gnSo.add(buildGeneSO(proteinVariantAnnotation.getUniprotAccession(), so)); if (StringUtils.isNotEmpty(proteinVariantAnnotation.getUniprotName())) { gnSo.add(buildGeneSO(proteinVariantAnnotation.getUniprotName(), so)); proteinKeywords.addAll(proteinVariantAnnotation.getKeywords()); addNotNull(xrefs, proteinVariantAnnotation.getUniprotName()); addNotNull(xrefs, proteinVariantAnnotation.getUniprotAccession()); addNotNull(xrefs, proteinVariantAnnotation.getUniprotVariantId());
if (StringUtils.isNotEmpty(protVarAnnotation.getUniprotName())) { uniprotName = protVarAnnotation.getUniprotName(); xrefs.add(uniprotName);
gnSo.add(buildGeneSO(proteinVariantAnnotation.getUniprotAccession(), so)); if (StringUtils.isNotEmpty(proteinVariantAnnotation.getUniprotName())) { gnSo.add(buildGeneSO(proteinVariantAnnotation.getUniprotName(), so)); putNotNull(ct, CT_AA_ALTERNATE_FIELD, proteinVariantAnnotation.getAlternate()); putNotNull(ct, CT_PROTEIN_UNIPROT_ACCESSION, proteinVariantAnnotation.getUniprotAccession()); putNotNull(ct, CT_PROTEIN_UNIPROT_NAME, proteinVariantAnnotation.getUniprotName()); putNotNull(ct, CT_PROTEIN_UNIPROT_VARIANT_ID, proteinVariantAnnotation.getUniprotVariantId()); putNotNull(ct, CT_PROTEIN_FUNCTIONAL_DESCRIPTION, proteinVariantAnnotation.getFunctionalDescription()); xrefs.add(convertXrefToStorage(proteinVariantAnnotation.getUniprotAccession(), "UniProt")); if (StringUtils.isNotEmpty(proteinVariantAnnotation.getUniprotName())) { xrefs.add(convertXrefToStorage(proteinVariantAnnotation.getUniprotName(), "UniProt"));
String inUniprotName = inCT.getProteinVariantAnnotation().getUniprotName() == null ? "" : inCT.getProteinVariantAnnotation().getUniprotName(); String outUniprotName = outCT.getProteinVariantAnnotation().getUniprotName() == null ? "" : outCT.getProteinVariantAnnotation().getUniprotName(); String inUniprotVariantId = inCT.getProteinVariantAnnotation().getUniprotVariantId() == null ? "" : inCT.getProteinVariantAnnotation().getUniprotVariantId(); String outUniprotVariantId = outCT.getProteinVariantAnnotation().getUniprotVariantId() == null ? "" : outCT.getProteinVariantAnnotation().getUniprotVariantId();
VariantAnnotationProto.ProteinVariantAnnotation.newBuilder() .setUniprotAccession(proteinAnnotation.getUniprotAccession()) .setUniprotName(proteinAnnotation.getUniprotName()) .setPosition(proteinAnnotation.getPosition()) .setReference(proteinAnnotation.getReference())