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.archaeopteryx.AptxUtil;
  36 import org.forester.io.parsers.nhx.NHXFormatException;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.PhylogenyNode;
  39 import org.forester.phylogeny.data.Accession;
  40 import org.forester.phylogeny.data.Annotation;
  41 import org.forester.phylogeny.data.DomainArchitecture;
  42 import org.forester.phylogeny.data.Identifier;
  43 import org.forester.phylogeny.data.Sequence;
  44 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  45 import org.forester.util.BasicTable;
  46 import org.forester.util.BasicTableParser;
  47 import org.forester.util.ForesterUtil;
  48
  49 public final class PhylogenyDecorator {
  50
  51     // From evoruby/lib/evo/apps/tseq_taxonomy_processor.rb:
  52     final private static String  TP_TAXONOMY_CODE                   = "TAXONOMY_CODE";
  53     final private static String  TP_TAXONOMY_ID                     = "TAXONOMY_ID";
  54     final private static String  TP_TAXONOMY_ID_PROVIDER            = "TAXONOMY_ID_PROVIDER";
  55     final private static String  TP_TAXONOMY_SN                     = "TAXONOMY_SN";
  56     final private static String  TP_TAXONOMY_CN                     = "TAXONOMY_CN";
  57     final private static String  TP_TAXONOMY_SYN                    = "TAXONOMY_SYN";
  58     final private static String  TP_SEQ_SYMBOL                      = "SEQ_SYMBOL";
  59     final private static String  TP_SEQ_ACCESSION                   = "SEQ_ACCESSION";
  60     final private static String  TP_SEQ_ACCESSION_SOURCE            = "SEQ_ACCESSION_SOURCE";
  61     final private static String  TP_SEQ_ANNOTATION_DESC             = "SEQ_ANNOTATION_DESC";
  62     final private static String  TP_SEQ_ANNOTATION_REF              = "SEQ_ANNOTATION_REF";
  63     final private static String  TP_SEQ_MOL_SEQ                     = "SEQ_MOL_SEQ";
  64     final private static String  TP_SEQ_NAME                        = "SEQ_NAME";
  65     final private static String  TP_NODE_NAME                       = "NODE_NAME";
  66     final private static Pattern NODENAME_SEQNUMBER_TAXDOMAINNUMBER = Pattern
  67                                                                             .compile( "^([a-fA-Z0-9]{1,5})_([A-Z0-9]{2,4}[A-Z])(\\d{1,4})$" );
  68     public final static boolean  SANITIZE                           = false;
  69     public final static boolean  VERBOSE                            = true;
  70
  71     private PhylogenyDecorator() {
  72         // Not needed.
  73     }
  74
  75     public static void decorate( final Phylogeny phylogeny,
  76                                  final Map<String, Map<String, String>> map,
  77                                  final boolean picky,
  78                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map )
  79             throws IllegalArgumentException {
  80         for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
  81             final PhylogenyNode node = iter.next();
  82             final String name = node.getName();
  83             if ( !ForesterUtil.isEmpty( name ) ) {
  84                 if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) ) {
  85                     Map<String, String> new_values = map.get( name );
  86                     int x = 0;
  87                     while ( ( new_values == null ) && ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 )
  88                             && ( x <= numbers_of_chars_allowed_to_remove_if_not_found_in_map ) ) {
  89                         new_values = map.get( name.substring( 0, name.length() - x ) );
  90                         ++x;
  91                     }
  92                     if ( new_values != null ) {
  93                         if ( new_values.containsKey( TP_TAXONOMY_CODE ) ) {
  94                             AptxUtil.ensurePresenceOfTaxonomy( node );
  95                             node.getNodeData().getTaxonomy().setTaxonomyCode( new_values.get( TP_TAXONOMY_CODE ) );
  96                         }
  97                         if ( new_values.containsKey( TP_TAXONOMY_ID )
  98                                 && new_values.containsKey( TP_TAXONOMY_ID_PROVIDER ) ) {
  99                             AptxUtil.ensurePresenceOfTaxonomy( node );
 100                             node.getNodeData()
 101                                     .getTaxonomy()
 102                                     .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ),
 103                                                                     new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) );
 104                         }
 105                         else if ( new_values.containsKey( TP_TAXONOMY_ID ) ) {
 106                             AptxUtil.ensurePresenceOfTaxonomy( node );
 107                             node.getNodeData().getTaxonomy()
 108                                     .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) );
 109                         }
 110                         if ( new_values.containsKey( TP_TAXONOMY_SN ) ) {
 111                             AptxUtil.ensurePresenceOfTaxonomy( node );
 112                             node.getNodeData().getTaxonomy().setScientificName( new_values.get( TP_TAXONOMY_SN ) );
 113                         }
 114                         if ( new_values.containsKey( TP_TAXONOMY_CN ) ) {
 115                             AptxUtil.ensurePresenceOfTaxonomy( node );
 116                             node.getNodeData().getTaxonomy().setCommonName( new_values.get( TP_TAXONOMY_CN ) );
 117                         }
 118                         if ( new_values.containsKey( TP_TAXONOMY_SYN ) ) {
 119                             AptxUtil.ensurePresenceOfTaxonomy( node );
 120                             node.getNodeData().getTaxonomy().getSynonyms().add( new_values.get( TP_TAXONOMY_SYN ) );
 121                         }
 122                         if ( new_values.containsKey( TP_SEQ_ACCESSION )
 123                                 && new_values.containsKey( TP_SEQ_ACCESSION_SOURCE ) ) {
 124                             AptxUtil.ensurePresenceOfSequence( node );
 125                             node.getNodeData()
 126                                     .getSequence()
 127                                     .setAccession( new Accession( new_values.get( TP_SEQ_ACCESSION ),
 128                                                                   new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) );
 129                         }
 130                         if ( new_values.containsKey( TP_SEQ_ANNOTATION_DESC ) ) {
 131                             AptxUtil.ensurePresenceOfSequence( node );
 132                             final Annotation ann = new Annotation( "?" );
 133                             ann.setDesc( new_values.get( TP_SEQ_ANNOTATION_DESC ) );
 134                             node.getNodeData().getSequence().addAnnotation( ann );
 135                         }
 136                         if ( new_values.containsKey( TP_SEQ_ANNOTATION_REF ) ) {
 137                             AptxUtil.ensurePresenceOfSequence( node );
 138                             final Annotation ann = new Annotation( new_values.get( TP_SEQ_ANNOTATION_REF ) );
 139                             node.getNodeData().getSequence().addAnnotation( ann );
 140                         }
 141                         if ( new_values.containsKey( TP_SEQ_SYMBOL ) ) {
 142                             AptxUtil.ensurePresenceOfSequence( node );
 143                             node.getNodeData().getSequence().setSymbol( new_values.get( TP_SEQ_SYMBOL ) );
 144                         }
 145                         if ( new_values.containsKey( TP_SEQ_NAME ) ) {
 146                             AptxUtil.ensurePresenceOfSequence( node );
 147                             node.getNodeData().getSequence().setName( new_values.get( TP_SEQ_NAME ) );
 148                         }
 149                         if ( new_values.containsKey( TP_SEQ_MOL_SEQ ) ) {
 150                             AptxUtil.ensurePresenceOfSequence( node );
 151                             node.getNodeData().getSequence().setMolecularSequence( new_values.get( TP_SEQ_MOL_SEQ ) );
 152                         }
 153                         if ( new_values.containsKey( TP_NODE_NAME ) ) {
 154                             node.setName( new_values.get( TP_NODE_NAME ) );
 155                         }
 156                     }
 157                 }
 158                 else if ( picky ) {
 159                     throw new IllegalArgumentException( "\"" + name + "\" not found in name map" );
 160                 }
 161             }
 162         }
 163     }
 164
 165     /**
 166      *
 167      *
 168      *
 169      *
 170      *
 171      * @param phylogeny
 172      * @param map
 173      *            maps names (in phylogeny) to new values
 174      * @param field
 175      * @param picky
 176      * @throws IllegalArgumentException
 177      * @throws NHXFormatException
 178      */
 179     public static void decorate( final Phylogeny phylogeny,
 180                                  final Map<String, String> map,
 181                                  final FIELD field,
 182                                  final boolean extract_bracketed_scientific_name,
 183                                  final boolean picky,
 184                                  final boolean cut_name_after_space,
 185                                  final boolean process_name_intelligently,
 186                                  final boolean process_similar_to,
 187                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 188                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException,
 189             NHXFormatException {
 190         PhylogenyDecorator.decorate( phylogeny,
 191                                      map,
 192                                      field,
 193                                      extract_bracketed_scientific_name,
 194                                      picky,
 195                                      null,
 196                                      cut_name_after_space,
 197                                      process_name_intelligently,
 198                                      process_similar_to,
 199                                      numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 200                                      move_domain_numbers_at_end_to_middle );
 201     }
 202
 203     /**
 204      *
 205      *
 206      *
 207      * @param phylogeny
 208      * @param map
 209      *            maps names (in phylogeny) to new values if intermediate_map is
 210      *            null otherwise maps intermediate value to new value
 211      * @param field
 212      * @param picky
 213      * @param intermediate_map
 214      *            maps name (in phylogeny) to a intermediate value
 215      * @throws IllegalArgumentException
 216      */
 217     public static void decorate( final Phylogeny phylogeny,
 218                                  final Map<String, String> map,
 219                                  final FIELD field,
 220                                  final boolean extract_bracketed_scientific_name,
 221                                  final boolean picky,
 222                                  final Map<String, String> intermediate_map,
 223                                  final boolean cut_name_after_space,
 224                                  final boolean process_name_intelligently,
 225                                  final boolean process_similar_to,
 226                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 227                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException {
 228         if ( extract_bracketed_scientific_name && ( field == FIELD.TAXONOMY_SCIENTIFIC_NAME ) ) {
 229             throw new IllegalArgumentException( "Attempt to extract bracketed scientific name together with data field pointing to scientific name" );
 230         }
 231         for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
 232             final PhylogenyNode node = iter.next();
 233             String name = node.getName();
 234             if ( !ForesterUtil.isEmpty( name ) ) {
 235                 if ( intermediate_map != null ) {
 236                     name = PhylogenyDecorator.extractIntermediate( intermediate_map, name );
 237                 }
 238                 if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) ) {
 239                     String new_value = map.get( name );
 240                     int x = 0;
 241                     while ( ( new_value == null ) && ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 )
 242                             && ( x <= numbers_of_chars_allowed_to_remove_if_not_found_in_map ) ) {
 243                         new_value = map.get( name.substring( 0, name.length() - x ) );
 244                         ++x;
 245                     }
 246                     if ( new_value != null ) {
 247                         new_value = new_value.trim();
 248                         new_value.replaceAll( "/\\s+/", " " );
 249                         if ( extract_bracketed_scientific_name && new_value.endsWith( "]" ) ) {
 250                             extractBracketedScientificNames( node, new_value );
 251                         }
 252                         switch ( field ) {
 253                             case SEQUENCE_ANNOTATION_DESC:
 254                                 if ( PhylogenyDecorator.VERBOSE ) {
 255                                     System.out.println( name + ": " + new_value );
 256                                 }
 257                                 if ( !node.getNodeData().isHasSequence() ) {
 258                                     node.getNodeData().setSequence( new Sequence() );
 259                                 }
 260                                 final Annotation annotation = new Annotation( "?" );
 261                                 annotation.setDesc( new_value );
 262                                 node.getNodeData().getSequence().addAnnotation( annotation );
 263                                 break;
 264                             case DOMAIN_STRUCTURE:
 265                                 if ( PhylogenyDecorator.VERBOSE ) {
 266                                     System.out.println( name + ": " + new_value );
 267                                 }
 268                                 if ( !node.getNodeData().isHasSequence() ) {
 269                                     node.getNodeData().setSequence( new Sequence() );
 270                                 }
 271                                 node.getNodeData().getSequence()
 272                                         .setDomainArchitecture( new DomainArchitecture( new_value ) );
 273                                 break;
 274                             case TAXONOMY_CODE:
 275                                 if ( PhylogenyDecorator.VERBOSE ) {
 276                                     System.out.println( name + ": " + new_value );
 277                                 }
 278                                 AptxUtil.ensurePresenceOfTaxonomy( node );
 279                                 node.getNodeData().getTaxonomy().setTaxonomyCode( new_value );
 280                                 break;
 281                             case TAXONOMY_SCIENTIFIC_NAME:
 282                                 if ( PhylogenyDecorator.VERBOSE ) {
 283                                     System.out.println( name + ": " + new_value );
 284                                 }
 285                                 AptxUtil.ensurePresenceOfTaxonomy( node );
 286                                 node.getNodeData().getTaxonomy().setScientificName( new_value );
 287                                 break;
 288                             case SEQUENCE_NAME:
 289                                 if ( PhylogenyDecorator.VERBOSE ) {
 290                                     System.out.println( name + ": " + new_value );
 291                                 }
 292                                 if ( !node.getNodeData().isHasSequence() ) {
 293                                     node.getNodeData().setSequence( new Sequence() );
 294                                 }
 295                                 node.getNodeData().getSequence().setName( new_value );
 296                                 break;
 297                             case NODE_NAME:
 298                                 if ( PhylogenyDecorator.VERBOSE ) {
 299                                     System.out.print( name + " -> " );
 300                                 }
 301                                 if ( cut_name_after_space ) {
 302                                     if ( PhylogenyDecorator.VERBOSE ) {
 303                                         System.out.print( new_value + " -> " );
 304                                     }
 305                                     new_value = PhylogenyDecorator.deleteAtFirstSpace( new_value );
 306                                 }
 307                                 else if ( process_name_intelligently ) {
 308                                     if ( PhylogenyDecorator.VERBOSE ) {
 309                                         System.out.print( new_value + " -> " );
 310                                     }
 311                                     new_value = PhylogenyDecorator.processNameIntelligently( new_value );
 312                                 }
 313                                 else if ( process_similar_to ) {
 314                                     if ( PhylogenyDecorator.VERBOSE ) {
 315                                         System.out.print( new_value + " -> " );
 316                                     }
 317                                     new_value = PhylogenyDecorator.processSimilarTo( new_value );
 318                                 }
 319                                 if ( PhylogenyDecorator.SANITIZE ) {
 320                                     new_value = PhylogenyDecorator.sanitize( new_value );
 321                                 }
 322                                 if ( PhylogenyDecorator.VERBOSE ) {
 323                                     System.out.println( new_value );
 324                                 }
 325                                 node.setName( new_value );
 326                                 break;
 327                             default:
 328                                 throw new RuntimeException( "unknown field \"" + field + "\"" );
 329                         }
 330                         if ( move_domain_numbers_at_end_to_middle && ( field != FIELD.NODE_NAME ) ) {
 331                             node.setName( moveDomainNumbersAtEnd( node.getName() ) );
 332                         }
 333                     }
 334                 }
 335                 else if ( picky ) {
 336                     throw new IllegalArgumentException( "\"" + name + "\" not found in name map" );
 337                 }
 338             }
 339         }
 340     }
 341
 342     public static void decorate( final Phylogeny[] phylogenies,
 343                                  final Map<String, Map<String, String>> map,
 344                                  final boolean picky,
 345                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map )
 346             throws IllegalArgumentException, NHXFormatException {
 347         for( int i = 0; i < phylogenies.length; ++i ) {
 348             PhylogenyDecorator.decorate( phylogenies[ i ],
 349                                          map,
 350                                          picky,
 351                                          numbers_of_chars_allowed_to_remove_if_not_found_in_map );
 352         }
 353     }
 354
 355     public static void decorate( final Phylogeny[] phylogenies,
 356                                  final Map<String, String> map,
 357                                  final FIELD field,
 358                                  final boolean extract_bracketed_scientific_name,
 359                                  final boolean picky,
 360                                  final boolean cut_name_after_space,
 361                                  final boolean process_name_intelligently,
 362                                  final boolean process_similar_to,
 363                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 364                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException,
 365             NHXFormatException {
 366         for( int i = 0; i < phylogenies.length; ++i ) {
 367             PhylogenyDecorator.decorate( phylogenies[ i ],
 368                                          map,
 369                                          field,
 370                                          extract_bracketed_scientific_name,
 371                                          picky,
 372                                          cut_name_after_space,
 373                                          process_name_intelligently,
 374                                          process_similar_to,
 375                                          numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 376                                          move_domain_numbers_at_end_to_middle );
 377         }
 378     }
 379
 380     public static void decorate( final Phylogeny[] phylogenies,
 381                                  final Map<String, String> map,
 382                                  final FIELD field,
 383                                  final boolean extract_bracketed_scientific_name,
 384                                  final boolean picky,
 385                                  final Map<String, String> intermediate_map,
 386                                  final boolean cut_name_after_space,
 387                                  final boolean process_name_intelligently,
 388                                  final boolean process_similar_to,
 389                                  final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 390                                  final boolean move_domain_numbers_at_end_to_middle ) throws IllegalArgumentException,
 391             NHXFormatException {
 392         for( int i = 0; i < phylogenies.length; ++i ) {
 393             PhylogenyDecorator.decorate( phylogenies[ i ],
 394                                          map,
 395                                          field,
 396                                          extract_bracketed_scientific_name,
 397                                          picky,
 398                                          intermediate_map,
 399                                          cut_name_after_space,
 400                                          process_name_intelligently,
 401                                          process_similar_to,
 402                                          numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 403                                          move_domain_numbers_at_end_to_middle );
 404         }
 405     }
 406
 407     private static String deleteAtFirstSpace( final String name ) {
 408         final int first_space = name.indexOf( " " );
 409         if ( first_space > 1 ) {
 410             return name.substring( 0, first_space ).trim();
 411         }
 412         return name;
 413     }
 414
 415     private static void extractBracketedScientificNames( final PhylogenyNode node, final String new_value ) {
 416         final int i = new_value.lastIndexOf( "[" );
 417         final String scientific_name = new_value.substring( i + 1, new_value.length() - 1 );
 418         AptxUtil.ensurePresenceOfTaxonomy( node );
 419         node.getNodeData().getTaxonomy().setScientificName( scientific_name );
 420     }
 421
 422     private static String extractIntermediate( final Map<String, String> intermediate_map, final String name ) {
 423         String new_name = null;
 424         if ( PhylogenyDecorator.VERBOSE ) {
 425             System.out.print( name + " => " );
 426         }
 427         if ( intermediate_map.containsKey( name ) ) {
 428             new_name = intermediate_map.get( name );
 429             if ( ForesterUtil.isEmpty( new_name ) ) {
 430                 throw new IllegalArgumentException( "\"" + name + "\" maps to null or empty string in secondary map" );
 431             }
 432         }
 433         else {
 434             throw new IllegalArgumentException( "\"" + name + "\" not found in name secondary map" );
 435         }
 436         if ( PhylogenyDecorator.VERBOSE ) {
 437             System.out.println( new_name + "  " );
 438         }
 439         return new_name;
 440     }
 441
 442     private static String moveDomainNumbersAtEnd( final String node_name ) {
 443         final Matcher m = NODENAME_SEQNUMBER_TAXDOMAINNUMBER.matcher( node_name );
 444         if ( m.matches() ) {
 445             final String seq_number = m.group( 1 );
 446             final String tax = m.group( 2 );
 447             final String domain_number = m.group( 3 );
 448             return seq_number + "_[" + domain_number + "]_" + tax;
 449         }
 450         else {
 451             return node_name;
 452         }
 453     }
 454
 455     public static Map<String, Map<String, String>> parseMappingTable( final File mapping_table_file )
 456             throws IOException {
 457         final Map<String, Map<String, String>> map = new HashMap<String, Map<String, String>>();
 458         BasicTable<String> mapping_table = null;
 459         mapping_table = BasicTableParser.parse( mapping_table_file, "\t", false );
 460         for( int row = 0; row < mapping_table.getNumberOfRows(); ++row ) {
 461             final Map<String, String> row_map = new HashMap<String, String>();
 462             String name = null;
 463             for( int col = 0; col < mapping_table.getNumberOfColumns(); ++col ) {
 464                 final String table_cell = mapping_table.getValue( col, row );
 465                 if ( col == 0 ) {
 466                     name = table_cell;
 467                 }
 468                 else if ( table_cell != null ) {
 469                     final String key = table_cell.substring( 0, table_cell.indexOf( ':' ) );
 470                     final String val = table_cell.substring( table_cell.indexOf( ':' ) + 1, table_cell.length() );
 471                     row_map.put( key, val );
 472                 }
 473             }
 474             map.put( name, row_map );
 475         }
 476         return map;
 477     }
 478
 479     private static String processNameIntelligently( final String name ) {
 480         final String[] s = name.split( " " );
 481         if ( s.length < 2 ) {
 482             return name;
 483         }
 484         else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "|" ) > 0 ) ) {
 485             return s[ 0 ];
 486         }
 487         else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "|" ) > 0 ) ) {
 488             return s[ 1 ];
 489         }
 490         else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "." ) > 0 ) ) {
 491             return s[ 0 ];
 492         }
 493         else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "." ) > 0 ) ) {
 494             return s[ 1 ];
 495         }
 496         else if ( s[ 0 ].indexOf( "_" ) > 0 ) {
 497             return s[ 0 ];
 498         }
 499         else if ( s[ 1 ].indexOf( "_" ) > 0 ) {
 500             return s[ 1 ];
 501         }
 502         else {
 503             return s[ 0 ];
 504         }
 505     }
 506
 507     private static String processSimilarTo( final String name ) {
 508         final int i = name.toLowerCase().indexOf( "similar to" );
 509         String similar_to = "";
 510         if ( i >= 0 ) {
 511             similar_to = " similarity=" + name.substring( i + 10 ).trim();
 512         }
 513         final String pi = processNameIntelligently( name );
 514         return pi + similar_to;
 515     }
 516
 517     private static String sanitize( String s ) {
 518         s = s.replace( ' ', '_' );
 519         s = s.replace( '(', '{' );
 520         s = s.replace( ')', '}' );
 521         s = s.replace( '[', '{' );
 522         s = s.replace( ']', '}' );
 523         s = s.replace( ',', '_' );
 524         return s;
 525     }
 526
 527     public static enum FIELD {
 528         NODE_NAME, SEQUENCE_ANNOTATION_DESC, DOMAIN_STRUCTURE, TAXONOMY_CODE, TAXONOMY_SCIENTIFIC_NAME, SEQUENCE_NAME;
 529     }
 530 }