private Score parseProteinSubstitutionScore(String predictorName, String scoreString) { String[] scoreFields = scoreString.split("[\\(\\)]"); return new Score(Double.valueOf(scoreFields[1]), predictorName, scoreFields[0]); }
private List<Score> getSubstitutionScores(TranscriptVariation transcriptVariation) { List<Score> substitionScores = null; if (transcriptVariation.getPolyphenScore() != null) { substitionScores = new ArrayList<>(); substitionScores.add(new Score((double) transcriptVariation.getPolyphenScore(), "Polyphen", null)); } if (transcriptVariation.getSiftScore() != null) { if (substitionScores == null) { substitionScores = new ArrayList<>(); } substitionScores.add(new Score((double) transcriptVariation.getSiftScore(), "Sift", null)); } return substitionScores; }
private Score buildScore(String source, Document document) { return new Score( getDefault(document, SCORE_SCORE_FIELD, 0.0), getDefault(document, SCORE_SOURCE_FIELD, source), getDefault(document, SCORE_DESCRIPTION_FIELD, (String) null) ); }
scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ss")), "sift", VariantAnnotationUtils.SIFT_DESCRIPTIONS.get(aaDocument.get("se")))); scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ps")), "polyphen", VariantAnnotationUtils.POLYPHEN_DESCRIPTIONS.get(aaDocument.get("pe"))));
@Override public Score build() { try { Score record = new Score(); record.score = fieldSetFlags()[0] ? this.score : (java.lang.Double) defaultValue(fields()[0]); record.source = fieldSetFlags()[1] ? this.source : (java.lang.String) defaultValue(fields()[1]); record.description = fieldSetFlags()[2] ? this.description : (java.lang.String) defaultValue(fields()[2]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ss")), "sift", VariantAnnotationUtils.SIFT_DESCRIPTIONS.get(aaDocument.get("se")))); scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ps")), "polyphen", VariantAnnotationUtils.POLYPHEN_DESCRIPTIONS.get(aaDocument.get("pe"))));
for (Float value : elem.getValue()) { if (value != null) { resultList.add(new Score(new Double(value), elem.getKey(), null));
for (Float value : elem.getValue()) { if (value != null) { resultList.add(new Score(new Double(value), elem.getKey(), null));
Score score = new Score(); score.setSource("sift"); if (StringUtils.isNotEmpty(fields[6])) { Score score = new Score(); score.setSource("polyphen"); if (StringUtils.isNotEmpty(fields[8])) { scores.add(new Score(variantSearchModel.getPhylop(), "phylop", "")); scores.add(new Score(variantSearchModel.getPhastCons(), "phastCons", "")); scores.add(new Score(variantSearchModel.getGerp(), "gerp", "")); scores.add(new Score(variantSearchModel.getCaddRaw(), "cadd_raw", "")); scores.add(new Score(variantSearchModel.getCaddScaled(), "cadd_scaled", ""));