2023             if ( printer_name.length() > 1 ) {
2024                 msg += " [" + printer_name + "]";
2025             }
2026             JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2027         }
2028         if ( !getOptions().isPrintUsingActualSize() ) {
2029             getControlPanel().showWhole();
2030         }
2031     }
2032
2033     private void printPhylogenyToPdf( final String file_name ) {
2034         if ( !getOptions().isPrintUsingActualSize() ) {
2035             getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
2036                                                              getOptions().getPrintSizeY(),
2037                                                              true );
2038             getCurrentTreePanel().resetPreferredSize();
2039             getCurrentTreePanel().repaint();
2040         }
2041         String pdf_written_to = "";
2042         boolean error = false;
2043         try {
2044             if ( getOptions().isPrintUsingActualSize() ) {
2045                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2046                                                                   getCurrentTreePanel(),
2047                                                                   getCurrentTreePanel().getWidth(),
2048                                                                   getCurrentTreePanel().getHeight() );
2049             }
2050             else {
2051                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2052                         .getPrintSizeX(), getOptions().getPrintSizeY() );
2053             }
2054         }
2055         catch ( final IOException e ) {
2056             error = true;
2057             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2058         }
2059         if ( !error ) {
2060             if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2061                 JOptionPane.showMessageDialog( this,
2062                                                "Wrote PDF to: " + pdf_written_to,
2063                                                "Information",
2064                                                JOptionPane.INFORMATION_MESSAGE );
2065             }
2066             else {
2067                 JOptionPane.showMessageDialog( this,
2068                                                "There was an unknown problem when attempting to write to PDF file: \""
2069                                                        + file_name + "\"",
2070                                                "Error",
2071                                                JOptionPane.ERROR_MESSAGE );
2072             }
2073         }
2074         if ( !getOptions().isPrintUsingActualSize() ) {
2075             getControlPanel().showWhole();
2076         }
2077     }
2078
2079     private void readPhylogeniesFromFile() {
2080         boolean exception = false;
2081         Phylogeny[] phys = null;
2082         // Set an initial directory if none set yet
2083         final File my_dir = getCurrentDir();
2084         _open_filechooser.setMultiSelectionEnabled( true );
2085         // Open file-open dialog and set current directory
2086         if ( my_dir != null ) {
2087             _open_filechooser.setCurrentDirectory( my_dir );
2088         }
2089         final int result = _open_filechooser.showOpenDialog( _contentpane );
2090         // All done: get the file
2091         final File[] files = _open_filechooser.getSelectedFiles();
2092         setCurrentDir( _open_filechooser.getCurrentDirectory() );
2093         boolean nhx_or_nexus = false;
2094         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2095             for( final File file : files ) {
2096                 if ( ( file != null ) && !file.isDirectory() ) {
2097                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2098                         _mainpanel.getCurrentTreePanel().setWaitCursor();
2099                     }
2100                     else {
2101                         _mainpanel.setWaitCursor();
2102                     }
2103                     if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2104                             || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2105                         try {
2106                             final NHXParser nhx = new NHXParser();
2107                             setSpecialOptionsForNhxParser( nhx );
2108                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
2109                             nhx_or_nexus = true;
2110                         }
2111                         catch ( final Exception e ) {
2112                             exception = true;
2113                             exceptionOccuredDuringOpenFile( e );
2114                         }
2115                     }
2116                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2117                         warnIfNotPhyloXmlValidation( getConfiguration() );
2118                         try {
2119                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
2120                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2121                         }
2122                         catch ( final Exception e ) {
2123                             exception = true;
2124                             exceptionOccuredDuringOpenFile( e );
2125                         }
2126                     }
2127                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2128                         try {
2129                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2130                         }
2131                         catch ( final Exception e ) {
2132                             exception = true;
2133                             exceptionOccuredDuringOpenFile( e );
2134                         }
2135                     }
2136                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2137                         try {
2138                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2139                             setSpecialOptionsForNexParser( nex );
2140                             phys = PhylogenyMethods.readPhylogenies( nex, file );
2141                             nhx_or_nexus = true;
2142                         }
2143                         catch ( final Exception e ) {
2144                             exception = true;
2145                             exceptionOccuredDuringOpenFile( e );
2146                         }
2147                     }
2148                     // "*.*":
2149                     else {
2150                         try {
2151                             final PhylogenyParser parser = ParserUtils
2152                                     .createParserDependingOnFileType( file, getConfiguration()
2153                                             .isValidatePhyloXmlAgainstSchema() );
2154                             if ( parser instanceof NexusPhylogeniesParser ) {
2155                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2156                                 setSpecialOptionsForNexParser( nex );
2157                                 nhx_or_nexus = true;
2158                             }
2159                             else if ( parser instanceof NHXParser ) {
2160                                 final NHXParser nhx = ( NHXParser ) parser;
2161                                 setSpecialOptionsForNhxParser( nhx );
2162                                 nhx_or_nexus = true;
2163                             }
2164                             else if ( parser instanceof PhyloXmlParser ) {
2165                                 warnIfNotPhyloXmlValidation( getConfiguration() );
2166                             }
2167                             phys = PhylogenyMethods.readPhylogenies( parser, file );
2168                         }
2169                         catch ( final Exception e ) {
2170                             exception = true;
2171                             exceptionOccuredDuringOpenFile( e );
2172                         }
2173                     }
2174                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2175                         _mainpanel.getCurrentTreePanel().setArrowCursor();
2176                     }
2177                     else {
2178                         _mainpanel.setArrowCursor();
2179                     }
2180                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2181                         boolean one_desc = false;
2182                         if ( nhx_or_nexus ) {
2183                             for( final Phylogeny phy : phys ) {
2184                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2185                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2186                                 }
2187                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2188                                     one_desc = true;
2189                                     break;
2190                                 }
2191                             }
2192                         }
2193                         AptxUtil.addPhylogeniesToTabs( phys,
2194                                                        file.getName(),
2195                                                        file.getAbsolutePath(),
2196                                                        getConfiguration(),
2197                                                        getMainPanel() );
2198                         _mainpanel.getControlPanel().showWhole();
2199                         if ( nhx_or_nexus && one_desc ) {
2200                             JOptionPane
2201                                     .showMessageDialog( this,
2202                                                         "One or more trees contain (a) node(s) with one descendant, "
2203                                                                 + ForesterUtil.LINE_SEPARATOR
2204                                                                 + "possibly indicating illegal parentheses within node names.",
2205                                                         "Warning: Possible Error in New Hampshire Formatted Data",
2206                                                         JOptionPane.WARNING_MESSAGE );
2207                         }
2208                     }
2209                 }
2210             }
2211         }
2212         activateSaveAllIfNeeded();
2213         System.gc();
2214     }
2215
2216     private void readSpeciesTreeFromFile() {
2217         Phylogeny t = null;
2218         boolean exception = false;
2219         final File my_dir = getCurrentDir();
2220         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2221         if ( my_dir != null ) {
2222             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2223         }
2224         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2225         final File file = _open_filechooser_for_species_tree.getSelectedFile();
2226         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2227             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2228                 try {
2229                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
2230                             .createPhyloXmlParserXsdValidating(), file );
2231                     t = trees[ 0 ];
2232                 }
2233                 catch ( final Exception e ) {
2234                     exception = true;
2235                     exceptionOccuredDuringOpenFile( e );
2236                 }
2237             }
2238             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2239                 try {
2240                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2241                     t = trees[ 0 ];
2242                 }
2243                 catch ( final Exception e ) {
2244                     exception = true;
2245                     exceptionOccuredDuringOpenFile( e );
2246                 }
2247             }
2248             // "*.*":
2249             else {
2250                 try {
2251                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
2252                             .createPhyloXmlParserXsdValidating(), file );
2253                     t = trees[ 0 ];
2254                 }
2255                 catch ( final Exception e ) {
2256                     exception = true;
2257                     exceptionOccuredDuringOpenFile( e );
2258                 }
2259             }
2260             if ( !exception && ( t != null ) && !t.isRooted() ) {
2261                 exception = true;
2262                 t = null;
2263                 JOptionPane.showMessageDialog( this,
2264                                                "Species tree is not rooted",
2265                                                "Species tree not loaded",
2266                                                JOptionPane.ERROR_MESSAGE );
2267             }
2268             if ( !exception && ( t != null ) ) {
2269                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2270                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2271                     final PhylogenyNode node = it.next();
2272                     if ( !node.getNodeData().isHasTaxonomy() ) {
2273                         exception = true;
2274                         t = null;
2275                         JOptionPane
2276                                 .showMessageDialog( this,
2277                                                     "Species tree contains external node(s) without taxonomy information",
2278                                                     "Species tree not loaded",
2279                                                     JOptionPane.ERROR_MESSAGE );
2280                         break;
2281                     }
2282                     else {
2283                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2284                             exception = true;
2285                             t = null;
2286                             JOptionPane.showMessageDialog( this,
2287                                                            "Taxonomy ["
2288                                                                    + node.getNodeData().getTaxonomy().asSimpleText()
2289                                                                    + "] is not unique in species tree",
2290                                                            "Species tree not loaded",
2291                                                            JOptionPane.ERROR_MESSAGE );
2292                             break;
2293                         }
2294                         else {
2295                             tax_set.add( node.getNodeData().getTaxonomy() );
2296                         }
2297                     }
2298                 }
2299             }
2300             if ( !exception && ( t != null ) ) {
2301                 setSpeciesTree( t );
2302                 JOptionPane.showMessageDialog( this,
2303                                                "Species tree successfully loaded",
2304                                                "Species tree loaded",
2305                                                JOptionPane.INFORMATION_MESSAGE );
2306             }
2307             _contentpane.repaint();
2308             System.gc();
2309         }
2310     }
2311
2312     private void setArrowCursor() {
2313         try {
2314             _mainpanel.getCurrentTreePanel().setArrowCursor();
2315         }
2316         catch ( final Exception ex ) {
2317             // Do nothing.
2318         }
2319     }
2320
2321     private void setCurrentDir( final File current_dir ) {
2322         _current_dir = current_dir;
2323     }
2324
2325     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2326         _min_not_collapse = min_not_collapse;
2327     }
2328
2329     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2330         _phylogenetic_inference_options = phylogenetic_inference_options;
2331     }
2332
2333     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2334         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2335         nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2336     }
2337
2338     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2339         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2340         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2341     }
2342
2343     private void writeAllToFile() {
2344         if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2345             return;
2346         }
2347         final File my_dir = getCurrentDir();
2348         if ( my_dir != null ) {
2349             _save_filechooser.setCurrentDirectory( my_dir );
2350         }
2351         _save_filechooser.setSelectedFile( new File( "" ) );
2352         final int result = _save_filechooser.showSaveDialog( _contentpane );
2353         final File file = _save_filechooser.getSelectedFile();
2354         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2355         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2356             if ( file.exists() ) {
2357                 final int i = JOptionPane.showConfirmDialog( this,
2358                                                              file + " already exists. Overwrite?",
2359                                                              "Warning",
2360                                                              JOptionPane.OK_CANCEL_OPTION,
2361                                                              JOptionPane.WARNING_MESSAGE );
2362                 if ( i != JOptionPane.OK_OPTION ) {
2363                     return;
2364                 }
2365                 else {
2366                     try {
2367                         file.delete();
2368                     }
2369                     catch ( final Exception e ) {
2370                         JOptionPane.showMessageDialog( this,
2371                                                        "Failed to delete: " + file,
2372                                                        "Error",
2373                                                        JOptionPane.WARNING_MESSAGE );
2374                     }
2375                 }
2376             }
2377             final int count = getMainPanel().getTabbedPane().getTabCount();
2378             final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2379             for( int i = 0; i < count; ++i ) {
2380                 final Phylogeny phy = getMainPanel().getPhylogeny( i );
2381                 if ( ForesterUtil.isEmpty( phy.getName() )
2382                         && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
2383                     phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
2384                 }
2385                 trees.add( phy );
2386                 getMainPanel().getTreePanels().get( i ).setEdited( false );
2387             }
2388             final PhylogenyWriter writer = new PhylogenyWriter();
2389             try {
2390                 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2391             }
2392             catch ( final IOException e ) {
2393                 JOptionPane.showMessageDialog( this,
2394                                                "Failed to write to: " + file,
2395                                                "Error",
2396                                                JOptionPane.WARNING_MESSAGE );
2397             }
2398         }
2399     }
2400
2401     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2402         try {
2403             final PhylogenyWriter writer = new PhylogenyWriter();
2404             writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2405         }
2406         catch ( final Exception e ) {
2407             exception = true;
2408             exceptionOccuredDuringSaveAs( e );
2409         }
2410         return exception;
2411     }
2412
2413     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2414         try {
2415             final PhylogenyWriter writer = new PhylogenyWriter();
2416             writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2417         }
2418         catch ( final Exception e ) {
2419             exception = true;
2420             exceptionOccuredDuringSaveAs( e );
2421         }
2422         return exception;
2423     }
2424
2425     private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2426         try {
2427             final PhylogenyWriter writer = new PhylogenyWriter();
2428             writer.toPhyloXML( file, t, 0 );
2429         }
2430         catch ( final Exception e ) {
2431             exception = true;
2432             exceptionOccuredDuringSaveAs( e );
2433         }
2434         return exception;
2435     }
2436
2437     private void writeToFile( final Phylogeny t ) {
2438         if ( t == null ) {
2439             return;
2440         }
2441         String initial_filename = null;
2442         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2443             try {
2444                 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2445             }
2446             catch ( final IOException e ) {
2447                 initial_filename = null;
2448             }
2449         }
2450         if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2451             _save_filechooser.setSelectedFile( new File( initial_filename ) );
2452         }
2453         else {
2454             _save_filechooser.setSelectedFile( new File( "" ) );
2455         }
2456         final File my_dir = getCurrentDir();
2457         if ( my_dir != null ) {
2458             _save_filechooser.setCurrentDirectory( my_dir );
2459         }
2460         final int result = _save_filechooser.showSaveDialog( _contentpane );
2461         final File file = _save_filechooser.getSelectedFile();
2462         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2463         boolean exception = false;
2464         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2465             if ( file.exists() ) {
2466                 final int i = JOptionPane.showConfirmDialog( this,
2467                                                              file + " already exists.\nOverwrite?",
2468                                                              "Overwrite?",
2469                                                              JOptionPane.OK_CANCEL_OPTION,
2470                                                              JOptionPane.QUESTION_MESSAGE );
2471                 if ( i != JOptionPane.OK_OPTION ) {
2472                     return;
2473                 }
2474                 else {
2475                     final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2476                     try {
2477                         ForesterUtil.copyFile( file, to );
2478                     }
2479                     catch ( final Exception e ) {
2480                         JOptionPane.showMessageDialog( this,
2481                                                        "Failed to create backup copy " + to,
2482                                                        "Failed to Create Backup Copy",
2483                                                        JOptionPane.WARNING_MESSAGE );
2484                     }
2485                     try {
2486                         file.delete();
2487                     }
2488                     catch ( final Exception e ) {
2489                         JOptionPane.showMessageDialog( this,
2490                                                        "Failed to delete: " + file,
2491                                                        "Failed to Delete",
2492                                                        JOptionPane.WARNING_MESSAGE );
2493                     }
2494                 }
2495             }
2496             if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2497                 exception = writeAsNewHampshire( t, exception, file );
2498             }
2499             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2500                 exception = writeAsPhyloXml( t, exception, file );
2501             }
2502             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2503                 exception = writeAsNexus( t, exception, file );
2504             }
2505             // "*.*":
2506             else {
2507                 final String file_name = file.getName().trim().toLowerCase();
2508                 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2509                         || file_name.endsWith( ".tree" ) ) {
2510                     exception = writeAsNewHampshire( t, exception, file );
2511                 }
2512                 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2513                     exception = writeAsNexus( t, exception, file );
2514                 }
2515                 // XML is default:
2516                 else {
2517                     exception = writeAsPhyloXml( t, exception, file );
2518                 }
2519             }
2520             if ( !exception ) {
2521                 getMainPanel().setTitleOfSelectedTab( file.getName() );
2522                 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2523                 getMainPanel().getCurrentTreePanel().setEdited( false );
2524             }
2525         }
2526     }
2527
2528     private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2529         if ( ( t == null ) || t.isEmpty() ) {
2530             return;
2531         }
2532         String initial_filename = "";
2533         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2534             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2535         }
2536         if ( initial_filename.indexOf( '.' ) > 0 ) {
2537             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2538         }
2539         initial_filename = initial_filename + "." + type;
2540         _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2541         final File my_dir = getCurrentDir();
2542         if ( my_dir != null ) {
2543             _writetographics_filechooser.setCurrentDirectory( my_dir );
2544         }
2545         final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2546         File file = _writetographics_filechooser.getSelectedFile();
2547         setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2548         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2549             if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2550                 file = new File( file.toString() + "." + type );
2551             }
2552             if ( file.exists() ) {
2553                 final int i = JOptionPane.showConfirmDialog( this,
2554                                                              file + " already exists. Overwrite?",
2555                                                              "Warning",
2556                                                              JOptionPane.OK_CANCEL_OPTION,
2557                                                              JOptionPane.WARNING_MESSAGE );
2558                 if ( i != JOptionPane.OK_OPTION ) {
2559                     return;
2560                 }
2561                 else {
2562                     try {
2563                         file.delete();
2564                     }
2565                     catch ( final Exception e ) {
2566                         JOptionPane.showMessageDialog( this,
2567                                                        "Failed to delete: " + file,
2568                                                        "Error",
2569                                                        JOptionPane.WARNING_MESSAGE );
2570                     }
2571                 }
2572             }
2573             writePhylogenyToGraphicsFile( file.toString(), type );
2574         }
2575     }
2576
2577     private void writeToPdf( final Phylogeny t ) {
2578         if ( ( t == null ) || t.isEmpty() ) {
2579             return;
2580         }
2581         String initial_filename = "";
2582         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2583             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2584         }
2585         if ( initial_filename.indexOf( '.' ) > 0 ) {
2586             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2587         }
2588         initial_filename = initial_filename + ".pdf";
2589         _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2590         final File my_dir = getCurrentDir();
2591         if ( my_dir != null ) {
2592             _writetopdf_filechooser.setCurrentDirectory( my_dir );
2593         }
2594         final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2595         File file = _writetopdf_filechooser.getSelectedFile();
2596         setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2597         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2598             if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2599                 file = new File( file.toString() + ".pdf" );
2600             }
2601             if ( file.exists() ) {
2602                 final int i = JOptionPane.showConfirmDialog( this,
2603                                                              file + " already exists. Overwrite?",
2604                                                              "WARNING",
2605                                                              JOptionPane.OK_CANCEL_OPTION,
2606                                                              JOptionPane.WARNING_MESSAGE );
2607                 if ( i != JOptionPane.OK_OPTION ) {
2608                     return;
2609                 }
2610             }
2611             printPhylogenyToPdf( file.toString() );
2612         }
2613     }
2614
2615     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2616         return new MainFrameApplication( phys, config );
2617     }
2618
2619     public static MainFrame createInstance( final Phylogeny[] phys,
2620                                             final Configuration config,
2621                                             final String title,
2622                                             final File current_dir ) {
2623         return new MainFrameApplication( phys, config, title, current_dir );
2624     }
2625
2626     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2627         return new MainFrameApplication( phys, config, title );
2628     }
2629
2630     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2631         return new MainFrameApplication( phys, config_file_name, title );
2632     }
2633
2634     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2635         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2636                 + o.getPrintSizeY() + ")" );
2637     }
2638
2639     static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2640         mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2641     }
2642
2643     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2644         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2645             JOptionPane
2646                     .showMessageDialog( null,
2647                                         ForesterUtil
2648                                                 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2649                                                            80 ),
2650                                         "Warning",
2651                                         JOptionPane.WARNING_MESSAGE );
2652         }
2653     }
2654 } // MainFrameApplication.
2655
2656 class DefaultFilter extends FileFilter {
2657
2658     @Override
2659     public boolean accept( final File f ) {
2660         final String file_name = f.getName().trim().toLowerCase();
2661         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2662                 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2663                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2664                 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2665                 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2666                 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2667                 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2668                 || file_name.endsWith( ".con" ) || f.isDirectory();
2669     }
2670
2671     @Override
2672     public String getDescription() {
2673         return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2674     }
2675 }
2676
2677 class GraphicsFileFilter extends FileFilter {
2678
2679     @Override
2680     public boolean accept( final File f ) {
2681         final String file_name = f.getName().trim().toLowerCase();
2682         return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2683                 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2684     }
2685
2686     @Override
2687     public String getDescription() {
2688         return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2689     }
2690 }
2691
2692 class MsaFileFilter extends FileFilter {
2693
2694     @Override
2695     public boolean accept( final File f ) {
2696         final String file_name = f.getName().trim().toLowerCase();
2697         return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2698                 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2699     }
2700
2701     @Override
2702     public String getDescription() {
2703         return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2704     }
2705 }
2706
2707 class NexusFilter extends FileFilter {
2708
2709     @Override
2710     public boolean accept( final File f ) {
2711         final String file_name = f.getName().trim().toLowerCase();
2712         return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2713                 || file_name.endsWith( ".tre" ) || f.isDirectory();
2714     }
2715
2716     @Override
2717     public String getDescription() {
2718         return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2719     }
2720 } // NexusFilter
2721
2722 class NHFilter extends FileFilter {
2723
2724     @Override
2725     public boolean accept( final File f ) {
2726         final String file_name = f.getName().trim().toLowerCase();
2727         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2728                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2729                 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2730                 || f.isDirectory();
2731     }
2732
2733     @Override
2734     public String getDescription() {
2735         return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2736     }
2737 } // NHFilter
2738
2739 class NHXFilter extends FileFilter {
2740
2741     @Override
2742     public boolean accept( final File f ) {
2743         final String file_name = f.getName().trim().toLowerCase();
2744         return file_name.endsWith( ".nhx" ) || f.isDirectory();
2745     }
2746
2747     @Override
2748     public String getDescription() {
2749         return "NHX files (*.nhx) [deprecated]";
2750     }
2751 }
2752
2753 class PdfFilter extends FileFilter {
2754
2755     @Override
2756     public boolean accept( final File f ) {
2757         return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2758     }
2759
2760     @Override
2761     public String getDescription() {
2762         return "PDF files (*.pdf)";
2763     }
2764 } // PdfFilter
2765
2766 class SequencesFileFilter extends FileFilter {
2767
2768     @Override
2769     public boolean accept( final File f ) {
2770         final String file_name = f.getName().trim().toLowerCase();
2771         return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2772                 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2773     }
2774
2775     @Override
2776     public String getDescription() {
2777         return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2778     }
2779 }
2780
2781 class TolFilter extends FileFilter {
2782
2783     @Override
2784     public boolean accept( final File f ) {
2785         final String file_name = f.getName().trim().toLowerCase();
2786         return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2787                 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2788     }
2789
2790     @Override
2791     public String getDescription() {
2792         return "Tree of Life files (*.tol, *.tolxml)";
2793     }
2794 } // TolFilter
2795
2796 class XMLFilter extends FileFilter {
2797
2798     @Override
2799     public boolean accept( final File f ) {
2800         final String file_name = f.getName().trim().toLowerCase();
2801         return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2802                 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2803     }
2804
2805     @Override
2806     public String getDescription() {
2807         return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
2808     }
2809 } // XMLFilter