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/*
 * 
 *
 */
package org.opencb.biodata.models.variant.stats;

import java.util.Arrays;

/**
 * Created by jmmut on 2015-12-02.
 *
 * @author Jose Miguel Mut Lopez <[email protected]>
 */
public class IdentityByState {
    public int[] ibs = {0, 0, 0};

    public void add(IdentityByState param) {
        for (int i = 0; i < ibs.length; i++) {
            ibs[i] += param.ibs[i];
        }
    }

    /**
     * Distance in genotype space.
     * As it is categorical, currently it is just computed as a ratio between shared genotypeCounters and total genotypeCounters.
     * Could also be euclidian distance with formula (taken from plink):
     * sqrt((IBSg.z1*0.5 + IBSg.z2*2)/(IBSg.z0+IBSg.z1+IBSg.z2*2));
     * @return
     */
    public double getDistance() {
        return (ibs[1] * 0.5 + ibs[2]) / (ibs[0] + ibs[1] + ibs[2]);
    }

    @Override
    public String toString() {
        return "IBS{" +
                "ibs=" + Arrays.toString(ibs) +
                '}';
    }

    public int[] getIbs() {
        return ibs;
    }

    public IdentityByState setIbs(int[] ibs) {
        this.ibs = ibs;
        return this;
    }
}