public void processResults(Future<List<QueryResult>> conservationFuture, List<QueryResult<VariantAnnotation>> variantAnnotationResultList) throws InterruptedException, ExecutionException { // try { while (!conservationFuture.isDone()) { Thread.sleep(1); } List<QueryResult> conservationQueryResults = conservationFuture.get(); if (conservationQueryResults != null) { for (int i = 0; i < variantAnnotationResultList.size(); i++) { variantAnnotationResultList.get(i).getResult().get(0) .setConservation((List<Score>) conservationQueryResults.get(i).getResult()); } } // } catch (ExecutionException e) { // } catch (InterruptedException | ExecutionException e) { // e.printStackTrace(); // } }
public void processResults(Future<List<QueryResult>> conservationFuture, List<QueryResult<VariantAnnotation>> variantAnnotationResultList) throws InterruptedException, ExecutionException { // try { while (!conservationFuture.isDone()) { Thread.sleep(1); } List<QueryResult> conservationQueryResults = conservationFuture.get(); if (conservationQueryResults != null) { for (int i = 0; i < variantAnnotationResultList.size(); i++) { variantAnnotationResultList.get(i).getResult().get(0) .setConservation((List<Score>) conservationQueryResults.get(i).getResult()); } } // } catch (ExecutionException e) { // } catch (InterruptedException | ExecutionException e) { // e.printStackTrace(); // } }
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); if (annotatorSet.contains("variation")) { destination.setId(origin.getId()); } if (annotatorSet.contains("consequenceType")) { destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); } if (annotatorSet.contains("conservation")) { destination.setConservation(origin.getConservation()); } // destination.setGeneExpression(origin.getGeneExpression()); // destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); if (annotatorSet.contains("populationFrequencies")) { destination.setPopulationFrequencies(origin.getPopulationFrequencies()); } // destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); if (annotatorSet.contains("clinical")) { destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); } if (annotatorSet.contains("functionalScore")) { destination.setFunctionalScore(origin.getFunctionalScore()); } }
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); if (annotatorSet.contains("variation")) { destination.setId(origin.getId()); } if (annotatorSet.contains("consequenceType")) { destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); } if (annotatorSet.contains("conservation")) { destination.setConservation(origin.getConservation()); } // destination.setGeneExpression(origin.getGeneExpression()); // destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); if (annotatorSet.contains("populationFrequencies")) { destination.setPopulationFrequencies(origin.getPopulationFrequencies()); } // destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); if (annotatorSet.contains("clinical")) { destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); } if (annotatorSet.contains("functionalScore")) { destination.setFunctionalScore(origin.getFunctionalScore()); } }
scores.add(new Score(variantSearchModel.getGerp(), "gerp", "")); variantAnnotation.setConservation(scores);
addScore(object, conservedRegionScores, PHYLOP, CONSERVED_REGION_PHYLOP_FIELD); addScore(object, conservedRegionScores, GERP, CONSERVED_REGION_GERP_FIELD); va.setConservation(conservedRegionScores);
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()); } }