*/
package jalview.datamodel.features;
-import jalview.datamodel.ContiguousI;
-import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.io.gff.SequenceOntologyI;
-
import java.util.ArrayList;
import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
+import intervalstore.api.IntervalI;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
/**
* A class that stores sequence features in a way that supports efficient
* querying by type and location (overlap). Intended for (but not limited to)
*/
public class SequenceFeatures implements SequenceFeaturesI
{
- /**
- * a comparator for sorting features by start position ascending
- */
- private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o1.getBegin(), o2.getBegin());
- }
- };
-
- /**
- * a comparator for sorting features by end position descending
- */
- private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o2.getEnd(), o1.getEnd());
- }
- };
-
/*
* map from feature type to structured store of features for that type
* null types are permitted (but not a good idea!)
List<FeatureStore> types = new ArrayList<>();
for (String theType : type)
{
- if (featureStore.containsKey(theType))
+ if (theType != null && featureStore.containsKey(theType))
{
types.add(featureStore.get(theType));
}
* @param features
* @param forwardStrand
*/
- public static void sortFeatures(List<SequenceFeature> features,
+ public static void sortFeatures(List<? extends IntervalI> features,
final boolean forwardStrand)
{
- Collections.sort(features, forwardStrand ? FORWARD_STRAND
- : REVERSE_STRAND);
+ Collections.sort(features,
+ forwardStrand
+ ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+ : IntervalI.COMPARE_END_DESC);
}
/**