for (Gene gene : geneList) { if (gene.getAnnotation().getDiseases() != null) { variantAnnotation.getGeneTraitAssociation().addAll(gene.getAnnotation().getDiseases());
for (Gene gene : geneList) { if (gene.getAnnotation().getDiseases() != null) { variantAnnotation.getGeneTraitAssociation().addAll(gene.getAnnotation().getDiseases());
if (variantAnnotation.getGeneTraitAssociation() != null) { for (GeneTraitAssociation geneTrait : variantAnnotation.getGeneTraitAssociation()) { addNotNull(geneTraitName, geneTrait.getName()); addNotNull(geneTraitId, geneTrait.getId());
if (variantAnnotation.getGeneTraitAssociation() != null && CollectionUtils.isNotEmpty(variantAnnotation.getGeneTraitAssociation())) { for (GeneTraitAssociation geneTraitAssociation : variantAnnotation.getGeneTraitAssociation()) { switch (geneTraitAssociation.getSource().toLowerCase()) { case "hpo":
Set<String> names = new HashSet<>(); Set<String> hpos = new HashSet<>(); if (variant.getAnnotation().getGeneTraitAssociation() != null) { for (GeneTraitAssociation geneTrait : variant.getAnnotation().getGeneTraitAssociation()) { ids.add(geneTrait.getId()); names.add(geneTrait.getName());
if (variantAnnotation.getGeneTraitAssociation() != null) { List<Document> geneTraitAssociations = new LinkedList<>(); for (GeneTraitAssociation geneTraitAssociation : variantAnnotation.getGeneTraitAssociation()) { if (geneTraitAssociation != null) { Document d = new Document();
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { if (origin != null) { destination.setId(origin.getId()); destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); destination.setConservation(origin.getConservation()); destination.setGeneExpression(origin.getGeneExpression()); destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); destination.setFunctionalScore(origin.getFunctionalScore()); } }