private VariantTraitAssociation convertToVariantTraitAssociation(List<EvidenceEntry> traitAssociation) { List<ClinVar> clinvarList = new ArrayList<>(); List<Cosmic> cosmicList = new ArrayList<>(traitAssociation.size()); for (EvidenceEntry evidenceEntry : traitAssociation) { switch (evidenceEntry.getSource().getName()) { case CLINVAR: clinvarList.add(parseClinvar(evidenceEntry)); break; case COSMIC: cosmicList.add(parseCosmic(evidenceEntry)); break; default: break; } } return new VariantTraitAssociation(clinvarList, null, cosmicList); }
private VariantTraitAssociation convertToVariantTraitAssociation(List<EvidenceEntry> traitAssociation) { List<ClinVar> clinvarList = new ArrayList<>(); List<Cosmic> cosmicList = new ArrayList<>(traitAssociation.size()); for (EvidenceEntry evidenceEntry : traitAssociation) { switch (evidenceEntry.getSource().getName()) { case CLINVAR: clinvarList.add(parseClinvar(evidenceEntry)); break; case COSMIC: cosmicList.add(parseCosmic(evidenceEntry)); break; default: break; } } return new VariantTraitAssociation(clinvarList, null, cosmicList); }
private VariantTraitAssociation parseClinicalData(Document clinicalData) { if (clinicalData != null) { int size = 0; VariantTraitAssociation variantTraitAssociation = new VariantTraitAssociation(); List cosmicDBList = (List) clinicalData.get(CLINICAL_COSMIC_FIELD); if (cosmicDBList != null) {
@Override public VariantTraitAssociation build() { try { VariantTraitAssociation record = new VariantTraitAssociation(); record.clinvar = fieldSetFlags()[0] ? this.clinvar : (java.util.List<org.opencb.biodata.models.variant.avro.ClinVar>) defaultValue(fields()[0]); record.gwas = fieldSetFlags()[1] ? this.gwas : (java.util.List<org.opencb.biodata.models.variant.avro.Gwas>) defaultValue(fields()[1]); record.cosmic = fieldSetFlags()[2] ? this.cosmic : (java.util.List<org.opencb.biodata.models.variant.avro.Cosmic>) defaultValue(fields()[2]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
VariantTraitAssociation variantTraitAssociation = new VariantTraitAssociation();