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

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