Seq.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 SEQ_H
#define SEQ_H

#include <iosfwd>
#include <string>
#include <exception>
#include <utility>

namespace Sequence
{
    class Seq
    {
      public:
        std::string name, seq;
        Seq(void);
        template <typename T>
        Seq(T &&name_, T &&seq_)
            : name(std::forward<T>(name_)), seq(std::forward<T>(seq_))
        {
        }
        Seq(const char * n, const char * s)
            : name(n),seq(s)
        {
        }
        Seq(const Seq &seq) = default;
        Seq(Seq &&seq) = default;
        virtual ~Seq() {}
        std::string GetName(void) const;
        std::string GetSeq(void) const;
        std::string substr(std::string::size_type beg,
                           std::string::size_type len) const;
        std::string substr(std::string::size_type beg) const;
        typedef std::string::iterator iterator;
        typedef std::string::const_iterator const_iterator;
        typedef std::string::reference reference;
        typedef std::string::const_reference const_reference;
        typedef std::string::size_type size_type;
        iterator begin();
        iterator end();
        const_iterator begin() const;
        const_iterator end() const;
        const_iterator cbegin() const;
        const_iterator cend() const;
        void Revcom(void);
        void Subseq(const unsigned &, const unsigned &);
        void Complement(void);
        size_type length(void) const;
        size_type size(void) const;
        size_type UngappedLength(void) const;
        bool IsGapped(void) const;
        reference operator[](const size_type &i);
        const_reference operator[](const size_type &i) const;
        bool operator==(const Seq &rhs) const;
        bool operator!=(const Seq &rhs) const;
        Seq &operator=(const Seq &rhs) = default;
        Seq &operator=(Seq &&rhs) = default;
        operator std::string() const;
        const char *c_str(void) const;
        virtual std::istream &read(std::istream &s) = 0;
        virtual std::ostream &print(std::ostream &s) const = 0;
    };

    std::ostream &operator<<(std::ostream &s, const Seq &c);
    std::istream &operator>>(std::istream &s, Seq &c);
}
#endif