org.snpeff.stats.TranslocationReport Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.stats;

import org.snpeff.interval.Gene;
import org.snpeff.interval.Transcript;
import org.snpeff.interval.VariantBnd;
import org.snpeff.vcf.VcfEffect;

/**
 * Pojo for translocation reports
 * @author pcingola
 */
public class TranslocationReport {

	Transcript tr1, tr2;
	VariantBnd var;
	VcfEffect veff;
	String svgPlot;

	public TranslocationReport(VariantBnd var, VcfEffect veff, Transcript tr1, Transcript tr2) {
		this.tr1 = tr1;
		this.tr2 = tr2;
		this.var = var;
		this.veff = veff;
	}

	public String getChr1() {
		return var.getChromosomeName();
	}

	public String getChr2() {
		return var.getEndPoint().getChromosomeName();
	}

	public String getGeneName1() {
		return ((Gene) tr1.getParent()).getGeneName();
	}

	public String getGeneName2() {
		return ((Gene) tr2.getParent()).getGeneName();
	}

	public String getHgvsC() {
		return veff.getHgvsC();
	}

	public String getHgvsP() {
		return veff.getHgvsP();
	}

	public String getImpact() {
		return veff.getImpact().toString();
	}

	public String getIndex() {
		return getChr1() + ":" + getPos1OneBased() //
				+ "-" + getChr2() + ":" + getPos2OneBased() //
				+ " " + getTrId1() + "-" + getTrId2() //
		;
	}

	/**
	 * Get position (as one-based coordinates)
	 */
	public int getPos1OneBased() {
		return var.getStart() + 1;
	}

	/**
	 * Get position (as one-based coordinates)
	 */
	public int getPos2OneBased() {
		return var.getEndPoint().getStart() + 1;
	}

	public String getSvgPlot() {
		return svgPlot;
	}

	public String getTrId1() {
		return tr1.getId();
	}

	public String getTrId2() {
		return tr2.getId();
	}

	public String getVariantEffect() {
		return veff.getEffString();
	}

	public String getVcfEffect() {
		return veff.toString();
	}

	public void setSvgPlot(String svgPlot) {
		this.svgPlot = svgPlot;
	}
}