@Test void testHoltOram() { Map<TermId, DiseaseToGeneAssociation> diseasemap = parser.getDiseaseToAssociationsMap(); TermId holtOramId = TermId.of("OMIM:142900"); assertTrue(diseasemap.containsKey(holtOramId)); DiseaseToGeneAssociation holtOramAssociation = diseasemap.get(holtOramId); List<Gene> geneList = holtOramAssociation.getGeneList(); assertEquals(1, geneList.size()); Gene gene = geneList.get(0); TermId tbx5Id = TermId.of("NCBIGene:6910"); assertEquals(tbx5Id, gene.getId()); String symbol = "TBX5"; assertEquals(symbol, gene.getSymbol()); }
public Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap() { return this.diseaseToAssociationsMap; }
HpoAssociationParser { public Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap() { return this.diseaseToAssociationsMap; } }
HpoAssociationParser { public Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap() { return this.diseaseToAssociationsMap; } 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 Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap() { return this.diseaseToAssociationsMap; } 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 Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap() { return this.diseaseToAssociationsMap; } 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);  }