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.GoAnnotation;
  70 import org.forester.archaeopteryx.tools.InferenceManager;
  71 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
  72 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
  73 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
  74 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
  75 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  76 import org.forester.archaeopteryx.webservices.WebservicesManager;
  77 import org.forester.io.parsers.FastaParser;
  78 import org.forester.io.parsers.GeneralMsaParser;
  79 import org.forester.io.parsers.PhylogenyParser;
  80 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  81 import org.forester.io.parsers.nhx.NHXParser;
  82 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  83 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  84 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  85 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  86 import org.forester.io.parsers.tol.TolParser;
  87 import org.forester.io.parsers.util.ParserUtils;
  88 import org.forester.io.writers.PhylogenyWriter;
  89 import org.forester.io.writers.SequenceWriter;
  90 import org.forester.msa.Msa;
  91 import org.forester.msa.MsaFormatException;
  92 import org.forester.phylogeny.Phylogeny;
  93 import org.forester.phylogeny.PhylogenyMethods;
  94 import org.forester.phylogeny.PhylogenyNode;
  95 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  96 import org.forester.phylogeny.data.Confidence;
  97 import org.forester.phylogeny.data.Taxonomy;
  98 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  99 import org.forester.phylogeny.factories.PhylogenyFactory;
 100 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 101 import org.forester.sequence.Sequence;
 102 import org.forester.util.BasicDescriptiveStatistics;
 103 import org.forester.util.BasicTable;
 104 import org.forester.util.BasicTableParser;
 105 import org.forester.util.DescriptiveStatistics;
 106 import org.forester.util.ForesterUtil;
 107 import org.forester.util.WindowsUtils;
 108
 109 public final class MainFrameApplication extends MainFrame {
 110
 111     static final String                      INFER_ANCESTOR_TAXONOMIES             = "Infer Ancestor Taxonomies";
 112     static final String                      OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
 113     private final static int                 FRAME_X_SIZE                          = 800;
 114     private final static int                 FRAME_Y_SIZE                          = 800;
 115     // Filters for the file-open dialog (classes defined in this file)
 116     private final static NHFilter            nhfilter                              = new NHFilter();
 117     private final static NHXFilter           nhxfilter                             = new NHXFilter();
 118     private final static XMLFilter           xmlfilter                             = new XMLFilter();
 119     private final static TolFilter           tolfilter                             = new TolFilter();
 120     private final static NexusFilter         nexusfilter                           = new NexusFilter();
 121     private final static PdfFilter           pdffilter                             = new PdfFilter();
 122     private final static GraphicsFileFilter  graphicsfilefilter                    = new GraphicsFileFilter();
 123     private final static MsaFileFilter       msafilter                             = new MsaFileFilter();
 124     private final static SequencesFileFilter seqsfilter                            = new SequencesFileFilter();
 125     private final static DefaultFilter       defaultfilter                         = new DefaultFilter();
 126     private static final long                serialVersionUID                      = -799735726778865234L;
 127     private final JFileChooser               _values_filechooser;
 128     private final JFileChooser               _sequences_filechooser;
 129     private final JFileChooser               _open_filechooser;
 130     private final JFileChooser               _msa_filechooser;
 131     private final JFileChooser               _seqs_pi_filechooser;
 132     private final JFileChooser               _open_filechooser_for_species_tree;
 133     private final JFileChooser               _save_filechooser;
 134     private final JFileChooser               _writetopdf_filechooser;
 135     private final JFileChooser               _writetographics_filechooser;
 136     // Application-only print menu items
 137     private JMenuItem                        _print_item;
 138     private JMenuItem                        _write_to_pdf_item;
 139     private JMenuItem                        _write_to_jpg_item;
 140     private JMenuItem                        _write_to_gif_item;
 141     private JMenuItem                        _write_to_tif_item;
 142     private JMenuItem                        _write_to_png_item;
 143     private JMenuItem                        _write_to_bmp_item;
 144     private File                             _current_dir;
 145     private ButtonGroup                      _radio_group_1;
 146     private ButtonGroup                      _radio_group_2;
 147     // Others:
 148     double                                   _min_not_collapse                     = Constants.MIN_NOT_COLLAPSE_DEFAULT;
 149     // Phylogeny Inference menu
 150     private JMenu                            _inference_menu;
 151     private JMenuItem                        _inference_from_msa_item;
 152     private JMenuItem                        _inference_from_seqs_item;
 153     // Phylogeny Inference
 154     private PhylogeneticInferenceOptions     _phylogenetic_inference_options       = null;
 155     private Msa                              _msa                                  = null;
 156     private File                             _msa_file                             = null;
 157     private List<Sequence>                   _seqs                                 = null;
 158     private File                             _seqs_file                            = null;
 159     JMenuItem                                _read_values_jmi;
 160     JMenuItem                                _read_seqs_jmi;
 161
 162     private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
 163         _configuration = config;
 164         if ( _configuration == null ) {
 165             throw new IllegalArgumentException( "configuration is null" );
 166         }
 167         setVisible( false );
 168         setOptions( Options.createInstance( _configuration ) );
 169         _mainpanel = new MainPanel( _configuration, this );
 170         _open_filechooser = null;
 171         _open_filechooser_for_species_tree = null;
 172         _save_filechooser = null;
 173         _writetopdf_filechooser = null;
 174         _writetographics_filechooser = null;
 175         _msa_filechooser = null;
 176         _seqs_pi_filechooser = null;
 177         _values_filechooser = null;
 178         _sequences_filechooser = null;
 179         _jmenubar = new JMenuBar();
 180         buildFileMenu();
 181         buildTypeMenu();
 182         _contentpane = getContentPane();
 183         _contentpane.setLayout( new BorderLayout() );
 184         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 185         // App is this big
 186         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 187         // The window listener
 188         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 189         addWindowListener( new WindowAdapter() {
 190
 191             @Override
 192             public void windowClosing( final WindowEvent e ) {
 193                 exit();
 194             }
 195         } );
 196         //   setVisible( true );
 197         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 198             AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
 199             validate();
 200             getMainPanel().getControlPanel().showWholeAll();
 201             getMainPanel().getControlPanel().showWhole();
 202         }
 203         //activateSaveAllIfNeeded();
 204         // ...and its children
 205         _contentpane.repaint();
 206     }
 207
 208     private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
 209         this( phys, config, title, null );
 210     }
 211
 212     private MainFrameApplication( final Phylogeny[] phys,
 213                                   final Configuration config,
 214                                   final String title,
 215                                   final File current_dir ) {
 216         super();
 217         _configuration = config;
 218         if ( _configuration == null ) {
 219             throw new IllegalArgumentException( "configuration is null" );
 220         }
 221         try {
 222             boolean synth_exception = false;
 223             if ( Constants.__SYNTH_LF ) {
 224                 try {
 225                     final SynthLookAndFeel synth = new SynthLookAndFeel();
 226                     synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
 227                                 MainFrameApplication.class );
 228                     UIManager.setLookAndFeel( synth );
 229                 }
 230                 catch ( final Exception ex ) {
 231                     synth_exception = true;
 232                     ForesterUtil.printWarningMessage( Constants.PRG_NAME,
 233                                                       "could not create synth look and feel: "
 234                                                               + ex.getLocalizedMessage() );
 235                 }
 236             }
 237             if ( !Constants.__SYNTH_LF || synth_exception ) {
 238                 if ( _configuration.isUseNativeUI() ) {
 239                     UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 240                 }
 241                 else {
 242                     UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 243                 }
 244             }
 245             //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
 246         }
 247         catch ( final UnsupportedLookAndFeelException e ) {
 248             AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
 249         }
 250         catch ( final ClassNotFoundException e ) {
 251             AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
 252         }
 253         catch ( final InstantiationException e ) {
 254             AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
 255         }
 256         catch ( final IllegalAccessException e ) {
 257             AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
 258         }
 259         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
 260             setCurrentDir( current_dir );
 261         }
 262         // hide until everything is ready
 263         setVisible( false );
 264         setOptions( Options.createInstance( _configuration ) );
 265         setInferenceManager( InferenceManager.createInstance( _configuration ) );
 266         setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
 267         //     _textframe = null; #~~~~
 268         // set title
 269         setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
 270         _mainpanel = new MainPanel( _configuration, this );
 271         // The file dialogs
 272         _open_filechooser = new JFileChooser();
 273         _open_filechooser.setCurrentDirectory( new File( "." ) );
 274         _open_filechooser.setMultiSelectionEnabled( false );
 275         _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 276         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
 277         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 278         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 279         _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
 280         _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
 281         _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
 282         _open_filechooser_for_species_tree = new JFileChooser();
 283         _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
 284         _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
 285         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 286         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
 287         _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
 288         _save_filechooser = new JFileChooser();
 289         _save_filechooser.setCurrentDirectory( new File( "." ) );
 290         _save_filechooser.setMultiSelectionEnabled( false );
 291         _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
 292         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 293         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 294         _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
 295         _writetopdf_filechooser = new JFileChooser();
 296         _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
 297         _writetographics_filechooser = new JFileChooser();
 298         _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
 299         // Msa:
 300         _msa_filechooser = new JFileChooser();
 301         _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
 302         _msa_filechooser.setCurrentDirectory( new File( "." ) );
 303         _msa_filechooser.setMultiSelectionEnabled( false );
 304         _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
 305         _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
 306         // Seqs:
 307         _seqs_pi_filechooser = new JFileChooser();
 308         _seqs_pi_filechooser.setName( "Read Sequences File" );
 309         _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
 310         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 311         _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
 312         _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
 313         // Expression
 314         _values_filechooser = new JFileChooser();
 315         _values_filechooser.setCurrentDirectory( new File( "." ) );
 316         _values_filechooser.setMultiSelectionEnabled( false );
 317         // Sequences
 318         _sequences_filechooser = new JFileChooser();
 319         _sequences_filechooser.setCurrentDirectory( new File( "." ) );
 320         _sequences_filechooser.setMultiSelectionEnabled( false );
 321         // build the menu bar
 322         _jmenubar = new JMenuBar();
 323         if ( !_configuration.isUseNativeUI() ) {
 324             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 325         }
 326         buildFileMenu();
 327         if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
 328             buildPhylogeneticInferenceMenu();
 329         }
 330         buildAnalysisMenu();
 331         buildToolsMenu();
 332         buildViewMenu();
 333         buildFontSizeMenu();
 334         buildOptionsMenu();
 335         buildTypeMenu();
 336         buildHelpMenu();
 337         setJMenuBar( _jmenubar );
 338         _jmenubar.add( _help_jmenu );
 339         _contentpane = getContentPane();
 340         _contentpane.setLayout( new BorderLayout() );
 341         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 342         // App is this big
 343         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 344         //        addWindowFocusListener( new WindowAdapter() {
 345         //
 346         //            @Override
 347         //            public void windowGainedFocus( WindowEvent e ) {
 348         //                requestFocusInWindow();
 349         //            }
 350         //        } );
 351         // The window listener
 352         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 353         addWindowListener( new WindowAdapter() {
 354
 355             @Override
 356             public void windowClosing( final WindowEvent e ) {
 357                 if ( isUnsavedDataPresent() ) {
 358                     final int r = JOptionPane.showConfirmDialog( null,
 359                                                                  "Exit despite potentially unsaved changes?",
 360                                                                  "Exit?",
 361                                                                  JOptionPane.YES_NO_OPTION );
 362                     if ( r != JOptionPane.YES_OPTION ) {
 363                         return;
 364                     }
 365                 }
 366                 else {
 367                     final int r = JOptionPane.showConfirmDialog( null,
 368                                                                  "Exit Archaeopteryx?",
 369                                                                  "Exit?",
 370                                                                  JOptionPane.YES_NO_OPTION );
 371                     if ( r != JOptionPane.YES_OPTION ) {
 372                         return;
 373                     }
 374                 }
 375                 exit();
 376             }
 377         } );
 378         // The component listener
 379         addComponentListener( new ComponentAdapter() {
 380
 381             @Override
 382             public void componentResized( final ComponentEvent e ) {
 383                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 384                     _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
 385                                                                                         .getWidth(),
 386                                                                                 _mainpanel.getCurrentTreePanel()
 387                                                                                         .getHeight(),
 388                                                                                 getOptions().isAllowFontSizeChange() );
 389                 }
 390             }
 391         } );
 392         requestFocusInWindow();
 393         // addKeyListener( this );
 394         setVisible( true );
 395         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 396             AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
 397             validate();
 398             getMainPanel().getControlPanel().showWholeAll();
 399             getMainPanel().getControlPanel().showWhole();
 400         }
 401         activateSaveAllIfNeeded();
 402         // ...and its children
 403         _contentpane.repaint();
 404         System.gc();
 405     }
 406
 407     private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
 408         // Reads the config file (false, false => not url, not applet):
 409         this( phys, new Configuration( config_file, false, false, true ), title );
 410     }
 411
 412     @Override
 413     public void actionPerformed( final ActionEvent e ) {
 414         try {
 415             super.actionPerformed( e );
 416             final Object o = e.getSource();
 417             // Handle app-specific actions here:
 418             if ( o == _open_item ) {
 419                 readPhylogeniesFromFile();
 420             }
 421             else if ( o == _save_item ) {
 422                 writeToFile( _mainpanel.getCurrentPhylogeny() );
 423                 // If subtree currently displayed, save it, instead of complete
 424                 // tree.
 425             }
 426             else if ( o == _new_item ) {
 427                 newTree();
 428             }
 429             else if ( o == _save_all_item ) {
 430                 writeAllToFile();
 431             }
 432             else if ( o == _close_item ) {
 433                 closeCurrentPane();
 434             }
 435             else if ( o == _write_to_pdf_item ) {
 436                 writeToPdf( _mainpanel.getCurrentPhylogeny() );
 437             }
 438             else if ( o == _write_to_jpg_item ) {
 439                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
 440             }
 441             else if ( o == _write_to_png_item ) {
 442                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
 443             }
 444             else if ( o == _write_to_gif_item ) {
 445                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
 446             }
 447             else if ( o == _write_to_tif_item ) {
 448                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
 449             }
 450             else if ( o == _write_to_bmp_item ) {
 451                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
 452             }
 453             else if ( o == _print_item ) {
 454                 print();
 455             }
 456             else if ( o == _load_species_tree_item ) {
 457                 readSpeciesTreeFromFile();
 458             }
 459             else if ( o == _lineage_inference ) {
 460                 if ( isSubtreeDisplayed() ) {
 461                     JOptionPane.showMessageDialog( this,
 462                                                    "Subtree is shown.",
 463                                                    "Cannot infer ancestral taxonomies",
 464                                                    JOptionPane.ERROR_MESSAGE );
 465                     return;
 466                 }
 467                 executeLineageInference();
 468             }
 469             else if ( o == _function_analysis ) {
 470                 executeFunctionAnalysis();
 471             }
 472             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
 473                 if ( isSubtreeDisplayed() ) {
 474                     return;
 475                 }
 476                 obtainDetailedTaxonomicInformation();
 477             }
 478             else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
 479                 if ( isSubtreeDisplayed() ) {
 480                     return;
 481                 }
 482                 obtainDetailedTaxonomicInformationDelete();
 483             }
 484             else if ( o == _obtain_seq_information_jmi ) {
 485                 obtainSequenceInformation();
 486             }
 487             else if ( o == _read_values_jmi ) {
 488                 if ( isSubtreeDisplayed() ) {
 489                     return;
 490                 }
 491                 addExpressionValuesFromFile();
 492             }
 493             else if ( o == _read_seqs_jmi ) {
 494                 if ( isSubtreeDisplayed() ) {
 495                     return;
 496                 }
 497                 addSequencesFromFile();
 498             }
 499             else if ( o == _move_node_names_to_tax_sn_jmi ) {
 500                 moveNodeNamesToTaxSn();
 501             }
 502             else if ( o == _move_node_names_to_seq_names_jmi ) {
 503                 moveNodeNamesToSeqNames();
 504             }
 505             else if ( o == _extract_tax_code_from_node_names_jmi ) {
 506                 extractTaxDataFromNodeNames();
 507             }
 508             else if ( o == _graphics_export_visible_only_cbmi ) {
 509                 updateOptions( getOptions() );
 510             }
 511             else if ( o == _antialias_print_cbmi ) {
 512                 updateOptions( getOptions() );
 513             }
 514             else if ( o == _print_black_and_white_cbmi ) {
 515                 updateOptions( getOptions() );
 516             }
 517             else if ( o == _print_using_actual_size_cbmi ) {
 518                 updateOptions( getOptions() );
 519             }
 520             else if ( o == _graphics_export_using_actual_size_cbmi ) {
 521                 updateOptions( getOptions() );
 522             }
 523             else if ( o == _print_size_mi ) {
 524                 choosePrintSize();
 525             }
 526             else if ( o == _choose_pdf_width_mi ) {
 527                 choosePdfWidth();
 528             }
 529             else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
 530                 updateOptions( getOptions() );
 531             }
 532             else if ( o == _replace_underscores_cbmi ) {
 533                 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
 534                     _extract_taxonomy_no_rbmi.setSelected( true );
 535                 }
 536                 updateOptions( getOptions() );
 537             }
 538             else if ( o == _collapse_below_threshold ) {
 539                 if ( isSubtreeDisplayed() ) {
 540                     return;
 541                 }
 542                 collapseBelowThreshold();
 543             }
 544             else if ( ( o == _extract_taxonomy_pfam_rbmi ) || ( o == _extract_taxonomy_yes_rbmi ) ) {
 545                 if ( _replace_underscores_cbmi != null ) {
 546                     _replace_underscores_cbmi.setSelected( false );
 547                 }
 548                 updateOptions( getOptions() );
 549             }
 550             else if ( o == _extract_taxonomy_no_rbmi ) {
 551                 updateOptions( getOptions() );
 552             }
 553             else if ( o == _inference_from_msa_item ) {
 554                 executePhyleneticInference( false );
 555             }
 556             else if ( o == _inference_from_seqs_item ) {
 557                 executePhyleneticInference( true );
 558             }
 559             _contentpane.repaint();
 560         }
 561         catch ( final Exception ex ) {
 562             AptxUtil.unexpectedException( ex );
 563         }
 564         catch ( final Error err ) {
 565             AptxUtil.unexpectedError( err );
 566         }
 567     }
 568
 569     public void end() {
 570         _mainpanel.terminate();
 571         _contentpane.removeAll();
 572         setVisible( false );
 573         dispose();
 574     }
 575
 576     @Override
 577     public MainPanel getMainPanel() {
 578         return _mainpanel;
 579     }
 580
 581     public Msa getMsa() {
 582         return _msa;
 583     }
 584
 585     public File getMsaFile() {
 586         return _msa_file;
 587     }
 588
 589     public List<Sequence> getSeqs() {
 590         return _seqs;
 591     }
 592
 593     public File getSeqsFile() {
 594         return _seqs_file;
 595     }
 596
 597     public void readMsaFromFile() {
 598         // Set an initial directory if none set yet
 599         final File my_dir = getCurrentDir();
 600         _msa_filechooser.setMultiSelectionEnabled( false );
 601         // Open file-open dialog and set current directory
 602         if ( my_dir != null ) {
 603             _msa_filechooser.setCurrentDirectory( my_dir );
 604         }
 605         final int result = _msa_filechooser.showOpenDialog( _contentpane );
 606         // All done: get the msa
 607         final File file = _msa_filechooser.getSelectedFile();
 608         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
 609         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 610             setMsaFile( null );
 611             setMsa( null );
 612             Msa msa = null;
 613             try {
 614                 final InputStream is = new FileInputStream( file );
 615                 if ( FastaParser.isLikelyFasta( file ) ) {
 616                     msa = FastaParser.parseMsa( is );
 617                 }
 618                 else {
 619                     msa = GeneralMsaParser.parse( is );
 620                 }
 621             }
 622             catch ( final MsaFormatException e ) {
 623                 setArrowCursor();
 624                 JOptionPane.showMessageDialog( this,
 625                                                e.getLocalizedMessage(),
 626                                                "Multiple sequence alignment format error",
 627                                                JOptionPane.ERROR_MESSAGE );
 628                 return;
 629             }
 630             catch ( final IOException e ) {
 631                 setArrowCursor();
 632                 JOptionPane.showMessageDialog( this,
 633                                                e.getLocalizedMessage(),
 634                                                "Failed to read multiple sequence alignment",
 635                                                JOptionPane.ERROR_MESSAGE );
 636                 return;
 637             }
 638             catch ( final IllegalArgumentException e ) {
 639                 setArrowCursor();
 640                 JOptionPane.showMessageDialog( this,
 641                                                e.getLocalizedMessage(),
 642                                                "Unexpected error during reading of multiple sequence alignment",
 643                                                JOptionPane.ERROR_MESSAGE );
 644                 return;
 645             }
 646             catch ( final Exception e ) {
 647                 setArrowCursor();
 648                 e.printStackTrace();
 649                 JOptionPane.showMessageDialog( this,
 650                                                e.getLocalizedMessage(),
 651                                                "Unexpected error during reading of multiple sequence alignment",
 652                                                JOptionPane.ERROR_MESSAGE );
 653                 return;
 654             }
 655             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
 656                 JOptionPane.showMessageDialog( this,
 657                                                "Multiple sequence alignment is empty",
 658                                                "Illegal Multiple Sequence Alignment",
 659                                                JOptionPane.ERROR_MESSAGE );
 660                 return;
 661             }
 662             if ( msa.getNumberOfSequences() < 4 ) {
 663                 JOptionPane.showMessageDialog( this,
 664                                                "Multiple sequence alignment needs to contain at least 3 sequences",
 665                                                "Illegal multiple sequence alignment",
 666                                                JOptionPane.ERROR_MESSAGE );
 667                 return;
 668             }
 669             if ( msa.getLength() < 2 ) {
 670                 JOptionPane.showMessageDialog( this,
 671                                                "Multiple sequence alignment needs to contain at least 2 residues",
 672                                                "Illegal multiple sequence alignment",
 673                                                JOptionPane.ERROR_MESSAGE );
 674                 return;
 675             }
 676             System.gc();
 677             setMsaFile( _msa_filechooser.getSelectedFile() );
 678             setMsa( msa );
 679         }
 680     }
 681
 682     public void readSeqsFromFileforPI() {
 683         // Set an initial directory if none set yet
 684         final File my_dir = getCurrentDir();
 685         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 686         // Open file-open dialog and set current directory
 687         if ( my_dir != null ) {
 688             _seqs_pi_filechooser.setCurrentDirectory( my_dir );
 689         }
 690         final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
 691         // All done: get the seqs
 692         final File file = _seqs_pi_filechooser.getSelectedFile();
 693         setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
 694         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 695             setSeqsFile( null );
 696             setSeqs( null );
 697             List<Sequence> seqs = null;
 698             try {
 699                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
 700                     seqs = FastaParser.parse( new FileInputStream( file ) );
 701                     for( final Sequence seq : seqs ) {
 702                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
 703                     }
 704                 }
 705                 else {
 706                     //TODO error
 707                 }
 708             }
 709             catch ( final MsaFormatException e ) {
 710                 setArrowCursor();
 711                 JOptionPane.showMessageDialog( this,
 712                                                e.getLocalizedMessage(),
 713                                                "Multiple sequence file format error",
 714                                                JOptionPane.ERROR_MESSAGE );
 715                 return;
 716             }
 717             catch ( final IOException e ) {
 718                 setArrowCursor();
 719                 JOptionPane.showMessageDialog( this,
 720                                                e.getLocalizedMessage(),
 721                                                "Failed to read multiple sequence file",
 722                                                JOptionPane.ERROR_MESSAGE );
 723                 return;
 724             }
 725             catch ( final IllegalArgumentException e ) {
 726                 setArrowCursor();
 727                 JOptionPane.showMessageDialog( this,
 728                                                e.getLocalizedMessage(),
 729                                                "Unexpected error during reading of multiple sequence file",
 730                                                JOptionPane.ERROR_MESSAGE );
 731                 return;
 732             }
 733             catch ( final Exception e ) {
 734                 setArrowCursor();
 735                 e.printStackTrace();
 736                 JOptionPane.showMessageDialog( this,
 737                                                e.getLocalizedMessage(),
 738                                                "Unexpected error during reading of multiple sequence file",
 739                                                JOptionPane.ERROR_MESSAGE );
 740                 return;
 741             }
 742             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 743                 JOptionPane.showMessageDialog( this,
 744                                                "Multiple sequence file is empty",
 745                                                "Illegal multiple sequence file",
 746                                                JOptionPane.ERROR_MESSAGE );
 747                 return;
 748             }
 749             if ( seqs.size() < 4 ) {
 750                 JOptionPane.showMessageDialog( this,
 751                                                "Multiple sequence file needs to contain at least 3 sequences",
 752                                                "Illegal multiple sequence file",
 753                                                JOptionPane.ERROR_MESSAGE );
 754                 return;
 755             }
 756             //  if ( msa.getLength() < 2 ) {
 757             //       JOptionPane.showMessageDialog( this,
 758             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
 759             //                                      "Illegal multiple sequence file",
 760             //                                      JOptionPane.ERROR_MESSAGE );
 761             //       return;
 762             //   }
 763             System.gc();
 764             setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
 765             setSeqs( seqs );
 766         }
 767     }
 768
 769     void buildAnalysisMenu() {
 770         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 771         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 772         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 773         _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
 774         customizeJMenuItem( _gsdi_item );
 775         customizeJMenuItem( _gsdir_item );
 776         customizeJMenuItem( _load_species_tree_item );
 777         _analysis_menu.addSeparator();
 778         _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 779         customizeJMenuItem( _lineage_inference );
 780         _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 781         _jmenubar.add( _analysis_menu );
 782     }
 783
 784     @Override
 785     void buildFileMenu() {
 786         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
 787         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
 788         _file_jmenu.addSeparator();
 789         _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
 790         _file_jmenu.addSeparator();
 791         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
 792         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
 793                 .getAvailablePhylogeniesWebserviceClients().size() ];
 794         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 795             final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
 796             _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
 797             _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
 798         }
 799         if ( getConfiguration().isEditable() ) {
 800             _file_jmenu.addSeparator();
 801             _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
 802             _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
 803         }
 804         _file_jmenu.addSeparator();
 805         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
 806         _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
 807         _save_all_item.setToolTipText( "Write all phylogenies to one file." );
 808         _save_all_item.setEnabled( false );
 809         _file_jmenu.addSeparator();
 810         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
 811         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
 812             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
 813         }
 814         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
 815         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
 816         if ( AptxUtil.canWriteFormat( "gif" ) ) {
 817             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
 818         }
 819         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
 820             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
 821         }
 822         _file_jmenu.addSeparator();
 823         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
 824         _file_jmenu.addSeparator();
 825         _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
 826         _close_item.setToolTipText( "To close the current pane." );
 827         _close_item.setEnabled( true );
 828         _file_jmenu.addSeparator();
 829         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 830         // For print in color option item
 831         customizeJMenuItem( _open_item );
 832         _open_item
 833                 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
 834         customizeJMenuItem( _open_url_item );
 835         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 836             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
 837         }
 838         customizeJMenuItem( _save_item );
 839         if ( getConfiguration().isEditable() ) {
 840             customizeJMenuItem( _new_item );
 841         }
 842         customizeJMenuItem( _close_item );
 843         customizeJMenuItem( _save_all_item );
 844         customizeJMenuItem( _write_to_pdf_item );
 845         customizeJMenuItem( _write_to_png_item );
 846         customizeJMenuItem( _write_to_jpg_item );
 847         customizeJMenuItem( _write_to_gif_item );
 848         customizeJMenuItem( _write_to_tif_item );
 849         customizeJMenuItem( _write_to_bmp_item );
 850         customizeJMenuItem( _print_item );
 851         customizeJMenuItem( _exit_item );
 852         _jmenubar.add( _file_jmenu );
 853     }
 854
 855     void buildOptionsMenu() {
 856         _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
 857         _options_jmenu.addChangeListener( new ChangeListener() {
 858
 859             @Override
 860             public void stateChanged( final ChangeEvent e ) {
 861                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 862                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 863                 MainFrame
 864                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 865                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 866                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 867                 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
 868                 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
 869                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 870                                                                      _show_scale_cbmi,
 871                                                                      _show_branch_length_values_cbmi,
 872                                                                      _non_lined_up_cladograms_rbmi,
 873                                                                      _uniform_cladograms_rbmi,
 874                                                                      _ext_node_dependent_cladogram_rbmi,
 875                                                                      _label_direction_cbmi );
 876                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 877                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 878                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 879             }
 880         } );
 881         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
 882         _options_jmenu
 883                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 884         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 885         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 886         _radio_group_1 = new ButtonGroup();
 887         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 888         _radio_group_1.add( _uniform_cladograms_rbmi );
 889         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 890         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
 891         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
 892         _options_jmenu
 893                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 894         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
 895         _options_jmenu
 896                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
 897         _options_jmenu
 898                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
 899         _options_jmenu
 900                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 901         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 902         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 903         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 904         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 905         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 906         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 907         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 908         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
 909         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
 910         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
 911         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 912             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 913         }
 914         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 915         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 916         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 917         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 918         _options_jmenu.addSeparator();
 919         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
 920         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
 921         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
 922         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 923         _options_jmenu.addSeparator();
 924         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
 925                                                       getConfiguration() ) );
 926         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
 927         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
 928         _options_jmenu
 929                 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
 930         _options_jmenu
 931                 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
 932         _options_jmenu
 933                 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
 934         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
 935         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
 936         _options_jmenu.addSeparator();
 937         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
 938         _options_jmenu
 939                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
 940         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
 941         //
 942         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
 943         _options_jmenu
 944                 .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
 945         _extract_taxonomy_pfam_rbmi
 946                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
 947         _options_jmenu
 948                 .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
 949         _extract_taxonomy_yes_rbmi
 950                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
 951         _radio_group_2 = new ButtonGroup();
 952         _radio_group_2.add( _extract_taxonomy_no_rbmi );
 953         _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
 954         _radio_group_2.add( _extract_taxonomy_yes_rbmi );
 955         //
 956         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
 957         _options_jmenu
 958                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
 959         _use_brackets_for_conf_in_nh_export_cbmi
 960                 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
 961         _options_jmenu
 962                 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
 963         customizeJMenuItem( _choose_font_mi );
 964         customizeJMenuItem( _choose_minimal_confidence_mi );
 965         customizeJMenuItem( _switch_colors_mi );
 966         customizeJMenuItem( _print_size_mi );
 967         customizeJMenuItem( _choose_pdf_width_mi );
 968         customizeJMenuItem( _overview_placment_mi );
 969         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 970                 .isShowDefaultNodeShapesExternal() );
 971         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 972                 .isShowDefaultNodeShapesInternal() );
 973         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
 974         customizeJMenuItem( _cycle_node_shape_mi );
 975         customizeJMenuItem( _cycle_node_fill_mi );
 976         customizeJMenuItem( _choose_node_size_mi );
 977         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 978         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 979         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 980         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 981         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 982         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 983         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 984         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 985                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 986         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 987                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 988         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 989                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 990         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 991         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 992         customizeCheckBoxMenuItem( _label_direction_cbmi,
 993                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 994         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
 995         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
 996         customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
 997                 .isInternalNumberAreConfidenceForNhParsing() );
 998         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
 999                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1000         customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
1001                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1002         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
1003                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1004         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1005         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1006         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1007         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1008         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1009         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1010                 .isGraphicsExportUsingActualSize() );
1011         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1012         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1013                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1014         customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1015                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1016         _jmenubar.add( _options_jmenu );
1017     }
1018
1019     void buildPhylogeneticInferenceMenu() {
1020         final InferenceManager im = getInferenceManager();
1021         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1022         _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1023         customizeJMenuItem( _inference_from_msa_item );
1024         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1025         if ( im.canDoMsa() ) {
1026             _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1027             customizeJMenuItem( _inference_from_seqs_item );
1028             _inference_from_seqs_item
1029                     .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1030         }
1031         else {
1032             _inference_menu
1033                     .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1034             customizeJMenuItem( _inference_from_seqs_item );
1035             _inference_from_seqs_item.setEnabled( false );
1036         }
1037         _jmenubar.add( _inference_menu );
1038     }
1039
1040     void buildToolsMenu() {
1041         _tools_menu = createMenu( "Tools", getConfiguration() );
1042         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1043         customizeJMenuItem( _confcolor_item );
1044         _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1045         customizeJMenuItem( _color_rank_jmi );
1046         _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1047         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1048         customizeJMenuItem( _taxcolor_item );
1049         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1050         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1051         customizeJMenuItem( _remove_branch_color_item );
1052         _tools_menu.addSeparator();
1053         _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1054         customizeJMenuItem( _annotate_item );
1055         _tools_menu.addSeparator();
1056         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1057         customizeJMenuItem( _midpoint_root_item );
1058         _tools_menu.addSeparator();
1059         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1060         customizeJMenuItem( _collapse_species_specific_subtrees );
1061         _tools_menu
1062                 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1063         customizeJMenuItem( _collapse_below_threshold );
1064         _collapse_below_threshold
1065                 .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)" );
1066         _tools_menu.addSeparator();
1067         _tools_menu
1068                 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
1069         customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1070         _extract_tax_code_from_node_names_jmi
1071                 .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'" );
1072         _tools_menu
1073                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1074         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1075         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1076         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1077         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1078         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1079         _tools_menu.addSeparator();
1080         _tools_menu
1081                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1082         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1083         _obtain_detailed_taxonomic_information_jmi
1084                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1085         _tools_menu
1086                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1087         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1088         _obtain_detailed_taxonomic_information_deleting_jmi
1089                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1090         _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1091         customizeJMenuItem( _obtain_seq_information_jmi );
1092         _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1093         _tools_menu.addSeparator();
1094         if ( !Constants.__RELEASE ) {
1095             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
1096             customizeJMenuItem( _function_analysis );
1097             _function_analysis
1098                     .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
1099             _tools_menu.addSeparator();
1100         }
1101         _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
1102         customizeJMenuItem( _read_values_jmi );
1103         _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
1104         _jmenubar.add( _tools_menu );
1105         _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
1106         customizeJMenuItem( _read_seqs_jmi );
1107         _read_seqs_jmi
1108                 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
1109         _jmenubar.add( _tools_menu );
1110     }
1111
1112     @Override
1113     void close() {
1114         if ( isUnsavedDataPresent() ) {
1115             final int r = JOptionPane.showConfirmDialog( this,
1116                                                          "Exit despite potentially unsaved changes?",
1117                                                          "Exit?",
1118                                                          JOptionPane.YES_NO_OPTION );
1119             if ( r != JOptionPane.YES_OPTION ) {
1120                 return;
1121             }
1122         }
1123         exit();
1124     }
1125
1126     void executeFunctionAnalysis() {
1127         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1128             return;
1129         }
1130         final GoAnnotation a = new GoAnnotation( this,
1131                                                  _mainpanel.getCurrentTreePanel(),
1132                                                  _mainpanel.getCurrentPhylogeny() );
1133         new Thread( a ).start();
1134     }
1135
1136     void executeLineageInference() {
1137         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1138             return;
1139         }
1140         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1141             JOptionPane.showMessageDialog( this,
1142                                            "Phylogeny is not rooted.",
1143                                            "Cannot infer ancestral taxonomies",
1144                                            JOptionPane.ERROR_MESSAGE );
1145             return;
1146         }
1147         final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1148                                                                                   _mainpanel.getCurrentTreePanel(),
1149                                                                                   _mainpanel.getCurrentPhylogeny()
1150                                                                                           .copy() );
1151         new Thread( inferrer ).start();
1152     }
1153
1154     void exit() {
1155         removeAllTextFrames();
1156         _mainpanel.terminate();
1157         _contentpane.removeAll();
1158         setVisible( false );
1159         dispose();
1160         System.exit( 0 );
1161     }
1162
1163     @Override
1164     void readPhylogeniesFromURL() {
1165         URL url = null;
1166         Phylogeny[] phys = null;
1167         final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1168         final String url_string = JOptionPane.showInputDialog( this,
1169                                                                message,
1170                                                                "Use URL/webservice to obtain a phylogeny",
1171                                                                JOptionPane.QUESTION_MESSAGE );
1172         boolean nhx_or_nexus = false;
1173         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1174             try {
1175                 url = new URL( url_string );
1176                 PhylogenyParser parser = null;
1177                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1178                     parser = new TolParser();
1179                 }
1180                 else {
1181                     parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1182                             .isValidatePhyloXmlAgainstSchema() );
1183                 }
1184                 if ( parser instanceof NexusPhylogeniesParser ) {
1185                     nhx_or_nexus = true;
1186                 }
1187                 else if ( parser instanceof NHXParser ) {
1188                     nhx_or_nexus = true;
1189                 }
1190                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1191                     _mainpanel.getCurrentTreePanel().setWaitCursor();
1192                 }
1193                 else {
1194                     _mainpanel.setWaitCursor();
1195                 }
1196                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1197                 phys = factory.create( url.openStream(), parser );
1198             }
1199             catch ( final MalformedURLException e ) {
1200                 JOptionPane.showMessageDialog( this,
1201                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1202                                                "Malformed URL",
1203                                                JOptionPane.ERROR_MESSAGE );
1204             }
1205             catch ( final IOException e ) {
1206                 JOptionPane.showMessageDialog( this,
1207                                                "Could not read from " + url + "\n"
1208                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1209                                                "Failed to read URL",
1210                                                JOptionPane.ERROR_MESSAGE );
1211             }
1212             catch ( final Exception e ) {
1213                 JOptionPane.showMessageDialog( this,
1214                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1215                                                "Unexpected Exception",
1216                                                JOptionPane.ERROR_MESSAGE );
1217             }
1218             finally {
1219                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1220                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1221                 }
1222                 else {
1223                     _mainpanel.setArrowCursor();
1224                 }
1225             }
1226             if ( ( phys != null ) && ( phys.length > 0 ) ) {
1227                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1228                     for( final Phylogeny phy : phys ) {
1229                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1230                     }
1231                 }
1232                 AptxUtil.addPhylogeniesToTabs( phys,
1233                                                new File( url.getFile() ).getName(),
1234                                                new File( url.getFile() ).toString(),
1235                                                getConfiguration(),
1236                                                getMainPanel() );
1237                 _mainpanel.getControlPanel().showWhole();
1238             }
1239         }
1240         activateSaveAllIfNeeded();
1241         System.gc();
1242     }
1243
1244     void setMsa( final Msa msa ) {
1245         _msa = msa;
1246     }
1247
1248     void setMsaFile( final File msa_file ) {
1249         _msa_file = msa_file;
1250     }
1251
1252     void setSeqs( final List<Sequence> seqs ) {
1253         _seqs = seqs;
1254     }
1255
1256     void setSeqsFile( final File seqs_file ) {
1257         _seqs_file = seqs_file;
1258     }
1259
1260     void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1261         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1262                                                                     _mainpanel.getCurrentTreePanel().getHeight(),
1263                                                                     true );
1264         String file_written_to = "";
1265         boolean error = false;
1266         try {
1267             file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1268                                                                      _mainpanel.getCurrentTreePanel().getWidth(),
1269                                                                      _mainpanel.getCurrentTreePanel().getHeight(),
1270                                                                      _mainpanel.getCurrentTreePanel(),
1271                                                                      _mainpanel.getControlPanel(),
1272                                                                      type,
1273                                                                      getOptions() );
1274         }
1275         catch ( final IOException e ) {
1276             error = true;
1277             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1278         }
1279         if ( !error ) {
1280             if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1281                 JOptionPane.showMessageDialog( this,
1282                                                "Wrote image to: " + file_written_to,
1283                                                "Graphics Export",
1284                                                JOptionPane.INFORMATION_MESSAGE );
1285             }
1286             else {
1287                 JOptionPane.showMessageDialog( this,
1288                                                "There was an unknown problem when attempting to write to an image file: \""
1289                                                        + file_name + "\"",
1290                                                "Error",
1291                                                JOptionPane.ERROR_MESSAGE );
1292             }
1293         }
1294         _contentpane.repaint();
1295     }
1296
1297     private void addExpressionValuesFromFile() {
1298         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1299             JOptionPane.showMessageDialog( this,
1300                                            "Need to load evolutionary tree first",
1301                                            "Can Not Read Expression Values",
1302                                            JOptionPane.WARNING_MESSAGE );
1303             return;
1304         }
1305         final File my_dir = getCurrentDir();
1306         if ( my_dir != null ) {
1307             _values_filechooser.setCurrentDirectory( my_dir );
1308         }
1309         final int result = _values_filechooser.showOpenDialog( _contentpane );
1310         final File file = _values_filechooser.getSelectedFile();
1311         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1312             BasicTable<String> t = null;
1313             try {
1314                 t = BasicTableParser.parse( file, '\t' );
1315                 if ( t.getNumberOfColumns() < 2 ) {
1316                     t = BasicTableParser.parse( file, ',' );
1317                 }
1318                 if ( t.getNumberOfColumns() < 2 ) {
1319                     t = BasicTableParser.parse( file, ' ' );
1320                 }
1321             }
1322             catch ( final IOException e ) {
1323                 JOptionPane.showMessageDialog( this,
1324                                                e.getMessage(),
1325                                                "Could Not Read Expression Value Table",
1326                                                JOptionPane.ERROR_MESSAGE );
1327                 return;
1328             }
1329             if ( t.getNumberOfColumns() < 2 ) {
1330                 JOptionPane.showMessageDialog( this,
1331                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
1332                                                "Problem with Expression Value Table",
1333                                                JOptionPane.ERROR_MESSAGE );
1334                 return;
1335             }
1336             if ( t.getNumberOfRows() < 1 ) {
1337                 JOptionPane.showMessageDialog( this,
1338                                                "Table contains zero rows",
1339                                                "Problem with Expression Value Table",
1340                                                JOptionPane.ERROR_MESSAGE );
1341                 return;
1342             }
1343             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1344             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1345                 JOptionPane.showMessageDialog( this,
1346                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1347                                                        + phy.getNumberOfExternalNodes() + " external nodes",
1348                                                "Warning",
1349                                                JOptionPane.WARNING_MESSAGE );
1350             }
1351             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1352             int not_found = 0;
1353             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1354                 final PhylogenyNode node = iter.next();
1355                 final String node_name = node.getName();
1356                 if ( !ForesterUtil.isEmpty( node_name ) ) {
1357                     int row = -1;
1358                     try {
1359                         row = t.findRow( node_name );
1360                     }
1361                     catch ( final IllegalArgumentException e ) {
1362                         JOptionPane
1363                                 .showMessageDialog( this,
1364                                                     e.getMessage(),
1365                                                     "Error Mapping Node Identifiers to Expression Value Identifiers",
1366                                                     JOptionPane.ERROR_MESSAGE );
1367                         return;
1368                     }
1369                     if ( row < 0 ) {
1370                         if ( node.isExternal() ) {
1371                             not_found++;
1372                         }
1373                         continue;
1374                     }
1375                     final List<Double> l = new ArrayList<Double>();
1376                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1377                         double d = -100;
1378                         try {
1379                             d = Double.parseDouble( t.getValueAsString( col, row ) );
1380                         }
1381                         catch ( final NumberFormatException e ) {
1382                             JOptionPane.showMessageDialog( this,
1383                                                            "Could not parse \"" + t.getValueAsString( col, row )
1384                                                                    + "\" into a decimal value",
1385                                                            "Issue with Expression Value Table",
1386                                                            JOptionPane.ERROR_MESSAGE );
1387                             return;
1388                         }
1389                         stats.addValue( d );
1390                         l.add( d );
1391                     }
1392                     if ( !l.isEmpty() ) {
1393                         if ( node.getNodeData().getProperties() != null ) {
1394                             node.getNodeData().getProperties()
1395                                     .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1396                         }
1397                         node.getNodeData().setVector( l );
1398                     }
1399                 }
1400             }
1401             if ( not_found > 0 ) {
1402                 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1403                         + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1404             }
1405             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1406         }
1407     }
1408
1409     private void addSequencesFromFile() {
1410         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1411             JOptionPane.showMessageDialog( this,
1412                                            "Need to load evolutionary tree first",
1413                                            "Can Not Read Sequences",
1414                                            JOptionPane.WARNING_MESSAGE );
1415             return;
1416         }
1417         final File my_dir = getCurrentDir();
1418         if ( my_dir != null ) {
1419             _sequences_filechooser.setCurrentDirectory( my_dir );
1420         }
1421         final int result = _sequences_filechooser.showOpenDialog( _contentpane );
1422         final File file = _sequences_filechooser.getSelectedFile();
1423         List<Sequence> seqs = null;
1424         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1425             try {
1426                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1427                     seqs = FastaParser.parse( new FileInputStream( file ) );
1428                 }
1429                 else {
1430                     JOptionPane.showMessageDialog( this,
1431                                                    "Format does not appear to be Fasta",
1432                                                    "Multiple sequence file format error",
1433                                                    JOptionPane.ERROR_MESSAGE );
1434                     return;
1435                 }
1436             }
1437             catch ( final MsaFormatException e ) {
1438                 setArrowCursor();
1439                 JOptionPane.showMessageDialog( this,
1440                                                e.getLocalizedMessage(),
1441                                                "Multiple sequence file format error",
1442                                                JOptionPane.ERROR_MESSAGE );
1443                 return;
1444             }
1445             catch ( final IOException e ) {
1446                 setArrowCursor();
1447                 JOptionPane.showMessageDialog( this,
1448                                                e.getLocalizedMessage(),
1449                                                "Failed to read multiple sequence file",
1450                                                JOptionPane.ERROR_MESSAGE );
1451                 return;
1452             }
1453             catch ( final Exception e ) {
1454                 setArrowCursor();
1455                 e.printStackTrace();
1456                 JOptionPane.showMessageDialog( this,
1457                                                e.getLocalizedMessage(),
1458                                                "Unexpected error during reading of multiple sequence file",
1459                                                JOptionPane.ERROR_MESSAGE );
1460                 return;
1461             }
1462             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1463                 JOptionPane.showMessageDialog( this,
1464                                                "Multiple sequence file is empty",
1465                                                "Empty multiple sequence file",
1466                                                JOptionPane.ERROR_MESSAGE );
1467                 setArrowCursor();
1468                 return;
1469             }
1470         }
1471         if ( seqs != null ) {
1472             for( final Sequence seq : seqs ) {
1473                 System.out.println( seq.getIdentifier() );
1474             }
1475             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1476             int total_counter = 0;
1477             int attached_counter = 0;
1478             for( final Sequence seq : seqs ) {
1479                 ++total_counter;
1480                 final String seq_name = seq.getIdentifier();
1481                 if ( !ForesterUtil.isEmpty( seq_name ) ) {
1482                     List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
1483                     if ( nodes.isEmpty() ) {
1484                         nodes = phy.getNodesViaSequenceSymbol( seq_name );
1485                     }
1486                     if ( nodes.isEmpty() ) {
1487                         nodes = phy.getNodes( seq_name );
1488                     }
1489                     if ( nodes.size() > 1 ) {
1490                         JOptionPane.showMessageDialog( this,
1491                                                        "Sequence name \"" + seq_name + "\" is not unique",
1492                                                        "Sequence name not unique",
1493                                                        JOptionPane.ERROR_MESSAGE );
1494                         setArrowCursor();
1495                         return;
1496                     }
1497                     final String[] a = seq_name.split( "\\s" );
1498                     if ( nodes.isEmpty() && ( a.length > 1 ) ) {
1499                         final String seq_name_split = a[ 0 ];
1500                         nodes = phy.getNodesViaSequenceName( seq_name_split );
1501                         if ( nodes.isEmpty() ) {
1502                             nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
1503                         }
1504                         if ( nodes.isEmpty() ) {
1505                             nodes = phy.getNodes( seq_name_split );
1506                         }
1507                         if ( nodes.size() > 1 ) {
1508                             JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
1509                                     + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
1510                             setArrowCursor();
1511                             return;
1512                         }
1513                     }
1514                     if ( nodes.size() == 1 ) {
1515                         ++attached_counter;
1516                         final PhylogenyNode n = nodes.get( 0 );
1517                         if ( !n.getNodeData().isHasSequence() ) {
1518                             n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
1519                         }
1520                         n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
1521                         if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
1522                             n.getNodeData().getSequence().setName( seq_name );
1523                         }
1524                     }
1525                 }
1526             }
1527             if ( attached_counter > 0 ) {
1528                 int ext_nodes = 0;
1529                 int ext_nodes_with_seq = 0;
1530                 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
1531                     ++ext_nodes;
1532                     final PhylogenyNode n = iter.next();
1533                     if ( n.getNodeData().isHasSequence()
1534                             && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
1535                         ++ext_nodes_with_seq;
1536                     }
1537                 }
1538                 final String s;
1539                 if ( ext_nodes == ext_nodes_with_seq ) {
1540                     s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
1541                 }
1542                 else {
1543                     s = ext_nodes_with_seq + " out of " + ext_nodes
1544                             + " external nodes now have a molecular sequence attached to them.";
1545                 }
1546                 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
1547                     JOptionPane.showMessageDialog( this,
1548                                                    "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
1549                                                    "All sequences attached",
1550                                                    JOptionPane.INFORMATION_MESSAGE );
1551                 }
1552                 else {
1553                     JOptionPane.showMessageDialog( this, "Attached " + attached_counter
1554                             + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
1555                             + " sequences attached", JOptionPane.WARNING_MESSAGE );
1556                 }
1557             }
1558             else {
1559                 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
1560                         + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
1561             }
1562         }
1563     }
1564
1565     private void choosePdfWidth() {
1566         final String s = ( String ) JOptionPane.showInputDialog( this,
1567                                                                  "Please enter the default line width for PDF export.\n"
1568                                                                          + "[current value: "
1569                                                                          + getOptions().getPrintLineWidth() + "]\n",
1570                                                                  "Line Width for PDF Export",
1571                                                                  JOptionPane.QUESTION_MESSAGE,
1572                                                                  null,
1573                                                                  null,
1574                                                                  getOptions().getPrintLineWidth() );
1575         if ( !ForesterUtil.isEmpty( s ) ) {
1576             boolean success = true;
1577             float f = 0.0f;
1578             final String m_str = s.trim();
1579             if ( !ForesterUtil.isEmpty( m_str ) ) {
1580                 try {
1581                     f = Float.parseFloat( m_str );
1582                 }
1583                 catch ( final Exception ex ) {
1584                     success = false;
1585                 }
1586             }
1587             else {
1588                 success = false;
1589             }
1590             if ( success && ( f > 0.0 ) ) {
1591                 getOptions().setPrintLineWidth( f );
1592             }
1593         }
1594     }
1595
1596     private void choosePrintSize() {
1597         final String s = ( String ) JOptionPane.showInputDialog( this,
1598                                                                  "Please enter values for width and height,\nseparated by a comma.\n"
1599                                                                          + "[current values: "
1600                                                                          + getOptions().getPrintSizeX() + ", "
1601                                                                          + getOptions().getPrintSizeY() + "]\n"
1602                                                                          + "[A4: " + Constants.A4_SIZE_X + ", "
1603                                                                          + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1604                                                                          + Constants.US_LETTER_SIZE_X + ", "
1605                                                                          + Constants.US_LETTER_SIZE_Y + "]",
1606                                                                  "Default Size for Graphics Export",
1607                                                                  JOptionPane.QUESTION_MESSAGE,
1608                                                                  null,
1609                                                                  null,
1610                                                                  getOptions().getPrintSizeX() + ", "
1611                                                                          + getOptions().getPrintSizeY() );
1612         if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1613             boolean success = true;
1614             int x = 0;
1615             int y = 0;
1616             final String[] str_ary = s.split( "," );
1617             if ( str_ary.length == 2 ) {
1618                 final String x_str = str_ary[ 0 ].trim();
1619                 final String y_str = str_ary[ 1 ].trim();
1620                 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1621                     try {
1622                         x = Integer.parseInt( x_str );
1623                         y = Integer.parseInt( y_str );
1624                     }
1625                     catch ( final Exception ex ) {
1626                         success = false;
1627                     }
1628                 }
1629                 else {
1630                     success = false;
1631                 }
1632             }
1633             else {
1634                 success = false;
1635             }
1636             if ( success && ( x > 1 ) && ( y > 1 ) ) {
1637                 getOptions().setPrintSizeX( x );
1638                 getOptions().setPrintSizeY( y );
1639             }
1640         }
1641     }
1642
1643     private void closeCurrentPane() {
1644         if ( getMainPanel().getCurrentTreePanel() != null ) {
1645             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1646                 final int r = JOptionPane.showConfirmDialog( this,
1647                                                              "Close tab despite potentially unsaved changes?",
1648                                                              "Close Tab?",
1649                                                              JOptionPane.YES_NO_OPTION );
1650                 if ( r != JOptionPane.YES_OPTION ) {
1651                     return;
1652                 }
1653             }
1654             getMainPanel().closeCurrentPane();
1655             activateSaveAllIfNeeded();
1656         }
1657     }
1658
1659     private void collapse( final Phylogeny phy, final double m ) {
1660         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1661         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1662         double min_support = Double.MAX_VALUE;
1663         boolean conf_present = false;
1664         while ( it.hasNext() ) {
1665             final PhylogenyNode n = it.next();
1666             if ( !n.isExternal() && !n.isRoot() ) {
1667                 final List<Confidence> c = n.getBranchData().getConfidences();
1668                 if ( ( c != null ) && ( c.size() > 0 ) ) {
1669                     conf_present = true;
1670                     double max = 0;
1671                     for( final Confidence confidence : c ) {
1672                         if ( confidence.getValue() > max ) {
1673                             max = confidence.getValue();
1674                         }
1675                     }
1676                     if ( max < getMinNotCollapseConfidenceValue() ) {
1677                         to_be_removed.add( n );
1678                     }
1679                     if ( max < min_support ) {
1680                         min_support = max;
1681                     }
1682                 }
1683             }
1684         }
1685         if ( conf_present ) {
1686             for( final PhylogenyNode node : to_be_removed ) {
1687                 PhylogenyMethods.removeNode( node, phy );
1688             }
1689             if ( to_be_removed.size() > 0 ) {
1690                 phy.externalNodesHaveChanged();
1691                 phy.clearHashIdToNodeMap();
1692                 phy.recalculateNumberOfExternalDescendants( true );
1693                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1694                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1695                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1696                 getCurrentTreePanel().setNodeInPreorderToNull();
1697                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1698                 getCurrentTreePanel().resetPreferredSize();
1699                 getCurrentTreePanel().setEdited( true );
1700                 getCurrentTreePanel().repaint();
1701                 repaint();
1702             }
1703             if ( to_be_removed.size() > 0 ) {
1704                 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1705                         + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1706                         + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1707             }
1708             else {
1709                 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1710                         + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1711             }
1712         }
1713         else {
1714             JOptionPane.showMessageDialog( this,
1715                                            "No branch collapsed because no confidence values present",
1716                                            "No confidence values present",
1717                                            JOptionPane.INFORMATION_MESSAGE );
1718         }
1719     }
1720
1721     private void collapseBelowThreshold() {
1722         if ( getCurrentTreePanel() != null ) {
1723             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1724             if ( ( phy != null ) && !phy.isEmpty() ) {
1725                 final String s = ( String ) JOptionPane.showInputDialog( this,
1726                                                                          "Please enter the minimum confidence value\n",
1727                                                                          "Minimal Confidence Value",
1728                                                                          JOptionPane.QUESTION_MESSAGE,
1729                                                                          null,
1730                                                                          null,
1731                                                                          getMinNotCollapseConfidenceValue() );
1732                 if ( !ForesterUtil.isEmpty( s ) ) {
1733                     boolean success = true;
1734                     double m = 0.0;
1735                     final String m_str = s.trim();
1736                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1737                         try {
1738                             m = Double.parseDouble( m_str );
1739                         }
1740                         catch ( final Exception ex ) {
1741                             success = false;
1742                         }
1743                     }
1744                     else {
1745                         success = false;
1746                     }
1747                     if ( success && ( m >= 0.0 ) ) {
1748                         setMinNotCollapseConfidenceValue( m );
1749                         collapse( phy, m );
1750                     }
1751                 }
1752             }
1753         }
1754     }
1755
1756     private PhyloXmlParser createPhyloXmlParser() {
1757         PhyloXmlParser xml_parser = null;
1758         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1759             try {
1760                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1761             }
1762             catch ( final Exception e ) {
1763                 JOptionPane.showMessageDialog( this,
1764                                                e.getLocalizedMessage(),
1765                                                "failed to create validating XML parser",
1766                                                JOptionPane.WARNING_MESSAGE );
1767             }
1768         }
1769         if ( xml_parser == null ) {
1770             xml_parser = new PhyloXmlParser();
1771         }
1772         return xml_parser;
1773     }
1774
1775     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1776         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1777                                                                       getPhylogeneticInferenceOptions(),
1778                                                                       from_unaligned_seqs );
1779         dialog.activate();
1780         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1781             if ( !from_unaligned_seqs ) {
1782                 if ( getMsa() != null ) {
1783                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1784                                                                                     getPhylogeneticInferenceOptions()
1785                                                                                             .copy(), this );
1786                     new Thread( inferrer ).start();
1787                 }
1788                 else {
1789                     JOptionPane.showMessageDialog( this,
1790                                                    "No multiple sequence alignment selected",
1791                                                    "Phylogenetic Inference Not Launched",
1792                                                    JOptionPane.WARNING_MESSAGE );
1793                 }
1794             }
1795             else {
1796                 if ( getSeqs() != null ) {
1797                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1798                                                                                     getPhylogeneticInferenceOptions()
1799                                                                                             .copy(), this );
1800                     new Thread( inferrer ).start();
1801                 }
1802                 else {
1803                     JOptionPane.showMessageDialog( this,
1804                                                    "No input sequences selected",
1805                                                    "Phylogenetic Inference Not Launched",
1806                                                    JOptionPane.WARNING_MESSAGE );
1807                 }
1808             }
1809         }
1810     }
1811
1812     private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1813         final StringBuilder sb = new StringBuilder();
1814         final StringBuilder sb_failed = new StringBuilder();
1815         int counter = 0;
1816         int counter_failed = 0;
1817         if ( getCurrentTreePanel() != null ) {
1818             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1819             if ( ( phy != null ) && !phy.isEmpty() ) {
1820                 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1821                 while ( it.hasNext() ) {
1822                     final PhylogenyNode n = it.next();
1823                     final String name = n.getName().trim();
1824                     if ( !ForesterUtil.isEmpty( name ) ) {
1825                         final String nt = ParserUtils
1826                                 .extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1827                         if ( !ForesterUtil.isEmpty( nt ) ) {
1828                             if ( counter < 15 ) {
1829                                 sb.append( name + ": " + nt + "\n" );
1830                             }
1831                             else if ( counter == 15 ) {
1832                                 sb.append( "...\n" );
1833                             }
1834                             counter++;
1835                         }
1836                         else {
1837                             if ( counter_failed < 15 ) {
1838                                 sb_failed.append( name + "\n" );
1839                             }
1840                             else if ( counter_failed == 15 ) {
1841                                 sb_failed.append( "...\n" );
1842                             }
1843                             counter_failed++;
1844                         }
1845                     }
1846                 }
1847                 if ( counter > 0 ) {
1848                     String failed = "";
1849                     String all = "all ";
1850                     if ( counter_failed > 0 ) {
1851                         all = "";
1852                         failed = "\nCould not extract taxonomic data for " + counter_failed
1853                                 + " named external nodes:\n" + sb_failed;
1854                     }
1855                     JOptionPane.showMessageDialog( this,
1856                                                    "Extracted taxonomic data from " + all + counter
1857                                                            + " named external nodes:\n" + sb.toString() + failed,
1858                                                    "Taxonomic Data Extraction Completed",
1859                                                    counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1860                                                            : JOptionPane.INFORMATION_MESSAGE );
1861                 }
1862                 else {
1863                     JOptionPane
1864                             .showMessageDialog( this,
1865                                                 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1866                                                         + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1867                                                         + "or nodes already have taxonomic data?\n",
1868                                                 "No Taxonomic Data Extracted",
1869                                                 JOptionPane.ERROR_MESSAGE );
1870                 }
1871             }
1872         }
1873     }
1874
1875     private ControlPanel getControlPanel() {
1876         return getMainPanel().getControlPanel();
1877     }
1878
1879     private File getCurrentDir() {
1880         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1881             if ( ForesterUtil.isWindows() ) {
1882                 try {
1883                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1884                 }
1885                 catch ( final Exception e ) {
1886                     _current_dir = null;
1887                 }
1888             }
1889         }
1890         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1891             if ( System.getProperty( "user.home" ) != null ) {
1892                 _current_dir = new File( System.getProperty( "user.home" ) );
1893             }
1894             else if ( System.getProperty( "user.dir" ) != null ) {
1895                 _current_dir = new File( System.getProperty( "user.dir" ) );
1896             }
1897         }
1898         return _current_dir;
1899     }
1900
1901     private double getMinNotCollapseConfidenceValue() {
1902         return _min_not_collapse;
1903     }
1904
1905     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1906         if ( _phylogenetic_inference_options == null ) {
1907             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1908         }
1909         return _phylogenetic_inference_options;
1910     }
1911
1912     private boolean isUnsavedDataPresent() {
1913         final List<TreePanel> tps = getMainPanel().getTreePanels();
1914         for( final TreePanel tp : tps ) {
1915             if ( tp.isEdited() ) {
1916                 return true;
1917             }
1918         }
1919         return false;
1920     }
1921
1922     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1923         if ( getCurrentTreePanel() != null ) {
1924             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1925             if ( ( phy != null ) && !phy.isEmpty() ) {
1926                 PhylogenyMethods
1927                         .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1928             }
1929         }
1930     }
1931
1932     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1933         if ( getCurrentTreePanel() != null ) {
1934             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1935             if ( ( phy != null ) && !phy.isEmpty() ) {
1936                 PhylogenyMethods.transferNodeNameToField( phy,
1937                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1938                                                           false );
1939             }
1940         }
1941     }
1942
1943     private void newTree() {
1944         final Phylogeny[] phys = new Phylogeny[ 1 ];
1945         final Phylogeny phy = new Phylogeny();
1946         final PhylogenyNode node = new PhylogenyNode();
1947         phy.setRoot( node );
1948         phy.setRooted( true );
1949         phys[ 0 ] = phy;
1950         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1951         _mainpanel.getControlPanel().showWhole();
1952         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1953         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1954         if ( getMainPanel().getMainFrame() == null ) {
1955             // Must be "E" applet version.
1956             ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1957                     .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1958         }
1959         else {
1960             getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1961         }
1962         activateSaveAllIfNeeded();
1963         System.gc();
1964     }
1965
1966     private void obtainDetailedTaxonomicInformation() {
1967         if ( getCurrentTreePanel() != null ) {
1968             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1969             if ( ( phy != null ) && !phy.isEmpty() ) {
1970                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1971                                                                        _mainpanel.getCurrentTreePanel(),
1972                                                                        phy.copy(),
1973                                                                        false,
1974                                                                        true );
1975                 new Thread( t ).start();
1976             }
1977         }
1978     }
1979
1980     private void obtainDetailedTaxonomicInformationDelete() {
1981         if ( getCurrentTreePanel() != null ) {
1982             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1983             if ( ( phy != null ) && !phy.isEmpty() ) {
1984                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1985                                                                        _mainpanel.getCurrentTreePanel(),
1986                                                                        phy.copy(),
1987                                                                        true,
1988                                                                        true );
1989                 new Thread( t ).start();
1990             }
1991         }
1992     }
1993
1994     private void obtainSequenceInformation() {
1995         if ( getCurrentTreePanel() != null ) {
1996             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1997             if ( ( phy != null ) && !phy.isEmpty() ) {
1998                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1999                                                                          _mainpanel.getCurrentTreePanel(),
2000                                                                          phy.copy() );
2001                 new Thread( u ).start();
2002             }
2003         }
2004     }
2005
2006     private void print() {
2007         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2008                 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2009             return;
2010         }
2011         if ( !getOptions().isPrintUsingActualSize() ) {
2012             getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
2013                                                              getOptions().getPrintSizeY() - 140,
2014                                                              true );
2015             getCurrentTreePanel().resetPreferredSize();
2016             getCurrentTreePanel().repaint();
2017         }
2018         final String job_name = Constants.PRG_NAME;
2019         boolean error = false;
2020         String printer_name = null;
2021         try {
2022             printer_name = Printer.print( getCurrentTreePanel(), job_name );
2023         }
2024         catch ( final Exception e ) {
2025             error = true;
2026             JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2027         }
2028         if ( !error && ( printer_name != null ) ) {
2029             String msg = "Printing data sent to printer";
2030             if ( printer_name.length() > 1 ) {
2031                 msg += " [" + printer_name + "]";
2032             }
2033             JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2034         }
2035         if ( !getOptions().isPrintUsingActualSize() ) {
2036             getControlPanel().showWhole();
2037         }
2038     }
2039
2040     private void printPhylogenyToPdf( final String file_name ) {
2041         if ( !getOptions().isPrintUsingActualSize() ) {
2042             getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
2043                                                              getOptions().getPrintSizeY(),
2044                                                              true );
2045             getCurrentTreePanel().resetPreferredSize();
2046             getCurrentTreePanel().repaint();
2047         }
2048         String pdf_written_to = "";
2049         boolean error = false;
2050         try {
2051             if ( getOptions().isPrintUsingActualSize() ) {
2052                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2053                                                                   getCurrentTreePanel(),
2054                                                                   getCurrentTreePanel().getWidth(),
2055                                                                   getCurrentTreePanel().getHeight() );
2056             }
2057             else {
2058                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2059                         .getPrintSizeX(), getOptions().getPrintSizeY() );
2060             }
2061         }
2062         catch ( final IOException e ) {
2063             error = true;
2064             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2065         }
2066         if ( !error ) {
2067             if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2068                 JOptionPane.showMessageDialog( this,
2069                                                "Wrote PDF to: " + pdf_written_to,
2070                                                "Information",
2071                                                JOptionPane.INFORMATION_MESSAGE );
2072             }
2073             else {
2074                 JOptionPane.showMessageDialog( this,
2075                                                "There was an unknown problem when attempting to write to PDF file: \""
2076                                                        + file_name + "\"",
2077                                                "Error",
2078                                                JOptionPane.ERROR_MESSAGE );
2079             }
2080         }
2081         if ( !getOptions().isPrintUsingActualSize() ) {
2082             getControlPanel().showWhole();
2083         }
2084     }
2085
2086     private void readPhylogeniesFromFile() {
2087         boolean exception = false;
2088         Phylogeny[] phys = null;
2089         // Set an initial directory if none set yet
2090         final File my_dir = getCurrentDir();
2091         _open_filechooser.setMultiSelectionEnabled( true );
2092         // Open file-open dialog and set current directory
2093         if ( my_dir != null ) {
2094             _open_filechooser.setCurrentDirectory( my_dir );
2095         }
2096         final int result = _open_filechooser.showOpenDialog( _contentpane );
2097         // All done: get the file
2098         final File[] files = _open_filechooser.getSelectedFiles();
2099         setCurrentDir( _open_filechooser.getCurrentDirectory() );
2100         boolean nhx_or_nexus = false;
2101         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2102             for( final File file : files ) {
2103                 if ( ( file != null ) && !file.isDirectory() ) {
2104                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2105                         _mainpanel.getCurrentTreePanel().setWaitCursor();
2106                     }
2107                     else {
2108                         _mainpanel.setWaitCursor();
2109                     }
2110                     if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2111                             || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2112                         try {
2113                             final NHXParser nhx = new NHXParser();
2114                             setSpecialOptionsForNhxParser( nhx );
2115                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
2116                             nhx_or_nexus = true;
2117                         }
2118                         catch ( final Exception e ) {
2119                             exception = true;
2120                             exceptionOccuredDuringOpenFile( e );
2121                         }
2122                     }
2123                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2124                         warnIfNotPhyloXmlValidation( getConfiguration() );
2125                         try {
2126                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
2127                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2128                         }
2129                         catch ( final Exception e ) {
2130                             exception = true;
2131                             exceptionOccuredDuringOpenFile( e );
2132                         }
2133                     }
2134                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2135                         try {
2136                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2137                         }
2138                         catch ( final Exception e ) {
2139                             exception = true;
2140                             exceptionOccuredDuringOpenFile( e );
2141                         }
2142                     }
2143                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2144                         try {
2145                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2146                             setSpecialOptionsForNexParser( nex );
2147                             phys = PhylogenyMethods.readPhylogenies( nex, file );
2148                             nhx_or_nexus = true;
2149                         }
2150                         catch ( final Exception e ) {
2151                             exception = true;
2152                             exceptionOccuredDuringOpenFile( e );
2153                         }
2154                     }
2155                     // "*.*":
2156                     else {
2157                         try {
2158                             final PhylogenyParser parser = ParserUtils
2159                                     .createParserDependingOnFileType( file, getConfiguration()
2160                                             .isValidatePhyloXmlAgainstSchema() );
2161                             if ( parser instanceof NexusPhylogeniesParser ) {
2162                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2163                                 setSpecialOptionsForNexParser( nex );
2164                                 nhx_or_nexus = true;
2165                             }
2166                             else if ( parser instanceof NHXParser ) {
2167                                 final NHXParser nhx = ( NHXParser ) parser;
2168                                 setSpecialOptionsForNhxParser( nhx );
2169                                 nhx_or_nexus = true;
2170                             }
2171                             else if ( parser instanceof PhyloXmlParser ) {
2172                                 warnIfNotPhyloXmlValidation( getConfiguration() );
2173                             }
2174                             phys = PhylogenyMethods.readPhylogenies( parser, file );
2175                         }
2176                         catch ( final Exception e ) {
2177                             exception = true;
2178                             exceptionOccuredDuringOpenFile( e );
2179                         }
2180                     }
2181                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2182                         _mainpanel.getCurrentTreePanel().setArrowCursor();
2183                     }
2184                     else {
2185                         _mainpanel.setArrowCursor();
2186                     }
2187                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2188                         boolean one_desc = false;
2189                         if ( nhx_or_nexus ) {
2190                             for( final Phylogeny phy : phys ) {
2191                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2192                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2193                                 }
2194                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2195                                     one_desc = true;
2196                                     break;
2197                                 }
2198                             }
2199                         }
2200                         AptxUtil.addPhylogeniesToTabs( phys,
2201                                                        file.getName(),
2202                                                        file.getAbsolutePath(),
2203                                                        getConfiguration(),
2204                                                        getMainPanel() );
2205                         _mainpanel.getControlPanel().showWhole();
2206                         if ( nhx_or_nexus && one_desc ) {
2207                             JOptionPane
2208                                     .showMessageDialog( this,
2209                                                         "One or more trees contain (a) node(s) with one descendant, "
2210                                                                 + ForesterUtil.LINE_SEPARATOR
2211                                                                 + "possibly indicating illegal parentheses within node names.",
2212                                                         "Warning: Possible Error in New Hampshire Formatted Data",
2213                                                         JOptionPane.WARNING_MESSAGE );
2214                         }
2215                     }
2216                 }
2217             }
2218         }
2219         activateSaveAllIfNeeded();
2220         System.gc();
2221     }
2222
2223     private void readSpeciesTreeFromFile() {
2224         Phylogeny t = null;
2225         boolean exception = false;
2226         final File my_dir = getCurrentDir();
2227         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2228         if ( my_dir != null ) {
2229             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2230         }
2231         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2232         final File file = _open_filechooser_for_species_tree.getSelectedFile();
2233         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2234             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2235                 try {
2236                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2237                     t = trees[ 0 ];
2238                 }
2239                 catch ( final Exception e ) {
2240                     exception = true;
2241                     exceptionOccuredDuringOpenFile( e );
2242                 }
2243             }
2244             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2245                 try {
2246                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2247                     t = trees[ 0 ];
2248                 }
2249                 catch ( final Exception e ) {
2250                     exception = true;
2251                     exceptionOccuredDuringOpenFile( e );
2252                 }
2253             }
2254             // "*.*":
2255             else {
2256                 try {
2257                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2258                     t = trees[ 0 ];
2259                 }
2260                 catch ( final Exception e ) {
2261                     exception = true;
2262                     exceptionOccuredDuringOpenFile( e );
2263                 }
2264             }
2265             if ( !exception && ( t != null ) && !t.isRooted() ) {
2266                 exception = true;
2267                 t = null;
2268                 JOptionPane.showMessageDialog( this,
2269                                                "Species tree is not rooted",
2270                                                "Species tree not loaded",
2271                                                JOptionPane.ERROR_MESSAGE );
2272             }
2273             if ( !exception && ( t != null ) ) {
2274                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2275                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2276                     final PhylogenyNode node = it.next();
2277                     if ( !node.getNodeData().isHasTaxonomy() ) {
2278                         exception = true;
2279                         t = null;
2280                         JOptionPane
2281                                 .showMessageDialog( this,
2282                                                     "Species tree contains external node(s) without taxonomy information",
2283                                                     "Species tree not loaded",
2284                                                     JOptionPane.ERROR_MESSAGE );
2285                         break;
2286                     }
2287                     else {
2288                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2289                             exception = true;
2290                             t = null;
2291                             JOptionPane.showMessageDialog( this,
2292                                                            "Taxonomy ["
2293                                                                    + node.getNodeData().getTaxonomy().asSimpleText()
2294                                                                    + "] is not unique in species tree",
2295                                                            "Species tree not loaded",
2296                                                            JOptionPane.ERROR_MESSAGE );
2297                             break;
2298                         }
2299                         else {
2300                             tax_set.add( node.getNodeData().getTaxonomy() );
2301                         }
2302                     }
2303                 }
2304             }
2305             if ( !exception && ( t != null ) ) {
2306                 setSpeciesTree( t );
2307                 JOptionPane.showMessageDialog( this,
2308                                                "Species tree successfully loaded",
2309                                                "Species tree loaded",
2310                                                JOptionPane.INFORMATION_MESSAGE );
2311             }
2312             _contentpane.repaint();
2313             System.gc();
2314         }
2315     }
2316
2317     private void setArrowCursor() {
2318         try {
2319             _mainpanel.getCurrentTreePanel().setArrowCursor();
2320         }
2321         catch ( final Exception ex ) {
2322             // Do nothing.
2323         }
2324     }
2325
2326     private void setCurrentDir( final File current_dir ) {
2327         _current_dir = current_dir;
2328     }
2329
2330     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2331         _min_not_collapse = min_not_collapse;
2332     }
2333
2334     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2335         _phylogenetic_inference_options = phylogenetic_inference_options;
2336     }
2337
2338     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2339         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2340         nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2341     }
2342
2343     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2344         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2345         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2346     }
2347
2348     private void writeAllToFile() {
2349         if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2350             return;
2351         }
2352         final File my_dir = getCurrentDir();
2353         if ( my_dir != null ) {
2354             _save_filechooser.setCurrentDirectory( my_dir );
2355         }
2356         _save_filechooser.setSelectedFile( new File( "" ) );
2357         final int result = _save_filechooser.showSaveDialog( _contentpane );
2358         final File file = _save_filechooser.getSelectedFile();
2359         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2360         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2361             if ( file.exists() ) {
2362                 final int i = JOptionPane.showConfirmDialog( this,
2363                                                              file + " already exists. Overwrite?",
2364                                                              "Warning",
2365                                                              JOptionPane.OK_CANCEL_OPTION,
2366                                                              JOptionPane.WARNING_MESSAGE );
2367                 if ( i != JOptionPane.OK_OPTION ) {
2368                     return;
2369                 }
2370                 else {
2371                     try {
2372                         file.delete();
2373                     }
2374                     catch ( final Exception e ) {
2375                         JOptionPane.showMessageDialog( this,
2376                                                        "Failed to delete: " + file,
2377                                                        "Error",
2378                                                        JOptionPane.WARNING_MESSAGE );
2379                     }
2380                 }
2381             }
2382             final int count = getMainPanel().getTabbedPane().getTabCount();
2383             final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2384             for( int i = 0; i < count; ++i ) {
2385                 final Phylogeny phy = getMainPanel().getPhylogeny( i );
2386                 if ( ForesterUtil.isEmpty( phy.getName() )
2387                         && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
2388                     phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
2389                 }
2390                 trees.add( phy );
2391                 getMainPanel().getTreePanels().get( i ).setEdited( false );
2392             }
2393             final PhylogenyWriter writer = new PhylogenyWriter();
2394             try {
2395                 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2396             }
2397             catch ( final IOException e ) {
2398                 JOptionPane.showMessageDialog( this,
2399                                                "Failed to write to: " + file,
2400                                                "Error",
2401                                                JOptionPane.WARNING_MESSAGE );
2402             }
2403         }
2404     }
2405
2406     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2407         try {
2408             final PhylogenyWriter writer = new PhylogenyWriter();
2409             writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2410         }
2411         catch ( final Exception e ) {
2412             exception = true;
2413             exceptionOccuredDuringSaveAs( e );
2414         }
2415         return exception;
2416     }
2417
2418     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2419         try {
2420             final PhylogenyWriter writer = new PhylogenyWriter();
2421             writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2422         }
2423         catch ( final Exception e ) {
2424             exception = true;
2425             exceptionOccuredDuringSaveAs( e );
2426         }
2427         return exception;
2428     }
2429
2430     private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2431         try {
2432             final PhylogenyWriter writer = new PhylogenyWriter();
2433             writer.toPhyloXML( file, t, 0 );
2434         }
2435         catch ( final Exception e ) {
2436             exception = true;
2437             exceptionOccuredDuringSaveAs( e );
2438         }
2439         return exception;
2440     }
2441
2442     private void writeToFile( final Phylogeny t ) {
2443         if ( t == null ) {
2444             return;
2445         }
2446         String initial_filename = null;
2447         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2448             try {
2449                 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2450             }
2451             catch ( final IOException e ) {
2452                 initial_filename = null;
2453             }
2454         }
2455         if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2456             _save_filechooser.setSelectedFile( new File( initial_filename ) );
2457         }
2458         else {
2459             _save_filechooser.setSelectedFile( new File( "" ) );
2460         }
2461         final File my_dir = getCurrentDir();
2462         if ( my_dir != null ) {
2463             _save_filechooser.setCurrentDirectory( my_dir );
2464         }
2465         final int result = _save_filechooser.showSaveDialog( _contentpane );
2466         final File file = _save_filechooser.getSelectedFile();
2467         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2468         boolean exception = false;
2469         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2470             if ( file.exists() ) {
2471                 final int i = JOptionPane.showConfirmDialog( this,
2472                                                              file + " already exists.\nOverwrite?",
2473                                                              "Overwrite?",
2474                                                              JOptionPane.OK_CANCEL_OPTION,
2475                                                              JOptionPane.QUESTION_MESSAGE );
2476                 if ( i != JOptionPane.OK_OPTION ) {
2477                     return;
2478                 }
2479                 else {
2480                     final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2481                     try {
2482                         ForesterUtil.copyFile( file, to );
2483                     }
2484                     catch ( final Exception e ) {
2485                         JOptionPane.showMessageDialog( this,
2486                                                        "Failed to create backup copy " + to,
2487                                                        "Failed to Create Backup Copy",
2488                                                        JOptionPane.WARNING_MESSAGE );
2489                     }
2490                     try {
2491                         file.delete();
2492                     }
2493                     catch ( final Exception e ) {
2494                         JOptionPane.showMessageDialog( this,
2495                                                        "Failed to delete: " + file,
2496                                                        "Failed to Delete",
2497                                                        JOptionPane.WARNING_MESSAGE );
2498                     }
2499                 }
2500             }
2501             if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2502                 exception = writeAsNewHampshire( t, exception, file );
2503             }
2504             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2505                 exception = writeAsPhyloXml( t, exception, file );
2506             }
2507             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2508                 exception = writeAsNexus( t, exception, file );
2509             }
2510             // "*.*":
2511             else {
2512                 final String file_name = file.getName().trim().toLowerCase();
2513                 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2514                         || file_name.endsWith( ".tree" ) ) {
2515                     exception = writeAsNewHampshire( t, exception, file );
2516                 }
2517                 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2518                     exception = writeAsNexus( t, exception, file );
2519                 }
2520                 // XML is default:
2521                 else {
2522                     exception = writeAsPhyloXml( t, exception, file );
2523                 }
2524             }
2525             if ( !exception ) {
2526                 getMainPanel().setTitleOfSelectedTab( file.getName() );
2527                 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2528                 getMainPanel().getCurrentTreePanel().setEdited( false );
2529             }
2530         }
2531     }
2532
2533     private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2534         if ( ( t == null ) || t.isEmpty() ) {
2535             return;
2536         }
2537         String initial_filename = "";
2538         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2539             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2540         }
2541         if ( initial_filename.indexOf( '.' ) > 0 ) {
2542             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2543         }
2544         initial_filename = initial_filename + "." + type;
2545         _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2546         final File my_dir = getCurrentDir();
2547         if ( my_dir != null ) {
2548             _writetographics_filechooser.setCurrentDirectory( my_dir );
2549         }
2550         final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2551         File file = _writetographics_filechooser.getSelectedFile();
2552         setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2553         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2554             if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2555                 file = new File( file.toString() + "." + type );
2556             }
2557             if ( file.exists() ) {
2558                 final int i = JOptionPane.showConfirmDialog( this,
2559                                                              file + " already exists. Overwrite?",
2560                                                              "Warning",
2561                                                              JOptionPane.OK_CANCEL_OPTION,
2562                                                              JOptionPane.WARNING_MESSAGE );
2563                 if ( i != JOptionPane.OK_OPTION ) {
2564                     return;
2565                 }
2566                 else {
2567                     try {
2568                         file.delete();
2569                     }
2570                     catch ( final Exception e ) {
2571                         JOptionPane.showMessageDialog( this,
2572                                                        "Failed to delete: " + file,
2573                                                        "Error",
2574                                                        JOptionPane.WARNING_MESSAGE );
2575                     }
2576                 }
2577             }
2578             writePhylogenyToGraphicsFile( file.toString(), type );
2579         }
2580     }
2581
2582     private void writeToPdf( final Phylogeny t ) {
2583         if ( ( t == null ) || t.isEmpty() ) {
2584             return;
2585         }
2586         String initial_filename = "";
2587         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2588             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2589         }
2590         if ( initial_filename.indexOf( '.' ) > 0 ) {
2591             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2592         }
2593         initial_filename = initial_filename + ".pdf";
2594         _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2595         final File my_dir = getCurrentDir();
2596         if ( my_dir != null ) {
2597             _writetopdf_filechooser.setCurrentDirectory( my_dir );
2598         }
2599         final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2600         File file = _writetopdf_filechooser.getSelectedFile();
2601         setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2602         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2603             if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2604                 file = new File( file.toString() + ".pdf" );
2605             }
2606             if ( file.exists() ) {
2607                 final int i = JOptionPane.showConfirmDialog( this,
2608                                                              file + " already exists. Overwrite?",
2609                                                              "WARNING",
2610                                                              JOptionPane.OK_CANCEL_OPTION,
2611                                                              JOptionPane.WARNING_MESSAGE );
2612                 if ( i != JOptionPane.OK_OPTION ) {
2613                     return;
2614                 }
2615             }
2616             printPhylogenyToPdf( file.toString() );
2617         }
2618     }
2619
2620     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2621         return new MainFrameApplication( phys, config );
2622     }
2623
2624     public static MainFrame createInstance( final Phylogeny[] phys,
2625                                             final Configuration config,
2626                                             final String title,
2627                                             final File current_dir ) {
2628         return new MainFrameApplication( phys, config, title, current_dir );
2629     }
2630
2631     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2632         return new MainFrameApplication( phys, config, title );
2633     }
2634
2635     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2636         return new MainFrameApplication( phys, config_file_name, title );
2637     }
2638
2639     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2640         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2641                 + o.getPrintSizeY() + ")" );
2642     }
2643
2644     static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2645         mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2646     }
2647
2648     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2649         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2650             JOptionPane
2651                     .showMessageDialog( null,
2652                                         ForesterUtil
2653                                                 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2654                                                            80 ),
2655                                         "Warning",
2656                                         JOptionPane.WARNING_MESSAGE );
2657         }
2658     }
2659 } // MainFrameApplication.
2660
2661 class DefaultFilter extends FileFilter {
2662
2663     @Override
2664     public boolean accept( final File f ) {
2665         final String file_name = f.getName().trim().toLowerCase();
2666         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2667                 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2668                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2669                 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2670                 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2671                 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2672                 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2673                 || file_name.endsWith( ".con" ) || f.isDirectory();
2674     }
2675
2676     @Override
2677     public String getDescription() {
2678         return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2679     }
2680 }
2681
2682 class GraphicsFileFilter extends FileFilter {
2683
2684     @Override
2685     public boolean accept( final File f ) {
2686         final String file_name = f.getName().trim().toLowerCase();
2687         return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2688                 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2689     }
2690
2691     @Override
2692     public String getDescription() {
2693         return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2694     }
2695 }
2696
2697 class MsaFileFilter extends FileFilter {
2698
2699     @Override
2700     public boolean accept( final File f ) {
2701         final String file_name = f.getName().trim().toLowerCase();
2702         return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2703                 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2704     }
2705
2706     @Override
2707     public String getDescription() {
2708         return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2709     }
2710 }
2711
2712 class NexusFilter extends FileFilter {
2713
2714     @Override
2715     public boolean accept( final File f ) {
2716         final String file_name = f.getName().trim().toLowerCase();
2717         return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2718                 || file_name.endsWith( ".tre" ) || f.isDirectory();
2719     }
2720
2721     @Override
2722     public String getDescription() {
2723         return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2724     }
2725 } // NexusFilter
2726
2727 class NHFilter extends FileFilter {
2728
2729     @Override
2730     public boolean accept( final File f ) {
2731         final String file_name = f.getName().trim().toLowerCase();
2732         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2733                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2734                 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2735                 || f.isDirectory();
2736     }
2737
2738     @Override
2739     public String getDescription() {
2740         return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2741     }
2742 } // NHFilter
2743
2744 class NHXFilter extends FileFilter {
2745
2746     @Override
2747     public boolean accept( final File f ) {
2748         final String file_name = f.getName().trim().toLowerCase();
2749         return file_name.endsWith( ".nhx" ) || f.isDirectory();
2750     }
2751
2752     @Override
2753     public String getDescription() {
2754         return "NHX files (*.nhx) [deprecated]";
2755     }
2756 }
2757
2758 class PdfFilter extends FileFilter {
2759
2760     @Override
2761     public boolean accept( final File f ) {
2762         return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2763     }
2764
2765     @Override
2766     public String getDescription() {
2767         return "PDF files (*.pdf)";
2768     }
2769 } // PdfFilter
2770
2771 class SequencesFileFilter extends FileFilter {
2772
2773     @Override
2774     public boolean accept( final File f ) {
2775         final String file_name = f.getName().trim().toLowerCase();
2776         return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2777                 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2778     }
2779
2780     @Override
2781     public String getDescription() {
2782         return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2783     }
2784 }
2785
2786 class TolFilter extends FileFilter {
2787
2788     @Override
2789     public boolean accept( final File f ) {
2790         final String file_name = f.getName().trim().toLowerCase();
2791         return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2792                 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2793     }
2794
2795     @Override
2796     public String getDescription() {
2797         return "Tree of Life files (*.tol, *.tolxml)";
2798     }
2799 } // TolFilter
2800
2801 class XMLFilter extends FileFilter {
2802
2803     @Override
2804     public boolean accept( final File f ) {
2805         final String file_name = f.getName().trim().toLowerCase();
2806         return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2807                 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2808     }
2809
2810     @Override
2811     public String getDescription() {
2812         return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
2813     }
2814 } // XMLFilter