segment.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_SEGMENT_HPP__
#define SHORE_IO_SEGMENT_HPP__

#include <iostream>
#include <string>

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

namespace shore {

class segment_reader
{
 private:

        bool m_is_gff;

        shore::row_reader m_reader;
        shore::segment m_current;

        void parse();

 public:

        typedef shore::segment current_type;

        segment_reader(const std::string &fn);

        segment_reader(const std::string &fn,
                       const std::string &id,const std::string &chr,
                       const std::string &pos,
                       const std::string &strand,const std::string &size,
                       const std::string &end=std::string());

        segment_reader(std::istream *const in,const bool is_gff=false);

        segment_reader(std::istream *const in,
                       const std::string &id,const std::string &chr,
                       const std::string &pos,
                       const std::string &strand,const std::string &size,
                       const std::string &end=std::string());

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

        const std::string &current_line() const;
        const std::string& get_header() const;

        bool is_gff() const;
        bool with_id();
        bool with_strand();
};

typedef shore::source<segment_reader> segment_source;

class segment_writer
{
 public:

        struct config
        {
                std::string filename;
                std::ostream *streamptr;
                bool wstrand;
                bool wsize;
                bool wcovminmax;
                bool wp;

                config(const std::string &fn=std::string(),
                           std::ostream *ostr=0,
                           bool strand=true,bool size=true,
                           bool covminmax=false,bool p=false)
                :filename(fn),streamptr(ostr),
                 wstrand(strand),wsize(size),wcovminmax(covminmax),wp(p)
                {}
        };
        
 private:

        shore::ostreams m_os;

        config m_conf;

        bool m_initialized;
        size_t m_numwritten;

 public:

        typedef shore::segment append_type;

        segment_writer(const config &conf);
        segment_writer(const std::string &fn,const bool strand=true,const bool size=true);
        segment_writer(std::ostream *const os,const bool strand=true,const bool size=true);
        ~segment_writer();

        void init(const bool covminmax,const bool p);

        void append(const shore::segment &seg);
        void flush();
};

typedef shore::sink<segment_writer> segment_sink;

} // namespace

#endif // SHORE_IO_SEGMENT_HPP__