private static boolean testPfamToGoParser( final File test_dir ) {
try {
final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator()
- + "pfam_to_go_test" ) );
+ + "pfam_to_go_test" ) );
final List<PfamToGoMapping> mappings = parser.parse();
if ( parser.getMappingCount() != 426 ) {
return false;
private static boolean testSuperTermCounting( final File test_dir ) {
try {
final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
- + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
+ + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
final List<GoTerm> all_go_terms = parser.parse();
if ( parser.getGoTermCount() != 27748 ) {
return false;
final List<GoTerm> categories = new ArrayList<GoTerm>();
final List<GoTerm> experiment_set = new ArrayList<GoTerm>();
experiment_set.add( new BasicGoTerm( new GoId( "GO:0005690" ), "snRNP U4atac", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0009698" ),
"phenylpropanoid metabolic process",
GoNameSpace.createUnassigned(),
false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0006915" ),
"apoptosis",
GoNameSpace.createUnassigned(),
false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0001783" ), "B cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
experiment_set.add( new BasicGoTerm( new GoId( "GO:0010658" ),
"striated muscle cell apoptosis",
GoNameSpace.createUnassigned(),
GoNameSpace.createUnassigned(),
false ) );
categories
- .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) );
+ .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0006915" ),
"apoptosis",
GoNameSpace.createUnassigned(),
false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0016326" ), "kinesin motor activity", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0005575" ), "cellular_component", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0032502" ), "developmental process", GoNameSpace
- .createUnassigned(), false ) );
+ .createUnassigned(), false ) );
categories.add( new BasicGoTerm( new GoId( "GO:0051094" ),
"positive regulation of developmental process",
GoNameSpace.createUnassigned(),
private static boolean testSuperTermGetting( final File test_dir ) {
try {
final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator()
- + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
+ + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM );
final List<GoTerm> go_terms = parser.parse();
if ( parser.getGoTermCount() != 27748 ) {
return false;