stringBuilder.append(variant.getAnnotation().getGeneDrugInteraction().stream() .map(GeneDrugInteraction::getDrugName).collect(Collectors.joining(","))); break;
stringBuilder.append(variant.getAnnotation().getGeneDrugInteraction().stream() .map(GeneDrugInteraction::getDrugName).collect(Collectors.joining(","))); break;
for (Gene gene : geneList) { if (gene.getAnnotation().getDrugs() != null) { variantAnnotation.getGeneDrugInteraction().addAll(gene.getAnnotation().getDrugs());
for (Gene gene : geneList) { if (gene.getAnnotation().getDrugs() != null) { variantAnnotation.getGeneDrugInteraction().addAll(gene.getAnnotation().getDrugs());
@Test public void testGetAllVariants_drugs() { //ANNOT_DRUG Query query; Map<String, Integer> drugs = new HashMap<>(); for (Variant variant : allVariants.getResult()) { if (variant.getAnnotation().getGeneDrugInteraction() != null) { Set<String> drugsInVariant = new HashSet<>(); for (GeneDrugInteraction drugInteraction : variant.getAnnotation().getGeneDrugInteraction()) { drugsInVariant.add(drugInteraction.getDrugName()); } for (String flag : drugsInVariant) { drugs.put(flag, drugs.getOrDefault(flag, 0) + 1); } } } int i = 0; for (Map.Entry<String, Integer> entry : drugs.entrySet()) { if (entry.getKey().contains(",")) { continue; } query = new Query(ANNOT_DRUG.key(), entry.getKey()); queryResult = query(query, null); assertEquals(entry.getKey(), entry.getValue().intValue(), queryResult.getNumResults()); if (++i > QUERIES_LIM) { break; } } }
if (variantAnnotation.getGeneDrugInteraction() != null) { for (GeneDrugInteraction drug : variantAnnotation.getGeneDrugInteraction()) { addNotNull(drugs, drug.getDrugName());
if (variantAnnotation.getGeneDrugInteraction() != null) { List<Document> drugGeneInteractions = new LinkedList<>(); List<GeneDrugInteraction> geneDrugInteractionList = variantAnnotation.getGeneDrugInteraction(); if (geneDrugInteractionList != null) { for (GeneDrugInteraction geneDrugInteraction : geneDrugInteractionList) {
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()); } }