refdict.hpp

/*
 * 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/>.
 */


#include <string>

#include "shore/datatype/datatypes.hpp"
#include "shore/datatype/coor.hpp"
#include "shore/processing/pipeline.hpp"

#include "shore/fmtio/text.hpp"

namespace shore {

class basic_refdict_reader
{
 private:

        enum Columns
        {
                COL_NUMID,
                COL_SIZE,
                COL_MD5,
                COL_STRID,
                COL_SUPP
        };

        shore::row_reader m_reader;

 public:

        basic_refdict_reader(const std::string &fn);
        bool next(refdict_entry &e);
        bool next(shore::refseq_region &r);
};

typedef shore::monolithic<basic_refdict_reader,refdict_entry> refdict_reader;

typedef shore::source<refdict_reader> refdict_source;

typedef shore::monolithic<basic_refdict_reader,
                          shore::refseq_region> refdict_region_reader;

typedef shore::source<refdict_region_reader> refdict_region_source;

}  // namespace shore