/*
* Copyright 2012-2015 Broad Institute, Inc.
* 
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
* 
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* 
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

package org.broadinstitute.gatk.utils.codecs.beagle;

import htsjdk.tribble.Feature;
import htsjdk.variant.variantcontext.Allele;

import java.util.ArrayList;
import java.util.Map;

public class BeagleFeature implements Feature {

    private String chr;
    private int start;
    private int end;

    Map<String, ArrayList<String>> sampleGenotypes;
    private Double r2Value;
    Map<String, ArrayList<String>> probLikelihoods;

    Allele AlleleA;
    Allele AlleleB;

    @Override
    public String getChr() {
        return getContig();
    }

    @Override
    public String getContig() {
        return chr;
    }

    @Override
    public int getStart() {
        return start;
    }

    @Override
    public int getEnd() {
        return end;
    }

    public Double getR2value() {
        return r2Value;
    }

    public Allele getAlleleA() {
        return AlleleA;
    }

    public Allele getAlleleB() {
        return AlleleB;
    }

    public Map<String, ArrayList<String>> getProbLikelihoods() {
        return probLikelihoods;
    }

    public Map<String, ArrayList<String>> getGenotypes() {
        return sampleGenotypes;        
    }

    protected void setChr(String chr) {
       this.chr = chr;
    }

    protected void setStart(int start) {
        this.start = start;
    }

    protected void setEnd(int end) {
        this.end = end;
    }

    protected void setR2value(double r2) {
        this.r2Value = r2;
    }

    protected void setAlleleA(String a, boolean isRef) {
        this.AlleleA = Allele.create(a, isRef);
    }

    protected void setAlleleB(String a, boolean isRef) {
        this.AlleleB = Allele.create(a, isRef);
    }

    protected void setProbLikelihoods(Map<String, ArrayList<String>> p) {
        this.probLikelihoods = p;
    }

    protected void setGenotypes(Map<String, ArrayList<String>> p) {
        this.sampleGenotypes = p;
    }
}
