/*
 * Copyright (c) 2007-2011 by The Broad Institute, Inc. and the Massachusetts Institute of
 * Technology.  All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
 * WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
 * WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
 * PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
 * OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
 * TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
 * OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
 * ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
 * THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
 * SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
 */

package edu.mit.broad.prodinfo.chromosome;

import edu.mit.broad.prodinfo.genomicplot.GenomicAnnotation;
import edu.mit.broad.prodinfo.genomicplot.TwoSubjectAnnotation;

public class BasicTwoSubjectAnnotation implements TwoSubjectAnnotation {
	private GenomicAnnotation a;
	private GenomicAnnotation b;
	
	public BasicTwoSubjectAnnotation() {
		a = new BasicGenomicAnnotation("A");
		b = new BasicGenomicAnnotation("B");
	}
	public GenomicAnnotation getA() {
		return a;
	}

	public int getAEnd() {
		return a.getEnd();
	}

	public String getAName() {
		return a.getName();
	}

	public int getAStart() {
		return a.getStart();
	}

	public GenomicAnnotation getB() {
		return b;
	}

	public int getBEnd() {
		return b.getEnd();
	}

	public String getBName() {
		return b.getName();
	}

	public int getBStart() {
		return b.getStart();
	}
	
	public void setA(GenomicAnnotation a) { this.a = a;}
	public void setB(GenomicAnnotation b) { this.b = b;}

	public boolean isDirect() {
		return !a.inReversedOrientation() && ! b.inReversedOrientation();
	}
	
	public String toString() {
		return getA().getChromosome() + ":" + getA().getStart() + "-" + getA().getEnd() + "\t("+(isDirect() ? "+" : "-")+")\t" + getB().getChromosome() + ":" + getB().getStart() + "-" + getB().getEnd();
	}

}
