Ms.hpp

/*
    Copyright 2008,2009,2011 St�phane De Mita and Mathieu Siol

    This file is part of the EggLib library.

    EggLib 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.

    EggLib 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 EggLib.  If not, see <http://www.gnu.org/licenses/>.
*/

#ifndef EGGLIB_GMS_HPP
#define EGGLIB_GMS_HPP

#include "DataMatrix.hpp"
#include <string>
#include <istream>

namespace egglib {

     class Ms {

      public:
         
        static DataMatrix get(std::string, unsigned int ns, bool separated=false);


        static DataMatrix get(std::istream& stream, unsigned int ns, bool separated=false);


        static std::string format(DataMatrix& dataMatrix, bool separated=false);
        
        
        static void format(std::ostream& stream, DataMatrix& dataMatrix, bool separated=false);


        static double tMRCA();


        static double prob();
    

        static std::string trees();

         
      private:
        // Line parser (the last \n is extracted and discarded - no error upon EOF)
        std::string next_line(std::istream& stream);
        
        static double _tMRCA;
        
        static double _prob;
        
        static std::string _trees;

        
        Ms() { }
        
        ~Ms() { }

        Ms(const Ms&) { }

        Ms& operator=(const Ms&) { return *this; }
                
    };
}
    
#endif