/** * Utility method to check whether a given annotation has been deprecated in a previous GATK release * * @param annotationName the annotation class name (not the full package) to check */ public static boolean isDeprecatedAnnotation(final String annotationName) { return deprecatedGATKAnnotations.containsKey(annotationName); }
/** * Utility method to check whether a given walker has been deprecated in a previous GATK release * * @param walkerName the walker class name (not the full package) to check */ public static boolean isDeprecatedWalker(final String walkerName) { return deprecatedGATKWalkers.containsKey(walkerName); }
public boolean containsKey(T oldUuid) { return map.containsKey(oldUuid); } }
@SuppressWarnings("unchecked") @Override public boolean contains(final Object o) { if (!(o instanceof Map.Entry)) return false; if (o instanceof Object2ObjectMap.Entry) { final Object2ObjectMap.Entry<K, V> e = (Object2ObjectMap.Entry<K, V>) o; final K k = e.getKey(); return map.containsKey(k) && java.util.Objects.equals(map.get(k), e.getValue()); } final Map.Entry<?, ?> e = (Map.Entry<?, ?>) o; final Object k = e.getKey(); final Object value = e.getValue(); return map.containsKey(k) && java.util.Objects.equals(map.get(k), (value)); } @SuppressWarnings("unchecked")
@Override public int get(K k, K cond) { if (!distributions.containsKey(cond)) { return 0; } return distributions.get(cond).get(k); }
@Override public Object2IntFrequencyDistribution<K> getConditionalDistribution(K cond) { if (distributions.containsKey(cond)) { return distributions.get(cond); } return new Object2IntFrequencyDistributionFastutil<K>(); }
if (this.loadedWorlds.containsKey(file.getName())) { return this.loadedWorlds.get(file.getName());
@Override public void set(K k, K cond, int v) { if (!distributions.containsKey(cond)) { Object2IntFrequencyDistributionFastutil<K> fd = new Object2IntFrequencyDistributionFastutil<K>(); fd.set(k, v); distributions.put(cond, fd); marginals.increment(k, v); sumOfAllCounts += v; } else { Object2IntFrequencyDistribution<K> fd = distributions.get(cond); int rv = fd.get(k); fd.set(k, v); distributions.put(cond, fd); marginals.increment(k, -rv + v); sumOfAllCounts = sumOfAllCounts - rv + v; } }