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

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.archaeopteryx;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Font;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ComponentAdapter;
  33 import java.awt.event.ComponentEvent;
  34 import java.awt.event.WindowAdapter;
  35 import java.awt.event.WindowEvent;
  36 import java.io.File;
  37 import java.io.FileInputStream;
  38 import java.io.IOException;
  39 import java.io.InputStream;
  40 import java.net.MalformedURLException;
  41 import java.net.URL;
  42 import java.util.ArrayList;
  43 import java.util.HashSet;
  44 import java.util.List;
  45 import java.util.Set;
  46
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.JCheckBoxMenuItem;
  49 import javax.swing.JFileChooser;
  50 import javax.swing.JMenu;
  51 import javax.swing.JMenuBar;
  52 import javax.swing.JMenuItem;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JRadioButtonMenuItem;
  55 import javax.swing.UIManager;
  56 import javax.swing.UnsupportedLookAndFeelException;
  57 import javax.swing.WindowConstants;
  58 import javax.swing.event.ChangeEvent;
  59 import javax.swing.event.ChangeListener;
  60 import javax.swing.filechooser.FileFilter;
  61 import javax.swing.plaf.synth.SynthLookAndFeel;
  62
  63 import org.forester.analysis.TaxonomyDataManager;
  64 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  65 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  66 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  67 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  68 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
  69 import org.forester.archaeopteryx.tools.GoAnnotation;
  70 import org.forester.archaeopteryx.tools.InferenceManager;
  71 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
  72 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
  73 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
  74 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
  75 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  76 import org.forester.archaeopteryx.webservices.WebservicesManager;
  77 import org.forester.io.parsers.FastaParser;
  78 import org.forester.io.parsers.GeneralMsaParser;
  79 import org.forester.io.parsers.PhylogenyParser;
  80 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  81 import org.forester.io.parsers.nhx.NHXParser;
  82 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  83 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  84 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  85 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  86 import org.forester.io.parsers.tol.TolParser;
  87 import org.forester.io.parsers.util.ParserUtils;
  88 import org.forester.io.writers.PhylogenyWriter;
  89 import org.forester.io.writers.SequenceWriter;
  90 import org.forester.msa.Msa;
  91 import org.forester.msa.MsaFormatException;
  92 import org.forester.phylogeny.Phylogeny;
  93 import org.forester.phylogeny.PhylogenyMethods;
  94 import org.forester.phylogeny.PhylogenyNode;
  95 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  96 import org.forester.phylogeny.data.Confidence;
  97 import org.forester.phylogeny.data.Taxonomy;
  98 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  99 import org.forester.phylogeny.factories.PhylogenyFactory;
 100 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 101 import org.forester.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.nhfilter );
 306         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
 307         _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
 308         _writetopdf_filechooser = new JFileChooser();
 309         _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
 310         _writetographics_filechooser = new JFileChooser();
 311         _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
 312         // Msa:
 313         _msa_filechooser = new JFileChooser();
 314         _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
 315         _msa_filechooser.setCurrentDirectory( new File( "." ) );
 316         _msa_filechooser.setMultiSelectionEnabled( false );
 317         _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
 318         _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
 319         // Seqs:
 320         _seqs_filechooser = new JFileChooser();
 321         _seqs_filechooser.setName( "Read Sequences File" );
 322         _seqs_filechooser.setCurrentDirectory( new File( "." ) );
 323         _seqs_filechooser.setMultiSelectionEnabled( false );
 324         _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() );
 325         _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
 326         // Expression
 327         _values_filechooser = new JFileChooser();
 328         _values_filechooser.setCurrentDirectory( new File( "." ) );
 329         _values_filechooser.setMultiSelectionEnabled( false );
 330         // build the menu bar
 331         _jmenubar = new JMenuBar();
 332         if ( !_configuration.isUseNativeUI() ) {
 333             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 334         }
 335         buildFileMenu();
 336         if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
 337             buildPhylogeneticInferenceMenu();
 338         }
 339         buildAnalysisMenu();
 340         buildToolsMenu();
 341         buildViewMenu();
 342         buildFontSizeMenu();
 343         buildOptionsMenu();
 344         buildTypeMenu();
 345         buildHelpMenu();
 346         setJMenuBar( _jmenubar );
 347         _jmenubar.add( _help_jmenu );
 348         _contentpane = getContentPane();
 349         _contentpane.setLayout( new BorderLayout() );
 350         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 351         // App is this big
 352         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 353         //        addWindowFocusListener( new WindowAdapter() {
 354         //
 355         //            @Override
 356         //            public void windowGainedFocus( WindowEvent e ) {
 357         //                requestFocusInWindow();
 358         //            }
 359         //        } );
 360         // The window listener
 361         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 362         addWindowListener( new WindowAdapter() {
 363
 364             @Override
 365             public void windowClosing( final WindowEvent e ) {
 366                 if ( isUnsavedDataPresent() ) {
 367                     final int r = JOptionPane.showConfirmDialog( null,
 368                                                                  "Exit despite potentially unsaved changes?",
 369                                                                  "Exit?",
 370                                                                  JOptionPane.YES_NO_OPTION );
 371                     if ( r != JOptionPane.YES_OPTION ) {
 372                         return;
 373                     }
 374                 }
 375                 else {
 376                     final int r = JOptionPane.showConfirmDialog( null,
 377                                                                  "Exit Archaeopteryx?",
 378                                                                  "Exit?",
 379                                                                  JOptionPane.YES_NO_OPTION );
 380                     if ( r != JOptionPane.YES_OPTION ) {
 381                         return;
 382                     }
 383                 }
 384                 exit();
 385             }
 386         } );
 387         // The component listener
 388         addComponentListener( new ComponentAdapter() {
 389
 390             @Override
 391             public void componentResized( final ComponentEvent e ) {
 392                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 393                     _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
 394                                                                                        .getWidth(),
 395                                                                                _mainpanel.getCurrentTreePanel()
 396                                                                                        .getHeight(),
 397                                                                                false );
 398                 }
 399             }
 400         } );
 401         requestFocusInWindow();
 402         // addKeyListener( this );
 403         setVisible( true );
 404         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 405             AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
 406             validate();
 407             getMainPanel().getControlPanel().showWholeAll();
 408             getMainPanel().getControlPanel().showWhole();
 409         }
 410         activateSaveAllIfNeeded();
 411         // ...and its children
 412         _contentpane.repaint();
 413         System.gc();
 414     }
 415
 416     private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
 417         // Reads the config file (false, false => not url, not applet):
 418         this( phys, new Configuration( config_file, false, false, true ), title );
 419     }
 420
 421     @Override
 422     public void actionPerformed( final ActionEvent e ) {
 423         try {
 424             super.actionPerformed( e );
 425             final Object o = e.getSource();
 426             // Handle app-specific actions here:
 427             if ( o == _open_item ) {
 428                 readPhylogeniesFromFile();
 429             }
 430             else if ( o == _save_item ) {
 431                 writeToFile( _mainpanel.getCurrentPhylogeny() );
 432                 // If subtree currently displayed, save it, instead of complete
 433                 // tree.
 434             }
 435             else if ( o == _new_item ) {
 436                 newTree();
 437             }
 438             else if ( o == _save_all_item ) {
 439                 writeAllToFile();
 440             }
 441             else if ( o == _close_item ) {
 442                 closeCurrentPane();
 443             }
 444             else if ( o == _write_to_pdf_item ) {
 445                 writeToPdf( _mainpanel.getCurrentPhylogeny() );
 446             }
 447             else if ( o == _write_to_jpg_item ) {
 448                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
 449             }
 450             else if ( o == _write_to_png_item ) {
 451                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
 452             }
 453             else if ( o == _write_to_gif_item ) {
 454                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
 455             }
 456             else if ( o == _write_to_tif_item ) {
 457                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
 458             }
 459             else if ( o == _write_to_bmp_item ) {
 460                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
 461             }
 462             else if ( o == _print_item ) {
 463                 print();
 464             }
 465             else if ( o == _load_species_tree_item ) {
 466                 readSpeciesTreeFromFile();
 467             }
 468             else if ( o == _lineage_inference ) {
 469                 if ( isSubtreeDisplayed() ) {
 470                     JOptionPane.showMessageDialog( this,
 471                                                    "Subtree is shown.",
 472                                                    "Cannot infer ancestral taxonomies",
 473                                                    JOptionPane.ERROR_MESSAGE );
 474                     return;
 475                 }
 476                 executeLineageInference();
 477             }
 478             else if ( o == _function_analysis ) {
 479                 executeFunctionAnalysis();
 480             }
 481             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
 482                 if ( isSubtreeDisplayed() ) {
 483                     return;
 484                 }
 485                 obtainDetailedTaxonomicInformation();
 486             }
 487             else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
 488                 if ( isSubtreeDisplayed() ) {
 489                     return;
 490                 }
 491                 obtainDetailedTaxonomicInformationDelete();
 492             }
 493             else if ( o == _obtain_seq_information_jmi ) {
 494                 obtainSequenceInformation();
 495             }
 496             else if ( o == _read_values_jmi ) {
 497                 if ( isSubtreeDisplayed() ) {
 498                     return;
 499                 }
 500                 addExpressionValuesFromFile();
 501             }
 502             else if ( o == _move_node_names_to_tax_sn_jmi ) {
 503                 moveNodeNamesToTaxSn();
 504             }
 505             else if ( o == _move_node_names_to_seq_names_jmi ) {
 506                 moveNodeNamesToSeqNames();
 507             }
 508             else if ( o == _extract_tax_code_from_node_names_jmi ) {
 509                 extractTaxDataFromNodeNames();
 510             }
 511             else if ( o == _gsdi_item ) {
 512                 if ( isSubtreeDisplayed() ) {
 513                     return;
 514                 }
 515                 executeGSDI();
 516             }
 517             else if ( o == _gsdir_item ) {
 518                 if ( isSubtreeDisplayed() ) {
 519                     return;
 520                 }
 521                 executeGSDIR();
 522             }
 523             else if ( o == _root_min_dups_item ) {
 524                 if ( isSubtreeDisplayed() ) {
 525                     return;
 526                 }
 527                 executeSDIR( false );
 528             }
 529             else if ( o == _root_min_cost_l_item ) {
 530                 if ( isSubtreeDisplayed() ) {
 531                     return;
 532                 }
 533                 executeSDIR( true );
 534             }
 535             else if ( o == _graphics_export_visible_only_cbmi ) {
 536                 updateOptions( getOptions() );
 537             }
 538             else if ( o == _antialias_print_cbmi ) {
 539                 updateOptions( getOptions() );
 540             }
 541             else if ( o == _print_black_and_white_cbmi ) {
 542                 updateOptions( getOptions() );
 543             }
 544             else if ( o == _print_using_actual_size_cbmi ) {
 545                 updateOptions( getOptions() );
 546             }
 547             else if ( o == _graphics_export_using_actual_size_cbmi ) {
 548                 updateOptions( getOptions() );
 549             }
 550             else if ( o == _print_size_mi ) {
 551                 choosePrintSize();
 552             }
 553             else if ( o == _choose_pdf_width_mi ) {
 554                 choosePdfWidth();
 555             }
 556             else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
 557                 updateOptions( getOptions() );
 558             }
 559             else if ( o == _replace_underscores_cbmi ) {
 560                 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
 561                     _extract_taxonomy_no_rbmi.setSelected( true );
 562                 }
 563                 updateOptions( getOptions() );
 564             }
 565             else if ( o == _collapse_below_threshold ) {
 566                 if ( isSubtreeDisplayed() ) {
 567                     return;
 568                 }
 569                 collapseBelowThreshold();
 570             }
 571             else if ( ( o == _extract_taxonomy_pfam_rbmi ) || ( o == _extract_taxonomy_yes_rbmi ) ) {
 572                 if ( _replace_underscores_cbmi != null ) {
 573                     _replace_underscores_cbmi.setSelected( false );
 574                 }
 575                 updateOptions( getOptions() );
 576             }
 577             else if ( o == _inference_from_msa_item ) {
 578                 executePhyleneticInference( false );
 579             }
 580             else if ( o == _inference_from_seqs_item ) {
 581                 executePhyleneticInference( true );
 582             }
 583             _contentpane.repaint();
 584         }
 585         catch ( final Exception ex ) {
 586             AptxUtil.unexpectedException( ex );
 587         }
 588         catch ( final Error err ) {
 589             AptxUtil.unexpectedError( err );
 590         }
 591     }
 592
 593     public void end() {
 594         _mainpanel.terminate();
 595         _contentpane.removeAll();
 596         setVisible( false );
 597         dispose();
 598     }
 599
 600     @Override
 601     public MainPanel getMainPanel() {
 602         return _mainpanel;
 603     }
 604
 605     public Msa getMsa() {
 606         return _msa;
 607     }
 608
 609     public File getMsaFile() {
 610         return _msa_file;
 611     }
 612
 613     public List<Sequence> getSeqs() {
 614         return _seqs;
 615     }
 616
 617     public File getSeqsFile() {
 618         return _seqs_file;
 619     }
 620
 621     public void readMsaFromFile() {
 622         // Set an initial directory if none set yet
 623         final File my_dir = getCurrentDir();
 624         _msa_filechooser.setMultiSelectionEnabled( false );
 625         // Open file-open dialog and set current directory
 626         if ( my_dir != null ) {
 627             _msa_filechooser.setCurrentDirectory( my_dir );
 628         }
 629         final int result = _msa_filechooser.showOpenDialog( _contentpane );
 630         // All done: get the msa
 631         final File file = _msa_filechooser.getSelectedFile();
 632         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
 633         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 634             setMsaFile( null );
 635             setMsa( null );
 636             Msa msa = null;
 637             try {
 638                 final InputStream is = new FileInputStream( file );
 639                 if ( FastaParser.isLikelyFasta( file ) ) {
 640                     msa = FastaParser.parseMsa( is );
 641                 }
 642                 else {
 643                     msa = GeneralMsaParser.parse( is );
 644                 }
 645             }
 646             catch ( final MsaFormatException e ) {
 647                 try {
 648                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 649                 }
 650                 catch ( final Exception ex ) {
 651                     // Do nothing.
 652                 }
 653                 JOptionPane.showMessageDialog( this,
 654                                                e.getLocalizedMessage(),
 655                                                "Multiple sequence alignment format error",
 656                                                JOptionPane.ERROR_MESSAGE );
 657                 return;
 658             }
 659             catch ( final IOException e ) {
 660                 try {
 661                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 662                 }
 663                 catch ( final Exception ex ) {
 664                     // Do nothing.
 665                 }
 666                 JOptionPane.showMessageDialog( this,
 667                                                e.getLocalizedMessage(),
 668                                                "Failed to read multiple sequence alignment",
 669                                                JOptionPane.ERROR_MESSAGE );
 670                 return;
 671             }
 672             catch ( final IllegalArgumentException e ) {
 673                 try {
 674                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 675                 }
 676                 catch ( final Exception ex ) {
 677                     // Do nothing.
 678                 }
 679                 JOptionPane.showMessageDialog( this,
 680                                                e.getLocalizedMessage(),
 681                                                "Unexpected error during reading of multiple sequence alignment",
 682                                                JOptionPane.ERROR_MESSAGE );
 683                 return;
 684             }
 685             catch ( final Exception e ) {
 686                 try {
 687                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 688                 }
 689                 catch ( final Exception ex ) {
 690                     // Do nothing.
 691                 }
 692                 e.printStackTrace();
 693                 JOptionPane.showMessageDialog( this,
 694                                                e.getLocalizedMessage(),
 695                                                "Unexpected error during reading of multiple sequence alignment",
 696                                                JOptionPane.ERROR_MESSAGE );
 697                 return;
 698             }
 699             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
 700                 JOptionPane.showMessageDialog( this,
 701                                                "Multiple sequence alignment is empty",
 702                                                "Illegal Multiple Sequence Alignment",
 703                                                JOptionPane.ERROR_MESSAGE );
 704                 return;
 705             }
 706             if ( msa.getNumberOfSequences() < 4 ) {
 707                 JOptionPane.showMessageDialog( this,
 708                                                "Multiple sequence alignment needs to contain at least 3 sequences",
 709                                                "Illegal multiple sequence alignment",
 710                                                JOptionPane.ERROR_MESSAGE );
 711                 return;
 712             }
 713             if ( msa.getLength() < 2 ) {
 714                 JOptionPane.showMessageDialog( this,
 715                                                "Multiple sequence alignment needs to contain at least 2 residues",
 716                                                "Illegal multiple sequence alignment",
 717                                                JOptionPane.ERROR_MESSAGE );
 718                 return;
 719             }
 720             System.gc();
 721             setMsaFile( _msa_filechooser.getSelectedFile() );
 722             setMsa( msa );
 723         }
 724     }
 725
 726     public void readSeqsFromFile() {
 727         // Set an initial directory if none set yet
 728         final File my_dir = getCurrentDir();
 729         _seqs_filechooser.setMultiSelectionEnabled( false );
 730         // Open file-open dialog and set current directory
 731         if ( my_dir != null ) {
 732             _seqs_filechooser.setCurrentDirectory( my_dir );
 733         }
 734         final int result = _seqs_filechooser.showOpenDialog( _contentpane );
 735         // All done: get the seqs
 736         final File file = _seqs_filechooser.getSelectedFile();
 737         setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
 738         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 739             setSeqsFile( null );
 740             setSeqs( null );
 741             List<Sequence> seqs = null;
 742             try {
 743                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
 744                     seqs = FastaParser.parse( new FileInputStream( file ) );
 745                     for( final Sequence seq : seqs ) {
 746                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
 747                     }
 748                 }
 749                 else {
 750                     //TODO error
 751                 }
 752             }
 753             catch ( final MsaFormatException e ) {
 754                 try {
 755                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 756                 }
 757                 catch ( final Exception ex ) {
 758                     // Do nothing.
 759                 }
 760                 JOptionPane.showMessageDialog( this,
 761                                                e.getLocalizedMessage(),
 762                                                "Multiple sequence file format error",
 763                                                JOptionPane.ERROR_MESSAGE );
 764                 return;
 765             }
 766             catch ( final IOException e ) {
 767                 try {
 768                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 769                 }
 770                 catch ( final Exception ex ) {
 771                     // Do nothing.
 772                 }
 773                 JOptionPane.showMessageDialog( this,
 774                                                e.getLocalizedMessage(),
 775                                                "Failed to read multiple sequence file",
 776                                                JOptionPane.ERROR_MESSAGE );
 777                 return;
 778             }
 779             catch ( final IllegalArgumentException e ) {
 780                 try {
 781                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 782                 }
 783                 catch ( final Exception ex ) {
 784                     // Do nothing.
 785                 }
 786                 JOptionPane.showMessageDialog( this,
 787                                                e.getLocalizedMessage(),
 788                                                "Unexpected error during reading of multiple sequence file",
 789                                                JOptionPane.ERROR_MESSAGE );
 790                 return;
 791             }
 792             catch ( final Exception e ) {
 793                 try {
 794                     _mainpanel.getCurrentTreePanel().setArrowCursor();
 795                 }
 796                 catch ( final Exception ex ) {
 797                     // Do nothing.
 798                 }
 799                 e.printStackTrace();
 800                 JOptionPane.showMessageDialog( this,
 801                                                e.getLocalizedMessage(),
 802                                                "Unexpected error during reading of multiple sequence file",
 803                                                JOptionPane.ERROR_MESSAGE );
 804                 return;
 805             }
 806             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 807                 JOptionPane.showMessageDialog( this,
 808                                                "Multiple sequence file is empty",
 809                                                "Illegal multiple sequence file",
 810                                                JOptionPane.ERROR_MESSAGE );
 811                 return;
 812             }
 813             if ( seqs.size() < 4 ) {
 814                 JOptionPane.showMessageDialog( this,
 815                                                "Multiple sequence file needs to contain at least 3 sequences",
 816                                                "Illegal multiple sequence file",
 817                                                JOptionPane.ERROR_MESSAGE );
 818                 return;
 819             }
 820             //  if ( msa.getLength() < 2 ) {
 821             //       JOptionPane.showMessageDialog( this,
 822             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
 823             //                                      "Illegal multiple sequence file",
 824             //                                      JOptionPane.ERROR_MESSAGE );
 825             //       return;
 826             //   }
 827             System.gc();
 828             setSeqsFile( _seqs_filechooser.getSelectedFile() );
 829             setSeqs( seqs );
 830         }
 831     }
 832
 833     void buildAnalysisMenu() {
 834         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 835         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 836         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
 837         _analysis_menu.addSeparator();
 838         _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
 839         _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
 840         _analysis_menu.addSeparator();
 841         _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
 842         customizeJMenuItem( _gsdi_item );
 843         customizeJMenuItem( _gsdir_item );
 844         customizeJMenuItem( _root_min_dups_item );
 845         customizeJMenuItem( _root_min_cost_l_item );
 846         customizeJMenuItem( _load_species_tree_item );
 847         _analysis_menu.addSeparator();
 848         _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 849         customizeJMenuItem( _lineage_inference );
 850         _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 851         _jmenubar.add( _analysis_menu );
 852     }
 853
 854     @Override
 855     void buildFileMenu() {
 856         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
 857         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
 858         _file_jmenu.addSeparator();
 859         _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
 860         _file_jmenu.addSeparator();
 861         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
 862         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
 863                 .getAvailablePhylogeniesWebserviceClients().size() ];
 864         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 865             final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
 866             _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
 867             _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
 868         }
 869         if ( getConfiguration().isEditable() ) {
 870             _file_jmenu.addSeparator();
 871             _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
 872             _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
 873         }
 874         _file_jmenu.addSeparator();
 875         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
 876         _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
 877         _save_all_item.setToolTipText( "Write all phylogenies to one file." );
 878         _save_all_item.setEnabled( false );
 879         _file_jmenu.addSeparator();
 880         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
 881         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
 882             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
 883         }
 884         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
 885         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
 886         if ( AptxUtil.canWriteFormat( "gif" ) ) {
 887             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
 888         }
 889         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
 890             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
 891         }
 892         _file_jmenu.addSeparator();
 893         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
 894         _file_jmenu.addSeparator();
 895         _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
 896         _close_item.setToolTipText( "To close the current pane." );
 897         _close_item.setEnabled( true );
 898         _file_jmenu.addSeparator();
 899         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 900         // For print in color option item
 901         customizeJMenuItem( _open_item );
 902         _open_item
 903                 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
 904         customizeJMenuItem( _open_url_item );
 905         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
 906             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
 907         }
 908         customizeJMenuItem( _save_item );
 909         if ( getConfiguration().isEditable() ) {
 910             customizeJMenuItem( _new_item );
 911         }
 912         customizeJMenuItem( _close_item );
 913         customizeJMenuItem( _save_all_item );
 914         customizeJMenuItem( _write_to_pdf_item );
 915         customizeJMenuItem( _write_to_png_item );
 916         customizeJMenuItem( _write_to_jpg_item );
 917         customizeJMenuItem( _write_to_gif_item );
 918         customizeJMenuItem( _write_to_tif_item );
 919         customizeJMenuItem( _write_to_bmp_item );
 920         customizeJMenuItem( _print_item );
 921         customizeJMenuItem( _exit_item );
 922         _jmenubar.add( _file_jmenu );
 923     }
 924
 925     void buildOptionsMenu() {
 926         _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
 927         _options_jmenu.addChangeListener( new ChangeListener() {
 928
 929             @Override
 930             public void stateChanged( final ChangeEvent e ) {
 931                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 932                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 933                 MainFrame
 934                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 935                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 936                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 937                 setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
 938                 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
 939                 MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
 940                                                                      _show_scale_cbmi,
 941                                                                      _show_branch_length_values_cbmi,
 942                                                                      _non_lined_up_cladograms_rbmi,
 943                                                                      _uniform_cladograms_rbmi,
 944                                                                      _ext_node_dependent_cladogram_rbmi,
 945                                                                      _label_direction_cbmi );
 946                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 947                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 948                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 949             }
 950         } );
 951         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
 952         _options_jmenu
 953                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 954         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 955         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
 956         _radio_group_1 = new ButtonGroup();
 957         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 958         _radio_group_1.add( _uniform_cladograms_rbmi );
 959         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 960         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
 961         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
 962         _options_jmenu
 963                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 964         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
 965         _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
 966         _options_jmenu
 967                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
 968         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 969         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 970         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 971         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
 972         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
 973         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
 974         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 975         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
 976         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
 977         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
 978         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 979             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
 980         }
 981         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 982         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 983         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 984         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 985         _options_jmenu.addSeparator();
 986         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
 987         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
 988         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
 989         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
 990         _options_jmenu.addSeparator();
 991         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
 992                                                       getConfiguration() ) );
 993         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
 994         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
 995         _options_jmenu
 996                 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
 997         _options_jmenu
 998                 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
 999         _options_jmenu
1000                 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
1001         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
1002         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
1003         _options_jmenu.addSeparator();
1004         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
1005         _options_jmenu
1006                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
1007         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
1008         //
1009         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
1010         _options_jmenu
1011                 .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
1012         _extract_taxonomy_pfam_rbmi
1013                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
1014         _options_jmenu
1015                 .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
1016         _extract_taxonomy_yes_rbmi
1017                 .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
1018         _radio_group_2 = new ButtonGroup();
1019         _radio_group_2.add( _extract_taxonomy_no_rbmi );
1020         _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
1021         _radio_group_2.add( _extract_taxonomy_yes_rbmi );
1022         //
1023         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
1024         _options_jmenu
1025                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
1026         _use_brackets_for_conf_in_nh_export_cbmi
1027                 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
1028         _options_jmenu
1029                 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
1030         customizeJMenuItem( _choose_font_mi );
1031         customizeJMenuItem( _choose_minimal_confidence_mi );
1032         customizeJMenuItem( _switch_colors_mi );
1033         customizeJMenuItem( _print_size_mi );
1034         customizeJMenuItem( _choose_pdf_width_mi );
1035         customizeJMenuItem( _overview_placment_mi );
1036         customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
1037         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
1038         customizeJMenuItem( _cycle_node_shape_mi );
1039         customizeJMenuItem( _cycle_node_fill_mi );
1040         customizeJMenuItem( _choose_node_size_mi );
1041         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
1042         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
1043         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
1044         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
1045         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
1046         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
1047         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
1048         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
1049                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
1050         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
1051                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1052         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
1053                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1054         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
1055         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1056         customizeCheckBoxMenuItem( _label_direction_cbmi,
1057                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1058         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1059         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1060         customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
1061                 .isInternalNumberAreConfidenceForNhParsing() );
1062         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1063                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1064         customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
1065                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
1066         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
1067                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1068         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1069         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1070         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1071         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1072         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
1073         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
1074                 .isGraphicsExportUsingActualSize() );
1075         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1076         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
1077                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1078         customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
1079                 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1080         _jmenubar.add( _options_jmenu );
1081     }
1082
1083     void buildPhylogeneticInferenceMenu() {
1084         final InferenceManager im = getInferenceManager();
1085         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1086         _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1087         customizeJMenuItem( _inference_from_msa_item );
1088         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1089         if ( im.canDoMsa() ) {
1090             _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1091             customizeJMenuItem( _inference_from_seqs_item );
1092             _inference_from_seqs_item
1093                     .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1094         }
1095         else {
1096             _inference_menu
1097                     .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
1098             customizeJMenuItem( _inference_from_seqs_item );
1099             _inference_from_seqs_item.setEnabled( false );
1100         }
1101         _jmenubar.add( _inference_menu );
1102     }
1103
1104     void buildToolsMenu() {
1105         _tools_menu = createMenu( "Tools", getConfiguration() );
1106         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
1107         customizeJMenuItem( _confcolor_item );
1108         _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
1109         customizeJMenuItem( _color_rank_jmi );
1110         _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
1111         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
1112         customizeJMenuItem( _taxcolor_item );
1113         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
1114         _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
1115         customizeJMenuItem( _remove_branch_color_item );
1116         _tools_menu.addSeparator();
1117         _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
1118         customizeJMenuItem( _annotate_item );
1119         _tools_menu.addSeparator();
1120         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
1121         customizeJMenuItem( _midpoint_root_item );
1122         _tools_menu.addSeparator();
1123         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
1124         customizeJMenuItem( _collapse_species_specific_subtrees );
1125         _tools_menu
1126                 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
1127         customizeJMenuItem( _collapse_below_threshold );
1128         _collapse_below_threshold
1129                 .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)" );
1130         _tools_menu.addSeparator();
1131         _tools_menu
1132                 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
1133         customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
1134         _extract_tax_code_from_node_names_jmi
1135                 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
1136         _tools_menu
1137                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
1138         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
1139         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
1140         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
1141         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
1142         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
1143         _tools_menu.addSeparator();
1144         _tools_menu
1145                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
1146         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
1147         _obtain_detailed_taxonomic_information_jmi
1148                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
1149         _tools_menu
1150                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
1151         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
1152         _obtain_detailed_taxonomic_information_deleting_jmi
1153                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
1154         _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
1155         customizeJMenuItem( _obtain_seq_information_jmi );
1156         _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
1157         _tools_menu.addSeparator();
1158         if ( !Constants.__RELEASE ) {
1159             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
1160             customizeJMenuItem( _function_analysis );
1161             _function_analysis
1162                     .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
1163             _tools_menu.addSeparator();
1164         }
1165         _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
1166         customizeJMenuItem( _read_values_jmi );
1167         _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
1168         _jmenubar.add( _tools_menu );
1169     }
1170
1171     @Override
1172     void close() {
1173         if ( isUnsavedDataPresent() ) {
1174             final int r = JOptionPane.showConfirmDialog( this,
1175                                                          "Exit despite potentially unsaved changes?",
1176                                                          "Exit?",
1177                                                          JOptionPane.YES_NO_OPTION );
1178             if ( r != JOptionPane.YES_OPTION ) {
1179                 return;
1180             }
1181         }
1182         exit();
1183     }
1184
1185     void executeFunctionAnalysis() {
1186         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1187             return;
1188         }
1189         final GoAnnotation a = new GoAnnotation( this,
1190                                                  _mainpanel.getCurrentTreePanel(),
1191                                                  _mainpanel.getCurrentPhylogeny() );
1192         new Thread( a ).start();
1193     }
1194
1195     void executeGSDI() {
1196         if ( !isOKforSDI( false, true ) ) {
1197             return;
1198         }
1199         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1200             JOptionPane.showMessageDialog( this,
1201                                            "Gene tree is not rooted.",
1202                                            "Cannot execute GSDI",
1203                                            JOptionPane.ERROR_MESSAGE );
1204             return;
1205         }
1206         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1207         gene_tree.setAllNodesToNotCollapse();
1208         gene_tree.recalculateNumberOfExternalDescendants( false );
1209         GSDI gsdi = null;
1210         final Phylogeny species_tree = _species_tree.copy();
1211         try {
1212             gsdi = new GSDI( gene_tree, species_tree, false, true, true );
1213         }
1214         catch ( final SDIException e ) {
1215             JOptionPane.showMessageDialog( this,
1216                                            e.getLocalizedMessage(),
1217                                            "Error during GSDI",
1218                                            JOptionPane.ERROR_MESSAGE );
1219             return;
1220         }
1221         catch ( final Exception e ) {
1222             AptxUtil.unexpectedException( e );
1223             return;
1224         }
1225         gene_tree.setRerootable( false );
1226         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1227         _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
1228         _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
1229         _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1230         _mainpanel.getCurrentTreePanel().setEdited( true );
1231         getControlPanel().setShowEvents( true );
1232         showWhole();
1233         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1234         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1235         showWhole();
1236         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1237         showWhole();
1238         _mainpanel.getCurrentTreePanel().setEdited( true );
1239         JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1240                 + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
1241                 + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
1242     }
1243
1244     void executeGSDIR() {
1245         if ( !isOKforSDI( false, true ) ) {
1246             return;
1247         }
1248         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1249         gene_tree.setAllNodesToNotCollapse();
1250         gene_tree.recalculateNumberOfExternalDescendants( false );
1251         GSDIR gsdir = null;
1252         final Phylogeny species_tree = _species_tree.copy();
1253         try {
1254             gsdir = new GSDIR( gene_tree, species_tree, true, true );
1255         }
1256         catch ( final SDIException e ) {
1257             JOptionPane.showMessageDialog( this,
1258                                            e.getLocalizedMessage(),
1259                                            "Error during GSDIR",
1260                                            JOptionPane.ERROR_MESSAGE );
1261             return;
1262         }
1263         catch ( final Exception e ) {
1264             AptxUtil.unexpectedException( e );
1265             return;
1266         }
1267         final List<Phylogeny> assigned_trees = gsdir.getMinDuplicationsSumGeneTrees();
1268         final List<Integer> shortests = GSDIR.getIndexesOfShortestTree( assigned_trees );
1269         final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) );
1270         result_gene_tree.setRerootable( false );
1271         result_gene_tree.clearHashIdToNodeMap();
1272         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1273         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1274         getControlPanel().setShowEvents( true );
1275         showWhole();
1276         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1277         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1278         showWhole();
1279         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1280         showWhole();
1281         _mainpanel.getCurrentTreePanel().setEdited( true );
1282         JOptionPane.showMessageDialog( this,
1283                                        "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
1284                                                + gsdir.getSpeciationsSum() + "\n"
1285                                                + "Number of root positions minimizing duplications sum: "
1286                                                + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n"
1287                                                + "Number of shortest trees: " + shortests.size(),
1288                                        "GSDIR successfully completed",
1289                                        JOptionPane.INFORMATION_MESSAGE );
1290     }
1291
1292     void executeLineageInference() {
1293         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1294             return;
1295         }
1296         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1297             JOptionPane.showMessageDialog( this,
1298                                            "Phylogeny is not rooted.",
1299                                            "Cannot infer ancestral taxonomies",
1300                                            JOptionPane.ERROR_MESSAGE );
1301             return;
1302         }
1303         final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1304                                                                                   _mainpanel.getCurrentTreePanel(),
1305                                                                                   _mainpanel.getCurrentPhylogeny()
1306                                                                                           .copy() );
1307         new Thread( inferrer ).start();
1308     }
1309
1310     void executeSDIR( final boolean minimize_cost ) {
1311         if ( !isOKforSDI( true, true ) ) {
1312             return;
1313         }
1314         Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1315         final SDIR sdiunrooted = new SDIR();
1316         gene_tree.setAllNodesToNotCollapse();
1317         gene_tree.recalculateNumberOfExternalDescendants( false );
1318         try {
1319             gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1320                                            !minimize_cost, // minimize sum of dups
1321                                            true, // minimize height
1322                                            true, // return tree(s)
1323                                            1 )[ 0 ]; // # of trees to return
1324         }
1325         catch ( final Exception e ) {
1326             JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1327             return;
1328         }
1329         final int duplications = sdiunrooted.getMinimalDuplications();
1330         gene_tree.setRerootable( false );
1331         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1332         getControlPanel().setShowEvents( true );
1333         showWhole();
1334         _mainpanel.getCurrentTreePanel().setEdited( true );
1335         JOptionPane.showMessageDialog( this,
1336                                        "Number of duplications: " + duplications,
1337                                        "SDIR successfully completed",
1338                                        JOptionPane.INFORMATION_MESSAGE );
1339     }
1340
1341     void exit() {
1342         removeAllTextFrames();
1343         _mainpanel.terminate();
1344         _contentpane.removeAll();
1345         setVisible( false );
1346         dispose();
1347         System.exit( 0 );
1348     }
1349
1350     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1351         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1352             return false;
1353         }
1354         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1355             JOptionPane.showMessageDialog( this,
1356                                            "No species tree loaded",
1357                                            "Cannot execute SDI",
1358                                            JOptionPane.ERROR_MESSAGE );
1359             return false;
1360         }
1361         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1362             JOptionPane.showMessageDialog( this,
1363                                            "Species tree is not completely binary",
1364                                            "Cannot execute SDI",
1365                                            JOptionPane.ERROR_MESSAGE );
1366             return false;
1367         }
1368         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1369             JOptionPane.showMessageDialog( this,
1370                                            "Gene tree is not completely binary",
1371                                            "Cannot execute SDI",
1372                                            JOptionPane.ERROR_MESSAGE );
1373             return false;
1374         }
1375         else {
1376             return true;
1377         }
1378     }
1379
1380     @Override
1381     void readPhylogeniesFromURL() {
1382         URL url = null;
1383         Phylogeny[] phys = null;
1384         final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
1385         final String url_string = JOptionPane.showInputDialog( this,
1386                                                                message,
1387                                                                "Use URL/webservice to obtain a phylogeny",
1388                                                                JOptionPane.QUESTION_MESSAGE );
1389         boolean nhx_or_nexus = false;
1390         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
1391             try {
1392                 url = new URL( url_string );
1393                 PhylogenyParser parser = null;
1394                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
1395                     parser = new TolParser();
1396                 }
1397                 else {
1398                     parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
1399                             .isValidatePhyloXmlAgainstSchema() );
1400                 }
1401                 if ( parser instanceof NexusPhylogeniesParser ) {
1402                     nhx_or_nexus = true;
1403                 }
1404                 else if ( parser instanceof NHXParser ) {
1405                     nhx_or_nexus = true;
1406                 }
1407                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1408                     _mainpanel.getCurrentTreePanel().setWaitCursor();
1409                 }
1410                 else {
1411                     _mainpanel.setWaitCursor();
1412                 }
1413                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1414                 phys = factory.create( url.openStream(), parser );
1415             }
1416             catch ( final MalformedURLException e ) {
1417                 JOptionPane.showMessageDialog( this,
1418                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
1419                                                "Malformed URL",
1420                                                JOptionPane.ERROR_MESSAGE );
1421             }
1422             catch ( final IOException e ) {
1423                 JOptionPane.showMessageDialog( this,
1424                                                "Could not read from " + url + "\n"
1425                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1426                                                "Failed to read URL",
1427                                                JOptionPane.ERROR_MESSAGE );
1428             }
1429             catch ( final Exception e ) {
1430                 JOptionPane.showMessageDialog( this,
1431                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
1432                                                "Unexpected Exception",
1433                                                JOptionPane.ERROR_MESSAGE );
1434             }
1435             finally {
1436                 if ( _mainpanel.getCurrentTreePanel() != null ) {
1437                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1438                 }
1439                 else {
1440                     _mainpanel.setArrowCursor();
1441                 }
1442             }
1443             if ( ( phys != null ) && ( phys.length > 0 ) ) {
1444                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1445                     for( final Phylogeny phy : phys ) {
1446                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1447                     }
1448                 }
1449                 AptxUtil.addPhylogeniesToTabs( phys,
1450                                                new File( url.getFile() ).getName(),
1451                                                new File( url.getFile() ).toString(),
1452                                                getConfiguration(),
1453                                                getMainPanel() );
1454                 _mainpanel.getControlPanel().showWhole();
1455             }
1456         }
1457         activateSaveAllIfNeeded();
1458         System.gc();
1459     }
1460
1461     void setMsa( final Msa msa ) {
1462         _msa = msa;
1463     }
1464
1465     void setMsaFile( final File msa_file ) {
1466         _msa_file = msa_file;
1467     }
1468
1469     void setSeqs( final List<Sequence> seqs ) {
1470         _seqs = seqs;
1471     }
1472
1473     void setSeqsFile( final File seqs_file ) {
1474         _seqs_file = seqs_file;
1475     }
1476
1477     void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
1478         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
1479                                                                    _mainpanel.getCurrentTreePanel().getHeight(),
1480                                                                    true );
1481         String file_written_to = "";
1482         boolean error = false;
1483         try {
1484             file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
1485                                                                      _mainpanel.getCurrentTreePanel().getWidth(),
1486                                                                      _mainpanel.getCurrentTreePanel().getHeight(),
1487                                                                      _mainpanel.getCurrentTreePanel(),
1488                                                                      _mainpanel.getControlPanel(),
1489                                                                      type,
1490                                                                      getOptions() );
1491         }
1492         catch ( final IOException e ) {
1493             error = true;
1494             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1495         }
1496         if ( !error ) {
1497             if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
1498                 JOptionPane.showMessageDialog( this,
1499                                                "Wrote image to: " + file_written_to,
1500                                                "Graphics Export",
1501                                                JOptionPane.INFORMATION_MESSAGE );
1502             }
1503             else {
1504                 JOptionPane.showMessageDialog( this,
1505                                                "There was an unknown problem when attempting to write to an image file: \""
1506                                                        + file_name + "\"",
1507                                                "Error",
1508                                                JOptionPane.ERROR_MESSAGE );
1509             }
1510         }
1511         _contentpane.repaint();
1512     }
1513
1514     private void addExpressionValuesFromFile() {
1515         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1516             JOptionPane.showMessageDialog( this,
1517                                            "Need to load evolutionary tree first",
1518                                            "Can Not Read Expression Values",
1519                                            JOptionPane.WARNING_MESSAGE );
1520             return;
1521         }
1522         final File my_dir = getCurrentDir();
1523         if ( my_dir != null ) {
1524             _values_filechooser.setCurrentDirectory( my_dir );
1525         }
1526         final int result = _values_filechooser.showOpenDialog( _contentpane );
1527         final File file = _values_filechooser.getSelectedFile();
1528         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1529             BasicTable<String> t = null;
1530             try {
1531                 t = BasicTableParser.parse( file, "\t" );
1532                 if ( t.getNumberOfColumns() < 2 ) {
1533                     t = BasicTableParser.parse( file, "," );
1534                 }
1535                 if ( t.getNumberOfColumns() < 2 ) {
1536                     t = BasicTableParser.parse( file, " " );
1537                 }
1538             }
1539             catch ( final IOException e ) {
1540                 JOptionPane.showMessageDialog( this,
1541                                                e.getMessage(),
1542                                                "Could Not Read Expression Value Table",
1543                                                JOptionPane.ERROR_MESSAGE );
1544                 return;
1545             }
1546             if ( t.getNumberOfColumns() < 2 ) {
1547                 JOptionPane.showMessageDialog( this,
1548                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
1549                                                "Problem with Expression Value Table",
1550                                                JOptionPane.ERROR_MESSAGE );
1551                 return;
1552             }
1553             if ( t.getNumberOfRows() < 1 ) {
1554                 JOptionPane.showMessageDialog( this,
1555                                                "Table contains zero rows",
1556                                                "Problem with Expression Value Table",
1557                                                JOptionPane.ERROR_MESSAGE );
1558                 return;
1559             }
1560             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1561             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1562                 JOptionPane.showMessageDialog( this,
1563                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1564                                                        + phy.getNumberOfExternalNodes() + " external nodes",
1565                                                "Warning",
1566                                                JOptionPane.WARNING_MESSAGE );
1567             }
1568             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1569             int not_found = 0;
1570             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1571                 final PhylogenyNode node = iter.next();
1572                 final String node_name = node.getName();
1573                 if ( !ForesterUtil.isEmpty( node_name ) ) {
1574                     int row = -1;
1575                     try {
1576                         row = t.findRow( node_name );
1577                     }
1578                     catch ( final IllegalArgumentException e ) {
1579                         JOptionPane
1580                                 .showMessageDialog( this,
1581                                                     e.getMessage(),
1582                                                     "Error Mapping Node Identifiers to Expression Value Identifiers",
1583                                                     JOptionPane.ERROR_MESSAGE );
1584                         return;
1585                     }
1586                     if ( row < 0 ) {
1587                         if ( node.isExternal() ) {
1588                             not_found++;
1589                         }
1590                         continue;
1591                     }
1592                     final List<Double> l = new ArrayList<Double>();
1593                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1594                         double d = -100;
1595                         try {
1596                             d = Double.parseDouble( t.getValueAsString( col, row ) );
1597                         }
1598                         catch ( final NumberFormatException e ) {
1599                             JOptionPane.showMessageDialog( this,
1600                                                            "Could not parse \"" + t.getValueAsString( col, row )
1601                                                                    + "\" into a decimal value",
1602                                                            "Issue with Expression Value Table",
1603                                                            JOptionPane.ERROR_MESSAGE );
1604                             return;
1605                         }
1606                         stats.addValue( d );
1607                         l.add( d );
1608                     }
1609                     if ( !l.isEmpty() ) {
1610                         if ( node.getNodeData().getProperties() != null ) {
1611                             node.getNodeData().getProperties()
1612                                     .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1613                         }
1614                         node.getNodeData().setVector( l );
1615                     }
1616                 }
1617             }
1618             if ( not_found > 0 ) {
1619                 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1620                         + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1621             }
1622             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1623         }
1624     }
1625
1626     private void choosePdfWidth() {
1627         final String s = ( String ) JOptionPane.showInputDialog( this,
1628                                                                  "Please enter the default line width for PDF export.\n"
1629                                                                          + "[current value: "
1630                                                                          + getOptions().getPrintLineWidth() + "]\n",
1631                                                                  "Line Width for PDF Export",
1632                                                                  JOptionPane.QUESTION_MESSAGE,
1633                                                                  null,
1634                                                                  null,
1635                                                                  getOptions().getPrintLineWidth() );
1636         if ( !ForesterUtil.isEmpty( s ) ) {
1637             boolean success = true;
1638             float f = 0.0f;
1639             final String m_str = s.trim();
1640             if ( !ForesterUtil.isEmpty( m_str ) ) {
1641                 try {
1642                     f = Float.parseFloat( m_str );
1643                 }
1644                 catch ( final Exception ex ) {
1645                     success = false;
1646                 }
1647             }
1648             else {
1649                 success = false;
1650             }
1651             if ( success && ( f > 0.0 ) ) {
1652                 getOptions().setPrintLineWidth( f );
1653             }
1654         }
1655     }
1656
1657     private void choosePrintSize() {
1658         final String s = ( String ) JOptionPane.showInputDialog( this,
1659                                                                  "Please enter values for width and height,\nseparated by a comma.\n"
1660                                                                          + "[current values: "
1661                                                                          + getOptions().getPrintSizeX() + ", "
1662                                                                          + getOptions().getPrintSizeY() + "]\n"
1663                                                                          + "[A4: " + Constants.A4_SIZE_X + ", "
1664                                                                          + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1665                                                                          + Constants.US_LETTER_SIZE_X + ", "
1666                                                                          + Constants.US_LETTER_SIZE_Y + "]",
1667                                                                  "Default Size for Graphics Export",
1668                                                                  JOptionPane.QUESTION_MESSAGE,
1669                                                                  null,
1670                                                                  null,
1671                                                                  getOptions().getPrintSizeX() + ", "
1672                                                                          + getOptions().getPrintSizeY() );
1673         if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1674             boolean success = true;
1675             int x = 0;
1676             int y = 0;
1677             final String[] str_ary = s.split( "," );
1678             if ( str_ary.length == 2 ) {
1679                 final String x_str = str_ary[ 0 ].trim();
1680                 final String y_str = str_ary[ 1 ].trim();
1681                 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1682                     try {
1683                         x = Integer.parseInt( x_str );
1684                         y = Integer.parseInt( y_str );
1685                     }
1686                     catch ( final Exception ex ) {
1687                         success = false;
1688                     }
1689                 }
1690                 else {
1691                     success = false;
1692                 }
1693             }
1694             else {
1695                 success = false;
1696             }
1697             if ( success && ( x > 1 ) && ( y > 1 ) ) {
1698                 getOptions().setPrintSizeX( x );
1699                 getOptions().setPrintSizeY( y );
1700             }
1701         }
1702     }
1703
1704     private void closeCurrentPane() {
1705         if ( getMainPanel().getCurrentTreePanel() != null ) {
1706             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1707                 final int r = JOptionPane.showConfirmDialog( this,
1708                                                              "Close tab despite potentially unsaved changes?",
1709                                                              "Close Tab?",
1710                                                              JOptionPane.YES_NO_OPTION );
1711                 if ( r != JOptionPane.YES_OPTION ) {
1712                     return;
1713                 }
1714             }
1715             getMainPanel().closeCurrentPane();
1716             activateSaveAllIfNeeded();
1717         }
1718     }
1719
1720     private void collapse( final Phylogeny phy, final double m ) {
1721         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1722         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1723         double min_support = Double.MAX_VALUE;
1724         boolean conf_present = false;
1725         while ( it.hasNext() ) {
1726             final PhylogenyNode n = it.next();
1727             if ( !n.isExternal() && !n.isRoot() ) {
1728                 final List<Confidence> c = n.getBranchData().getConfidences();
1729                 if ( ( c != null ) && ( c.size() > 0 ) ) {
1730                     conf_present = true;
1731                     double max = 0;
1732                     for( final Confidence confidence : c ) {
1733                         if ( confidence.getValue() > max ) {
1734                             max = confidence.getValue();
1735                         }
1736                     }
1737                     if ( max < getMinNotCollapseConfidenceValue() ) {
1738                         to_be_removed.add( n );
1739                     }
1740                     if ( max < min_support ) {
1741                         min_support = max;
1742                     }
1743                 }
1744             }
1745         }
1746         if ( conf_present ) {
1747             for( final PhylogenyNode node : to_be_removed ) {
1748                 PhylogenyMethods.removeNode( node, phy );
1749             }
1750             if ( to_be_removed.size() > 0 ) {
1751                 phy.externalNodesHaveChanged();
1752                 phy.clearHashIdToNodeMap();
1753                 phy.recalculateNumberOfExternalDescendants( true );
1754                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1755                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1756                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1757                 getCurrentTreePanel().setNodeInPreorderToNull();
1758                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1759                 getCurrentTreePanel().resetPreferredSize();
1760                 getCurrentTreePanel().setEdited( true );
1761                 getCurrentTreePanel().repaint();
1762                 repaint();
1763             }
1764             if ( to_be_removed.size() > 0 ) {
1765                 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1766                         + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1767                         + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1768             }
1769             else {
1770                 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1771                         + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1772             }
1773         }
1774         else {
1775             JOptionPane.showMessageDialog( this,
1776                                            "No branch collapsed because no confidence values present",
1777                                            "No confidence values present",
1778                                            JOptionPane.INFORMATION_MESSAGE );
1779         }
1780     }
1781
1782     private void collapseBelowThreshold() {
1783         if ( getCurrentTreePanel() != null ) {
1784             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1785             if ( ( phy != null ) && !phy.isEmpty() ) {
1786                 final String s = ( String ) JOptionPane.showInputDialog( this,
1787                                                                          "Please enter the minimum confidence value\n",
1788                                                                          "Minimal Confidence Value",
1789                                                                          JOptionPane.QUESTION_MESSAGE,
1790                                                                          null,
1791                                                                          null,
1792                                                                          getMinNotCollapseConfidenceValue() );
1793                 if ( !ForesterUtil.isEmpty( s ) ) {
1794                     boolean success = true;
1795                     double m = 0.0;
1796                     final String m_str = s.trim();
1797                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1798                         try {
1799                             m = Double.parseDouble( m_str );
1800                         }
1801                         catch ( final Exception ex ) {
1802                             success = false;
1803                         }
1804                     }
1805                     else {
1806                         success = false;
1807                     }
1808                     if ( success && ( m >= 0.0 ) ) {
1809                         setMinNotCollapseConfidenceValue( m );
1810                         collapse( phy, m );
1811                     }
1812                 }
1813             }
1814         }
1815     }
1816
1817     private PhyloXmlParser createPhyloXmlParser() {
1818         PhyloXmlParser xml_parser = null;
1819         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1820             try {
1821                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1822             }
1823             catch ( final Exception e ) {
1824                 JOptionPane.showMessageDialog( this,
1825                                                e.getLocalizedMessage(),
1826                                                "failed to create validating XML parser",
1827                                                JOptionPane.WARNING_MESSAGE );
1828             }
1829         }
1830         if ( xml_parser == null ) {
1831             xml_parser = new PhyloXmlParser();
1832         }
1833         return xml_parser;
1834     }
1835
1836     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1837         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1838                                                                       getPhylogeneticInferenceOptions(),
1839                                                                       from_unaligned_seqs );
1840         dialog.activate();
1841         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1842             if ( !from_unaligned_seqs ) {
1843                 if ( getMsa() != null ) {
1844                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1845                                                                                     getPhylogeneticInferenceOptions()
1846                                                                                             .copy(), this );
1847                     new Thread( inferrer ).start();
1848                 }
1849                 else {
1850                     JOptionPane.showMessageDialog( this,
1851                                                    "No multiple sequence alignment selected",
1852                                                    "Phylogenetic Inference Not Launched",
1853                                                    JOptionPane.WARNING_MESSAGE );
1854                 }
1855             }
1856             else {
1857                 if ( getSeqs() != null ) {
1858                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1859                                                                                     getPhylogeneticInferenceOptions()
1860                                                                                             .copy(), this );
1861                     new Thread( inferrer ).start();
1862                 }
1863                 else {
1864                     JOptionPane.showMessageDialog( this,
1865                                                    "No input sequences selected",
1866                                                    "Phylogenetic Inference Not Launched",
1867                                                    JOptionPane.WARNING_MESSAGE );
1868                 }
1869             }
1870         }
1871     }
1872
1873     private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1874         final StringBuilder sb = new StringBuilder();
1875         final StringBuilder sb_failed = new StringBuilder();
1876         int counter = 0;
1877         int counter_failed = 0;
1878         if ( getCurrentTreePanel() != null ) {
1879             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1880             if ( ( phy != null ) && !phy.isEmpty() ) {
1881                 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1882                 while ( it.hasNext() ) {
1883                     final PhylogenyNode n = it.next();
1884                     final String name = n.getName().trim();
1885                     if ( !ForesterUtil.isEmpty( name ) ) {
1886                         final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES );
1887                         if ( !ForesterUtil.isEmpty( nt ) ) {
1888                             if ( counter < 15 ) {
1889                                 sb.append( name + ": " + nt + "\n" );
1890                             }
1891                             else if ( counter == 15 ) {
1892                                 sb.append( "...\n" );
1893                             }
1894                             counter++;
1895                         }
1896                         else {
1897                             if ( counter_failed < 15 ) {
1898                                 sb_failed.append( name + "\n" );
1899                             }
1900                             else if ( counter_failed == 15 ) {
1901                                 sb_failed.append( "...\n" );
1902                             }
1903                             counter_failed++;
1904                         }
1905                     }
1906                 }
1907                 if ( counter > 0 ) {
1908                     String failed = "";
1909                     String all = "all ";
1910                     if ( counter_failed > 0 ) {
1911                         all = "";
1912                         failed = "\nCould not extract taxonomic data for " + counter_failed
1913                                 + " named external nodes:\n" + sb_failed;
1914                     }
1915                     JOptionPane.showMessageDialog( this,
1916                                                    "Extracted taxonomic data from " + all + counter
1917                                                            + " named external nodes:\n" + sb.toString() + failed,
1918                                                    "Taxonomic Data Extraction Completed",
1919                                                    counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1920                                                            : JOptionPane.INFORMATION_MESSAGE );
1921                 }
1922                 else {
1923                     JOptionPane
1924                             .showMessageDialog( this,
1925                                                 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1926                                                         + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1927                                                         + "or nodes already have taxonomic data?\n",
1928                                                 "No Taxonomic Data Extracted",
1929                                                 JOptionPane.ERROR_MESSAGE );
1930                 }
1931             }
1932         }
1933     }
1934
1935     private ControlPanel getControlPanel() {
1936         return getMainPanel().getControlPanel();
1937     }
1938
1939     private File getCurrentDir() {
1940         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1941             if ( ForesterUtil.isWindowns() ) {
1942                 try {
1943                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1944                 }
1945                 catch ( final Exception e ) {
1946                     _current_dir = null;
1947                 }
1948             }
1949         }
1950         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1951             if ( System.getProperty( "user.home" ) != null ) {
1952                 _current_dir = new File( System.getProperty( "user.home" ) );
1953             }
1954             else if ( System.getProperty( "user.dir" ) != null ) {
1955                 _current_dir = new File( System.getProperty( "user.dir" ) );
1956             }
1957         }
1958         return _current_dir;
1959     }
1960
1961     private double getMinNotCollapseConfidenceValue() {
1962         return _min_not_collapse;
1963     }
1964
1965     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1966         if ( _phylogenetic_inference_options == null ) {
1967             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1968         }
1969         return _phylogenetic_inference_options;
1970     }
1971
1972     private boolean isUnsavedDataPresent() {
1973         final List<TreePanel> tps = getMainPanel().getTreePanels();
1974         for( final TreePanel tp : tps ) {
1975             if ( tp.isEdited() ) {
1976                 return true;
1977             }
1978         }
1979         return false;
1980     }
1981
1982     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1983         if ( getCurrentTreePanel() != null ) {
1984             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1985             if ( ( phy != null ) && !phy.isEmpty() ) {
1986                 PhylogenyMethods
1987                         .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1988             }
1989         }
1990     }
1991
1992     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1993         if ( getCurrentTreePanel() != null ) {
1994             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1995             if ( ( phy != null ) && !phy.isEmpty() ) {
1996                 PhylogenyMethods.transferNodeNameToField( phy,
1997                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1998                                                           false );
1999             }
2000         }
2001     }
2002
2003     private void newTree() {
2004         final Phylogeny[] phys = new Phylogeny[ 1 ];
2005         final Phylogeny phy = new Phylogeny();
2006         final PhylogenyNode node = new PhylogenyNode();
2007         phy.setRoot( node );
2008         phy.setRooted( true );
2009         phys[ 0 ] = phy;
2010         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
2011         _mainpanel.getControlPanel().showWhole();
2012         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2013         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2014         if ( getMainPanel().getMainFrame() == null ) {
2015             // Must be "E" applet version.
2016             ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
2017                     .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2018         }
2019         else {
2020             getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
2021         }
2022         activateSaveAllIfNeeded();
2023         System.gc();
2024     }
2025
2026     private void obtainDetailedTaxonomicInformation() {
2027         if ( getCurrentTreePanel() != null ) {
2028             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2029             if ( ( phy != null ) && !phy.isEmpty() ) {
2030                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
2031                                                                        _mainpanel.getCurrentTreePanel(),
2032                                                                        phy.copy(),
2033                                                                        false,
2034                                                                        true );
2035                 new Thread( t ).start();
2036             }
2037         }
2038     }
2039
2040     private void obtainDetailedTaxonomicInformationDelete() {
2041         if ( getCurrentTreePanel() != null ) {
2042             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2043             if ( ( phy != null ) && !phy.isEmpty() ) {
2044                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
2045                                                                        _mainpanel.getCurrentTreePanel(),
2046                                                                        phy.copy(),
2047                                                                        true,
2048                                                                        true );
2049                 new Thread( t ).start();
2050             }
2051         }
2052     }
2053
2054     private void obtainSequenceInformation() {
2055         if ( getCurrentTreePanel() != null ) {
2056             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
2057             if ( ( phy != null ) && !phy.isEmpty() ) {
2058                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
2059                                                                          _mainpanel.getCurrentTreePanel(),
2060                                                                          phy.copy() );
2061                 new Thread( u ).start();
2062             }
2063         }
2064     }
2065
2066     private void print() {
2067         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
2068                 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2069             return;
2070         }
2071         if ( !getOptions().isPrintUsingActualSize() ) {
2072             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
2073                                                             getOptions().getPrintSizeY() - 140,
2074                                                             true );
2075             getCurrentTreePanel().resetPreferredSize();
2076             getCurrentTreePanel().repaint();
2077         }
2078         final String job_name = Constants.PRG_NAME;
2079         boolean error = false;
2080         String printer_name = null;
2081         try {
2082             printer_name = Printer.print( getCurrentTreePanel(), job_name );
2083         }
2084         catch ( final Exception e ) {
2085             error = true;
2086             JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
2087         }
2088         if ( !error && ( printer_name != null ) ) {
2089             String msg = "Printing data sent to printer";
2090             if ( printer_name.length() > 1 ) {
2091                 msg += " [" + printer_name + "]";
2092             }
2093             JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
2094         }
2095         if ( !getOptions().isPrintUsingActualSize() ) {
2096             getControlPanel().showWhole();
2097         }
2098     }
2099
2100     private void printPhylogenyToPdf( final String file_name ) {
2101         if ( !getOptions().isPrintUsingActualSize() ) {
2102             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
2103                                                             getOptions().getPrintSizeY(),
2104                                                             true );
2105             getCurrentTreePanel().resetPreferredSize();
2106             getCurrentTreePanel().repaint();
2107         }
2108         String pdf_written_to = "";
2109         boolean error = false;
2110         try {
2111             if ( getOptions().isPrintUsingActualSize() ) {
2112                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
2113                                                                   getCurrentTreePanel(),
2114                                                                   getCurrentTreePanel().getWidth(),
2115                                                                   getCurrentTreePanel().getHeight() );
2116             }
2117             else {
2118                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
2119                         .getPrintSizeX(), getOptions().getPrintSizeY() );
2120             }
2121         }
2122         catch ( final IOException e ) {
2123             error = true;
2124             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2125         }
2126         if ( !error ) {
2127             if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
2128                 JOptionPane.showMessageDialog( this,
2129                                                "Wrote PDF to: " + pdf_written_to,
2130                                                "Information",
2131                                                JOptionPane.INFORMATION_MESSAGE );
2132             }
2133             else {
2134                 JOptionPane.showMessageDialog( this,
2135                                                "There was an unknown problem when attempting to write to PDF file: \""
2136                                                        + file_name + "\"",
2137                                                "Error",
2138                                                JOptionPane.ERROR_MESSAGE );
2139             }
2140         }
2141         if ( !getOptions().isPrintUsingActualSize() ) {
2142             getControlPanel().showWhole();
2143         }
2144     }
2145
2146     private void readPhylogeniesFromFile() {
2147         boolean exception = false;
2148         Phylogeny[] phys = null;
2149         // Set an initial directory if none set yet
2150         final File my_dir = getCurrentDir();
2151         _open_filechooser.setMultiSelectionEnabled( true );
2152         // Open file-open dialog and set current directory
2153         if ( my_dir != null ) {
2154             _open_filechooser.setCurrentDirectory( my_dir );
2155         }
2156         final int result = _open_filechooser.showOpenDialog( _contentpane );
2157         // All done: get the file
2158         final File[] files = _open_filechooser.getSelectedFiles();
2159         setCurrentDir( _open_filechooser.getCurrentDirectory() );
2160         boolean nhx_or_nexus = false;
2161         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2162             for( final File file : files ) {
2163                 if ( ( file != null ) && !file.isDirectory() ) {
2164                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2165                         _mainpanel.getCurrentTreePanel().setWaitCursor();
2166                     }
2167                     else {
2168                         _mainpanel.setWaitCursor();
2169                     }
2170                     if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
2171                             || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
2172                         try {
2173                             final NHXParser nhx = new NHXParser();
2174                             setSpecialOptionsForNhxParser( nhx );
2175                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
2176                             nhx_or_nexus = true;
2177                         }
2178                         catch ( final Exception e ) {
2179                             exception = true;
2180                             exceptionOccuredDuringOpenFile( e );
2181                         }
2182                     }
2183                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2184                         warnIfNotPhyloXmlValidation( getConfiguration() );
2185                         try {
2186                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
2187                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
2188                         }
2189                         catch ( final Exception e ) {
2190                             exception = true;
2191                             exceptionOccuredDuringOpenFile( e );
2192                         }
2193                     }
2194                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
2195                         try {
2196                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2197                         }
2198                         catch ( final Exception e ) {
2199                             exception = true;
2200                             exceptionOccuredDuringOpenFile( e );
2201                         }
2202                     }
2203                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2204                         try {
2205                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
2206                             setSpecialOptionsForNexParser( nex );
2207                             phys = PhylogenyMethods.readPhylogenies( nex, file );
2208                             nhx_or_nexus = true;
2209                         }
2210                         catch ( final Exception e ) {
2211                             exception = true;
2212                             exceptionOccuredDuringOpenFile( e );
2213                         }
2214                     }
2215                     // "*.*":
2216                     else {
2217                         try {
2218                             final PhylogenyParser parser = ParserUtils
2219                                     .createParserDependingOnFileType( file, getConfiguration()
2220                                             .isValidatePhyloXmlAgainstSchema() );
2221                             if ( parser instanceof NexusPhylogeniesParser ) {
2222                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
2223                                 setSpecialOptionsForNexParser( nex );
2224                                 nhx_or_nexus = true;
2225                             }
2226                             else if ( parser instanceof NHXParser ) {
2227                                 final NHXParser nhx = ( NHXParser ) parser;
2228                                 setSpecialOptionsForNhxParser( nhx );
2229                                 nhx_or_nexus = true;
2230                             }
2231                             else if ( parser instanceof PhyloXmlParser ) {
2232                                 warnIfNotPhyloXmlValidation( getConfiguration() );
2233                             }
2234                             phys = PhylogenyMethods.readPhylogenies( parser, file );
2235                         }
2236                         catch ( final Exception e ) {
2237                             exception = true;
2238                             exceptionOccuredDuringOpenFile( e );
2239                         }
2240                     }
2241                     if ( _mainpanel.getCurrentTreePanel() != null ) {
2242                         _mainpanel.getCurrentTreePanel().setArrowCursor();
2243                     }
2244                     else {
2245                         _mainpanel.setArrowCursor();
2246                     }
2247                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
2248                         boolean one_desc = false;
2249                         if ( nhx_or_nexus ) {
2250                             for( final Phylogeny phy : phys ) {
2251                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2252                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2253                                 }
2254                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
2255                                     one_desc = true;
2256                                     break;
2257                                 }
2258                             }
2259                         }
2260                         AptxUtil.addPhylogeniesToTabs( phys,
2261                                                        file.getName(),
2262                                                        file.getAbsolutePath(),
2263                                                        getConfiguration(),
2264                                                        getMainPanel() );
2265                         _mainpanel.getControlPanel().showWhole();
2266                         if ( nhx_or_nexus && one_desc ) {
2267                             JOptionPane
2268                                     .showMessageDialog( this,
2269                                                         "One or more trees contain (a) node(s) with one descendant, "
2270                                                                 + ForesterUtil.LINE_SEPARATOR
2271                                                                 + "possibly indicating illegal parentheses within node names.",
2272                                                         "Warning: Possible Error in New Hampshire Formatted Data",
2273                                                         JOptionPane.WARNING_MESSAGE );
2274                         }
2275                     }
2276                 }
2277             }
2278         }
2279         activateSaveAllIfNeeded();
2280         System.gc();
2281     }
2282
2283     private void readSpeciesTreeFromFile() {
2284         Phylogeny t = null;
2285         boolean exception = false;
2286         final File my_dir = getCurrentDir();
2287         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2288         if ( my_dir != null ) {
2289             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2290         }
2291         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2292         final File file = _open_filechooser_for_species_tree.getSelectedFile();
2293         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2294             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2295                 try {
2296                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2297                     t = trees[ 0 ];
2298                 }
2299                 catch ( final Exception e ) {
2300                     exception = true;
2301                     exceptionOccuredDuringOpenFile( e );
2302                 }
2303             }
2304             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2305                 try {
2306                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2307                     t = trees[ 0 ];
2308                 }
2309                 catch ( final Exception e ) {
2310                     exception = true;
2311                     exceptionOccuredDuringOpenFile( e );
2312                 }
2313             }
2314             // "*.*":
2315             else {
2316                 try {
2317                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2318                     t = trees[ 0 ];
2319                 }
2320                 catch ( final Exception e ) {
2321                     exception = true;
2322                     exceptionOccuredDuringOpenFile( e );
2323                 }
2324             }
2325             if ( !exception && ( t != null ) && !t.isRooted() ) {
2326                 exception = true;
2327                 t = null;
2328                 JOptionPane.showMessageDialog( this,
2329                                                "Species tree is not rooted",
2330                                                "Species tree not loaded",
2331                                                JOptionPane.ERROR_MESSAGE );
2332             }
2333             if ( !exception && ( t != null ) ) {
2334                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2335                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2336                     final PhylogenyNode node = it.next();
2337                     if ( !node.getNodeData().isHasTaxonomy() ) {
2338                         exception = true;
2339                         t = null;
2340                         JOptionPane
2341                                 .showMessageDialog( this,
2342                                                     "Species tree contains external node(s) without taxonomy information",
2343                                                     "Species tree not loaded",
2344                                                     JOptionPane.ERROR_MESSAGE );
2345                         break;
2346                     }
2347                     else {
2348                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2349                             exception = true;
2350                             t = null;
2351                             JOptionPane.showMessageDialog( this,
2352                                                            "Taxonomy ["
2353                                                                    + node.getNodeData().getTaxonomy().asSimpleText()
2354                                                                    + "] is not unique in species tree",
2355                                                            "Species tree not loaded",
2356                                                            JOptionPane.ERROR_MESSAGE );
2357                             break;
2358                         }
2359                         else {
2360                             tax_set.add( node.getNodeData().getTaxonomy() );
2361                         }
2362                     }
2363                 }
2364             }
2365             if ( !exception && ( t != null ) ) {
2366                 _species_tree = t;
2367                 JOptionPane.showMessageDialog( this,
2368                                                "Species tree successfully loaded",
2369                                                "Species tree loaded",
2370                                                JOptionPane.INFORMATION_MESSAGE );
2371             }
2372             _contentpane.repaint();
2373             System.gc();
2374         }
2375     }
2376
2377     private void setCurrentDir( final File current_dir ) {
2378         _current_dir = current_dir;
2379     }
2380
2381     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2382         _min_not_collapse = min_not_collapse;
2383     }
2384
2385     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2386         _phylogenetic_inference_options = phylogenetic_inference_options;
2387     }
2388
2389     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2390         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2391         nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2392     }
2393
2394     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2395         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2396         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
2397     }
2398
2399     private void writeAllToFile() {
2400         if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2401             return;
2402         }
2403         final File my_dir = getCurrentDir();
2404         if ( my_dir != null ) {
2405             _save_filechooser.setCurrentDirectory( my_dir );
2406         }
2407         _save_filechooser.setSelectedFile( new File( "" ) );
2408         final int result = _save_filechooser.showSaveDialog( _contentpane );
2409         final File file = _save_filechooser.getSelectedFile();
2410         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2411         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2412             if ( file.exists() ) {
2413                 final int i = JOptionPane.showConfirmDialog( this,
2414                                                              file + " already exists. Overwrite?",
2415                                                              "Warning",
2416                                                              JOptionPane.OK_CANCEL_OPTION,
2417                                                              JOptionPane.WARNING_MESSAGE );
2418                 if ( i != JOptionPane.OK_OPTION ) {
2419                     return;
2420                 }
2421                 else {
2422                     try {
2423                         file.delete();
2424                     }
2425                     catch ( final Exception e ) {
2426                         JOptionPane.showMessageDialog( this,
2427                                                        "Failed to delete: " + file,
2428                                                        "Error",
2429                                                        JOptionPane.WARNING_MESSAGE );
2430                     }
2431                 }
2432             }
2433             final int count = getMainPanel().getTabbedPane().getTabCount();
2434             final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2435             for( int i = 0; i < count; ++i ) {
2436                 trees.add( getMainPanel().getPhylogeny( i ) );
2437                 getMainPanel().getTreePanels().get( i ).setEdited( false );
2438             }
2439             final PhylogenyWriter writer = new PhylogenyWriter();
2440             try {
2441                 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2442             }
2443             catch ( final IOException e ) {
2444                 JOptionPane.showMessageDialog( this,
2445                                                "Failed to write to: " + file,
2446                                                "Error",
2447                                                JOptionPane.WARNING_MESSAGE );
2448             }
2449         }
2450     }
2451
2452     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2453         try {
2454             final PhylogenyWriter writer = new PhylogenyWriter();
2455             writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2456         }
2457         catch ( final Exception e ) {
2458             exception = true;
2459             exceptionOccuredDuringSaveAs( e );
2460         }
2461         return exception;
2462     }
2463
2464     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2465         try {
2466             final PhylogenyWriter writer = new PhylogenyWriter();
2467             writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2468         }
2469         catch ( final Exception e ) {
2470             exception = true;
2471             exceptionOccuredDuringSaveAs( e );
2472         }
2473         return exception;
2474     }
2475
2476     private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2477         try {
2478             final PhylogenyWriter writer = new PhylogenyWriter();
2479             writer.toPhyloXML( file, t, 0 );
2480         }
2481         catch ( final Exception e ) {
2482             exception = true;
2483             exceptionOccuredDuringSaveAs( e );
2484         }
2485         return exception;
2486     }
2487
2488     private void writeToFile( final Phylogeny t ) {
2489         if ( t == null ) {
2490             return;
2491         }
2492         String initial_filename = null;
2493         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2494             try {
2495                 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2496             }
2497             catch ( final IOException e ) {
2498                 initial_filename = null;
2499             }
2500         }
2501         if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2502             _save_filechooser.setSelectedFile( new File( initial_filename ) );
2503         }
2504         else {
2505             _save_filechooser.setSelectedFile( new File( "" ) );
2506         }
2507         final File my_dir = getCurrentDir();
2508         if ( my_dir != null ) {
2509             _save_filechooser.setCurrentDirectory( my_dir );
2510         }
2511         final int result = _save_filechooser.showSaveDialog( _contentpane );
2512         final File file = _save_filechooser.getSelectedFile();
2513         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2514         boolean exception = false;
2515         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2516             if ( file.exists() ) {
2517                 final int i = JOptionPane.showConfirmDialog( this,
2518                                                              file + " already exists.\nOverwrite?",
2519                                                              "Overwrite?",
2520                                                              JOptionPane.OK_CANCEL_OPTION,
2521                                                              JOptionPane.QUESTION_MESSAGE );
2522                 if ( i != JOptionPane.OK_OPTION ) {
2523                     return;
2524                 }
2525                 else {
2526                     final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2527                     try {
2528                         ForesterUtil.copyFile( file, to );
2529                     }
2530                     catch ( final Exception e ) {
2531                         JOptionPane.showMessageDialog( this,
2532                                                        "Failed to create backup copy " + to,
2533                                                        "Failed to Create Backup Copy",
2534                                                        JOptionPane.WARNING_MESSAGE );
2535                     }
2536                     try {
2537                         file.delete();
2538                     }
2539                     catch ( final Exception e ) {
2540                         JOptionPane.showMessageDialog( this,
2541                                                        "Failed to delete: " + file,
2542                                                        "Failed to Delete",
2543                                                        JOptionPane.WARNING_MESSAGE );
2544                     }
2545                 }
2546             }
2547             if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2548                 exception = writeAsNewHampshire( t, exception, file );
2549             }
2550             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2551                 exception = writeAsPhyloXml( t, exception, file );
2552             }
2553             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2554                 exception = writeAsNexus( t, exception, file );
2555             }
2556             // "*.*":
2557             else {
2558                 final String file_name = file.getName().trim().toLowerCase();
2559                 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2560                         || file_name.endsWith( ".tree" ) ) {
2561                     exception = writeAsNewHampshire( t, exception, file );
2562                 }
2563                 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2564                     exception = writeAsNexus( t, exception, file );
2565                 }
2566                 // XML is default:
2567                 else {
2568                     exception = writeAsPhyloXml( t, exception, file );
2569                 }
2570             }
2571             if ( !exception ) {
2572                 getMainPanel().setTitleOfSelectedTab( file.getName() );
2573                 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2574                 getMainPanel().getCurrentTreePanel().setEdited( false );
2575             }
2576         }
2577     }
2578
2579     private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2580         if ( ( t == null ) || t.isEmpty() ) {
2581             return;
2582         }
2583         String initial_filename = "";
2584         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2585             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2586         }
2587         if ( initial_filename.indexOf( '.' ) > 0 ) {
2588             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2589         }
2590         initial_filename = initial_filename + "." + type;
2591         _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2592         final File my_dir = getCurrentDir();
2593         if ( my_dir != null ) {
2594             _writetographics_filechooser.setCurrentDirectory( my_dir );
2595         }
2596         final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2597         File file = _writetographics_filechooser.getSelectedFile();
2598         setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2599         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2600             if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2601                 file = new File( file.toString() + "." + type );
2602             }
2603             if ( file.exists() ) {
2604                 final int i = JOptionPane.showConfirmDialog( this,
2605                                                              file + " already exists. Overwrite?",
2606                                                              "Warning",
2607                                                              JOptionPane.OK_CANCEL_OPTION,
2608                                                              JOptionPane.WARNING_MESSAGE );
2609                 if ( i != JOptionPane.OK_OPTION ) {
2610                     return;
2611                 }
2612                 else {
2613                     try {
2614                         file.delete();
2615                     }
2616                     catch ( final Exception e ) {
2617                         JOptionPane.showMessageDialog( this,
2618                                                        "Failed to delete: " + file,
2619                                                        "Error",
2620                                                        JOptionPane.WARNING_MESSAGE );
2621                     }
2622                 }
2623             }
2624             writePhylogenyToGraphicsFile( file.toString(), type );
2625         }
2626     }
2627
2628     private void writeToPdf( final Phylogeny t ) {
2629         if ( ( t == null ) || t.isEmpty() ) {
2630             return;
2631         }
2632         String initial_filename = "";
2633         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2634             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2635         }
2636         if ( initial_filename.indexOf( '.' ) > 0 ) {
2637             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2638         }
2639         initial_filename = initial_filename + ".pdf";
2640         _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2641         final File my_dir = getCurrentDir();
2642         if ( my_dir != null ) {
2643             _writetopdf_filechooser.setCurrentDirectory( my_dir );
2644         }
2645         final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2646         File file = _writetopdf_filechooser.getSelectedFile();
2647         setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2648         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2649             if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2650                 file = new File( file.toString() + ".pdf" );
2651             }
2652             if ( file.exists() ) {
2653                 final int i = JOptionPane.showConfirmDialog( this,
2654                                                              file + " already exists. Overwrite?",
2655                                                              "WARNING",
2656                                                              JOptionPane.OK_CANCEL_OPTION,
2657                                                              JOptionPane.WARNING_MESSAGE );
2658                 if ( i != JOptionPane.OK_OPTION ) {
2659                     return;
2660                 }
2661             }
2662             printPhylogenyToPdf( file.toString() );
2663         }
2664     }
2665
2666     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2667         return new MainFrameApplication( phys, config );
2668     }
2669
2670     public static MainFrame createInstance( final Phylogeny[] phys,
2671                                             final Configuration config,
2672                                             final String title,
2673                                             final File current_dir ) {
2674         return new MainFrameApplication( phys, config, title, current_dir );
2675     }
2676
2677     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2678         return new MainFrameApplication( phys, config, title );
2679     }
2680
2681     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2682         return new MainFrameApplication( phys, config_file_name, title );
2683     }
2684
2685     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2686         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2687                 + o.getPrintSizeY() + ")" );
2688     }
2689
2690     static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2691         mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2692     }
2693
2694     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2695         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2696             JOptionPane
2697                     .showMessageDialog( null,
2698                                         ForesterUtil
2699                                                 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2700                                                            80 ),
2701                                         "Warning",
2702                                         JOptionPane.WARNING_MESSAGE );
2703         }
2704     }
2705 } // MainFrameApplication.
2706
2707 class DefaultFilter extends FileFilter {
2708
2709     @Override
2710     public boolean accept( final File f ) {
2711         final String file_name = f.getName().trim().toLowerCase();
2712         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2713                 || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )
2714                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
2715                 || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
2716                 || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
2717                 || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
2718                 || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
2719                 || file_name.endsWith( ".con" ) || f.isDirectory();
2720     }
2721
2722     @Override
2723     public String getDescription() {
2724         return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";
2725     }
2726 }
2727
2728 class GraphicsFileFilter extends FileFilter {
2729
2730     @Override
2731     public boolean accept( final File f ) {
2732         final String file_name = f.getName().trim().toLowerCase();
2733         return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
2734                 || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
2735     }
2736
2737     @Override
2738     public String getDescription() {
2739         return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
2740     }
2741 }
2742
2743 class MsaFileFilter extends FileFilter {
2744
2745     @Override
2746     public boolean accept( final File f ) {
2747         final String file_name = f.getName().trim().toLowerCase();
2748         return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )
2749                 || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();
2750     }
2751
2752     @Override
2753     public String getDescription() {
2754         return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";
2755     }
2756 }
2757
2758 class NexusFilter extends FileFilter {
2759
2760     @Override
2761     public boolean accept( final File f ) {
2762         final String file_name = f.getName().trim().toLowerCase();
2763         return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2764                 || file_name.endsWith( ".tre" ) || f.isDirectory();
2765     }
2766
2767     @Override
2768     public String getDescription() {
2769         return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2770     }
2771 } // NexusFilter
2772
2773 class NHFilter extends FileFilter {
2774
2775     @Override
2776     public boolean accept( final File f ) {
2777         final String file_name = f.getName().trim().toLowerCase();
2778         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2779                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2780                 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2781                 || f.isDirectory();
2782     }
2783
2784     @Override
2785     public String getDescription() {
2786         return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2787     }
2788 } // NHFilter
2789
2790 class NHXFilter extends FileFilter {
2791
2792     @Override
2793     public boolean accept( final File f ) {
2794         final String file_name = f.getName().trim().toLowerCase();
2795         return file_name.endsWith( ".nhx" ) || f.isDirectory();
2796     }
2797
2798     @Override
2799     public String getDescription() {
2800         return "NHX files (*.nhx)";
2801     }
2802 }
2803
2804 class PdfFilter extends FileFilter {
2805
2806     @Override
2807     public boolean accept( final File f ) {
2808         return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2809     }
2810
2811     @Override
2812     public String getDescription() {
2813         return "PDF files (*.pdf)";
2814     }
2815 } // PdfFilter
2816
2817 class SequencesFileFilter extends FileFilter {
2818
2819     @Override
2820     public boolean accept( final File f ) {
2821         final String file_name = f.getName().trim().toLowerCase();
2822         return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )
2823                 || file_name.endsWith( ".seqs" ) || f.isDirectory();
2824     }
2825
2826     @Override
2827     public String getDescription() {
2828         return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";
2829     }
2830 }
2831
2832 class TolFilter extends FileFilter {
2833
2834     @Override
2835     public boolean accept( final File f ) {
2836         final String file_name = f.getName().trim().toLowerCase();
2837         return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2838                 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2839     }
2840
2841     @Override
2842     public String getDescription() {
2843         return "Tree of Life files (*.tol, *.tolxml)";
2844     }
2845 } // TolFilter
2846
2847 class XMLFilter extends FileFilter {
2848
2849     @Override
2850     public boolean accept( final File f ) {
2851         final String file_name = f.getName().trim().toLowerCase();
2852         return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2853                 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2854     }
2855
2856     @Override
2857     public String getDescription() {
2858         return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
2859     }
2860 } // XMLFilter