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