org.mskcc.shenkers.data.interval.GIntervalTreeMap.java Source code

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Here is the source code for org.mskcc.shenkers.data.interval.GIntervalTreeMap.java

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package org.mskcc.shenkers.data.interval;

import com.google.common.collect.Maps;
import htsjdk.samtools.util.IntervalTree;
import htsjdk.samtools.util.IntervalTree.Node;
import htsjdk.samtools.util.IntervalTreeMap;
import htsjdk.tribble.annotation.Strand;
import htsjdk.tribble.bed.BEDFeature;
import htsjdk.tribble.bed.SimpleBEDFeature;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.Spliterators;
import java.util.concurrent.ConcurrentHashMap;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import jersey.repackaged.com.google.common.collect.Iterators;
import org.apache.commons.lang3.builder.HashCodeBuilder;

/**
 *
 * @author sol
 */
public class GIntervalTreeMap<T> {

    Map<ChrStrand, IntervalTree<T>> intervals = new HashMap<ChrStrand, IntervalTree<T>>();

    final IntervalTree<T> empty = new IntervalTree<T>();

    public GIntervalTreeMap() {
    }

    public void add(String chr, int start, int end) {
        add(chr, start, end, Strand.NONE, null);
    }

    public void add(String chr, int start, int end, Strand strand) {
        add(chr, start, end, strand, null);
    }

    public void add(String chr, int start, int end, Strand strand, T value) {
        intervals.computeIfAbsent(new ChrStrand(chr, strand), k -> new IntervalTree<T>()).put(start, end, value);
    }

    public Iterator<Node<T>> queryNodes(String chr, int start, int end) {
        return Iterators.concat(queryNodes(chr, start, end, Strand.POSITIVE),
                queryNodes(chr, start, end, Strand.NEGATIVE), queryNodes(chr, start, end, Strand.NONE));
    }

    public Iterator<Node<T>> queryNodes(String chr, int start, int end, Strand strand) {
        return intervals.getOrDefault(new ChrStrand(chr, strand), empty).overlappers(start, end);
    }

    public Iterator<IntervalFeature<T>> query(String chr, int start, int end, Strand strand) {
        return Iterators.transform(queryNodes(chr, start, end, strand),
                n -> new IntervalFeatureImpl<T>(chr, n.getStart(), n.getEnd(), strand, n.getValue()));
    }

    public Iterator<IntervalFeature<T>> query(String chr, int start, int end) {
        return Iterators.concat(query(chr, start, end, Strand.POSITIVE), query(chr, start, end, Strand.NEGATIVE),
                query(chr, start, end, Strand.NONE));
    }

    public Stream<Node<T>> streamOverlapNodes(String chr, int start, int end) {
        boolean parallel = false;
        int characteristics = 0;
        return StreamSupport.stream(
                Spliterators.spliteratorUnknownSize(queryNodes(chr, start, end), characteristics), parallel);
    }

    public Stream<Node<T>> streamOverlapNodes(String chr, int start, int end, Strand strand) {
        boolean parallel = false;
        int characteristics = 0;
        return StreamSupport.stream(
                Spliterators.spliteratorUnknownSize(queryNodes(chr, start, end, strand), characteristics),
                parallel);
    }

    public Stream<IntervalFeature<T>> streamOverlaps(String chr, int start, int end) {
        boolean parallel = false;
        int characteristics = 0;
        return StreamSupport.stream(Spliterators.spliteratorUnknownSize(query(chr, start, end), characteristics),
                parallel);
    }

    public Stream<IntervalFeature<T>> streamOverlaps(String chr, int start, int end, Strand strand) {
        return streamOverlapNodes(chr, start, end, strand)
                .map(n -> new IntervalFeatureImpl<T>(chr, n.getStart(), n.getEnd(), strand, n.getValue()));
    }
}