/*
* The MIT License
*
* Copyright (c) 2010 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import htsjdk.samtools.SAMException;
import htsjdk.samtools.SAMSequenceDictionary;
import java.util.Iterator;
/**
* @author alecw@broadinstitute.org
*/
public class IntervalUtil {
/** Return true if the sequence/position lie in the provided interval. */
public static boolean contains(final Interval interval, final String sequenceName, final long position) {
return interval.getSequence().equals(sequenceName) && (position >= interval.getStart() && position <= interval.getEnd());
}
/** Return true if the sequence/position lie in the provided interval list. */
public static boolean contains(final IntervalList intervalList, final String sequenceName, final long position) {
for (final Interval interval : intervalList.getUniqueIntervals()) {
if (contains(interval, sequenceName, position))
return true;
}
return false;
}
/**
* Throws RuntimeException if the given intervals are not locus ordered and non-overlapping
* @param intervals
* @param sequenceDictionary used to determine order of sequences
*/
public static void assertOrderedNonOverlapping(final Iterator<Interval> intervals, final SAMSequenceDictionary sequenceDictionary) {
if (!intervals.hasNext()) {
return;
}
Interval prevInterval = intervals.next();
int prevSequenceIndex = sequenceDictionary.getSequenceIndex(prevInterval.getSequence());
while (intervals.hasNext()) {
final Interval interval = intervals.next();
if (prevInterval.intersects(interval)) {
throw new SAMException("Intervals should not overlap: " + prevInterval + "; " + interval);
}
final int thisSequenceIndex = sequenceDictionary.getSequenceIndex(interval.getSequence());
if (prevSequenceIndex > thisSequenceIndex ||
(prevSequenceIndex == thisSequenceIndex && prevInterval.compareTo(interval) >= 0)) {
throw new SAMException("Intervals not in order: " + prevInterval + "; " + interval);
}
prevInterval = interval;
prevSequenceIndex = thisSequenceIndex;
}
}
}