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