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.PhylogenyNodeI.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_uniprot_seq_information_jmi ) {
 559                 obtainUniProtSequenceInformation();
 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( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
 946         customizeJMenuItem( _infer_common_sn_names_item );
 947         _tools_menu.addSeparator();
 948         _tools_menu
 949                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
 950         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
 951         _obtain_detailed_taxonomic_information_jmi
 952                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
 953         _tools_menu
 954                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
 955         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
 956         _obtain_detailed_taxonomic_information_deleting_jmi
 957                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
 958         _tools_menu.add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
 959         customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
 960         _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
 961         _tools_menu.addSeparator();
 962         if ( !Constants.__RELEASE ) {
 963             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
 964             customizeJMenuItem( _function_analysis );
 965             _function_analysis
 966                     .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
 967             _tools_menu.addSeparator();
 968         }
 969         _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
 970         customizeJMenuItem( _read_values_jmi );
 971         _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
 972         _jmenubar.add( _tools_menu );
 973     }
 974
 975     private void choosePdfWidth() {
 976         final String s = ( String ) JOptionPane.showInputDialog( this,
 977                                                                  "Please enter the default line width for PDF export.\n"
 978                                                                          + "[current value: "
 979                                                                          + getOptions().getPrintLineWidth() + "]\n",
 980                                                                  "Line Width for PDF Export",
 981                                                                  JOptionPane.QUESTION_MESSAGE,
 982                                                                  null,
 983                                                                  null,
 984                                                                  getOptions().getPrintLineWidth() );
 985         if ( !ForesterUtil.isEmpty( s ) ) {
 986             boolean success = true;
 987             float f = 0.0f;
 988             final String m_str = s.trim();
 989             if ( !ForesterUtil.isEmpty( m_str ) ) {
 990                 try {
 991                     f = Float.parseFloat( m_str );
 992                 }
 993                 catch ( final Exception ex ) {
 994                     success = false;
 995                 }
 996             }
 997             else {
 998                 success = false;
 999             }
1000             if ( success && ( f > 0.0 ) ) {
1001                 getOptions().setPrintLineWidth( f );
1002             }
1003         }
1004     }
1005
1006     private void choosePrintSize() {
1007         final String s = ( String ) JOptionPane.showInputDialog( this,
1008                                                                  "Please enter values for width and height,\nseparated by a comma.\n"
1009                                                                          + "[current values: "
1010                                                                          + getOptions().getPrintSizeX() + ", "
1011                                                                          + getOptions().getPrintSizeY() + "]\n"
1012                                                                          + "[A4: " + Constants.A4_SIZE_X + ", "
1013                                                                          + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
1014                                                                          + Constants.US_LETTER_SIZE_X + ", "
1015                                                                          + Constants.US_LETTER_SIZE_Y + "]",
1016                                                                  "Default Size for Graphics Export",
1017                                                                  JOptionPane.QUESTION_MESSAGE,
1018                                                                  null,
1019                                                                  null,
1020                                                                  getOptions().getPrintSizeX() + ", "
1021                                                                          + getOptions().getPrintSizeY() );
1022         if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
1023             boolean success = true;
1024             int x = 0;
1025             int y = 0;
1026             final String[] str_ary = s.split( "," );
1027             if ( str_ary.length == 2 ) {
1028                 final String x_str = str_ary[ 0 ].trim();
1029                 final String y_str = str_ary[ 1 ].trim();
1030                 if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
1031                     try {
1032                         x = Integer.parseInt( x_str );
1033                         y = Integer.parseInt( y_str );
1034                     }
1035                     catch ( final Exception ex ) {
1036                         success = false;
1037                     }
1038                 }
1039                 else {
1040                     success = false;
1041                 }
1042             }
1043             else {
1044                 success = false;
1045             }
1046             if ( success && ( x > 1 ) && ( y > 1 ) ) {
1047                 getOptions().setPrintSizeX( x );
1048                 getOptions().setPrintSizeY( y );
1049             }
1050         }
1051     }
1052
1053     @Override
1054     void close() {
1055         if ( isUnsavedDataPresent() ) {
1056             final int r = JOptionPane.showConfirmDialog( this,
1057                                                          "Exit despite potentially unsaved changes?",
1058                                                          "Exit?",
1059                                                          JOptionPane.YES_NO_OPTION );
1060             if ( r != JOptionPane.YES_OPTION ) {
1061                 return;
1062             }
1063         }
1064         exit();
1065     }
1066
1067     private void closeCurrentPane() {
1068         if ( getMainPanel().getCurrentTreePanel() != null ) {
1069             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
1070                 final int r = JOptionPane.showConfirmDialog( this,
1071                                                              "Close tab despite potentially unsaved changes?",
1072                                                              "Close Tab?",
1073                                                              JOptionPane.YES_NO_OPTION );
1074                 if ( r != JOptionPane.YES_OPTION ) {
1075                     return;
1076                 }
1077             }
1078             getMainPanel().closeCurrentPane();
1079             activateSaveAllIfNeeded();
1080         }
1081     }
1082
1083     private void collapse( final Phylogeny phy, final double m ) {
1084         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1085         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1086         double min_support = Double.MAX_VALUE;
1087         boolean conf_present = false;
1088         while ( it.hasNext() ) {
1089             final PhylogenyNode n = it.next();
1090             if ( !n.isExternal() && !n.isRoot() ) {
1091                 final List<Confidence> c = n.getBranchData().getConfidences();
1092                 if ( ( c != null ) && ( c.size() > 0 ) ) {
1093                     conf_present = true;
1094                     double max = 0;
1095                     for( final Confidence confidence : c ) {
1096                         if ( confidence.getValue() > max ) {
1097                             max = confidence.getValue();
1098                         }
1099                     }
1100                     if ( max < getMinNotCollapseConfidenceValue() ) {
1101                         to_be_removed.add( n );
1102                     }
1103                     if ( max < min_support ) {
1104                         min_support = max;
1105                     }
1106                 }
1107             }
1108         }
1109         if ( conf_present ) {
1110             for( final PhylogenyNode node : to_be_removed ) {
1111                 PhylogenyMethods.removeNode( node, phy );
1112             }
1113             if ( to_be_removed.size() > 0 ) {
1114                 phy.externalNodesHaveChanged();
1115                 phy.clearHashIdToNodeMap();
1116                 phy.recalculateNumberOfExternalDescendants( true );
1117                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1118                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1119                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1120                 getCurrentTreePanel().setNodeInPreorderToNull();
1121                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1122                 getCurrentTreePanel().resetPreferredSize();
1123                 getCurrentTreePanel().setEdited( true );
1124                 getCurrentTreePanel().repaint();
1125                 repaint();
1126             }
1127             if ( to_be_removed.size() > 0 ) {
1128                 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
1129                         + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
1130                         + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
1131             }
1132             else {
1133                 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
1134                         + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
1135             }
1136         }
1137         else {
1138             JOptionPane.showMessageDialog( this,
1139                                            "No branch collapsed because no confidence values present",
1140                                            "No confidence values present",
1141                                            JOptionPane.INFORMATION_MESSAGE );
1142         }
1143     }
1144
1145     private void collapseBelowThreshold() {
1146         if ( getCurrentTreePanel() != null ) {
1147             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1148             if ( ( phy != null ) && !phy.isEmpty() ) {
1149                 final String s = ( String ) JOptionPane.showInputDialog( this,
1150                                                                          "Please enter the minimum confidence value\n",
1151                                                                          "Minimal Confidence Value",
1152                                                                          JOptionPane.QUESTION_MESSAGE,
1153                                                                          null,
1154                                                                          null,
1155                                                                          getMinNotCollapseConfidenceValue() );
1156                 if ( !ForesterUtil.isEmpty( s ) ) {
1157                     boolean success = true;
1158                     double m = 0.0;
1159                     final String m_str = s.trim();
1160                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1161                         try {
1162                             m = Double.parseDouble( m_str );
1163                         }
1164                         catch ( final Exception ex ) {
1165                             success = false;
1166                         }
1167                     }
1168                     else {
1169                         success = false;
1170                     }
1171                     if ( success && ( m >= 0.0 ) ) {
1172                         setMinNotCollapseConfidenceValue( m );
1173                         collapse( phy, m );
1174                     }
1175                 }
1176             }
1177         }
1178     }
1179
1180     private PhyloXmlParser createPhyloXmlParser() {
1181         PhyloXmlParser xml_parser = null;
1182         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1183             try {
1184                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1185             }
1186             catch ( final Exception e ) {
1187                 JOptionPane.showMessageDialog( this,
1188                                                e.getLocalizedMessage(),
1189                                                "failed to create validating XML parser",
1190                                                JOptionPane.WARNING_MESSAGE );
1191             }
1192         }
1193         if ( xml_parser == null ) {
1194             xml_parser = new PhyloXmlParser();
1195         }
1196         return xml_parser;
1197     }
1198
1199     void executeGSDI() {
1200         if ( !isOKforSDI( false, true ) ) {
1201             return;
1202         }
1203         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1204             JOptionPane.showMessageDialog( this,
1205                                            "Gene tree is not rooted.",
1206                                            "Cannot execute GSDI",
1207                                            JOptionPane.ERROR_MESSAGE );
1208             return;
1209         }
1210         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1211         gene_tree.setAllNodesToNotCollapse();
1212         gene_tree.recalculateNumberOfExternalDescendants( false );
1213         GSDI gsdi = null;
1214         try {
1215             gsdi = new GSDI( gene_tree, _species_tree.copy(), false, true, true );
1216         }
1217         catch ( final Exception e ) {
1218             JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
1219         }
1220         gene_tree.setRerootable( false );
1221         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1222         _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
1223         _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
1224         _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1225         _mainpanel.getCurrentTreePanel().setEdited( true );
1226         getControlPanel().setShowEvents( true );
1227         showWhole();
1228         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1229         _mainpanel.addPhylogenyInNewTab( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null );
1230         showWhole();
1231         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1232         showWhole();
1233         _mainpanel.getCurrentTreePanel().setEdited( true );
1234         JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1235                 + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
1236                 + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
1237     }
1238
1239     void executeFunctionAnalysis() {
1240         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1241             return;
1242         }
1243         final GoAnnotation a = new GoAnnotation( this,
1244                                                  _mainpanel.getCurrentTreePanel(),
1245                                                  _mainpanel.getCurrentPhylogeny() );
1246         new Thread( a ).start();
1247     }
1248
1249     void executeLineageInference() {
1250         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1251             return;
1252         }
1253         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
1254             JOptionPane.showMessageDialog( this,
1255                                            "Phylogeny is not rooted.",
1256                                            "Cannot infer ancestral taxonomies",
1257                                            JOptionPane.ERROR_MESSAGE );
1258             return;
1259         }
1260         final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
1261                                                                                   _mainpanel.getCurrentTreePanel(),
1262                                                                                   _mainpanel.getCurrentPhylogeny()
1263                                                                                           .copy() );
1264         new Thread( inferrer ).start();
1265     }
1266
1267     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1268         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1269                                                                       getPhylogeneticInferenceOptions(),
1270                                                                       from_unaligned_seqs );
1271         dialog.activate();
1272         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1273             if ( !from_unaligned_seqs ) {
1274                 if ( getMsa() != null ) {
1275                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1276                                                                                     getPhylogeneticInferenceOptions()
1277                                                                                             .copy(), this );
1278                     new Thread( inferrer ).start();
1279                 }
1280                 else {
1281                     JOptionPane.showMessageDialog( this,
1282                                                    "No multiple sequence alignment selected",
1283                                                    "Phylogenetic Inference Not Launched",
1284                                                    JOptionPane.WARNING_MESSAGE );
1285                 }
1286             }
1287             else {
1288                 if ( getSeqs() != null ) {
1289                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1290                                                                                     getPhylogeneticInferenceOptions()
1291                                                                                             .copy(), this );
1292                     new Thread( inferrer ).start();
1293                 }
1294                 else {
1295                     JOptionPane.showMessageDialog( this,
1296                                                    "No input sequences selected",
1297                                                    "Phylogenetic Inference Not Launched",
1298                                                    JOptionPane.WARNING_MESSAGE );
1299                 }
1300             }
1301         }
1302     }
1303
1304     void executeSDIR( final boolean minimize_cost ) {
1305         if ( !isOKforSDI( true, true ) ) {
1306             return;
1307         }
1308         Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1309         final SDIR sdiunrooted = new SDIR();
1310         gene_tree.setAllNodesToNotCollapse();
1311         gene_tree.recalculateNumberOfExternalDescendants( false );
1312         try {
1313             gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
1314                                            !minimize_cost, // minimize sum of dups
1315                                            true, // minimize height
1316                                            true, // return tree(s)
1317                                            1 )[ 0 ]; // # of trees to return
1318         }
1319         catch ( final Exception e ) {
1320             JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
1321             return;
1322         }
1323         final int duplications = sdiunrooted.getMinimalDuplications();
1324         gene_tree.setRerootable( false );
1325         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
1326         getControlPanel().setShowEvents( true );
1327         showWhole();
1328         _mainpanel.getCurrentTreePanel().setEdited( true );
1329         JOptionPane.showMessageDialog( this,
1330                                        "Number of duplications: " + duplications,
1331                                        "SDIR successfully completed",
1332                                        JOptionPane.INFORMATION_MESSAGE );
1333     }
1334
1335     void exit() {
1336         removeAllTextFrames();
1337         _mainpanel.terminate();
1338         _contentpane.removeAll();
1339         setVisible( false );
1340         dispose();
1341         System.exit( 0 );
1342     }
1343
1344     public void end() {
1345         _mainpanel.terminate();
1346         _contentpane.removeAll();
1347         setVisible( false );
1348         dispose();
1349     }
1350
1351     private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
1352         if ( getCurrentTreePanel() != null ) {
1353             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1354             if ( ( phy != null ) && !phy.isEmpty() ) {
1355                 final PhylogenyNodeIterator it = phy.iteratorPostorder();
1356                 while ( it.hasNext() ) {
1357                     final PhylogenyNode n = it.next();
1358                     final String name = n.getName().trim();
1359                     if ( !ForesterUtil.isEmpty( name ) ) {
1360                         final String code = ParserUtils
1361                                 .extractTaxonomyCodeFromNodeName( name, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
1362                         if ( !ForesterUtil.isEmpty( code ) ) {
1363                             PhylogenyMethods.setTaxonomyCode( n, code );
1364                         }
1365                     }
1366                 }
1367             }
1368         }
1369     }
1370
1371     private ControlPanel getControlPanel() {
1372         return getMainPanel().getControlPanel();
1373     }
1374
1375     private File getCurrentDir() {
1376         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1377             if ( ForesterUtil.isWindowns() ) {
1378                 try {
1379                     _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
1380                 }
1381                 catch ( final Exception e ) {
1382                     _current_dir = null;
1383                 }
1384             }
1385         }
1386         if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
1387             if ( System.getProperty( "user.home" ) != null ) {
1388                 _current_dir = new File( System.getProperty( "user.home" ) );
1389             }
1390             else if ( System.getProperty( "user.dir" ) != null ) {
1391                 _current_dir = new File( System.getProperty( "user.dir" ) );
1392             }
1393         }
1394         return _current_dir;
1395     }
1396
1397     @Override
1398     public MainPanel getMainPanel() {
1399         return _mainpanel;
1400     }
1401
1402     private double getMinNotCollapseConfidenceValue() {
1403         return _min_not_collapse;
1404     }
1405
1406     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1407         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1408             return false;
1409         }
1410         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1411             JOptionPane.showMessageDialog( this,
1412                                            "No species tree loaded",
1413                                            "Cannot execute SDI",
1414                                            JOptionPane.ERROR_MESSAGE );
1415             return false;
1416         }
1417         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1418             JOptionPane.showMessageDialog( this,
1419                                            "Species tree is not completely binary",
1420                                            "Cannot execute SDI",
1421                                            JOptionPane.ERROR_MESSAGE );
1422             return false;
1423         }
1424         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1425             JOptionPane.showMessageDialog( this,
1426                                            "Gene tree is not completely binary",
1427                                            "Cannot execute SDI",
1428                                            JOptionPane.ERROR_MESSAGE );
1429             return false;
1430         }
1431         else {
1432             return true;
1433         }
1434     }
1435
1436     private boolean isUnsavedDataPresent() {
1437         final List<TreePanel> tps = getMainPanel().getTreePanels();
1438         for( final TreePanel tp : tps ) {
1439             if ( tp.isEdited() ) {
1440                 return true;
1441             }
1442         }
1443         return false;
1444     }
1445
1446     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1447         if ( getCurrentTreePanel() != null ) {
1448             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1449             if ( ( phy != null ) && !phy.isEmpty() ) {
1450                 PhylogenyMethods
1451                         .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
1452             }
1453         }
1454     }
1455
1456     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1457         if ( getCurrentTreePanel() != null ) {
1458             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1459             if ( ( phy != null ) && !phy.isEmpty() ) {
1460                 PhylogenyMethods.transferNodeNameToField( phy,
1461                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1462                                                           false );
1463             }
1464         }
1465     }
1466
1467     private void newTree() {
1468         final Phylogeny[] phys = new Phylogeny[ 1 ];
1469         final Phylogeny phy = new Phylogeny();
1470         final PhylogenyNode node = new PhylogenyNode();
1471         phy.setRoot( node );
1472         phy.setRooted( true );
1473         phys[ 0 ] = phy;
1474         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1475         _mainpanel.getControlPanel().showWhole();
1476         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1477         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1478         if ( getMainPanel().getMainFrame() == null ) {
1479             // Must be "E" applet version.
1480             ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1481                     .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1482         }
1483         else {
1484             getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1485         }
1486         activateSaveAllIfNeeded();
1487         System.gc();
1488     }
1489
1490     private void obtainDetailedTaxonomicInformation() {
1491         if ( getCurrentTreePanel() != null ) {
1492             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1493             if ( ( phy != null ) && !phy.isEmpty() ) {
1494                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1495                                                                        _mainpanel.getCurrentTreePanel(),
1496                                                                        phy.copy(),
1497                                                                        false,
1498                                                                        true );
1499                 new Thread( t ).start();
1500             }
1501         }
1502     }
1503
1504     private void obtainDetailedTaxonomicInformationDelete() {
1505         if ( getCurrentTreePanel() != null ) {
1506             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1507             if ( ( phy != null ) && !phy.isEmpty() ) {
1508                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1509                                                                        _mainpanel.getCurrentTreePanel(),
1510                                                                        phy.copy(),
1511                                                                        true,
1512                                                                        true );
1513                 new Thread( t ).start();
1514             }
1515         }
1516     }
1517
1518     private void obtainUniProtSequenceInformation() {
1519         if ( getCurrentTreePanel() != null ) {
1520             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1521             if ( ( phy != null ) && !phy.isEmpty() ) {
1522                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1523                                                                          _mainpanel.getCurrentTreePanel(),
1524                                                                          phy.copy() );
1525                 new Thread( u ).start();
1526             }
1527         }
1528     }
1529
1530     private void print() {
1531         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
1532                 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
1533             return;
1534         }
1535         if ( !getOptions().isPrintUsingActualSize() ) {
1536             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
1537                                                             getOptions().getPrintSizeY() - 140,
1538                                                             true );
1539             getCurrentTreePanel().resetPreferredSize();
1540             getCurrentTreePanel().repaint();
1541         }
1542         final String job_name = Constants.PRG_NAME;
1543         boolean error = false;
1544         String printer_name = null;
1545         try {
1546             printer_name = Printer.print( getCurrentTreePanel(), job_name );
1547         }
1548         catch ( final Exception e ) {
1549             error = true;
1550             JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
1551         }
1552         if ( !error && ( printer_name != null ) ) {
1553             String msg = "Printing data sent to printer";
1554             if ( printer_name.length() > 1 ) {
1555                 msg += " [" + printer_name + "]";
1556             }
1557             JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
1558         }
1559         if ( !getOptions().isPrintUsingActualSize() ) {
1560             getControlPanel().showWhole();
1561         }
1562     }
1563
1564     private void printPhylogenyToPdf( final String file_name ) {
1565         if ( !getOptions().isPrintUsingActualSize() ) {
1566             getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
1567                                                             getOptions().getPrintSizeY(),
1568                                                             true );
1569             getCurrentTreePanel().resetPreferredSize();
1570             getCurrentTreePanel().repaint();
1571         }
1572         String pdf_written_to = "";
1573         boolean error = false;
1574         try {
1575             if ( getOptions().isPrintUsingActualSize() ) {
1576                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
1577                                                                   getCurrentTreePanel(),
1578                                                                   getCurrentTreePanel().getWidth(),
1579                                                                   getCurrentTreePanel().getHeight() );
1580             }
1581             else {
1582                 pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
1583                         .getPrintSizeX(), getOptions().getPrintSizeY() );
1584             }
1585         }
1586         catch ( final IOException e ) {
1587             error = true;
1588             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
1589         }
1590         if ( !error ) {
1591             if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
1592                 JOptionPane.showMessageDialog( this,
1593                                                "Wrote PDF to: " + pdf_written_to,
1594                                                "Information",
1595                                                JOptionPane.INFORMATION_MESSAGE );
1596             }
1597             else {
1598                 JOptionPane.showMessageDialog( this,
1599                                                "There was an unknown problem when attempting to write to PDF file: \""
1600                                                        + file_name + "\"",
1601                                                "Error",
1602                                                JOptionPane.ERROR_MESSAGE );
1603             }
1604         }
1605         if ( !getOptions().isPrintUsingActualSize() ) {
1606             getControlPanel().showWhole();
1607         }
1608     }
1609
1610     private void addExpressionValuesFromFile() {
1611         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
1612             JOptionPane.showMessageDialog( this,
1613                                            "Need to load evolutionary tree first",
1614                                            "Can Not Read Expression Values",
1615                                            JOptionPane.WARNING_MESSAGE );
1616             return;
1617         }
1618         final File my_dir = getCurrentDir();
1619         if ( my_dir != null ) {
1620             _values_filechooser.setCurrentDirectory( my_dir );
1621         }
1622         final int result = _values_filechooser.showOpenDialog( _contentpane );
1623         final File file = _values_filechooser.getSelectedFile();
1624         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1625             BasicTable<String> t = null;
1626             try {
1627                 t = BasicTableParser.parse( file, "\t" );
1628                 if ( t.getNumberOfColumns() < 2 ) {
1629                     t = BasicTableParser.parse( file, "," );
1630                 }
1631                 if ( t.getNumberOfColumns() < 2 ) {
1632                     t = BasicTableParser.parse( file, " " );
1633                 }
1634             }
1635             catch ( final IOException e ) {
1636                 JOptionPane.showMessageDialog( this,
1637                                                e.getMessage(),
1638                                                "Could Not Read Expression Value Table",
1639                                                JOptionPane.ERROR_MESSAGE );
1640                 return;
1641             }
1642             if ( t.getNumberOfColumns() < 2 ) {
1643                 JOptionPane.showMessageDialog( this,
1644                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
1645                                                "Problem with Expression Value Table",
1646                                                JOptionPane.ERROR_MESSAGE );
1647                 return;
1648             }
1649             if ( t.getNumberOfRows() < 1 ) {
1650                 JOptionPane.showMessageDialog( this,
1651                                                "Table contains zero rows",
1652                                                "Problem with Expression Value Table",
1653                                                JOptionPane.ERROR_MESSAGE );
1654                 return;
1655             }
1656             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1657             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
1658                 JOptionPane.showMessageDialog( this,
1659                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
1660                                                        + phy.getNumberOfExternalNodes() + " external nodes",
1661                                                "Warning",
1662                                                JOptionPane.WARNING_MESSAGE );
1663             }
1664             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1665             int not_found = 0;
1666             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
1667                 final PhylogenyNode node = iter.next();
1668                 final String node_name = node.getName();
1669                 if ( !ForesterUtil.isEmpty( node_name ) ) {
1670                     int row = -1;
1671                     try {
1672                         row = t.findRow( node_name );
1673                     }
1674                     catch ( final IllegalArgumentException e ) {
1675                         JOptionPane
1676                                 .showMessageDialog( this,
1677                                                     e.getMessage(),
1678                                                     "Error Mapping Node Identifiers to Expression Value Identifiers",
1679                                                     JOptionPane.ERROR_MESSAGE );
1680                         return;
1681                     }
1682                     if ( row < 0 ) {
1683                         if ( node.isExternal() ) {
1684                             not_found++;
1685                         }
1686                         continue;
1687                     }
1688                     final List<Double> l = new ArrayList<Double>();
1689                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
1690                         double d = -100;
1691                         try {
1692                             d = Double.parseDouble( t.getValueAsString( col, row ) );
1693                         }
1694                         catch ( final NumberFormatException e ) {
1695                             JOptionPane.showMessageDialog( this,
1696                                                            "Could not parse \"" + t.getValueAsString( col, row )
1697                                                                    + "\" into a decimal value",
1698                                                            "Issue with Expression Value Table",
1699                                                            JOptionPane.ERROR_MESSAGE );
1700                             return;
1701                         }
1702                         stats.addValue( d );
1703                         l.add( d );
1704                     }
1705                     if ( !l.isEmpty() ) {
1706                         if ( node.getNodeData().getProperties() != null ) {
1707                             node.getNodeData().getProperties()
1708                                     .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
1709                         }
1710                         node.getNodeData().setVector( l );
1711                     }
1712                 }
1713             }
1714             if ( not_found > 0 ) {
1715                 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
1716                         + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
1717             }
1718             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
1719         }
1720     }
1721
1722     private void readPhylogeniesFromFile() {
1723         boolean exception = false;
1724         Phylogeny[] phys = null;
1725         // Set an initial directory if none set yet
1726         final File my_dir = getCurrentDir();
1727         _open_filechooser.setMultiSelectionEnabled( true );
1728         // Open file-open dialog and set current directory
1729         if ( my_dir != null ) {
1730             _open_filechooser.setCurrentDirectory( my_dir );
1731         }
1732         final int result = _open_filechooser.showOpenDialog( _contentpane );
1733         // All done: get the file
1734         final File[] files = _open_filechooser.getSelectedFiles();
1735         setCurrentDir( _open_filechooser.getCurrentDirectory() );
1736         boolean nhx_or_nexus = false;
1737         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1738             for( final File file : files ) {
1739                 if ( ( file != null ) && !file.isDirectory() ) {
1740                     if ( _mainpanel.getCurrentTreePanel() != null ) {
1741                         _mainpanel.getCurrentTreePanel().setWaitCursor();
1742                     }
1743                     else {
1744                         _mainpanel.setWaitCursor();
1745                     }
1746                     if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
1747                             || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
1748                         try {
1749                             final NHXParser nhx = new NHXParser();
1750                             setSpecialOptionsForNhxParser( nhx );
1751                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
1752                             nhx_or_nexus = true;
1753                         }
1754                         catch ( final Exception e ) {
1755                             exception = true;
1756                             exceptionOccuredDuringOpenFile( e );
1757                         }
1758                     }
1759                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
1760                         warnIfNotPhyloXmlValidation( getConfiguration() );
1761                         try {
1762                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
1763                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
1764                         }
1765                         catch ( final Exception e ) {
1766                             exception = true;
1767                             exceptionOccuredDuringOpenFile( e );
1768                         }
1769                     }
1770                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
1771                         try {
1772                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1773                         }
1774                         catch ( final Exception e ) {
1775                             exception = true;
1776                             exceptionOccuredDuringOpenFile( e );
1777                         }
1778                     }
1779                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
1780                         try {
1781                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
1782                             setSpecialOptionsForNexParser( nex );
1783                             phys = PhylogenyMethods.readPhylogenies( nex, file );
1784                             nhx_or_nexus = true;
1785                         }
1786                         catch ( final Exception e ) {
1787                             exception = true;
1788                             exceptionOccuredDuringOpenFile( e );
1789                         }
1790                     }
1791                     // "*.*":
1792                     else {
1793                         try {
1794                             final PhylogenyParser parser = ParserUtils
1795                                     .createParserDependingOnFileType( file, getConfiguration()
1796                                             .isValidatePhyloXmlAgainstSchema() );
1797                             if ( parser instanceof NexusPhylogeniesParser ) {
1798                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
1799                                 setSpecialOptionsForNexParser( nex );
1800                                 nhx_or_nexus = true;
1801                             }
1802                             else if ( parser instanceof NHXParser ) {
1803                                 final NHXParser nhx = ( NHXParser ) parser;
1804                                 setSpecialOptionsForNhxParser( nhx );
1805                                 nhx_or_nexus = true;
1806                             }
1807                             else if ( parser instanceof PhyloXmlParser ) {
1808                                 warnIfNotPhyloXmlValidation( getConfiguration() );
1809                             }
1810                             phys = PhylogenyMethods.readPhylogenies( parser, file );
1811                         }
1812                         catch ( final Exception e ) {
1813                             exception = true;
1814                             exceptionOccuredDuringOpenFile( e );
1815                         }
1816                     }
1817                     if ( _mainpanel.getCurrentTreePanel() != null ) {
1818                         _mainpanel.getCurrentTreePanel().setArrowCursor();
1819                     }
1820                     else {
1821                         _mainpanel.setArrowCursor();
1822                     }
1823                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
1824                         boolean one_desc = false;
1825                         if ( nhx_or_nexus ) {
1826                             for( final Phylogeny phy : phys ) {
1827                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1828                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
1829                                 }
1830                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
1831                                     one_desc = true;
1832                                     break;
1833                                 }
1834                             }
1835                         }
1836                         AptxUtil.addPhylogeniesToTabs( phys,
1837                                                        file.getName(),
1838                                                        file.getAbsolutePath(),
1839                                                        getConfiguration(),
1840                                                        getMainPanel() );
1841                         _mainpanel.getControlPanel().showWhole();
1842                         if ( nhx_or_nexus && one_desc ) {
1843                             JOptionPane
1844                                     .showMessageDialog( this,
1845                                                         "One or more trees contain (a) node(s) with one descendant, "
1846                                                                 + ForesterUtil.LINE_SEPARATOR
1847                                                                 + "possibly indicating illegal parentheses within node names.",
1848                                                         "Warning: Possible Error in New Hampshire Formatted Data",
1849                                                         JOptionPane.WARNING_MESSAGE );
1850                         }
1851                     }
1852                 }
1853             }
1854         }
1855         activateSaveAllIfNeeded();
1856         System.gc();
1857     }
1858
1859     public void readSeqsFromFile() {
1860         // Set an initial directory if none set yet
1861         final File my_dir = getCurrentDir();
1862         _seqs_filechooser.setMultiSelectionEnabled( false );
1863         // Open file-open dialog and set current directory
1864         if ( my_dir != null ) {
1865             _seqs_filechooser.setCurrentDirectory( my_dir );
1866         }
1867         final int result = _seqs_filechooser.showOpenDialog( _contentpane );
1868         // All done: get the seqs
1869         final File file = _seqs_filechooser.getSelectedFile();
1870         setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
1871         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1872             setSeqsFile( null );
1873             setSeqs( null );
1874             List<Sequence> seqs = null;
1875             try {
1876                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
1877                     seqs = FastaParser.parse( new FileInputStream( file ) );
1878                     for( final Sequence seq : seqs ) {
1879                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
1880                     }
1881                 }
1882                 else {
1883                     //TODO error
1884                 }
1885             }
1886             catch ( final MsaFormatException e ) {
1887                 try {
1888                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1889                 }
1890                 catch ( final Exception ex ) {
1891                     // Do nothing.
1892                 }
1893                 JOptionPane.showMessageDialog( this,
1894                                                e.getLocalizedMessage(),
1895                                                "Multiple sequence file format error",
1896                                                JOptionPane.ERROR_MESSAGE );
1897                 return;
1898             }
1899             catch ( final IOException e ) {
1900                 try {
1901                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1902                 }
1903                 catch ( final Exception ex ) {
1904                     // Do nothing.
1905                 }
1906                 JOptionPane.showMessageDialog( this,
1907                                                e.getLocalizedMessage(),
1908                                                "Failed to read multiple sequence file",
1909                                                JOptionPane.ERROR_MESSAGE );
1910                 return;
1911             }
1912             catch ( final IllegalArgumentException e ) {
1913                 try {
1914                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1915                 }
1916                 catch ( final Exception ex ) {
1917                     // Do nothing.
1918                 }
1919                 JOptionPane.showMessageDialog( this,
1920                                                e.getLocalizedMessage(),
1921                                                "Unexpected error during reading of multiple sequence file",
1922                                                JOptionPane.ERROR_MESSAGE );
1923                 return;
1924             }
1925             catch ( final Exception e ) {
1926                 try {
1927                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1928                 }
1929                 catch ( final Exception ex ) {
1930                     // Do nothing.
1931                 }
1932                 e.printStackTrace();
1933                 JOptionPane.showMessageDialog( this,
1934                                                e.getLocalizedMessage(),
1935                                                "Unexpected error during reading of multiple sequence file",
1936                                                JOptionPane.ERROR_MESSAGE );
1937                 return;
1938             }
1939             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
1940                 JOptionPane.showMessageDialog( this,
1941                                                "Multiple sequence file is empty",
1942                                                "Illegal multiple sequence file",
1943                                                JOptionPane.ERROR_MESSAGE );
1944                 return;
1945             }
1946             if ( seqs.size() < 4 ) {
1947                 JOptionPane.showMessageDialog( this,
1948                                                "Multiple sequence file needs to contain at least 3 sequences",
1949                                                "Illegal multiple sequence file",
1950                                                JOptionPane.ERROR_MESSAGE );
1951                 return;
1952             }
1953             //  if ( msa.getLength() < 2 ) {
1954             //       JOptionPane.showMessageDialog( this,
1955             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
1956             //                                      "Illegal multiple sequence file",
1957             //                                      JOptionPane.ERROR_MESSAGE );
1958             //       return;
1959             //   }
1960             System.gc();
1961             setSeqsFile( _seqs_filechooser.getSelectedFile() );
1962             setSeqs( seqs );
1963         }
1964     }
1965
1966     public void readMsaFromFile() {
1967         // Set an initial directory if none set yet
1968         final File my_dir = getCurrentDir();
1969         _msa_filechooser.setMultiSelectionEnabled( false );
1970         // Open file-open dialog and set current directory
1971         if ( my_dir != null ) {
1972             _msa_filechooser.setCurrentDirectory( my_dir );
1973         }
1974         final int result = _msa_filechooser.showOpenDialog( _contentpane );
1975         // All done: get the msa
1976         final File file = _msa_filechooser.getSelectedFile();
1977         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
1978         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
1979             setMsaFile( null );
1980             setMsa( null );
1981             Msa msa = null;
1982             try {
1983                 final InputStream is = new FileInputStream( file );
1984                 if ( FastaParser.isLikelyFasta( file ) ) {
1985                     msa = FastaParser.parseMsa( is );
1986                 }
1987                 else {
1988                     msa = GeneralMsaParser.parse( is );
1989                 }
1990             }
1991             catch ( final MsaFormatException e ) {
1992                 try {
1993                     _mainpanel.getCurrentTreePanel().setArrowCursor();
1994                 }
1995                 catch ( final Exception ex ) {
1996                     // Do nothing.
1997                 }
1998                 JOptionPane.showMessageDialog( this,
1999                                                e.getLocalizedMessage(),
2000                                                "Multiple sequence alignment format error",
2001                                                JOptionPane.ERROR_MESSAGE );
2002                 return;
2003             }
2004             catch ( final IOException e ) {
2005                 try {
2006                     _mainpanel.getCurrentTreePanel().setArrowCursor();
2007                 }
2008                 catch ( final Exception ex ) {
2009                     // Do nothing.
2010                 }
2011                 JOptionPane.showMessageDialog( this,
2012                                                e.getLocalizedMessage(),
2013                                                "Failed to read multiple sequence alignment",
2014                                                JOptionPane.ERROR_MESSAGE );
2015                 return;
2016             }
2017             catch ( final IllegalArgumentException e ) {
2018                 try {
2019                     _mainpanel.getCurrentTreePanel().setArrowCursor();
2020                 }
2021                 catch ( final Exception ex ) {
2022                     // Do nothing.
2023                 }
2024                 JOptionPane.showMessageDialog( this,
2025                                                e.getLocalizedMessage(),
2026                                                "Unexpected error during reading of multiple sequence alignment",
2027                                                JOptionPane.ERROR_MESSAGE );
2028                 return;
2029             }
2030             catch ( final Exception e ) {
2031                 try {
2032                     _mainpanel.getCurrentTreePanel().setArrowCursor();
2033                 }
2034                 catch ( final Exception ex ) {
2035                     // Do nothing.
2036                 }
2037                 e.printStackTrace();
2038                 JOptionPane.showMessageDialog( this,
2039                                                e.getLocalizedMessage(),
2040                                                "Unexpected error during reading of multiple sequence alignment",
2041                                                JOptionPane.ERROR_MESSAGE );
2042                 return;
2043             }
2044             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
2045                 JOptionPane.showMessageDialog( this,
2046                                                "Multiple sequence alignment is empty",
2047                                                "Illegal Multiple Sequence Alignment",
2048                                                JOptionPane.ERROR_MESSAGE );
2049                 return;
2050             }
2051             if ( msa.getNumberOfSequences() < 4 ) {
2052                 JOptionPane.showMessageDialog( this,
2053                                                "Multiple sequence alignment needs to contain at least 3 sequences",
2054                                                "Illegal multiple sequence alignment",
2055                                                JOptionPane.ERROR_MESSAGE );
2056                 return;
2057             }
2058             if ( msa.getLength() < 2 ) {
2059                 JOptionPane.showMessageDialog( this,
2060                                                "Multiple sequence alignment needs to contain at least 2 residues",
2061                                                "Illegal multiple sequence alignment",
2062                                                JOptionPane.ERROR_MESSAGE );
2063                 return;
2064             }
2065             System.gc();
2066             setMsaFile( _msa_filechooser.getSelectedFile() );
2067             setMsa( msa );
2068         }
2069     }
2070
2071     @Override
2072     void readPhylogeniesFromURL() {
2073         URL url = null;
2074         Phylogeny[] phys = null;
2075         final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
2076         final String url_string = JOptionPane.showInputDialog( this,
2077                                                                message,
2078                                                                "Use URL/webservice to obtain a phylogeny",
2079                                                                JOptionPane.QUESTION_MESSAGE );
2080         boolean nhx_or_nexus = false;
2081         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
2082             try {
2083                 url = new URL( url_string );
2084                 PhylogenyParser parser = null;
2085                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
2086                     parser = new TolParser();
2087                 }
2088                 else {
2089                     parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
2090                             .isValidatePhyloXmlAgainstSchema() );
2091                 }
2092                 if ( parser instanceof NexusPhylogeniesParser ) {
2093                     nhx_or_nexus = true;
2094                 }
2095                 else if ( parser instanceof NHXParser ) {
2096                     nhx_or_nexus = true;
2097                 }
2098                 if ( _mainpanel.getCurrentTreePanel() != null ) {
2099                     _mainpanel.getCurrentTreePanel().setWaitCursor();
2100                 }
2101                 else {
2102                     _mainpanel.setWaitCursor();
2103                 }
2104                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2105                 phys = factory.create( url.openStream(), parser );
2106             }
2107             catch ( final MalformedURLException e ) {
2108                 JOptionPane.showMessageDialog( this,
2109                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
2110                                                "Malformed URL",
2111                                                JOptionPane.ERROR_MESSAGE );
2112             }
2113             catch ( final IOException e ) {
2114                 JOptionPane.showMessageDialog( this,
2115                                                "Could not read from " + url + "\n"
2116                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2117                                                "Failed to read URL",
2118                                                JOptionPane.ERROR_MESSAGE );
2119             }
2120             catch ( final Exception e ) {
2121                 JOptionPane.showMessageDialog( this,
2122                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2123                                                "Unexpected Exception",
2124                                                JOptionPane.ERROR_MESSAGE );
2125             }
2126             finally {
2127                 if ( _mainpanel.getCurrentTreePanel() != null ) {
2128                     _mainpanel.getCurrentTreePanel().setArrowCursor();
2129                 }
2130                 else {
2131                     _mainpanel.setArrowCursor();
2132                 }
2133             }
2134             if ( ( phys != null ) && ( phys.length > 0 ) ) {
2135                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2136                     for( final Phylogeny phy : phys ) {
2137                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
2138                     }
2139                 }
2140                 AptxUtil.addPhylogeniesToTabs( phys,
2141                                                new File( url.getFile() ).getName(),
2142                                                new File( url.getFile() ).toString(),
2143                                                getConfiguration(),
2144                                                getMainPanel() );
2145                 _mainpanel.getControlPanel().showWhole();
2146             }
2147         }
2148         activateSaveAllIfNeeded();
2149         System.gc();
2150     }
2151
2152     private void readSpeciesTreeFromFile() {
2153         Phylogeny t = null;
2154         boolean exception = false;
2155         final File my_dir = getCurrentDir();
2156         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
2157         if ( my_dir != null ) {
2158             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
2159         }
2160         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
2161         final File file = _open_filechooser_for_species_tree.getSelectedFile();
2162         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2163             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
2164                 try {
2165                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2166                     t = trees[ 0 ];
2167                 }
2168                 catch ( final Exception e ) {
2169                     exception = true;
2170                     exceptionOccuredDuringOpenFile( e );
2171                 }
2172             }
2173             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
2174                 try {
2175                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
2176                     t = trees[ 0 ];
2177                 }
2178                 catch ( final Exception e ) {
2179                     exception = true;
2180                     exceptionOccuredDuringOpenFile( e );
2181                 }
2182             }
2183             // "*.*":
2184             else {
2185                 try {
2186                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
2187                     t = trees[ 0 ];
2188                 }
2189                 catch ( final Exception e ) {
2190                     exception = true;
2191                     exceptionOccuredDuringOpenFile( e );
2192                 }
2193             }
2194             if ( !exception && ( t != null ) && !t.isRooted() ) {
2195                 exception = true;
2196                 t = null;
2197                 JOptionPane.showMessageDialog( this,
2198                                                "Species tree is not rooted",
2199                                                "Species tree not loaded",
2200                                                JOptionPane.ERROR_MESSAGE );
2201             }
2202             if ( !exception && ( t != null ) ) {
2203                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
2204                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
2205                     final PhylogenyNode node = it.next();
2206                     if ( !node.getNodeData().isHasTaxonomy() ) {
2207                         exception = true;
2208                         t = null;
2209                         JOptionPane
2210                                 .showMessageDialog( this,
2211                                                     "Species tree contains external node(s) without taxonomy information",
2212                                                     "Species tree not loaded",
2213                                                     JOptionPane.ERROR_MESSAGE );
2214                         break;
2215                     }
2216                     else {
2217                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
2218                             exception = true;
2219                             t = null;
2220                             JOptionPane.showMessageDialog( this,
2221                                                            "Taxonomy ["
2222                                                                    + node.getNodeData().getTaxonomy().asSimpleText()
2223                                                                    + "] is not unique in species tree",
2224                                                            "Species tree not loaded",
2225                                                            JOptionPane.ERROR_MESSAGE );
2226                             break;
2227                         }
2228                         else {
2229                             tax_set.add( node.getNodeData().getTaxonomy() );
2230                         }
2231                     }
2232                 }
2233             }
2234             if ( !exception && ( t != null ) ) {
2235                 _species_tree = t;
2236                 JOptionPane.showMessageDialog( this,
2237                                                "Species tree successfully loaded",
2238                                                "Species tree loaded",
2239                                                JOptionPane.INFORMATION_MESSAGE );
2240             }
2241             _contentpane.repaint();
2242             System.gc();
2243         }
2244     }
2245
2246     private void setCurrentDir( final File current_dir ) {
2247         _current_dir = current_dir;
2248     }
2249
2250     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
2251         _min_not_collapse = min_not_collapse;
2252     }
2253
2254     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
2255         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2256     }
2257
2258     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
2259         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
2260         PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
2261         if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
2262             te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
2263         }
2264         nhx.setTaxonomyExtraction( te );
2265     }
2266
2267     private void writeAllToFile() {
2268         if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
2269             return;
2270         }
2271         final File my_dir = getCurrentDir();
2272         if ( my_dir != null ) {
2273             _save_filechooser.setCurrentDirectory( my_dir );
2274         }
2275         _save_filechooser.setSelectedFile( new File( "" ) );
2276         final int result = _save_filechooser.showSaveDialog( _contentpane );
2277         final File file = _save_filechooser.getSelectedFile();
2278         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2279         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2280             if ( file.exists() ) {
2281                 final int i = JOptionPane.showConfirmDialog( this,
2282                                                              file + " already exists. Overwrite?",
2283                                                              "Warning",
2284                                                              JOptionPane.OK_CANCEL_OPTION,
2285                                                              JOptionPane.WARNING_MESSAGE );
2286                 if ( i != JOptionPane.OK_OPTION ) {
2287                     return;
2288                 }
2289                 else {
2290                     try {
2291                         file.delete();
2292                     }
2293                     catch ( final Exception e ) {
2294                         JOptionPane.showMessageDialog( this,
2295                                                        "Failed to delete: " + file,
2296                                                        "Error",
2297                                                        JOptionPane.WARNING_MESSAGE );
2298                     }
2299                 }
2300             }
2301             final int count = getMainPanel().getTabbedPane().getTabCount();
2302             final List<Phylogeny> trees = new ArrayList<Phylogeny>();
2303             for( int i = 0; i < count; ++i ) {
2304                 trees.add( getMainPanel().getPhylogeny( i ) );
2305                 getMainPanel().getTreePanels().get( i ).setEdited( false );
2306             }
2307             final PhylogenyWriter writer = new PhylogenyWriter();
2308             try {
2309                 writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
2310             }
2311             catch ( final IOException e ) {
2312                 JOptionPane.showMessageDialog( this,
2313                                                "Failed to write to: " + file,
2314                                                "Error",
2315                                                JOptionPane.WARNING_MESSAGE );
2316             }
2317         }
2318     }
2319
2320     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
2321         try {
2322             final PhylogenyWriter writer = new PhylogenyWriter();
2323             writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
2324         }
2325         catch ( final Exception e ) {
2326             exception = true;
2327             exceptionOccuredDuringSaveAs( e );
2328         }
2329         return exception;
2330     }
2331
2332     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
2333         try {
2334             final PhylogenyWriter writer = new PhylogenyWriter();
2335             writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
2336         }
2337         catch ( final Exception e ) {
2338             exception = true;
2339             exceptionOccuredDuringSaveAs( e );
2340         }
2341         return exception;
2342     }
2343
2344     private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
2345         try {
2346             final PhylogenyWriter writer = new PhylogenyWriter();
2347             writer.toNewHampshireX( t, file );
2348         }
2349         catch ( final Exception e ) {
2350             exception = true;
2351             exceptionOccuredDuringSaveAs( e );
2352         }
2353         return exception;
2354     }
2355
2356     private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
2357         try {
2358             final PhylogenyWriter writer = new PhylogenyWriter();
2359             writer.toPhyloXML( file, t, 0 );
2360         }
2361         catch ( final Exception e ) {
2362             exception = true;
2363             exceptionOccuredDuringSaveAs( e );
2364         }
2365         return exception;
2366     }
2367
2368     void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
2369         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
2370                                                                    _mainpanel.getCurrentTreePanel().getHeight(),
2371                                                                    true );
2372         String file_written_to = "";
2373         boolean error = false;
2374         try {
2375             file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
2376                                                                      _mainpanel.getCurrentTreePanel().getWidth(),
2377                                                                      _mainpanel.getCurrentTreePanel().getHeight(),
2378                                                                      _mainpanel.getCurrentTreePanel(),
2379                                                                      _mainpanel.getControlPanel(),
2380                                                                      type,
2381                                                                      getOptions() );
2382         }
2383         catch ( final IOException e ) {
2384             error = true;
2385             JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
2386         }
2387         if ( !error ) {
2388             if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
2389                 JOptionPane.showMessageDialog( this,
2390                                                "Wrote image to: " + file_written_to,
2391                                                "Graphics Export",
2392                                                JOptionPane.INFORMATION_MESSAGE );
2393             }
2394             else {
2395                 JOptionPane.showMessageDialog( this,
2396                                                "There was an unknown problem when attempting to write to an image file: \""
2397                                                        + file_name + "\"",
2398                                                "Error",
2399                                                JOptionPane.ERROR_MESSAGE );
2400             }
2401         }
2402         _contentpane.repaint();
2403     }
2404
2405     private void writeToFile( final Phylogeny t ) {
2406         if ( t == null ) {
2407             return;
2408         }
2409         String initial_filename = null;
2410         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2411             try {
2412                 initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
2413             }
2414             catch ( final IOException e ) {
2415                 initial_filename = null;
2416             }
2417         }
2418         if ( !ForesterUtil.isEmpty( initial_filename ) ) {
2419             _save_filechooser.setSelectedFile( new File( initial_filename ) );
2420         }
2421         else {
2422             _save_filechooser.setSelectedFile( new File( "" ) );
2423         }
2424         final File my_dir = getCurrentDir();
2425         if ( my_dir != null ) {
2426             _save_filechooser.setCurrentDirectory( my_dir );
2427         }
2428         final int result = _save_filechooser.showSaveDialog( _contentpane );
2429         final File file = _save_filechooser.getSelectedFile();
2430         setCurrentDir( _save_filechooser.getCurrentDirectory() );
2431         boolean exception = false;
2432         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2433             if ( file.exists() ) {
2434                 final int i = JOptionPane.showConfirmDialog( this,
2435                                                              file + " already exists.\nOverwrite?",
2436                                                              "Overwrite?",
2437                                                              JOptionPane.OK_CANCEL_OPTION,
2438                                                              JOptionPane.QUESTION_MESSAGE );
2439                 if ( i != JOptionPane.OK_OPTION ) {
2440                     return;
2441                 }
2442                 else {
2443                     final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
2444                     try {
2445                         ForesterUtil.copyFile( file, to );
2446                     }
2447                     catch ( final Exception e ) {
2448                         JOptionPane.showMessageDialog( this,
2449                                                        "Failed to create backup copy " + to,
2450                                                        "Failed to Create Backup Copy",
2451                                                        JOptionPane.WARNING_MESSAGE );
2452                     }
2453                     try {
2454                         file.delete();
2455                     }
2456                     catch ( final Exception e ) {
2457                         JOptionPane.showMessageDialog( this,
2458                                                        "Failed to delete: " + file,
2459                                                        "Failed to Delete",
2460                                                        JOptionPane.WARNING_MESSAGE );
2461                     }
2462                 }
2463             }
2464             if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
2465                 exception = writeAsNewHampshire( t, exception, file );
2466             }
2467             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
2468                 exception = writeAsNHX( t, exception, file );
2469             }
2470             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
2471                 exception = writeAsPhyloXml( t, exception, file );
2472             }
2473             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
2474                 exception = writeAsNexus( t, exception, file );
2475             }
2476             // "*.*":
2477             else {
2478                 final String file_name = file.getName().trim().toLowerCase();
2479                 if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2480                         || file_name.endsWith( ".tree" ) ) {
2481                     exception = writeAsNewHampshire( t, exception, file );
2482                 }
2483                 else if ( file_name.endsWith( ".nhx" ) ) {
2484                     exception = writeAsNHX( t, exception, file );
2485                 }
2486                 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
2487                     exception = writeAsNexus( t, exception, file );
2488                 }
2489                 // XML is default:
2490                 else {
2491                     exception = writeAsPhyloXml( t, exception, file );
2492                 }
2493             }
2494             if ( !exception ) {
2495                 getMainPanel().setTitleOfSelectedTab( file.getName() );
2496                 getMainPanel().getCurrentTreePanel().setTreeFile( file );
2497                 getMainPanel().getCurrentTreePanel().setEdited( false );
2498             }
2499         }
2500     }
2501
2502     private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
2503         if ( ( t == null ) || t.isEmpty() ) {
2504             return;
2505         }
2506         String initial_filename = "";
2507         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2508             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2509         }
2510         if ( initial_filename.indexOf( '.' ) > 0 ) {
2511             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2512         }
2513         initial_filename = initial_filename + "." + type;
2514         _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
2515         final File my_dir = getCurrentDir();
2516         if ( my_dir != null ) {
2517             _writetographics_filechooser.setCurrentDirectory( my_dir );
2518         }
2519         final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
2520         File file = _writetographics_filechooser.getSelectedFile();
2521         setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
2522         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2523             if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
2524                 file = new File( file.toString() + "." + type );
2525             }
2526             if ( file.exists() ) {
2527                 final int i = JOptionPane.showConfirmDialog( this,
2528                                                              file + " already exists. Overwrite?",
2529                                                              "Warning",
2530                                                              JOptionPane.OK_CANCEL_OPTION,
2531                                                              JOptionPane.WARNING_MESSAGE );
2532                 if ( i != JOptionPane.OK_OPTION ) {
2533                     return;
2534                 }
2535                 else {
2536                     try {
2537                         file.delete();
2538                     }
2539                     catch ( final Exception e ) {
2540                         JOptionPane.showMessageDialog( this,
2541                                                        "Failed to delete: " + file,
2542                                                        "Error",
2543                                                        JOptionPane.WARNING_MESSAGE );
2544                     }
2545                 }
2546             }
2547             writePhylogenyToGraphicsFile( file.toString(), type );
2548         }
2549     }
2550
2551     private void writeToPdf( final Phylogeny t ) {
2552         if ( ( t == null ) || t.isEmpty() ) {
2553             return;
2554         }
2555         String initial_filename = "";
2556         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
2557             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
2558         }
2559         if ( initial_filename.indexOf( '.' ) > 0 ) {
2560             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
2561         }
2562         initial_filename = initial_filename + ".pdf";
2563         _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
2564         final File my_dir = getCurrentDir();
2565         if ( my_dir != null ) {
2566             _writetopdf_filechooser.setCurrentDirectory( my_dir );
2567         }
2568         final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
2569         File file = _writetopdf_filechooser.getSelectedFile();
2570         setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
2571         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
2572             if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
2573                 file = new File( file.toString() + ".pdf" );
2574             }
2575             if ( file.exists() ) {
2576                 final int i = JOptionPane.showConfirmDialog( this,
2577                                                              file + " already exists. Overwrite?",
2578                                                              "WARNING",
2579                                                              JOptionPane.OK_CANCEL_OPTION,
2580                                                              JOptionPane.WARNING_MESSAGE );
2581                 if ( i != JOptionPane.OK_OPTION ) {
2582                     return;
2583                 }
2584             }
2585             printPhylogenyToPdf( file.toString() );
2586         }
2587     }
2588
2589     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2590         return new MainFrameApplication( phys, config, title );
2591     }
2592
2593     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2594         return new MainFrameApplication( phys, config );
2595     }
2596
2597     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2598         return new MainFrameApplication( phys, config_file_name, title );
2599     }
2600
2601     public static MainFrame createInstance( final Phylogeny[] phys,
2602                                             final Configuration config,
2603                                             final String title,
2604                                             final File current_dir ) {
2605         return new MainFrameApplication( phys, config, title, current_dir );
2606     }
2607
2608     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
2609         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
2610                 + o.getPrintSizeY() + ")" );
2611     }
2612
2613     static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
2614         mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
2615     }
2616
2617     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2618         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2619             JOptionPane
2620                     .showMessageDialog( null,
2621                                         ForesterUtil
2622                                                 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2623                                                            80 ),
2624                                         "Warning",
2625                                         JOptionPane.WARNING_MESSAGE );
2626         }
2627     }
2628
2629     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
2630         _phylogenetic_inference_options = phylogenetic_inference_options;
2631     }
2632
2633     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
2634         if ( _phylogenetic_inference_options == null ) {
2635             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
2636         }
2637         return _phylogenetic_inference_options;
2638     }
2639
2640     public Msa getMsa() {
2641         return _msa;
2642     }
2643
2644     void setMsa( final Msa msa ) {
2645         _msa = msa;
2646     }
2647
2648     void setMsaFile( final File msa_file ) {
2649         _msa_file = msa_file;
2650     }
2651
2652     public File getMsaFile() {
2653         return _msa_file;
2654     }
2655
2656     public List<Sequence> getSeqs() {
2657         return _seqs;
2658     }
2659
2660     void setSeqs( final List<Sequence> seqs ) {
2661         _seqs = seqs;
2662     }
2663
2664     void setSeqsFile( final File seqs_file ) {
2665         _seqs_file = seqs_file;
2666     }
2667
2668     public File getSeqsFile() {
2669         return _seqs_file;
2670     }
2671 } // MainFrameApplication.
2672
2673 class NexusFilter extends FileFilter {
2674
2675     @Override
2676     public boolean accept( final File f ) {
2677         final String file_name = f.getName().trim().toLowerCase();
2678         return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
2679                 || file_name.endsWith( ".tre" ) || f.isDirectory();
2680     }
2681
2682     @Override
2683     public String getDescription() {
2684         return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
2685     }
2686 } // NexusFilter
2687
2688 class NHFilter extends FileFilter {
2689
2690     @Override
2691     public boolean accept( final File f ) {
2692         final String file_name = f.getName().trim().toLowerCase();
2693         return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
2694                 || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
2695                 || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )
2696                 || f.isDirectory();
2697     }
2698
2699     @Override
2700     public String getDescription() {
2701         return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";
2702     }
2703 } // NHFilter
2704
2705 class NHXFilter extends FileFilter {
2706
2707     @Override
2708     public boolean accept( final File f ) {
2709         final String file_name = f.getName().trim().toLowerCase();
2710         return file_name.endsWith( ".nhx" ) || f.isDirectory();
2711     }
2712
2713     @Override
2714     public String getDescription() {
2715         return "NHX files (*.nhx)";
2716     }
2717 }
2718
2719 class PdfFilter extends FileFilter {
2720
2721     @Override
2722     public boolean accept( final File f ) {
2723         return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
2724     }
2725
2726     @Override
2727     public String getDescription() {
2728         return "PDF files (*.pdf)";
2729     }
2730 } // PdfFilter
2731
2732 class TolFilter extends FileFilter {
2733
2734     @Override
2735     public boolean accept( final File f ) {
2736         final String file_name = f.getName().trim().toLowerCase();
2737         return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
2738                 .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
2739     }
2740
2741     @Override
2742     public String getDescription() {
2743         return "Tree of Life files (*.tol, *.tolxml)";
2744     }
2745 } // TolFilter
2746
2747 class XMLFilter extends FileFilter {
2748
2749     @Override
2750     public boolean accept( final File f ) {
2751         final String file_name = f.getName().trim().toLowerCase();
2752         return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )
2753                 || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
2754     }
2755
2756     @Override
2757     public String getDescription() {
2758         return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";
2759     }
2760 } // XMLFilter