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Variant annotation and effect prediction package.

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package org.snpeff.interval;

import org.snpeff.snpEffect.EffectType;

/**
 * Interval for a splice site acceptor
 *
 * Note: Splice sites donnor are defined as the last 2 bases of an intron
 * Reference: http://en.wikipedia.org/wiki/RNA_splicing
 *
 * @author pcingola
 *
 */
public class SpliceSiteAcceptor extends SpliceSite {

	private static final long serialVersionUID = -7416687954435361328L;

	public SpliceSiteAcceptor() {
		super();
		type = EffectType.SPLICE_SITE_ACCEPTOR;
	}

	public SpliceSiteAcceptor(Intron parent, int start, int end, boolean strandMinus, String id) {
		super(parent, start, end, strandMinus, id);
		type = EffectType.SPLICE_SITE_ACCEPTOR;
	}

	@Override
	public boolean intersectsCoreSpliceSite(Marker marker) {
		if (size() <= CORE_SPLICE_SITE_SIZE) return true;

		if (!getChromosomeName().equals(marker.getChromosomeName())) return false; // Not in the same chromosome? They do not intersect

		int coreStart, coreEnd;
		if (isStrandPlus()) {
			coreEnd = end;
			coreStart = coreEnd - CORE_SPLICE_SITE_SIZE + 1;
		} else {
			coreStart = start;
			coreEnd = coreStart + CORE_SPLICE_SITE_SIZE - 1;
		}

		return marker.intersects(coreStart, coreEnd);
	}
}