@Test void testGeneIdToGeneSymbol(){ Map<TermId, String> geneMap = parser.getGeneIdToSymbolMap(); assertEquals(geneMap.get(TermId.of("NCBIGene:2690")),"GHR"); assertEquals(geneMap.get(TermId.of("NCBIGene:2200")),"FBN1"); }
public Map<TermId,String> getGeneIdToSymbolMap() { return this.geneIdToSymbolMap;}
HpoAssociationParser { public Map<TermId,String> getGeneIdToSymbolMap() { return this.geneIdToSymbolMap;} }
HpoAssociationParser { public Map<TermId,String> getGeneIdToSymbolMap() { return this.geneIdToSymbolMap;} 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,String> getGeneIdToSymbolMap() { return this.geneIdToSymbolMap;} 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,String> getGeneIdToSymbolMap() { return this.geneIdToSymbolMap;} 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);  }