mummer.hpp

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/*
 * Copyright 2008,2009,2010,2011,2012 Stephan Ossowski, Korbinian Schneeberger,
 * Felix Ott, Joerg Hagmann, Alf Scotland, Sebastian Bender
 * 
 * This file is part of SHORE.
 * 
 * SHORE 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.
 * 
 * SHORE 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 SHORE.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef SHORE_IO_MUMMER_HPP__
#define SHORE_IO_MUMMER_HPP__

#include <map>
#include <string>
#include <vector>

#include "shore/datatype/datatypes.hpp"
#include "shore/stream/streams.hpp"
#include "shore/fmtio/text.hpp"

namespace shore {

class delta_reader
{
 private:

        shore::line_reader m_lr;
        std::string m_splitbuf[7];

        shore::delta_record m_current;
        bool m_hasdata;

        void init();

 public:

        typedef shore::delta_record current_type;

        delta_reader(const std::string& fn);
        delta_reader(std::istream*const in);

        const shore::delta_record& current() const;
        bool has_data() const;
        void next();
};

typedef shore::source<delta_reader> delta_source;

class wga_parser
{
 public:

 private:

        std::map<std::string,shore::sequence_record> m_ref;
        std::map<std::string,shore::sequence_record> m_qry;

        shore::wga_record m_current;
        bool m_hasdata;

        std::string m_mmbuf_ref;
        std::string m_mmbuf_qry;

        std::vector<int> m_deltabuf;

 public:

        typedef shore::delta_record append_type;
        typedef shore::wga_record current_type;

        wga_parser(const std::string& seqfn1,const std::string& seqfn2);

        const shore::wga_record& current() const;
        bool has_data() const;
        void next();

        void append(const shore::delta_record& d);
        void flush();
};

} // namespace

#endif // SHORE_IO_MUMMER_HPP__