import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
*/
public class SequenceFeatures implements SequenceFeaturesI
{
- /**
- * a comparator for sorting features by start position ascending
- */
- private static Comparator<IntervalI> FORWARD_STRAND = new Comparator<IntervalI>()
- {
- @Override
- public int compare(IntervalI o1, IntervalI o2)
- {
- return Integer.compare(o1.getBegin(), o2.getBegin());
- }
- };
-
- /**
- * a comparator for sorting features by end position descending
- */
- private static Comparator<IntervalI> REVERSE_STRAND = new Comparator<IntervalI>()
- {
- @Override
- public int compare(IntervalI o1, IntervalI o2)
- {
- return Integer.compare(o2.getEnd(), o1.getEnd());
- }
- };
/*
* map from feature type to structured store of features for that type
* @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);
+ IntervalI.sortIntervals(features, forwardStrand);
}
/**
* {@inheritDoc}
*/
@Override
- public boolean shiftFeatures(int shift)
+ public boolean shiftFeatures(int fromPosition, int shiftBy)
{
boolean modified = false;
for (FeatureStore fs : featureStore.values())
{
- modified |= fs.shiftFeatures(shift);
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
}
return modified;
}
-}
\ No newline at end of file
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
+ }
+}