PedigreeAlleles.h

/*
 *  Copyright (C) 2010  Regents of the University of Michigan
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef __PEDALLELES_H__
#define __PEDALLELES_H__

#include "LongInt.h"

class Alleles
{
public:
    char   one;
    char   two;

    Alleles()
    {
        one = two = 0;
    }

    char & operator [](int i)
    {
        return (i == 1) ? one : two;
    }

    // is the genotype fully defined?
    bool isKnown()
    {
        return (one * two) != 0;
    }
    bool isHeterozygous()
    {
        return isKnown() && (one != two);
    }
    bool isHomozygous()
    {
        return isKnown() && (one == two);
    }
    bool hasAllele(int a)
    {
        return (one == a) || (two == a);
    }

    // in a bi-allelic system (a, NOT a)
    bool isHeterozygousFor(int a)
    {
        return isHeterozygous() && hasAllele(a);
    }
    bool isHomozygousFor(int a)
    {
        return !(isHeterozygousFor(a));
    }

    // how may alleles a in this genotype?
    int countAlleles(int a)
    {
        return ((one == a) ? 1 : 0) + ((two == a) ? 1 : 0);
    }

    // what is the other allele, assuming genotype is (a, X)
    int otherAllele(int a)
    {
        return ((one == a) ? two : one);
    }

    // are two unordered genotypes identical?
    int identicalTo(Alleles & al)
    {
        return ((al.one == one) && (al.two == two)) ||
               ((al.two == one) && (al.one == two));
    }

    // how many alleles are identical by state
    int countIBS(Alleles & al)
    {
        return (one == al.one) ?
               ((two == al.two) ? 2 : 1) :
                       ((one == al.two) ?
                        ((two == al.one) ? 2 : 1) :
                        (((two == al.one) || (two == al.two)) ? 1 : 0));
    }

    int operator == (Alleles & rhs)
{
        return identicalTo(rhs);
    }
    int operator != (Alleles & rhs)
    {
        return !identicalTo(rhs);
    }

    char Hi()
    {
        return one > two ? one : two;
    }
    char Lo()
    {
        return one > two ? two : one;
    }

    int SequenceCoded()
    {
        return isKnown() ? Hi() *(Hi() - 1) / 2 + Lo() : 0;
    }

    longint BinaryCoded()
    {
        if (isKnown())
        {
            longint allele1(1);
            longint allele2(1);

            allele1 <<= one - 1;
            allele2 <<= two - 1;

            return allele1 | allele2;
        }
        else
            return NOTZERO;
    }

    void Intersect(Alleles & geno)
    {
        char a1 = Lo(), a2 = Hi();
        char b1 = geno.Lo(), b2 = geno.Hi();

        if (a1 == b1 && a2 == b2)
            return;
        if (a1 == b1 || a1 == b2)
            one = two = a1;
        else if (a2 == b1 || a2 == b2)
            one = two = a2;
        else
            one = two = 0;
    }

    void Intersect(char allele)
    {
        if (one != allele && two != allele)
            one = two = 0;
        else
            one = two = allele;
    }

    bool AddAllele(char allele)
    {
        if (one == allele || two == allele)
            return true;

        if (one != 0 && two != 0)
            return false;

        if (one == 0) one = allele;
        else two = allele;
        return true;
    }

    void Wipe()
    {
        one = two = 0;
    }
};

#endif