forester/java/src/org/forester/go/TestGo.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.go;
  27
  28 import java.io.File;
  29 import java.util.ArrayList;
  30 import java.util.List;
  31 import java.util.Map;
  32 import java.util.SortedSet;
  33
  34 import org.forester.util.ForesterUtil;
  35
  36 public class TestGo {
  37
  38     private final static double ZERO_DIFF = 1.0E-9;
  39
  40     public static boolean isEqual( final double a, final double b ) {
  41         return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
  42     }
  43
  44     public static boolean test( final File test_dir ) {
  45         System.out.print( "  GO ID: " );
  46         if ( !testGoId() ) {
  47             System.out.println( "failed." );
  48             return false;
  49         }
  50         System.out.println( "OK." );
  51         System.out.print( "  Namespace: " );
  52         if ( !testNamespace() ) {
  53             System.out.println( "failed." );
  54             return false;
  55         }
  56         System.out.println( "OK." );
  57         System.out.print( "  Basic GO term: " );
  58         if ( !testBasicGoTerm() ) {
  59             System.out.println( "failed." );
  60             return false;
  61         }
  62         System.out.println( "OK." );
  63         System.out.print( "  OBO parser: " );
  64         if ( !testOBOparser( test_dir ) ) {
  65             System.out.println( "failed." );
  66             return false;
  67         }
  68         System.out.println( "OK." );
  69         System.out.print( "  Pfam to GO mapping: " );
  70         if ( !testPfamToGoMapping() ) {
  71             System.out.println( "failed." );
  72             return false;
  73         }
  74         System.out.println( "OK." );
  75         System.out.print( "  Pfam to GO parser: " );
  76         if ( !testPfamToGoParser( test_dir ) ) {
  77             System.out.println( "failed." );
  78             return false;
  79         }
  80         System.out.println( "OK." );
  81         System.out.print( "  Super terms: " );
  82         if ( !testSuperTermGetting( test_dir ) ) {
  83             System.out.println( "failed." );
  84             return false;
  85         }
  86         System.out.println( "OK." );
  87         System.out.print( "  Super term counting: " );
  88         if ( !testSuperTermCounting( test_dir ) ) {
  89             System.out.println( "failed." );
  90             return false;
  91         }
  92         System.out.println( "OK." );
  93         return true;
  94     }
  95
  96     private static boolean testBasicGoTerm() {
  97         try {
  98             final GoTerm gt1 = new BasicGoTerm( "GO:0047579",
  99                                                 "4-hydroxymandelate oxidase activity",
 100                                                 "molecular_function",
 101                                                 false );
 102             final GoTerm gt2 = new BasicGoTerm( "GO:0047579",
 103                                                 "4-hydroxymandelate oxidase activity",
 104                                                 "molecular_function",
 105                                                 false );
 106             final GoTerm gt3 = new BasicGoTerm( "GO:0047579", "?", "molecular_function", true );
 107             final GoTerm gt4 = new BasicGoTerm( "GO:0047579",
 108                                                 "4-hydroxymandelate oxidase activity",
 109                                                 "biological_process",
 110                                                 false );
 111             final GoTerm gt5 = new BasicGoTerm( "GO:0047578",
 112                                                 "4-hydroxymandelate oxidase activity",
 113                                                 "molecular_function",
 114                                                 false );
 115             if ( !gt1.equals( gt2 ) ) {
 116                 return false;
 117             }
 118             if ( !gt1.equals( gt3 ) ) {
 119                 return false;
 120             }
 121             if ( gt1.equals( gt4 ) ) {
 122                 return false;
 123             }
 124             if ( gt1.hashCode() != gt4.hashCode() ) {
 125                 return false;
 126             }
 127             if ( gt1.equals( gt5 ) ) {
 128                 return false;
 129             }
 130             final GoTerm gt6 = ( GoTerm ) gt5.copy();
 131             if ( !gt6.equals( gt5 ) ) {
 132                 return false;
 133             }
 134         }
 135         catch ( final Exception e ) {
 136             e.printStackTrace( System.out );
 137             return false;
 138         }
 139         return true;
 140     }
 141
 142     private static boolean testGoId() {
 143         try {
 144             final GoId id1 = new GoId( "GO:0042617" );
 145             final GoId id2 = new GoId( "GO:0042630" );
 146             final GoId id3 = new GoId( "GO:0042630" );
 147             if ( id1.equals( id2 ) ) {
 148                 return false;
 149             }
 150             if ( !id2.equals( id3 ) ) {
 151                 return false;
 152             }
 153             if ( !id1.toString().equals( "GO:0042617" ) ) {
 154                 return false;
 155             }
 156             if ( id2.hashCode() != id3.hashCode() ) {
 157                 return false;
 158             }
 159             if ( id1.hashCode() == id2.hashCode() ) {
 160                 return false;
 161             }
 162         }
 163         catch ( final Exception e ) {
 164             e.printStackTrace( System.out );
 165             return false;
 166         }
 167         return true;
 168     }
 169
 170     private static boolean testNamespace() {
 171         try {
 172             final GoNameSpace b = new GoNameSpace( "Biological_process" );
 173             final GoNameSpace c = new GoNameSpace( "Cellular_Component" );
 174             final GoNameSpace m = new GoNameSpace( "molecular_function" );
 175             final GoNameSpace m2 = new GoNameSpace( GoNameSpace.GoNamespaceType.MOLECULAR_FUNCTION );
 176             if ( b.equals( c ) ) {
 177                 return false;
 178             }
 179             if ( !m.equals( m2 ) ) {
 180                 return false;
 181             }
 182             if ( !b.toString().equals( "biological_process" ) ) {
 183                 return false;
 184             }
 185             if ( !c.toString().equals( "cellular_component" ) ) {
 186                 return false;
 187             }
 188             if ( !m.toString().equals( "molecular_function" ) ) {
 189                 return false;
 190             }
 191         }
 192         catch ( final Exception e ) {
 193             e.printStackTrace( System.out );
 194             return false;
 195         }
 196         return true;
 197     }
 198
 199     private static boolean testOBOparser( final File test_dir ) {
 200         try {
 201             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator() + "obo_test" ),
 202                                                     OBOparser.ReturnType.BASIC_GO_TERM );
 203             final List<GoTerm> go_terms = parser.parse();
 204             if ( parser.getGoTermCount() != 26 ) {
 205                 return false;
 206             }
 207             final GoTerm g0 = go_terms.get( 0 );
 208             final GoTerm g1 = go_terms.get( 1 );
 209             final GoTerm g3 = go_terms.get( 2 );
 210             final GoTerm g2 = go_terms.get( 25 );
 211             if ( !g0.getComment().equals( "" ) ) {
 212                 return false;
 213             }
 214             if ( !g0.getDefinition()
 215                     .equals( "\"The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton.\" [GOC:mcc, PMID:10873824, PMID:11389764]" ) ) {
 216                 return false;
 217             }
 218             if ( !g0.getGoId().getId().equals( "GO:0000001" ) ) {
 219                 return false;
 220             }
 221             if ( g0.getGoNameSpace().equals( GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) ) {
 222                 return false;
 223             }
 224             if ( g0.getGoNameSpace().getType() != GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) {
 225                 return false;
 226             }
 227             if ( g0.getGoRelationships().size() != 0 ) {
 228                 return false;
 229             }
 230             if ( g0.getGoXRefs().size() != 0 ) {
 231                 return false;
 232             }
 233             if ( !g0.getName().equals( "mitochondrion inheritance" ) ) {
 234                 return false;
 235             }
 236             if ( g0.getSuperGoIds().size() != 2 ) {
 237                 return false;
 238             }
 239             if ( !g0.isObsolete() ) {
 240                 return false;
 241             }
 242             if ( !g1.getComment().equals( "comment" ) ) {
 243                 return false;
 244             }
 245             if ( !g1.getDefinition()
 246                     .equals( "\"The maintenance of the structure and integrity of the mitochondrial genome.\" [GOC:ai]" ) ) {
 247                 return false;
 248             }
 249             if ( !g1.getGoId().getId().equals( "GO:0000002" ) ) {
 250                 return false;
 251             }
 252             if ( g1.getGoNameSpace().equals( GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) ) {
 253                 return false;
 254             }
 255             if ( g1.getGoNameSpace().getType() != GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) {
 256                 return false;
 257             }
 258             if ( g1.getGoRelationships().size() != 1 ) {
 259                 return false;
 260             }
 261             if ( g1.getGoXRefs().size() != 5 ) {
 262                 return false;
 263             }
 264             if ( !g1.getName().equals( "mitochondrial genome maintenance" ) ) {
 265                 return false;
 266             }
 267             if ( g1.getSuperGoIds().size() != 1 ) {
 268                 return false;
 269             }
 270             if ( g1.isObsolete() ) {
 271                 return false;
 272             }
 273             if ( !g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "EC:2.4.1.-" ) ) ) {
 274                 return false;
 275             }
 276             if ( !g1.getGoXRefs().get( 0 ).getXRef().equals( "2.4.1.-" ) ) {
 277                 return false;
 278             }
 279             if ( g1.getGoXRefs().get( 0 ).getType() != GoXRef.Type.EC ) {
 280                 return false;
 281             }
 282             if ( g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "EC:2.4.1.1" ) ) ) {
 283                 return false;
 284             }
 285             if ( g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "Reactome:2.4.1.-" ) ) ) {
 286                 return false;
 287             }
 288             if ( !g1.getGoXRefs().get( 1 ).equals( new BasicGoXRef( "Reactome:7672" ) ) ) {
 289                 return false;
 290             }
 291             if ( !g1.getGoXRefs().get( 2 ).equals( new BasicGoXRef( "MetaCyc:SIROHEME-FERROCHELAT-RXN" ) ) ) {
 292                 return false;
 293             }
 294             if ( !g1.getGoXRefs().get( 3 ).equals( new BasicGoXRef( "RESID:AA02376" ) ) ) {
 295                 return false;
 296             }
 297             if ( !g1.getGoXRefs().get( 4 ).equals( new BasicGoXRef( "UM-BBD_enzymeID:e0271" ) ) ) {
 298                 return false;
 299             }
 300             if ( !g1.getGoRelationships().get( 0 ).equals( new BasicGoRelationship( "part_of GO:0007052" ) ) ) {
 301                 return false;
 302             }
 303             if ( !g1.getGoRelationships().get( 0 ).getGoId().equals( new GoId( "GO:0007052" ) ) ) {
 304                 return false;
 305             }
 306             if ( !g1.getGoRelationships().get( 0 ).getGoId().getId().equals( "GO:0007052" ) ) {
 307                 return false;
 308             }
 309             if ( g1.getGoRelationships().get( 0 ).getType() != GoRelationship.Type.PART_OF ) {
 310                 return false;
 311             }
 312             if ( g1.getGoRelationships().get( 0 ).equals( new BasicGoRelationship( "part_of GO:1007052" ) ) ) {
 313                 return false;
 314             }
 315             if ( !g1.getSuperGoIds().get( 0 ).equals( new GoId( "GO:0007005" ) ) ) {
 316                 return false;
 317             }
 318             if ( g1.getSuperGoIds().get( 0 ).equals( new GoId( "GO:1007005" ) ) ) {
 319                 return false;
 320             }
 321             if ( !g2.getGoId().getId().equals( "GO:0000030" ) ) {
 322                 return false;
 323             }
 324             if ( !g2.getGoId().equals( new GoId( "GO:0000030" ) ) ) {
 325                 return false;
 326             }
 327             if ( g2.getGoId().getId().equals( "GO:0000031" ) ) {
 328                 return false;
 329             }
 330             if ( g2.getGoId().equals( new GoId( "GO:0000031" ) ) ) {
 331                 return false;
 332             }
 333             if ( g3.getGoSubsets().size() != 3 ) {
 334                 return false;
 335             }
 336             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "goslim_generic" ) ) ) {
 337                 return false;
 338             }
 339             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "goslim_plant" ) ) ) {
 340                 return false;
 341             }
 342             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "gosubset_prok" ) ) ) {
 343                 return false;
 344             }
 345             if ( g3.getGoSubsets().contains( new BasicGoSubset( "goslim_candida" ) ) ) {
 346                 return false;
 347             }
 348         }
 349         catch ( final Exception e ) {
 350             e.printStackTrace( System.out );
 351             return false;
 352         }
 353         return true;
 354     }
 355
 356     private static boolean testPfamToGoMapping() {
 357         try {
 358             final PfamToGoMapping pg0 = new PfamToGoMapping( "A", new GoId( "GO:0000001" ) );
 359             final PfamToGoMapping pg1 = new PfamToGoMapping( "A", new GoId( "GO:0000001" ) );
 360             final PfamToGoMapping pg2 = new PfamToGoMapping( "B", new GoId( "GO:0000001" ) );
 361             final PfamToGoMapping pg3 = new PfamToGoMapping( "A", new GoId( "GO:0000002" ) );
 362             final PfamToGoMapping pg4 = new PfamToGoMapping( "B", new GoId( "GO:0000002" ) );
 363             if ( !pg0.equals( pg0 ) ) {
 364                 return false;
 365             }
 366             if ( !pg0.equals( pg1 ) ) {
 367                 return false;
 368             }
 369             if ( pg0.equals( pg2 ) ) {
 370                 return false;
 371             }
 372             if ( pg0.equals( pg3 ) ) {
 373                 return false;
 374             }
 375             if ( pg0.equals( pg4 ) ) {
 376                 return false;
 377             }
 378             if ( pg0.compareTo( pg3 ) != 0 ) {
 379                 return false;
 380             }
 381             if ( pg0.compareTo( pg2 ) >= 0 ) {
 382                 return false;
 383             }
 384             if ( pg2.compareTo( pg0 ) <= 0 ) {
 385                 return false;
 386             }
 387         }
 388         catch ( final Exception e ) {
 389             e.printStackTrace( System.out );
 390             return false;
 391         }
 392         return true;
 393     }
 394
 395     private static boolean testPfamToGoParser( final File test_dir ) {
 396         try {
 397             final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator()
 398                     + "pfam_to_go_test" ) );
 399             final List<PfamToGoMapping> mappings = parser.parse();
 400             if ( parser.getMappingCount() != 426 ) {
 401                 return false;
 402             }
 403             if ( mappings.size() != 426 ) {
 404                 return false;
 405             }
 406             final PfamToGoMapping m0 = mappings.get( 0 );
 407             final PfamToGoMapping m1 = mappings.get( 1 );
 408             final PfamToGoMapping m2 = mappings.get( 2 );
 409             final PfamToGoMapping m3 = mappings.get( 3 );
 410             final PfamToGoMapping m4 = mappings.get( 4 );
 411             final PfamToGoMapping m5 = mappings.get( 5 );
 412             final PfamToGoMapping m424 = mappings.get( 424 );
 413             final PfamToGoMapping m425 = mappings.get( 425 );
 414             if ( !m0.getKey().equals( "7tm_1" ) ) {
 415                 return false;
 416             }
 417             if ( !m0.getValue().equals( new GoId( "GO:0001584" ) ) ) {
 418                 return false;
 419             }
 420             if ( m0.getKey().equals( "7tm_x" ) ) {
 421                 return false;
 422             }
 423             if ( m0.getValue().equals( new GoId( "GO:0001585" ) ) ) {
 424                 return false;
 425             }
 426             if ( !m1.getKey().equals( "7tm_1" ) ) {
 427                 return false;
 428             }
 429             if ( !m1.getValue().equals( new GoId( "GO:0007186" ) ) ) {
 430                 return false;
 431             }
 432             if ( !m2.getKey().equals( "7tm_1" ) ) {
 433                 return false;
 434             }
 435             if ( !m2.getValue().equals( new GoId( "GO:0016021" ) ) ) {
 436                 return false;
 437             }
 438             if ( !m3.getKey().equals( "7tm_2" ) ) {
 439                 return false;
 440             }
 441             if ( !m3.getValue().equals( new GoId( "GO:0004930" ) ) ) {
 442                 return false;
 443             }
 444             if ( !m4.getKey().equals( "7tm_2" ) ) {
 445                 return false;
 446             }
 447             if ( !m4.getValue().equals( new GoId( "GO:0016020" ) ) ) {
 448                 return false;
 449             }
 450             if ( !m5.getKey().equals( "7tm_3" ) ) {
 451                 return false;
 452             }
 453             if ( !m5.getValue().equals( new GoId( "GO:0008067" ) ) ) {
 454                 return false;
 455             }
 456             if ( !m424.getKey().equals( "OMPdecase" ) ) {
 457                 return false;
 458             }
 459             if ( !m424.getValue().equals( new GoId( "GO:0006207" ) ) ) {
 460                 return false;
 461             }
 462             if ( !m425.getKey().equals( "Bac_DNA_binding" ) ) {
 463                 return false;
 464             }
 465             if ( !m425.getValue().equals( new GoId( "GO:0003677" ) ) ) {
 466                 return false;
 467             }
 468         }
 469         catch ( final Exception e ) {
 470             e.printStackTrace( System.out );
 471             return false;
 472         }
 473         return true;
 474     }
 475
 476     private static boolean testSuperTermCounting( final File test_dir ) {
 477         try {
 478             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
 479                     + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
 480             final List<GoTerm> all_go_terms = parser.parse();
 481             if ( parser.getGoTermCount() != 27748 ) {
 482                 return false;
 483             }
 484             final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( all_go_terms );
 485             final List<GoTerm> categories = new ArrayList<GoTerm>();
 486             final List<GoTerm> experiment_set = new ArrayList<GoTerm>();
 487             experiment_set.add( new BasicGoTerm( new GoId( "GO:0005690" ), "snRNP U4atac", GoNameSpace
 488                     .createUnassigned(), false ) );
 489             experiment_set.add( new BasicGoTerm( new GoId( "GO:0009698" ),
 490                                                  "phenylpropanoid metabolic process",
 491                                                  GoNameSpace.createUnassigned(),
 492                                                  false ) );
 493             experiment_set.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
 494                     .createUnassigned(), false ) );
 495             experiment_set.add( new BasicGoTerm( new GoId( "GO:0006915" ),
 496                                                  "apoptosis",
 497                                                  GoNameSpace.createUnassigned(),
 498                                                  false ) );
 499             experiment_set.add( new BasicGoTerm( new GoId( "GO:0001783" ), "B cell apoptosis", GoNameSpace
 500                     .createUnassigned(), false ) );
 501             experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
 502                     .createUnassigned(), false ) );
 503             experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
 504                     .createUnassigned(), false ) );
 505             experiment_set.add( new BasicGoTerm( new GoId( "GO:0010658" ),
 506                                                  "striated muscle cell apoptosis",
 507                                                  GoNameSpace.createUnassigned(),
 508                                                  false ) );
 509             experiment_set.add( new BasicGoTerm( new GoId( "GO:0043065" ),
 510                                                  "positive regulation of apoptosis",
 511                                                  GoNameSpace.createUnassigned(),
 512                                                  false ) );
 513             categories
 514                     .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) );
 515             categories.add( new BasicGoTerm( new GoId( "GO:0006915" ),
 516                                              "apoptosis",
 517                                              GoNameSpace.createUnassigned(),
 518                                              false ) );
 519             categories.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
 520                     .createUnassigned(), false ) );
 521             categories.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
 522                     .createUnassigned(), false ) );
 523             categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace
 524                     .createUnassigned(), false ) );
 525             categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace
 526                     .createUnassigned(), false ) );
 527             categories.add( new BasicGoTerm( new GoId( "GO:0016326" ), "kinesin motor activity", GoNameSpace
 528                     .createUnassigned(), false ) );
 529             categories.add( new BasicGoTerm( new GoId( "GO:0005575" ), "cellular_component", GoNameSpace
 530                     .createUnassigned(), false ) );
 531             categories.add( new BasicGoTerm( new GoId( "GO:0032502" ), "developmental process", GoNameSpace
 532                     .createUnassigned(), false ) );
 533             categories.add( new BasicGoTerm( new GoId( "GO:0051094" ),
 534                                              "positive regulation of developmental process",
 535                                              GoNameSpace.createUnassigned(),
 536                                              false ) );
 537             categories.add( new BasicGoTerm( new GoId( "GO:0048522" ),
 538                                              "positive regulation of cellular process",
 539                                              GoNameSpace.createUnassigned(),
 540                                              false ) );
 541             final Map<GoId, Integer> counts = GoUtils.countCategories( categories, experiment_set, goid_to_term_map );
 542             // death
 543             if ( counts.get( new GoId( "GO:0016265" ) ) != 5 ) {
 544                 return false;
 545             }
 546             // apoptosis
 547             if ( counts.get( new GoId( "GO:0006915" ) ) != 5 ) {
 548                 return false;
 549             }
 550             // biological_process
 551             if ( counts.get( new GoId( "GO:0008150" ) ) != 8 ) {
 552                 return false;
 553             }
 554             // muscle cell apoptosis
 555             if ( counts.get( new GoId( "GO:0010657" ) ) != 3 ) {
 556                 return false;
 557             }
 558             // striated muscle cell apoptosis
 559             if ( counts.get( new GoId( "GO:0010658" ) ) != 1 ) {
 560                 return false;
 561             }
 562             // o-xylene biosynthetic process
 563             if ( counts.get( new GoId( "GO:0046242" ) ) != 0 ) {
 564                 return false;
 565             }
 566             // kinesin motor activity
 567             if ( counts.get( new GoId( "GO:0016326" ) ) != 0 ) {
 568                 return false;
 569             }
 570             // cellular_component
 571             if ( counts.get( new GoId( "GO:0005575" ) ) != 1 ) {
 572                 return false;
 573             }
 574             // developmental process
 575             if ( counts.get( new GoId( "GO:0032502" ) ) != 5 ) {
 576                 return false;
 577             }
 578             // positive regulation of developmental process
 579             if ( counts.get( new GoId( "GO:0051094" ) ) != 1 ) {
 580                 return false;
 581             }
 582             // positive regulation of cellular process
 583             if ( counts.get( new GoId( "GO:0048522" ) ) != 1 ) {
 584                 return false;
 585             }
 586             final List<GoId> categories_id = new ArrayList<GoId>();
 587             final List<GoId> experiment_set_id = new ArrayList<GoId>();
 588             experiment_set_id.add( new GoId( "GO:0005690" ) );
 589             experiment_set_id.add( new GoId( "GO:0009698" ) );
 590             experiment_set_id.add( new GoId( "GO:0008150" ) );
 591             experiment_set_id.add( new GoId( "GO:0006915" ) );
 592             experiment_set_id.add( new GoId( "GO:0001783" ) );
 593             experiment_set_id.add( new GoId( "GO:0010657" ) );
 594             experiment_set_id.add( new GoId( "GO:0010657" ) );
 595             experiment_set_id.add( new GoId( "GO:0010658" ) );
 596             categories_id.add( new GoId( "GO:0016265" ) );
 597             categories_id.add( new GoId( "GO:0006915" ) );
 598             categories_id.add( new GoId( "GO:0008150" ) );
 599             categories_id.add( new GoId( "GO:0010657" ) );
 600             categories_id.add( new GoId( "GO:0010658" ) );
 601             categories_id.add( new GoId( "GO:0046242" ) );
 602             categories_id.add( new GoId( "GO:0016326" ) );
 603             categories_id.add( new GoId( "GO:0005575" ) );
 604             final Map<GoId, Integer> counts_id = GoUtils.countCategoriesId( categories_id,
 605                                                                             experiment_set_id,
 606                                                                             goid_to_term_map );
 607             // death
 608             if ( counts_id.get( new GoId( "GO:0016265" ) ) != 5 ) {
 609                 return false;
 610             }
 611             // apoptosis
 612             if ( counts_id.get( new GoId( "GO:0006915" ) ) != 5 ) {
 613                 return false;
 614             }
 615             // biological_process
 616             if ( counts_id.get( new GoId( "GO:0008150" ) ) != 7 ) {
 617                 return false;
 618             }
 619             // muscle cell apoptosis
 620             if ( counts_id.get( new GoId( "GO:0010657" ) ) != 3 ) {
 621                 return false;
 622             }
 623             // striated muscle cell apoptosis
 624             if ( counts_id.get( new GoId( "GO:0010658" ) ) != 1 ) {
 625                 return false;
 626             }
 627             // o-xylene biosynthetic process
 628             if ( counts_id.get( new GoId( "GO:0046242" ) ) != 0 ) {
 629                 return false;
 630             }
 631             // kinesin motor activity
 632             if ( counts_id.get( new GoId( "GO:0016326" ) ) != 0 ) {
 633                 return false;
 634             }
 635             // cellular_componen
 636             if ( counts_id.get( new GoId( "GO:0005575" ) ) != 1 ) {
 637                 return false;
 638             }
 639         }
 640         catch ( final Exception e ) {
 641             e.printStackTrace( System.out );
 642             return false;
 643         }
 644         return true;
 645     }
 646
 647     private static boolean testSuperTermGetting( final File test_dir ) {
 648         try {
 649             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
 650                     + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
 651             final List<GoTerm> go_terms = parser.parse();
 652             if ( parser.getGoTermCount() != 27748 ) {
 653                 return false;
 654             }
 655             final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
 656             final SortedSet<GoTerm> b_cell_selection = GoUtils.getAllSuperGoTerms( new GoId( "GO:0002339" ),
 657                                                                                    goid_to_term_map );
 658             if ( b_cell_selection.size() != 2 ) {
 659                 return false;
 660             }
 661             if ( !b_cell_selection.contains( new BasicGoTerm( new GoId( "GO:0002376" ),
 662                                                               "immune system process",
 663                                                               GoNameSpace.createBiologicalProcess(),
 664                                                               false ) ) ) {
 665                 return false;
 666             }
 667             if ( !b_cell_selection.contains( new BasicGoTerm( new GoId( "GO:0008150" ),
 668                                                               "biological process",
 669                                                               GoNameSpace.createBiologicalProcess(),
 670                                                               false ) ) ) {
 671                 return false;
 672             }
 673             final SortedSet<GoTerm> b_cell_differentation = GoUtils.getAllSuperGoTerms( new GoId( "GO:0030183" ),
 674                                                                                         goid_to_term_map );
 675             if ( b_cell_differentation.size() != 12 ) {
 676                 return false;
 677             }
 678             final SortedSet<GoTerm> biological_process = GoUtils.getAllSuperGoTerms( new GoId( "GO:0008150" ),
 679                                                                                      goid_to_term_map );
 680             if ( biological_process.size() != 0 ) {
 681                 return false;
 682             }
 683             final SortedSet<GoTerm> protein_aa_phosphorylation = GoUtils.getAllSuperGoTerms( new GoId( "GO:0006468" ),
 684                                                                                              goid_to_term_map );
 685             if ( protein_aa_phosphorylation.size() != 16 ) {
 686                 return false;
 687             }
 688         }
 689         catch ( final Exception e ) {
 690             e.printStackTrace( System.out );
 691             return false;
 692         }
 693         return true;
 694     }
 695 }