private String parseGeneName(EvidenceEntry evidenceEntry) { if (evidenceEntry.getGenomicFeatures() != null && !evidenceEntry.getGenomicFeatures().isEmpty() && evidenceEntry.getGenomicFeatures().get(0).getXrefs() != null) { // There may be more than one genomic feature for cosmic evidence entries. However, the actual gene symbol // is expected to be found at index 0. return evidenceEntry.getGenomicFeatures().get(0).getXrefs().get(SYMBOL); } return null; }
private String parseGeneName(EvidenceEntry evidenceEntry) { if (evidenceEntry.getGenomicFeatures() != null && !evidenceEntry.getGenomicFeatures().isEmpty() && evidenceEntry.getGenomicFeatures().get(0).getXrefs() != null) { // There may be more than one genomic feature for cosmic evidence entries. However, the actual gene symbol // is expected to be found at index 0. return evidenceEntry.getGenomicFeatures().get(0).getXrefs().get(SYMBOL); } return null; }
private ClinVar parseClinvar(EvidenceEntry evidenceEntry) { String clinicalSignificance = getAdditionalProperty(evidenceEntry, CLINICAL_SIGNIFICANCE_IN_SOURCE_FILE); List<String> traitList = null; if (evidenceEntry.getHeritableTraits() != null) { traitList = evidenceEntry .getHeritableTraits() .stream() .map((heritableTrait) -> heritableTrait.getTrait()) .collect(Collectors.toList()); } List<String> geneNameList = null; if (evidenceEntry.getGenomicFeatures() != null) { geneNameList = evidenceEntry .getGenomicFeatures() .stream() .map((genomicFeature) -> genomicFeature.getXrefs().get(SYMBOL)) .collect(Collectors.toList()); } String reviewStatus = getAdditionalProperty(evidenceEntry, REVIEW_STATUS_IN_SOURCE_FILE); return new ClinVar(evidenceEntry.getId(), clinicalSignificance, traitList, geneNameList, reviewStatus); }
private ClinVar parseClinvar(EvidenceEntry evidenceEntry) { String clinicalSignificance = getAdditionalProperty(evidenceEntry, CLINICAL_SIGNIFICANCE_IN_SOURCE_FILE); List<String> traitList = null; if (evidenceEntry.getHeritableTraits() != null) { traitList = evidenceEntry .getHeritableTraits() .stream() .map((heritableTrait) -> heritableTrait.getTrait()) .collect(Collectors.toList()); } List<String> geneNameList = null; if (evidenceEntry.getGenomicFeatures() != null) { geneNameList = evidenceEntry .getGenomicFeatures() .stream() .map((genomicFeature) -> genomicFeature.getXrefs().get(SYMBOL)) .collect(Collectors.toList()); } String reviewStatus = getAdditionalProperty(evidenceEntry, REVIEW_STATUS_IN_SOURCE_FILE); return new ClinVar(evidenceEntry.getId(), clinicalSignificance, traitList, geneNameList, reviewStatus); }
return false; if (evidenceEntry1.getGenomicFeatures() != null ? !evidenceEntry1.getGenomicFeatures().equals(evidenceEntry2.getGenomicFeatures()) : evidenceEntry2.getGenomicFeatures() != null) { return false;
evidenceEntry.setBibliography(Collections.emptyList()); if (evidenceEntry.getGenomicFeatures() == null) { evidenceEntry.setGenomicFeatures(Collections.emptyList());
if (evidenceEntry.getGenomicFeatures() == null) { evidenceEntry.setGenomicFeatures(Collections.emptyList());
if (evidenceEntry.getGenomicFeatures() == null) { evidenceEntry.setGenomicFeatures(Collections.emptyList());