entry : featureStore.entrySet())
{
- if (!entry.getValue().isEmpty())
+ String type = entry.getKey();
+ if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
{
- types.add(entry.getKey());
+ types.add(type);
}
}
return types;
}
/**
+ * Answers true if the given type matches one of the specified terms (or is a
+ * sub-type of one in the Sequence Ontology), or if no terms are supplied.
+ * Answers false if filter terms are specified and the given term does not
+ * match any of them.
+ *
+ * @param type
+ * @param soTerm
+ * @return
+ */
+ protected boolean isOntologyTerm(String type, String... soTerm)
+ {
+ if (soTerm == null || soTerm.length == 0)
+ {
+ return true;
+ }
+ 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;
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMinimumScore(positional)
+ : Float.NaN;
}
/**
@@ -338,7 +444,129 @@ public class SequenceFeatures implements SequenceFeaturesI
@Override
public float getMaximumScore(String type, boolean positional)
{
- return featureStore.containsKey(type) ? featureStore.get(type)
- .getMaximumScore(positional) : Float.NaN;
+ 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)
+ {
+ IntervalI.sortIntervals(features, forwardStrand);
+ }
+
+ /**
+ * {@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 (FeatureStoreI 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 (FeatureStoreI fs : featureStore.values())
+ {
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
+ }
+ return modified;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
}
+
+ /**
+ * Simplified find for features associated with a given position.
+ *
+ * JavaScript set to not use IntervalI, but easily testable by setting false
+ * to true in javadoc
+ *
+ * FeatureRenderer has checked already that featureStore does contain type.
+ *
+ * @author Bob Hanson 2019.07.30
+ */
+ @Override
+ public List findFeatures(int pos, String type,
+ List list)
+ {
+ FeatureStoreI fs = featureStore.get(type);
+ return fs.findOverlappingFeatures(pos, pos, list);
+ }
+
+ // Chrome; developer console closed
+
+ // BH 2019.08.01 useIntervalStore true, redraw false:
+ // Platform: timer mark 13.848 0.367 overviewrender 16000 pixels row:14
+ // Platform: timer mark 15.391 0.39 overviewrender 16000 pixels row:14
+ // Platform: timer mark 16.498 0.39 overviewrender 16000 pixels row:14
+ // Platform: timer mark 17.596 0.401 overviewrender 16000 pixels row:14
+ // Platform: timer mark 18.738 0.363 overviewrender 16000 pixels row:14
+ // Platform: timer mark 19.659 0.358 overviewrender 16000 pixels row:14
+ // Platform: timer mark 20.737 0.359 overviewrender 16000 pixels row:14
+ // Platform: timer mark 21.797 0.391 overviewrender 16000 pixels row:14
+ // Platform: timer mark 22.851 0.361 overviewrender 16000 pixels row:14
+ // Platform: timer mark 24.019 0.395 overviewrender 16000 pixels row:14
+
+ // BH 2019.08.01 useIntervalStore false, redraw false:
+ // Platform: timer mark 19.011 0.181 overviewrender 16000 pixels row:14
+ // Platform: timer mark 20.311 0.183 overviewrender 16000 pixels row:14
+ // Platform: timer mark 21.368 0.175 overviewrender 16000 pixels row:14
+ // Platform: timer mark 22.347 0.178 overviewrender 16000 pixels row:14
+ // Platform: timer mark 23.605 0.216 overviewrender 16000 pixels row:14
+ // Platform: timer mark 24.836 0.191 overviewrender 16000 pixels row:14
+ // Platform: timer mark 26.016 0.181 overviewrender 16000 pixels row:14
+ // Platform: timer mark 27.278 0.178 overviewrender 16000 pixels row:14
+ // Platform: timer mark 28.158 0.181 overviewrender 16000 pixels row:14
+ // Platform: timer mark 29.227 0.196 overviewrender 16000 pixels row:14
+ // Platform: timer mark 30.1 0.171 overviewrender 16000 pixels row:14
+ // Platform: timer mark 31.684 0.196 overviewrender 16000 pixels row:14
+ // Platform: timer mark 32.779 0.18 overviewrender 16000 pixels row:14
+ // Platform: timer mark 52.355 0.185 overviewrender 16000 pixels row:14
+ // Platform: timer mark 53.829 0.186 overviewrender 16000 pixels row:14
+
+ /**
+ * @author Bob Hanson 2019.08.01
+ */
+ @Override
+ public boolean hasFeatures(String type)
+ {
+ return featureStore.containsKey(type);
+ }
+
}