test_class.declarator: ontology
test_class.modifier: private final
test_class.original_string: private final ImmutableOntology ontology;
test_class.type: ImmutableOntology
test_class.var_name: ontology
test_class.declarator: id1
test_class.modifier: private final
test_class.original_string: private final TermId id1;
test_class.type: TermId
test_class.var_name: id1
test_class.declarator: id2
test_class.modifier: private final
test_class.original_string: private final TermId id2;
test_class.type: TermId
test_class.var_name: id2
test_class.declarator: id3
test_class.modifier: private final
test_class.original_string: private final TermId id3;
test_class.type: TermId
test_class.var_name: id3
test_class.declarator: id4
test_class.modifier: private final
test_class.original_string: private final TermId id4;
test_class.type: TermId
test_class.var_name: id4
test_class.declarator: id5
test_class.modifier: private final
test_class.original_string: private final TermId id5;
test_class.type: TermId
test_class.var_name: id5
test_class.file: phenol-core/src/test/java/org/monarchinitiative/phenol/ontology/algo/OntologyAlgorithmTest.java
test_class.identifier: OntologyAlgorithmTest
test_case.body: @Test
    public void testReturnChildrenWithoutOriginalTerm() {
      // id5 has 3 children: id2->id5, id3-> id5, id4->id5
      Set<TermId> expected = ImmutableSet.of(id2, id3, id4);
      assertEquals(expected, getChildTerms(ontology, id5, false));
    }
test_case.class_method_signature: OntologyAlgorithmTest.testReturnChildrenWithoutOriginalTerm()
test_case.full_signature: @Test public void testReturnChildrenWithoutOriginalTerm()
test_case.identifier: testReturnChildrenWithoutOriginalTerm
test_case.invocations: of assertEquals getChildTerms
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testReturnChildrenWithoutOriginalTerm()
focal_class.declarator: logger = LoggerFactory.getLogger(OntologyAlgorithm.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(OntologyAlgorithm.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.file: phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/algo/OntologyAlgorithm.java
focal_class.identifier: OntologyAlgorithm
focal_class.class_method_signature: OntologyAlgorithm.OntologyAlgorithm()
focal_class.full_signature: private  OntologyAlgorithm()
focal_class.identifier: OntologyAlgorithm
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.signature:  OntologyAlgorithm()
focal_class.class_method_signature: OntologyAlgorithm.existsPath(
        Ontology ontology,
        final TermId sourceID,
        TermId destID)
focal_class.full_signature: public static boolean existsPath(
        Ontology ontology,
        final TermId sourceID,
        TermId destID)
focal_class.identifier: existsPath
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        final TermId sourceID,
        TermId destID)
focal_class.return: boolean
focal_class.signature: boolean existsPath(
        Ontology ontology,
        final TermId sourceID,
        TermId destID)
focal_class.class_method_signature: OntologyAlgorithm.getChildTerms(
      Ontology ontology, TermId parentTermId)
focal_class.full_signature: public static Set<TermId> getChildTerms(
      Ontology ontology, TermId parentTermId)
focal_class.identifier: getChildTerms
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId parentTermId)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getChildTerms(
      Ontology ontology, TermId parentTermId)
focal_class.class_method_signature: OntologyAlgorithm.getChildTerms(
        Ontology ontology,
        TermId parentTermId,
        boolean includeOriginalTerm)
focal_class.full_signature: public static Set<TermId> getChildTerms(
        Ontology ontology,
        TermId parentTermId,
        boolean includeOriginalTerm)
focal_class.identifier: getChildTerms
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        TermId parentTermId,
        boolean includeOriginalTerm)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getChildTerms(
        Ontology ontology,
        TermId parentTermId,
        boolean includeOriginalTerm)
focal_class.class_method_signature: OntologyAlgorithm.getChildTerms(
      Ontology ontology, Set<TermId> parentTermIdSet)
focal_class.full_signature: public static Set<TermId> getChildTerms(
      Ontology ontology, Set<TermId> parentTermIdSet)
focal_class.identifier: getChildTerms
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, Set<TermId> parentTermIdSet)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getChildTerms(
      Ontology ontology, Set<TermId> parentTermIdSet)
focal_class.class_method_signature: OntologyAlgorithm.getParentTerms(
      Ontology ontology, Set<TermId> childTermIdSet)
focal_class.full_signature: public static Set<TermId> getParentTerms(
      Ontology ontology, Set<TermId> childTermIdSet)
focal_class.identifier: getParentTerms
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, Set<TermId> childTermIdSet)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getParentTerms(
      Ontology ontology, Set<TermId> childTermIdSet)
focal_class.class_method_signature: OntologyAlgorithm.getParentTerms(
        Ontology ontology,
        Set<TermId> childTermIdSet,
        boolean includeOriginalTerm)
focal_class.full_signature: public static Set<TermId> getParentTerms(
        Ontology ontology,
        Set<TermId> childTermIdSet,
        boolean includeOriginalTerm)
focal_class.identifier: getParentTerms
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        Set<TermId> childTermIdSet,
        boolean includeOriginalTerm)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getParentTerms(
        Ontology ontology,
        Set<TermId> childTermIdSet,
        boolean includeOriginalTerm)
focal_class.class_method_signature: OntologyAlgorithm.getDescendents(
      Ontology ontology, TermId parentTermId)
focal_class.full_signature: public static Set<TermId> getDescendents(
      Ontology ontology, TermId parentTermId)
focal_class.identifier: getDescendents
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId parentTermId)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getDescendents(
      Ontology ontology, TermId parentTermId)
focal_class.class_method_signature: OntologyAlgorithm.getParentTerms(
        Ontology ontology,
        TermId childTermId,
        boolean includeOriginalTerm)
focal_class.full_signature: public static Set<TermId> getParentTerms(
        Ontology ontology,
        TermId childTermId,
        boolean includeOriginalTerm)
focal_class.identifier: getParentTerms
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        TermId childTermId,
        boolean includeOriginalTerm)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getParentTerms(
        Ontology ontology,
        TermId childTermId,
        boolean includeOriginalTerm)
focal_class.class_method_signature: OntologyAlgorithm.getAncestorTerms(
        Ontology ontology,
        TermId rootTerm,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.full_signature: public static Set<TermId> getAncestorTerms(
        Ontology ontology,
        TermId rootTerm,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.identifier: getAncestorTerms
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        TermId rootTerm,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getAncestorTerms(
        Ontology ontology,
        TermId rootTerm,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.class_method_signature: OntologyAlgorithm.getAncestorTerms(
        Ontology ontology,
        TermId rootTerm,
        TermId child,
        boolean includeOriginalTerm)
focal_class.full_signature: public static Set<TermId> getAncestorTerms(
        Ontology ontology,
        TermId rootTerm,
        TermId child,
        boolean includeOriginalTerm)
focal_class.identifier: getAncestorTerms
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        TermId rootTerm,
        TermId child,
        boolean includeOriginalTerm)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getAncestorTerms(
        Ontology ontology,
        TermId rootTerm,
        TermId child,
        boolean includeOriginalTerm)
focal_class.class_method_signature: OntologyAlgorithm.getAncestorTerms(
        Ontology ontology,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.full_signature: public static Set<TermId> getAncestorTerms(
        Ontology ontology,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.identifier: getAncestorTerms
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getAncestorTerms(
        Ontology ontology,
        Set<TermId> children,
        boolean includeOriginalTerm)
focal_class.class_method_signature: OntologyAlgorithm.getAncestorTerms(
        Ontology ontology,
        TermId child,
        boolean includeOriginalTerm)
focal_class.full_signature: public static Set<TermId> getAncestorTerms(
        Ontology ontology,
        TermId child,
        boolean includeOriginalTerm)
focal_class.identifier: getAncestorTerms
focal_class.modifiers: public static
focal_class.parameters: (
        Ontology ontology,
        TermId child,
        boolean includeOriginalTerm)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getAncestorTerms(
        Ontology ontology,
        TermId child,
        boolean includeOriginalTerm)
focal_class.class_method_signature: OntologyAlgorithm.getParentTerms(
      Ontology ontology, TermId childTermId)
focal_class.full_signature: public static Set<TermId> getParentTerms(
      Ontology ontology, TermId childTermId)
focal_class.identifier: getParentTerms
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId childTermId)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getParentTerms(
      Ontology ontology, TermId childTermId)
focal_class.class_method_signature: OntologyAlgorithm.getAncestorTerms(
      Ontology ontology, TermId childTermId)
focal_class.full_signature: public static Set<TermId> getAncestorTerms(
      Ontology ontology, TermId childTermId)
focal_class.identifier: getAncestorTerms
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId childTermId)
focal_class.return: Set<TermId>
focal_class.signature: Set<TermId> getAncestorTerms(
      Ontology ontology, TermId childTermId)
focal_class.class_method_signature: OntologyAlgorithm.isSubclass(
      Ontology ontology, TermId source, TermId dest)
focal_class.full_signature: public static boolean isSubclass(
      Ontology ontology, TermId source, TermId dest)
focal_class.identifier: isSubclass
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId source, TermId dest)
focal_class.return: boolean
focal_class.signature: boolean isSubclass(
      Ontology ontology, TermId source, TermId dest)
focal_class.class_method_signature: OntologyAlgorithm.termsAreSiblings(
      Ontology ontology, TermId t1, TermId t2)
focal_class.full_signature: public static boolean termsAreSiblings(
      Ontology ontology, TermId t1, TermId t2)
focal_class.identifier: termsAreSiblings
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId t1, TermId t2)
focal_class.return: boolean
focal_class.signature: boolean termsAreSiblings(
      Ontology ontology, TermId t1, TermId t2)
focal_class.class_method_signature: OntologyAlgorithm.termsAreRelated(
      Ontology ontology, TermId t1, TermId t2)
focal_class.full_signature: public static boolean termsAreRelated(
      Ontology ontology, TermId t1, TermId t2)
focal_class.identifier: termsAreRelated
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId t1, TermId t2)
focal_class.return: boolean
focal_class.signature: boolean termsAreRelated(
      Ontology ontology, TermId t1, TermId t2)
focal_class.class_method_signature: OntologyAlgorithm.termsAreUnrelated(
      Ontology ontology, TermId t1, TermId t2)
focal_class.full_signature: public static boolean termsAreUnrelated(
      Ontology ontology, TermId t1, TermId t2)
focal_class.identifier: termsAreUnrelated
focal_class.modifiers: public static
focal_class.parameters: (
      Ontology ontology, TermId t1, TermId t2)
focal_class.return: boolean
focal_class.signature: boolean termsAreUnrelated(
      Ontology ontology, TermId t1, TermId t2)
focal_method.body: public static Set<TermId> getChildTerms(
      Ontology ontology, TermId parentTermId) {
      return getChildTerms(ontology, parentTermId, true);
    }
focal_method.class_method_signature: OntologyAlgorithm.getChildTerms(
      Ontology ontology, TermId parentTermId)
focal_method.full_signature: public static Set<TermId> getChildTerms(
      Ontology ontology, TermId parentTermId)
focal_method.identifier: getChildTerms
focal_method.invocations: getChildTerms
focal_method.modifiers: public static
focal_method.parameters: (
      Ontology ontology, TermId parentTermId)
focal_method.return: Set<TermId>
focal_method.signature: Set<TermId> getChildTerms(
      Ontology ontology, TermId parentTermId)