public Set<String> getSamplesName() { requireSamplesPosition(); return samplesPosition.keySet(); }
public List<String> getOrderedSamplesName() { requireSamplesPosition(); return new ArrayList<>(samplesPosition.keySet()); }
@Deprecated public Map<String, Map<String, String>> getSamplesDataAsMap() { requireSamplesPosition(); Map<String, Map<String, String>> samplesDataMap = new HashMap<>(); for (Map.Entry<String, Integer> entry : samplesPosition.entrySet()) { samplesDataMap.put(entry.getKey(), getSampleDataAsMap(entry.getKey())); } return Collections.unmodifiableMap(samplesDataMap); }
public List<String> getSampleData(String sampleName) { requireSamplesPosition(); Integer samplePosition = samplesPosition.get(sampleName); if (samplePosition == null) { return null; } else { return getSampleData(samplePosition); } }
public String getSampleData(String sampleName, String field) { requireSamplesPosition(); if (samplesPosition.containsKey(sampleName)) { Map<String, Integer> formatPositions = getFormatPositions(); if (formatPositions.containsKey(field)) { List<String> sampleData = impl.getSamplesData().get(samplesPosition.get(sampleName)); Integer formatIdx = formatPositions.get(field); return formatIdx < sampleData.size() ? sampleData.get(formatIdx) : null; } } return null; }
public Map<String, String> getSampleDataAsMap(String sampleName) { requireSamplesPosition(); if (samplesPosition.containsKey(sampleName)) { HashMap<String, String> sampleDataMap = new HashMap<>(); Iterator<String> iterator = getFormat().iterator(); List<String> sampleDataList = impl.getSamplesData().get(samplesPosition.get(sampleName)); for (String data : sampleDataList) { sampleDataMap.put(iterator.next(), data); } return Collections.unmodifiableMap(sampleDataMap); } return null; }
public StudyEntry addSampleData(String sampleName, String format, String value, String defaultValue) { requireSamplesPosition(); Integer formatIdx = getFormatPositions().get(format); Integer samplePosition = getSamplesPosition().get(sampleName); return addSampleData(samplePosition, formatIdx, value, defaultValue); }