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

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