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Variant annotation and effect prediction package.

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package org.snpeff.interval;

import org.snpeff.interval.tree.IntervalForest;

/**
 * A 'BND' variant (i.e. translocation) consisting of two endpoints
 *
 * @author pcingola
 */
public class VariantBnd extends Variant {

	private static final long serialVersionUID = 1L;
	Marker endPoint;
	boolean left; // Is endPoint oriented to the left?
	boolean before; // Is endPoint before ALT?

	public VariantBnd() {
		super();
	}

	public VariantBnd(Marker parent, int start, String ref, String alt, Chromosome chrTr, int startTr, boolean left, boolean before) {
		super(parent, start, ref, alt);
		endPoint = new Marker(chrTr, startTr, startTr);
		endPoint.setStrandMinus(left);
		this.left = left;
		this.before = before;
		variantType = VariantType.BND;
	}

	public Marker getEndPoint() {
		return endPoint;
	}

	public boolean isBefore() {
		return before;
	}

	@Override
	public boolean isBnd() {
		return true;
	}

	public boolean isLeft() {
		return left;
	}

	@Override
	public boolean isStructural() {
		return true;
	}

	/**
	 * Return a collection of intervals that intersect both ends of this variant
	 */
	@Override
	public Markers query(IntervalForest intervalForest) {
		Markers res1 = intervalForest.query(this);
		Markers res2 = intervalForest.query(endPoint);
		res1.add(res2);
		return res1;
	}

	@Override
	public Variant realignLeft() {
		// Do not realign translocations
		return this;
	}

	@Override
	public String toString() {
		String sep = left ? "]" : "[";
		String trPos = sep + endPoint.getChromosomeName() + ":" + endPoint.getStart() + sep;

		return "chr" + getChromosomeName() //
				+ ":" + start //
				+ "_" + getReference() //
				+ "/" //
				+ (before ? trPos + getAlt() : getAlt() + trPos) //
		;
	}

}