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 testDiseasetoGene() {
      Multimap<TermId, TermId> diseaseMap = parser.getDiseaseToGeneIdMap();
      Collection<TermId> genes = diseaseMap.get(TermId.of("OMIM:143890"));
      assertEquals(genes.size(), 7);
    }
test_case.class_method_signature: HpoAssociationParserTest.testDiseasetoGene()
test_case.full_signature: @Test void testDiseasetoGene()
test_case.identifier: testDiseasetoGene
test_case.invocations: getDiseaseToGeneIdMap get of assertEquals size
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void testDiseasetoGene()
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> getDiseaseToGeneIdMap() { return this.diseaseToGeneMap; }
focal_method.class_method_signature: HpoAssociationParser.getDiseaseToGeneIdMap()
focal_method.full_signature: public Multimap<TermId,TermId> getDiseaseToGeneIdMap()
focal_method.identifier: getDiseaseToGeneIdMap
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: Multimap<TermId,TermId>
focal_method.signature: Multimap<TermId,TermId> getDiseaseToGeneIdMap()