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         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
 272             setCurrentDir( current_dir );
 273         }
 274         // hide until everything is ready
 275         setVisible( false );
 276         setOptions( Options.createInstance( _configuration ) );
 277         setInferenceManager( InferenceManager.createInstance( _configuration ) );
 278         setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
 279         //     _textframe = null; #~~~~
 280         _species_tree = null;
 281         // set title
 282         setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
 283         _mainpanel = new MainPanel( _configuration, this );
 284         // The file dialogs
 285         _open_filechooser = new JFileChooser();
 286         _open_filechooser.setCurrentDirectory( new File( "." ) );
 287         _open_filechooser.setMultiSelectionEnabled( false );
 288         _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 289         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
 290         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 291         _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 292         _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
 293         _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
 294         _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
 295         _open_filechooser_for_species_tree = new JFileChooser();
 296         _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
 297         _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
 298         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
 299         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
 300         _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
 301         _save_filechooser = new JFileChooser();
 302         _save_filechooser.setCurrentDirectory( new File( "." ) );
 303         _save_filechooser.setMultiSelectionEnabled( false );
 304         _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
 305         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
 306         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
 307         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 308         _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
 309         _writetopdf_filechooser = new JFileChooser();
 310         _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
 311         _writetographics_filechooser = new JFileChooser();
 312         _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
 313         // Msa:
 314         _msa_filechooser = new JFileChooser();
 315         _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
 316         _msa_filechooser.setCurrentDirectory( new File( "." ) );
 317         _msa_filechooser.setMultiSelectionEnabled( false );
 318         _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
 319         _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
 320         // Seqs:
 321         _seqs_filechooser = new JFileChooser();
 322         _seqs_filechooser.setName( "Read Sequences File" );
 323         _seqs_filechooser.setCurrentDirectory( new File( "." ) );
 324         _seqs_filechooser.setMultiSelectionEnabled( false );
 325         _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() );
 326         _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
 327         // Expression
 328         _values_filechooser = new JFileChooser();
 329         _values_filechooser.setCurrentDirectory( new File( "." ) );
 330         _values_filechooser.setMultiSelectionEnabled( false );
 331         // build the menu bar
 332         _jmenubar = new JMenuBar();
 333         if ( !_configuration.isUseNativeUI() ) {
 334             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 335         }
 336         buildFileMenu();
 337         if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
 338             buildPhylogeneticInferenceMenu();
 339         }
 340         buildAnalysisMenu();
 341         buildToolsMenu();
 342         buildViewMenu();
 343         buildFontSizeMenu();
 344         buildOptionsMenu();
 345         buildTypeMenu();
 346         buildHelpMenu();
 347         setJMenuBar( _jmenubar );
 348         _jmenubar.add( _help_jmenu );
 349         _contentpane = getContentPane();
 350         _contentpane.setLayout( new BorderLayout() );
 351         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 352         // App is this big
 353         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 354         //        addWindowFocusListener( new WindowAdapter() {
 355         //
 356         //            @Override
 357         //            public void windowGainedFocus( WindowEvent e ) {
 358         //                requestFocusInWindow();
 359         //            }
 360         //        } );
 361         // The window listener
 362         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 363         addWindowListener( new WindowAdapter() {
 364
 365             @Override
 366             public void windowClosing( final WindowEvent e ) {
 367                 if ( isUnsavedDataPresent() ) {
 368                     final int r = JOptionPane.showConfirmDialog( null,
 369                                                                  "Exit despite potentially unsaved changes?",
 370                                                                  "Exit?",
 371                                                                  JOptionPane.YES_NO_OPTION );
 372                     if ( r != JOptionPane.YES_OPTION ) {
 373                         return;
 374                     }
 375                 }
 376                 else {
 377                     final int r = JOptionPane.showConfirmDialog( null,
 378                                                                  "Exit Archaeopteryx?",
 379                                                                  "Exit?",
 380                                                                  JOptionPane.YES_NO_OPTION );
 381                     if ( r != JOptionPane.YES_OPTION ) {
 382                         return;
 383                     }
 384                 }
 385                 exit();
 386             }
 387         } );
 388         // The component listener
 389         addComponentListener( new ComponentAdapter() {
 390
 391             @Override
 392             public void componentResized( final ComponentEvent e ) {
 393                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 394                     _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
 395                                                                                        .getWidth(),
 396                                                                                _mainpanel.getCurrentTreePanel()
 397                                                                                        .getHeight(),
 398                                                                                false );
 399                 }
 400             }
 401         } );
 402         requestFocusInWindow();
 403         // addKeyListener( this );
 404         setVisible( true );
 405         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 406             AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
 407             validate();
 408             getMainPanel().getControlPanel().showWholeAll();
 409             getMainPanel().getControlPanel().showWhole();
 410         }
 411         activateSaveAllIfNeeded();
 412         // ...and its children
 413         _contentpane.repaint();
 414         System.gc();
 415     }
 416
 417     private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
 418         // Reads the config file (false, false => not url, not applet):
 419         this( phys, new Configuration( config_file, false, false, true ), title );
 420     }
 421
 422     @Override
 423     public void actionPerformed( final ActionEvent e ) {
 424         try {
 425             super.actionPerformed( e );
 426             final Object o = e.getSource();
 427             // Handle app-specific actions here:
 428             if ( o == _open_item ) {
 429                 readPhylogeniesFromFile();
 430             }
 431             else if ( o == _save_item ) {
 432                 writeToFile( _mainpanel.getCurrentPhylogeny() );
 433                 // If subtree currently displayed, save it, instead of complete
 434                 // tree.
 435             }
 436             else if ( o == _new_item ) {
 437                 newTree();
 438             }
 439             else if ( o == _save_all_item ) {
 440                 writeAllToFile();
 441             }
 442             else if ( o == _close_item ) {
 443                 closeCurrentPane();
 444             }
 445             else if ( o == _write_to_pdf_item ) {
 446                 writeToPdf( _mainpanel.getCurrentPhylogeny() );
 447             }
 448             else if ( o == _write_to_jpg_item ) {
 449                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
 450             }
 451             else if ( o == _write_to_png_item ) {
 452                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
 453             }
 454             else if ( o == _write_to_gif_item ) {
 455                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
 456             }
 457             else if ( o == _write_to_tif_item ) {
 458                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
 459             }
 460             else if ( o == _write_to_bmp_item ) {
 461                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
 462             }
 463             else if ( o == _print_item ) {
 464                 print();
 465             }
 466             else if ( o == _load_species_tree_item ) {
 467                 readSpeciesTreeFromFile();
 468             }
 469             else if ( o == _lineage_inference ) {
 470                 if ( isSubtreeDisplayed() ) {
 471                     JOptionPane.showMessageDialog( this,
 472                                                    "Subtree is shown.",
 473                                                    "Cannot infer ancestral taxonomies",
 474                                                    JOptionPane.ERROR_MESSAGE );
 475                     return;
 476                 }
 477                 executeLineageInference();
 478             }
 479             else if ( o == _function_analysis ) {
 480                 executeFunctionAnalysis();
 481             }
 482             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
 483                 if ( isSubtreeDisplayed() ) {
 484                     return;
 485                 }
 486                 obtainDetailedTaxonomicInformation();
 487             }
 488             else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
 489                 if ( isSubtreeDisplayed() ) {
 490                     return;
 491                 }
 492                 obtainDetailedTaxonomicInformationDelete();
 493             }
 494             else if ( o == _obtain_seq_information_jmi ) {
 495                 obtainSequenceInformation();
 496             }
 497             else if ( o == _read_values_jmi ) {
 498                 if ( isSubtreeDisplayed() ) {
 499                     return;
 500                 }
 501                 addExpressionValuesFromFile();
 502             }
 503             else if ( o == _move_node_names_to_tax_sn_jmi ) {
 504                 moveNodeNamesToTaxSn();
 505             }
 506             else if ( o == _move_node_names_to_seq_names_jmi ) {
 507                 moveNodeNamesToSeqNames();
 508             }
 509             else if ( o == _extract_tax_code_from_node_names_jmi ) {
 510                 extractTaxDataFromNodeNames();
 511             }
 512             else if ( o == _gsdi_item ) {
 513                 if ( isSubtreeDisplayed() ) {
 514                     return;
 515                 }
 516                 executeGSDI();
 517             }
 518             else if ( o == _gsdir_item ) {
 519                 if ( isSubtreeDisplayed() ) {
 520                     return;
 521                 }
 522                 executeGSDIR();
 523             }
 524             else if ( o == _root_min_dups_item ) {
 525                 if ( isSubtreeDisplayed() ) {
 526                     return;
 527                 }
 528                 executeSDIR( false );
 529             }
 530             else if ( o == _root_min_cost_l_item ) {
 531                 if ( isSubtreeDisplayed() ) {
 532                     return;
 533                 }
 534                 executeSDIR( true );
 535             }
 536             else if ( o == _graphics_export_visible_only_cbmi ) {
 537                 updateOptions( getOptions() );
 538             }
 539             else if ( o == _antialias_print_cbmi ) {
 540                 updateOptions( getOptions() );
 541             }
 542             else if ( o == _print_black_and_white_cbmi ) {
 543                 updateOptions( getOptions() );
 544             }
 545             else if ( o == _print_using_actual_size_cbmi ) {
 546                 updateOptions( getOptions() );
 547             }
 548             else if ( o == _graphics_export_using_actual_size_cbmi ) {
 549                 updateOptions( getOptions() );
 550             }
 551             else if ( o == _print_size_mi ) {
 552                 choosePrintSize();
 553             }
 554             else if ( o == _choose_pdf_width_mi ) {
 555                 choosePdfWidth();
 556             }
 557             else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
 558                 updateOptions( getOptions() );
 559             }
 560             else if ( o == _replace_underscores_cbmi ) {
 561                 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
 562                     _extract_taxonomy_no_rbmi.setSelected( true );
 563                 }
 564                 updateOptions( getOptions() );
 565             }
 566             else if ( o == _collapse_below_threshold ) {
 567                 if ( isSubtreeDisplayed() ) {
 568                     return;
 569                 }
 570                 collapseBelowThreshold();
 571             }
 572             else if ( ( o == _extract_taxonomy_pfam_rbmi ) || ( o == _extract_taxonomy_yes_rbmi ) ) {
 573                 if ( _replace_underscores_cbmi != null ) {
 574                     _replace_underscores_cbmi.setSelected( false );
 575                 }
 576                 updateOptions( getOptions() );
 577             }
 578             else if ( o == _inference_from_msa_item ) {
 579                 executePhyleneticInference( false );
 580             }
 581             else if ( o == _inference_from_seqs_item ) {
 582                 executePhyleneticInference( true );
 583             }
 584             _contentpane.repaint();
 585         }
 586         catch ( final Exception ex ) {
 587             AptxUtil.unexpectedException( ex );
 588         }
 589         catch ( final Error err ) {
 590             AptxUtil.unexpectedError( err );
 591         }
 592     }
 593
 594     public void end() {
 595         _mainpanel.terminate();
 596         _contentpane.removeAll();
 597         setVisible( false );
 598         dispose();
 599     }
 600
 601     @Override
 602     public MainPanel getMainPanel() {
 603         return _mainpanel;
 604     }
 605
 606     public Msa getMsa() {
 607         return _msa;
 608     }
 609
 610     public File getMsaFile() {
 611         return _msa_file;
 612     }
 613
 614     public List<Sequence> getSeqs() {
 615         return _seqs;
 616     }
 617
 618     public File getSeqsFile() {
 619         return _seqs_file;
 620     }
 621
 622     public void readMsaFromFile() {
 623         // Set an initial directory if none set yet
 624         final File my_dir = getCurrentDir();
 625         _msa_filechooser.setMultiSelectionEnabled( false );
 626         // Open file-open dialog and set current directory
 627         if ( my_dir != null ) {
 628             _msa_filechooser.setCurrentDirectory( my_dir );
 629         }
 630         final int result = _msa_filechooser.showOpenDialog( _contentpane );
 631         // All done: get the msa
 632         final File file = _msa_filechooser.getSelectedFile();
 633         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
 634         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 635             setMsaFile( null );
 636             setMsa( null );
 637             Msa msa = null;
 638             try {
 639                 final InputStream is = new FileInputStream( file );
 640                 if ( FastaParser.isLikelyFasta( file ) ) {
 641                     msa = FastaParser.parseMsa( is );
 642                 }
 643                 else {
 644                     msa = GeneralMsaParser.parse( is );
 645                 }
 646             }
 647             catch ( final MsaFormatException e ) {
 648                 try {
 649                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 650                 }
 651                 catch ( final Exception ex ) {
 652                     // Do nothing.
 653                 }
 654                 JOptionPane.showMessageDialog( this,
 655                                                e.getLocalizedMessage(),
 656                                                "Multiple sequence alignment format error",
 657                                                JOptionPane.ERROR_MESSAGE );
 658                 return;
 659             }
 660             catch ( final IOException e ) {
 661                 try {
 662                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 663                 }
 664                 catch ( final Exception ex ) {
 665                     // Do nothing.
 666                 }
 667                 JOptionPane.showMessageDialog( this,
 668                                                e.getLocalizedMessage(),
 669                                                "Failed to read multiple sequence alignment",
 670                                                JOptionPane.ERROR_MESSAGE );
 671                 return;
 672             }
 673             catch ( final IllegalArgumentException e ) {
 674                 try {
 675                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 676                 }
 677                 catch ( final Exception ex ) {
 678                     // Do nothing.
 679                 }
 680                 JOptionPane.showMessageDialog( this,
 681                                                e.getLocalizedMessage(),
 682                                                "Unexpected error during reading of multiple sequence alignment",
 683                                                JOptionPane.ERROR_MESSAGE );
 684                 return;
 685             }
 686             catch ( final Exception e ) {
 687                 try {
 688                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 689                 }
 690                 catch ( final Exception ex ) {
 691                     // Do nothing.
 692                 }
 693                 e.printStackTrace();
 694                 JOptionPane.showMessageDialog( this,
 695                                                e.getLocalizedMessage(),
 696                                                "Unexpected error during reading of multiple sequence alignment",
 697                                                JOptionPane.ERROR_MESSAGE );
 698                 return;
 699             }
 700             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
 701                 JOptionPane.showMessageDialog( this,
 702                                                "Multiple sequence alignment is empty",
 703                                                "Illegal Multiple Sequence Alignment",
 704                                                JOptionPane.ERROR_MESSAGE );
 705                 return;
 706             }
 707             if ( msa.getNumberOfSequences() < 4 ) {
 708                 JOptionPane.showMessageDialog( this,
 709                                                "Multiple sequence alignment needs to contain at least 3 sequences",
 710                                                "Illegal multiple sequence alignment",
 711                                                JOptionPane.ERROR_MESSAGE );
 712                 return;
 713             }
 714             if ( msa.getLength() < 2 ) {
 715                 JOptionPane.showMessageDialog( this,
 716                                                "Multiple sequence alignment needs to contain at least 2 residues",
 717                                                "Illegal multiple sequence alignment",
 718                                                JOptionPane.ERROR_MESSAGE );
 719                 return;
 720             }
 721             System.gc();
 722             setMsaFile( _msa_filechooser.getSelectedFile() );
 723             setMsa( msa );
 724         }
 725     }
 726
 727     public void readSeqsFromFile() {
 728         // Set an initial directory if none set yet
 729         final File my_dir = getCurrentDir();
 730         _seqs_filechooser.setMultiSelectionEnabled( false );
 731         // Open file-open dialog and set current directory
 732         if ( my_dir != null ) {
 733             _seqs_filechooser.setCurrentDirectory( my_dir );
 734         }
 735         final int result = _seqs_filechooser.showOpenDialog( _contentpane );
 736         // All done: get the seqs
 737         final File file = _seqs_filechooser.getSelectedFile();
 738         setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
 739         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 740             setSeqsFile( null );
 741             setSeqs( null );
 742             List<Sequence> seqs = null;
 743             try {
 744                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
 745                     seqs = FastaParser.parse( new FileInputStream( file ) );
 746                     for( final Sequence seq : seqs ) {
 747                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
 748                     }
 749                 }
 750                 else {
 751                     //TODO error
 752                 }
 753             }
 754             catch ( final MsaFormatException e ) {
 755                 try {
 756                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 757                 }
 758                 catch ( final Exception ex ) {
 759                     // Do nothing.
 760                 }
 761                 JOptionPane.showMessageDialog( this,
 762                                                e.getLocalizedMessage(),
 763                                                "Multiple sequence file format error",
 764                                                JOptionPane.ERROR_MESSAGE );
 765                 return;
 766             }
 767             catch ( final IOException e ) {
 768                 try {
 769                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 770                 }
 771                 catch ( final Exception ex ) {
 772                     // Do nothing.
 773                 }
 774                 JOptionPane.showMessageDialog( this,
 775                                                e.getLocalizedMessage(),
 776                                                "Failed to read multiple sequence file",
 777                                                JOptionPane.ERROR_MESSAGE );
 778                 return;
 779             }
 780             catch ( final IllegalArgumentException e ) {
 781                 try {
 782                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 783                 }
 784                 catch ( final Exception ex ) {
 785                     // Do nothing.
 786                 }
 787                 JOptionPane.showMessageDialog( this,
 788                                                e.getLocalizedMessage(),
 789                                                "Unexpected error during reading of multiple sequence file",
 790                                                JOptionPane.ERROR_MESSAGE );
 791                 return;
 792             }
 793             catch ( final Exception e ) {
 794                 try {
 795                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 796                 }
 797                 catch ( final Exception ex ) {
 798                     // Do nothing.
 799                 }
 800                 e.printStackTrace();
 801                 JOptionPane.showMessageDialog( this,
 802                                                e.getLocalizedMessage(),
 803                                                "Unexpected error during reading of multiple sequence file",
 804                                                JOptionPane.ERROR_MESSAGE );
 805                 return;
 806             }
 807             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 808                 JOptionPane.showMessageDialog( this,
 809                                                "Multiple sequence file is empty",
 810                                                "Illegal multiple sequence file",
 811                                                JOptionPane.ERROR_MESSAGE );
 812                 return;
 813             }
 814             if ( seqs.size() < 4 ) {
 815                 JOptionPane.showMessageDialog( this,
 816                                                "Multiple sequence file needs to contain at least 3 sequences",
 817                                                "Illegal multiple sequence file",
 818                                                JOptionPane.ERROR_MESSAGE );
 819                 return;
 820             }
 821             //  if ( msa.getLength() < 2 ) {
 822             //       JOptionPane.showMessageDialog( this,
 823             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
 824             //                                      "Illegal multiple sequence file",
 825             //                                      JOptionPane.ERROR_MESSAGE );
 826             //       return;
 827             //   }
 828             System.gc();
 829             setSeqsFile( _seqs_filechooser.getSelectedFile() );
 830             setSeqs( seqs );
 831         }
 832     }
 833
 834     void buildAnalysisMenu() {
 835         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 836         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 837         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
 838         _analysis_menu.addSeparator();
 839         _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
 840         _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
 841         _analysis_menu.addSeparator();
 842         _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
 843         customizeJMenuItem( _gsdi_item );
 844         customizeJMenuItem( _gsdir_item );
 845         customizeJMenuItem( _root_min_dups_item );
 846         customizeJMenuItem( _root_min_cost_l_item );
 847         customizeJMenuItem( _load_species_tree_item );
 848         _analysis_menu.addSeparator();
 849         _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 850         customizeJMenuItem( _lineage_inference );
 851         _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 852         _jmenubar.add( _analysis_menu );
 853     }
 854
 855     @Override
 856     void buildFileMenu() {
 857         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
 858         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
 859         _file_jmenu.addSeparator();
 860         _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
 861         _file_jmenu.addSeparator();
 862         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
 863         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
 864                 .getAvailablePhylogeniesWebserviceClients().size() ];
 865         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 866             final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
 867             _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
 868             _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
 869         }
 870         if ( getConfiguration().isEditable() ) {
 871             _file_jmenu.addSeparator();
 872             _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
 873             _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
 874         }
 875         _file_jmenu.addSeparator();
 876         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
 877         _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
 878         _save_all_item.setToolTipText( "Write all phylogenies to one file." );
 879         _save_all_item.setEnabled( false );
 880         _file_jmenu.addSeparator();
 881         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
 882         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
 883             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
 884         }
 885         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
 886         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
 887         if ( AptxUtil.canWriteFormat( "gif" ) ) {
 888             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
 889         }
 890         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
 891             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
 892         }
 893         _file_jmenu.addSeparator();
 894         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
 895         _file_jmenu.addSeparator();
 896         _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
 897         _close_item.setToolTipText( "To close the current pane." );
 898         _close_item.setEnabled( true );
 899         _file_jmenu.addSeparator();
 900         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 901         // For print in color option item
 902         customizeJMenuItem( _open_item );
 903         _open_item
 904                 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
 905         customizeJMenuItem( _open_url_item );
 906         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 907             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
 908         }
 909         customizeJMenuItem( _save_item );
 910         if ( getConfiguration().isEditable() ) {
 911             customizeJMenuItem( _new_item );
 912         }
 913         customizeJMenuItem( _close_item );
 914         customizeJMenuItem( _save_all_item );
 915         customizeJMenuItem( _write_to_pdf_item );
 916         customizeJMenuItem( _write_to_png_item );
 917         customizeJMenuItem( _write_to_jpg_item );
 918         customizeJMenuItem( _write_to_gif_item );
 919         customizeJMenuItem( _write_to_tif_item );
 920         customizeJMenuItem( _write_to_bmp_item );
 921         customizeJMenuItem( _print_item );
 922         customizeJMenuItem( _exit_item );
 923         _jmenubar.add( _file_jmenu );
 924     }
 925
 926     void buildOptionsMenu() {
 927         _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
 928         _options_jmenu.addChangeListener( new ChangeListener() {
 929
 930             @Override
 931             public void stateChanged( final ChangeEvent e ) {
 932                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 933                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 934                 MainFrame
 935                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 936                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 937                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 938                 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
 939                 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
 940                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 941                                                                      _show_scale_cbmi,
 942                                                                      _show_branch_length_values_cbmi,
 943                                                                      _non_lined_up_cladograms_rbmi,
 944                                                                      _uniform_cladograms_rbmi,
 945                                                                      _ext_node_dependent_cladogram_rbmi,
 946                                                                      _label_direction_cbmi );
 947                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 948                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 949                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 950             }
 951         } );
 952         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
 953         _options_jmenu
 954                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 955         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 956         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 957         _radio_group_1 = new ButtonGroup();
 958         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 959         _radio_group_1.add( _uniform_cladograms_rbmi );
 960         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 961         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
 962         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
 963         _options_jmenu
 964                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 965         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
 966         _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
 967         _options_jmenu
 968                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 969         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 970         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 971         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 972         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 973         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 974         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 975         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 976         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
 977         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
 978         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
 979         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 980             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 981         }
 982         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 983         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 984         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 985         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 986         _options_jmenu.addSeparator();
 987         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
 988         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
 989         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
 990         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 991         _options_jmenu.addSeparator();
 992         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
 993                                                       getConfiguration() ) );
 994         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
 995         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
 996         _options_jmenu
 997                 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
 998         _options_jmenu
 999                 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
1000         _options_jmenu
1001                 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
1002         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
1003         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
1004         _options_jmenu.addSeparator();
1005         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
1006         _options_jmenu
1007                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
1008         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
1009         //
1010         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
1011         _options_jmenu
1012                 .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
1013         _extract_taxonomy_pfam_rbmi
1014                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
1015         _options_jmenu
1016                 .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
1017         _extract_taxonomy_yes_rbmi
1018                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
1019         _radio_group_2 = new ButtonGroup();
1020         _radio_group_2.add( _extract_taxonomy_no_rbmi );
1021         _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
1022         _radio_group_2.add( _extract_taxonomy_yes_rbmi );
1023         //
1024         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
1025         _options_jmenu
1026                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
1027         _use_brackets_for_conf_in_nh_export_cbmi
1028                 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
1029         _options_jmenu
1030                 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
1031         customizeJMenuItem( _choose_font_mi );
1032         customizeJMenuItem( _choose_minimal_confidence_mi );
1033         customizeJMenuItem( _switch_colors_mi );
1034         customizeJMenuItem( _print_size_mi );
1035         customizeJMenuItem( _choose_pdf_width_mi );
1036         customizeJMenuItem( _overview_placment_mi );
1037         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
1038         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
1039         customizeJMenuItem( _cycle_node_shape_mi );
1040         customizeJMenuItem( _cycle_node_fill_mi );
1041         customizeJMenuItem( _choose_node_size_mi );
1042         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
1043         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
1044         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
1045         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
1046         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
1047         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
1048         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
1049         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
1050                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
1051         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
1052                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1053         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
1054                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1055         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
1056         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1057         customizeCheckBoxMenuItem( _label_direction_cbmi,
1058                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1059         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1060         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1061         customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1062                 .isInternalNumberAreConfidenceForNhParsing() );
1063         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1064                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1065         customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
1066                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
1067         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
1068                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1069         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1070         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1071         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1072         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1073         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1074         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1075                 .isGraphicsExportUsingActualSize() );
1076         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1077         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1078                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1079         customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1080                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1081         _jmenubar.add( _options_jmenu );
1082     }
1083
1084     void buildPhylogeneticInferenceMenu() {
1085         final InferenceManager im = getInferenceManager();
1086         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1087         _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1088         customizeJMenuItem( _inference_from_msa_item );
1089         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1090         if ( im.canDoMsa() ) {
1091             _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1092             customizeJMenuItem( _inference_from_seqs_item );
1093             _inference_from_seqs_item
1094                     .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1095         }
1096         else {
1097             _inference_menu
1098                     .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1099             customizeJMenuItem( _inference_from_seqs_item );
1100             _inference_from_seqs_item.setEnabled( false );
1101         }
1102         _jmenubar.add( _inference_menu );
1103     }
1104
1105     void buildToolsMenu() {
1106         _tools_menu = createMenu( "Tools", getConfiguration() );
1107         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1108         customizeJMenuItem( _confcolor_item );
1109         _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1110         customizeJMenuItem( _color_rank_jmi );
1111         _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1112         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1113         customizeJMenuItem( _taxcolor_item );
1114         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1115         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1116         customizeJMenuItem( _remove_branch_color_item );
1117         _tools_menu.addSeparator();
1118         _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1119         customizeJMenuItem( _annotate_item );
1120         _tools_menu.addSeparator();
1121         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1122         customizeJMenuItem( _midpoint_root_item );
1123         _tools_menu.addSeparator();
1124         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1125         customizeJMenuItem( _collapse_species_specific_subtrees );
1126         _tools_menu
1127                 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1128         customizeJMenuItem( _collapse_below_threshold );
1129         _collapse_below_threshold
1130                 .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)" );
1131         _tools_menu.addSeparator();
1132         _tools_menu
1133                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1134         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1135         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1136         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1137         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1138         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1139         _tools_menu
1140                 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes or Ids from Node Names" ) );
1141         customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1142         _extract_tax_code_from_node_names_jmi
1143                 .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI', or Uniprot identifiers from nodes names in the form of 'xyz_1234567'" );
1144         _tools_menu.addSeparator();
1145         _tools_menu
1146                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1147         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1148         _obtain_detailed_taxonomic_information_jmi
1149                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1150         _tools_menu
1151                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1152         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1153         _obtain_detailed_taxonomic_information_deleting_jmi
1154                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1155         _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1156         customizeJMenuItem( _obtain_seq_information_jmi );
1157         _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1158         _tools_menu.addSeparator();
1159         if ( !Constants.__RELEASE ) {
1160             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
1161             customizeJMenuItem( _function_analysis );
1162             _function_analysis
1163                     .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
1164             _tools_menu.addSeparator();
1165         }
1166         _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
1167         customizeJMenuItem( _read_values_jmi );
1168         _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
1169         _jmenubar.add( _tools_menu );
1170     }
1171
1172     @Override
1173     void close() {
1174         if ( isUnsavedDataPresent() ) {
1175             final int r = JOptionPane.showConfirmDialog( this,
1176                                                          "Exit despite potentially unsaved changes?",
1177                                                          "Exit?",
1178                                                          JOptionPane.YES_NO_OPTION );
1179             if ( r != JOptionPane.YES_OPTION ) {
1180                 return;
1181             }
1182         }
1183         exit();
1184     }
1185
1186     void executeFunctionAnalysis() {
1187         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1188             return;
1189         }
1190         final GoAnnotation a = new GoAnnotation( this,
1191                                                  _mainpanel.getCurrentTreePanel(),
1192                                                  _mainpanel.getCurrentPhylogeny() );
1193         new Thread( a ).start();
1194     }
1195
1196     void executeGSDI() {
1197         if ( !isOKforSDI( false, true ) ) {
1198             return;
1199         }
1200         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1201             JOptionPane.showMessageDialog( this,
1202                                            "Gene tree is not rooted.",
1203                                            "Cannot execute GSDI",
1204                                            JOptionPane.ERROR_MESSAGE );
1205             return;
1206         }
1207         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1208         gene_tree.setAllNodesToNotCollapse();
1209         gene_tree.recalculateNumberOfExternalDescendants( false );
1210         GSDI gsdi = null;
1211         final Phylogeny species_tree = _species_tree.copy();
1212         try {
1213             gsdi = new GSDI( gene_tree, species_tree, false, true, true );
1214         }
1215         catch ( final SDIException e ) {
1216             JOptionPane.showMessageDialog( this,
1217                                            e.getLocalizedMessage(),
1218                                            "Error during GSDI",
1219                                            JOptionPane.ERROR_MESSAGE );
1220             return;
1221         }
1222         catch ( final Exception e ) {
1223             AptxUtil.unexpectedException( e );
1224             return;
1225         }
1226         gene_tree.setRerootable( false );
1227         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1228         _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
1229         _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
1230         _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1231         _mainpanel.getCurrentTreePanel().setEdited( true );
1232         getControlPanel().setShowEvents( true );
1233         showWhole();
1234         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1235         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1236         showWhole();
1237         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1238         showWhole();
1239         _mainpanel.getCurrentTreePanel().setEdited( true );
1240         JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1241                 + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
1242                 + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
1243     }
1244
1245     void executeGSDIR() {
1246         if ( !isOKforSDI( false, true ) ) {
1247             return;
1248         }
1249         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1250         gene_tree.setAllNodesToNotCollapse();
1251         gene_tree.recalculateNumberOfExternalDescendants( false );
1252         GSDIR gsdir = null;
1253         final Phylogeny species_tree = _species_tree.copy();
1254         try {
1255             gsdir = new GSDIR( gene_tree, species_tree, true, true );
1256         }
1257         catch ( final SDIException e ) {
1258             JOptionPane.showMessageDialog( this,
1259                                            e.getLocalizedMessage(),
1260                                            "Error during GSDIR",
1261                                            JOptionPane.ERROR_MESSAGE );
1262             return;
1263         }
1264         catch ( final Exception e ) {
1265             AptxUtil.unexpectedException( e );
1266             return;
1267         }
1268         final List<Phylogeny> assigned_trees = gsdir.getMinDuplicationsSumGeneTrees();
1269         final List<Integer> shortests = GSDIR.getIndexesOfShortestTree( assigned_trees );
1270         final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) );
1271         result_gene_tree.setRerootable( false );
1272         result_gene_tree.clearHashIdToNodeMap();
1273         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1274         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1275         getControlPanel().setShowEvents( true );
1276         showWhole();
1277         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1278         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1279         showWhole();
1280         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1281         showWhole();
1282         _mainpanel.getCurrentTreePanel().setEdited( true );
1283         JOptionPane.showMessageDialog( this,
1284                                        "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
1285                                                + gsdir.getSpeciationsSum() + "\n"
1286                                                + "Number of root positions minimizing duplications sum: "
1287                                                + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n"
1288                                                + "Number of shortest trees: " + shortests.size(),
1289                                        "GSDIR successfully completed",
1290                                        JOptionPane.INFORMATION_MESSAGE );
1291     }
1292
1293     void executeLineageInference() {
1294         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1295             return;
1296         }
1297         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1298             JOptionPane.showMessageDialog( this,
1299                                            "Phylogeny is not rooted.",
1300                                            "Cannot infer ancestral taxonomies",
1301                                            JOptionPane.ERROR_MESSAGE );
1302             return;
1303         }
1304         final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1305                                                                                   _mainpanel.getCurrentTreePanel(),
1306                                                                                   _mainpanel.getCurrentPhylogeny()
1307                                                                                           .copy() );
1308         new Thread( inferrer ).start();
1309     }
1310
1311     void executeSDIR( final boolean minimize_cost ) {
1312         if ( !isOKforSDI( true, true ) ) {
1313             return;
1314         }
1315         Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1316         final SDIR sdiunrooted = new SDIR();
1317         gene_tree.setAllNodesToNotCollapse();
1318         gene_tree.recalculateNumberOfExternalDescendants( false );
1319         try {
1320             gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1321                                            !minimize_cost, // minimize sum of dups
1322                                            true, // minimize height
1323                                            true, // return tree(s)
1324                                            1 )[ 0 ]; // # of trees to return
1325         }
1326         catch ( final Exception e ) {
1327             JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1328             return;
1329         }
1330         final int duplications = sdiunrooted.getMinimalDuplications();
1331         gene_tree.setRerootable( false );
1332         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1333         getControlPanel().setShowEvents( true );
1334         showWhole();
1335         _mainpanel.getCurrentTreePanel().setEdited( true );
1336         JOptionPane.showMessageDialog( this,
1337                                        "Number of duplications: " + duplications,
1338                                        "SDIR successfully completed",
1339                                        JOptionPane.INFORMATION_MESSAGE );
1340     }
1341
1342     void exit() {
1343         removeAllTextFrames();
1344         _mainpanel.terminate();
1345         _contentpane.removeAll();
1346         setVisible( false );
1347         dispose();
1348         System.exit( 0 );
1349     }
1350
1351     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1352         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1353             return false;
1354         }
1355         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1356             JOptionPane.showMessageDialog( this,
1357                                            "No species tree loaded",
1358                                            "Cannot execute SDI",
1359                                            JOptionPane.ERROR_MESSAGE );
1360             return false;
1361         }
1362         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1363             JOptionPane.showMessageDialog( this,
1364                                            "Species tree is not completely binary",
1365                                            "Cannot execute SDI",
1366                                            JOptionPane.ERROR_MESSAGE );
1367             return false;
1368         }
1369         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1370             JOptionPane.showMessageDialog( this,
1371                                            "Gene tree is not completely binary",
1372                                            "Cannot execute SDI",
1373                                            JOptionPane.ERROR_MESSAGE );
1374             return false;
1375         }
1376         else {
1377             return true;
1378         }
1379     }
1380
1381     @Override
1382     void readPhylogeniesFromURL() {
1383         URL url = null;
1384         Phylogeny[] phys = null;
1385         final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1386         final String url_string = JOptionPane.showInputDialog( this,
1387                                                                message,
1388                                                                "Use URL/webservice to obtain a phylogeny",
1389                                                                JOptionPane.QUESTION_MESSAGE );
1390         boolean nhx_or_nexus = false;
1391         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1392             try {
1393                 url = new URL( url_string );
1394                 PhylogenyParser parser = null;
1395                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1396                     parser = new TolParser();
1397                 }
1398                 else {
1399                     parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1400                             .isValidatePhyloXmlAgainstSchema() );
1401                 }
1402                 if ( parser instanceof NexusPhylogeniesParser ) {
1403                     nhx_or_nexus = true;
1404                 }
1405                 else if ( parser instanceof NHXParser ) {
1406                     nhx_or_nexus = true;
1407                 }
1408                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1409                     _mainpanel.getCurrentTreePanel().setWaitCursor();
1410                 }
1411                 else {
1412                     _mainpanel.setWaitCursor();
1413                 }
1414                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1415                 phys = factory.create( url.openStream(), parser );
1416             }
1417             catch ( final MalformedURLException e ) {
1418                 JOptionPane.showMessageDialog( this,
1419                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1420                                                "Malformed URL",
1421                                                JOptionPane.ERROR_MESSAGE );
1422             }
1423             catch ( final IOException e ) {
1424                 JOptionPane.showMessageDialog( this,
1425                                                "Could not read from " + url + "\n"
1426                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1427                                                "Failed to read URL",
1428                                                JOptionPane.ERROR_MESSAGE );
1429             }
1430             catch ( final Exception e ) {
1431                 JOptionPane.showMessageDialog( this,
1432                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1433                                                "Unexpected Exception",
1434                                                JOptionPane.ERROR_MESSAGE );
1435             }
1436             finally {
1437                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1438                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1439                 }
1440                 else {
1441                     _mainpanel.setArrowCursor();
1442                 }
1443             }
1444             if ( ( phys != null ) && ( phys.length > 0 ) ) {
1445                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1446                     for( final Phylogeny phy : phys ) {
1447                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1448                     }
1449                 }
1450                 AptxUtil.addPhylogeniesToTabs( phys,
1451                                                new File( url.getFile() ).getName(),
1452                                                new File( url.getFile() ).toString(),
1453                                                getConfiguration(),
1454                                                getMainPanel() );
1455                 _mainpanel.getControlPanel().showWhole();
1456             }
1457         }
1458         activateSaveAllIfNeeded();
1459         System.gc();
1460     }
1461
1462     void setMsa( final Msa msa ) {
1463         _msa = msa;
1464     }
1465
1466     void setMsaFile( final File msa_file ) {
1467         _msa_file = msa_file;
1468     }
1469
1470     void setSeqs( final List<Sequence> seqs ) {
1471         _seqs = seqs;
1472     }
1473
1474     void setSeqsFile( final File seqs_file ) {
1475         _seqs_file = seqs_file;
1476     }
1477
1478     void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1479         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1480                                                                    _mainpanel.getCurrentTreePanel().getHeight(),
1481                                                                    true );
1482         String file_written_to = "";
1483         boolean error = false;
1484         try {
1485             file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1486                                                                      _mainpanel.getCurrentTreePanel().getWidth(),
1487                                                                      _mainpanel.getCurrentTreePanel().getHeight(),
1488                                                                      _mainpanel.getCurrentTreePanel(),
1489                                                                      _mainpanel.getControlPanel(),
1490                                                                      type,
1491                                                                      getOptions() );
1492         }
1493         catch ( final IOException e ) {
1494             error = true;
1495             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1496         }
1497         if ( !error ) {
1498             if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1499                 JOptionPane.showMessageDialog( this,
1500                                                "Wrote image to: " + file_written_to,
1501                                                "Graphics Export",
1502                                                JOptionPane.INFORMATION_MESSAGE );
1503             }
1504             else {
1505                 JOptionPane.showMessageDialog( this,
1506                                                "There was an unknown problem when attempting to write to an image file: \""
1507                                                        + file_name + "\"",
1508                                                "Error",
1509                                                JOptionPane.ERROR_MESSAGE );
1510             }
1511         }
1512         _contentpane.repaint();
1513     }
1514
1515     private void addExpressionValuesFromFile() {
1516         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1517             JOptionPane.showMessageDialog( this,
1518                                            "Need to load evolutionary tree first",
1519                                            "Can Not Read Expression Values",
1520                                            JOptionPane.WARNING_MESSAGE );
1521             return;
1522         }
1523         final File my_dir = getCurrentDir();
1524         if ( my_dir != null ) {
1525             _values_filechooser.setCurrentDirectory( my_dir );
1526         }
1527         final int result = _values_filechooser.showOpenDialog( _contentpane );
1528         final File file = _values_filechooser.getSelectedFile();
1529         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1530             BasicTable<String> t = null;
1531             try {
1532                 t = BasicTableParser.parse( file, "\t" );
1533                 if ( t.getNumberOfColumns() < 2 ) {
1534                     t = BasicTableParser.parse( file, "," );
1535                 }
1536                 if ( t.getNumberOfColumns() < 2 ) {
1537                     t = BasicTableParser.parse( file, " " );
1538                 }
1539             }
1540             catch ( final IOException e ) {
1541                 JOptionPane.showMessageDialog( this,
1542                                                e.getMessage(),
1543                                                "Could Not Read Expression Value Table",
1544                                                JOptionPane.ERROR_MESSAGE );
1545                 return;
1546             }
1547             if ( t.getNumberOfColumns() < 2 ) {
1548                 JOptionPane.showMessageDialog( this,
1549                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
1550                                                "Problem with Expression Value Table",
1551                                                JOptionPane.ERROR_MESSAGE );
1552                 return;
1553             }
1554             if ( t.getNumberOfRows() < 1 ) {
1555                 JOptionPane.showMessageDialog( this,
1556                                                "Table contains zero rows",
1557                                                "Problem with Expression Value Table",
1558                                                JOptionPane.ERROR_MESSAGE );
1559                 return;
1560             }
1561             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1562             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1563                 JOptionPane.showMessageDialog( this,
1564                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1565                                                        + phy.getNumberOfExternalNodes() + " external nodes",
1566                                                "Warning",
1567                                                JOptionPane.WARNING_MESSAGE );
1568             }
1569             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1570             int not_found = 0;
1571             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1572                 final PhylogenyNode node = iter.next();
1573                 final String node_name = node.getName();
1574                 if ( !ForesterUtil.isEmpty( node_name ) ) {
1575                     int row = -1;
1576                     try {
1577                         row = t.findRow( node_name );
1578                     }
1579                     catch ( final IllegalArgumentException e ) {
1580                         JOptionPane
1581                                 .showMessageDialog( this,
1582                                                     e.getMessage(),
1583                                                     "Error Mapping Node Identifiers to Expression Value Identifiers",
1584                                                     JOptionPane.ERROR_MESSAGE );
1585                         return;
1586                     }
1587                     if ( row < 0 ) {
1588                         if ( node.isExternal() ) {
1589                             not_found++;
1590                         }
1591                         continue;
1592                     }
1593                     final List<Double> l = new ArrayList<Double>();
1594                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1595                         double d = -100;
1596                         try {
1597                             d = Double.parseDouble( t.getValueAsString( col, row ) );
1598                         }
1599                         catch ( final NumberFormatException e ) {
1600                             JOptionPane.showMessageDialog( this,
1601                                                            "Could not parse \"" + t.getValueAsString( col, row )
1602                                                                    + "\" into a decimal value",
1603                                                            "Issue with Expression Value Table",
1604                                                            JOptionPane.ERROR_MESSAGE );
1605                             return;
1606                         }
1607                         stats.addValue( d );
1608                         l.add( d );
1609                     }
1610                     if ( !l.isEmpty() ) {
1611                         if ( node.getNodeData().getProperties() != null ) {
1612                             node.getNodeData().getProperties()
1613                                     .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1614                         }
1615                         node.getNodeData().setVector( l );
1616                     }
1617                 }
1618             }
1619             if ( not_found > 0 ) {
1620                 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1621                         + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1622             }
1623             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1624         }
1625     }
1626
1627     private void choosePdfWidth() {
1628         final String s = ( String ) JOptionPane.showInputDialog( this,
1629                                                                  "Please enter the default line width for PDF export.\n"
1630                                                                          + "[current value: "
1631                                                                          + getOptions().getPrintLineWidth() + "]\n",
1632                                                                  "Line Width for PDF Export",
1633                                                                  JOptionPane.QUESTION_MESSAGE,
1634                                                                  null,
1635                                                                  null,
1636                                                                  getOptions().getPrintLineWidth() );
1637         if ( !ForesterUtil.isEmpty( s ) ) {
1638             boolean success = true;
1639             float f = 0.0f;
1640             final String m_str = s.trim();
1641             if ( !ForesterUtil.isEmpty( m_str ) ) {
1642                 try {
1643                     f = Float.parseFloat( m_str );
1644                 }
1645                 catch ( final Exception ex ) {
1646                     success = false;
1647                 }
1648             }
1649             else {
1650                 success = false;
1651             }
1652             if ( success && ( f > 0.0 ) ) {
1653                 getOptions().setPrintLineWidth( f );
1654             }
1655         }
1656     }
1657
1658     private void choosePrintSize() {
1659         final String s = ( String ) JOptionPane.showInputDialog( this,
1660                                                                  "Please enter values for width and height,\nseparated by a comma.\n"
1661                                                                          + "[current values: "
1662                                                                          + getOptions().getPrintSizeX() + ", "
1663                                                                          + getOptions().getPrintSizeY() + "]\n"
1664                                                                          + "[A4: " + Constants.A4_SIZE_X + ", "
1665                                                                          + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1666                                                                          + Constants.US_LETTER_SIZE_X + ", "
1667                                                                          + Constants.US_LETTER_SIZE_Y + "]",
1668                                                                  "Default Size for Graphics Export",
1669                                                                  JOptionPane.QUESTION_MESSAGE,
1670                                                                  null,
1671                                                                  null,
1672                                                                  getOptions().getPrintSizeX() + ", "
1673                                                                          + getOptions().getPrintSizeY() );
1674         if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1675             boolean success = true;
1676             int x = 0;
1677             int y = 0;
1678             final String[] str_ary = s.split( "," );
1679             if ( str_ary.length == 2 ) {
1680                 final String x_str = str_ary[ 0 ].trim();
1681                 final String y_str = str_ary[ 1 ].trim();
1682                 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1683                     try {
1684                         x = Integer.parseInt( x_str );
1685                         y = Integer.parseInt( y_str );
1686                     }
1687                     catch ( final Exception ex ) {
1688                         success = false;
1689                     }
1690                 }
1691                 else {
1692                     success = false;
1693                 }
1694             }
1695             else {
1696                 success = false;
1697             }
1698             if ( success && ( x > 1 ) && ( y > 1 ) ) {
1699                 getOptions().setPrintSizeX( x );
1700                 getOptions().setPrintSizeY( y );
1701             }
1702         }
1703     }
1704
1705     private void closeCurrentPane() {
1706         if ( getMainPanel().getCurrentTreePanel() != null ) {
1707             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1708                 final int r = JOptionPane.showConfirmDialog( this,
1709                                                              "Close tab despite potentially unsaved changes?",
1710                                                              "Close Tab?",
1711                                                              JOptionPane.YES_NO_OPTION );
1712                 if ( r != JOptionPane.YES_OPTION ) {
1713                     return;
1714                 }
1715             }
1716             getMainPanel().closeCurrentPane();
1717             activateSaveAllIfNeeded();
1718         }
1719     }
1720
1721     private void collapse( final Phylogeny phy, final double m ) {
1722         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1723         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1724         double min_support = Double.MAX_VALUE;
1725         boolean conf_present = false;
1726         while ( it.hasNext() ) {
1727             final PhylogenyNode n = it.next();
1728             if ( !n.isExternal() && !n.isRoot() ) {
1729                 final List<Confidence> c = n.getBranchData().getConfidences();
1730                 if ( ( c != null ) && ( c.size() > 0 ) ) {
1731                     conf_present = true;
1732                     double max = 0;
1733                     for( final Confidence confidence : c ) {
1734                         if ( confidence.getValue() > max ) {
1735                             max = confidence.getValue();
1736                         }
1737                     }
1738                     if ( max < getMinNotCollapseConfidenceValue() ) {
1739                         to_be_removed.add( n );
1740                     }
1741                     if ( max < min_support ) {
1742                         min_support = max;
1743                     }
1744                 }
1745             }
1746         }
1747         if ( conf_present ) {
1748             for( final PhylogenyNode node : to_be_removed ) {
1749                 PhylogenyMethods.removeNode( node, phy );
1750             }
1751             if ( to_be_removed.size() > 0 ) {
1752                 phy.externalNodesHaveChanged();
1753                 phy.clearHashIdToNodeMap();
1754                 phy.recalculateNumberOfExternalDescendants( true );
1755                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1756                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1757                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1758                 getCurrentTreePanel().setNodeInPreorderToNull();
1759                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1760                 getCurrentTreePanel().resetPreferredSize();
1761                 getCurrentTreePanel().setEdited( true );
1762                 getCurrentTreePanel().repaint();
1763                 repaint();
1764             }
1765             if ( to_be_removed.size() > 0 ) {
1766                 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1767                         + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1768                         + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1769             }
1770             else {
1771                 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1772                         + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1773             }
1774         }
1775         else {
1776             JOptionPane.showMessageDialog( this,
1777                                            "No branch collapsed because no confidence values present",
1778                                            "No confidence values present",
1779                                            JOptionPane.INFORMATION_MESSAGE );
1780         }
1781     }
1782
1783     private void collapseBelowThreshold() {
1784         if ( getCurrentTreePanel() != null ) {
1785             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1786             if ( ( phy != null ) && !phy.isEmpty() ) {
1787                 final String s = ( String ) JOptionPane.showInputDialog( this,
1788                                                                          "Please enter the minimum confidence value\n",
1789                                                                          "Minimal Confidence Value",
1790                                                                          JOptionPane.QUESTION_MESSAGE,
1791                                                                          null,
1792                                                                          null,
1793                                                                          getMinNotCollapseConfidenceValue() );
1794                 if ( !ForesterUtil.isEmpty( s ) ) {
1795                     boolean success = true;
1796                     double m = 0.0;
1797                     final String m_str = s.trim();
1798                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1799                         try {
1800                             m = Double.parseDouble( m_str );
1801                         }
1802                         catch ( final Exception ex ) {
1803                             success = false;
1804                         }
1805                     }
1806                     else {
1807                         success = false;
1808                     }
1809                     if ( success && ( m >= 0.0 ) ) {
1810                         setMinNotCollapseConfidenceValue( m );
1811                         collapse( phy, m );
1812                     }
1813                 }
1814             }
1815         }
1816     }
1817
1818     private PhyloXmlParser createPhyloXmlParser() {
1819         PhyloXmlParser xml_parser = null;
1820         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1821             try {
1822                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1823             }
1824             catch ( final Exception e ) {
1825                 JOptionPane.showMessageDialog( this,
1826                                                e.getLocalizedMessage(),
1827                                                "failed to create validating XML parser",
1828                                                JOptionPane.WARNING_MESSAGE );
1829             }
1830         }
1831         if ( xml_parser == null ) {
1832             xml_parser = new PhyloXmlParser();
1833         }
1834         return xml_parser;
1835     }
1836
1837     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1838         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1839                                                                       getPhylogeneticInferenceOptions(),
1840                                                                       from_unaligned_seqs );
1841         dialog.activate();
1842         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1843             if ( !from_unaligned_seqs ) {
1844                 if ( getMsa() != null ) {
1845                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1846                                                                                     getPhylogeneticInferenceOptions()
1847                                                                                             .copy(), this );
1848                     new Thread( inferrer ).start();
1849                 }
1850                 else {
1851                     JOptionPane.showMessageDialog( this,
1852                                                    "No multiple sequence alignment selected",
1853                                                    "Phylogenetic Inference Not Launched",
1854                                                    JOptionPane.WARNING_MESSAGE );
1855                 }
1856             }
1857             else {
1858                 if ( getSeqs() != null ) {
1859                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1860                                                                                     getPhylogeneticInferenceOptions()
1861                                                                                             .copy(), this );
1862                     new Thread( inferrer ).start();
1863                 }
1864                 else {
1865                     JOptionPane.showMessageDialog( this,
1866                                                    "No input sequences selected",
1867                                                    "Phylogenetic Inference Not Launched",
1868                                                    JOptionPane.WARNING_MESSAGE );
1869                 }
1870             }
1871         }
1872     }
1873
1874     private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1875         final StringBuilder sb = new StringBuilder();
1876         final StringBuilder sb_failed = new StringBuilder();
1877         int counter = 0;
1878         int counter_failed = 0;
1879         if ( getCurrentTreePanel() != null ) {
1880             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1881             if ( ( phy != null ) && !phy.isEmpty() ) {
1882                 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1883                 while ( it.hasNext() ) {
1884                     final PhylogenyNode n = it.next();
1885                     final String name = n.getName().trim();
1886                     if ( !ForesterUtil.isEmpty( name ) ) {
1887                         final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES );
1888                         if ( !ForesterUtil.isEmpty( nt ) ) {
1889                             if ( counter < 15 ) {
1890                                 sb.append( name + ": " + nt + "\n" );
1891                             }
1892                             else if ( counter == 15 ) {
1893                                 sb.append( "...\n" );
1894                             }
1895                             counter++;
1896                         }
1897                         else {
1898                             if ( counter_failed < 15 ) {
1899                                 sb_failed.append( name + "\n" );
1900                             }
1901                             else if (  counter_failed == 15 ) {
1902                                 sb_failed.append( "...\n" );
1903                             }
1904                             counter_failed++;
1905                         }
1906                     }
1907                 }
1908                 if ( counter > 0 ) {
1909                     String failed = "";
1910                     if ( counter_failed > 0 ) {
1911                         failed = "\nDid not extract taxonomic data for "  + counter_failed + " (named) external nodes:\n" + sb_failed;
1912
1913                     }
1914                     JOptionPane.showMessageDialog( this,
1915                                                    "Successfully extracted taxonomic data from " + counter
1916                                                            + " external nodes:\n" + sb.toString() + failed,
1917                                                    "Taxonomic Data Extraction Successfully Completed",
1918                                                    JOptionPane.INFORMATION_MESSAGE );
1919                 }
1920                 else {
1921                     JOptionPane
1922                             .showMessageDialog( this,
1923                                                 "Could not extract any taxonomic data, maybe node names are empty\nor not in the form \"XYZ_CAEEL\", \"XYZ_CAEEL/12-394\", or \"XYZ_1234567\"?",
1924                                                 "No Taxonomic Data Extracted",
1925                                                 JOptionPane.WARNING_MESSAGE );
1926                 }
1927             }
1928         }
1929     }
1930
1931     private ControlPanel getControlPanel() {
1932         return getMainPanel().getControlPanel();
1933     }
1934
1935     private File getCurrentDir() {
1936         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1937             if ( ForesterUtil.isWindowns() ) {
1938                 try {
1939                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1940                 }
1941                 catch ( final Exception e ) {
1942                     _current_dir = null;
1943                 }
1944             }
1945         }
1946         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1947             if ( System.getProperty( "user.home" ) != null ) {
1948                 _current_dir = new File( System.getProperty( "user.home" ) );
1949             }
1950             else if ( System.getProperty( "user.dir" ) != null ) {
1951                 _current_dir = new File( System.getProperty( "user.dir" ) );
1952             }
1953         }
1954         return _current_dir;
1955     }
1956
1957     private double getMinNotCollapseConfidenceValue() {
1958         return _min_not_collapse;
1959     }
1960
1961     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1962         if ( _phylogenetic_inference_options == null ) {
1963             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1964         }
1965         return _phylogenetic_inference_options;
1966     }
1967
1968     private boolean isUnsavedDataPresent() {
1969         final List<TreePanel> tps = getMainPanel().getTreePanels();
1970         for( final TreePanel tp : tps ) {
1971             if ( tp.isEdited() ) {
1972                 return true;
1973             }
1974         }
1975         return false;
1976     }
1977
1978     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1979         if ( getCurrentTreePanel() != null ) {
1980             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1981             if ( ( phy != null ) && !phy.isEmpty() ) {
1982                 PhylogenyMethods
1983                         .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1984             }
1985         }
1986     }
1987
1988     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1989         if ( getCurrentTreePanel() != null ) {
1990             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1991             if ( ( phy != null ) && !phy.isEmpty() ) {
1992                 PhylogenyMethods.transferNodeNameToField( phy,
1993                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1994                                                           false );
1995             }
1996         }
1997     }
1998
1999     private void newTree() {
2000         final Phylogeny[] phys = new Phylogeny[ 1 ];
2001         final Phylogeny phy = new Phylogeny();
2002         final PhylogenyNode node = new PhylogenyNode();
2003         phy.setRoot( node );
2004         phy.setRooted( true );
2005         phys[ 0 ] = phy;
2006         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
2007         _mainpanel.getControlPanel().showWhole();
2008         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2009         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2010         if ( getMainPanel().getMainFrame() == null ) {
2011             // Must be "E" applet version.
2012             ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
2013                     .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2014         }
2015         else {
2016             getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2017         }
2018         activateSaveAllIfNeeded();
2019         System.gc();
2020     }
2021
2022     private void obtainDetailedTaxonomicInformation() {
2023         if ( getCurrentTreePanel() != null ) {
2024             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2025             if ( ( phy != null ) && !phy.isEmpty() ) {
2026                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
2027                                                                        _mainpanel.getCurrentTreePanel(),
2028                                                                        phy.copy(),
2029                                                                        false,
2030                                                                        true );
2031                 new Thread( t ).start();
2032             }
2033         }
2034     }
2035
2036     private void obtainDetailedTaxonomicInformationDelete() {
2037         if ( getCurrentTreePanel() != null ) {
2038             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2039             if ( ( phy != null ) && !phy.isEmpty() ) {
2040                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
2041                                                                        _mainpanel.getCurrentTreePanel(),
2042                                                                        phy.copy(),
2043                                                                        true,
2044                                                                        true );
2045                 new Thread( t ).start();
2046             }
2047         }
2048     }
2049
2050     private void obtainSequenceInformation() {
2051         if ( getCurrentTreePanel() != null ) {
2052             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2053             if ( ( phy != null ) && !phy.isEmpty() ) {
2054                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
2055                                                                          _mainpanel.getCurrentTreePanel(),
2056                                                                          phy.copy() );
2057                 new Thread( u ).start();
2058             }
2059         }
2060     }
2061
2062     private void print() {
2063         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2064                 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2065             return;
2066         }
2067         if ( !getOptions().isPrintUsingActualSize() ) {
2068             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
2069                                                             getOptions().getPrintSizeY() - 140,
2070                                                             true );
2071             getCurrentTreePanel().resetPreferredSize();
2072             getCurrentTreePanel().repaint();
2073         }
2074         final String job_name = Constants.PRG_NAME;
2075         boolean error = false;
2076         String printer_name = null;
2077         try {
2078             printer_name = Printer.print( getCurrentTreePanel(), job_name );
2079         }
2080         catch ( final Exception e ) {
2081             error = true;
2082             JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2083         }
2084         if ( !error && ( printer_name != null ) ) {
2085             String msg = "Printing data sent to printer";
2086             if ( printer_name.length() > 1 ) {
2087                 msg += " [" + printer_name + "]";
2088             }
2089             JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2090         }
2091         if ( !getOptions().isPrintUsingActualSize() ) {
2092             getControlPanel().showWhole();
2093         }
2094     }
2095
2096     private void printPhylogenyToPdf( final String file_name ) {
2097         if ( !getOptions().isPrintUsingActualSize() ) {
2098             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
2099                                                             getOptions().getPrintSizeY(),
2100                                                             true );
2101             getCurrentTreePanel().resetPreferredSize();
2102             getCurrentTreePanel().repaint();
2103         }
2104         String pdf_written_to = "";
2105         boolean error = false;
2106         try {
2107             if ( getOptions().isPrintUsingActualSize() ) {
2108                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2109                                                                   getCurrentTreePanel(),
2110                                                                   getCurrentTreePanel().getWidth(),
2111                                                                   getCurrentTreePanel().getHeight() );
2112             }
2113             else {
2114                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2115                         .getPrintSizeX(), getOptions().getPrintSizeY() );
2116             }
2117         }
2118         catch ( final IOException e ) {
2119             error = true;
2120             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2121         }
2122         if ( !error ) {
2123             if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2124                 JOptionPane.showMessageDialog( this,
2125                                                "Wrote PDF to: " + pdf_written_to,
2126                                                "Information",
2127                                                JOptionPane.INFORMATION_MESSAGE );
2128             }
2129             else {
2130                 JOptionPane.showMessageDialog( this,
2131                                                "There was an unknown problem when attempting to write to PDF file: \""
2132                                                        + file_name + "\"",
2133                                                "Error",
2134                                                JOptionPane.ERROR_MESSAGE );
2135             }
2136         }
2137         if ( !getOptions().isPrintUsingActualSize() ) {
2138             getControlPanel().showWhole();
2139         }
2140     }
2141
2142     private void readPhylogeniesFromFile() {
2143         boolean exception = false;
2144         Phylogeny[] phys = null;
2145         // Set an initial directory if none set yet
2146         final File my_dir = getCurrentDir();
2147         _open_filechooser.setMultiSelectionEnabled( true );
2148         // Open file-open dialog and set current directory
2149         if ( my_dir != null ) {
2150             _open_filechooser.setCurrentDirectory( my_dir );
2151         }
2152         final int result = _open_filechooser.showOpenDialog( _contentpane );
2153         // All done: get the file
2154         final File[] files = _open_filechooser.getSelectedFiles();
2155         setCurrentDir( _open_filechooser.getCurrentDirectory() );
2156         boolean nhx_or_nexus = false;
2157         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2158             for( final File file : files ) {
2159                 if ( ( file != null ) && !file.isDirectory() ) {
2160                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2161                         _mainpanel.getCurrentTreePanel().setWaitCursor();
2162                     }
2163                     else {
2164                         _mainpanel.setWaitCursor();
2165                     }
2166                     if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2167                             || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2168                         try {
2169                             final NHXParser nhx = new NHXParser();
2170                             setSpecialOptionsForNhxParser( nhx );
2171                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
2172                             nhx_or_nexus = true;
2173                         }
2174                         catch ( final Exception e ) {
2175                             exception = true;
2176                             exceptionOccuredDuringOpenFile( e );
2177                         }
2178                     }
2179                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2180                         warnIfNotPhyloXmlValidation( getConfiguration() );
2181                         try {
2182                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
2183                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2184                         }
2185                         catch ( final Exception e ) {
2186                             exception = true;
2187                             exceptionOccuredDuringOpenFile( e );
2188                         }
2189                     }
2190                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2191                         try {
2192                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2193                         }
2194                         catch ( final Exception e ) {
2195                             exception = true;
2196                             exceptionOccuredDuringOpenFile( e );
2197                         }
2198                     }
2199                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2200                         try {
2201                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2202                             setSpecialOptionsForNexParser( nex );
2203                             phys = PhylogenyMethods.readPhylogenies( nex, file );
2204                             nhx_or_nexus = true;
2205                         }
2206                         catch ( final Exception e ) {
2207                             exception = true;
2208                             exceptionOccuredDuringOpenFile( e );
2209                         }
2210                     }
2211                     // "*.*":
2212                     else {
2213                         try {
2214                             final PhylogenyParser parser = ParserUtils
2215                                     .createParserDependingOnFileType( file, getConfiguration()
2216                                             .isValidatePhyloXmlAgainstSchema() );
2217                             if ( parser instanceof NexusPhylogeniesParser ) {
2218                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2219                                 setSpecialOptionsForNexParser( nex );
2220                                 nhx_or_nexus = true;
2221                             }
2222                             else if ( parser instanceof NHXParser ) {
2223                                 final NHXParser nhx = ( NHXParser ) parser;
2224                                 setSpecialOptionsForNhxParser( nhx );
2225                                 nhx_or_nexus = true;
2226                             }
2227                             else if ( parser instanceof PhyloXmlParser ) {
2228                                 warnIfNotPhyloXmlValidation( getConfiguration() );
2229                             }
2230                             phys = PhylogenyMethods.readPhylogenies( parser, file );
2231                         }
2232                         catch ( final Exception e ) {
2233                             exception = true;
2234                             exceptionOccuredDuringOpenFile( e );
2235                         }
2236                     }
2237                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2238                         _mainpanel.getCurrentTreePanel().setArrowCursor();
2239                     }
2240                     else {
2241                         _mainpanel.setArrowCursor();
2242                     }
2243                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2244                         boolean one_desc = false;
2245                         if ( nhx_or_nexus ) {
2246                             for( final Phylogeny phy : phys ) {
2247                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2248                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2249                                 }
2250                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2251                                     one_desc = true;
2252                                     break;
2253                                 }
2254                             }
2255                         }
2256                         AptxUtil.addPhylogeniesToTabs( phys,
2257                                                        file.getName(),
2258                                                        file.getAbsolutePath(),
2259                                                        getConfiguration(),
2260                                                        getMainPanel() );
2261                         _mainpanel.getControlPanel().showWhole();
2262                         if ( nhx_or_nexus && one_desc ) {
2263                             JOptionPane
2264                                     .showMessageDialog( this,
2265                                                         "One or more trees contain (a) node(s) with one descendant, "
2266                                                                 + ForesterUtil.LINE_SEPARATOR
2267                                                                 + "possibly indicating illegal parentheses within node names.",
2268                                                         "Warning: Possible Error in New Hampshire Formatted Data",
2269                                                         JOptionPane.WARNING_MESSAGE );
2270                         }
2271                     }
2272                 }
2273             }
2274         }
2275         activateSaveAllIfNeeded();
2276         System.gc();
2277     }
2278
2279     private void readSpeciesTreeFromFile() {
2280         Phylogeny t = null;
2281         boolean exception = false;
2282         final File my_dir = getCurrentDir();
2283         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2284         if ( my_dir != null ) {
2285             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2286         }
2287         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2288         final File file = _open_filechooser_for_species_tree.getSelectedFile();
2289         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2290             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2291                 try {
2292                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2293                     t = trees[ 0 ];
2294                 }
2295                 catch ( final Exception e ) {
2296                     exception = true;
2297                     exceptionOccuredDuringOpenFile( e );
2298                 }
2299             }
2300             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2301                 try {
2302                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2303                     t = trees[ 0 ];
2304                 }
2305                 catch ( final Exception e ) {
2306                     exception = true;
2307                     exceptionOccuredDuringOpenFile( e );
2308                 }
2309             }
2310             // "*.*":
2311             else {
2312                 try {
2313                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2314                     t = trees[ 0 ];
2315                 }
2316                 catch ( final Exception e ) {
2317                     exception = true;
2318                     exceptionOccuredDuringOpenFile( e );
2319                 }
2320             }
2321             if ( !exception && ( t != null ) && !t.isRooted() ) {
2322                 exception = true;
2323                 t = null;
2324                 JOptionPane.showMessageDialog( this,
2325                                                "Species tree is not rooted",
2326                                                "Species tree not loaded",
2327                                                JOptionPane.ERROR_MESSAGE );
2328             }
2329             if ( !exception && ( t != null ) ) {
2330                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2331                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2332                     final PhylogenyNode node = it.next();
2333                     if ( !node.getNodeData().isHasTaxonomy() ) {
2334                         exception = true;
2335                         t = null;
2336                         JOptionPane
2337                                 .showMessageDialog( this,
2338                                                     "Species tree contains external node(s) without taxonomy information",
2339                                                     "Species tree not loaded",
2340                                                     JOptionPane.ERROR_MESSAGE );
2341                         break;
2342                     }
2343                     else {
2344                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2345                             exception = true;
2346                             t = null;
2347                             JOptionPane.showMessageDialog( this,
2348                                                            "Taxonomy ["
2349                                                                    + node.getNodeData().getTaxonomy().asSimpleText()
2350                                                                    + "] is not unique in species tree",
2351                                                            "Species tree not loaded",
2352                                                            JOptionPane.ERROR_MESSAGE );
2353                             break;
2354                         }
2355                         else {
2356                             tax_set.add( node.getNodeData().getTaxonomy() );
2357                         }
2358                     }
2359                 }
2360             }
2361             if ( !exception && ( t != null ) ) {
2362                 _species_tree = t;
2363                 JOptionPane.showMessageDialog( this,
2364                                                "Species tree successfully loaded",
2365                                                "Species tree loaded",
2366                                                JOptionPane.INFORMATION_MESSAGE );
2367             }
2368             _contentpane.repaint();
2369             System.gc();
2370         }
2371     }
2372
2373     private void setCurrentDir( final File current_dir ) {
2374         _current_dir = current_dir;
2375     }
2376
2377     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2378         _min_not_collapse = min_not_collapse;
2379     }
2380
2381     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2382         _phylogenetic_inference_options = phylogenetic_inference_options;
2383     }
2384
2385     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2386         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2387         nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2388     }
2389
2390     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2391         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2392         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2393     }
2394
2395     private void writeAllToFile() {
2396         if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2397             return;
2398         }
2399         final File my_dir = getCurrentDir();
2400         if ( my_dir != null ) {
2401             _save_filechooser.setCurrentDirectory( my_dir );
2402         }
2403         _save_filechooser.setSelectedFile( new File( "" ) );
2404         final int result = _save_filechooser.showSaveDialog( _contentpane );
2405         final File file = _save_filechooser.getSelectedFile();
2406         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2407         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2408             if ( file.exists() ) {
2409                 final int i = JOptionPane.showConfirmDialog( this,
2410                                                              file + " already exists. Overwrite?",
2411                                                              "Warning",
2412                                                              JOptionPane.OK_CANCEL_OPTION,
2413                                                              JOptionPane.WARNING_MESSAGE );
2414                 if ( i != JOptionPane.OK_OPTION ) {
2415                     return;
2416                 }
2417                 else {
2418                     try {
2419                         file.delete();
2420                     }
2421                     catch ( final Exception e ) {
2422                         JOptionPane.showMessageDialog( this,
2423                                                        "Failed to delete: " + file,
2424                                                        "Error",
2425                                                        JOptionPane.WARNING_MESSAGE );
2426                     }
2427                 }
2428             }
2429             final int count = getMainPanel().getTabbedPane().getTabCount();
2430             final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2431             for( int i = 0; i < count; ++i ) {
2432                 trees.add( getMainPanel().getPhylogeny( i ) );
2433                 getMainPanel().getTreePanels().get( i ).setEdited( false );
2434             }
2435             final PhylogenyWriter writer = new PhylogenyWriter();
2436             try {
2437                 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2438             }
2439             catch ( final IOException e ) {
2440                 JOptionPane.showMessageDialog( this,
2441                                                "Failed to write to: " + file,
2442                                                "Error",
2443                                                JOptionPane.WARNING_MESSAGE );
2444             }
2445         }
2446     }
2447
2448     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2449         try {
2450             final PhylogenyWriter writer = new PhylogenyWriter();
2451             writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2452         }
2453         catch ( final Exception e ) {
2454             exception = true;
2455             exceptionOccuredDuringSaveAs( e );
2456         }
2457         return exception;
2458     }
2459
2460     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2461         try {
2462             final PhylogenyWriter writer = new PhylogenyWriter();
2463             writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2464         }
2465         catch ( final Exception e ) {
2466             exception = true;
2467             exceptionOccuredDuringSaveAs( e );
2468         }
2469         return exception;
2470     }
2471
2472     private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
2473         try {
2474             final PhylogenyWriter writer = new PhylogenyWriter();
2475             writer.toNewHampshireX( t, file );
2476         }
2477         catch ( final Exception e ) {
2478             exception = true;
2479             exceptionOccuredDuringSaveAs( e );
2480         }
2481         return exception;
2482     }
2483
2484     private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2485         try {
2486             final PhylogenyWriter writer = new PhylogenyWriter();
2487             writer.toPhyloXML( file, t, 0 );
2488         }
2489         catch ( final Exception e ) {
2490             exception = true;
2491             exceptionOccuredDuringSaveAs( e );
2492         }
2493         return exception;
2494     }
2495
2496     private void writeToFile( final Phylogeny t ) {
2497         if ( t == null ) {
2498             return;
2499         }
2500         String initial_filename = null;
2501         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2502             try {
2503                 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2504             }
2505             catch ( final IOException e ) {
2506                 initial_filename = null;
2507             }
2508         }
2509         if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2510             _save_filechooser.setSelectedFile( new File( initial_filename ) );
2511         }
2512         else {
2513             _save_filechooser.setSelectedFile( new File( "" ) );
2514         }
2515         final File my_dir = getCurrentDir();
2516         if ( my_dir != null ) {
2517             _save_filechooser.setCurrentDirectory( my_dir );
2518         }
2519         final int result = _save_filechooser.showSaveDialog( _contentpane );
2520         final File file = _save_filechooser.getSelectedFile();
2521         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2522         boolean exception = false;
2523         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2524             if ( file.exists() ) {
2525                 final int i = JOptionPane.showConfirmDialog( this,
2526                                                              file + " already exists.\nOverwrite?",
2527                                                              "Overwrite?",
2528                                                              JOptionPane.OK_CANCEL_OPTION,
2529                                                              JOptionPane.QUESTION_MESSAGE );
2530                 if ( i != JOptionPane.OK_OPTION ) {
2531                     return;
2532                 }
2533                 else {
2534                     final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2535                     try {
2536                         ForesterUtil.copyFile( file, to );
2537                     }
2538                     catch ( final Exception e ) {
2539                         JOptionPane.showMessageDialog( this,
2540                                                        "Failed to create backup copy " + to,
2541                                                        "Failed to Create Backup Copy",
2542                                                        JOptionPane.WARNING_MESSAGE );
2543                     }
2544                     try {
2545                         file.delete();
2546                     }
2547                     catch ( final Exception e ) {
2548                         JOptionPane.showMessageDialog( this,
2549                                                        "Failed to delete: " + file,
2550                                                        "Failed to Delete",
2551                                                        JOptionPane.WARNING_MESSAGE );
2552                     }
2553                 }
2554             }
2555             if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2556                 exception = writeAsNewHampshire( t, exception, file );
2557             }
2558             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
2559                 exception = writeAsNHX( t, exception, file );
2560             }
2561             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2562                 exception = writeAsPhyloXml( t, exception, file );
2563             }
2564             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2565                 exception = writeAsNexus( t, exception, file );
2566             }
2567             // "*.*":
2568             else {
2569                 final String file_name = file.getName().trim().toLowerCase();
2570                 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2571                         || file_name.endsWith( ".tree" ) ) {
2572                     exception = writeAsNewHampshire( t, exception, file );
2573                 }
2574                 else if ( file_name.endsWith( ".nhx" ) ) {
2575                     exception = writeAsNHX( t, exception, file );
2576                 }
2577                 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2578                     exception = writeAsNexus( t, exception, file );
2579                 }
2580                 // XML is default:
2581                 else {
2582                     exception = writeAsPhyloXml( t, exception, file );
2583                 }
2584             }
2585             if ( !exception ) {
2586                 getMainPanel().setTitleOfSelectedTab( file.getName() );
2587                 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2588                 getMainPanel().getCurrentTreePanel().setEdited( false );
2589             }
2590         }
2591     }
2592
2593     private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2594         if ( ( t == null ) || t.isEmpty() ) {
2595             return;
2596         }
2597         String initial_filename = "";
2598         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2599             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2600         }
2601         if ( initial_filename.indexOf( '.' ) > 0 ) {
2602             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2603         }
2604         initial_filename = initial_filename + "." + type;
2605         _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2606         final File my_dir = getCurrentDir();
2607         if ( my_dir != null ) {
2608             _writetographics_filechooser.setCurrentDirectory( my_dir );
2609         }
2610         final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2611         File file = _writetographics_filechooser.getSelectedFile();
2612         setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2613         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2614             if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2615                 file = new File( file.toString() + "." + type );
2616             }
2617             if ( file.exists() ) {
2618                 final int i = JOptionPane.showConfirmDialog( this,
2619                                                              file + " already exists. Overwrite?",
2620                                                              "Warning",
2621                                                              JOptionPane.OK_CANCEL_OPTION,
2622                                                              JOptionPane.WARNING_MESSAGE );
2623                 if ( i != JOptionPane.OK_OPTION ) {
2624                     return;
2625                 }
2626                 else {
2627                     try {
2628                         file.delete();
2629                     }
2630                     catch ( final Exception e ) {
2631                         JOptionPane.showMessageDialog( this,
2632                                                        "Failed to delete: " + file,
2633                                                        "Error",
2634                                                        JOptionPane.WARNING_MESSAGE );
2635                     }
2636                 }
2637             }
2638             writePhylogenyToGraphicsFile( file.toString(), type );
2639         }
2640     }
2641
2642     private void writeToPdf( final Phylogeny t ) {
2643         if ( ( t == null ) || t.isEmpty() ) {
2644             return;
2645         }
2646         String initial_filename = "";
2647         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2648             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2649         }
2650         if ( initial_filename.indexOf( '.' ) > 0 ) {
2651             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2652         }
2653         initial_filename = initial_filename + ".pdf";
2654         _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2655         final File my_dir = getCurrentDir();
2656         if ( my_dir != null ) {
2657             _writetopdf_filechooser.setCurrentDirectory( my_dir );
2658         }
2659         final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2660         File file = _writetopdf_filechooser.getSelectedFile();
2661         setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2662         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2663             if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2664                 file = new File( file.toString() + ".pdf" );
2665             }
2666             if ( file.exists() ) {
2667                 final int i = JOptionPane.showConfirmDialog( this,
2668                                                              file + " already exists. Overwrite?",
2669                                                              "WARNING",
2670                                                              JOptionPane.OK_CANCEL_OPTION,
2671                                                              JOptionPane.WARNING_MESSAGE );
2672                 if ( i != JOptionPane.OK_OPTION ) {
2673                     return;
2674                 }
2675             }
2676             printPhylogenyToPdf( file.toString() );
2677         }
2678     }
2679
2680     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2681         return new MainFrameApplication( phys, config );
2682     }
2683
2684     public static MainFrame createInstance( final Phylogeny[] phys,
2685                                             final Configuration config,
2686                                             final String title,
2687                                             final File current_dir ) {
2688         return new MainFrameApplication( phys, config, title, current_dir );
2689     }
2690
2691     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2692         return new MainFrameApplication( phys, config, title );
2693     }
2694
2695     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2696         return new MainFrameApplication( phys, config_file_name, title );
2697     }
2698
2699     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2700         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2701                 + o.getPrintSizeY() + ")" );
2702     }
2703
2704     static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2705         mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2706     }
2707
2708     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2709         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2710             JOptionPane
2711                     .showMessageDialog( null,
2712                                         ForesterUtil
2713                                                 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2714                                                            80 ),
2715                                         "Warning",
2716                                         JOptionPane.WARNING_MESSAGE );
2717         }
2718     }
2719 } // MainFrameApplication.
2720
2721 class DefaultFilter extends FileFilter {
2722
2723     @Override
2724     public boolean accept( final File f ) {
2725         final String file_name = f.getName().trim().toLowerCase();
2726         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2727                 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2728                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2729                 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2730                 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2731                 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2732                 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2733                 || file_name.endsWith( ".con" ) || f.isDirectory();
2734     }
2735
2736     @Override
2737     public String getDescription() {
2738         return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2739     }
2740 }
2741
2742 class GraphicsFileFilter extends FileFilter {
2743
2744     @Override
2745     public boolean accept( final File f ) {
2746         final String file_name = f.getName().trim().toLowerCase();
2747         return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2748                 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2749     }
2750
2751     @Override
2752     public String getDescription() {
2753         return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2754     }
2755 }
2756
2757 class MsaFileFilter extends FileFilter {
2758
2759     @Override
2760     public boolean accept( final File f ) {
2761         final String file_name = f.getName().trim().toLowerCase();
2762         return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2763                 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2764     }
2765
2766     @Override
2767     public String getDescription() {
2768         return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2769     }
2770 }
2771
2772 class NexusFilter extends FileFilter {
2773
2774     @Override
2775     public boolean accept( final File f ) {
2776         final String file_name = f.getName().trim().toLowerCase();
2777         return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2778                 || file_name.endsWith( ".tre" ) || f.isDirectory();
2779     }
2780
2781     @Override
2782     public String getDescription() {
2783         return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2784     }
2785 } // NexusFilter
2786
2787 class NHFilter extends FileFilter {
2788
2789     @Override
2790     public boolean accept( final File f ) {
2791         final String file_name = f.getName().trim().toLowerCase();
2792         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2793                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2794                 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2795                 || f.isDirectory();
2796     }
2797
2798     @Override
2799     public String getDescription() {
2800         return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2801     }
2802 } // NHFilter
2803
2804 class NHXFilter extends FileFilter {
2805
2806     @Override
2807     public boolean accept( final File f ) {
2808         final String file_name = f.getName().trim().toLowerCase();
2809         return file_name.endsWith( ".nhx" ) || f.isDirectory();
2810     }
2811
2812     @Override
2813     public String getDescription() {
2814         return "NHX files (*.nhx)";
2815     }
2816 }
2817
2818 class PdfFilter extends FileFilter {
2819
2820     @Override
2821     public boolean accept( final File f ) {
2822         return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2823     }
2824
2825     @Override
2826     public String getDescription() {
2827         return "PDF files (*.pdf)";
2828     }
2829 } // PdfFilter
2830
2831 class SequencesFileFilter extends FileFilter {
2832
2833     @Override
2834     public boolean accept( final File f ) {
2835         final String file_name = f.getName().trim().toLowerCase();
2836         return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2837                 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2838     }
2839
2840     @Override
2841     public String getDescription() {
2842         return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2843     }
2844 }
2845
2846 class TolFilter extends FileFilter {
2847
2848     @Override
2849     public boolean accept( final File f ) {
2850         final String file_name = f.getName().trim().toLowerCase();
2851         return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2852                 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2853     }
2854
2855     @Override
2856     public String getDescription() {
2857         return "Tree of Life files (*.tol, *.tolxml)";
2858     }
2859 } // TolFilter
2860
2861 class XMLFilter extends FileFilter {
2862
2863     @Override
2864     public boolean accept( final File f ) {
2865         final String file_name = f.getName().trim().toLowerCase();
2866         return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2867                 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2868     }
2869
2870     @Override
2871     public String getDescription() {
2872         return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
2873     }
2874 } // XMLFilter