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

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

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package org.mskcc.shenkers.data.interval;

import com.google.common.collect.BoundType;
import com.google.common.collect.Range;
import com.google.common.collect.RangeMap;
import com.google.common.collect.RangeSet;
import com.google.common.collect.TreeRangeMap;
import com.google.common.collect.TreeRangeSet;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalTreeMap;
import java.util.Map;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

/**
 *
 * @author sol
 */
public class RangeTools {

    private static final Logger logger = LogManager.getLogger();

    public static RangeSet<Integer> asClosed(RangeSet<Integer> s) {
        RangeSet<Integer> closedIntervalSet = TreeRangeSet.create();
        for (Range<Integer> r : s.asRanges()) {
            closedIntervalSet.add(asClosed(r));
        }
        return closedIntervalSet;
    }

    public static <T> RangeMap<Integer, T> asClosed(RangeMap<Integer, T> s) {
        RangeMap<Integer, T> closedIntervalSet = TreeRangeMap.create();
        Map<Range<Integer>, T> map = s.asMapOfRanges();
        for (Map.Entry<Range<Integer>, T> r : map.entrySet()) {
            closedIntervalSet.put(asClosed(r.getKey()), r.getValue());
        }
        return closedIntervalSet;
    }

    public static Range<Integer> asClosed(Range<Integer> r) {
        return Range.closed(r.lowerBoundType() == BoundType.OPEN ? r.lowerEndpoint() + 1 : r.lowerEndpoint(),
                r.upperBoundType() == BoundType.OPEN ? r.upperEndpoint() - 1 : r.upperEndpoint());
    }

    public static int length(Range<Integer> i) {
        return i.upperEndpoint() - i.lowerEndpoint() + 1;
    }

    public static double lengthReal(Range<Double> i) {
        return i.upperEndpoint() - i.lowerEndpoint();
    }
}