test_class.declarator: parser
test_class.modifier: private
test_class.original_string: private HpoAssociationParser parser;
test_class.type: HpoAssociationParser
test_class.var_name: parser
test_class.file: phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/assoc/HpoAssociationParserTest.java
test_class.identifier: HpoAssociationParserTest
test_case.body: @Test
    void testFbn1() {
      Multimap<TermId, TermId> mmap = parser.getGeneToDiseaseIdMap();
      TermId Fbn1Id = TermId.of("NCBIGene:2200");
      assertTrue(mmap.containsKey(Fbn1Id));
      Collection<TermId> diseaseIdCollection = mmap.get(Fbn1Id);
      assertEquals(8, diseaseIdCollection.size());
      TermId acromicricDysplasia = TermId.of("OMIM:102370");
      assertTrue(diseaseIdCollection.contains(acromicricDysplasia));
      TermId ectopiaLentis = TermId.of("OMIM:129600");
      assertTrue(diseaseIdCollection.contains(ectopiaLentis));
      TermId geleophysicDysplasia2 = TermId.of("OMIM:614185");
      assertTrue(diseaseIdCollection.contains(geleophysicDysplasia2));
      TermId marfanLipodystrophySyndrome = TermId.of("OMIM:616914");
      assertTrue(diseaseIdCollection.contains(marfanLipodystrophySyndrome));
      TermId marfanSyndrome = TermId.of("OMIM:154700");
      assertTrue(diseaseIdCollection.contains(marfanSyndrome));
      TermId massSyndrome = TermId.of("OMIM:604308");
      assertTrue(diseaseIdCollection.contains(massSyndrome));
      TermId stiffSkinSyndrome = TermId.of("OMIM:184900");
      assertTrue(diseaseIdCollection.contains(stiffSkinSyndrome));
      TermId weillMarchesani2 = TermId.of("OMIM:608328");
      assertTrue(diseaseIdCollection.contains(weillMarchesani2));
    }
test_case.class_method_signature: HpoAssociationParserTest.testFbn1()
test_case.full_signature: @Test void testFbn1()
test_case.identifier: testFbn1
test_case.invocations: getGeneToDiseaseIdMap of assertTrue containsKey get assertEquals size of assertTrue contains of assertTrue contains of assertTrue contains of assertTrue contains of assertTrue contains of assertTrue contains of assertTrue contains of assertTrue contains
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void testFbn1()
focal_class.declarator: hpoOntology
focal_class.modifier: private final
focal_class.original_string: private final Ontology hpoOntology;
focal_class.type: Ontology
focal_class.var_name: hpoOntology
focal_class.declarator: homoSapiensGeneInfoFile
focal_class.modifier: private final
focal_class.original_string: private final File homoSapiensGeneInfoFile;
focal_class.type: File
focal_class.var_name: homoSapiensGeneInfoFile
focal_class.declarator: mim2geneMedgenFile
focal_class.modifier: private final
focal_class.original_string: private final File mim2geneMedgenFile;
focal_class.type: File
focal_class.var_name: mim2geneMedgenFile
focal_class.declarator: orphaToGeneFile
focal_class.modifier: private final
focal_class.original_string: private final File orphaToGeneFile;
focal_class.type: File
focal_class.var_name: orphaToGeneFile
focal_class.declarator: phenotypeDotHpoaFile
focal_class.modifier: private final
focal_class.original_string: private final File phenotypeDotHpoaFile;
focal_class.type: File
focal_class.var_name: phenotypeDotHpoaFile
focal_class.declarator: geneIdToSymbolMap
focal_class.modifier: private
focal_class.original_string: private Map<TermId, String> geneIdToSymbolMap;
focal_class.type: Map<TermId, String>
focal_class.var_name: geneIdToSymbolMap
focal_class.declarator: diseaseToGeneMap
focal_class.modifier: private
focal_class.original_string: private ImmutableMultimap<TermId,TermId> diseaseToGeneMap;
focal_class.type: ImmutableMultimap<TermId,TermId>
focal_class.var_name: diseaseToGeneMap
focal_class.declarator: geneToDiseaseMap
focal_class.modifier: private
focal_class.original_string: private ImmutableMultimap<TermId,TermId> geneToDiseaseMap;
focal_class.type: ImmutableMultimap<TermId,TermId>
focal_class.var_name: geneToDiseaseMap
focal_class.declarator: diseaseToAssociationsMap
focal_class.modifier: private
focal_class.original_string: private ImmutableMap<TermId, DiseaseToGeneAssociation> diseaseToAssociationsMap;
focal_class.type: ImmutableMap<TermId, DiseaseToGeneAssociation>
focal_class.var_name: diseaseToAssociationsMap
focal_class.declarator: phenotypeToGeneList
focal_class.modifier: private
focal_class.original_string: private ImmutableList<HpoGeneAnnotation> phenotypeToGeneList;
focal_class.type: ImmutableList<HpoGeneAnnotation>
focal_class.var_name: phenotypeToGeneList
focal_class.declarator: associationList
focal_class.modifier: private
focal_class.original_string: private List<DiseaseToGeneAssociation> associationList;
focal_class.type: List<DiseaseToGeneAssociation>
focal_class.var_name: associationList
focal_class.file: phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/assoc/HpoAssociationParser.java
focal_class.identifier: HpoAssociationParser
focal_class.class_method_signature: HpoAssociationParser.HpoAssociationParser(String geneInfoPath,
                                String mim2geneMedgenPath,
                                String orphaToGenePath,
                                String phenotypeHpoaPath,
                                Ontology hpoOntology)
focal_class.full_signature: public  HpoAssociationParser(String geneInfoPath,
                                String mim2geneMedgenPath,
                                String orphaToGenePath,
                                String phenotypeHpoaPath,
                                Ontology hpoOntology)
focal_class.identifier: HpoAssociationParser
focal_class.modifiers: public
focal_class.parameters: (String geneInfoPath,
                                String mim2geneMedgenPath,
                                String orphaToGenePath,
                                String phenotypeHpoaPath,
                                Ontology hpoOntology)
focal_class.signature:  HpoAssociationParser(String geneInfoPath,
                                String mim2geneMedgenPath,
                                String orphaToGenePath,
                                String phenotypeHpoaPath,
                                Ontology hpoOntology)
focal_class.class_method_signature: HpoAssociationParser.HpoAssociationParser(String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology)
focal_class.full_signature: public  HpoAssociationParser(String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology)
focal_class.identifier: HpoAssociationParser
focal_class.modifiers: public
focal_class.parameters: (String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology)
focal_class.signature:  HpoAssociationParser(String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology)
focal_class.class_method_signature: HpoAssociationParser.HpoAssociationParser(File geneInfoFile,
                                File mim2geneMedgenFile,
                                File orphaToGeneFile,
                                File phenotypeHpoaFile,
                                Ontology hpoOntology)
focal_class.full_signature: public  HpoAssociationParser(File geneInfoFile,
                                File mim2geneMedgenFile,
                                File orphaToGeneFile,
                                File phenotypeHpoaFile,
                                Ontology hpoOntology)
focal_class.identifier: HpoAssociationParser
focal_class.modifiers: public
focal_class.parameters: (File geneInfoFile,
                                File mim2geneMedgenFile,
                                File orphaToGeneFile,
                                File phenotypeHpoaFile,
                                Ontology hpoOntology)
focal_class.signature:  HpoAssociationParser(File geneInfoFile,
                                File mim2geneMedgenFile,
                                File orphaToGeneFile,
                                File phenotypeHpoaFile,
                                Ontology hpoOntology)
focal_class.class_method_signature: HpoAssociationParser.ingestPhenotypeHpoaFile()
focal_class.full_signature: private void ingestPhenotypeHpoaFile()
focal_class.identifier: ingestPhenotypeHpoaFile
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void ingestPhenotypeHpoaFile()
focal_class.class_method_signature: HpoAssociationParser.getDiseaseToAssociationsMap()
focal_class.full_signature: public Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap()
focal_class.identifier: getDiseaseToAssociationsMap
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Map<TermId,DiseaseToGeneAssociation>
focal_class.signature: Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap()
focal_class.class_method_signature: HpoAssociationParser.getGeneIdToSymbolMap()
focal_class.full_signature: public Map<TermId,String> getGeneIdToSymbolMap()
focal_class.identifier: getGeneIdToSymbolMap
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Map<TermId,String>
focal_class.signature: Map<TermId,String> getGeneIdToSymbolMap()
focal_class.class_method_signature: HpoAssociationParser.getDiseaseToGeneIdMap()
focal_class.full_signature: public Multimap<TermId,TermId> getDiseaseToGeneIdMap()
focal_class.identifier: getDiseaseToGeneIdMap
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Multimap<TermId,TermId>
focal_class.signature: Multimap<TermId,TermId> getDiseaseToGeneIdMap()
focal_class.class_method_signature: HpoAssociationParser.getGeneToDiseaseIdMap()
focal_class.full_signature: public Multimap<TermId,TermId> getGeneToDiseaseIdMap()
focal_class.identifier: getGeneToDiseaseIdMap
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Multimap<TermId,TermId>
focal_class.signature: Multimap<TermId,TermId> getGeneToDiseaseIdMap()
focal_class.class_method_signature: HpoAssociationParser.getPhenotypeToGene()
focal_class.full_signature: public List<HpoGeneAnnotation> getPhenotypeToGene()
focal_class.identifier: getPhenotypeToGene
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<HpoGeneAnnotation>
focal_class.signature: List<HpoGeneAnnotation> getPhenotypeToGene()
focal_class.class_method_signature: HpoAssociationParser.setTermToGene(Multimap<TermId, TermId> phenotypeToDisease)
focal_class.full_signature: public void setTermToGene(Multimap<TermId, TermId> phenotypeToDisease)
focal_class.identifier: setTermToGene
focal_class.modifiers: public
focal_class.parameters: (Multimap<TermId, TermId> phenotypeToDisease)
focal_class.return: void
focal_class.signature: void setTermToGene(Multimap<TermId, TermId> phenotypeToDisease)
focal_class.class_method_signature: HpoAssociationParser.setAssociationMaps()
focal_class.full_signature: private void setAssociationMaps()
focal_class.identifier: setAssociationMaps
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setAssociationMaps()
focal_class.class_method_signature: HpoAssociationParser.ingestDisease2GeneAssociations()
focal_class.full_signature: private void ingestDisease2GeneAssociations()
focal_class.identifier: ingestDisease2GeneAssociations
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void ingestDisease2GeneAssociations()
focal_method.body: public Multimap<TermId,TermId> getGeneToDiseaseIdMap() { return this.geneToDiseaseMap; }
focal_method.class_method_signature: HpoAssociationParser.getGeneToDiseaseIdMap()
focal_method.full_signature: public Multimap<TermId,TermId> getGeneToDiseaseIdMap()
focal_method.identifier: getGeneToDiseaseIdMap
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: Multimap<TermId,TermId>
focal_method.signature: Multimap<TermId,TermId> getGeneToDiseaseIdMap()