@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)); }
public Multimap<TermId,TermId> getGeneToDiseaseIdMap() { return this.geneToDiseaseMap; }
HpoAssociationParser { public Multimap<TermId,TermId> getGeneToDiseaseIdMap() { return this.geneToDiseaseMap; } }
HpoAssociationParser { public Multimap<TermId,TermId> getGeneToDiseaseIdMap() { return this.geneToDiseaseMap; } HpoAssociationParser(String geneInfoPath,
                              String mim2geneMedgenPath,
                              String orphaToGenePath,
                              String phenotypeHpoaPath,
                              Ontology hpoOntology);  HpoAssociationParser(String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology);  HpoAssociationParser(File geneInfoFile,
                              File mim2geneMedgenFile,
                              File orphaToGeneFile,
                              File phenotypeHpoaFile,
                              Ontology hpoOntology); }
HpoAssociationParser { public Multimap<TermId,TermId> getGeneToDiseaseIdMap() { return this.geneToDiseaseMap; } HpoAssociationParser(String geneInfoPath,
                              String mim2geneMedgenPath,
                              String orphaToGenePath,
                              String phenotypeHpoaPath,
                              Ontology hpoOntology);  HpoAssociationParser(String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology);  HpoAssociationParser(File geneInfoFile,
                              File mim2geneMedgenFile,
                              File orphaToGeneFile,
                              File phenotypeHpoaFile,
                              Ontology hpoOntology); Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap(); Map<TermId,String> getGeneIdToSymbolMap(); Multimap<TermId,TermId> getDiseaseToGeneIdMap(); Multimap<TermId,TermId> getGeneToDiseaseIdMap(); List<HpoGeneAnnotation> getPhenotypeToGene(); void setTermToGene(Multimap<TermId, TermId> phenotypeToDisease); }
HpoAssociationParser { public Multimap<TermId,TermId> getGeneToDiseaseIdMap() { return this.geneToDiseaseMap; } HpoAssociationParser(String geneInfoPath,
                              String mim2geneMedgenPath,
                              String orphaToGenePath,
                              String phenotypeHpoaPath,
                              Ontology hpoOntology);  HpoAssociationParser(String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology);  HpoAssociationParser(File geneInfoFile,
                              File mim2geneMedgenFile,
                              File orphaToGeneFile,
                              File phenotypeHpoaFile,
                              Ontology hpoOntology); Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap(); Map<TermId,String> getGeneIdToSymbolMap(); Multimap<TermId,TermId> getDiseaseToGeneIdMap(); Multimap<TermId,TermId> getGeneToDiseaseIdMap(); List<HpoGeneAnnotation> getPhenotypeToGene(); void setTermToGene(Multimap<TermId, TermId> phenotypeToDisease);  }