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

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