SimpleSNP.hpp

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/*

Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu

Remove the brackets to email me.

This file is part of libsequence.

libsequence 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.

libsequence 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
long with libsequence.  If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef __SIMPLE_SNP_HPP__
#define __SIMPLE_SNP_HPP__

#include <Sequence/PolyTable.hpp>

namespace Sequence
{
    class __attribute__((deprecated)) SimpleSNP : public PolyTable
    {
      private:
        std::vector<std::string> _names;
        bool Diploid, isoFemale;
        bool haveOutgroup;

      public:
        SimpleSNP(SimpleSNP &&);
        SimpleSNP(const bool diploid = 0, const bool isofemale = 0)
            : PolyTable(), Diploid(diploid), isoFemale(isofemale),
              haveOutgroup(false)
        {
        }
        ~SimpleSNP(void) {}

        SimpleSNP &operator=(SimpleSNP &&);

        bool outgroup(void) const;
        void set_outgroup(const bool &b);
        std::string label(unsigned i) const;
        std::istream &read(std::istream &s);
        std::ostream &print(std::ostream &o) const;
    };
    typedef SimpleSNP Hudson2001;
}
#endif