.setDisplayConsequenceType(getMostSevereConsequenceType(normalizedVariantList.get(i) .getAnnotation().getConsequenceTypes())); } catch (UnsupportedURLVariantFormat e) {
.setDisplayConsequenceType(getMostSevereConsequenceType(normalizedVariantList.get(i) .getAnnotation().getConsequenceTypes())); } catch (UnsupportedURLVariantFormat e) {
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()); } }
switch (fields[0]) { case "DCT": variantAnnotation.setDisplayConsequenceType(fields[1]); break; case "HGVS":
.setDisplayConsequenceType(getMostSevereConsequenceType(variant0.getAnnotation() .getConsequenceTypes())); .setDisplayConsequenceType(getMostSevereConsequenceType(variant1.getAnnotation() .getConsequenceTypes())); .setDisplayConsequenceType(getMostSevereConsequenceType(variant2.getAnnotation() .getConsequenceTypes()));
.setDisplayConsequenceType(getMostSevereConsequenceType(variant0.getAnnotation() .getConsequenceTypes())); .setDisplayConsequenceType(getMostSevereConsequenceType(variant1.getAnnotation() .getConsequenceTypes())); .setDisplayConsequenceType(getMostSevereConsequenceType(variant2.getAnnotation() .getConsequenceTypes()));
Integer displaySO = object.getInteger(DISPLAY_CONSEQUENCE_TYPE_FIELD); if (displaySO != null) { va.setDisplayConsequenceType(ConsequenceTypeMappings.accessionToTerm.get(displaySO));
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()); } }