Fasta.hpp

/*
    Copyright 2008-2009 Stéphane De Mita, 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_FASTA_HPP
#define EGGLIB_FASTA_HPP

#include <istream>
#include <iostream>
#include <string>
#include "Container.hpp"

namespace egglib {

    class Fasta {

      public:

        static Container parsef(const char* fname, bool importGroupLabels=false);


        static void parsef(const char* fname, Container& container, bool importGroupLabels=false);


        static Container parse(const std::string& str, bool importGroupLabels=false);


        static void parse(const std::string& str, Container& container, bool importGroupLabels=false);


        static Container parse(std::istream& stream, bool importGroupLabels=false);


        static void parse(std::istream& stream, Container& container, bool importGroupLabels=false);
        
        
        static void formatf(const char* fname, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50);


        static void format(std::ostream& file, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50);


        static std::string format(const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50);

          
          
      protected:
        
        Fasta() { }
        
        Fasta(const Fasta& source) { }
        
        Fasta& operator=(const Fasta& source) { return *this; }
        
        virtual ~Fasta() { }

        
    };
}

#endif