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

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.archaeopteryx;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Font;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ComponentAdapter;
  33 import java.awt.event.ComponentEvent;
  34 import java.awt.event.WindowAdapter;
  35 import java.awt.event.WindowEvent;
  36 import java.io.File;
  37 import java.io.FileInputStream;
  38 import java.io.IOException;
  39 import java.io.InputStream;
  40 import java.net.MalformedURLException;
  41 import java.net.URL;
  42 import java.util.ArrayList;
  43 import java.util.HashSet;
  44 import java.util.List;
  45 import java.util.Set;
  46
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.JCheckBoxMenuItem;
  49 import javax.swing.JFileChooser;
  50 import javax.swing.JMenu;
  51 import javax.swing.JMenuBar;
  52 import javax.swing.JMenuItem;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JRadioButtonMenuItem;
  55 import javax.swing.UIManager;
  56 import javax.swing.UnsupportedLookAndFeelException;
  57 import javax.swing.WindowConstants;
  58 import javax.swing.event.ChangeEvent;
  59 import javax.swing.event.ChangeListener;
  60
  61 import org.forester.analysis.TaxonomyDataManager;
  62 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  63 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  64 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  65 import org.forester.archaeopteryx.tools.InferenceManager;
  66 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
  67 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
  68 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
  69 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
  70 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  71 import org.forester.archaeopteryx.webservices.WebservicesManager;
  72 import org.forester.io.parsers.FastaParser;
  73 import org.forester.io.parsers.GeneralMsaParser;
  74 import org.forester.io.parsers.PhylogenyParser;
  75 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  76 import org.forester.io.parsers.nhx.NHXParser;
  77 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  78 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  79 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  80 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  81 import org.forester.io.parsers.tol.TolParser;
  82 import org.forester.io.parsers.util.ParserUtils;
  83 import org.forester.io.writers.SequenceWriter;
  84 import org.forester.msa.Msa;
  85 import org.forester.msa.MsaFormatException;
  86 import org.forester.phylogeny.Phylogeny;
  87 import org.forester.phylogeny.PhylogenyMethods;
  88 import org.forester.phylogeny.PhylogenyNode;
  89 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  90 import org.forester.phylogeny.data.Confidence;
  91 import org.forester.phylogeny.data.PhylogenyDataUtil;
  92 import org.forester.phylogeny.data.Sequence;
  93 import org.forester.phylogeny.data.Taxonomy;
  94 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  95 import org.forester.phylogeny.factories.PhylogenyFactory;
  96 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  97 import org.forester.sequence.MolecularSequence;
  98 import org.forester.util.BasicDescriptiveStatistics;
  99 import org.forester.util.BasicTable;
 100 import org.forester.util.BasicTableParser;
 101 import org.forester.util.DescriptiveStatistics;
 102 import org.forester.util.ForesterUtil;
 103
 104 public final class MainFrameApplication extends MainFrame {
 105
 106     private final static int             FRAME_X_SIZE                    = 800;
 107     private final static int             FRAME_Y_SIZE                    = 800;
 108     // Filters for the file-open dialog (classes defined in this file)
 109     private static final long            serialVersionUID                = -799735726778865234L;
 110     private static final boolean         PREPROCESS_TREES                = false;
 111     private final JFileChooser           _values_filechooser;
 112     private final JFileChooser           _sequences_filechooser;
 113     private final JFileChooser           _open_filechooser;
 114     private final JFileChooser           _msa_filechooser;
 115     private final JFileChooser           _seqs_pi_filechooser;
 116     private final JFileChooser           _open_filechooser_for_species_tree;
 117     // Application-only print menu items
 118     private JMenuItem                    _collapse_below_threshold;
 119     private JMenuItem                    _collapse_below_branch_length;
 120     private ButtonGroup                  _radio_group_1;
 121     private ButtonGroup                  _radio_group_2;
 122     // Others:
 123     double                               _min_not_collapse               = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT;
 124     double                               _min_not_collapse_bl            = 0.001;
 125     // Phylogeny Inference menu
 126     private JMenu                        _inference_menu;
 127     private JMenuItem                    _inference_from_msa_item;
 128     private JMenuItem                    _inference_from_seqs_item;
 129     // Phylogeny Inference
 130     private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
 131     private Msa                          _msa                            = null;
 132     private File                         _msa_file                       = null;
 133     private List<MolecularSequence>      _seqs                           = null;
 134     private File                         _seqs_file                      = null;
 135     JMenuItem                            _read_values_jmi;
 136     JMenuItem                            _read_seqs_jmi;
 137
 138     private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
 139         _configuration = config;
 140         if ( _configuration == null ) {
 141             throw new IllegalArgumentException( "configuration is null" );
 142         }
 143         setVisible( false );
 144         setOptions( Options.createInstance( _configuration ) );
 145         _mainpanel = new MainPanel( _configuration, this );
 146         _open_filechooser = null;
 147         _open_filechooser_for_species_tree = null;
 148         _save_filechooser = null;
 149         _writetopdf_filechooser = null;
 150         _writetographics_filechooser = null;
 151         _msa_filechooser = null;
 152         _seqs_pi_filechooser = null;
 153         _values_filechooser = null;
 154         _sequences_filechooser = null;
 155         _jmenubar = new JMenuBar();
 156         buildFileMenu();
 157         buildTypeMenu();
 158         _contentpane = getContentPane();
 159         _contentpane.setLayout( new BorderLayout() );
 160         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 161         // App is this big
 162         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 163         // The window listener
 164         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 165         addWindowListener( new WindowAdapter() {
 166
 167             @Override
 168             public void windowClosing( final WindowEvent e ) {
 169                 exit();
 170             }
 171         } );
 172         //   setVisible( true );
 173         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 174             AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
 175             validate();
 176             getMainPanel().getControlPanel().showWholeAll();
 177             getMainPanel().getControlPanel().showWhole();
 178         }
 179         //activateSaveAllIfNeeded();
 180         // ...and its children
 181         _contentpane.repaint();
 182     }
 183
 184     private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
 185         this( phys, config, title, null );
 186     }
 187
 188     private MainFrameApplication( final Phylogeny[] phys,
 189                                   final Configuration config,
 190                                   final String title,
 191                                   final File current_dir ) {
 192         super();
 193         _configuration = config;
 194         if ( _configuration == null ) {
 195             throw new IllegalArgumentException( "configuration is null" );
 196         }
 197         try {
 198             if ( _configuration.isUseNativeUI() ) {
 199                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 200             }
 201             else {
 202                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 203             }
 204         }
 205         catch ( final UnsupportedLookAndFeelException e ) {
 206             AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
 207         }
 208         catch ( final ClassNotFoundException e ) {
 209             AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
 210         }
 211         catch ( final InstantiationException e ) {
 212             AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
 213         }
 214         catch ( final IllegalAccessException e ) {
 215             AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
 216         }
 217         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
 218             setCurrentDir( current_dir );
 219         }
 220         // hide until everything is ready
 221         setVisible( false );
 222         setOptions( Options.createInstance( _configuration ) );
 223         setInferenceManager( InferenceManager.createInstance( _configuration ) );
 224         setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
 225         // set title
 226         setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" );
 227         _mainpanel = new MainPanel( _configuration, this );
 228         // The file dialogs
 229         _open_filechooser = new JFileChooser();
 230         _open_filechooser.setMultiSelectionEnabled( true );
 231         _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );
 232         _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );
 233         _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
 234         _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
 235         _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );
 236         _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
 237         _open_filechooser.setFileFilter( MainFrame.defaultfilter );
 238         _open_filechooser_for_species_tree = new JFileChooser();
 239         _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
 240         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );
 241         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );
 242         _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );
 243         // Msa:
 244         _msa_filechooser = new JFileChooser();
 245         _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
 246         _msa_filechooser.setMultiSelectionEnabled( false );
 247         _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
 248         _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );
 249         // Seqs:
 250         _seqs_pi_filechooser = new JFileChooser();
 251         _seqs_pi_filechooser.setName( "Read Sequences File" );
 252         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 253         _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
 254         _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );
 255         // Expression
 256         _values_filechooser = new JFileChooser();
 257         _values_filechooser.setMultiSelectionEnabled( false );
 258         // Sequences
 259         _sequences_filechooser = new JFileChooser();
 260         _sequences_filechooser.setMultiSelectionEnabled( false );
 261         try {
 262             final String home_dir = System.getProperty( "user.home" );
 263             _open_filechooser.setCurrentDirectory( new File( home_dir ) );
 264             _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) );
 265             _msa_filechooser.setCurrentDirectory( new File( home_dir ) );
 266             _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) );
 267             _values_filechooser.setCurrentDirectory( new File( home_dir ) );
 268             _sequences_filechooser.setCurrentDirectory( new File( home_dir ) );
 269         }
 270         catch ( final Exception e ) {
 271             e.printStackTrace();
 272             // Do nothing. Not important.
 273         }
 274         // build the menu bar
 275         _jmenubar = new JMenuBar();
 276         if ( !_configuration.isUseNativeUI() ) {
 277             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 278         }
 279         buildFileMenu();
 280         if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
 281             buildPhylogeneticInferenceMenu();
 282         }
 283         buildAnalysisMenu();
 284         buildToolsMenu();
 285         buildViewMenu();
 286         buildFontSizeMenu();
 287         buildOptionsMenu();
 288         buildTypeMenu();
 289         buildHelpMenu();
 290         setJMenuBar( _jmenubar );
 291         _jmenubar.add( _help_jmenu );
 292         _contentpane = getContentPane();
 293         _contentpane.setLayout( new BorderLayout() );
 294         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 295         // App is this big
 296         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 297         //        addWindowFocusListener( new WindowAdapter() {
 298         //
 299         //            @Override
 300         //            public void windowGainedFocus( WindowEvent e ) {
 301         //                requestFocusInWindow();
 302         //            }
 303         //        } );
 304         // The window listener
 305         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 306         addWindowListener( new WindowAdapter() {
 307
 308             @Override
 309             public void windowClosing( final WindowEvent e ) {
 310                 if ( isUnsavedDataPresent() ) {
 311                     final int r = JOptionPane.showConfirmDialog( null,
 312                                                                  "Exit despite potentially unsaved changes?",
 313                                                                  "Exit?",
 314                                                                  JOptionPane.YES_NO_OPTION );
 315                     if ( r != JOptionPane.YES_OPTION ) {
 316                         return;
 317                     }
 318                 }
 319                 else {
 320                     final int r = JOptionPane
 321                             .showConfirmDialog( null, "Exit Archaeopteryx?", "Exit?", JOptionPane.YES_NO_OPTION );
 322                     if ( r != JOptionPane.YES_OPTION ) {
 323                         return;
 324                     }
 325                 }
 326                 exit();
 327             }
 328         } );
 329         // The component listener
 330         addComponentListener( new ComponentAdapter() {
 331
 332             @Override
 333             public void componentResized( final ComponentEvent e ) {
 334                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 335                     _mainpanel.getCurrentTreePanel()
 336                             .calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
 337                                                         _mainpanel.getCurrentTreePanel().getHeight() );
 338                 }
 339             }
 340         } );
 341         requestFocusInWindow();
 342         // addKeyListener( this );
 343         setVisible( true );
 344         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 345             AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
 346             validate();
 347             getMainPanel().getControlPanel().showWholeAll();
 348             getMainPanel().getControlPanel().showWhole();
 349         }
 350         activateSaveAllIfNeeded();
 351         // ...and its children
 352         _contentpane.repaint();
 353         System.gc();
 354     }
 355
 356     private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
 357         // Reads the config file (false, false => not url, not applet):
 358         this( phys, new Configuration( config_file, false, false, true ), title );
 359     }
 360
 361     @Override
 362     public void actionPerformed( final ActionEvent e ) {
 363         try {
 364             super.actionPerformed( e );
 365             final Object o = e.getSource();
 366             // Handle app-specific actions here:
 367             if ( o == _open_item ) {
 368                 readPhylogeniesFromFile();
 369             }
 370             if ( o == _open_url_item ) {
 371                 readPhylogeniesFromURL();
 372             }
 373             else if ( o == _new_item ) {
 374                 newTree();
 375             }
 376             else if ( o == _close_item ) {
 377                 closeCurrentPane();
 378             }
 379             else if ( o == _load_species_tree_item ) {
 380                 readSpeciesTreeFromFile();
 381             }
 382             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
 383                 if ( isSubtreeDisplayed() ) {
 384                     return;
 385                 }
 386                 obtainDetailedTaxonomicInformation();
 387             }
 388             else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
 389                 if ( isSubtreeDisplayed() ) {
 390                     return;
 391                 }
 392                 obtainDetailedTaxonomicInformationDelete();
 393             }
 394             else if ( o == _obtain_seq_information_jmi ) {
 395                 obtainSequenceInformation();
 396             }
 397             else if ( o == _read_values_jmi ) {
 398                 if ( isSubtreeDisplayed() ) {
 399                     return;
 400                 }
 401                 addExpressionValuesFromFile();
 402             }
 403             else if ( o == _read_seqs_jmi ) {
 404                 if ( isSubtreeDisplayed() ) {
 405                     return;
 406                 }
 407                 addSequencesFromFile();
 408             }
 409             else if ( o == _move_node_names_to_tax_sn_jmi ) {
 410                 moveNodeNamesToTaxSn();
 411             }
 412             else if ( o == _move_node_names_to_seq_names_jmi ) {
 413                 moveNodeNamesToSeqNames();
 414             }
 415             else if ( o == _extract_tax_code_from_node_names_jmi ) {
 416                 extractTaxDataFromNodeNames();
 417             }
 418             else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
 419                 updateOptions( getOptions() );
 420             }
 421             else if ( o == _replace_underscores_cbmi ) {
 422                 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
 423                     _extract_taxonomy_no_rbmi.setSelected( true );
 424                 }
 425                 updateOptions( getOptions() );
 426             }
 427             else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
 428                 updateOptions( getOptions() );
 429             }
 430             else if ( o == _collapse_below_threshold ) {
 431                 if ( isSubtreeDisplayed() ) {
 432                     return;
 433                 }
 434                 collapseBelowThreshold();
 435             }
 436
 437             else if ( o == _collapse_below_branch_length ) {
 438                 if ( isSubtreeDisplayed() ) {
 439                     return;
 440                 }
 441                 collapseBelowBranchLengthThreshold();
 442             }
 443             else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
 444                     || ( o == _extract_taxonomy_agressive_rbmi ) ) {
 445                 if ( _replace_underscores_cbmi != null ) {
 446                     _replace_underscores_cbmi.setSelected( false );
 447                 }
 448                 updateOptions( getOptions() );
 449             }
 450             else if ( o == _extract_taxonomy_no_rbmi ) {
 451                 updateOptions( getOptions() );
 452             }
 453             else if ( o == _inference_from_msa_item ) {
 454                 executePhyleneticInference( false );
 455             }
 456             else if ( o == _inference_from_seqs_item ) {
 457                 executePhyleneticInference( true );
 458             }
 459             _contentpane.repaint();
 460         }
 461         catch ( final Exception ex ) {
 462             AptxUtil.unexpectedException( ex );
 463         }
 464         catch ( final Error err ) {
 465             AptxUtil.unexpectedError( err );
 466         }
 467     }
 468
 469     public void end() {
 470         _mainpanel.terminate();
 471         _contentpane.removeAll();
 472         setVisible( false );
 473         dispose();
 474     }
 475
 476     @Override
 477     public MainPanel getMainPanel() {
 478         return _mainpanel;
 479     }
 480
 481     public Msa getMsa() {
 482         return _msa;
 483     }
 484
 485     public File getMsaFile() {
 486         return _msa_file;
 487     }
 488
 489     public List<MolecularSequence> getSeqs() {
 490         return _seqs;
 491     }
 492
 493     public File getSeqsFile() {
 494         return _seqs_file;
 495     }
 496
 497     public void readMsaFromFile() {
 498         // Set an initial directory if none set yet
 499         final File my_dir = getCurrentDir();
 500         _msa_filechooser.setMultiSelectionEnabled( false );
 501         // Open file-open dialog and set current directory
 502         if ( my_dir != null ) {
 503             _msa_filechooser.setCurrentDirectory( my_dir );
 504         }
 505         final int result = _msa_filechooser.showOpenDialog( _contentpane );
 506         // All done: get the msa
 507         final File file = _msa_filechooser.getSelectedFile();
 508         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
 509         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 510             setMsaFile( null );
 511             setMsa( null );
 512             Msa msa = null;
 513             try {
 514                 final InputStream is = new FileInputStream( file );
 515                 if ( FastaParser.isLikelyFasta( file ) ) {
 516                     msa = FastaParser.parseMsa( is );
 517                 }
 518                 else {
 519                     msa = GeneralMsaParser.parse( is );
 520                 }
 521             }
 522             catch ( final MsaFormatException e ) {
 523                 setArrowCursor();
 524                 JOptionPane.showMessageDialog( this,
 525                                                e.getLocalizedMessage(),
 526                                                "Multiple sequence alignment format error",
 527                                                JOptionPane.ERROR_MESSAGE );
 528                 return;
 529             }
 530             catch ( final IOException e ) {
 531                 setArrowCursor();
 532                 JOptionPane.showMessageDialog( this,
 533                                                e.getLocalizedMessage(),
 534                                                "Failed to read multiple sequence alignment",
 535                                                JOptionPane.ERROR_MESSAGE );
 536                 return;
 537             }
 538             catch ( final IllegalArgumentException e ) {
 539                 setArrowCursor();
 540                 JOptionPane.showMessageDialog( this,
 541                                                e.getLocalizedMessage(),
 542                                                "Unexpected error during reading of multiple sequence alignment",
 543                                                JOptionPane.ERROR_MESSAGE );
 544                 return;
 545             }
 546             catch ( final Exception e ) {
 547                 setArrowCursor();
 548                 e.printStackTrace();
 549                 JOptionPane.showMessageDialog( this,
 550                                                e.getLocalizedMessage(),
 551                                                "Unexpected error during reading of multiple sequence alignment",
 552                                                JOptionPane.ERROR_MESSAGE );
 553                 return;
 554             }
 555             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
 556                 JOptionPane.showMessageDialog( this,
 557                                                "Multiple sequence alignment is empty",
 558                                                "Illegal Multiple Sequence Alignment",
 559                                                JOptionPane.ERROR_MESSAGE );
 560                 return;
 561             }
 562             if ( msa.getNumberOfSequences() < 4 ) {
 563                 JOptionPane.showMessageDialog( this,
 564                                                "Multiple sequence alignment needs to contain at least 3 sequences",
 565                                                "Illegal multiple sequence alignment",
 566                                                JOptionPane.ERROR_MESSAGE );
 567                 return;
 568             }
 569             if ( msa.getLength() < 2 ) {
 570                 JOptionPane.showMessageDialog( this,
 571                                                "Multiple sequence alignment needs to contain at least 2 residues",
 572                                                "Illegal multiple sequence alignment",
 573                                                JOptionPane.ERROR_MESSAGE );
 574                 return;
 575             }
 576             System.gc();
 577             setMsaFile( _msa_filechooser.getSelectedFile() );
 578             setMsa( msa );
 579         }
 580     }
 581
 582     public void readSeqsFromFileforPI() {
 583         // Set an initial directory if none set yet
 584         final File my_dir = getCurrentDir();
 585         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 586         // Open file-open dialog and set current directory
 587         if ( my_dir != null ) {
 588             _seqs_pi_filechooser.setCurrentDirectory( my_dir );
 589         }
 590         final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
 591         // All done: get the seqs
 592         final File file = _seqs_pi_filechooser.getSelectedFile();
 593         setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
 594         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 595             setSeqsFile( null );
 596             setSeqs( null );
 597             List<MolecularSequence> seqs = null;
 598             try {
 599                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
 600                     seqs = FastaParser.parse( new FileInputStream( file ) );
 601                     for( final MolecularSequence seq : seqs ) {
 602                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
 603                     }
 604                 }
 605                 else {
 606                     //TODO error
 607                 }
 608             }
 609             catch ( final MsaFormatException e ) {
 610                 setArrowCursor();
 611                 JOptionPane.showMessageDialog( this,
 612                                                e.getLocalizedMessage(),
 613                                                "Multiple sequence file format error",
 614                                                JOptionPane.ERROR_MESSAGE );
 615                 return;
 616             }
 617             catch ( final IOException e ) {
 618                 setArrowCursor();
 619                 JOptionPane.showMessageDialog( this,
 620                                                e.getLocalizedMessage(),
 621                                                "Failed to read multiple sequence file",
 622                                                JOptionPane.ERROR_MESSAGE );
 623                 return;
 624             }
 625             catch ( final IllegalArgumentException e ) {
 626                 setArrowCursor();
 627                 JOptionPane.showMessageDialog( this,
 628                                                e.getLocalizedMessage(),
 629                                                "Unexpected error during reading of multiple sequence file",
 630                                                JOptionPane.ERROR_MESSAGE );
 631                 return;
 632             }
 633             catch ( final Exception e ) {
 634                 setArrowCursor();
 635                 e.printStackTrace();
 636                 JOptionPane.showMessageDialog( this,
 637                                                e.getLocalizedMessage(),
 638                                                "Unexpected error during reading of multiple sequence file",
 639                                                JOptionPane.ERROR_MESSAGE );
 640                 return;
 641             }
 642             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 643                 JOptionPane.showMessageDialog( this,
 644                                                "Multiple sequence file is empty",
 645                                                "Illegal multiple sequence file",
 646                                                JOptionPane.ERROR_MESSAGE );
 647                 return;
 648             }
 649             if ( seqs.size() < 4 ) {
 650                 JOptionPane.showMessageDialog( this,
 651                                                "Multiple sequence file needs to contain at least 3 sequences",
 652                                                "Illegal multiple sequence file",
 653                                                JOptionPane.ERROR_MESSAGE );
 654                 return;
 655             }
 656             //  if ( msa.getLength() < 2 ) {
 657             //       JOptionPane.showMessageDialog( this,
 658             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
 659             //                                      "Illegal multiple sequence file",
 660             //                                      JOptionPane.ERROR_MESSAGE );
 661             //       return;
 662             //   }
 663             System.gc();
 664             setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
 665             setSeqs( seqs );
 666         }
 667     }
 668
 669     private void addExpressionValuesFromFile() {
 670         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
 671             JOptionPane.showMessageDialog( this,
 672                                            "Need to load evolutionary tree first",
 673                                            "Can Not Read Expression Values",
 674                                            JOptionPane.WARNING_MESSAGE );
 675             return;
 676         }
 677         final File my_dir = getCurrentDir();
 678         if ( my_dir != null ) {
 679             _values_filechooser.setCurrentDirectory( my_dir );
 680         }
 681         final int result = _values_filechooser.showOpenDialog( _contentpane );
 682         final File file = _values_filechooser.getSelectedFile();
 683         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
 684             BasicTable<String> t = null;
 685             try {
 686                 t = BasicTableParser.parse( file, '\t' );
 687                 if ( t.getNumberOfColumns() < 2 ) {
 688                     t = BasicTableParser.parse( file, ',' );
 689                 }
 690                 if ( t.getNumberOfColumns() < 2 ) {
 691                     t = BasicTableParser.parse( file, ' ' );
 692                 }
 693             }
 694             catch ( final IOException e ) {
 695                 JOptionPane.showMessageDialog( this,
 696                                                e.getMessage(),
 697                                                "Could Not Read Expression Value Table",
 698                                                JOptionPane.ERROR_MESSAGE );
 699                 return;
 700             }
 701             if ( t.getNumberOfColumns() < 2 ) {
 702                 JOptionPane.showMessageDialog( this,
 703                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
 704                                                "Problem with Expression Value Table",
 705                                                JOptionPane.ERROR_MESSAGE );
 706                 return;
 707             }
 708             if ( t.getNumberOfRows() < 1 ) {
 709                 JOptionPane.showMessageDialog( this,
 710                                                "Table contains zero rows",
 711                                                "Problem with Expression Value Table",
 712                                                JOptionPane.ERROR_MESSAGE );
 713                 return;
 714             }
 715             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
 716             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
 717                 JOptionPane.showMessageDialog( this,
 718                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
 719                                                        + phy.getNumberOfExternalNodes() + " external nodes",
 720                                                "Warning",
 721                                                JOptionPane.WARNING_MESSAGE );
 722             }
 723             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 724             int not_found = 0;
 725             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
 726                 final PhylogenyNode node = iter.next();
 727                 final String node_name = node.getName();
 728                 if ( !ForesterUtil.isEmpty( node_name ) ) {
 729                     int row = -1;
 730                     try {
 731                         row = t.findRow( node_name );
 732                     }
 733                     catch ( final IllegalArgumentException e ) {
 734                         JOptionPane.showMessageDialog( this,
 735                                                        e.getMessage(),
 736                                                        "Error Mapping Node Identifiers to Expression Value Identifiers",
 737                                                        JOptionPane.ERROR_MESSAGE );
 738                         return;
 739                     }
 740                     if ( row < 0 ) {
 741                         if ( node.isExternal() ) {
 742                             not_found++;
 743                         }
 744                         continue;
 745                     }
 746                     final List<Double> l = new ArrayList<Double>();
 747                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
 748                         double d = -100;
 749                         try {
 750                             d = Double.parseDouble( t.getValueAsString( col, row ) );
 751                         }
 752                         catch ( final NumberFormatException e ) {
 753                             JOptionPane.showMessageDialog( this,
 754                                                            "Could not parse \"" + t.getValueAsString( col, row )
 755                                                                    + "\" into a decimal value",
 756                                                            "Issue with Expression Value Table",
 757                                                            JOptionPane.ERROR_MESSAGE );
 758                             return;
 759                         }
 760                         stats.addValue( d );
 761                         l.add( d );
 762                     }
 763                     if ( !l.isEmpty() ) {
 764                         if ( node.getNodeData().getProperties() != null ) {
 765                             node.getNodeData().getProperties()
 766                                     .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
 767                         }
 768                         node.getNodeData().setVector( l );
 769                     }
 770                 }
 771             }
 772             if ( not_found > 0 ) {
 773                 JOptionPane
 774                         .showMessageDialog( this,
 775                                             "Could not fine expression values for " + not_found + " external node(s)",
 776                                             "Warning",
 777                                             JOptionPane.WARNING_MESSAGE );
 778             }
 779             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
 780         }
 781     }
 782
 783     private void addSequencesFromFile() {
 784         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
 785             JOptionPane.showMessageDialog( this,
 786                                            "Need to load evolutionary tree first",
 787                                            "Can Not Read Sequences",
 788                                            JOptionPane.WARNING_MESSAGE );
 789             return;
 790         }
 791         final File my_dir = getCurrentDir();
 792         if ( my_dir != null ) {
 793             _sequences_filechooser.setCurrentDirectory( my_dir );
 794         }
 795         final int result = _sequences_filechooser.showOpenDialog( _contentpane );
 796         final File file = _sequences_filechooser.getSelectedFile();
 797         List<MolecularSequence> seqs = null;
 798         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 799             try {
 800                 final FileInputStream fis1 = new FileInputStream( file );
 801                 if ( FastaParser.isLikelyFasta( fis1 ) ) {
 802                     final FileInputStream fis2 = new FileInputStream( file );
 803                     seqs = FastaParser.parse( fis2 );
 804                     try {
 805                         fis2.close();
 806                     }
 807                     catch ( final Exception e ) {
 808                         // Ignore.
 809                     }
 810                 }
 811                 else {
 812                     JOptionPane.showMessageDialog( this,
 813                                                    "Format does not appear to be Fasta",
 814                                                    "Multiple sequence file format error",
 815                                                    JOptionPane.ERROR_MESSAGE );
 816                     return;
 817                 }
 818                 try {
 819                     fis1.close();
 820                 }
 821                 catch ( final Exception e ) {
 822                     // Ignore.
 823                 }
 824             }
 825             catch ( final MsaFormatException e ) {
 826                 setArrowCursor();
 827                 JOptionPane.showMessageDialog( this,
 828                                                e.getLocalizedMessage(),
 829                                                "Multiple sequence file format error",
 830                                                JOptionPane.ERROR_MESSAGE );
 831                 return;
 832             }
 833             catch ( final IOException e ) {
 834                 setArrowCursor();
 835                 JOptionPane.showMessageDialog( this,
 836                                                e.getLocalizedMessage(),
 837                                                "Failed to read multiple sequence file",
 838                                                JOptionPane.ERROR_MESSAGE );
 839                 return;
 840             }
 841             catch ( final Exception e ) {
 842                 setArrowCursor();
 843                 e.printStackTrace();
 844                 JOptionPane.showMessageDialog( this,
 845                                                e.getLocalizedMessage(),
 846                                                "Unexpected error during reading of multiple sequence file",
 847                                                JOptionPane.ERROR_MESSAGE );
 848                 return;
 849             }
 850             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 851                 JOptionPane.showMessageDialog( this,
 852                                                "Multiple sequence file is empty",
 853                                                "Empty multiple sequence file",
 854                                                JOptionPane.ERROR_MESSAGE );
 855                 setArrowCursor();
 856                 return;
 857             }
 858         }
 859         if ( seqs != null ) {
 860             for( final MolecularSequence seq : seqs ) {
 861                 System.out.println( seq.getIdentifier() );
 862             }
 863             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
 864             int total_counter = 0;
 865             int attached_counter = 0;
 866             for( final MolecularSequence seq : seqs ) {
 867                 ++total_counter;
 868                 final String seq_name = seq.getIdentifier();
 869                 if ( !ForesterUtil.isEmpty( seq_name ) ) {
 870                     List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
 871                     if ( nodes.isEmpty() ) {
 872                         nodes = phy.getNodesViaSequenceSymbol( seq_name );
 873                     }
 874                     if ( nodes.isEmpty() ) {
 875                         nodes = phy.getNodesViaGeneName( seq_name );
 876                     }
 877                     if ( nodes.isEmpty() ) {
 878                         nodes = phy.getNodes( seq_name );
 879                     }
 880                     if ( nodes.size() > 1 ) {
 881                         JOptionPane.showMessageDialog( this,
 882                                                        "Sequence name \"" + seq_name + "\" is not unique",
 883                                                        "Sequence name not unique",
 884                                                        JOptionPane.ERROR_MESSAGE );
 885                         setArrowCursor();
 886                         return;
 887                     }
 888                     final String[] a = seq_name.split( "\\s" );
 889                     if ( nodes.isEmpty() && ( a.length > 1 ) ) {
 890                         final String seq_name_split = a[ 0 ];
 891                         nodes = phy.getNodesViaSequenceName( seq_name_split );
 892                         if ( nodes.isEmpty() ) {
 893                             nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
 894                         }
 895                         if ( nodes.isEmpty() ) {
 896                             nodes = phy.getNodes( seq_name_split );
 897                         }
 898                         if ( nodes.size() > 1 ) {
 899                             JOptionPane.showMessageDialog( this,
 900                                                            "Split sequence name \"" + seq_name_split
 901                                                                    + "\" is not unique",
 902                                                            "Sequence name not unique",
 903                                                            JOptionPane.ERROR_MESSAGE );
 904                             setArrowCursor();
 905                             return;
 906                         }
 907                     }
 908                     if ( nodes.size() == 1 ) {
 909                         ++attached_counter;
 910                         final PhylogenyNode n = nodes.get( 0 );
 911                         if ( !n.getNodeData().isHasSequence() ) {
 912                             n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
 913                         }
 914                         n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
 915                         if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
 916                             n.getNodeData().getSequence().setName( seq_name );
 917                         }
 918                     }
 919                 }
 920             }
 921             if ( attached_counter > 0 ) {
 922                 int ext_nodes = 0;
 923                 int ext_nodes_with_seq = 0;
 924                 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 925                     ++ext_nodes;
 926                     final PhylogenyNode n = iter.next();
 927                     if ( n.getNodeData().isHasSequence()
 928                             && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
 929                         ++ext_nodes_with_seq;
 930                     }
 931                 }
 932                 final String s;
 933                 if ( ext_nodes == ext_nodes_with_seq ) {
 934                     s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
 935                 }
 936                 else {
 937                     s = ext_nodes_with_seq + " out of " + ext_nodes
 938                             + " external nodes now have a molecular sequence attached to them.";
 939                 }
 940                 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
 941                     JOptionPane.showMessageDialog( this,
 942                                                    "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
 943                                                    "All sequences attached",
 944                                                    JOptionPane.INFORMATION_MESSAGE );
 945                 }
 946                 else {
 947                     JOptionPane.showMessageDialog( this,
 948                                                    "Attached " + attached_counter + " sequences out of a total of "
 949                                                            + total_counter + " sequences.\n" + s,
 950                                                    attached_counter + " sequences attached",
 951                                                    JOptionPane.WARNING_MESSAGE );
 952                 }
 953             }
 954             else {
 955                 JOptionPane.showMessageDialog( this,
 956                                                "No maching tree node for any of the " + total_counter + " sequences",
 957                                                "Could not attach any sequences",
 958                                                JOptionPane.ERROR_MESSAGE );
 959             }
 960         }
 961     }
 962
 963     private void closeCurrentPane() {
 964         if ( getMainPanel().getCurrentTreePanel() != null ) {
 965             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
 966                 final int r = JOptionPane.showConfirmDialog( this,
 967                                                              "Close tab despite potentially unsaved changes?",
 968                                                              "Close Tab?",
 969                                                              JOptionPane.YES_NO_OPTION );
 970                 if ( r != JOptionPane.YES_OPTION ) {
 971                     return;
 972                 }
 973             }
 974             getMainPanel().closeCurrentPane();
 975             activateSaveAllIfNeeded();
 976         }
 977     }
 978
 979     private void collapseBelowThreshold( final Phylogeny phy ) {
 980         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 981         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
 982         double min_support = Double.MAX_VALUE;
 983         boolean conf_present = false;
 984         while ( it.hasNext() ) {
 985             final PhylogenyNode n = it.next();
 986             if ( !n.isExternal() && !n.isRoot() ) {
 987                 final List<Confidence> c = n.getBranchData().getConfidences();
 988                 if ( ( c != null ) && ( c.size() > 0 ) ) {
 989                     conf_present = true;
 990                     double max = 0;
 991                     for( final Confidence confidence : c ) {
 992                         if ( confidence.getValue() > max ) {
 993                             max = confidence.getValue();
 994                         }
 995                     }
 996                     if ( max < getMinNotCollapseConfidenceValue() ) {
 997                         to_be_removed.add( n );
 998                     }
 999                     if ( max < min_support ) {
1000                         min_support = max;
1001                     }
1002                 }
1003             }
1004         }
1005         if ( conf_present ) {
1006             for( final PhylogenyNode node : to_be_removed ) {
1007                 PhylogenyMethods.removeNode( node, phy );
1008             }
1009             if ( to_be_removed.size() > 0 ) {
1010                 phy.externalNodesHaveChanged();
1011                 phy.clearHashIdToNodeMap();
1012                 phy.recalculateNumberOfExternalDescendants( true );
1013                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1014                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1015                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1016                 getCurrentTreePanel().setNodeInPreorderToNull();
1017                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1018                 getCurrentTreePanel().resetPreferredSize();
1019                 getCurrentTreePanel().setEdited( true );
1020                 getCurrentTreePanel().repaint();
1021                 repaint();
1022             }
1023             if ( to_be_removed.size() > 0 ) {
1024                 JOptionPane.showMessageDialog( this,
1025                                                "Collapsed " + to_be_removed.size()
1026                                                        + " branches with\nconfidence values below "
1027                                                        + getMinNotCollapseConfidenceValue(),
1028                                                "Collapsed " + to_be_removed.size() + " branches",
1029                                                JOptionPane.INFORMATION_MESSAGE );
1030             }
1031             else {
1032                 JOptionPane.showMessageDialog( this,
1033                                                "No branch collapsed,\nminimum confidence value per branch is "
1034                                                        + min_support,
1035                                                "No branch collapsed",
1036                                                JOptionPane.INFORMATION_MESSAGE );
1037             }
1038         }
1039         else {
1040             JOptionPane.showMessageDialog( this,
1041                                            "No branch collapsed because no confidence values present",
1042                                            "No confidence values present",
1043                                            JOptionPane.INFORMATION_MESSAGE );
1044         }
1045     }
1046
1047     private void collapseBelowBranchLengthThreshold() {
1048         if ( getCurrentTreePanel() != null ) {
1049             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1050             if ( ( phy != null ) && !phy.isEmpty() ) {
1051                 final String s = ( String ) JOptionPane.showInputDialog( this,
1052                                                                          "Please enter the minimum branch length value\n",
1053                                                                          "Minimal Branch Length Value",
1054                                                                          JOptionPane.QUESTION_MESSAGE,
1055                                                                          null,
1056                                                                          null,
1057                                                                          getMinNotCollapseBlValue() );
1058                 if ( !ForesterUtil.isEmpty( s ) ) {
1059                     boolean success = true;
1060                     double m = 0.0;
1061                     final String m_str = s.trim();
1062                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1063                         try {
1064                             m = Double.parseDouble( m_str );
1065                         }
1066                         catch ( final Exception ex ) {
1067                             success = false;
1068                         }
1069                     }
1070                     else {
1071                         success = false;
1072                     }
1073                     if ( success && ( m >= 0.0 ) ) {
1074                         setMinNotCollapseBlValue( m );
1075                         collapseBl( phy );
1076                     }
1077                 }
1078             }
1079         }
1080     }
1081
1082     private void collapseBelowThreshold() {
1083         if ( getCurrentTreePanel() != null ) {
1084             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1085             if ( ( phy != null ) && !phy.isEmpty() ) {
1086                 final String s = ( String ) JOptionPane.showInputDialog( this,
1087                                                                          "Please enter the minimum confidence value\n",
1088                                                                          "Minimal Confidence Value",
1089                                                                          JOptionPane.QUESTION_MESSAGE,
1090                                                                          null,
1091                                                                          null,
1092                                                                          getMinNotCollapseConfidenceValue() );
1093                 if ( !ForesterUtil.isEmpty( s ) ) {
1094                     boolean success = true;
1095                     double m = 0.0;
1096                     final String m_str = s.trim();
1097                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1098                         try {
1099                             m = Double.parseDouble( m_str );
1100                         }
1101                         catch ( final Exception ex ) {
1102                             success = false;
1103                         }
1104                     }
1105                     else {
1106                         success = false;
1107                     }
1108                     if ( success && ( m >= 0.0 ) ) {
1109                         setMinNotCollapseConfidenceValue( m );
1110                         collapseBelowThreshold( phy );
1111                     }
1112                 }
1113             }
1114         }
1115     }
1116
1117     private void collapseBl( final Phylogeny phy ) {
1118         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1119         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1120         double min_bl = Double.MAX_VALUE;
1121         boolean bl_present = false;
1122         while ( it.hasNext() ) {
1123             final PhylogenyNode n = it.next();
1124             if ( !n.isExternal() && !n.isRoot() ) {
1125                 final double bl = n.getDistanceToParent();
1126                 if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
1127                     bl_present = true;
1128                     if ( bl < getMinNotCollapseBlValue() ) {
1129                         to_be_removed.add( n );
1130                     }
1131                     if ( bl < min_bl ) {
1132                         min_bl = bl;
1133                     }
1134                 }
1135             }
1136         }
1137         if ( bl_present ) {
1138             for( final PhylogenyNode node : to_be_removed ) {
1139                 PhylogenyMethods.removeNode( node, phy );
1140             }
1141             if ( to_be_removed.size() > 0 ) {
1142                 phy.externalNodesHaveChanged();
1143                 phy.clearHashIdToNodeMap();
1144                 phy.recalculateNumberOfExternalDescendants( true );
1145                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1146                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1147                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1148                 getCurrentTreePanel().setNodeInPreorderToNull();
1149                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1150                 getCurrentTreePanel().resetPreferredSize();
1151                 getCurrentTreePanel().setEdited( true );
1152                 getCurrentTreePanel().repaint();
1153                 repaint();
1154             }
1155             if ( to_be_removed.size() > 0 ) {
1156                 JOptionPane.showMessageDialog( this,
1157                                                "Collapsed " + to_be_removed.size()
1158                                                        + " branches with\nbranch length values below "
1159                                                        + getMinNotCollapseBlValue(),
1160                                                "Collapsed " + to_be_removed.size() + " branches",
1161                                                JOptionPane.INFORMATION_MESSAGE );
1162             }
1163             else {
1164                 JOptionPane.showMessageDialog( this,
1165                                                "No branch collapsed,\nminimum branch length is " + min_bl,
1166                                                "No branch collapsed",
1167                                                JOptionPane.INFORMATION_MESSAGE );
1168             }
1169         }
1170         else {
1171             JOptionPane.showMessageDialog( this,
1172                                            "No branch collapsed because no branch length values present",
1173                                            "No branch length values present",
1174                                            JOptionPane.INFORMATION_MESSAGE );
1175         }
1176     }
1177
1178     private PhyloXmlParser createPhyloXmlParser() {
1179         PhyloXmlParser xml_parser = null;
1180         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1181             try {
1182                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1183             }
1184             catch ( final Exception e ) {
1185                 JOptionPane.showMessageDialog( this,
1186                                                e.getLocalizedMessage(),
1187                                                "failed to create validating XML parser",
1188                                                JOptionPane.WARNING_MESSAGE );
1189             }
1190         }
1191         if ( xml_parser == null ) {
1192             xml_parser = PhyloXmlParser.createPhyloXmlParser();
1193         }
1194         return xml_parser;
1195     }
1196
1197     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1198         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1199                                                                       getPhylogeneticInferenceOptions(),
1200                                                                       from_unaligned_seqs );
1201         dialog.activate();
1202         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1203             if ( !from_unaligned_seqs ) {
1204                 if ( getMsa() != null ) {
1205                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1206                                                                                     getPhylogeneticInferenceOptions()
1207                                                                                             .copy(),
1208                                                                                     this );
1209                     new Thread( inferrer ).start();
1210                 }
1211                 else {
1212                     JOptionPane.showMessageDialog( this,
1213                                                    "No multiple sequence alignment selected",
1214                                                    "Phylogenetic Inference Not Launched",
1215                                                    JOptionPane.WARNING_MESSAGE );
1216                 }
1217             }
1218             else {
1219                 if ( getSeqs() != null ) {
1220                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1221                                                                                     getPhylogeneticInferenceOptions()
1222                                                                                             .copy(),
1223                                                                                     this );
1224                     new Thread( inferrer ).start();
1225                 }
1226                 else {
1227                     JOptionPane.showMessageDialog( this,
1228                                                    "No input sequences selected",
1229                                                    "Phylogenetic Inference Not Launched",
1230                                                    JOptionPane.WARNING_MESSAGE );
1231                 }
1232             }
1233         }
1234     }
1235
1236     private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1237         final StringBuilder sb = new StringBuilder();
1238         final StringBuilder sb_failed = new StringBuilder();
1239         int counter = 0;
1240         int counter_failed = 0;
1241         if ( getCurrentTreePanel() != null ) {
1242             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1243             if ( ( phy != null ) && !phy.isEmpty() ) {
1244                 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1245                 while ( it.hasNext() ) {
1246                     final PhylogenyNode n = it.next();
1247                     final String name = n.getName().trim();
1248                     if ( !ForesterUtil.isEmpty( name ) ) {
1249                         final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
1250                                                                                        TAXONOMY_EXTRACTION.AGGRESSIVE );
1251                         if ( !ForesterUtil.isEmpty( nt ) ) {
1252                             if ( counter < 15 ) {
1253                                 sb.append( name + ": " + nt + "\n" );
1254                             }
1255                             else if ( counter == 15 ) {
1256                                 sb.append( "...\n" );
1257                             }
1258                             counter++;
1259                         }
1260                         else {
1261                             if ( counter_failed < 15 ) {
1262                                 sb_failed.append( name + "\n" );
1263                             }
1264                             else if ( counter_failed == 15 ) {
1265                                 sb_failed.append( "...\n" );
1266                             }
1267                             counter_failed++;
1268                         }
1269                     }
1270                 }
1271                 if ( counter > 0 ) {
1272                     String failed = "";
1273                     String all = "all ";
1274                     if ( counter_failed > 0 ) {
1275                         all = "";
1276                         failed = "\nCould not extract taxonomic data for " + counter_failed + " named external nodes:\n"
1277                                 + sb_failed;
1278                     }
1279                     JOptionPane.showMessageDialog( this,
1280                                                    "Extracted taxonomic data from " + all + counter
1281                                                            + " named external nodes:\n" + sb.toString() + failed,
1282                                                    "Taxonomic Data Extraction Completed",
1283                                                    counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1284                                                            : JOptionPane.INFORMATION_MESSAGE );
1285                 }
1286                 else {
1287                     JOptionPane.showMessageDialog( this,
1288                                                    "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1289                                                            + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1290                                                            + "or nodes already have taxonomic data?\n",
1291                                                    "No Taxonomic Data Extracted",
1292                                                    JOptionPane.ERROR_MESSAGE );
1293                 }
1294             }
1295         }
1296     }
1297
1298     private double getMinNotCollapseBlValue() {
1299         return _min_not_collapse_bl;
1300     }
1301
1302     private double getMinNotCollapseConfidenceValue() {
1303         return _min_not_collapse;
1304     }
1305
1306     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1307         if ( _phylogenetic_inference_options == null ) {
1308             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1309         }
1310         return _phylogenetic_inference_options;
1311     }
1312
1313     private boolean isUnsavedDataPresent() {
1314         final List<TreePanel> tps = getMainPanel().getTreePanels();
1315         for( final TreePanel tp : tps ) {
1316             if ( tp.isEdited() ) {
1317                 return true;
1318             }
1319         }
1320         return false;
1321     }
1322
1323     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1324         if ( getCurrentTreePanel() != null ) {
1325             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1326             if ( ( phy != null ) && !phy.isEmpty() ) {
1327                 PhylogenyMethods.transferNodeNameToField( phy,
1328                                                           PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME,
1329                                                           false );
1330             }
1331         }
1332     }
1333
1334     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1335         if ( getCurrentTreePanel() != null ) {
1336             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1337             if ( ( phy != null ) && !phy.isEmpty() ) {
1338                 PhylogenyMethods.transferNodeNameToField( phy,
1339                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1340                                                           false );
1341             }
1342         }
1343     }
1344
1345     private void newTree() {
1346         final Phylogeny[] phys = new Phylogeny[ 1 ];
1347         final Phylogeny phy = new Phylogeny();
1348         final PhylogenyNode node = new PhylogenyNode();
1349         phy.setRoot( node );
1350         phy.setRooted( true );
1351         phys[ 0 ] = phy;
1352         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1353         _mainpanel.getControlPanel().showWhole();
1354         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1355         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1356         if ( getMainPanel().getMainFrame() == null ) {
1357             // Must be "E" applet version.
1358             ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
1359                     .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1360         }
1361         else {
1362             getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1363         }
1364         activateSaveAllIfNeeded();
1365         System.gc();
1366     }
1367
1368     private void obtainDetailedTaxonomicInformation() {
1369         if ( getCurrentTreePanel() != null ) {
1370             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1371             if ( ( phy != null ) && !phy.isEmpty() ) {
1372                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1373                                                                        _mainpanel.getCurrentTreePanel(),
1374                                                                        phy.copy(),
1375                                                                        false,
1376                                                                        true );
1377                 new Thread( t ).start();
1378             }
1379         }
1380     }
1381
1382     private void obtainDetailedTaxonomicInformationDelete() {
1383         if ( getCurrentTreePanel() != null ) {
1384             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1385             if ( ( phy != null ) && !phy.isEmpty() ) {
1386                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1387                                                                        _mainpanel.getCurrentTreePanel(),
1388                                                                        phy.copy(),
1389                                                                        true,
1390                                                                        true );
1391                 new Thread( t ).start();
1392             }
1393         }
1394     }
1395
1396     private void obtainSequenceInformation() {
1397         if ( getCurrentTreePanel() != null ) {
1398             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1399             if ( ( phy != null ) && !phy.isEmpty() ) {
1400                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1401                                                                          _mainpanel.getCurrentTreePanel(),
1402                                                                          phy.copy() );
1403                 new Thread( u ).start();
1404             }
1405         }
1406     }
1407
1408     private void preProcessTreesUponReading( final Phylogeny[] phys ) {
1409         for( final Phylogeny phy : phys ) {
1410             if ( ( phy != null ) && !phy.isEmpty() ) {
1411                 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
1412                     final PhylogenyNode n = it.next();
1413                     if ( n.isExternal() ) {
1414                         if ( n.getNodeData().isHasSequence() ) {
1415                             final Sequence s = n.getNodeData().getSequence();
1416                             if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {
1417                                 if ( ( s.getAccession() != null )
1418                                         && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {
1419                                     s.setGeneName( s.getAccession().getValue() );
1420                                 }
1421                                 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
1422                                     s.setGeneName( n.getName() );
1423                                 }
1424                             }
1425                         }
1426                     }
1427                 }
1428             }
1429         }
1430     }
1431
1432     private void readPhylogeniesFromFile() {
1433         boolean exception = false;
1434         Phylogeny[] phys = null;
1435         // Set an initial directory if none set yet
1436         final File my_dir = getCurrentDir();
1437         // Open file-open dialog and set current directory
1438         if ( my_dir != null ) {
1439             _open_filechooser.setCurrentDirectory( my_dir );
1440         }
1441         final int result = _open_filechooser.showOpenDialog( _contentpane );
1442         // All done: get the file
1443         final File[] files = _open_filechooser.getSelectedFiles();
1444         setCurrentDir( _open_filechooser.getCurrentDirectory() );
1445         boolean nhx_or_nexus = false;
1446         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1447             for( final File file : files ) {
1448                 if ( ( file != null ) && !file.isDirectory() ) {
1449                     if ( _mainpanel.getCurrentTreePanel() != null ) {
1450                         _mainpanel.getCurrentTreePanel().setWaitCursor();
1451                     }
1452                     else {
1453                         _mainpanel.setWaitCursor();
1454                     }
1455                     if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )
1456                             || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {
1457                         try {
1458                             final NHXParser nhx = new NHXParser();
1459                             setSpecialOptionsForNhxParser( nhx );
1460                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
1461                             nhx_or_nexus = true;
1462                         }
1463                         catch ( final Exception e ) {
1464                             exception = true;
1465                             exceptionOccuredDuringOpenFile( e );
1466                         }
1467                     }
1468                     else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
1469                         warnIfNotPhyloXmlValidation( getConfiguration() );
1470                         try {
1471                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
1472                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
1473                         }
1474                         catch ( final Exception e ) {
1475                             exception = true;
1476                             exceptionOccuredDuringOpenFile( e );
1477                         }
1478                     }
1479                     else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {
1480                         try {
1481                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1482                         }
1483                         catch ( final Exception e ) {
1484                             exception = true;
1485                             exceptionOccuredDuringOpenFile( e );
1486                         }
1487                     }
1488                     else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
1489                         try {
1490                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
1491                             setSpecialOptionsForNexParser( nex );
1492                             phys = PhylogenyMethods.readPhylogenies( nex, file );
1493                             nhx_or_nexus = true;
1494                         }
1495                         catch ( final Exception e ) {
1496                             exception = true;
1497                             exceptionOccuredDuringOpenFile( e );
1498                         }
1499                     }
1500                     // "*.*":
1501                     else {
1502                         try {
1503                             final PhylogenyParser parser = ParserUtils
1504                                     .createParserDependingOnFileType( file,
1505                                                                       getConfiguration()
1506                                                                               .isValidatePhyloXmlAgainstSchema() );
1507                             if ( parser instanceof NexusPhylogeniesParser ) {
1508                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
1509                                 setSpecialOptionsForNexParser( nex );
1510                                 nhx_or_nexus = true;
1511                             }
1512                             else if ( parser instanceof NHXParser ) {
1513                                 final NHXParser nhx = ( NHXParser ) parser;
1514                                 setSpecialOptionsForNhxParser( nhx );
1515                                 nhx_or_nexus = true;
1516                             }
1517                             else if ( parser instanceof PhyloXmlParser ) {
1518                                 warnIfNotPhyloXmlValidation( getConfiguration() );
1519                             }
1520                             phys = PhylogenyMethods.readPhylogenies( parser, file );
1521                         }
1522                         catch ( final Exception e ) {
1523                             exception = true;
1524                             exceptionOccuredDuringOpenFile( e );
1525                         }
1526                     }
1527                     if ( _mainpanel.getCurrentTreePanel() != null ) {
1528                         _mainpanel.getCurrentTreePanel().setArrowCursor();
1529                     }
1530                     else {
1531                         _mainpanel.setArrowCursor();
1532                     }
1533                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
1534                         boolean one_desc = false;
1535                         if ( nhx_or_nexus ) {
1536                             for( final Phylogeny phy : phys ) {
1537                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1538                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
1539                                 }
1540                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
1541                                     one_desc = true;
1542                                     break;
1543                                 }
1544                             }
1545                         }
1546                         if ( PREPROCESS_TREES ) {
1547                             preProcessTreesUponReading( phys );
1548                         }
1549                         AptxUtil.addPhylogeniesToTabs( phys,
1550                                                        file.getName(),
1551                                                        file.getAbsolutePath(),
1552                                                        getConfiguration(),
1553                                                        getMainPanel() );
1554                         _mainpanel.getControlPanel().showWhole();
1555                         if ( nhx_or_nexus && one_desc ) {
1556                             JOptionPane.showMessageDialog( this,
1557                                                            "One or more trees contain (a) node(s) with one descendant, "
1558                                                                    + ForesterUtil.LINE_SEPARATOR
1559                                                                    + "possibly indicating illegal parentheses within node names.",
1560                                                            "Warning: Possible Error in New Hampshire Formatted Data",
1561                                                            JOptionPane.WARNING_MESSAGE );
1562                         }
1563                     }
1564                 }
1565             }
1566         }
1567         activateSaveAllIfNeeded();
1568         System.gc();
1569     }
1570
1571     private void readSpeciesTreeFromFile() {
1572         Phylogeny t = null;
1573         boolean exception = false;
1574         final File my_dir = getCurrentDir();
1575         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
1576         if ( my_dir != null ) {
1577             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
1578         }
1579         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
1580         final File file = _open_filechooser_for_species_tree.getSelectedFile();
1581         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1582             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {
1583                 try {
1584                     final Phylogeny[] trees = PhylogenyMethods
1585                             .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
1586                     t = trees[ 0 ];
1587                 }
1588                 catch ( final Exception e ) {
1589                     exception = true;
1590                     exceptionOccuredDuringOpenFile( e );
1591                 }
1592             }
1593             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {
1594                 try {
1595                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1596                     t = trees[ 0 ];
1597                 }
1598                 catch ( final Exception e ) {
1599                     exception = true;
1600                     exceptionOccuredDuringOpenFile( e );
1601                 }
1602             }
1603             // "*.*":
1604             else {
1605                 try {
1606                     final Phylogeny[] trees = PhylogenyMethods
1607                             .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
1608                     t = trees[ 0 ];
1609                 }
1610                 catch ( final Exception e ) {
1611                     exception = true;
1612                     exceptionOccuredDuringOpenFile( e );
1613                 }
1614             }
1615             if ( !exception && ( t != null ) && !t.isRooted() ) {
1616                 exception = true;
1617                 t = null;
1618                 JOptionPane.showMessageDialog( this,
1619                                                "Species tree is not rooted",
1620                                                "Species tree not loaded",
1621                                                JOptionPane.ERROR_MESSAGE );
1622             }
1623             if ( !exception && ( t != null ) ) {
1624                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
1625                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
1626                     final PhylogenyNode node = it.next();
1627                     if ( !node.getNodeData().isHasTaxonomy() ) {
1628                         exception = true;
1629                         t = null;
1630                         JOptionPane.showMessageDialog( this,
1631                                                        "Species tree contains external node(s) without taxonomy information",
1632                                                        "Species tree not loaded",
1633                                                        JOptionPane.ERROR_MESSAGE );
1634                         break;
1635                     }
1636                     else {
1637                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
1638                             exception = true;
1639                             t = null;
1640                             JOptionPane
1641                                     .showMessageDialog( this,
1642                                                         "Taxonomy [" + node.getNodeData().getTaxonomy().asSimpleText()
1643                                                                 + "] is not unique in species tree",
1644                                                         "Species tree not loaded",
1645                                                         JOptionPane.ERROR_MESSAGE );
1646                             break;
1647                         }
1648                         else {
1649                             tax_set.add( node.getNodeData().getTaxonomy() );
1650                         }
1651                     }
1652                 }
1653             }
1654             if ( !exception && ( t != null ) ) {
1655                 setSpeciesTree( t );
1656                 JOptionPane.showMessageDialog( this,
1657                                                "Species tree successfully loaded",
1658                                                "Species tree loaded",
1659                                                JOptionPane.INFORMATION_MESSAGE );
1660             }
1661             _contentpane.repaint();
1662             System.gc();
1663         }
1664     }
1665
1666     private void setArrowCursor() {
1667         try {
1668             _mainpanel.getCurrentTreePanel().setArrowCursor();
1669         }
1670         catch ( final Exception ex ) {
1671             // Do nothing.
1672         }
1673     }
1674
1675     private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {
1676         _min_not_collapse_bl = min_not_collapse_bl;
1677     }
1678
1679     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
1680         _min_not_collapse = min_not_collapse;
1681     }
1682
1683     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
1684         _phylogenetic_inference_options = phylogenetic_inference_options;
1685     }
1686
1687     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
1688         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
1689         nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
1690         nex.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() );
1691     }
1692
1693     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
1694         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
1695         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
1696         nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
1697         nhx.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() );
1698     }
1699
1700     void buildAnalysisMenu() {
1701         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
1702         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
1703         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
1704         _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
1705         customizeJMenuItem( _gsdi_item );
1706         customizeJMenuItem( _gsdir_item );
1707         customizeJMenuItem( _load_species_tree_item );
1708         _analysis_menu.addSeparator();
1709         _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
1710         customizeJMenuItem( _lineage_inference );
1711         _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
1712         _jmenubar.add( _analysis_menu );
1713     }
1714
1715     @Override
1716     void buildFileMenu() {
1717         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
1718         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
1719         _file_jmenu.addSeparator();
1720         _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
1721         _file_jmenu.addSeparator();
1722         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
1723         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
1724                 .getAvailablePhylogeniesWebserviceClients().size() ];
1725         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
1726             final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
1727             _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
1728             _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
1729         }
1730         if ( getConfiguration().isEditable() ) {
1731             _file_jmenu.addSeparator();
1732             _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
1733             _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
1734         }
1735         _file_jmenu.addSeparator();
1736         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
1737         _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
1738         _save_all_item.setToolTipText( "Write all phylogenies to one file." );
1739         _save_all_item.setEnabled( false );
1740         _file_jmenu.addSeparator();
1741         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
1742         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" )
1743                 || AptxUtil.canWriteFormat( "TIF" ) ) {
1744             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
1745         }
1746         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
1747         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
1748         if ( AptxUtil.canWriteFormat( "gif" ) ) {
1749             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
1750         }
1751         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
1752             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
1753         }
1754         _file_jmenu.addSeparator();
1755         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
1756         _file_jmenu.addSeparator();
1757         _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
1758         _close_item.setToolTipText( "To close the current pane." );
1759         _close_item.setEnabled( true );
1760         _file_jmenu.addSeparator();
1761         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
1762         customizeJMenuItem( _open_item );
1763         _open_item.setFont( new Font( _open_item.getFont().getFontName(),
1764                                       Font.BOLD,
1765                                       _open_item.getFont().getSize() + 4 ) );
1766         customizeJMenuItem( _open_url_item );
1767         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
1768             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
1769         }
1770         customizeJMenuItem( _save_item );
1771         if ( getConfiguration().isEditable() ) {
1772             customizeJMenuItem( _new_item );
1773         }
1774         customizeJMenuItem( _close_item );
1775         customizeJMenuItem( _save_all_item );
1776         customizeJMenuItem( _write_to_pdf_item );
1777         customizeJMenuItem( _write_to_png_item );
1778         customizeJMenuItem( _write_to_jpg_item );
1779         customizeJMenuItem( _write_to_gif_item );
1780         customizeJMenuItem( _write_to_tif_item );
1781         customizeJMenuItem( _write_to_bmp_item );
1782         customizeJMenuItem( _print_item );
1783         customizeJMenuItem( _exit_item );
1784         _jmenubar.add( _file_jmenu );
1785     }
1786
1787     void buildOptionsMenu() {
1788         _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
1789         _options_jmenu.addChangeListener( new ChangeListener() {
1790
1791             @Override
1792             public void stateChanged( final ChangeEvent e ) {
1793                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
1794                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
1795                 MainFrame.setTextMinSupportMenuItem( _choose_minimal_confidence_mi,
1796                                                      getOptions(),
1797                                                      getCurrentTreePanel() );
1798                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi,
1799                                                          MainFrame.createCurrentFontDesc( getMainPanel()
1800                                                                  .getTreeFontSet() ) );
1801                 //  MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
1802                 MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
1803                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
1804                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
1805                 MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );
1806                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
1807                 try {
1808                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
1809                     getMainPanel().getControlPanel().setVisibilityOfX();
1810                 }
1811                 catch ( final Exception ignore ) {
1812                     // do nothing, not important.
1813                 }
1814             }
1815         } );
1816         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
1817         _options_jmenu
1818                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
1819         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
1820         _radio_group_1 = new ButtonGroup();
1821         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
1822          _radio_group_1.add( _non_lined_up_cladograms_rbmi );
1823         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
1824         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
1825         _options_jmenu
1826                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
1827         _options_jmenu
1828                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
1829         _options_jmenu
1830                 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
1831
1832         _options_jmenu
1833         .add( _collapsed_with_average_height_cbmi = new JCheckBoxMenuItem( "Proportional Height of Collapsed Subtrees" ) );
1834
1835
1836         _options_jmenu
1837                 .add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
1838
1839
1840
1841         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
1842             _options_jmenu
1843                     .add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
1844             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
1845         }
1846         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
1847         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
1848         _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
1849         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
1850         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
1851         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
1852         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
1853         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
1854         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
1855         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
1856         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
1857         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
1858         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
1859         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
1860         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
1861         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
1862         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
1863         _options_jmenu.addSeparator();
1864         _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );
1865         _options_jmenu.addSeparator();
1866         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
1867         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
1868         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
1869         _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
1870         _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
1871         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
1872         _options_jmenu
1873                 .add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
1874         _options_jmenu.addSeparator();
1875         _options_jmenu
1876                 .add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), getConfiguration() ) );
1877         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
1878         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
1879         _options_jmenu
1880                 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
1881         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
1882         _options_jmenu.addSeparator();
1883         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );
1884         _options_jmenu
1885                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
1886         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
1887         _options_jmenu
1888                 .add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) );
1889         _parse_beast_style_extended_nexus_tags_cbmi
1890                 .setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" );
1891         _options_jmenu
1892                 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
1893         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
1894         _options_jmenu
1895                 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
1896         _options_jmenu
1897                 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
1898         _options_jmenu
1899                 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
1900         _extract_taxonomy_pfam_strict_rbmi
1901                 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
1902         _extract_taxonomy_pfam_relaxed_rbmi
1903                 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
1904         _extract_taxonomy_agressive_rbmi
1905                 .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
1906         _radio_group_2 = new ButtonGroup();
1907         _radio_group_2.add( _extract_taxonomy_no_rbmi );
1908         _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
1909         _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
1910         _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
1911         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );
1912         _options_jmenu
1913                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
1914         _use_brackets_for_conf_in_nh_export_cbmi
1915                 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
1916         _options_jmenu
1917                 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
1918         customizeJMenuItem( _choose_font_mi );
1919         customizeJMenuItem( _choose_minimal_confidence_mi );
1920         customizeJMenuItem( _switch_colors_mi );
1921         customizeJMenuItem( _choose_pdf_width_mi );
1922         customizeJMenuItem( _overview_placment_mi );
1923         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi,
1924                                    getOptions().isShowDefaultNodeShapesExternal() );
1925         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi,
1926                                    getOptions().isShowDefaultNodeShapesInternal() );
1927         customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi,
1928                                    getOptions().isShowDefaultNodeShapesForMarkedNodes() );
1929         customizeJMenuItem( _cycle_node_shape_mi );
1930         customizeJMenuItem( _cycle_node_fill_mi );
1931         customizeJMenuItem( _choose_node_size_mi );
1932         customizeJMenuItem( _cycle_data_return );
1933         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch,
1934                                    getOptions().isColorLabelsSameAsParentBranch() );
1935         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
1936         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
1937         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
1938         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
1939         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
1940         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
1941         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
1942         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
1943         customizeCheckBoxMenuItem( _collapsed_with_average_height_cbmi, getOptions().isCollapsedWithAverageHeigh() );
1944         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
1945                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
1946         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
1947                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP );
1948         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1949         customizeCheckBoxMenuItem( _label_direction_cbmi,
1950                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1951         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1952         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1953         customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi,
1954                                    getOptions().isInternalNumberAreConfidenceForNhParsing() );
1955         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1956                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1957         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
1958                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1959         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
1960                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1961         customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
1962                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
1963         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1964         customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi,
1965                                    getOptions().isReplaceUnderscoresInNhParsing() );
1966         customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
1967         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1968         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1969         customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi,
1970                                    getOptions().isColorAllFoundNodesWhenColoringSubtree() );
1971         customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi,
1972                                    getOptions().isParseBeastStyleExtendedNexusTags() );
1973         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1974         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1975         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi,
1976                                    getOptions()
1977                                            .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1978         customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi,
1979                                    getOptions()
1980                                            .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1981         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
1982         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
1983         _jmenubar.add( _options_jmenu );
1984     }
1985
1986     void buildPhylogeneticInferenceMenu() {
1987         final InferenceManager im = getInferenceManager();
1988         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1989         _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1990         customizeJMenuItem( _inference_from_msa_item );
1991         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1992         if ( im.canDoMsa() ) {
1993             _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1994             customizeJMenuItem( _inference_from_seqs_item );
1995             _inference_from_seqs_item
1996                     .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1997         }
1998         else {
1999             _inference_menu
2000                     .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
2001             customizeJMenuItem( _inference_from_seqs_item );
2002             _inference_from_seqs_item.setEnabled( false );
2003         }
2004         _jmenubar.add( _inference_menu );
2005     }
2006
2007     void buildToolsMenu() {
2008         _tools_menu = createMenu( "Tools", getConfiguration() );
2009         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
2010         customizeJMenuItem( _confcolor_item );
2011         _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
2012         customizeJMenuItem( _color_rank_jmi );
2013         _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
2014         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
2015         customizeJMenuItem( _taxcolor_item );
2016         _tools_menu.addSeparator();
2017         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
2018         _remove_visual_styles_item
2019                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
2020         customizeJMenuItem( _remove_visual_styles_item );
2021         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
2022         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
2023         customizeJMenuItem( _remove_branch_color_item );
2024         _tools_menu.addSeparator();
2025         _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
2026         customizeJMenuItem( _annotate_item );
2027         _tools_menu.addSeparator();
2028         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
2029         customizeJMenuItem( _midpoint_root_item );
2030         _tools_menu.addSeparator();
2031         _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );
2032         _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );
2033         customizeJMenuItem( _delete_selected_nodes_item );
2034         _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );
2035         _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
2036         customizeJMenuItem( _delete_not_selected_nodes_item );
2037         _tools_menu.addSeparator();
2038         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Single Taxonomy-Subtrees" ) );
2039         customizeJMenuItem( _collapse_species_specific_subtrees );
2040         _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse subtrees associated with only one taxonomy (such as species specific subtrees)" );
2041         _tools_menu
2042                 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
2043         customizeJMenuItem( _collapse_below_threshold );
2044         _collapse_below_threshold
2045                 .setToolTipText( "To (permanently) 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)" );
2046         //
2047         _tools_menu
2048                 .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
2049         customizeJMenuItem( _collapse_below_branch_length );
2050         _collapse_below_branch_length
2051                 .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
2052         //
2053         _tools_menu.addSeparator();
2054         _tools_menu
2055                 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
2056         customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
2057         _extract_tax_code_from_node_names_jmi
2058                 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
2059         _tools_menu
2060                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
2061         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
2062         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
2063         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
2064         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
2065         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
2066         _tools_menu.addSeparator();
2067         _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
2068         customizeJMenuItem( _obtain_seq_information_jmi );
2069         _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
2070         _tools_menu
2071                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
2072         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
2073         _obtain_detailed_taxonomic_information_jmi
2074                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
2075         _tools_menu
2076                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
2077         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
2078         _obtain_detailed_taxonomic_information_deleting_jmi
2079                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
2080         _tools_menu.addSeparator();
2081         _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
2082         customizeJMenuItem( _read_values_jmi );
2083         _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
2084         _jmenubar.add( _tools_menu );
2085         _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
2086         customizeJMenuItem( _read_seqs_jmi );
2087         _read_seqs_jmi
2088                 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
2089         _jmenubar.add( _tools_menu );
2090     }
2091
2092     @Override
2093     void close() {
2094         if ( isUnsavedDataPresent() ) {
2095             final int r = JOptionPane.showConfirmDialog( this,
2096                                                          "Exit despite potentially unsaved changes?",
2097                                                          "Exit?",
2098                                                          JOptionPane.YES_NO_OPTION );
2099             if ( r != JOptionPane.YES_OPTION ) {
2100                 return;
2101             }
2102         }
2103         exit();
2104     }
2105
2106     void exit() {
2107         removeAllTextFrames();
2108         _mainpanel.terminate();
2109         _contentpane.removeAll();
2110         setVisible( false );
2111         dispose();
2112         // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.
2113     }
2114
2115     void readPhylogeniesFromURL() {
2116         URL url = null;
2117         Phylogeny[] phys = null;
2118         final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
2119         final String url_string = JOptionPane
2120                 .showInputDialog( this,
2121                                   message,
2122                                   "Use URL/webservice to obtain a phylogeny",
2123                                   JOptionPane.QUESTION_MESSAGE );
2124         boolean nhx_or_nexus = false;
2125         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
2126             try {
2127                 url = new URL( url_string );
2128                 PhylogenyParser parser = null;
2129                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
2130                     parser = new TolParser();
2131                 }
2132                 else {
2133                     parser = ParserUtils
2134                             .createParserDependingOnUrlContents( url,
2135                                                                  getConfiguration().isValidatePhyloXmlAgainstSchema() );
2136                 }
2137                 if ( parser instanceof NexusPhylogeniesParser ) {
2138                     nhx_or_nexus = true;
2139                 }
2140                 else if ( parser instanceof NHXParser ) {
2141                     nhx_or_nexus = true;
2142                 }
2143                 if ( _mainpanel.getCurrentTreePanel() != null ) {
2144                     _mainpanel.getCurrentTreePanel().setWaitCursor();
2145                 }
2146                 else {
2147                     _mainpanel.setWaitCursor();
2148                 }
2149                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2150                 phys = factory.create( url.openStream(), parser );
2151             }
2152             catch ( final MalformedURLException e ) {
2153                 JOptionPane.showMessageDialog( this,
2154                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
2155                                                "Malformed URL",
2156                                                JOptionPane.ERROR_MESSAGE );
2157             }
2158             catch ( final IOException e ) {
2159                 JOptionPane.showMessageDialog( this,
2160                                                "Could not read from " + url + "\n"
2161                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2162                                                "Failed to read URL",
2163                                                JOptionPane.ERROR_MESSAGE );
2164             }
2165             catch ( final Exception e ) {
2166                 JOptionPane.showMessageDialog( this,
2167                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2168                                                "Unexpected Exception",
2169                                                JOptionPane.ERROR_MESSAGE );
2170             }
2171             finally {
2172                 if ( _mainpanel.getCurrentTreePanel() != null ) {
2173                     _mainpanel.getCurrentTreePanel().setArrowCursor();
2174                 }
2175                 else {
2176                     _mainpanel.setArrowCursor();
2177                 }
2178             }
2179             if ( ( phys != null ) && ( phys.length > 0 ) ) {
2180                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2181                     for( final Phylogeny phy : phys ) {
2182                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
2183                     }
2184                 }
2185                 AptxUtil.addPhylogeniesToTabs( phys,
2186                                                new File( url.getFile() ).getName(),
2187                                                new File( url.getFile() ).toString(),
2188                                                getConfiguration(),
2189                                                getMainPanel() );
2190                 _mainpanel.getControlPanel().showWhole();
2191             }
2192         }
2193         activateSaveAllIfNeeded();
2194         System.gc();
2195     }
2196
2197     void setMsa( final Msa msa ) {
2198         _msa = msa;
2199     }
2200
2201     void setMsaFile( final File msa_file ) {
2202         _msa_file = msa_file;
2203     }
2204
2205     void setSeqs( final List<MolecularSequence> seqs ) {
2206         _seqs = seqs;
2207     }
2208
2209     void setSeqsFile( final File seqs_file ) {
2210         _seqs_file = seqs_file;
2211     }
2212
2213     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2214         return new MainFrameApplication( phys, config );
2215     }
2216
2217     public static MainFrame createInstance( final Phylogeny[] phys,
2218                                             final Configuration config,
2219                                             final String title,
2220                                             final File current_dir ) {
2221         return new MainFrameApplication( phys, config, title, current_dir );
2222     }
2223
2224     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2225         return new MainFrameApplication( phys, config, title );
2226     }
2227
2228     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2229         return new MainFrameApplication( phys, config_file_name, title );
2230     }
2231
2232     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2233         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2234             JOptionPane.showMessageDialog( null,
2235                                            ForesterUtil.wordWrap(
2236                                                                   "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2237                                                                   80 ),
2238                                            "Warning",
2239                                            JOptionPane.WARNING_MESSAGE );
2240         }
2241     }
2242 } // MainFrameApplication.