if (StringUtils.isNotEmpty(proteinVariantAnnotation.getUniprotAccession())) { gnSo.add(buildGeneSO(proteinVariantAnnotation.getUniprotAccession(), so)); addNotNull(xrefs, proteinVariantAnnotation.getUniprotAccession()); addNotNull(xrefs, proteinVariantAnnotation.getUniprotVariantId());
if (StringUtils.isNotEmpty(protVarAnnotation.getUniprotAccession())) { uniprotAccession = protVarAnnotation.getUniprotAccession(); xrefs.add(uniprotAccession); traits.add("KW" + FIELD_SEP + protVarAnnotation.getUniprotAccession() + FIELD_SEP + keyword);
if (StringUtils.isNotEmpty(proteinVariantAnnotation.getUniprotAccession())) { gnSo.add(buildGeneSO(proteinVariantAnnotation.getUniprotAccession(), so)); putNotNull(ct, CT_AA_REFERENCE_FIELD, proteinVariantAnnotation.getReference()); 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()); if (StringUtils.isNotEmpty(proteinVariantAnnotation.getUniprotAccession())) { xrefs.add(convertXrefToStorage(proteinVariantAnnotation.getUniprotAccession(), "UniProt"));
checkScore(inCT.getProteinVariantAnnotation().getSubstitutionScores(), outCT.getProteinVariantAnnotation().getSubstitutionScores(), "polyphen"); String inUniprotAccession = inCT.getProteinVariantAnnotation().getUniprotAccession() == null ? "" : inCT.getProteinVariantAnnotation().getUniprotAccession(); String outUniprotAccession = outCT.getProteinVariantAnnotation().getUniprotAccession() == null ? "" : outCT.getProteinVariantAnnotation().getUniprotAccession(); String inUniprotName = inCT.getProteinVariantAnnotation().getUniprotName() == null ? "" : inCT.getProteinVariantAnnotation().getUniprotName(); String outUniprotName = outCT.getProteinVariantAnnotation().getUniprotName() == null ? "" : outCT.getProteinVariantAnnotation().getUniprotName();
VariantAnnotationProto.ProteinVariantAnnotation.Builder builder = VariantAnnotationProto.ProteinVariantAnnotation.newBuilder() .setUniprotAccession(proteinAnnotation.getUniprotAccession()) .setUniprotName(proteinAnnotation.getUniprotName()) .setPosition(proteinAnnotation.getPosition())