forester/java/src/org/forester/application/decorator.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 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.application;
  27
  28 import java.io.File;
  29 import java.io.FileInputStream;
  30 import java.io.IOException;
  31 import java.util.ArrayList;
  32 import java.util.HashMap;
  33 import java.util.Iterator;
  34 import java.util.List;
  35 import java.util.Map;
  36 import java.util.Map.Entry;
  37
  38 import org.forester.io.parsers.FastaParser;
  39 import org.forester.io.parsers.PhylogenyParser;
  40 import org.forester.io.parsers.util.ParserUtils;
  41 import org.forester.io.writers.PhylogenyWriter;
  42 import org.forester.phylogeny.Phylogeny;
  43 import org.forester.phylogeny.PhylogenyMethods;
  44 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  45 import org.forester.phylogeny.data.Identifier;
  46 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  47 import org.forester.phylogeny.factories.PhylogenyFactory;
  48 import org.forester.sequence.Sequence;
  49 import org.forester.tools.PhylogenyDecorator;
  50 import org.forester.tools.PhylogenyDecorator.FIELD;
  51 import org.forester.util.BasicTable;
  52 import org.forester.util.BasicTableParser;
  53 import org.forester.util.CommandLineArguments;
  54 import org.forester.util.ForesterUtil;
  55
  56 public final class decorator {
  57
  58     private static final String SEQUENCE_NAME_FIELD                     = "s";
  59     private static final String MOL_SEQ                                 = "m";
  60     private static final String TAXONOMY_CODE_FIELD                     = "c";
  61     private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD          = "sn";
  62     private static final String DS_FILED                                = "d";
  63     private static final String SEQUENCE_ANNOTATION_DESC                = "a";
  64     private static final String NODE_NAME_FIELD                         = "n";
  65     final static private String PICKY_OPTION                            = "p";
  66     final static private String FIELD_OPTION                            = "f";
  67     final static private String TRIM_AFTER_TILDE_OPTION                 = "t";
  68     final static private String VERBOSE_OPTION                          = "ve";
  69     final static private String TREE_NAME_OPTION                        = "pn";
  70     final static private String TREE_ID_OPTION                          = "pi";
  71     final static private String TREE_DESC_OPTION                        = "pd";
  72     final static private String MIDPOINT_ROOT_OPTION                    = "mp";
  73     final static private String ORDER_TREE_OPTION                       = "or";
  74     final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION  = "sn";
  75     final static private String EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION = "tc";
  76     final static private String PROCESS_NAME_INTELLIGENTLY_OPTION       = "x";
  77     final static private String PROCESS_SIMILAR_TO_OPTION               = "xs";
  78     final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION       = "c";
  79     final static private String ALLOW_REMOVAL_OF_CHARS_OPTION           = "r";
  80     final static private String ADVANCED_TABLE_OPTION                   = "table";
  81     final static private String KEY_COLUMN                              = "k";
  82     final static private String VALUE_COLUMN                            = "v";
  83     final static private String MAPPING_FILE_SEPARATOR_OPTION           = "s";
  84     final static private char   MAPPING_FILE_SEPARATOR_DEFAULT          = '\t';
  85     final static private String PRG_NAME                                = "decorator";
  86     final static private String PRG_VERSION                             = "1.16";
  87     final static private String PRG_DATE                                = "131113";
  88
  89     public static void main( final String args[] ) {
  90         ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE );
  91         if ( ( args.length < 4 ) || ( args.length > 12 ) ) {
  92             decorator.argumentsError();
  93         }
  94         CommandLineArguments cla = null;
  95         try {
  96             cla = new CommandLineArguments( args );
  97         }
  98         catch ( final Exception e ) {
  99             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
 100         }
 101         if ( ( cla.getNumberOfNames() < 3 ) || ( cla.getNumberOfNames() > 4 ) ) {
 102             decorator.argumentsError();
 103         }
 104         final File phylogenies_infile = cla.getFile( 0 );
 105         final File mapping_infile = cla.getFile( 1 );
 106         final File phylogenies_outfile = cla.getFile( 2 );
 107         if ( phylogenies_outfile.exists() ) {
 108             ForesterUtil.fatalError( PRG_NAME, "[" + phylogenies_outfile + "] already exists" );
 109         }
 110         final List<String> allowed_options = new ArrayList<String>();
 111         allowed_options.add( decorator.ADVANCED_TABLE_OPTION );
 112         allowed_options.add( decorator.PICKY_OPTION );
 113         allowed_options.add( decorator.FIELD_OPTION );
 114         allowed_options.add( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION );
 115         allowed_options.add( decorator.PROCESS_SIMILAR_TO_OPTION );
 116         allowed_options.add( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION );
 117         allowed_options.add( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
 118         allowed_options.add( decorator.KEY_COLUMN );
 119         allowed_options.add( decorator.VALUE_COLUMN );
 120         allowed_options.add( decorator.MAPPING_FILE_SEPARATOR_OPTION );
 121         allowed_options.add( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION );
 122         allowed_options.add( decorator.EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION );
 123         allowed_options.add( decorator.TREE_NAME_OPTION );
 124         allowed_options.add( decorator.TREE_ID_OPTION );
 125         allowed_options.add( decorator.TREE_DESC_OPTION );
 126         allowed_options.add( decorator.TRIM_AFTER_TILDE_OPTION );
 127         allowed_options.add( decorator.ORDER_TREE_OPTION );
 128         allowed_options.add( decorator.MIDPOINT_ROOT_OPTION );
 129         allowed_options.add( decorator.VERBOSE_OPTION );
 130         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 131         if ( dissallowed_options.length() > 0 ) {
 132             ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options );
 133         }
 134         final boolean advanced_table = cla.isOptionSet( decorator.ADVANCED_TABLE_OPTION );
 135         if ( !advanced_table ) {
 136             final List<String> mandatory_options = new ArrayList<String>();
 137             mandatory_options.add( decorator.FIELD_OPTION );
 138             final String missing_options = cla.validateMandatoryOptionsAsString( mandatory_options );
 139             if ( missing_options.length() > 0 ) {
 140                 ForesterUtil.fatalError( decorator.PRG_NAME, "missing option(s): " + missing_options );
 141             }
 142         }
 143         final boolean picky = cla.isOptionSet( decorator.PICKY_OPTION );
 144         char separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
 145         if ( cla.isOptionSet( decorator.MAPPING_FILE_SEPARATOR_OPTION ) ) {
 146             if ( advanced_table ) {
 147                 argumentsError();
 148             }
 149             separator = cla.getOptionValueAsChar( decorator.MAPPING_FILE_SEPARATOR_OPTION );
 150         }
 151         int key_column = 0;
 152         int value_column = 1;
 153         String field_str = "";
 154         FIELD field = FIELD.NODE_NAME;
 155         int numbers_of_chars_allowed_to_remove_if_not_found_in_map = -1;
 156         boolean cut_name_after_space = false;
 157         boolean process_name_intelligently = false;
 158         boolean process_similar_to = false;
 159         boolean extract_bracketed_scientific_name = false;
 160         boolean extract_bracketed_tax_code = false;
 161         boolean trim_after_tilde = false;
 162         boolean order_tree = false;
 163         boolean midpoint_root = false;
 164         boolean verbose = false;
 165         String tree_name = "";
 166         String tree_id = "";
 167         String tree_desc = "";
 168         try {
 169             if ( cla.isOptionSet( decorator.TREE_NAME_OPTION ) ) {
 170                 tree_name = cla.getOptionValueAsCleanString( decorator.TREE_NAME_OPTION );
 171             }
 172             if ( cla.isOptionSet( decorator.TREE_ID_OPTION ) ) {
 173                 tree_id = cla.getOptionValueAsCleanString( decorator.TREE_ID_OPTION );
 174             }
 175             if ( cla.isOptionSet( decorator.TREE_DESC_OPTION ) ) {
 176                 tree_desc = cla.getOptionValueAsCleanString( decorator.TREE_DESC_OPTION );
 177             }
 178             if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION ) ) {
 179                 if ( advanced_table ) {
 180                     argumentsError();
 181                 }
 182                 extract_bracketed_scientific_name = true;
 183             }
 184             if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION ) ) {
 185                 if ( advanced_table ) {
 186                     argumentsError();
 187                 }
 188                 extract_bracketed_tax_code = true;
 189             }
 190             if ( cla.isOptionSet( decorator.KEY_COLUMN ) ) {
 191                 if ( advanced_table ) {
 192                     argumentsError();
 193                 }
 194                 key_column = cla.getOptionValueAsInt( decorator.KEY_COLUMN );
 195             }
 196             if ( cla.isOptionSet( decorator.VALUE_COLUMN ) ) {
 197                 if ( advanced_table ) {
 198                     argumentsError();
 199                 }
 200                 value_column = cla.getOptionValueAsInt( decorator.VALUE_COLUMN );
 201             }
 202             if ( cla.isOptionSet( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION ) ) {
 203                 if ( advanced_table ) {
 204                     argumentsError();
 205                 }
 206                 cut_name_after_space = true;
 207             }
 208             if ( cla.isOptionSet( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION ) ) {
 209                 if ( advanced_table ) {
 210                     argumentsError();
 211                 }
 212                 process_name_intelligently = true;
 213             }
 214             if ( cla.isOptionSet( decorator.PROCESS_SIMILAR_TO_OPTION ) ) {
 215                 if ( advanced_table ) {
 216                     argumentsError();
 217                 }
 218                 process_similar_to = true;
 219             }
 220             if ( cla.isOptionSet( decorator.TRIM_AFTER_TILDE_OPTION ) ) {
 221                 if ( advanced_table ) {
 222                     argumentsError();
 223                 }
 224                 trim_after_tilde = true;
 225             }
 226             if ( cla.isOptionSet( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ) ) {
 227                 numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla
 228                         .getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
 229             }
 230             if ( cla.isOptionSet( decorator.MIDPOINT_ROOT_OPTION ) ) {
 231                 midpoint_root = true;
 232             }
 233             if ( cla.isOptionSet( decorator.ORDER_TREE_OPTION ) ) {
 234                 order_tree = true;
 235             }
 236             if ( cla.isOptionSet( decorator.VERBOSE_OPTION ) ) {
 237                 verbose = true;
 238             }
 239             if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) {
 240                 field_str = cla.getOptionValue( decorator.FIELD_OPTION );
 241                 if ( field_str.equals( NODE_NAME_FIELD ) ) {
 242                     field = FIELD.NODE_NAME;
 243                 }
 244                 else if ( field_str.equals( SEQUENCE_ANNOTATION_DESC ) ) {
 245                     field = FIELD.SEQUENCE_ANNOTATION_DESC;
 246                 }
 247                 else if ( field_str.equals( DS_FILED ) ) {
 248                     field = FIELD.DOMAIN_STRUCTURE;
 249                     extract_bracketed_scientific_name = false;
 250                     extract_bracketed_tax_code = false;
 251                 }
 252                 else if ( field_str.equals( TAXONOMY_CODE_FIELD ) ) {
 253                     field = FIELD.TAXONOMY_CODE;
 254                 }
 255                 else if ( field_str.equals( SEQUENCE_NAME_FIELD ) ) {
 256                     field = FIELD.SEQUENCE_NAME;
 257                 }
 258                 else if ( field_str.equals( MOL_SEQ ) ) {
 259                     field = FIELD.MOL_SEQ;
 260                 }
 261                 else if ( field_str.equals( TAXONOMY_SCIENTIFIC_NAME_FIELD ) ) {
 262                     field = FIELD.TAXONOMY_SCIENTIFIC_NAME;
 263                     extract_bracketed_scientific_name = false;
 264                     extract_bracketed_tax_code = false;
 265                 }
 266                 else {
 267                     ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
 268                             + "\" option: \"" + field_str + "\"" );
 269                 }
 270             }
 271         }
 272         catch ( final Exception e ) {
 273             ForesterUtil.fatalError( decorator.PRG_NAME, "error in command line: " + e.getMessage() );
 274         }
 275         if ( ( field != FIELD.NODE_NAME ) && ( cut_name_after_space || process_name_intelligently ) ) {
 276             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x or -c option without -f=n" );
 277         }
 278         if ( ( field != FIELD.NODE_NAME ) && process_similar_to ) {
 279             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
 280                     + " option without -f=n" );
 281         }
 282         if ( cut_name_after_space && process_name_intelligently ) {
 283             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x and -c option together" );
 284         }
 285         if ( process_similar_to && process_name_intelligently ) {
 286             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
 287                     + " and -x option together" );
 288         }
 289         if ( process_similar_to && cut_name_after_space ) {
 290             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
 291                     + " and -c option together" );
 292         }
 293         if ( extract_bracketed_scientific_name && extract_bracketed_tax_code ) {
 294             argumentsError();
 295         }
 296         Phylogeny[] phylogenies = null;
 297         try {
 298             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 299             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogenies_infile, true );
 300             phylogenies = factory.create( phylogenies_infile, pp );
 301         }
 302         catch ( final Exception e ) {
 303             ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
 304                     + "] [" + e.getMessage() + "]" );
 305         }
 306         Map<String, String> map = null;
 307         if ( !advanced_table ) {
 308             if ( field != FIELD.MOL_SEQ ) {
 309                 BasicTable<String> mapping_table = null;
 310                 try {
 311                     mapping_table = BasicTableParser.parse( mapping_infile, separator, true, false );
 312                 }
 313                 catch ( final Exception e ) {
 314                     ForesterUtil.fatalError( decorator.PRG_NAME,
 315                                              "failed to read [" + mapping_infile + "] [" + e.getMessage() + "]" );
 316                 }
 317                 if ( ( key_column < 0 ) || ( key_column >= mapping_table.getNumberOfColumns() ) ) {
 318                     ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for key column" );
 319                 }
 320                 if ( ( value_column < 0 ) || ( value_column >= mapping_table.getNumberOfColumns() ) ) {
 321                     ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for value column" );
 322                 }
 323                 if ( mapping_table.isEmpty() || ( mapping_table.getNumberOfColumns() < 1 ) ) {
 324                     ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table is empty" );
 325                 }
 326                 if ( mapping_table.getNumberOfColumns() == 1 ) {
 327                     ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table has only one column" );
 328                 }
 329                 map = mapping_table.getColumnsAsMap( key_column, value_column );
 330                 if ( verbose ) {
 331                     final Iterator<Entry<String, String>> iter = map.entrySet().iterator();
 332                     System.out.println();
 333                     while ( iter.hasNext() ) {
 334                         final Entry<String, String> e = iter.next();
 335                         System.out.println( e.getKey() + " => " + e.getValue() );
 336                     }
 337                     System.out.println();
 338                 }
 339             }
 340             else {
 341                 map = readFastaFileIntoMap( mapping_infile, verbose );
 342             }
 343         }
 344         if ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id )
 345                 || !ForesterUtil.isEmpty( tree_desc ) ) {
 346             if ( ( phylogenies.length > 1 )
 347                     && ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
 348                 ForesterUtil.fatalError( decorator.PRG_NAME,
 349                                          "attempt to set same name or id on more than one phylogeny" );
 350             }
 351             if ( !ForesterUtil.isEmpty( tree_name ) ) {
 352                 phylogenies[ 0 ].setName( tree_name );
 353             }
 354             if ( !ForesterUtil.isEmpty( tree_id ) ) {
 355                 final String[] s_ary = tree_id.split( ":" );
 356                 phylogenies[ 0 ].setIdentifier( new Identifier( s_ary[ 1 ], s_ary[ 0 ] ) );
 357             }
 358             if ( !ForesterUtil.isEmpty( tree_desc ) ) {
 359                 for( final Phylogeny phylogenie : phylogenies ) {
 360                     phylogenie.setDescription( tree_desc );
 361                 }
 362             }
 363         }
 364         try {
 365             if ( advanced_table ) {
 366                 Map<String, Map<String, String>> table = null;
 367                 try {
 368                     table = PhylogenyDecorator.parseMappingTable( mapping_infile );
 369                 }
 370                 catch ( final IOException e ) {
 371                     ForesterUtil.fatalError( decorator.PRG_NAME,
 372                                              "failed to read \"" + mapping_infile + "\" [" + e.getMessage() + "]" );
 373                 }
 374                 PhylogenyDecorator.decorate( phylogenies,
 375                                              table,
 376                                              picky,
 377                                              numbers_of_chars_allowed_to_remove_if_not_found_in_map );
 378             }
 379             else {
 380                 PhylogenyDecorator.decorate( phylogenies,
 381                                              map,
 382                                              field,
 383                                              extract_bracketed_scientific_name,
 384                                              extract_bracketed_tax_code,
 385                                              picky,
 386                                              cut_name_after_space,
 387                                              process_name_intelligently,
 388                                              process_similar_to,
 389                                              numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 390                                              trim_after_tilde,
 391                                              verbose );
 392             }
 393         }
 394         catch ( final NullPointerException e ) {
 395             ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
 396         }
 397         catch ( final Exception e ) {
 398             ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() );
 399         }
 400         if ( midpoint_root || order_tree ) {
 401             for( final Phylogeny phy : phylogenies ) {
 402                 if ( midpoint_root ) {
 403                     PhylogenyMethods.midpointRoot( phy );
 404                 }
 405                 if ( order_tree ) {
 406                     PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.TAXONOMY );
 407                 }
 408             }
 409         }
 410         try {
 411             final PhylogenyWriter w = new PhylogenyWriter();
 412             w.toPhyloXML( phylogenies, 0, phylogenies_outfile, ForesterUtil.getLineSeparator() );
 413         }
 414         catch ( final IOException e ) {
 415             ForesterUtil.fatalError( decorator.PRG_NAME, "failed to write output [" + e.getMessage() + "]" );
 416         }
 417         System.out.println();
 418         ForesterUtil.programMessage( PRG_NAME, "wrote: " + phylogenies_outfile );
 419         ForesterUtil.programMessage( PRG_NAME, "OK." );
 420     }
 421
 422     private static Map<String, String> readFastaFileIntoMap( final File mapping_infile, final boolean verbose ) {
 423         List<Sequence> seqs = null;
 424         try {
 425             seqs = FastaParser.parse( new FileInputStream( mapping_infile ) );
 426         }
 427         catch ( final IOException e ) {
 428             ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read fasta-file from [" + mapping_infile + "] ["
 429                     + e.getMessage() + "]" );
 430         }
 431         if ( ForesterUtil.isEmpty( seqs ) ) {
 432             ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
 433                     + "] is devoid of fasta-formatted sequences" );
 434         }
 435         final Map<String, String> map = new HashMap<String, String>();
 436         for( final Sequence seq : seqs ) {
 437             if ( ForesterUtil.isEmpty( seq.getIdentifier() ) ) {
 438                 ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
 439                         + "] contains sequence with empty identifier" );
 440             }
 441             if ( map.containsKey( seq.getIdentifier() ) ) {
 442                 ForesterUtil.fatalError( decorator.PRG_NAME, "sequence identifier [" + seq.getIdentifier()
 443                         + "] is not unique" );
 444             }
 445             if ( seq.getLength() < 1 ) {
 446                 ForesterUtil.fatalError( decorator.PRG_NAME, "sequence [" + seq.getIdentifier() + "] is empty" );
 447             }
 448             map.put( seq.getIdentifier(), seq.getMolecularSequenceAsString() );
 449             if ( verbose ) {
 450                 System.out.println( seq.getIdentifier() + " => " + seq.getMolecularSequenceAsString() );
 451             }
 452         }
 453         return map;
 454     }
 455
 456     private static void argumentsError() {
 457         System.out.println();
 458         System.out.println( decorator.PRG_NAME + " -" + ADVANCED_TABLE_OPTION + " | -f=<c> <phylogenies infile> "
 459                 + "[mapping table file|fasta-file] <phylogenies outfile>" );
 460         System.out.println();
 461         System.out.println( "options:" );
 462         System.out.println();
 463         System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=<c>)" );
 464         System.out.println( " -r=<n> : allow to remove up to n characters from the end of the names" );
 465         System.out.println( "          in phylogenies infile if not found (in map) otherwise" );
 466         System.out.println( " -p     : picky, fails if node name not found in mapping table" );
 467         System.out.println( " -" + TREE_NAME_OPTION + "=<s>: name for the phylogeny" );
 468         System.out.println( " -" + TREE_ID_OPTION + "=<s>: identifier for the phylogeny (in the form provider:value)" );
 469         System.out.println( " -" + TREE_DESC_OPTION + "=<s>: description for phylogenies" );
 470         System.out.println();
 471         System.out.println();
 472         System.out.println( "advanced options, only available if -" + ADVANCED_TABLE_OPTION + " is not used:" );
 473         System.out.println();
 474         System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
 475         System.out.println( "                                " + SEQUENCE_ANNOTATION_DESC
 476                 + " : sequence annotation description" );
 477         System.out.println( "                                " + DS_FILED + " : domain structure" );
 478         System.out.println( "                                " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
 479         System.out.println( "                                " + TAXONOMY_SCIENTIFIC_NAME_FIELD
 480                 + ": taxonomy scientific name" );
 481         System.out.println( "                                " + SEQUENCE_NAME_FIELD + " : sequence name" );
 482         System.out.println( "                                " + MOL_SEQ + " : molecular sequence" );
 483         System.out.println( " -k=<n> : key column in mapping table (0 based)," );
 484         System.out.println( "          names of the node to be decorated - default is 0" );
 485         System.out.println( " -v=<n> : value column in mapping table (0 based)," );
 486         System.out.println( "          data which with to decorate - default is 1" );
 487         System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
 488                 + "    : to extract bracketed scientific names, e.g. [Nematostella vectensis]" );
 489         System.out.println( " -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION
 490                 + "    : to extract bracketed taxonomic codes, e.g. [NEMVE]" );
 491         System.out.println( " -s=<c> : column separator in mapping file, default is tab" );
 492         System.out.println( " -x     : process name \"intelligently\" (only for -f=n)" );
 493         System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION
 494                 + "    : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" );
 495         System.out.println( " -c     : cut name after first space (only for -f=n)" );
 496         System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
 497                 + "     : trim node name to be replaced after tilde" );
 498         System.out.println( " -" + decorator.MIDPOINT_ROOT_OPTION + "    : to midpoint-root the tree" );
 499         System.out.println( " -" + decorator.ORDER_TREE_OPTION + "    : to order tree branches" );
 500         System.out.println( " -" + decorator.VERBOSE_OPTION + "    : verbose" );
 501         System.out.println();
 502         System.exit( -1 );
 503     }
 504 }