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.protein.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.getDefinition()
 216                     .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]" ) ) {
 217                 return false;
 218             }
 219             if ( !g0.getGoId().getId().equals( "GO:0000001" ) ) {
 220                 return false;
 221             }
 222             if ( g0.getGoNameSpace().equals( GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) ) {
 223                 return false;
 224             }
 225             if ( g0.getGoNameSpace().getType() != GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) {
 226                 return false;
 227             }
 228             if ( g0.getGoRelationships().size() != 0 ) {
 229                 return false;
 230             }
 231             if ( g0.getGoXRefs().size() != 0 ) {
 232                 return false;
 233             }
 234             if ( !g0.getName().equals( "mitochondrion inheritance" ) ) {
 235                 return false;
 236             }
 237             if ( g0.getSuperGoIds().size() != 2 ) {
 238                 return false;
 239             }
 240             if ( !g0.isObsolete() ) {
 241                 return false;
 242             }
 243             if ( !g1.getComment().equals( "comment" ) ) {
 244                 return false;
 245             }
 246             if ( !g1.getDefinition()
 247                     .equals( "\"The maintenance of the structure and integrity of the mitochondrial genome.\" [GOC:ai]" ) ) {
 248                 return false;
 249             }
 250             if ( !g1.getGoId().getId().equals( "GO:0000002" ) ) {
 251                 return false;
 252             }
 253             if ( g1.getGoNameSpace().equals( GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) ) {
 254                 return false;
 255             }
 256             if ( g1.getGoNameSpace().getType() != GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS ) {
 257                 return false;
 258             }
 259             if ( g1.getGoRelationships().size() != 1 ) {
 260                 return false;
 261             }
 262             if ( g1.getGoXRefs().size() != 5 ) {
 263                 return false;
 264             }
 265             if ( !g1.getName().equals( "mitochondrial genome maintenance" ) ) {
 266                 return false;
 267             }
 268             if ( g1.getSuperGoIds().size() != 1 ) {
 269                 return false;
 270             }
 271             if ( g1.isObsolete() ) {
 272                 return false;
 273             }
 274             if ( !g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "EC:2.4.1.-" ) ) ) {
 275                 return false;
 276             }
 277             if ( !g1.getGoXRefs().get( 0 ).getXRef().equals( "2.4.1.-" ) ) {
 278                 return false;
 279             }
 280             if ( g1.getGoXRefs().get( 0 ).getType() != GoXRef.Type.EC ) {
 281                 return false;
 282             }
 283             if ( g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "EC:2.4.1.1" ) ) ) {
 284                 return false;
 285             }
 286             if ( g1.getGoXRefs().get( 0 ).equals( new BasicGoXRef( "Reactome:2.4.1.-" ) ) ) {
 287                 return false;
 288             }
 289             if ( !g1.getGoXRefs().get( 1 ).equals( new BasicGoXRef( "Reactome:7672" ) ) ) {
 290                 return false;
 291             }
 292             if ( !g1.getGoXRefs().get( 2 ).equals( new BasicGoXRef( "MetaCyc:SIROHEME-FERROCHELAT-RXN" ) ) ) {
 293                 return false;
 294             }
 295             if ( !g1.getGoXRefs().get( 3 ).equals( new BasicGoXRef( "RESID:AA02376" ) ) ) {
 296                 return false;
 297             }
 298             if ( !g1.getGoXRefs().get( 4 ).equals( new BasicGoXRef( "UM-BBD_enzymeID:e0271" ) ) ) {
 299                 return false;
 300             }
 301             if ( !g1.getGoRelationships().get( 0 ).equals( new BasicGoRelationship( "part_of GO:0007052" ) ) ) {
 302                 return false;
 303             }
 304             if ( !g1.getGoRelationships().get( 0 ).getGoId().equals( new GoId( "GO:0007052" ) ) ) {
 305                 return false;
 306             }
 307             if ( !g1.getGoRelationships().get( 0 ).getGoId().getId().equals( "GO:0007052" ) ) {
 308                 return false;
 309             }
 310             if ( g1.getGoRelationships().get( 0 ).getType() != GoRelationship.Type.PART_OF ) {
 311                 return false;
 312             }
 313             if ( g1.getGoRelationships().get( 0 ).equals( new BasicGoRelationship( "part_of GO:1007052" ) ) ) {
 314                 return false;
 315             }
 316             if ( !g1.getSuperGoIds().get( 0 ).equals( new GoId( "GO:0007005" ) ) ) {
 317                 return false;
 318             }
 319             if ( g1.getSuperGoIds().get( 0 ).equals( new GoId( "GO:1007005" ) ) ) {
 320                 return false;
 321             }
 322             if ( !g2.getGoId().getId().equals( "GO:0000030" ) ) {
 323                 return false;
 324             }
 325             if ( !g2.getGoId().equals( new GoId( "GO:0000030" ) ) ) {
 326                 return false;
 327             }
 328             if ( g2.getGoId().getId().equals( "GO:0000031" ) ) {
 329                 return false;
 330             }
 331             if ( g2.getGoId().equals( new GoId( "GO:0000031" ) ) ) {
 332                 return false;
 333             }
 334             if ( g3.getGoSubsets().size() != 3 ) {
 335                 return false;
 336             }
 337             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "goslim_generic" ) ) ) {
 338                 return false;
 339             }
 340             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "goslim_plant" ) ) ) {
 341                 return false;
 342             }
 343             if ( !g3.getGoSubsets().contains( new BasicGoSubset( "gosubset_prok" ) ) ) {
 344                 return false;
 345             }
 346             if ( g3.getGoSubsets().contains( new BasicGoSubset( "goslim_candida" ) ) ) {
 347                 return false;
 348             }
 349         }
 350         catch ( final Exception e ) {
 351             e.printStackTrace( System.out );
 352             return false;
 353         }
 354         return true;
 355     }
 356
 357     private static boolean testPfamToGoMapping() {
 358         try {
 359             final PfamToGoMapping pg0 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
 360             final PfamToGoMapping pg1 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
 361             final PfamToGoMapping pg2 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000001" ) );
 362             final PfamToGoMapping pg3 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000002" ) );
 363             final PfamToGoMapping pg4 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000002" ) );
 364             if ( !pg0.equals( pg0 ) ) {
 365                 return false;
 366             }
 367             if ( !pg0.equals( pg1 ) ) {
 368                 return false;
 369             }
 370             if ( pg0.equals( pg2 ) ) {
 371                 return false;
 372             }
 373             if ( pg0.equals( pg3 ) ) {
 374                 return false;
 375             }
 376             if ( pg0.equals( pg4 ) ) {
 377                 return false;
 378             }
 379             if ( pg0.compareTo( pg3 ) != 0 ) {
 380                 return false;
 381             }
 382             if ( pg0.compareTo( pg2 ) >= 0 ) {
 383                 return false;
 384             }
 385             if ( pg2.compareTo( pg0 ) <= 0 ) {
 386                 return false;
 387             }
 388         }
 389         catch ( final Exception e ) {
 390             e.printStackTrace( System.out );
 391             return false;
 392         }
 393         return true;
 394     }
 395
 396     private static boolean testPfamToGoParser( final File test_dir ) {
 397         try {
 398             final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator()
 399                     + "pfam_to_go_test" ) );
 400             final List<PfamToGoMapping> mappings = parser.parse();
 401             if ( parser.getMappingCount() != 426 ) {
 402                 return false;
 403             }
 404             if ( mappings.size() != 426 ) {
 405                 return false;
 406             }
 407             final PfamToGoMapping m0 = mappings.get( 0 );
 408             final PfamToGoMapping m1 = mappings.get( 1 );
 409             final PfamToGoMapping m2 = mappings.get( 2 );
 410             final PfamToGoMapping m3 = mappings.get( 3 );
 411             final PfamToGoMapping m4 = mappings.get( 4 );
 412             final PfamToGoMapping m5 = mappings.get( 5 );
 413             final PfamToGoMapping m424 = mappings.get( 424 );
 414             final PfamToGoMapping m425 = mappings.get( 425 );
 415             if ( !m0.getKey().equals( new DomainId( "7tm_1" ) ) ) {
 416                 return false;
 417             }
 418             if ( !m0.getValue().equals( new GoId( "GO:0001584" ) ) ) {
 419                 return false;
 420             }
 421             if ( m0.getKey().equals( new DomainId( "7tm_x" ) ) ) {
 422                 return false;
 423             }
 424             if ( m0.getValue().equals( new GoId( "GO:0001585" ) ) ) {
 425                 return false;
 426             }
 427             if ( !m1.getKey().equals( new DomainId( "7tm_1" ) ) ) {
 428                 return false;
 429             }
 430             if ( !m1.getValue().equals( new GoId( "GO:0007186" ) ) ) {
 431                 return false;
 432             }
 433             if ( !m2.getKey().equals( new DomainId( "7tm_1" ) ) ) {
 434                 return false;
 435             }
 436             if ( !m2.getValue().equals( new GoId( "GO:0016021" ) ) ) {
 437                 return false;
 438             }
 439             if ( !m3.getKey().equals( new DomainId( "7tm_2" ) ) ) {
 440                 return false;
 441             }
 442             if ( !m3.getValue().equals( new GoId( "GO:0004930" ) ) ) {
 443                 return false;
 444             }
 445             if ( !m4.getKey().equals( new DomainId( "7tm_2" ) ) ) {
 446                 return false;
 447             }
 448             if ( !m4.getValue().equals( new GoId( "GO:0016020" ) ) ) {
 449                 return false;
 450             }
 451             if ( !m5.getKey().equals( new DomainId( "7tm_3" ) ) ) {
 452                 return false;
 453             }
 454             if ( !m5.getValue().equals( new GoId( "GO:0008067" ) ) ) {
 455                 return false;
 456             }
 457             if ( !m424.getKey().equals( new DomainId( "OMPdecase" ) ) ) {
 458                 return false;
 459             }
 460             if ( !m424.getValue().equals( new GoId( "GO:0006207" ) ) ) {
 461                 return false;
 462             }
 463             if ( !m425.getKey().equals( new DomainId( "Bac_DNA_binding" ) ) ) {
 464                 return false;
 465             }
 466             if ( !m425.getValue().equals( new GoId( "GO:0003677" ) ) ) {
 467                 return false;
 468             }
 469         }
 470         catch ( final Exception e ) {
 471             e.printStackTrace( System.out );
 472             return false;
 473         }
 474         return true;
 475     }
 476
 477     private static boolean testSuperTermCounting( final File test_dir ) {
 478         try {
 479             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
 480                     + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
 481             final List<GoTerm> all_go_terms = parser.parse();
 482             if ( parser.getGoTermCount() != 27748 ) {
 483                 return false;
 484             }
 485             final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( all_go_terms );
 486             final List<GoTerm> categories = new ArrayList<GoTerm>();
 487             final List<GoTerm> experiment_set = new ArrayList<GoTerm>();
 488             experiment_set.add( new BasicGoTerm( new GoId( "GO:0005690" ), "snRNP U4atac", GoNameSpace
 489                     .createUnassigned(), false ) );
 490             experiment_set.add( new BasicGoTerm( new GoId( "GO:0009698" ),
 491                                                  "phenylpropanoid metabolic process",
 492                                                  GoNameSpace.createUnassigned(),
 493                                                  false ) );
 494             experiment_set.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
 495                     .createUnassigned(), false ) );
 496             experiment_set.add( new BasicGoTerm( new GoId( "GO:0006915" ),
 497                                                  "apoptosis",
 498                                                  GoNameSpace.createUnassigned(),
 499                                                  false ) );
 500             experiment_set.add( new BasicGoTerm( new GoId( "GO:0001783" ), "B cell apoptosis", GoNameSpace
 501                     .createUnassigned(), false ) );
 502             experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle 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:0010658" ),
 507                                                  "striated muscle cell apoptosis",
 508                                                  GoNameSpace.createUnassigned(),
 509                                                  false ) );
 510             experiment_set.add( new BasicGoTerm( new GoId( "GO:0043065" ),
 511                                                  "positive regulation of apoptosis",
 512                                                  GoNameSpace.createUnassigned(),
 513                                                  false ) );
 514             categories
 515                     .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) );
 516             categories.add( new BasicGoTerm( new GoId( "GO:0006915" ),
 517                                              "apoptosis",
 518                                              GoNameSpace.createUnassigned(),
 519                                              false ) );
 520             categories.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
 521                     .createUnassigned(), false ) );
 522             categories.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
 523                     .createUnassigned(), false ) );
 524             categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace
 525                     .createUnassigned(), false ) );
 526             categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace
 527                     .createUnassigned(), false ) );
 528             categories.add( new BasicGoTerm( new GoId( "GO:0016326" ), "kinesin motor activity", GoNameSpace
 529                     .createUnassigned(), false ) );
 530             categories.add( new BasicGoTerm( new GoId( "GO:0005575" ), "cellular_component", GoNameSpace
 531                     .createUnassigned(), false ) );
 532             categories.add( new BasicGoTerm( new GoId( "GO:0032502" ), "developmental process", GoNameSpace
 533                     .createUnassigned(), false ) );
 534             categories.add( new BasicGoTerm( new GoId( "GO:0051094" ),
 535                                              "positive regulation of developmental process",
 536                                              GoNameSpace.createUnassigned(),
 537                                              false ) );
 538             categories.add( new BasicGoTerm( new GoId( "GO:0048522" ),
 539                                              "positive regulation of cellular process",
 540                                              GoNameSpace.createUnassigned(),
 541                                              false ) );
 542             final Map<GoId, Integer> counts = GoUtils.countCategories( categories, experiment_set, goid_to_term_map );
 543             // death
 544             if ( counts.get( new GoId( "GO:0016265" ) ) != 5 ) {
 545                 return false;
 546             }
 547             // apoptosis
 548             if ( counts.get( new GoId( "GO:0006915" ) ) != 5 ) {
 549                 return false;
 550             }
 551             // biological_process
 552             if ( counts.get( new GoId( "GO:0008150" ) ) != 8 ) {
 553                 return false;
 554             }
 555             // muscle cell apoptosis
 556             if ( counts.get( new GoId( "GO:0010657" ) ) != 3 ) {
 557                 return false;
 558             }
 559             // striated muscle cell apoptosis
 560             if ( counts.get( new GoId( "GO:0010658" ) ) != 1 ) {
 561                 return false;
 562             }
 563             // o-xylene biosynthetic process
 564             if ( counts.get( new GoId( "GO:0046242" ) ) != 0 ) {
 565                 return false;
 566             }
 567             // kinesin motor activity
 568             if ( counts.get( new GoId( "GO:0016326" ) ) != 0 ) {
 569                 return false;
 570             }
 571             // cellular_component
 572             if ( counts.get( new GoId( "GO:0005575" ) ) != 1 ) {
 573                 return false;
 574             }
 575             // developmental process
 576             if ( counts.get( new GoId( "GO:0032502" ) ) != 5 ) {
 577                 return false;
 578             }
 579             // positive regulation of developmental process
 580             if ( counts.get( new GoId( "GO:0051094" ) ) != 1 ) {
 581                 return false;
 582             }
 583             // positive regulation of cellular process
 584             if ( counts.get( new GoId( "GO:0048522" ) ) != 1 ) {
 585                 return false;
 586             }
 587             final List<GoId> categories_id = new ArrayList<GoId>();
 588             final List<GoId> experiment_set_id = new ArrayList<GoId>();
 589             experiment_set_id.add( new GoId( "GO:0005690" ) );
 590             experiment_set_id.add( new GoId( "GO:0009698" ) );
 591             experiment_set_id.add( new GoId( "GO:0008150" ) );
 592             experiment_set_id.add( new GoId( "GO:0006915" ) );
 593             experiment_set_id.add( new GoId( "GO:0001783" ) );
 594             experiment_set_id.add( new GoId( "GO:0010657" ) );
 595             experiment_set_id.add( new GoId( "GO:0010657" ) );
 596             experiment_set_id.add( new GoId( "GO:0010658" ) );
 597             categories_id.add( new GoId( "GO:0016265" ) );
 598             categories_id.add( new GoId( "GO:0006915" ) );
 599             categories_id.add( new GoId( "GO:0008150" ) );
 600             categories_id.add( new GoId( "GO:0010657" ) );
 601             categories_id.add( new GoId( "GO:0010658" ) );
 602             categories_id.add( new GoId( "GO:0046242" ) );
 603             categories_id.add( new GoId( "GO:0016326" ) );
 604             categories_id.add( new GoId( "GO:0005575" ) );
 605             final Map<GoId, Integer> counts_id = GoUtils.countCategoriesId( categories_id,
 606                                                                             experiment_set_id,
 607                                                                             goid_to_term_map );
 608             // death
 609             if ( counts_id.get( new GoId( "GO:0016265" ) ) != 5 ) {
 610                 return false;
 611             }
 612             // apoptosis
 613             if ( counts_id.get( new GoId( "GO:0006915" ) ) != 5 ) {
 614                 return false;
 615             }
 616             // biological_process
 617             if ( counts_id.get( new GoId( "GO:0008150" ) ) != 7 ) {
 618                 return false;
 619             }
 620             // muscle cell apoptosis
 621             if ( counts_id.get( new GoId( "GO:0010657" ) ) != 3 ) {
 622                 return false;
 623             }
 624             // striated muscle cell apoptosis
 625             if ( counts_id.get( new GoId( "GO:0010658" ) ) != 1 ) {
 626                 return false;
 627             }
 628             // o-xylene biosynthetic process
 629             if ( counts_id.get( new GoId( "GO:0046242" ) ) != 0 ) {
 630                 return false;
 631             }
 632             // kinesin motor activity
 633             if ( counts_id.get( new GoId( "GO:0016326" ) ) != 0 ) {
 634                 return false;
 635             }
 636             // cellular_componen
 637             if ( counts_id.get( new GoId( "GO:0005575" ) ) != 1 ) {
 638                 return false;
 639             }
 640         }
 641         catch ( final Exception e ) {
 642             e.printStackTrace( System.out );
 643             return false;
 644         }
 645         return true;
 646     }
 647
 648     private static boolean testSuperTermGetting( final File test_dir ) {
 649         try {
 650             final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
 651                     + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
 652             final List<GoTerm> go_terms = parser.parse();
 653             if ( parser.getGoTermCount() != 27748 ) {
 654                 return false;
 655             }
 656             final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
 657             final SortedSet<GoTerm> b_cell_selection = GoUtils.getAllSuperGoTerms( new GoId( "GO:0002339" ),
 658                                                                                    goid_to_term_map );
 659             if ( b_cell_selection.size() != 2 ) {
 660                 return false;
 661             }
 662             if ( !b_cell_selection.contains( new BasicGoTerm( new GoId( "GO:0002376" ),
 663                                                               "immune system process",
 664                                                               GoNameSpace.createBiologicalProcess(),
 665                                                               false ) ) ) {
 666                 return false;
 667             }
 668             if ( !b_cell_selection.contains( new BasicGoTerm( new GoId( "GO:0008150" ),
 669                                                               "biological process",
 670                                                               GoNameSpace.createBiologicalProcess(),
 671                                                               false ) ) ) {
 672                 return false;
 673             }
 674             final SortedSet<GoTerm> b_cell_differentation = GoUtils.getAllSuperGoTerms( new GoId( "GO:0030183" ),
 675                                                                                         goid_to_term_map );
 676             if ( b_cell_differentation.size() != 12 ) {
 677                 return false;
 678             }
 679             final SortedSet<GoTerm> biological_process = GoUtils.getAllSuperGoTerms( new GoId( "GO:0008150" ),
 680                                                                                      goid_to_term_map );
 681             if ( biological_process.size() != 0 ) {
 682                 return false;
 683             }
 684             final SortedSet<GoTerm> protein_aa_phosphorylation = GoUtils.getAllSuperGoTerms( new GoId( "GO:0006468" ),
 685                                                                                              goid_to_term_map );
 686             if ( protein_aa_phosphorylation.size() != 16 ) {
 687                 return false;
 688             }
 689         }
 690         catch ( final Exception e ) {
 691             e.printStackTrace( System.out );
 692             return false;
 693         }
 694         return true;
 695     }
 696 }