gff.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_GFF_HPP__
#define SHORE_IO_GFF_HPP__

#include <set>
#include <map>
#include <string>

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

namespace shore {

class gff_reader
{
 private:

        shore::row_reader m_reader;

        shore::annotation_entry m_current;
        std::string m_attrbuf;


        void parse();

 public:

        typedef shore::annotation_entry current_type;

        gff_reader(std::istream*const in);

        gff_reader(const std::string& fn);

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

typedef shore::source<gff_reader> gff_source;

class gff_writer
{
 public:

        static const std::string HEADER;

 private:

        shore::ostreams m_os;
        
        std::string m_default_source;
        std::string m_default_type;

        long m_id;
        int m_chr;

        bool m_signed_scores;
        bool m_enumerate;

        std::map<int,std::string> m_chrtrans;

        shore::alignment_helper m_ah;
        std::string m_buf;

 public:

        typedef shore::annotation_entry append_type;

        gff_writer(const std::string &fn,
                   const std::string& default_type="region",
                   const bool signed_scores=true,const bool enumerate=false);

        gff_writer(std::ostream*const os,
                   const std::string& default_type="region",
                   const bool signed_scores=true,const bool enumerate=false);

        void signed_scores(const bool s)
        {
                m_signed_scores=s;
        }

        void append(const shore::segment &seg);
        void append(const shore::coverage &cov);
        void append(const shore::alignment &aln);
        void append(const shore::annotation_entry &ae);
        void flush();
};

typedef shore::sink<gff_writer> gff_sink;

} // namespace

#endif // SHORE_IO_GFF_HPP__