();
- for (FeatureStore featureSet : featureStore.values())
+ if (soTerm == null || soTerm.length == 0)
{
- groups.addAll(featureSet.getFeatureGroups());
+ return true;
}
- return groups;
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
+ for (String term : soTerm)
+ {
+ if (type.equals(term) || so.isA(type, term))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public float getMinimumScore(String type, boolean positional)
+ {
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMinimumScore(positional)
+ : Float.NaN;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public float getMaximumScore(String type, boolean positional)
+ {
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMaximumScore(positional)
+ : Float.NaN;
+ }
+
+ /**
+ * A convenience method to sort features by start position ascending (if on
+ * forward strand), or end position descending (if on reverse strand)
+ *
+ * @param features
+ * @param forwardStrand
+ */
+ public static void sortFeatures(List features,
+ final boolean forwardStrand)
+ {
+ Collections.sort(features,
+ forwardStrand ? IntervalI.COMPARE_BEGIN_ASC
+ : IntervalI.COMPARE_END_DESC);
+ }
+
+ /**
+ * {@inheritDoc} This method is 'semi-optimised': it only inspects features
+ * for types that include the specified group, but has to inspect every
+ * feature of those types for matching feature group. This is efficient unless
+ * a sequence has features that share the same type but are in different
+ * groups - an unlikely case.
+ *
+ * For example, if RESNUM feature is created with group = PDBID, then features
+ * would only be retrieved for those sequences associated with the target
+ * PDBID (group).
+ */
+ @Override
+ public List getFeaturesForGroup(boolean positional,
+ String group, String... type)
+ {
+ List result = new ArrayList<>();
+ for (FeatureStore featureSet : varargToTypes(type))
+ {
+ if (featureSet.getFeatureGroups(positional).contains(group))
+ {
+ result.addAll(featureSet.getFeaturesForGroup(positional, group));
+ }
+ }
+ return result;
}
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean shiftFeatures(int fromPosition, int shiftBy)
+ {
+ boolean modified = false;
+ for (FeatureStore fs : featureStore.values())
+ {
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
+ }
+ return modified;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
+ }
+
+ @Override
+ public List findFeatures(int pos, String type,
+ List list)
+ {
+ FeatureStore fs = featureStore.get(type);
+ if (fs == null)
+ {
+ return list == null ? new ArrayList<>() : list;
+ }
+ return fs.findFeatures(pos, pos, list);
+ }
+
+ @Override
+ public boolean hasFeatures(String type)
+ {
+ return featureStore.containsKey(type)
+ && !featureStore.get(type).isEmpty();
+ }
+
}