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 SimpleSNP:public PolyTable
    {
    private:
      mutable bool Diploid,isoFemale;
      bool haveOutgroup;
      std::vector<std::string> _names;
    public:
      SimpleSNP (const bool diploid =0,const bool isofemale=0)  : PolyTable(),
          Diploid(diploid),isoFemale(isofemale),haveOutgroup(false)
      {}
      ~ SimpleSNP (void) {}
     
      bool outgroup(void) const;
      void set_outgroup( const bool & b );
      std::string label(unsigned i) const;
      std::istream & read (std::istream & s) throw (Sequence::badFormat,std::exception);
      std::ostream & print(std::ostream &o) const;
    };
    typedef SimpleSNP Hudson2001;
}
#endif

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