private void addProteinSubstitutionScore(ConsequenceType consequenceType, Score score) { ProteinVariantAnnotation proteinVariantAnnotation = consequenceType.getProteinVariantAnnotation(); List<Score> proteinSubstitionScores; if(proteinVariantAnnotation==null) { proteinVariantAnnotation = new ProteinVariantAnnotation(); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); proteinSubstitionScores = new ArrayList<>(); proteinVariantAnnotation.setSubstitutionScores(proteinSubstitionScores); } else { proteinSubstitionScores = proteinVariantAnnotation.getSubstitutionScores(); } proteinSubstitionScores.add(score); }
.append(consequenceType.getProteinVariantAnnotation().getAlternate()); stringBuilder.append(FIELD_SEPARATOR); if (consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { List<String> sift = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("sift")) .map(Score::getDescription) List<String> polyphen = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("polyphen")) .map(Score::getDescription)
case "sift": if (consequenceType.getProteinVariantAnnotation() != null && consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { List<Double> sift = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("sift")) .map(Score::getScore) case "polyphen": if (consequenceType.getProteinVariantAnnotation() != null && consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { List<Double> polyphen = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("polyphen")) .map(Score::getScore)
case "sift": if (consequenceType.getProteinVariantAnnotation() != null && consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { List<Double> sift = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("sift")) .map(Score::getScore) case "polyphen": if (consequenceType.getProteinVariantAnnotation() != null && consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { List<Double> polyphen = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("polyphen")) .map(Score::getScore)
@Override protected Iterable<T> featureValueOf(VariantAnnotation actual) { if (actual.getConsequenceTypes() != null) { Set<T> set = new HashSet<>(); for (ConsequenceType ct : actual.getConsequenceTypes()) { if (ct != null && ct.getProteinVariantAnnotation() != null && ct.getProteinVariantAnnotation().getSubstitutionScores() != null) { for (Score score : ct.getProteinVariantAnnotation().getSubstitutionScores()) { if (score != null && source.equals(score.getSource())) { set.add(mapper.apply(score)); } } } } return set; } return Collections.emptyList(); } };
for (ConsequenceType consequenceType : consequenceTypes) { if (consequenceType.getProteinVariantAnnotation() != null && consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { for (Score score : consequenceType.getProteinVariantAnnotation().getSubstitutionScores()) { String source = score.getSource(); if (("sift").equals(source)) {
} else { Score sift = getScore(protVarAnnotation.getSubstitutionScores(), "sift"); Score polyph = getScore(protVarAnnotation.getSubstitutionScores(), "polyphen"); trans.append(FIELD_SEP); if (sift != null) {
&& ListUtils.isNotEmpty(consequenceType.getProteinVariantAnnotation().getSubstitutionScores()) && ListUtils.isNotEmpty(variant.getAnnotation().getFunctionalScore()) && ListUtils.isNotEmpty(variant.getAnnotation().getConservation())) { double scaledCadd = Double.MIN_VALUE; double gerp = Double.MIN_VALUE; for (Score score: consequenceType.getProteinVariantAnnotation().getSubstitutionScores()) { switch (score.getSource()) { case "sift":
if (proteinVariantAnnotation.getSubstitutionScores() != null) { for (Score score : proteinVariantAnnotation.getSubstitutionScores()) { if (score.getSource().equalsIgnoreCase("sift")) { addNotNull(sift, score.getScore());
putNotNull(ct, CT_PROTEIN_FUNCTIONAL_DESCRIPTION, proteinVariantAnnotation.getFunctionalDescription()); if (proteinVariantAnnotation.getSubstitutionScores() != null) { List<Document> proteinSubstitutionScores = new LinkedList<>(); for (Score score : proteinVariantAnnotation.getSubstitutionScores()) { if (score != null) { if (score.getSource().equals(POLYPHEN)) {
checkScore(inCT.getProteinVariantAnnotation().getSubstitutionScores(), outCT.getProteinVariantAnnotation().getSubstitutionScores(), "sift"); checkScore(inCT.getProteinVariantAnnotation().getSubstitutionScores(), outCT.getProteinVariantAnnotation().getSubstitutionScores(), "polyphen");
.setFunctionalDescription(proteinAnnotation.getFunctionalDescription()); List<Score> substitutionScores = proteinAnnotation.getSubstitutionScores(); if (substitutionScores != null) { for (Score score: substitutionScores) {