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

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: www.phylosoft.org/forester
  26
  27 package org.forester.archaeopteryx;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Font;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ComponentAdapter;
  33 import java.awt.event.ComponentEvent;
  34 import java.awt.event.WindowAdapter;
  35 import java.awt.event.WindowEvent;
  36 import java.io.File;
  37 import java.io.FileInputStream;
  38 import java.io.IOException;
  39 import java.io.InputStream;
  40 import java.net.MalformedURLException;
  41 import java.net.URL;
  42 import java.util.ArrayList;
  43 import java.util.HashSet;
  44 import java.util.List;
  45 import java.util.Set;
  46
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.JCheckBoxMenuItem;
  49 import javax.swing.JFileChooser;
  50 import javax.swing.JMenu;
  51 import javax.swing.JMenuBar;
  52 import javax.swing.JMenuItem;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JRadioButtonMenuItem;
  55 import javax.swing.UIManager;
  56 import javax.swing.UnsupportedLookAndFeelException;
  57 import javax.swing.WindowConstants;
  58 import javax.swing.event.ChangeEvent;
  59 import javax.swing.event.ChangeListener;
  60 import javax.swing.filechooser.FileFilter;
  61 import javax.swing.plaf.synth.SynthLookAndFeel;
  62
  63 import org.forester.analysis.TaxonomyDataManager;
  64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
  69 import org.forester.archaeopteryx.tools.GoAnnotation;
  70 import org.forester.archaeopteryx.tools.InferenceManager;
  71 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
  72 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
  73 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
  74 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
  75 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  76 import org.forester.archaeopteryx.webservices.WebservicesManager;
  77 import org.forester.io.parsers.FastaParser;
  78 import org.forester.io.parsers.GeneralMsaParser;
  79 import org.forester.io.parsers.PhylogenyParser;
  80 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  81 import org.forester.io.parsers.nhx.NHXParser;
  82 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  83 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  84 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  85 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  86 import org.forester.io.parsers.tol.TolParser;
  87 import org.forester.io.parsers.util.ParserUtils;
  88 import org.forester.io.writers.PhylogenyWriter;
  89 import org.forester.io.writers.SequenceWriter;
  90 import org.forester.msa.Msa;
  91 import org.forester.msa.MsaFormatException;
  92 import org.forester.phylogeny.Phylogeny;
  93 import org.forester.phylogeny.PhylogenyMethods;
  94 import org.forester.phylogeny.PhylogenyNode;
  95 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  96 import org.forester.phylogeny.data.Confidence;
  97 import org.forester.phylogeny.data.Taxonomy;
  98 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  99 import org.forester.phylogeny.factories.PhylogenyFactory;
 100 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 101 import org.forester.sdi.GSDI;
 102 import org.forester.sdi.GSDIR;
 103 import org.forester.sdi.SDIException;
 104 import org.forester.sdi.SDIR;
 105 import org.forester.sequence.Sequence;
 106 import org.forester.util.BasicDescriptiveStatistics;
 107 import org.forester.util.BasicTable;
 108 import org.forester.util.BasicTableParser;
 109 import org.forester.util.DescriptiveStatistics;
 110 import org.forester.util.ForesterUtil;
 111 import org.forester.util.WindowsUtils;
 112
 113 public final class MainFrameApplication extends MainFrame {
 114
 115     static final String                      INFER_ANCESTOR_TAXONOMIES             = "Infer Ancestor Taxonomies";
 116     static final String                      OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
 117     private final static int                 FRAME_X_SIZE                          = 800;
 118     private final static int                 FRAME_Y_SIZE                          = 800;
 119     // Filters for the file-open dialog (classes defined in this file)
 120     private final static NHFilter            nhfilter                              = new NHFilter();
 121     private final static NHXFilter           nhxfilter                             = new NHXFilter();
 122     private final static XMLFilter           xmlfilter                             = new XMLFilter();
 123     private final static TolFilter           tolfilter                             = new TolFilter();
 124     private final static NexusFilter         nexusfilter                           = new NexusFilter();
 125     private final static PdfFilter           pdffilter                             = new PdfFilter();
 126     private final static GraphicsFileFilter  graphicsfilefilter                    = new GraphicsFileFilter();
 127     private final static MsaFileFilter       msafilter                             = new MsaFileFilter();
 128     private final static SequencesFileFilter seqsfilter                            = new SequencesFileFilter();
 129     private final static DefaultFilter       defaultfilter                         = new DefaultFilter();
 130     private static final long                serialVersionUID                      = -799735726778865234L;
 131     private final JFileChooser               _values_filechooser;
 132     private final JFileChooser               _open_filechooser;
 133     private final JFileChooser               _msa_filechooser;
 134     private final JFileChooser               _seqs_filechooser;
 135     private final JFileChooser               _open_filechooser_for_species_tree;
 136     private final JFileChooser               _save_filechooser;
 137     private final JFileChooser               _writetopdf_filechooser;
 138     private final JFileChooser               _writetographics_filechooser;
 139     // Analysis menu
 140     private JMenu                            _analysis_menu;
 141     private JMenuItem                        _load_species_tree_item;
 142     private JMenuItem                        _gsdi_item;
 143     private JMenuItem                        _gsdir_item;
 144     private JMenuItem                        _root_min_dups_item;
 145     private JMenuItem                        _root_min_cost_l_item;
 146     private JMenuItem                        _lineage_inference;
 147     private JMenuItem                        _function_analysis;
 148     // Application-only print menu items
 149     private JMenuItem                        _print_item;
 150     private JMenuItem                        _write_to_pdf_item;
 151     private JMenuItem                        _write_to_jpg_item;
 152     private JMenuItem                        _write_to_gif_item;
 153     private JMenuItem                        _write_to_tif_item;
 154     private JMenuItem                        _write_to_png_item;
 155     private JMenuItem                        _write_to_bmp_item;
 156     private Phylogeny                        _species_tree;
 157     private File                             _current_dir;
 158     private ButtonGroup                      _radio_group_1;
 159     private ButtonGroup                      _radio_group_2;
 160     // Others:
 161     double                                   _min_not_collapse                     = Constants.MIN_NOT_COLLAPSE_DEFAULT;
 162     // Phylogeny Inference menu
 163     private JMenu                            _inference_menu;
 164     private JMenuItem                        _inference_from_msa_item;
 165     private JMenuItem                        _inference_from_seqs_item;
 166     // Phylogeny Inference
 167     private PhylogeneticInferenceOptions     _phylogenetic_inference_options       = null;
 168     private Msa                              _msa                                  = null;
 169     private File                             _msa_file                             = null;
 170     private List<Sequence>                   _seqs                                 = null;
 171     private File                             _seqs_file                            = null;
 172     // expression values menu:
 173     JMenuItem                                _read_values_jmi;
 174
 175     private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
 176         _configuration = config;
 177         if ( _configuration == null ) {
 178             throw new IllegalArgumentException( "configuration is null" );
 179         }
 180         setVisible( false );
 181         setOptions( Options.createInstance( _configuration ) );
 182         _mainpanel = new MainPanel( _configuration, this );
 183         _open_filechooser = null;
 184         _open_filechooser_for_species_tree = null;
 185         _save_filechooser = null;
 186         _writetopdf_filechooser = null;
 187         _writetographics_filechooser = null;
 188         _msa_filechooser = null;
 189         _seqs_filechooser = null;
 190         _values_filechooser = null;
 191         _jmenubar = new JMenuBar();
 192         buildFileMenu();
 193         buildTypeMenu();
 194         _contentpane = getContentPane();
 195         _contentpane.setLayout( new BorderLayout() );
 196         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 197         // App is this big
 198         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 199         // The window listener
 200         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 201         addWindowListener( new WindowAdapter() {
 202
 203             @Override
 204             public void windowClosing( final WindowEvent e ) {
 205                 exit();
 206             }
 207         } );
 208         //   setVisible( true );
 209         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 210             AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
 211             validate();
 212             getMainPanel().getControlPanel().showWholeAll();
 213             getMainPanel().getControlPanel().showWhole();
 214         }
 215         //activateSaveAllIfNeeded();
 216         // ...and its children
 217         _contentpane.repaint();
 218     }
 219
 220     private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
 221         this( phys, config, title, null );
 222     }
 223
 224     private MainFrameApplication( final Phylogeny[] phys,
 225                                   final Configuration config,
 226                                   final String title,
 227                                   final File current_dir ) {
 228         super();
 229         _configuration = config;
 230         if ( _configuration == null ) {
 231             throw new IllegalArgumentException( "configuration is null" );
 232         }
 233         try {
 234             boolean synth_exception = false;
 235             if ( Constants.__SYNTH_LF ) {
 236                 try {
 237                     final SynthLookAndFeel synth = new SynthLookAndFeel();
 238                     synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
 239                                 MainFrameApplication.class );
 240                     UIManager.setLookAndFeel( synth );
 241                 }
 242                 catch ( final Exception ex ) {
 243                     synth_exception = true;
 244                     ForesterUtil.printWarningMessage( Constants.PRG_NAME,
 245                                                       "could not create synth look and feel: "
 246                                                               + ex.getLocalizedMessage() );
 247                 }
 248             }
 249             if ( !Constants.__SYNTH_LF || synth_exception ) {
 250                 if ( _configuration.isUseNativeUI() ) {
 251                     UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 252                 }
 253                 else {
 254                     UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 255                 }
 256             }
 257             //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
 258         }
 259         catch ( final UnsupportedLookAndFeelException e ) {
 260             AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
 261         }
 262         catch ( final ClassNotFoundException e ) {
 263             AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
 264         }
 265         catch ( final InstantiationException e ) {
 266             AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
 267         }
 268         catch ( final IllegalAccessException e ) {
 269             AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
 270         }
 271         catch ( final Exception e ) {
 272             AptxUtil.dieWithSystemError( e.toString() );
 273         }
 274         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
 275             setCurrentDir( current_dir );
 276         }
 277         // hide until everything is ready
 278         setVisible( false );
 279         setOptions( Options.createInstance( _configuration ) );
 280         setInferenceManager( InferenceManager.createInstance( _configuration ) );
 281         setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
 282         //     _textframe = null; #~~~~
 283         _species_tree = null;
 284         // set title
 285         setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
 286         _mainpanel = new MainPanel( _configuration, this );
 287         // The file dialogs
 288         _open_filechooser = new JFileChooser();
 289         _open_filechooser.setCurrentDirectory( new File( "." ) );
 290         _open_filechooser.setMultiSelectionEnabled( false );
 291         _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 292         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
 293         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 294         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 295         _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
 296         _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
 297         _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
 298         _open_filechooser_for_species_tree = new JFileChooser();
 299         _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
 300         _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
 301         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 302         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
 303         _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
 304         _save_filechooser = new JFileChooser();
 305         _save_filechooser.setCurrentDirectory( new File( "." ) );
 306         _save_filechooser.setMultiSelectionEnabled( false );
 307         _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
 308         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
 309         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 310         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 311         _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
 312         _writetopdf_filechooser = new JFileChooser();
 313         _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
 314         _writetographics_filechooser = new JFileChooser();
 315         _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
 316         // Msa:
 317         _msa_filechooser = new JFileChooser();
 318         _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
 319         _msa_filechooser.setCurrentDirectory( new File( "." ) );
 320         _msa_filechooser.setMultiSelectionEnabled( false );
 321         _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
 322         _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
 323         // Seqs:
 324         _seqs_filechooser = new JFileChooser();
 325         _seqs_filechooser.setName( "Read Sequences File" );
 326         _seqs_filechooser.setCurrentDirectory( new File( "." ) );
 327         _seqs_filechooser.setMultiSelectionEnabled( false );
 328         _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() );
 329         _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
 330         // Expression
 331         _values_filechooser = new JFileChooser();
 332         _values_filechooser.setCurrentDirectory( new File( "." ) );
 333         _values_filechooser.setMultiSelectionEnabled( false );
 334         // build the menu bar
 335         _jmenubar = new JMenuBar();
 336         if ( !_configuration.isUseNativeUI() ) {
 337             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 338         }
 339         buildFileMenu();
 340         if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
 341             buildPhylogeneticInferenceMenu();
 342         }
 343         buildAnalysisMenu();
 344         buildToolsMenu();
 345         buildViewMenu();
 346         buildFontSizeMenu();
 347         buildOptionsMenu();
 348         buildTypeMenu();
 349         buildHelpMenu();
 350         setJMenuBar( _jmenubar );
 351         _jmenubar.add( _help_jmenu );
 352         _contentpane = getContentPane();
 353         _contentpane.setLayout( new BorderLayout() );
 354         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 355         // App is this big
 356         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 357         //        addWindowFocusListener( new WindowAdapter() {
 358         //
 359         //            @Override
 360         //            public void windowGainedFocus( WindowEvent e ) {
 361         //                requestFocusInWindow();
 362         //            }
 363         //        } );
 364         // The window listener
 365         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 366         addWindowListener( new WindowAdapter() {
 367
 368             @Override
 369             public void windowClosing( final WindowEvent e ) {
 370                 if ( isUnsavedDataPresent() ) {
 371                     final int r = JOptionPane.showConfirmDialog( null,
 372                                                                  "Exit despite potentially unsaved changes?",
 373                                                                  "Exit?",
 374                                                                  JOptionPane.YES_NO_OPTION );
 375                     if ( r != JOptionPane.YES_OPTION ) {
 376                         return;
 377                     }
 378                 }
 379                 else {
 380                     final int r = JOptionPane.showConfirmDialog( null,
 381                                                                  "Exit Archaeopteryx?",
 382                                                                  "Exit?",
 383                                                                  JOptionPane.YES_NO_OPTION );
 384                     if ( r != JOptionPane.YES_OPTION ) {
 385                         return;
 386                     }
 387                 }
 388                 exit();
 389             }
 390         } );
 391         // The component listener
 392         addComponentListener( new ComponentAdapter() {
 393
 394             @Override
 395             public void componentResized( final ComponentEvent e ) {
 396                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 397                     _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
 398                                                                                        .getWidth(),
 399                                                                                _mainpanel.getCurrentTreePanel()
 400                                                                                        .getHeight(),
 401                                                                                false );
 402                 }
 403             }
 404         } );
 405         requestFocusInWindow();
 406         // addKeyListener( this );
 407         setVisible( true );
 408         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 409             AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
 410             validate();
 411             getMainPanel().getControlPanel().showWholeAll();
 412             getMainPanel().getControlPanel().showWhole();
 413         }
 414         activateSaveAllIfNeeded();
 415         // ...and its children
 416         _contentpane.repaint();
 417         System.gc();
 418     }
 419
 420     private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
 421         // Reads the config file (false, false => not url, not applet):
 422         this( phys, new Configuration( config_file, false, false, true ), title );
 423     }
 424
 425     @Override
 426     public void actionPerformed( final ActionEvent e ) {
 427         try {
 428             super.actionPerformed( e );
 429             final Object o = e.getSource();
 430             // Handle app-specific actions here:
 431             if ( o == _open_item ) {
 432                 readPhylogeniesFromFile();
 433             }
 434             else if ( o == _save_item ) {
 435                 writeToFile( _mainpanel.getCurrentPhylogeny() );
 436                 // If subtree currently displayed, save it, instead of complete
 437                 // tree.
 438             }
 439             else if ( o == _new_item ) {
 440                 newTree();
 441             }
 442             else if ( o == _save_all_item ) {
 443                 writeAllToFile();
 444             }
 445             else if ( o == _close_item ) {
 446                 closeCurrentPane();
 447             }
 448             else if ( o == _write_to_pdf_item ) {
 449                 writeToPdf( _mainpanel.getCurrentPhylogeny() );
 450             }
 451             else if ( o == _write_to_jpg_item ) {
 452                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
 453             }
 454             else if ( o == _write_to_png_item ) {
 455                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
 456             }
 457             else if ( o == _write_to_gif_item ) {
 458                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
 459             }
 460             else if ( o == _write_to_tif_item ) {
 461                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
 462             }
 463             else if ( o == _write_to_bmp_item ) {
 464                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
 465             }
 466             else if ( o == _print_item ) {
 467                 print();
 468             }
 469             else if ( o == _load_species_tree_item ) {
 470                 readSpeciesTreeFromFile();
 471             }
 472             else if ( o == _lineage_inference ) {
 473                 if ( isSubtreeDisplayed() ) {
 474                     JOptionPane.showMessageDialog( this,
 475                                                    "Subtree is shown.",
 476                                                    "Cannot infer ancestral taxonomies",
 477                                                    JOptionPane.ERROR_MESSAGE );
 478                     return;
 479                 }
 480                 executeLineageInference();
 481             }
 482             else if ( o == _function_analysis ) {
 483                 executeFunctionAnalysis();
 484             }
 485             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
 486                 if ( isSubtreeDisplayed() ) {
 487                     return;
 488                 }
 489                 obtainDetailedTaxonomicInformation();
 490             }
 491             else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
 492                 if ( isSubtreeDisplayed() ) {
 493                     return;
 494                 }
 495                 obtainDetailedTaxonomicInformationDelete();
 496             }
 497             else if ( o == _obtain_seq_information_jmi ) {
 498                 obtainSequenceInformation();
 499             }
 500             else if ( o == _read_values_jmi ) {
 501                 if ( isSubtreeDisplayed() ) {
 502                     return;
 503                 }
 504                 addExpressionValuesFromFile();
 505             }
 506             else if ( o == _move_node_names_to_tax_sn_jmi ) {
 507                 moveNodeNamesToTaxSn();
 508             }
 509             else if ( o == _move_node_names_to_seq_names_jmi ) {
 510                 moveNodeNamesToSeqNames();
 511             }
 512             else if ( o == _extract_tax_code_from_node_names_jmi ) {
 513                 extractTaxCodeFromNodeNames();
 514             }
 515             else if ( o == _gsdi_item ) {
 516                 if ( isSubtreeDisplayed() ) {
 517                     return;
 518                 }
 519                 executeGSDI();
 520             }
 521             else if ( o == _gsdir_item ) {
 522                 if ( isSubtreeDisplayed() ) {
 523                     return;
 524                 }
 525                 executeGSDIR();
 526             }
 527             else if ( o == _root_min_dups_item ) {
 528                 if ( isSubtreeDisplayed() ) {
 529                     return;
 530                 }
 531                 executeSDIR( false );
 532             }
 533             else if ( o == _root_min_cost_l_item ) {
 534                 if ( isSubtreeDisplayed() ) {
 535                     return;
 536                 }
 537                 executeSDIR( true );
 538             }
 539             else if ( o == _graphics_export_visible_only_cbmi ) {
 540                 updateOptions( getOptions() );
 541             }
 542             else if ( o == _antialias_print_cbmi ) {
 543                 updateOptions( getOptions() );
 544             }
 545             else if ( o == _print_black_and_white_cbmi ) {
 546                 updateOptions( getOptions() );
 547             }
 548             else if ( o == _print_using_actual_size_cbmi ) {
 549                 updateOptions( getOptions() );
 550             }
 551             else if ( o == _graphics_export_using_actual_size_cbmi ) {
 552                 updateOptions( getOptions() );
 553             }
 554             else if ( o == _print_size_mi ) {
 555                 choosePrintSize();
 556             }
 557             else if ( o == _choose_pdf_width_mi ) {
 558                 choosePdfWidth();
 559             }
 560             else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
 561                 updateOptions( getOptions() );
 562             }
 563             else if ( o == _replace_underscores_cbmi ) {
 564                 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
 565                     _extract_taxonomy_no_rbmi.setSelected( true );
 566                 }
 567                 updateOptions( getOptions() );
 568             }
 569             else if ( o == _collapse_below_threshold ) {
 570                 if ( isSubtreeDisplayed() ) {
 571                     return;
 572                 }
 573                 collapseBelowThreshold();
 574             }
 575             else if ( ( o == _extract_taxonomy_pfam_rbmi ) || ( o == _extract_taxonomy_yes_rbmi ) ) {
 576                 if ( _replace_underscores_cbmi != null ) {
 577                     _replace_underscores_cbmi.setSelected( false );
 578                 }
 579                 updateOptions( getOptions() );
 580             }
 581             else if ( o == _inference_from_msa_item ) {
 582                 executePhyleneticInference( false );
 583             }
 584             else if ( o == _inference_from_seqs_item ) {
 585                 executePhyleneticInference( true );
 586             }
 587             _contentpane.repaint();
 588         }
 589         catch ( final Exception ex ) {
 590             AptxUtil.unexpectedException( ex );
 591         }
 592         catch ( final Error err ) {
 593             AptxUtil.unexpectedError( err );
 594         }
 595     }
 596
 597     public void end() {
 598         _mainpanel.terminate();
 599         _contentpane.removeAll();
 600         setVisible( false );
 601         dispose();
 602     }
 603
 604     @Override
 605     public MainPanel getMainPanel() {
 606         return _mainpanel;
 607     }
 608
 609     public Msa getMsa() {
 610         return _msa;
 611     }
 612
 613     public File getMsaFile() {
 614         return _msa_file;
 615     }
 616
 617     public List<Sequence> getSeqs() {
 618         return _seqs;
 619     }
 620
 621     public File getSeqsFile() {
 622         return _seqs_file;
 623     }
 624
 625     public void readMsaFromFile() {
 626         // Set an initial directory if none set yet
 627         final File my_dir = getCurrentDir();
 628         _msa_filechooser.setMultiSelectionEnabled( false );
 629         // Open file-open dialog and set current directory
 630         if ( my_dir != null ) {
 631             _msa_filechooser.setCurrentDirectory( my_dir );
 632         }
 633         final int result = _msa_filechooser.showOpenDialog( _contentpane );
 634         // All done: get the msa
 635         final File file = _msa_filechooser.getSelectedFile();
 636         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
 637         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 638             setMsaFile( null );
 639             setMsa( null );
 640             Msa msa = null;
 641             try {
 642                 final InputStream is = new FileInputStream( file );
 643                 if ( FastaParser.isLikelyFasta( file ) ) {
 644                     msa = FastaParser.parseMsa( is );
 645                 }
 646                 else {
 647                     msa = GeneralMsaParser.parse( is );
 648                 }
 649             }
 650             catch ( final MsaFormatException e ) {
 651                 try {
 652                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 653                 }
 654                 catch ( final Exception ex ) {
 655                     // Do nothing.
 656                 }
 657                 JOptionPane.showMessageDialog( this,
 658                                                e.getLocalizedMessage(),
 659                                                "Multiple sequence alignment format error",
 660                                                JOptionPane.ERROR_MESSAGE );
 661                 return;
 662             }
 663             catch ( final IOException e ) {
 664                 try {
 665                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 666                 }
 667                 catch ( final Exception ex ) {
 668                     // Do nothing.
 669                 }
 670                 JOptionPane.showMessageDialog( this,
 671                                                e.getLocalizedMessage(),
 672                                                "Failed to read multiple sequence alignment",
 673                                                JOptionPane.ERROR_MESSAGE );
 674                 return;
 675             }
 676             catch ( final IllegalArgumentException e ) {
 677                 try {
 678                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 679                 }
 680                 catch ( final Exception ex ) {
 681                     // Do nothing.
 682                 }
 683                 JOptionPane.showMessageDialog( this,
 684                                                e.getLocalizedMessage(),
 685                                                "Unexpected error during reading of multiple sequence alignment",
 686                                                JOptionPane.ERROR_MESSAGE );
 687                 return;
 688             }
 689             catch ( final Exception e ) {
 690                 try {
 691                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 692                 }
 693                 catch ( final Exception ex ) {
 694                     // Do nothing.
 695                 }
 696                 e.printStackTrace();
 697                 JOptionPane.showMessageDialog( this,
 698                                                e.getLocalizedMessage(),
 699                                                "Unexpected error during reading of multiple sequence alignment",
 700                                                JOptionPane.ERROR_MESSAGE );
 701                 return;
 702             }
 703             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
 704                 JOptionPane.showMessageDialog( this,
 705                                                "Multiple sequence alignment is empty",
 706                                                "Illegal Multiple Sequence Alignment",
 707                                                JOptionPane.ERROR_MESSAGE );
 708                 return;
 709             }
 710             if ( msa.getNumberOfSequences() < 4 ) {
 711                 JOptionPane.showMessageDialog( this,
 712                                                "Multiple sequence alignment needs to contain at least 3 sequences",
 713                                                "Illegal multiple sequence alignment",
 714                                                JOptionPane.ERROR_MESSAGE );
 715                 return;
 716             }
 717             if ( msa.getLength() < 2 ) {
 718                 JOptionPane.showMessageDialog( this,
 719                                                "Multiple sequence alignment needs to contain at least 2 residues",
 720                                                "Illegal multiple sequence alignment",
 721                                                JOptionPane.ERROR_MESSAGE );
 722                 return;
 723             }
 724             System.gc();
 725             setMsaFile( _msa_filechooser.getSelectedFile() );
 726             setMsa( msa );
 727         }
 728     }
 729
 730     public void readSeqsFromFile() {
 731         // Set an initial directory if none set yet
 732         final File my_dir = getCurrentDir();
 733         _seqs_filechooser.setMultiSelectionEnabled( false );
 734         // Open file-open dialog and set current directory
 735         if ( my_dir != null ) {
 736             _seqs_filechooser.setCurrentDirectory( my_dir );
 737         }
 738         final int result = _seqs_filechooser.showOpenDialog( _contentpane );
 739         // All done: get the seqs
 740         final File file = _seqs_filechooser.getSelectedFile();
 741         setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
 742         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 743             setSeqsFile( null );
 744             setSeqs( null );
 745             List<Sequence> seqs = null;
 746             try {
 747                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
 748                     seqs = FastaParser.parse( new FileInputStream( file ) );
 749                     for( final Sequence seq : seqs ) {
 750                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
 751                     }
 752                 }
 753                 else {
 754                     //TODO error
 755                 }
 756             }
 757             catch ( final MsaFormatException e ) {
 758                 try {
 759                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 760                 }
 761                 catch ( final Exception ex ) {
 762                     // Do nothing.
 763                 }
 764                 JOptionPane.showMessageDialog( this,
 765                                                e.getLocalizedMessage(),
 766                                                "Multiple sequence file format error",
 767                                                JOptionPane.ERROR_MESSAGE );
 768                 return;
 769             }
 770             catch ( final IOException e ) {
 771                 try {
 772                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 773                 }
 774                 catch ( final Exception ex ) {
 775                     // Do nothing.
 776                 }
 777                 JOptionPane.showMessageDialog( this,
 778                                                e.getLocalizedMessage(),
 779                                                "Failed to read multiple sequence file",
 780                                                JOptionPane.ERROR_MESSAGE );
 781                 return;
 782             }
 783             catch ( final IllegalArgumentException e ) {
 784                 try {
 785                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 786                 }
 787                 catch ( final Exception ex ) {
 788                     // Do nothing.
 789                 }
 790                 JOptionPane.showMessageDialog( this,
 791                                                e.getLocalizedMessage(),
 792                                                "Unexpected error during reading of multiple sequence file",
 793                                                JOptionPane.ERROR_MESSAGE );
 794                 return;
 795             }
 796             catch ( final Exception e ) {
 797                 try {
 798                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 799                 }
 800                 catch ( final Exception ex ) {
 801                     // Do nothing.
 802                 }
 803                 e.printStackTrace();
 804                 JOptionPane.showMessageDialog( this,
 805                                                e.getLocalizedMessage(),
 806                                                "Unexpected error during reading of multiple sequence file",
 807                                                JOptionPane.ERROR_MESSAGE );
 808                 return;
 809             }
 810             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 811                 JOptionPane.showMessageDialog( this,
 812                                                "Multiple sequence file is empty",
 813                                                "Illegal multiple sequence file",
 814                                                JOptionPane.ERROR_MESSAGE );
 815                 return;
 816             }
 817             if ( seqs.size() < 4 ) {
 818                 JOptionPane.showMessageDialog( this,
 819                                                "Multiple sequence file needs to contain at least 3 sequences",
 820                                                "Illegal multiple sequence file",
 821                                                JOptionPane.ERROR_MESSAGE );
 822                 return;
 823             }
 824             //  if ( msa.getLength() < 2 ) {
 825             //       JOptionPane.showMessageDialog( this,
 826             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
 827             //                                      "Illegal multiple sequence file",
 828             //                                      JOptionPane.ERROR_MESSAGE );
 829             //       return;
 830             //   }
 831             System.gc();
 832             setSeqsFile( _seqs_filechooser.getSelectedFile() );
 833             setSeqs( seqs );
 834         }
 835     }
 836
 837     void buildAnalysisMenu() {
 838         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 839         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 840         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
 841         _analysis_menu.addSeparator();
 842         _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
 843         _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
 844         _analysis_menu.addSeparator();
 845         _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
 846         customizeJMenuItem( _gsdi_item );
 847         customizeJMenuItem( _gsdir_item );
 848         customizeJMenuItem( _root_min_dups_item );
 849         customizeJMenuItem( _root_min_cost_l_item );
 850         customizeJMenuItem( _load_species_tree_item );
 851         _analysis_menu.addSeparator();
 852         _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 853         customizeJMenuItem( _lineage_inference );
 854         _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 855         _jmenubar.add( _analysis_menu );
 856     }
 857
 858     @Override
 859     void buildFileMenu() {
 860         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
 861         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
 862         _file_jmenu.addSeparator();
 863         _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
 864         _file_jmenu.addSeparator();
 865         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
 866         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
 867                 .getAvailablePhylogeniesWebserviceClients().size() ];
 868         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 869             final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
 870             _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
 871             _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
 872         }
 873         if ( getConfiguration().isEditable() ) {
 874             _file_jmenu.addSeparator();
 875             _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
 876             _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
 877         }
 878         _file_jmenu.addSeparator();
 879         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
 880         _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
 881         _save_all_item.setToolTipText( "Write all phylogenies to one file." );
 882         _save_all_item.setEnabled( false );
 883         _file_jmenu.addSeparator();
 884         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
 885         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
 886             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
 887         }
 888         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
 889         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
 890         if ( AptxUtil.canWriteFormat( "gif" ) ) {
 891             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
 892         }
 893         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
 894             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
 895         }
 896         _file_jmenu.addSeparator();
 897         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
 898         _file_jmenu.addSeparator();
 899         _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
 900         _close_item.setToolTipText( "To close the current pane." );
 901         _close_item.setEnabled( true );
 902         _file_jmenu.addSeparator();
 903         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 904         // For print in color option item
 905         customizeJMenuItem( _open_item );
 906         _open_item
 907                 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
 908         customizeJMenuItem( _open_url_item );
 909         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 910             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
 911         }
 912         customizeJMenuItem( _save_item );
 913         if ( getConfiguration().isEditable() ) {
 914             customizeJMenuItem( _new_item );
 915         }
 916         customizeJMenuItem( _close_item );
 917         customizeJMenuItem( _save_all_item );
 918         customizeJMenuItem( _write_to_pdf_item );
 919         customizeJMenuItem( _write_to_png_item );
 920         customizeJMenuItem( _write_to_jpg_item );
 921         customizeJMenuItem( _write_to_gif_item );
 922         customizeJMenuItem( _write_to_tif_item );
 923         customizeJMenuItem( _write_to_bmp_item );
 924         customizeJMenuItem( _print_item );
 925         customizeJMenuItem( _exit_item );
 926         _jmenubar.add( _file_jmenu );
 927     }
 928
 929     void buildOptionsMenu() {
 930         _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
 931         _options_jmenu.addChangeListener( new ChangeListener() {
 932
 933             @Override
 934             public void stateChanged( final ChangeEvent e ) {
 935                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 936                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 937                 MainFrame
 938                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 939                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 940                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 941                 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
 942                 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
 943                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 944                                                                      _show_scale_cbmi,
 945                                                                      _show_branch_length_values_cbmi,
 946                                                                      _non_lined_up_cladograms_rbmi,
 947                                                                      _uniform_cladograms_rbmi,
 948                                                                      _ext_node_dependent_cladogram_rbmi,
 949                                                                      _label_direction_cbmi );
 950                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 951                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 952                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 953             }
 954         } );
 955         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
 956         _options_jmenu
 957                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 958         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 959         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 960         _radio_group_1 = new ButtonGroup();
 961         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 962         _radio_group_1.add( _uniform_cladograms_rbmi );
 963         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 964         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
 965         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
 966         _options_jmenu
 967                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 968         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
 969         _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
 970         _options_jmenu
 971                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 972         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 973         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 974         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 975         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 976         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 977         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 978         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 979         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
 980         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
 981         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
 982         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 983             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 984         }
 985         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 986         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 987         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 988         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 989         _options_jmenu.addSeparator();
 990         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
 991         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
 992         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
 993         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 994         _options_jmenu.addSeparator();
 995         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
 996                                                       getConfiguration() ) );
 997         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
 998         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
 999         _options_jmenu
1000                 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
1001         _options_jmenu
1002                 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
1003         _options_jmenu
1004                 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
1005         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
1006         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
1007         _options_jmenu.addSeparator();
1008         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
1009         _options_jmenu
1010                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
1011         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
1012         //
1013         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
1014         _options_jmenu
1015                 .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
1016         _extract_taxonomy_pfam_rbmi
1017                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
1018         _options_jmenu
1019                 .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
1020         _extract_taxonomy_yes_rbmi
1021                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
1022         _radio_group_2 = new ButtonGroup();
1023         _radio_group_2.add( _extract_taxonomy_no_rbmi );
1024         _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
1025         _radio_group_2.add( _extract_taxonomy_yes_rbmi );
1026         //
1027         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
1028         _options_jmenu
1029                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
1030         _use_brackets_for_conf_in_nh_export_cbmi
1031                 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
1032         _options_jmenu
1033                 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
1034         customizeJMenuItem( _choose_font_mi );
1035         customizeJMenuItem( _choose_minimal_confidence_mi );
1036         customizeJMenuItem( _switch_colors_mi );
1037         customizeJMenuItem( _print_size_mi );
1038         customizeJMenuItem( _choose_pdf_width_mi );
1039         customizeJMenuItem( _overview_placment_mi );
1040         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
1041         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
1042         customizeJMenuItem( _cycle_node_shape_mi );
1043         customizeJMenuItem( _cycle_node_fill_mi );
1044         customizeJMenuItem( _choose_node_size_mi );
1045         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
1046         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
1047         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
1048         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
1049         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
1050         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
1051         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
1052         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
1053                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
1054         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
1055                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1056         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
1057                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1058         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
1059         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1060         customizeCheckBoxMenuItem( _label_direction_cbmi,
1061                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1062         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1063         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1064         customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1065                 .isInternalNumberAreConfidenceForNhParsing() );
1066         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1067                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1068         customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
1069                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
1070         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
1071                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1072         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1073         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1074         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1075         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1076         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1077         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1078                 .isGraphicsExportUsingActualSize() );
1079         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1080         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1081                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1082         customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1083                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1084         _jmenubar.add( _options_jmenu );
1085     }
1086
1087     void buildPhylogeneticInferenceMenu() {
1088         final InferenceManager im = getInferenceManager();
1089         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1090         _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1091         customizeJMenuItem( _inference_from_msa_item );
1092         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1093         if ( im.canDoMsa() ) {
1094             _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1095             customizeJMenuItem( _inference_from_seqs_item );
1096             _inference_from_seqs_item
1097                     .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1098         }
1099         else {
1100             _inference_menu
1101                     .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1102             customizeJMenuItem( _inference_from_seqs_item );
1103             _inference_from_seqs_item.setEnabled( false );
1104         }
1105         _jmenubar.add( _inference_menu );
1106     }
1107
1108     void buildToolsMenu() {
1109         _tools_menu = createMenu( "Tools", getConfiguration() );
1110         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1111         customizeJMenuItem( _confcolor_item );
1112         _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1113         customizeJMenuItem( _color_rank_jmi );
1114         _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1115         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1116         customizeJMenuItem( _taxcolor_item );
1117         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1118         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1119         customizeJMenuItem( _remove_branch_color_item );
1120         _tools_menu.addSeparator();
1121         _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1122         customizeJMenuItem( _annotate_item );
1123         _tools_menu.addSeparator();
1124         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1125         customizeJMenuItem( _midpoint_root_item );
1126         _tools_menu.addSeparator();
1127         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1128         customizeJMenuItem( _collapse_species_specific_subtrees );
1129         _tools_menu
1130                 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1131         customizeJMenuItem( _collapse_below_threshold );
1132         _collapse_below_threshold
1133                 .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)" );
1134         _tools_menu.addSeparator();
1135         _tools_menu
1136                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1137         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1138         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1139         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1140         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1141         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1142         _tools_menu
1143                 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes from Node Names" ) );
1144         customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1145         _extract_tax_code_from_node_names_jmi
1146                 .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" );
1147         _tools_menu.addSeparator();
1148         _tools_menu
1149                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1150         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1151         _obtain_detailed_taxonomic_information_jmi
1152                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1153         _tools_menu
1154                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1155         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1156         _obtain_detailed_taxonomic_information_deleting_jmi
1157                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1158         _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1159         customizeJMenuItem( _obtain_seq_information_jmi );
1160         _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1161         _tools_menu.addSeparator();
1162         if ( !Constants.__RELEASE ) {
1163             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
1164             customizeJMenuItem( _function_analysis );
1165             _function_analysis
1166                     .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
1167             _tools_menu.addSeparator();
1168         }
1169         _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
1170         customizeJMenuItem( _read_values_jmi );
1171         _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
1172         _jmenubar.add( _tools_menu );
1173     }
1174
1175     @Override
1176     void close() {
1177         if ( isUnsavedDataPresent() ) {
1178             final int r = JOptionPane.showConfirmDialog( this,
1179                                                          "Exit despite potentially unsaved changes?",
1180                                                          "Exit?",
1181                                                          JOptionPane.YES_NO_OPTION );
1182             if ( r != JOptionPane.YES_OPTION ) {
1183                 return;
1184             }
1185         }
1186         exit();
1187     }
1188
1189     void executeFunctionAnalysis() {
1190         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1191             return;
1192         }
1193         final GoAnnotation a = new GoAnnotation( this,
1194                                                  _mainpanel.getCurrentTreePanel(),
1195                                                  _mainpanel.getCurrentPhylogeny() );
1196         new Thread( a ).start();
1197     }
1198
1199     void executeGSDI() {
1200         if ( !isOKforSDI( false, true ) ) {
1201             return;
1202         }
1203         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1204             JOptionPane.showMessageDialog( this,
1205                                            "Gene tree is not rooted.",
1206                                            "Cannot execute GSDI",
1207                                            JOptionPane.ERROR_MESSAGE );
1208             return;
1209         }
1210         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1211         gene_tree.setAllNodesToNotCollapse();
1212         gene_tree.recalculateNumberOfExternalDescendants( false );
1213         GSDI gsdi = null;
1214         final Phylogeny species_tree = _species_tree.copy();
1215         try {
1216             gsdi = new GSDI( gene_tree, species_tree, false, true, true );
1217         }
1218         catch ( final SDIException e ) {
1219             JOptionPane.showMessageDialog( this,
1220                                            e.getLocalizedMessage(),
1221                                            "Error during GSDI",
1222                                            JOptionPane.ERROR_MESSAGE );
1223             return;
1224         }
1225         catch ( final Exception e ) {
1226             AptxUtil.unexpectedException( e );
1227             return;
1228         }
1229         gene_tree.setRerootable( false );
1230         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1231         _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
1232         _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
1233         _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1234         _mainpanel.getCurrentTreePanel().setEdited( true );
1235         getControlPanel().setShowEvents( true );
1236         showWhole();
1237         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1238         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1239         showWhole();
1240         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1241         showWhole();
1242         _mainpanel.getCurrentTreePanel().setEdited( true );
1243         JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1244                 + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
1245                 + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
1246     }
1247
1248     void executeGSDIR() {
1249         if ( !isOKforSDI( false, true ) ) {
1250             return;
1251         }
1252         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1253         gene_tree.setAllNodesToNotCollapse();
1254         gene_tree.recalculateNumberOfExternalDescendants( false );
1255         GSDIR gsdir = null;
1256         final Phylogeny species_tree = _species_tree.copy();
1257         try {
1258             gsdir = new GSDIR( gene_tree, species_tree, true, true );
1259         }
1260         catch ( final SDIException e ) {
1261             JOptionPane.showMessageDialog( this,
1262                                            e.getLocalizedMessage(),
1263                                            "Error during GSDIR",
1264                                            JOptionPane.ERROR_MESSAGE );
1265             return;
1266         }
1267         catch ( final Exception e ) {
1268             AptxUtil.unexpectedException( e );
1269             return;
1270         }
1271         final List<Phylogeny> assigned_trees = gsdir.getMinDuplicationsSumGeneTrees();
1272         final List<Integer> shortests = GSDIR.getIndexesOfShortestTree( assigned_trees );
1273         final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) );
1274         result_gene_tree.setRerootable( false );
1275         result_gene_tree.clearHashIdToNodeMap();
1276         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1277         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1278         getControlPanel().setShowEvents( true );
1279         showWhole();
1280         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1281         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1282         showWhole();
1283         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1284         showWhole();
1285         _mainpanel.getCurrentTreePanel().setEdited( true );
1286         JOptionPane.showMessageDialog( this,
1287                                        "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
1288                                                + gsdir.getSpeciationsSum() + "\n"
1289                                                + "Number of root positions minimizing duplications sum: "
1290                                                + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n"
1291                                                + "Number of shortest trees: " + shortests.size(),
1292                                        "GSDIR successfully completed",
1293                                        JOptionPane.INFORMATION_MESSAGE );
1294     }
1295
1296     void executeLineageInference() {
1297         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1298             return;
1299         }
1300         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1301             JOptionPane.showMessageDialog( this,
1302                                            "Phylogeny is not rooted.",
1303                                            "Cannot infer ancestral taxonomies",
1304                                            JOptionPane.ERROR_MESSAGE );
1305             return;
1306         }
1307         final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1308                                                                                   _mainpanel.getCurrentTreePanel(),
1309                                                                                   _mainpanel.getCurrentPhylogeny()
1310                                                                                           .copy() );
1311         new Thread( inferrer ).start();
1312     }
1313
1314     void executeSDIR( final boolean minimize_cost ) {
1315         if ( !isOKforSDI( true, true ) ) {
1316             return;
1317         }
1318         Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1319         final SDIR sdiunrooted = new SDIR();
1320         gene_tree.setAllNodesToNotCollapse();
1321         gene_tree.recalculateNumberOfExternalDescendants( false );
1322         try {
1323             gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1324                                            !minimize_cost, // minimize sum of dups
1325                                            true, // minimize height
1326                                            true, // return tree(s)
1327                                            1 )[ 0 ]; // # of trees to return
1328         }
1329         catch ( final Exception e ) {
1330             JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1331             return;
1332         }
1333         final int duplications = sdiunrooted.getMinimalDuplications();
1334         gene_tree.setRerootable( false );
1335         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1336         getControlPanel().setShowEvents( true );
1337         showWhole();
1338         _mainpanel.getCurrentTreePanel().setEdited( true );
1339         JOptionPane.showMessageDialog( this,
1340                                        "Number of duplications: " + duplications,
1341                                        "SDIR successfully completed",
1342                                        JOptionPane.INFORMATION_MESSAGE );
1343     }
1344
1345     void exit() {
1346         removeAllTextFrames();
1347         _mainpanel.terminate();
1348         _contentpane.removeAll();
1349         setVisible( false );
1350         dispose();
1351         System.exit( 0 );
1352     }
1353
1354     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1355         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1356             return false;
1357         }
1358         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1359             JOptionPane.showMessageDialog( this,
1360                                            "No species tree loaded",
1361                                            "Cannot execute SDI",
1362                                            JOptionPane.ERROR_MESSAGE );
1363             return false;
1364         }
1365         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1366             JOptionPane.showMessageDialog( this,
1367                                            "Species tree is not completely binary",
1368                                            "Cannot execute SDI",
1369                                            JOptionPane.ERROR_MESSAGE );
1370             return false;
1371         }
1372         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1373             JOptionPane.showMessageDialog( this,
1374                                            "Gene tree is not completely binary",
1375                                            "Cannot execute SDI",
1376                                            JOptionPane.ERROR_MESSAGE );
1377             return false;
1378         }
1379         else {
1380             return true;
1381         }
1382     }
1383
1384     @Override
1385     void readPhylogeniesFromURL() {
1386         URL url = null;
1387         Phylogeny[] phys = null;
1388         final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1389         final String url_string = JOptionPane.showInputDialog( this,
1390                                                                message,
1391                                                                "Use URL/webservice to obtain a phylogeny",
1392                                                                JOptionPane.QUESTION_MESSAGE );
1393         boolean nhx_or_nexus = false;
1394         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1395             try {
1396                 url = new URL( url_string );
1397                 PhylogenyParser parser = null;
1398                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1399                     parser = new TolParser();
1400                 }
1401                 else {
1402                     parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1403                             .isValidatePhyloXmlAgainstSchema() );
1404                 }
1405                 if ( parser instanceof NexusPhylogeniesParser ) {
1406                     nhx_or_nexus = true;
1407                 }
1408                 else if ( parser instanceof NHXParser ) {
1409                     nhx_or_nexus = true;
1410                 }
1411                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1412                     _mainpanel.getCurrentTreePanel().setWaitCursor();
1413                 }
1414                 else {
1415                     _mainpanel.setWaitCursor();
1416                 }
1417                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1418                 phys = factory.create( url.openStream(), parser );
1419             }
1420             catch ( final MalformedURLException e ) {
1421                 JOptionPane.showMessageDialog( this,
1422                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1423                                                "Malformed URL",
1424                                                JOptionPane.ERROR_MESSAGE );
1425             }
1426             catch ( final IOException e ) {
1427                 JOptionPane.showMessageDialog( this,
1428                                                "Could not read from " + url + "\n"
1429                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1430                                                "Failed to read URL",
1431                                                JOptionPane.ERROR_MESSAGE );
1432             }
1433             catch ( final Exception e ) {
1434                 JOptionPane.showMessageDialog( this,
1435                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1436                                                "Unexpected Exception",
1437                                                JOptionPane.ERROR_MESSAGE );
1438             }
1439             finally {
1440                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1441                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1442                 }
1443                 else {
1444                     _mainpanel.setArrowCursor();
1445                 }
1446             }
1447             if ( ( phys != null ) && ( phys.length > 0 ) ) {
1448                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1449                     for( final Phylogeny phy : phys ) {
1450                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1451                     }
1452                 }
1453                 AptxUtil.addPhylogeniesToTabs( phys,
1454                                                new File( url.getFile() ).getName(),
1455                                                new File( url.getFile() ).toString(),
1456                                                getConfiguration(),
1457                                                getMainPanel() );
1458                 _mainpanel.getControlPanel().showWhole();
1459             }
1460         }
1461         activateSaveAllIfNeeded();
1462         System.gc();
1463     }
1464
1465     void setMsa( final Msa msa ) {
1466         _msa = msa;
1467     }
1468
1469     void setMsaFile( final File msa_file ) {
1470         _msa_file = msa_file;
1471     }
1472
1473     void setSeqs( final List<Sequence> seqs ) {
1474         _seqs = seqs;
1475     }
1476
1477     void setSeqsFile( final File seqs_file ) {
1478         _seqs_file = seqs_file;
1479     }
1480
1481     void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1482         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1483                                                                    _mainpanel.getCurrentTreePanel().getHeight(),
1484                                                                    true );
1485         String file_written_to = "";
1486         boolean error = false;
1487         try {
1488             file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1489                                                                      _mainpanel.getCurrentTreePanel().getWidth(),
1490                                                                      _mainpanel.getCurrentTreePanel().getHeight(),
1491                                                                      _mainpanel.getCurrentTreePanel(),
1492                                                                      _mainpanel.getControlPanel(),
1493                                                                      type,
1494                                                                      getOptions() );
1495         }
1496         catch ( final IOException e ) {
1497             error = true;
1498             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1499         }
1500         if ( !error ) {
1501             if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1502                 JOptionPane.showMessageDialog( this,
1503                                                "Wrote image to: " + file_written_to,
1504                                                "Graphics Export",
1505                                                JOptionPane.INFORMATION_MESSAGE );
1506             }
1507             else {
1508                 JOptionPane.showMessageDialog( this,
1509                                                "There was an unknown problem when attempting to write to an image file: \""
1510                                                        + file_name + "\"",
1511                                                "Error",
1512                                                JOptionPane.ERROR_MESSAGE );
1513             }
1514         }
1515         _contentpane.repaint();
1516     }
1517
1518     private void addExpressionValuesFromFile() {
1519         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1520             JOptionPane.showMessageDialog( this,
1521                                            "Need to load evolutionary tree first",
1522                                            "Can Not Read Expression Values",
1523                                            JOptionPane.WARNING_MESSAGE );
1524             return;
1525         }
1526         final File my_dir = getCurrentDir();
1527         if ( my_dir != null ) {
1528             _values_filechooser.setCurrentDirectory( my_dir );
1529         }
1530         final int result = _values_filechooser.showOpenDialog( _contentpane );
1531         final File file = _values_filechooser.getSelectedFile();
1532         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1533             BasicTable<String> t = null;
1534             try {
1535                 t = BasicTableParser.parse( file, "\t" );
1536                 if ( t.getNumberOfColumns() < 2 ) {
1537                     t = BasicTableParser.parse( file, "," );
1538                 }
1539                 if ( t.getNumberOfColumns() < 2 ) {
1540                     t = BasicTableParser.parse( file, " " );
1541                 }
1542             }
1543             catch ( final IOException e ) {
1544                 JOptionPane.showMessageDialog( this,
1545                                                e.getMessage(),
1546                                                "Could Not Read Expression Value Table",
1547                                                JOptionPane.ERROR_MESSAGE );
1548                 return;
1549             }
1550             if ( t.getNumberOfColumns() < 2 ) {
1551                 JOptionPane.showMessageDialog( this,
1552                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
1553                                                "Problem with Expression Value Table",
1554                                                JOptionPane.ERROR_MESSAGE );
1555                 return;
1556             }
1557             if ( t.getNumberOfRows() < 1 ) {
1558                 JOptionPane.showMessageDialog( this,
1559                                                "Table contains zero rows",
1560                                                "Problem with Expression Value Table",
1561                                                JOptionPane.ERROR_MESSAGE );
1562                 return;
1563             }
1564             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1565             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1566                 JOptionPane.showMessageDialog( this,
1567                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1568                                                        + phy.getNumberOfExternalNodes() + " external nodes",
1569                                                "Warning",
1570                                                JOptionPane.WARNING_MESSAGE );
1571             }
1572             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1573             int not_found = 0;
1574             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1575                 final PhylogenyNode node = iter.next();
1576                 final String node_name = node.getName();
1577                 if ( !ForesterUtil.isEmpty( node_name ) ) {
1578                     int row = -1;
1579                     try {
1580                         row = t.findRow( node_name );
1581                     }
1582                     catch ( final IllegalArgumentException e ) {
1583                         JOptionPane
1584                                 .showMessageDialog( this,
1585                                                     e.getMessage(),
1586                                                     "Error Mapping Node Identifiers to Expression Value Identifiers",
1587                                                     JOptionPane.ERROR_MESSAGE );
1588                         return;
1589                     }
1590                     if ( row < 0 ) {
1591                         if ( node.isExternal() ) {
1592                             not_found++;
1593                         }
1594                         continue;
1595                     }
1596                     final List<Double> l = new ArrayList<Double>();
1597                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1598                         double d = -100;
1599                         try {
1600                             d = Double.parseDouble( t.getValueAsString( col, row ) );
1601                         }
1602                         catch ( final NumberFormatException e ) {
1603                             JOptionPane.showMessageDialog( this,
1604                                                            "Could not parse \"" + t.getValueAsString( col, row )
1605                                                                    + "\" into a decimal value",
1606                                                            "Issue with Expression Value Table",
1607                                                            JOptionPane.ERROR_MESSAGE );
1608                             return;
1609                         }
1610                         stats.addValue( d );
1611                         l.add( d );
1612                     }
1613                     if ( !l.isEmpty() ) {
1614                         if ( node.getNodeData().getProperties() != null ) {
1615                             node.getNodeData().getProperties()
1616                                     .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1617                         }
1618                         node.getNodeData().setVector( l );
1619                     }
1620                 }
1621             }
1622             if ( not_found > 0 ) {
1623                 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1624                         + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1625             }
1626             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1627         }
1628     }
1629
1630     private void choosePdfWidth() {
1631         final String s = ( String ) JOptionPane.showInputDialog( this,
1632                                                                  "Please enter the default line width for PDF export.\n"
1633                                                                          + "[current value: "
1634                                                                          + getOptions().getPrintLineWidth() + "]\n",
1635                                                                  "Line Width for PDF Export",
1636                                                                  JOptionPane.QUESTION_MESSAGE,
1637                                                                  null,
1638                                                                  null,
1639                                                                  getOptions().getPrintLineWidth() );
1640         if ( !ForesterUtil.isEmpty( s ) ) {
1641             boolean success = true;
1642             float f = 0.0f;
1643             final String m_str = s.trim();
1644             if ( !ForesterUtil.isEmpty( m_str ) ) {
1645                 try {
1646                     f = Float.parseFloat( m_str );
1647                 }
1648                 catch ( final Exception ex ) {
1649                     success = false;
1650                 }
1651             }
1652             else {
1653                 success = false;
1654             }
1655             if ( success && ( f > 0.0 ) ) {
1656                 getOptions().setPrintLineWidth( f );
1657             }
1658         }
1659     }
1660
1661     private void choosePrintSize() {
1662         final String s = ( String ) JOptionPane.showInputDialog( this,
1663                                                                  "Please enter values for width and height,\nseparated by a comma.\n"
1664                                                                          + "[current values: "
1665                                                                          + getOptions().getPrintSizeX() + ", "
1666                                                                          + getOptions().getPrintSizeY() + "]\n"
1667                                                                          + "[A4: " + Constants.A4_SIZE_X + ", "
1668                                                                          + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1669                                                                          + Constants.US_LETTER_SIZE_X + ", "
1670                                                                          + Constants.US_LETTER_SIZE_Y + "]",
1671                                                                  "Default Size for Graphics Export",
1672                                                                  JOptionPane.QUESTION_MESSAGE,
1673                                                                  null,
1674                                                                  null,
1675                                                                  getOptions().getPrintSizeX() + ", "
1676                                                                          + getOptions().getPrintSizeY() );
1677         if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1678             boolean success = true;
1679             int x = 0;
1680             int y = 0;
1681             final String[] str_ary = s.split( "," );
1682             if ( str_ary.length == 2 ) {
1683                 final String x_str = str_ary[ 0 ].trim();
1684                 final String y_str = str_ary[ 1 ].trim();
1685                 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1686                     try {
1687                         x = Integer.parseInt( x_str );
1688                         y = Integer.parseInt( y_str );
1689                     }
1690                     catch ( final Exception ex ) {
1691                         success = false;
1692                     }
1693                 }
1694                 else {
1695                     success = false;
1696                 }
1697             }
1698             else {
1699                 success = false;
1700             }
1701             if ( success && ( x > 1 ) && ( y > 1 ) ) {
1702                 getOptions().setPrintSizeX( x );
1703                 getOptions().setPrintSizeY( y );
1704             }
1705         }
1706     }
1707
1708     private void closeCurrentPane() {
1709         if ( getMainPanel().getCurrentTreePanel() != null ) {
1710             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1711                 final int r = JOptionPane.showConfirmDialog( this,
1712                                                              "Close tab despite potentially unsaved changes?",
1713                                                              "Close Tab?",
1714                                                              JOptionPane.YES_NO_OPTION );
1715                 if ( r != JOptionPane.YES_OPTION ) {
1716                     return;
1717                 }
1718             }
1719             getMainPanel().closeCurrentPane();
1720             activateSaveAllIfNeeded();
1721         }
1722     }
1723
1724     private void collapse( final Phylogeny phy, final double m ) {
1725         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1726         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1727         double min_support = Double.MAX_VALUE;
1728         boolean conf_present = false;
1729         while ( it.hasNext() ) {
1730             final PhylogenyNode n = it.next();
1731             if ( !n.isExternal() && !n.isRoot() ) {
1732                 final List<Confidence> c = n.getBranchData().getConfidences();
1733                 if ( ( c != null ) && ( c.size() > 0 ) ) {
1734                     conf_present = true;
1735                     double max = 0;
1736                     for( final Confidence confidence : c ) {
1737                         if ( confidence.getValue() > max ) {
1738                             max = confidence.getValue();
1739                         }
1740                     }
1741                     if ( max < getMinNotCollapseConfidenceValue() ) {
1742                         to_be_removed.add( n );
1743                     }
1744                     if ( max < min_support ) {
1745                         min_support = max;
1746                     }
1747                 }
1748             }
1749         }
1750         if ( conf_present ) {
1751             for( final PhylogenyNode node : to_be_removed ) {
1752                 PhylogenyMethods.removeNode( node, phy );
1753             }
1754             if ( to_be_removed.size() > 0 ) {
1755                 phy.externalNodesHaveChanged();
1756                 phy.clearHashIdToNodeMap();
1757                 phy.recalculateNumberOfExternalDescendants( true );
1758                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1759                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1760                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1761                 getCurrentTreePanel().setNodeInPreorderToNull();
1762                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1763                 getCurrentTreePanel().resetPreferredSize();
1764                 getCurrentTreePanel().setEdited( true );
1765                 getCurrentTreePanel().repaint();
1766                 repaint();
1767             }
1768             if ( to_be_removed.size() > 0 ) {
1769                 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1770                         + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1771                         + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1772             }
1773             else {
1774                 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1775                         + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1776             }
1777         }
1778         else {
1779             JOptionPane.showMessageDialog( this,
1780                                            "No branch collapsed because no confidence values present",
1781                                            "No confidence values present",
1782                                            JOptionPane.INFORMATION_MESSAGE );
1783         }
1784     }
1785
1786     private void collapseBelowThreshold() {
1787         if ( getCurrentTreePanel() != null ) {
1788             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1789             if ( ( phy != null ) && !phy.isEmpty() ) {
1790                 final String s = ( String ) JOptionPane.showInputDialog( this,
1791                                                                          "Please enter the minimum confidence value\n",
1792                                                                          "Minimal Confidence Value",
1793                                                                          JOptionPane.QUESTION_MESSAGE,
1794                                                                          null,
1795                                                                          null,
1796                                                                          getMinNotCollapseConfidenceValue() );
1797                 if ( !ForesterUtil.isEmpty( s ) ) {
1798                     boolean success = true;
1799                     double m = 0.0;
1800                     final String m_str = s.trim();
1801                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1802                         try {
1803                             m = Double.parseDouble( m_str );
1804                         }
1805                         catch ( final Exception ex ) {
1806                             success = false;
1807                         }
1808                     }
1809                     else {
1810                         success = false;
1811                     }
1812                     if ( success && ( m >= 0.0 ) ) {
1813                         setMinNotCollapseConfidenceValue( m );
1814                         collapse( phy, m );
1815                     }
1816                 }
1817             }
1818         }
1819     }
1820
1821     private PhyloXmlParser createPhyloXmlParser() {
1822         PhyloXmlParser xml_parser = null;
1823         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1824             try {
1825                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1826             }
1827             catch ( final Exception e ) {
1828                 JOptionPane.showMessageDialog( this,
1829                                                e.getLocalizedMessage(),
1830                                                "failed to create validating XML parser",
1831                                                JOptionPane.WARNING_MESSAGE );
1832             }
1833         }
1834         if ( xml_parser == null ) {
1835             xml_parser = new PhyloXmlParser();
1836         }
1837         return xml_parser;
1838     }
1839
1840     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1841         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1842                                                                       getPhylogeneticInferenceOptions(),
1843                                                                       from_unaligned_seqs );
1844         dialog.activate();
1845         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1846             if ( !from_unaligned_seqs ) {
1847                 if ( getMsa() != null ) {
1848                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1849                                                                                     getPhylogeneticInferenceOptions()
1850                                                                                             .copy(), this );
1851                     new Thread( inferrer ).start();
1852                 }
1853                 else {
1854                     JOptionPane.showMessageDialog( this,
1855                                                    "No multiple sequence alignment selected",
1856                                                    "Phylogenetic Inference Not Launched",
1857                                                    JOptionPane.WARNING_MESSAGE );
1858                 }
1859             }
1860             else {
1861                 if ( getSeqs() != null ) {
1862                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1863                                                                                     getPhylogeneticInferenceOptions()
1864                                                                                             .copy(), this );
1865                     new Thread( inferrer ).start();
1866                 }
1867                 else {
1868                     JOptionPane.showMessageDialog( this,
1869                                                    "No input sequences selected",
1870                                                    "Phylogenetic Inference Not Launched",
1871                                                    JOptionPane.WARNING_MESSAGE );
1872                 }
1873             }
1874         }
1875     }
1876
1877     private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
1878         if ( getCurrentTreePanel() != null ) {
1879             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1880             if ( ( phy != null ) && !phy.isEmpty() ) {
1881                 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1882                 while ( it.hasNext() ) {
1883                     final PhylogenyNode n = it.next();
1884                     final String name = n.getName().trim();
1885                     if ( !ForesterUtil.isEmpty( name ) ) {
1886                         final String code = ParserUtils
1887                                 .extractTaxonomyCodeFromNodeName( name, NHXParser.TAXONOMY_EXTRACTION.YES );
1888                         if ( !ForesterUtil.isEmpty( code ) ) {
1889                             PhylogenyMethods.setTaxonomyCode( n, code );
1890                         }
1891                     }
1892                 }
1893             }
1894         }
1895     }
1896
1897     private ControlPanel getControlPanel() {
1898         return getMainPanel().getControlPanel();
1899     }
1900
1901     private File getCurrentDir() {
1902         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1903             if ( ForesterUtil.isWindowns() ) {
1904                 try {
1905                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1906                 }
1907                 catch ( final Exception e ) {
1908                     _current_dir = null;
1909                 }
1910             }
1911         }
1912         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1913             if ( System.getProperty( "user.home" ) != null ) {
1914                 _current_dir = new File( System.getProperty( "user.home" ) );
1915             }
1916             else if ( System.getProperty( "user.dir" ) != null ) {
1917                 _current_dir = new File( System.getProperty( "user.dir" ) );
1918             }
1919         }
1920         return _current_dir;
1921     }
1922
1923     private double getMinNotCollapseConfidenceValue() {
1924         return _min_not_collapse;
1925     }
1926
1927     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1928         if ( _phylogenetic_inference_options == null ) {
1929             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1930         }
1931         return _phylogenetic_inference_options;
1932     }
1933
1934     private boolean isUnsavedDataPresent() {
1935         final List<TreePanel> tps = getMainPanel().getTreePanels();
1936         for( final TreePanel tp : tps ) {
1937             if ( tp.isEdited() ) {
1938                 return true;
1939             }
1940         }
1941         return false;
1942     }
1943
1944     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1945         if ( getCurrentTreePanel() != null ) {
1946             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1947             if ( ( phy != null ) && !phy.isEmpty() ) {
1948                 PhylogenyMethods
1949                         .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1950             }
1951         }
1952     }
1953
1954     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1955         if ( getCurrentTreePanel() != null ) {
1956             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1957             if ( ( phy != null ) && !phy.isEmpty() ) {
1958                 PhylogenyMethods.transferNodeNameToField( phy,
1959                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1960                                                           false );
1961             }
1962         }
1963     }
1964
1965     private void newTree() {
1966         final Phylogeny[] phys = new Phylogeny[ 1 ];
1967         final Phylogeny phy = new Phylogeny();
1968         final PhylogenyNode node = new PhylogenyNode();
1969         phy.setRoot( node );
1970         phy.setRooted( true );
1971         phys[ 0 ] = phy;
1972         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1973         _mainpanel.getControlPanel().showWhole();
1974         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1975         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1976         if ( getMainPanel().getMainFrame() == null ) {
1977             // Must be "E" applet version.
1978             ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1979                     .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1980         }
1981         else {
1982             getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1983         }
1984         activateSaveAllIfNeeded();
1985         System.gc();
1986     }
1987
1988     private void obtainDetailedTaxonomicInformation() {
1989         if ( getCurrentTreePanel() != null ) {
1990             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1991             if ( ( phy != null ) && !phy.isEmpty() ) {
1992                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1993                                                                        _mainpanel.getCurrentTreePanel(),
1994                                                                        phy.copy(),
1995                                                                        false,
1996                                                                        true );
1997                 new Thread( t ).start();
1998             }
1999         }
2000     }
2001
2002     private void obtainDetailedTaxonomicInformationDelete() {
2003         if ( getCurrentTreePanel() != null ) {
2004             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2005             if ( ( phy != null ) && !phy.isEmpty() ) {
2006                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
2007                                                                        _mainpanel.getCurrentTreePanel(),
2008                                                                        phy.copy(),
2009                                                                        true,
2010                                                                        true );
2011                 new Thread( t ).start();
2012             }
2013         }
2014     }
2015
2016     private void obtainSequenceInformation() {
2017         if ( getCurrentTreePanel() != null ) {
2018             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2019             if ( ( phy != null ) && !phy.isEmpty() ) {
2020                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
2021                                                                          _mainpanel.getCurrentTreePanel(),
2022                                                                          phy.copy() );
2023                 new Thread( u ).start();
2024             }
2025         }
2026     }
2027
2028     private void print() {
2029         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2030                 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2031             return;
2032         }
2033         if ( !getOptions().isPrintUsingActualSize() ) {
2034             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
2035                                                             getOptions().getPrintSizeY() - 140,
2036                                                             true );
2037             getCurrentTreePanel().resetPreferredSize();
2038             getCurrentTreePanel().repaint();
2039         }
2040         final String job_name = Constants.PRG_NAME;
2041         boolean error = false;
2042         String printer_name = null;
2043         try {
2044             printer_name = Printer.print( getCurrentTreePanel(), job_name );
2045         }
2046         catch ( final Exception e ) {
2047             error = true;
2048             JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2049         }
2050         if ( !error && ( printer_name != null ) ) {
2051             String msg = "Printing data sent to printer";
2052             if ( printer_name.length() > 1 ) {
2053                 msg += " [" + printer_name + "]";
2054             }
2055             JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2056         }
2057         if ( !getOptions().isPrintUsingActualSize() ) {
2058             getControlPanel().showWhole();
2059         }
2060     }
2061
2062     private void printPhylogenyToPdf( final String file_name ) {
2063         if ( !getOptions().isPrintUsingActualSize() ) {
2064             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
2065                                                             getOptions().getPrintSizeY(),
2066                                                             true );
2067             getCurrentTreePanel().resetPreferredSize();
2068             getCurrentTreePanel().repaint();
2069         }
2070         String pdf_written_to = "";
2071         boolean error = false;
2072         try {
2073             if ( getOptions().isPrintUsingActualSize() ) {
2074                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2075                                                                   getCurrentTreePanel(),
2076                                                                   getCurrentTreePanel().getWidth(),
2077                                                                   getCurrentTreePanel().getHeight() );
2078             }
2079             else {
2080                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2081                         .getPrintSizeX(), getOptions().getPrintSizeY() );
2082             }
2083         }
2084         catch ( final IOException e ) {
2085             error = true;
2086             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2087         }
2088         if ( !error ) {
2089             if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2090                 JOptionPane.showMessageDialog( this,
2091                                                "Wrote PDF to: " + pdf_written_to,
2092                                                "Information",
2093                                                JOptionPane.INFORMATION_MESSAGE );
2094             }
2095             else {
2096                 JOptionPane.showMessageDialog( this,
2097                                                "There was an unknown problem when attempting to write to PDF file: \""
2098                                                        + file_name + "\"",
2099                                                "Error",
2100                                                JOptionPane.ERROR_MESSAGE );
2101             }
2102         }
2103         if ( !getOptions().isPrintUsingActualSize() ) {
2104             getControlPanel().showWhole();
2105         }
2106     }
2107
2108     private void readPhylogeniesFromFile() {
2109         boolean exception = false;
2110         Phylogeny[] phys = null;
2111         // Set an initial directory if none set yet
2112         final File my_dir = getCurrentDir();
2113         _open_filechooser.setMultiSelectionEnabled( true );
2114         // Open file-open dialog and set current directory
2115         if ( my_dir != null ) {
2116             _open_filechooser.setCurrentDirectory( my_dir );
2117         }
2118         final int result = _open_filechooser.showOpenDialog( _contentpane );
2119         // All done: get the file
2120         final File[] files = _open_filechooser.getSelectedFiles();
2121         setCurrentDir( _open_filechooser.getCurrentDirectory() );
2122         boolean nhx_or_nexus = false;
2123         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2124             for( final File file : files ) {
2125                 if ( ( file != null ) && !file.isDirectory() ) {
2126                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2127                         _mainpanel.getCurrentTreePanel().setWaitCursor();
2128                     }
2129                     else {
2130                         _mainpanel.setWaitCursor();
2131                     }
2132                     if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2133                             || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2134                         try {
2135                             final NHXParser nhx = new NHXParser();
2136                             setSpecialOptionsForNhxParser( nhx );
2137                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
2138                             nhx_or_nexus = true;
2139                         }
2140                         catch ( final Exception e ) {
2141                             exception = true;
2142                             exceptionOccuredDuringOpenFile( e );
2143                         }
2144                     }
2145                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2146                         warnIfNotPhyloXmlValidation( getConfiguration() );
2147                         try {
2148                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
2149                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2150                         }
2151                         catch ( final Exception e ) {
2152                             exception = true;
2153                             exceptionOccuredDuringOpenFile( e );
2154                         }
2155                     }
2156                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2157                         try {
2158                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2159                         }
2160                         catch ( final Exception e ) {
2161                             exception = true;
2162                             exceptionOccuredDuringOpenFile( e );
2163                         }
2164                     }
2165                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2166                         try {
2167                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2168                             setSpecialOptionsForNexParser( nex );
2169                             phys = PhylogenyMethods.readPhylogenies( nex, file );
2170                             nhx_or_nexus = true;
2171                         }
2172                         catch ( final Exception e ) {
2173                             exception = true;
2174                             exceptionOccuredDuringOpenFile( e );
2175                         }
2176                     }
2177                     // "*.*":
2178                     else {
2179                         try {
2180                             final PhylogenyParser parser = ParserUtils
2181                                     .createParserDependingOnFileType( file, getConfiguration()
2182                                             .isValidatePhyloXmlAgainstSchema() );
2183                             if ( parser instanceof NexusPhylogeniesParser ) {
2184                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2185                                 setSpecialOptionsForNexParser( nex );
2186                                 nhx_or_nexus = true;
2187                             }
2188                             else if ( parser instanceof NHXParser ) {
2189                                 final NHXParser nhx = ( NHXParser ) parser;
2190                                 setSpecialOptionsForNhxParser( nhx );
2191                                 nhx_or_nexus = true;
2192                             }
2193                             else if ( parser instanceof PhyloXmlParser ) {
2194                                 warnIfNotPhyloXmlValidation( getConfiguration() );
2195                             }
2196                             phys = PhylogenyMethods.readPhylogenies( parser, file );
2197                         }
2198                         catch ( final Exception e ) {
2199                             exception = true;
2200                             exceptionOccuredDuringOpenFile( e );
2201                         }
2202                     }
2203                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2204                         _mainpanel.getCurrentTreePanel().setArrowCursor();
2205                     }
2206                     else {
2207                         _mainpanel.setArrowCursor();
2208                     }
2209                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2210                         boolean one_desc = false;
2211                         if ( nhx_or_nexus ) {
2212                             for( final Phylogeny phy : phys ) {
2213                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2214                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2215                                 }
2216                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2217                                     one_desc = true;
2218                                     break;
2219                                 }
2220                             }
2221                         }
2222                         AptxUtil.addPhylogeniesToTabs( phys,
2223                                                        file.getName(),
2224                                                        file.getAbsolutePath(),
2225                                                        getConfiguration(),
2226                                                        getMainPanel() );
2227                         _mainpanel.getControlPanel().showWhole();
2228                         if ( nhx_or_nexus && one_desc ) {
2229                             JOptionPane
2230                                     .showMessageDialog( this,
2231                                                         "One or more trees contain (a) node(s) with one descendant, "
2232                                                                 + ForesterUtil.LINE_SEPARATOR
2233                                                                 + "possibly indicating illegal parentheses within node names.",
2234                                                         "Warning: Possible Error in New Hampshire Formatted Data",
2235                                                         JOptionPane.WARNING_MESSAGE );
2236                         }
2237                     }
2238                 }
2239             }
2240         }
2241         activateSaveAllIfNeeded();
2242         System.gc();
2243     }
2244
2245     private void readSpeciesTreeFromFile() {
2246         Phylogeny t = null;
2247         boolean exception = false;
2248         final File my_dir = getCurrentDir();
2249         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2250         if ( my_dir != null ) {
2251             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2252         }
2253         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2254         final File file = _open_filechooser_for_species_tree.getSelectedFile();
2255         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2256             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2257                 try {
2258                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2259                     t = trees[ 0 ];
2260                 }
2261                 catch ( final Exception e ) {
2262                     exception = true;
2263                     exceptionOccuredDuringOpenFile( e );
2264                 }
2265             }
2266             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2267                 try {
2268                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2269                     t = trees[ 0 ];
2270                 }
2271                 catch ( final Exception e ) {
2272                     exception = true;
2273                     exceptionOccuredDuringOpenFile( e );
2274                 }
2275             }
2276             // "*.*":
2277             else {
2278                 try {
2279                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2280                     t = trees[ 0 ];
2281                 }
2282                 catch ( final Exception e ) {
2283                     exception = true;
2284                     exceptionOccuredDuringOpenFile( e );
2285                 }
2286             }
2287             if ( !exception && ( t != null ) && !t.isRooted() ) {
2288                 exception = true;
2289                 t = null;
2290                 JOptionPane.showMessageDialog( this,
2291                                                "Species tree is not rooted",
2292                                                "Species tree not loaded",
2293                                                JOptionPane.ERROR_MESSAGE );
2294             }
2295             if ( !exception && ( t != null ) ) {
2296                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2297                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2298                     final PhylogenyNode node = it.next();
2299                     if ( !node.getNodeData().isHasTaxonomy() ) {
2300                         exception = true;
2301                         t = null;
2302                         JOptionPane
2303                                 .showMessageDialog( this,
2304                                                     "Species tree contains external node(s) without taxonomy information",
2305                                                     "Species tree not loaded",
2306                                                     JOptionPane.ERROR_MESSAGE );
2307                         break;
2308                     }
2309                     else {
2310                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2311                             exception = true;
2312                             t = null;
2313                             JOptionPane.showMessageDialog( this,
2314                                                            "Taxonomy ["
2315                                                                    + node.getNodeData().getTaxonomy().asSimpleText()
2316                                                                    + "] is not unique in species tree",
2317                                                            "Species tree not loaded",
2318                                                            JOptionPane.ERROR_MESSAGE );
2319                             break;
2320                         }
2321                         else {
2322                             tax_set.add( node.getNodeData().getTaxonomy() );
2323                         }
2324                     }
2325                 }
2326             }
2327             if ( !exception && ( t != null ) ) {
2328                 _species_tree = t;
2329                 JOptionPane.showMessageDialog( this,
2330                                                "Species tree successfully loaded",
2331                                                "Species tree loaded",
2332                                                JOptionPane.INFORMATION_MESSAGE );
2333             }
2334             _contentpane.repaint();
2335             System.gc();
2336         }
2337     }
2338
2339     private void setCurrentDir( final File current_dir ) {
2340         _current_dir = current_dir;
2341     }
2342
2343     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2344         _min_not_collapse = min_not_collapse;
2345     }
2346
2347     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2348         _phylogenetic_inference_options = phylogenetic_inference_options;
2349     }
2350
2351     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2352         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2353     }
2354
2355     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2356         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2357         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2358     }
2359
2360     private void writeAllToFile() {
2361         if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2362             return;
2363         }
2364         final File my_dir = getCurrentDir();
2365         if ( my_dir != null ) {
2366             _save_filechooser.setCurrentDirectory( my_dir );
2367         }
2368         _save_filechooser.setSelectedFile( new File( "" ) );
2369         final int result = _save_filechooser.showSaveDialog( _contentpane );
2370         final File file = _save_filechooser.getSelectedFile();
2371         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2372         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2373             if ( file.exists() ) {
2374                 final int i = JOptionPane.showConfirmDialog( this,
2375                                                              file + " already exists. Overwrite?",
2376                                                              "Warning",
2377                                                              JOptionPane.OK_CANCEL_OPTION,
2378                                                              JOptionPane.WARNING_MESSAGE );
2379                 if ( i != JOptionPane.OK_OPTION ) {
2380                     return;
2381                 }
2382                 else {
2383                     try {
2384                         file.delete();
2385                     }
2386                     catch ( final Exception e ) {
2387                         JOptionPane.showMessageDialog( this,
2388                                                        "Failed to delete: " + file,
2389                                                        "Error",
2390                                                        JOptionPane.WARNING_MESSAGE );
2391                     }
2392                 }
2393             }
2394             final int count = getMainPanel().getTabbedPane().getTabCount();
2395             final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2396             for( int i = 0; i < count; ++i ) {
2397                 trees.add( getMainPanel().getPhylogeny( i ) );
2398                 getMainPanel().getTreePanels().get( i ).setEdited( false );
2399             }
2400             final PhylogenyWriter writer = new PhylogenyWriter();
2401             try {
2402                 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2403             }
2404             catch ( final IOException e ) {
2405                 JOptionPane.showMessageDialog( this,
2406                                                "Failed to write to: " + file,
2407                                                "Error",
2408                                                JOptionPane.WARNING_MESSAGE );
2409             }
2410         }
2411     }
2412
2413     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2414         try {
2415             final PhylogenyWriter writer = new PhylogenyWriter();
2416             writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2417         }
2418         catch ( final Exception e ) {
2419             exception = true;
2420             exceptionOccuredDuringSaveAs( e );
2421         }
2422         return exception;
2423     }
2424
2425     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2426         try {
2427             final PhylogenyWriter writer = new PhylogenyWriter();
2428             writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2429         }
2430         catch ( final Exception e ) {
2431             exception = true;
2432             exceptionOccuredDuringSaveAs( e );
2433         }
2434         return exception;
2435     }
2436
2437     private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
2438         try {
2439             final PhylogenyWriter writer = new PhylogenyWriter();
2440             writer.toNewHampshireX( t, file );
2441         }
2442         catch ( final Exception e ) {
2443             exception = true;
2444             exceptionOccuredDuringSaveAs( e );
2445         }
2446         return exception;
2447     }
2448
2449     private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2450         try {
2451             final PhylogenyWriter writer = new PhylogenyWriter();
2452             writer.toPhyloXML( file, t, 0 );
2453         }
2454         catch ( final Exception e ) {
2455             exception = true;
2456             exceptionOccuredDuringSaveAs( e );
2457         }
2458         return exception;
2459     }
2460
2461     private void writeToFile( final Phylogeny t ) {
2462         if ( t == null ) {
2463             return;
2464         }
2465         String initial_filename = null;
2466         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2467             try {
2468                 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2469             }
2470             catch ( final IOException e ) {
2471                 initial_filename = null;
2472             }
2473         }
2474         if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2475             _save_filechooser.setSelectedFile( new File( initial_filename ) );
2476         }
2477         else {
2478             _save_filechooser.setSelectedFile( new File( "" ) );
2479         }
2480         final File my_dir = getCurrentDir();
2481         if ( my_dir != null ) {
2482             _save_filechooser.setCurrentDirectory( my_dir );
2483         }
2484         final int result = _save_filechooser.showSaveDialog( _contentpane );
2485         final File file = _save_filechooser.getSelectedFile();
2486         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2487         boolean exception = false;
2488         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2489             if ( file.exists() ) {
2490                 final int i = JOptionPane.showConfirmDialog( this,
2491                                                              file + " already exists.\nOverwrite?",
2492                                                              "Overwrite?",
2493                                                              JOptionPane.OK_CANCEL_OPTION,
2494                                                              JOptionPane.QUESTION_MESSAGE );
2495                 if ( i != JOptionPane.OK_OPTION ) {
2496                     return;
2497                 }
2498                 else {
2499                     final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2500                     try {
2501                         ForesterUtil.copyFile( file, to );
2502                     }
2503                     catch ( final Exception e ) {
2504                         JOptionPane.showMessageDialog( this,
2505                                                        "Failed to create backup copy " + to,
2506                                                        "Failed to Create Backup Copy",
2507                                                        JOptionPane.WARNING_MESSAGE );
2508                     }
2509                     try {
2510                         file.delete();
2511                     }
2512                     catch ( final Exception e ) {
2513                         JOptionPane.showMessageDialog( this,
2514                                                        "Failed to delete: " + file,
2515                                                        "Failed to Delete",
2516                                                        JOptionPane.WARNING_MESSAGE );
2517                     }
2518                 }
2519             }
2520             if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2521                 exception = writeAsNewHampshire( t, exception, file );
2522             }
2523             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
2524                 exception = writeAsNHX( t, exception, file );
2525             }
2526             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2527                 exception = writeAsPhyloXml( t, exception, file );
2528             }
2529             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2530                 exception = writeAsNexus( t, exception, file );
2531             }
2532             // "*.*":
2533             else {
2534                 final String file_name = file.getName().trim().toLowerCase();
2535                 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2536                         || file_name.endsWith( ".tree" ) ) {
2537                     exception = writeAsNewHampshire( t, exception, file );
2538                 }
2539                 else if ( file_name.endsWith( ".nhx" ) ) {
2540                     exception = writeAsNHX( t, exception, file );
2541                 }
2542                 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2543                     exception = writeAsNexus( t, exception, file );
2544                 }
2545                 // XML is default:
2546                 else {
2547                     exception = writeAsPhyloXml( t, exception, file );
2548                 }
2549             }
2550             if ( !exception ) {
2551                 getMainPanel().setTitleOfSelectedTab( file.getName() );
2552                 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2553                 getMainPanel().getCurrentTreePanel().setEdited( false );
2554             }
2555         }
2556     }
2557
2558     private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2559         if ( ( t == null ) || t.isEmpty() ) {
2560             return;
2561         }
2562         String initial_filename = "";
2563         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2564             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2565         }
2566         if ( initial_filename.indexOf( '.' ) > 0 ) {
2567             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2568         }
2569         initial_filename = initial_filename + "." + type;
2570         _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2571         final File my_dir = getCurrentDir();
2572         if ( my_dir != null ) {
2573             _writetographics_filechooser.setCurrentDirectory( my_dir );
2574         }
2575         final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2576         File file = _writetographics_filechooser.getSelectedFile();
2577         setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2578         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2579             if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2580                 file = new File( file.toString() + "." + type );
2581             }
2582             if ( file.exists() ) {
2583                 final int i = JOptionPane.showConfirmDialog( this,
2584                                                              file + " already exists. Overwrite?",
2585                                                              "Warning",
2586                                                              JOptionPane.OK_CANCEL_OPTION,
2587                                                              JOptionPane.WARNING_MESSAGE );
2588                 if ( i != JOptionPane.OK_OPTION ) {
2589                     return;
2590                 }
2591                 else {
2592                     try {
2593                         file.delete();
2594                     }
2595                     catch ( final Exception e ) {
2596                         JOptionPane.showMessageDialog( this,
2597                                                        "Failed to delete: " + file,
2598                                                        "Error",
2599                                                        JOptionPane.WARNING_MESSAGE );
2600                     }
2601                 }
2602             }
2603             writePhylogenyToGraphicsFile( file.toString(), type );
2604         }
2605     }
2606
2607     private void writeToPdf( final Phylogeny t ) {
2608         if ( ( t == null ) || t.isEmpty() ) {
2609             return;
2610         }
2611         String initial_filename = "";
2612         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2613             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2614         }
2615         if ( initial_filename.indexOf( '.' ) > 0 ) {
2616             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2617         }
2618         initial_filename = initial_filename + ".pdf";
2619         _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2620         final File my_dir = getCurrentDir();
2621         if ( my_dir != null ) {
2622             _writetopdf_filechooser.setCurrentDirectory( my_dir );
2623         }
2624         final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2625         File file = _writetopdf_filechooser.getSelectedFile();
2626         setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2627         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2628             if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2629                 file = new File( file.toString() + ".pdf" );
2630             }
2631             if ( file.exists() ) {
2632                 final int i = JOptionPane.showConfirmDialog( this,
2633                                                              file + " already exists. Overwrite?",
2634                                                              "WARNING",
2635                                                              JOptionPane.OK_CANCEL_OPTION,
2636                                                              JOptionPane.WARNING_MESSAGE );
2637                 if ( i != JOptionPane.OK_OPTION ) {
2638                     return;
2639                 }
2640             }
2641             printPhylogenyToPdf( file.toString() );
2642         }
2643     }
2644
2645     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2646         return new MainFrameApplication( phys, config );
2647     }
2648
2649     public static MainFrame createInstance( final Phylogeny[] phys,
2650                                             final Configuration config,
2651                                             final String title,
2652                                             final File current_dir ) {
2653         return new MainFrameApplication( phys, config, title, current_dir );
2654     }
2655
2656     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2657         return new MainFrameApplication( phys, config, title );
2658     }
2659
2660     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2661         return new MainFrameApplication( phys, config_file_name, title );
2662     }
2663
2664     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2665         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2666                 + o.getPrintSizeY() + ")" );
2667     }
2668
2669     static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2670         mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2671     }
2672
2673     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2674         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2675             JOptionPane
2676                     .showMessageDialog( null,
2677                                         ForesterUtil
2678                                                 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2679                                                            80 ),
2680                                         "Warning",
2681                                         JOptionPane.WARNING_MESSAGE );
2682         }
2683     }
2684 } // MainFrameApplication.
2685
2686 class DefaultFilter 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( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2692                 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2693                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2694                 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2695                 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2696                 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2697                 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2698                 || file_name.endsWith( ".con" ) || f.isDirectory();
2699     }
2700
2701     @Override
2702     public String getDescription() {
2703         return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2704     }
2705 }
2706
2707 class GraphicsFileFilter extends FileFilter {
2708
2709     @Override
2710     public boolean accept( final File f ) {
2711         final String file_name = f.getName().trim().toLowerCase();
2712         return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2713                 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2714     }
2715
2716     @Override
2717     public String getDescription() {
2718         return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2719     }
2720 }
2721
2722 class MsaFileFilter extends FileFilter {
2723
2724     @Override
2725     public boolean accept( final File f ) {
2726         final String file_name = f.getName().trim().toLowerCase();
2727         return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2728                 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2729     }
2730
2731     @Override
2732     public String getDescription() {
2733         return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2734     }
2735 }
2736
2737 class NexusFilter extends FileFilter {
2738
2739     @Override
2740     public boolean accept( final File f ) {
2741         final String file_name = f.getName().trim().toLowerCase();
2742         return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2743                 || file_name.endsWith( ".tre" ) || f.isDirectory();
2744     }
2745
2746     @Override
2747     public String getDescription() {
2748         return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2749     }
2750 } // NexusFilter
2751
2752 class NHFilter extends FileFilter {
2753
2754     @Override
2755     public boolean accept( final File f ) {
2756         final String file_name = f.getName().trim().toLowerCase();
2757         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2758                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2759                 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2760                 || f.isDirectory();
2761     }
2762
2763     @Override
2764     public String getDescription() {
2765         return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2766     }
2767 } // NHFilter
2768
2769 class NHXFilter extends FileFilter {
2770
2771     @Override
2772     public boolean accept( final File f ) {
2773         final String file_name = f.getName().trim().toLowerCase();
2774         return file_name.endsWith( ".nhx" ) || f.isDirectory();
2775     }
2776
2777     @Override
2778     public String getDescription() {
2779         return "NHX files (*.nhx)";
2780     }
2781 }
2782
2783 class PdfFilter extends FileFilter {
2784
2785     @Override
2786     public boolean accept( final File f ) {
2787         return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2788     }
2789
2790     @Override
2791     public String getDescription() {
2792         return "PDF files (*.pdf)";
2793     }
2794 } // PdfFilter
2795
2796 class SequencesFileFilter extends FileFilter {
2797
2798     @Override
2799     public boolean accept( final File f ) {
2800         final String file_name = f.getName().trim().toLowerCase();
2801         return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2802                 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2803     }
2804
2805     @Override
2806     public String getDescription() {
2807         return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2808     }
2809 }
2810
2811 class TolFilter extends FileFilter {
2812
2813     @Override
2814     public boolean accept( final File f ) {
2815         final String file_name = f.getName().trim().toLowerCase();
2816         return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2817                 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2818     }
2819
2820     @Override
2821     public String getDescription() {
2822         return "Tree of Life files (*.tol, *.tolxml)";
2823     }
2824 } // TolFilter
2825
2826 class XMLFilter extends FileFilter {
2827
2828     @Override
2829     public boolean accept( final File f ) {
2830         final String file_name = f.getName().trim().toLowerCase();
2831         return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2832                 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2833     }
2834
2835     @Override
2836     public String getDescription() {
2837         return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
2838     }
2839 } // XMLFilter