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: www.phylosoft.org/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.surfacing.DomainId;
  35 import org.forester.util.ForesterUtil;
  36
  37 public class TestGo {
  38
  39     private final static double ZERO_DIFF = 1.0E-9;
  40
  41     public static boolean isEqual( final double a, final double b ) {
  42         return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
  43     }
  44
  45     public static boolean test( final File test_dir ) {
  46         System.out.print( "  GO ID: " );
  47         if ( !testGoId() ) {
  48             System.out.println( "failed." );
  49             return false;
  50         }
  51         System.out.println( "OK." );
  52         System.out.print( "  Namespace: " );
  53         if ( !testNamespace() ) {
  54             System.out.println( "failed." );
  55             return false;
  56         }
  57         System.out.println( "OK." );
  58         System.out.print( "  Basic GO term: " );
  59         if ( !testBasicGoTerm() ) {
  60             System.out.println( "failed." );
  61             return false;
  62         }
  63         System.out.println( "OK." );
  64         System.out.print( "  OBO parser: " );
  65         if ( !testOBOparser( test_dir ) ) {
  66             System.out.println( "failed." );
  67             return false;
  68         }
  69         System.out.println( "OK." );
  70         System.out.print( "  Pfam to GO mapping: " );
  71         if ( !testPfamToGoMapping() ) {
  72             System.out.println( "failed." );
  73             return false;
  74         }
  75         System.out.println( "OK." );
  76         System.out.print( "  Pfam to GO parser: " );
  77         if ( !testPfamToGoParser( test_dir ) ) {
  78             System.out.println( "failed." );
  79             return false;
  80         }
  81         System.out.println( "OK." );
  82         System.out.print( "  Super terms: " );
  83         if ( !testSuperTermGetting( test_dir ) ) {
  84             System.out.println( "failed." );
  85             return false;
  86         }
  87         System.out.println( "OK." );
  88         System.out.print( "  Super term counting: " );
  89         if ( !testSuperTermCounting( test_dir ) ) {
  90             System.out.println( "failed." );
  91             return false;
  92         }
  93         System.out.println( "OK." );
  94         return true;
  95     }
  96
  97     private static boolean testBasicGoTerm() {
  98         try {
  99             final GoTerm gt1 = new BasicGoTerm( "GO:0047579",
 100                                                 "4-hydroxymandelate oxidase activity",
 101                                                 "molecular_function",
 102                                                 false );
 103             final GoTerm gt2 = new BasicGoTerm( "GO:0047579",
 104                                                 "4-hydroxymandelate oxidase activity",
 105                                                 "molecular_function",
 106                                                 false );
 107             final GoTerm gt3 = new BasicGoTerm( "GO:0047579", "?", "molecular_function", true );
 108             final GoTerm gt4 = new BasicGoTerm( "GO:0047579",
 109                                                 "4-hydroxymandelate oxidase activity",
 110                                                 "biological_process",
 111                                                 false );
 112             final GoTerm gt5 = new BasicGoTerm( "GO:0047578",
 113                                                 "4-hydroxymandelate oxidase activity",
 114                                                 "molecular_function",
 115                                                 false );
 116             if ( !gt1.equals( gt2 ) ) {
 117                 return false;
 118             }
 119             if ( !gt1.equals( gt3 ) ) {
 120                 return false;
 121             }
 122             if ( gt1.equals( gt4 ) ) {
 123                 return false;
 124             }
 125             if ( gt1.hashCode() != gt4.hashCode() ) {
 126                 return false;
 127             }
 128             if ( gt1.equals( gt5 ) ) {
 129                 return false;
 130             }
 131             final GoTerm gt6 = ( GoTerm ) gt5.copy();
 132             if ( !gt6.equals( gt5 ) ) {
 133                 return false;
 134             }
 135         }
 136         catch ( final Exception e ) {
 137             e.printStackTrace( System.out );
 138             return false;
 139         }
 140         return true;
 141     }
 142
 143     private static boolean testGoId() {
 144         try {
 145             final GoId id1 = new GoId( "GO:0042617" );
 146             final GoId id2 = new GoId( "GO:0042630" );
 147             final GoId id3 = new GoId( "GO:0042630" );
 148             if ( id1.equals( id2 ) ) {
 149                 return false;
 150             }
 151             if ( !id2.equals( id3 ) ) {
 152                 return false;
 153             }
 154             if ( !id1.toString().equals( "GO:0042617" ) ) {
 155                 return false;
 156             }
 157             if ( id2.hashCode() != id3.hashCode() ) {
 158                 return false;
 159             }
 160             if ( id1.hashCode() == id2.hashCode() ) {
 161                 return false;
 162             }
 163         }
 164         catch ( final Exception e ) {
 165             e.printStackTrace( System.out );
 166             return false;
 167         }
 168         return true;
 169     }
 170
 171     private static boolean testNamespace() {
 172         try {
 173             final GoNameSpace b = new GoNameSpace( "Biological_process" );
 174             final GoNameSpace c = new GoNameSpace( "Cellular_Component" );
 175             final GoNameSpace m = new GoNameSpace( "molecular_function" );
 176             final GoNameSpace m2 = new GoNameSpace( GoNameSpace.GoNamespaceType.MOLECULAR_FUNCTION );
 177             if ( b.equals( c ) ) {
 178                 return false;
 179             }
 180             if ( !m.equals( m2 ) ) {
 181                 return false;
 182             }
 183             if ( !b.toString().equals( "biological_process" ) ) {
 184                 return false;
 185             }
 186             if ( !c.toString().equals( "cellular_component" ) ) {
 187                 return false;
 188             }
 189             if ( !m.toString().equals( "molecular_function" ) ) {
 190                 return false;
 191             }
 192         }
 193         catch ( final Exception e ) {
 194             e.printStackTrace( System.out );
 195             return false;
 196         }
 197         return true;
 198     }
 199
 200     private static boolean testOBOparser( final File test_dir ) {
 201         try {
 202             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator() + "obo_test" ),
 203                                                     OBOparser.ReturnType.BASIC_GO_TERM );
 204             final List<GoTerm> go_terms = parser.parse();
 205             if ( parser.getGoTermCount() != 26 ) {
 206                 return false;
 207             }
 208             final GoTerm g0 = go_terms.get( 0 );
 209             final GoTerm g1 = go_terms.get( 1 );
 210             final GoTerm g3 = go_terms.get( 2 );
 211             final GoTerm g2 = go_terms.get( 25 );
 212             if ( !g0.getComment().equals( "" ) ) {
 213                 return false;
 214             }
 215             if ( !g0
 216                     .getDefinition()
 217                     .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]" ) ) {
 218                 return false;
 219             }
 220             if ( !g0.getGoId().getId().equals( "GO:0000001" ) ) {
 221                 return false;
 222             }
 223             if ( g0.getGoNameSpace().equals( GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) ) {
 224                 return false;
 225             }
 226             if ( g0.getGoNameSpace().getType() != GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) {
 227                 return false;
 228             }
 229             if ( g0.getGoRelationships().size() != 0 ) {
 230                 return false;
 231             }
 232             if ( g0.getGoXRefs().size() != 0 ) {
 233                 return false;
 234             }
 235             if ( !g0.getName().equals( "mitochondrion inheritance" ) ) {
 236                 return false;
 237             }
 238             if ( g0.getSuperGoIds().size() != 2 ) {
 239                 return false;
 240             }
 241             if ( !g0.isObsolete() ) {
 242                 return false;
 243             }
 244             if ( !g1.getComment().equals( "comment" ) ) {
 245                 return false;
 246             }
 247             if ( !g1
 248                     .getDefinition()
 249                     .equals( "\"The maintenance of the structure and integrity of the mitochondrial genome.\" [GOC:ai]" ) ) {
 250                 return false;
 251             }
 252             if ( !g1.getGoId().getId().equals( "GO:0000002" ) ) {
 253                 return false;
 254             }
 255             if ( g1.getGoNameSpace().equals( GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) ) {
 256                 return false;
 257             }
 258             if ( g1.getGoNameSpace().getType() != GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) {
 259                 return false;
 260             }
 261             if ( g1.getGoRelationships().size() != 1 ) {
 262                 return false;
 263             }
 264             if ( g1.getGoXRefs().size() != 5 ) {
 265                 return false;
 266             }
 267             if ( !g1.getName().equals( "mitochondrial genome maintenance" ) ) {
 268                 return false;
 269             }
 270             if ( g1.getSuperGoIds().size() != 1 ) {
 271                 return false;
 272             }
 273             if ( g1.isObsolete() ) {
 274                 return false;
 275             }
 276             if ( !g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "EC:2.4.1.-" ) ) ) {
 277                 return false;
 278             }
 279             if ( !g1.getGoXRefs().get( 0 ).getXRef().equals( "2.4.1.-" ) ) {
 280                 return false;
 281             }
 282             if ( g1.getGoXRefs().get( 0 ).getType() != GoXRef.Type.EC ) {
 283                 return false;
 284             }
 285             if ( g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "EC:2.4.1.1" ) ) ) {
 286                 return false;
 287             }
 288             if ( g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "Reactome:2.4.1.-" ) ) ) {
 289                 return false;
 290             }
 291             if ( !g1.getGoXRefs().get( 1 ).equals( new BasicGoXRef( "Reactome:7672" ) ) ) {
 292                 return false;
 293             }
 294             if ( !g1.getGoXRefs().get( 2 ).equals( new BasicGoXRef( "MetaCyc:SIROHEME-FERROCHELAT-RXN" ) ) ) {
 295                 return false;
 296             }
 297             if ( !g1.getGoXRefs().get( 3 ).equals( new BasicGoXRef( "RESID:AA02376" ) ) ) {
 298                 return false;
 299             }
 300             if ( !g1.getGoXRefs().get( 4 ).equals( new BasicGoXRef( "UM-BBD_enzymeID:e0271" ) ) ) {
 301                 return false;
 302             }
 303             if ( !g1.getGoRelationships().get( 0 ).equals( new BasicGoRelationship( "part_of GO:0007052" ) ) ) {
 304                 return false;
 305             }
 306             if ( !g1.getGoRelationships().get( 0 ).getGoId().equals( new GoId( "GO:0007052" ) ) ) {
 307                 return false;
 308             }
 309             if ( !g1.getGoRelationships().get( 0 ).getGoId().getId().equals( "GO:0007052" ) ) {
 310                 return false;
 311             }
 312             if ( g1.getGoRelationships().get( 0 ).getType() != GoRelationship.Type.PART_OF ) {
 313                 return false;
 314             }
 315             if ( g1.getGoRelationships().get( 0 ).equals( new BasicGoRelationship( "part_of GO:1007052" ) ) ) {
 316                 return false;
 317             }
 318             if ( !g1.getSuperGoIds().get( 0 ).equals( new GoId( "GO:0007005" ) ) ) {
 319                 return false;
 320             }
 321             if ( g1.getSuperGoIds().get( 0 ).equals( new GoId( "GO:1007005" ) ) ) {
 322                 return false;
 323             }
 324             if ( !g2.getGoId().getId().equals( "GO:0000030" ) ) {
 325                 return false;
 326             }
 327             if ( !g2.getGoId().equals( new GoId( "GO:0000030" ) ) ) {
 328                 return false;
 329             }
 330             if ( g2.getGoId().getId().equals( "GO:0000031" ) ) {
 331                 return false;
 332             }
 333             if ( g2.getGoId().equals( new GoId( "GO:0000031" ) ) ) {
 334                 return false;
 335             }
 336             if ( g3.getGoSubsets().size() != 3 ) {
 337                 return false;
 338             }
 339             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "goslim_generic" ) ) ) {
 340                 return false;
 341             }
 342             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "goslim_plant" ) ) ) {
 343                 return false;
 344             }
 345             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "gosubset_prok" ) ) ) {
 346                 return false;
 347             }
 348             if ( g3.getGoSubsets().contains( new BasicGoSubset( "goslim_candida" ) ) ) {
 349                 return false;
 350             }
 351         }
 352         catch ( final Exception e ) {
 353             e.printStackTrace( System.out );
 354             return false;
 355         }
 356         return true;
 357     }
 358
 359     private static boolean testPfamToGoMapping() {
 360         try {
 361             final PfamToGoMapping pg0 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
 362             final PfamToGoMapping pg1 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
 363             final PfamToGoMapping pg2 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000001" ) );
 364             final PfamToGoMapping pg3 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000002" ) );
 365             final PfamToGoMapping pg4 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000002" ) );
 366             if ( !pg0.equals( pg0 ) ) {
 367                 return false;
 368             }
 369             if ( !pg0.equals( pg1 ) ) {
 370                 return false;
 371             }
 372             if ( pg0.equals( pg2 ) ) {
 373                 return false;
 374             }
 375             if ( pg0.equals( pg3 ) ) {
 376                 return false;
 377             }
 378             if ( pg0.equals( pg4 ) ) {
 379                 return false;
 380             }
 381             if ( pg0.compareTo( pg3 ) != 0 ) {
 382                 return false;
 383             }
 384             if ( pg0.compareTo( pg2 ) >= 0 ) {
 385                 return false;
 386             }
 387             if ( pg2.compareTo( pg0 ) <= 0 ) {
 388                 return false;
 389             }
 390         }
 391         catch ( final Exception e ) {
 392             e.printStackTrace( System.out );
 393             return false;
 394         }
 395         return true;
 396     }
 397
 398     private static boolean testPfamToGoParser( final File test_dir ) {
 399         try {
 400             final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator()
 401                     + "pfam_to_go_test" ) );
 402             final List<PfamToGoMapping> mappings = parser.parse();
 403             if ( parser.getMappingCount() != 426 ) {
 404                 return false;
 405             }
 406             if ( mappings.size() != 426 ) {
 407                 return false;
 408             }
 409             final PfamToGoMapping m0 = mappings.get( 0 );
 410             final PfamToGoMapping m1 = mappings.get( 1 );
 411             final PfamToGoMapping m2 = mappings.get( 2 );
 412             final PfamToGoMapping m3 = mappings.get( 3 );
 413             final PfamToGoMapping m4 = mappings.get( 4 );
 414             final PfamToGoMapping m5 = mappings.get( 5 );
 415             final PfamToGoMapping m424 = mappings.get( 424 );
 416             final PfamToGoMapping m425 = mappings.get( 425 );
 417             if ( !m0.getKey().equals( new DomainId( "7tm_1" ) ) ) {
 418                 return false;
 419             }
 420             if ( !m0.getValue().equals( new GoId( "GO:0001584" ) ) ) {
 421                 return false;
 422             }
 423             if ( m0.getKey().equals( new DomainId( "7tm_x" ) ) ) {
 424                 return false;
 425             }
 426             if ( m0.getValue().equals( new GoId( "GO:0001585" ) ) ) {
 427                 return false;
 428             }
 429             if ( !m1.getKey().equals( new DomainId( "7tm_1" ) ) ) {
 430                 return false;
 431             }
 432             if ( !m1.getValue().equals( new GoId( "GO:0007186" ) ) ) {
 433                 return false;
 434             }
 435             if ( !m2.getKey().equals( new DomainId( "7tm_1" ) ) ) {
 436                 return false;
 437             }
 438             if ( !m2.getValue().equals( new GoId( "GO:0016021" ) ) ) {
 439                 return false;
 440             }
 441             if ( !m3.getKey().equals( new DomainId( "7tm_2" ) ) ) {
 442                 return false;
 443             }
 444             if ( !m3.getValue().equals( new GoId( "GO:0004930" ) ) ) {
 445                 return false;
 446             }
 447             if ( !m4.getKey().equals( new DomainId( "7tm_2" ) ) ) {
 448                 return false;
 449             }
 450             if ( !m4.getValue().equals( new GoId( "GO:0016020" ) ) ) {
 451                 return false;
 452             }
 453             if ( !m5.getKey().equals( new DomainId( "7tm_3" ) ) ) {
 454                 return false;
 455             }
 456             if ( !m5.getValue().equals( new GoId( "GO:0008067" ) ) ) {
 457                 return false;
 458             }
 459             if ( !m424.getKey().equals( new DomainId( "OMPdecase" ) ) ) {
 460                 return false;
 461             }
 462             if ( !m424.getValue().equals( new GoId( "GO:0006207" ) ) ) {
 463                 return false;
 464             }
 465             if ( !m425.getKey().equals( new DomainId( "Bac_DNA_binding" ) ) ) {
 466                 return false;
 467             }
 468             if ( !m425.getValue().equals( new GoId( "GO:0003677" ) ) ) {
 469                 return false;
 470             }
 471         }
 472         catch ( final Exception e ) {
 473             e.printStackTrace( System.out );
 474             return false;
 475         }
 476         return true;
 477     }
 478
 479     private static boolean testSuperTermCounting( final File test_dir ) {
 480         try {
 481             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
 482                     + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
 483             final List<GoTerm> all_go_terms = parser.parse();
 484             if ( parser.getGoTermCount() != 27748 ) {
 485                 return false;
 486             }
 487             final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( all_go_terms );
 488             final List<GoTerm> categories = new ArrayList<GoTerm>();
 489             final List<GoTerm> experiment_set = new ArrayList<GoTerm>();
 490             experiment_set.add( new BasicGoTerm( new GoId( "GO:0005690" ), "snRNP U4atac", GoNameSpace
 491                     .createUnassigned(), false ) );
 492             experiment_set.add( new BasicGoTerm( new GoId( "GO:0009698" ),
 493                                                  "phenylpropanoid metabolic process",
 494                                                  GoNameSpace.createUnassigned(),
 495                                                  false ) );
 496             experiment_set.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
 497                     .createUnassigned(), false ) );
 498             experiment_set.add( new BasicGoTerm( new GoId( "GO:0006915" ),
 499                                                  "apoptosis",
 500                                                  GoNameSpace.createUnassigned(),
 501                                                  false ) );
 502             experiment_set.add( new BasicGoTerm( new GoId( "GO:0001783" ), "B cell apoptosis", GoNameSpace
 503                     .createUnassigned(), false ) );
 504             experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
 505                     .createUnassigned(), false ) );
 506             experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
 507                     .createUnassigned(), false ) );
 508             experiment_set.add( new BasicGoTerm( new GoId( "GO:0010658" ),
 509                                                  "striated muscle cell apoptosis",
 510                                                  GoNameSpace.createUnassigned(),
 511                                                  false ) );
 512             experiment_set.add( new BasicGoTerm( new GoId( "GO:0043065" ),
 513                                                  "positive regulation of apoptosis",
 514                                                  GoNameSpace.createUnassigned(),
 515                                                  false ) );
 516             categories
 517                     .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) );
 518             categories.add( new BasicGoTerm( new GoId( "GO:0006915" ),
 519                                              "apoptosis",
 520                                              GoNameSpace.createUnassigned(),
 521                                              false ) );
 522             categories.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
 523                     .createUnassigned(), false ) );
 524             categories.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
 525                     .createUnassigned(), false ) );
 526             categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace
 527                     .createUnassigned(), false ) );
 528             categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace
 529                     .createUnassigned(), false ) );
 530             categories.add( new BasicGoTerm( new GoId( "GO:0016326" ), "kinesin motor activity", GoNameSpace
 531                     .createUnassigned(), false ) );
 532             categories.add( new BasicGoTerm( new GoId( "GO:0005575" ), "cellular_component", GoNameSpace
 533                     .createUnassigned(), false ) );
 534             categories.add( new BasicGoTerm( new GoId( "GO:0032502" ), "developmental process", GoNameSpace
 535                     .createUnassigned(), false ) );
 536             categories.add( new BasicGoTerm( new GoId( "GO:0051094" ),
 537                                              "positive regulation of developmental process",
 538                                              GoNameSpace.createUnassigned(),
 539                                              false ) );
 540             categories.add( new BasicGoTerm( new GoId( "GO:0048522" ),
 541                                              "positive regulation of cellular process",
 542                                              GoNameSpace.createUnassigned(),
 543                                              false ) );
 544             final Map<GoId, Integer> counts = GoUtils.countCategories( categories, experiment_set, goid_to_term_map );
 545             // death
 546             if ( counts.get( new GoId( "GO:0016265" ) ) != 5 ) {
 547                 return false;
 548             }
 549             // apoptosis
 550             if ( counts.get( new GoId( "GO:0006915" ) ) != 5 ) {
 551                 return false;
 552             }
 553             // biological_process
 554             if ( counts.get( new GoId( "GO:0008150" ) ) != 8 ) {
 555                 return false;
 556             }
 557             // muscle cell apoptosis
 558             if ( counts.get( new GoId( "GO:0010657" ) ) != 3 ) {
 559                 return false;
 560             }
 561             // striated muscle cell apoptosis
 562             if ( counts.get( new GoId( "GO:0010658" ) ) != 1 ) {
 563                 return false;
 564             }
 565             // o-xylene biosynthetic process
 566             if ( counts.get( new GoId( "GO:0046242" ) ) != 0 ) {
 567                 return false;
 568             }
 569             // kinesin motor activity
 570             if ( counts.get( new GoId( "GO:0016326" ) ) != 0 ) {
 571                 return false;
 572             }
 573             // cellular_component
 574             if ( counts.get( new GoId( "GO:0005575" ) ) != 1 ) {
 575                 return false;
 576             }
 577             // developmental process
 578             if ( counts.get( new GoId( "GO:0032502" ) ) != 5 ) {
 579                 return false;
 580             }
 581             // positive regulation of developmental process
 582             if ( counts.get( new GoId( "GO:0051094" ) ) != 1 ) {
 583                 return false;
 584             }
 585             // positive regulation of cellular process
 586             if ( counts.get( new GoId( "GO:0048522" ) ) != 1 ) {
 587                 return false;
 588             }
 589             final List<GoId> categories_id = new ArrayList<GoId>();
 590             final List<GoId> experiment_set_id = new ArrayList<GoId>();
 591             experiment_set_id.add( new GoId( "GO:0005690" ) );
 592             experiment_set_id.add( new GoId( "GO:0009698" ) );
 593             experiment_set_id.add( new GoId( "GO:0008150" ) );
 594             experiment_set_id.add( new GoId( "GO:0006915" ) );
 595             experiment_set_id.add( new GoId( "GO:0001783" ) );
 596             experiment_set_id.add( new GoId( "GO:0010657" ) );
 597             experiment_set_id.add( new GoId( "GO:0010657" ) );
 598             experiment_set_id.add( new GoId( "GO:0010658" ) );
 599             categories_id.add( new GoId( "GO:0016265" ) );
 600             categories_id.add( new GoId( "GO:0006915" ) );
 601             categories_id.add( new GoId( "GO:0008150" ) );
 602             categories_id.add( new GoId( "GO:0010657" ) );
 603             categories_id.add( new GoId( "GO:0010658" ) );
 604             categories_id.add( new GoId( "GO:0046242" ) );
 605             categories_id.add( new GoId( "GO:0016326" ) );
 606             categories_id.add( new GoId( "GO:0005575" ) );
 607             final Map<GoId, Integer> counts_id = GoUtils.countCategoriesId( categories_id,
 608                                                                             experiment_set_id,
 609                                                                             goid_to_term_map );
 610             // death
 611             if ( counts_id.get( new GoId( "GO:0016265" ) ) != 5 ) {
 612                 return false;
 613             }
 614             // apoptosis
 615             if ( counts_id.get( new GoId( "GO:0006915" ) ) != 5 ) {
 616                 return false;
 617             }
 618             // biological_process
 619             if ( counts_id.get( new GoId( "GO:0008150" ) ) != 7 ) {
 620                 return false;
 621             }
 622             // muscle cell apoptosis
 623             if ( counts_id.get( new GoId( "GO:0010657" ) ) != 3 ) {
 624                 return false;
 625             }
 626             // striated muscle cell apoptosis
 627             if ( counts_id.get( new GoId( "GO:0010658" ) ) != 1 ) {
 628                 return false;
 629             }
 630             // o-xylene biosynthetic process
 631             if ( counts_id.get( new GoId( "GO:0046242" ) ) != 0 ) {
 632                 return false;
 633             }
 634             // kinesin motor activity
 635             if ( counts_id.get( new GoId( "GO:0016326" ) ) != 0 ) {
 636                 return false;
 637             }
 638             // cellular_componen
 639             if ( counts_id.get( new GoId( "GO:0005575" ) ) != 1 ) {
 640                 return false;
 641             }
 642         }
 643         catch ( final Exception e ) {
 644             e.printStackTrace( System.out );
 645             return false;
 646         }
 647         return true;
 648     }
 649
 650     private static boolean testSuperTermGetting( final File test_dir ) {
 651         try {
 652             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
 653                     + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
 654             final List<GoTerm> go_terms = parser.parse();
 655             if ( parser.getGoTermCount() != 27748 ) {
 656                 return false;
 657             }
 658             final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
 659             final SortedSet<GoTerm> b_cell_selection = GoUtils.getAllSuperGoTerms( new GoId( "GO:0002339" ),
 660                                                                                    goid_to_term_map );
 661             if ( b_cell_selection.size() != 2 ) {
 662                 return false;
 663             }
 664             if ( !b_cell_selection.contains( new BasicGoTerm( new GoId( "GO:0002376" ),
 665                                                               "immune system process",
 666                                                               GoNameSpace.createBiologicalProcess(),
 667                                                               false ) ) ) {
 668                 return false;
 669             }
 670             if ( !b_cell_selection.contains( new BasicGoTerm( new GoId( "GO:0008150" ),
 671                                                               "biological process",
 672                                                               GoNameSpace.createBiologicalProcess(),
 673                                                               false ) ) ) {
 674                 return false;
 675             }
 676             final SortedSet<GoTerm> b_cell_differentation = GoUtils.getAllSuperGoTerms( new GoId( "GO:0030183" ),
 677                                                                                         goid_to_term_map );
 678             if ( b_cell_differentation.size() != 12 ) {
 679                 return false;
 680             }
 681             final SortedSet<GoTerm> biological_process = GoUtils.getAllSuperGoTerms( new GoId( "GO:0008150" ),
 682                                                                                      goid_to_term_map );
 683             if ( biological_process.size() != 0 ) {
 684                 return false;
 685             }
 686             final SortedSet<GoTerm> protein_aa_phosphorylation = GoUtils.getAllSuperGoTerms( new GoId( "GO:0006468" ),
 687                                                                                              goid_to_term_map );
 688             if ( protein_aa_phosphorylation.size() != 16 ) {
 689                 return false;
 690             }
 691         }
 692         catch ( final Exception e ) {
 693             e.printStackTrace( System.out );
 694             return false;
 695         }
 696         return true;
 697     }
 698 }