forester/java/src/org/forester/tools/PhylogenyDecorator.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: www.phylosoft.org/forester
  25
  26 package org.forester.tools;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.util.HashMap;
  31 import java.util.Map;
  32 import java.util.regex.Matcher;
  33 import java.util.regex.Pattern;
  34
  35 import org.forester.io.parsers.nhx.NHXFormatException;
  36 import org.forester.phylogeny.Phylogeny;
  37 import org.forester.phylogeny.PhylogenyNode;
  38 import org.forester.phylogeny.data.Accession;
  39 import org.forester.phylogeny.data.Annotation;
  40 import org.forester.phylogeny.data.DomainArchitecture;
  41 import org.forester.phylogeny.data.Identifier;
  42 import org.forester.phylogeny.data.Sequence;
  43 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  44 import org.forester.util.BasicTable;
  45 import org.forester.util.BasicTableParser;
  46 import org.forester.util.ForesterUtil;
  47
  48 public final class PhylogenyDecorator {
  49
  50     // From evoruby/lib/evo/apps/tseq_taxonomy_processor.rb:
  51     final private static String  TP_TAXONOMY_CODE                   = "TAXONOMY_CODE";
  52     final private static String  TP_TAXONOMY_ID                     = "TAXONOMY_ID";
  53     final private static String  TP_TAXONOMY_ID_PROVIDER            = "TAXONOMY_ID_PROVIDER";
  54     final private static String  TP_TAXONOMY_SN                     = "TAXONOMY_SN";
  55     final private static String  TP_TAXONOMY_CN                     = "TAXONOMY_CN";
  56     final private static String  TP_TAXONOMY_SYN                    = "TAXONOMY_SYN";
  57     final private static String  TP_SEQ_SYMBOL                      = "SEQ_SYMBOL";
  58     final private static String  TP_SEQ_ACCESSION                   = "SEQ_ACCESSION";
  59     final private static String  TP_SEQ_ACCESSION_SOURCE            = "SEQ_ACCESSION_SOURCE";
  60     final private static String  TP_SEQ_ANNOTATION_DESC             = "SEQ_ANNOTATION_DESC";
  61     final private static String  TP_SEQ_ANNOTATION_REF              = "SEQ_ANNOTATION_REF";
  62     final private static String  TP_SEQ_MOL_SEQ                     = "SEQ_MOL_SEQ";
  63     final private static String  TP_SEQ_NAME                        = "SEQ_NAME";
  64     final private static String  TP_NODE_NAME                       = "NODE_NAME";
  65     final private static Pattern NODENAME_SEQNUMBER_TAXDOMAINNUMBER = Pattern
  66                                                                             .compile( "^([a-fA-Z0-9]{1,5})_([A-Z0-9]{2,4}[A-Z])(\\d{1,4})$" );
  67     public final static boolean  SANITIZE                           = false;
  68     public final static boolean  VERBOSE                            = true;
  69
  70     private PhylogenyDecorator() {
  71         // Not needed.
  72     }
  73
  74     public static void decorate( final Phylogeny phylogeny,
  75                                  final Map<String, Map<String, String>> map,
  76                                  final boolean picky,
  77                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map )
  78             throws IllegalArgumentException {
  79         for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
  80             final PhylogenyNode node = iter.next();
  81             final String name = node.getName();
  82             if ( !ForesterUtil.isEmpty( name ) ) {
  83                 if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) ) {
  84                     Map<String, String> new_values = map.get( name );
  85                     int x = 0;
  86                     while ( ( new_values == null ) && ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 )
  87                             && ( x <= numbers_of_chars_allowed_to_remove_if_not_found_in_map ) ) {
  88                         new_values = map.get( name.substring( 0, name.length() - x ) );
  89                         ++x;
  90                     }
  91                     if ( new_values != null ) {
  92                         if ( new_values.containsKey( TP_TAXONOMY_CODE ) ) {
  93                             ForesterUtil.ensurePresenceOfTaxonomy( node );
  94                             node.getNodeData().getTaxonomy().setTaxonomyCode( new_values.get( TP_TAXONOMY_CODE ) );
  95                         }
  96                         if ( new_values.containsKey( TP_TAXONOMY_ID )
  97                                 && new_values.containsKey( TP_TAXONOMY_ID_PROVIDER ) ) {
  98                             ForesterUtil.ensurePresenceOfTaxonomy( node );
  99                             node.getNodeData()
 100                                     .getTaxonomy()
 101                                     .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ),
 102                                                                     new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) );
 103                         }
 104                         else if ( new_values.containsKey( TP_TAXONOMY_ID ) ) {
 105                             ForesterUtil.ensurePresenceOfTaxonomy( node );
 106                             node.getNodeData().getTaxonomy()
 107                                     .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) );
 108                         }
 109                         if ( new_values.containsKey( TP_TAXONOMY_SN ) ) {
 110                             ForesterUtil.ensurePresenceOfTaxonomy( node );
 111                             node.getNodeData().getTaxonomy().setScientificName( new_values.get( TP_TAXONOMY_SN ) );
 112                         }
 113                         if ( new_values.containsKey( TP_TAXONOMY_CN ) ) {
 114                             ForesterUtil.ensurePresenceOfTaxonomy( node );
 115                             node.getNodeData().getTaxonomy().setCommonName( new_values.get( TP_TAXONOMY_CN ) );
 116                         }
 117                         if ( new_values.containsKey( TP_TAXONOMY_SYN ) ) {
 118                             ForesterUtil.ensurePresenceOfTaxonomy( node );
 119                             node.getNodeData().getTaxonomy().getSynonyms().add( new_values.get( TP_TAXONOMY_SYN ) );
 120                         }
 121                         if ( new_values.containsKey( TP_SEQ_ACCESSION )
 122                                 && new_values.containsKey( TP_SEQ_ACCESSION_SOURCE ) ) {
 123                             ForesterUtil.ensurePresenceOfSequence( node );
 124                             node.getNodeData()
 125                                     .getSequence()
 126                                     .setAccession( new Accession( new_values.get( TP_SEQ_ACCESSION ),
 127                                                                   new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) );
 128                         }
 129                         if ( new_values.containsKey( TP_SEQ_ANNOTATION_DESC ) ) {
 130                             ForesterUtil.ensurePresenceOfSequence( node );
 131                             final Annotation ann = new Annotation( "?" );
 132                             ann.setDesc( new_values.get( TP_SEQ_ANNOTATION_DESC ) );
 133                             node.getNodeData().getSequence().addAnnotation( ann );
 134                         }
 135                         if ( new_values.containsKey( TP_SEQ_ANNOTATION_REF ) ) {
 136                             ForesterUtil.ensurePresenceOfSequence( node );
 137                             final Annotation ann = new Annotation( new_values.get( TP_SEQ_ANNOTATION_REF ) );
 138                             node.getNodeData().getSequence().addAnnotation( ann );
 139                         }
 140                         if ( new_values.containsKey( TP_SEQ_SYMBOL ) ) {
 141                             ForesterUtil.ensurePresenceOfSequence( node );
 142                             node.getNodeData().getSequence().setSymbol( new_values.get( TP_SEQ_SYMBOL ) );
 143                         }
 144                         if ( new_values.containsKey( TP_SEQ_NAME ) ) {
 145                             ForesterUtil.ensurePresenceOfSequence( node );
 146                             node.getNodeData().getSequence().setName( new_values.get( TP_SEQ_NAME ) );
 147                         }
 148                         if ( new_values.containsKey( TP_SEQ_MOL_SEQ ) ) {
 149                             ForesterUtil.ensurePresenceOfSequence( node );
 150                             node.getNodeData().getSequence().setMolecularSequence( new_values.get( TP_SEQ_MOL_SEQ ) );
 151                         }
 152                         if ( new_values.containsKey( TP_NODE_NAME ) ) {
 153                             node.setName( new_values.get( TP_NODE_NAME ) );
 154                         }
 155                     }
 156                 }
 157                 else if ( picky ) {
 158                     throw new IllegalArgumentException( "\"" + name + "\" not found in name map" );
 159                 }
 160             }
 161         }
 162     }
 163
 164     /**
 165      *
 166      *
 167      *
 168      *
 169      *
 170      * @param phylogeny
 171      * @param map
 172      *            maps names (in phylogeny) to new values
 173      * @param field
 174      * @param picky
 175      * @throws IllegalArgumentException
 176      * @throws NHXFormatException
 177      */
 178     public static void decorate( final Phylogeny phylogeny,
 179                                  final Map<String, String> map,
 180                                  final FIELD field,
 181                                  final boolean extract_bracketed_scientific_name,
 182                                  final boolean picky,
 183                                  final boolean cut_name_after_space,
 184                                  final boolean process_name_intelligently,
 185                                  final boolean process_similar_to,
 186                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 187                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException,
 188             NHXFormatException {
 189         PhylogenyDecorator.decorate( phylogeny,
 190                                      map,
 191                                      field,
 192                                      extract_bracketed_scientific_name,
 193                                      picky,
 194                                      null,
 195                                      cut_name_after_space,
 196                                      process_name_intelligently,
 197                                      process_similar_to,
 198                                      numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 199                                      move_domain_numbers_at_end_to_middle );
 200     }
 201
 202     /**
 203      *
 204      *
 205      *
 206      * @param phylogeny
 207      * @param map
 208      *            maps names (in phylogeny) to new values if intermediate_map is
 209      *            null otherwise maps intermediate value to new value
 210      * @param field
 211      * @param picky
 212      * @param intermediate_map
 213      *            maps name (in phylogeny) to a intermediate value
 214      * @throws IllegalArgumentException
 215      */
 216     public static void decorate( final Phylogeny phylogeny,
 217                                  final Map<String, String> map,
 218                                  final FIELD field,
 219                                  final boolean extract_bracketed_scientific_name,
 220                                  final boolean picky,
 221                                  final Map<String, String> intermediate_map,
 222                                  final boolean cut_name_after_space,
 223                                  final boolean process_name_intelligently,
 224                                  final boolean process_similar_to,
 225                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 226                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException {
 227         if ( extract_bracketed_scientific_name && ( field == FIELD.TAXONOMY_SCIENTIFIC_NAME ) ) {
 228             throw new IllegalArgumentException( "Attempt to extract bracketed scientific name together with data field pointing to scientific name" );
 229         }
 230         for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
 231             final PhylogenyNode node = iter.next();
 232             String name = node.getName();
 233             if ( !ForesterUtil.isEmpty( name ) ) {
 234                 if ( intermediate_map != null ) {
 235                     name = PhylogenyDecorator.extractIntermediate( intermediate_map, name );
 236                 }
 237                 if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) ) {
 238                     String new_value = map.get( name );
 239                     int x = 0;
 240                     while ( ( new_value == null ) && ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 )
 241                             && ( x <= numbers_of_chars_allowed_to_remove_if_not_found_in_map ) ) {
 242                         new_value = map.get( name.substring( 0, name.length() - x ) );
 243                         ++x;
 244                     }
 245                     if ( new_value != null ) {
 246                         new_value = new_value.trim();
 247                         new_value.replaceAll( "/\\s+/", " " );
 248                         if ( extract_bracketed_scientific_name && new_value.endsWith( "]" ) ) {
 249                             extractBracketedScientificNames( node, new_value );
 250                         }
 251                         switch ( field ) {
 252                             case SEQUENCE_ANNOTATION_DESC:
 253                                 if ( PhylogenyDecorator.VERBOSE ) {
 254                                     System.out.println( name + ": " + new_value );
 255                                 }
 256                                 if ( !node.getNodeData().isHasSequence() ) {
 257                                     node.getNodeData().setSequence( new Sequence() );
 258                                 }
 259                                 final Annotation annotation = new Annotation( "?" );
 260                                 annotation.setDesc( new_value );
 261                                 node.getNodeData().getSequence().addAnnotation( annotation );
 262                                 break;
 263                             case DOMAIN_STRUCTURE:
 264                                 if ( PhylogenyDecorator.VERBOSE ) {
 265                                     System.out.println( name + ": " + new_value );
 266                                 }
 267                                 if ( !node.getNodeData().isHasSequence() ) {
 268                                     node.getNodeData().setSequence( new Sequence() );
 269                                 }
 270                                 node.getNodeData().getSequence()
 271                                         .setDomainArchitecture( new DomainArchitecture( new_value ) );
 272                                 break;
 273                             case TAXONOMY_CODE:
 274                                 if ( PhylogenyDecorator.VERBOSE ) {
 275                                     System.out.println( name + ": " + new_value );
 276                                 }
 277                                 ForesterUtil.ensurePresenceOfTaxonomy( node );
 278                                 node.getNodeData().getTaxonomy().setTaxonomyCode( new_value );
 279                                 break;
 280                             case TAXONOMY_SCIENTIFIC_NAME:
 281                                 if ( PhylogenyDecorator.VERBOSE ) {
 282                                     System.out.println( name + ": " + new_value );
 283                                 }
 284                                 ForesterUtil.ensurePresenceOfTaxonomy( node );
 285                                 node.getNodeData().getTaxonomy().setScientificName( new_value );
 286                                 break;
 287                             case SEQUENCE_NAME:
 288                                 if ( PhylogenyDecorator.VERBOSE ) {
 289                                     System.out.println( name + ": " + new_value );
 290                                 }
 291                                 if ( !node.getNodeData().isHasSequence() ) {
 292                                     node.getNodeData().setSequence( new Sequence() );
 293                                 }
 294                                 node.getNodeData().getSequence().setName( new_value );
 295                                 break;
 296                             case NODE_NAME:
 297                                 if ( PhylogenyDecorator.VERBOSE ) {
 298                                     System.out.print( name + " -> " );
 299                                 }
 300                                 if ( cut_name_after_space ) {
 301                                     if ( PhylogenyDecorator.VERBOSE ) {
 302                                         System.out.print( new_value + " -> " );
 303                                     }
 304                                     new_value = PhylogenyDecorator.deleteAtFirstSpace( new_value );
 305                                 }
 306                                 else if ( process_name_intelligently ) {
 307                                     if ( PhylogenyDecorator.VERBOSE ) {
 308                                         System.out.print( new_value + " -> " );
 309                                     }
 310                                     new_value = PhylogenyDecorator.processNameIntelligently( new_value );
 311                                 }
 312                                 else if ( process_similar_to ) {
 313                                     if ( PhylogenyDecorator.VERBOSE ) {
 314                                         System.out.print( new_value + " -> " );
 315                                     }
 316                                     new_value = PhylogenyDecorator.processSimilarTo( new_value );
 317                                 }
 318                                 if ( PhylogenyDecorator.SANITIZE ) {
 319                                     new_value = PhylogenyDecorator.sanitize( new_value );
 320                                 }
 321                                 if ( PhylogenyDecorator.VERBOSE ) {
 322                                     System.out.println( new_value );
 323                                 }
 324                                 node.setName( new_value );
 325                                 break;
 326                             default:
 327                                 throw new RuntimeException( "unknown field \"" + field + "\"" );
 328                         }
 329                         if ( move_domain_numbers_at_end_to_middle && ( field != FIELD.NODE_NAME ) ) {
 330                             node.setName( moveDomainNumbersAtEnd( node.getName() ) );
 331                         }
 332                     }
 333                 }
 334                 else if ( picky ) {
 335                     throw new IllegalArgumentException( "\"" + name + "\" not found in name map" );
 336                 }
 337             }
 338         }
 339     }
 340
 341     public static void decorate( final Phylogeny[] phylogenies,
 342                                  final Map<String, Map<String, String>> map,
 343                                  final boolean picky,
 344                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map )
 345             throws IllegalArgumentException, NHXFormatException {
 346         for( int i = 0; i < phylogenies.length; ++i ) {
 347             PhylogenyDecorator.decorate( phylogenies[ i ],
 348                                          map,
 349                                          picky,
 350                                          numbers_of_chars_allowed_to_remove_if_not_found_in_map );
 351         }
 352     }
 353
 354     public static void decorate( final Phylogeny[] phylogenies,
 355                                  final Map<String, String> map,
 356                                  final FIELD field,
 357                                  final boolean extract_bracketed_scientific_name,
 358                                  final boolean picky,
 359                                  final boolean cut_name_after_space,
 360                                  final boolean process_name_intelligently,
 361                                  final boolean process_similar_to,
 362                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 363                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException,
 364             NHXFormatException {
 365         for( int i = 0; i < phylogenies.length; ++i ) {
 366             PhylogenyDecorator.decorate( phylogenies[ i ],
 367                                          map,
 368                                          field,
 369                                          extract_bracketed_scientific_name,
 370                                          picky,
 371                                          cut_name_after_space,
 372                                          process_name_intelligently,
 373                                          process_similar_to,
 374                                          numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 375                                          move_domain_numbers_at_end_to_middle );
 376         }
 377     }
 378
 379     public static void decorate( final Phylogeny[] phylogenies,
 380                                  final Map<String, String> map,
 381                                  final FIELD field,
 382                                  final boolean extract_bracketed_scientific_name,
 383                                  final boolean picky,
 384                                  final Map<String, String> intermediate_map,
 385                                  final boolean cut_name_after_space,
 386                                  final boolean process_name_intelligently,
 387                                  final boolean process_similar_to,
 388                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 389                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException,
 390             NHXFormatException {
 391         for( int i = 0; i < phylogenies.length; ++i ) {
 392             PhylogenyDecorator.decorate( phylogenies[ i ],
 393                                          map,
 394                                          field,
 395                                          extract_bracketed_scientific_name,
 396                                          picky,
 397                                          intermediate_map,
 398                                          cut_name_after_space,
 399                                          process_name_intelligently,
 400                                          process_similar_to,
 401                                          numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 402                                          move_domain_numbers_at_end_to_middle );
 403         }
 404     }
 405
 406     private static String deleteAtFirstSpace( final String name ) {
 407         final int first_space = name.indexOf( " " );
 408         if ( first_space > 1 ) {
 409             return name.substring( 0, first_space ).trim();
 410         }
 411         return name;
 412     }
 413
 414     private static void extractBracketedScientificNames( final PhylogenyNode node, final String new_value ) {
 415         final int i = new_value.lastIndexOf( "[" );
 416         final String scientific_name = new_value.substring( i + 1, new_value.length() - 1 );
 417         ForesterUtil.ensurePresenceOfTaxonomy( node );
 418         node.getNodeData().getTaxonomy().setScientificName( scientific_name );
 419     }
 420
 421     private static String extractIntermediate( final Map<String, String> intermediate_map, final String name ) {
 422         String new_name = null;
 423         if ( PhylogenyDecorator.VERBOSE ) {
 424             System.out.print( name + " => " );
 425         }
 426         if ( intermediate_map.containsKey( name ) ) {
 427             new_name = intermediate_map.get( name );
 428             if ( ForesterUtil.isEmpty( new_name ) ) {
 429                 throw new IllegalArgumentException( "\"" + name + "\" maps to null or empty string in secondary map" );
 430             }
 431         }
 432         else {
 433             throw new IllegalArgumentException( "\"" + name + "\" not found in name secondary map" );
 434         }
 435         if ( PhylogenyDecorator.VERBOSE ) {
 436             System.out.println( new_name + "  " );
 437         }
 438         return new_name;
 439     }
 440
 441     private static String moveDomainNumbersAtEnd( final String node_name ) {
 442         final Matcher m = NODENAME_SEQNUMBER_TAXDOMAINNUMBER.matcher( node_name );
 443         if ( m.matches() ) {
 444             final String seq_number = m.group( 1 );
 445             final String tax = m.group( 2 );
 446             final String domain_number = m.group( 3 );
 447             return seq_number + "_[" + domain_number + "]_" + tax;
 448         }
 449         else {
 450             return node_name;
 451         }
 452     }
 453
 454     public static Map<String, Map<String, String>> parseMappingTable( final File mapping_table_file )
 455             throws IOException {
 456         final Map<String, Map<String, String>> map = new HashMap<String, Map<String, String>>();
 457         BasicTable<String> mapping_table = null;
 458         mapping_table = BasicTableParser.parse( mapping_table_file, "\t", false );
 459         for( int row = 0; row < mapping_table.getNumberOfRows(); ++row ) {
 460             final Map<String, String> row_map = new HashMap<String, String>();
 461             String name = null;
 462             for( int col = 0; col < mapping_table.getNumberOfColumns(); ++col ) {
 463                 final String table_cell = mapping_table.getValue( col, row );
 464                 if ( col == 0 ) {
 465                     name = table_cell;
 466                 }
 467                 else if ( table_cell != null ) {
 468                     final String key = table_cell.substring( 0, table_cell.indexOf( ':' ) );
 469                     final String val = table_cell.substring( table_cell.indexOf( ':' ) + 1, table_cell.length() );
 470                     row_map.put( key, val );
 471                 }
 472             }
 473             map.put( name, row_map );
 474         }
 475         return map;
 476     }
 477
 478     private static String processNameIntelligently( final String name ) {
 479         final String[] s = name.split( " " );
 480         if ( s.length < 2 ) {
 481             return name;
 482         }
 483         else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "|" ) > 0 ) ) {
 484             return s[ 0 ];
 485         }
 486         else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "|" ) > 0 ) ) {
 487             return s[ 1 ];
 488         }
 489         else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "." ) > 0 ) ) {
 490             return s[ 0 ];
 491         }
 492         else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "." ) > 0 ) ) {
 493             return s[ 1 ];
 494         }
 495         else if ( s[ 0 ].indexOf( "_" ) > 0 ) {
 496             return s[ 0 ];
 497         }
 498         else if ( s[ 1 ].indexOf( "_" ) > 0 ) {
 499             return s[ 1 ];
 500         }
 501         else {
 502             return s[ 0 ];
 503         }
 504     }
 505
 506     private static String processSimilarTo( final String name ) {
 507         final int i = name.toLowerCase().indexOf( "similar to" );
 508         String similar_to = "";
 509         if ( i >= 0 ) {
 510             similar_to = " similarity=" + name.substring( i + 10 ).trim();
 511         }
 512         final String pi = processNameIntelligently( name );
 513         return pi + similar_to;
 514     }
 515
 516     private static String sanitize( String s ) {
 517         s = s.replace( ' ', '_' );
 518         s = s.replace( '(', '{' );
 519         s = s.replace( ')', '}' );
 520         s = s.replace( '[', '{' );
 521         s = s.replace( ']', '}' );
 522         s = s.replace( ',', '_' );
 523         return s;
 524     }
 525
 526     public static enum FIELD {
 527         NODE_NAME, SEQUENCE_ANNOTATION_DESC, DOMAIN_STRUCTURE, TAXONOMY_CODE, TAXONOMY_SCIENTIFIC_NAME, SEQUENCE_NAME;
 528     }
 529 }