*/
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.Set;
import java.util.TreeMap;
+import intervalstore.api.IntervalI;
+
/**
* A class that stores sequence features in a way that supports efficient
* querying by type and location (overlap). Intended for (but not limited to)
/**
* a comparator for sorting features by start position ascending
*/
- private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
+ private static Comparator<IntervalI> FORWARD_STRAND = new Comparator<IntervalI>()
{
@Override
- public int compare(ContiguousI o1, ContiguousI o2)
+ 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<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
+ private static Comparator<IntervalI> REVERSE_STRAND = new Comparator<IntervalI>()
{
@Override
- public int compare(ContiguousI o1, ContiguousI o2)
+ public int compare(IntervalI o1, IntervalI o2)
{
return Integer.compare(o2.getEnd(), o1.getEnd());
}