public StudyEntry(String fileId, String studyId) { this(studyId, new ArrayList<>(), null); if (fileId != null) { setFileId(fileId); } }
/** * @deprecated Use {@link #StudyEntry(String, List, List)} */ @Deprecated public StudyEntry(String fileId, String studyId, List<String> secondaryAlternates, List<String> format) { this.impl = new org.opencb.biodata.models.variant.avro.StudyEntry(studyId, new ArrayList<>(), null, format, new ArrayList<>(), new LinkedHashMap<>(), new ArrayList<>()); setSecondaryAlternatesAlleles(secondaryAlternates); if (fileId != null) { setFileId(fileId); } }
StudyEntry entry = new StudyEntry(metadata.getId(), secondaryAlternatesMap, Arrays.asList(format.split(":"))); VariantFileMetadata fileMetadata = new VariantFileMetadata(metadata.getFiles().get(0)); entry.setFileId(fileMetadata.getId()); variant.addStudyEntry(entry);
/** * @param n * @return studyEntryList */ public List<StudyEntry> getStudies(int n) { int studyID = 2; int fieldID = 3; List<StudyEntry> studyEntryList = new ArrayList<>(); StudyEntry studyEntry = new StudyEntry(); studyEntry.setStudyId(Integer.toString(studyID)); studyEntry.setFileId(Integer.toString(fieldID)); Map<String, String> attributes = genAttributes(); studyEntry.setAttributes(attributes); studyEntry.setFormat(getFormat()); List<List<String>> sampleList = new ArrayList<>(getFormat().size()); for (int i = 0; i < n; i++) { sampleList.add(getRandomample()); } studyEntry.setSamplesData(sampleList); studyEntryList.add(studyEntry); return studyEntryList; }