genome_region_reader.hpp

Go to the documentation of this file.

#ifndef GENESIS_POPULATION_FORMAT_GENOME_REGION_READER_H_
#define GENESIS_POPULATION_FORMAT_GENOME_REGION_READER_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 Lucas Czech
 
    This program 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.
 
    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/population/genome_locus_set.hpp"
#include "genesis/population/genome_region.hpp"
#include "genesis/population/genome_region_list.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/io/input_stream.hpp"
 
#include <cstdint>
#include <functional>
#include <string>
#include <utility>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Genome Region Reader
// =================================================================================================
 
class GenomeRegionReader
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    GenomeRegionReader() = default;
    ~GenomeRegionReader() = default;
 
    GenomeRegionReader( GenomeRegionReader const& ) = default;
    GenomeRegionReader( GenomeRegionReader&& )      = default;
 
    GenomeRegionReader& operator= ( GenomeRegionReader const& ) = default;
    GenomeRegionReader& operator= ( GenomeRegionReader&& )      = default;
 
    // ---------------------------------------------------------------------
    //     Reading
    // ---------------------------------------------------------------------
 
    GenomeLocusSet read_as_genome_locus_set(
        std::shared_ptr< utils::BaseInputSource > source
    ) const;
 
    GenomeRegionList read_as_genome_region_list(
        std::shared_ptr< utils::BaseInputSource > source,
        bool merge = false
    ) const;
 
    void read_as_genome_region_list(
        std::shared_ptr< utils::BaseInputSource > source,
        GenomeRegionList& target,
        bool merge = false
    ) const;
 
    // -------------------------------------------------------------------------
    //     Settings
    // -------------------------------------------------------------------------
 
    bool zero_based() const
    {
        return zero_based_;
    }
 
    GenomeRegionReader& zero_based( bool value )
    {
        zero_based_ = value;
        return *this;
    }
 
    bool end_exclusive() const
    {
        return end_exclusive_;
    }
 
    GenomeRegionReader& end_exclusive( bool value )
    {
        end_exclusive_ = value;
        return *this;
    }
 
    // -------------------------------------------------------------------------
    //     Internal Helpers
    // -------------------------------------------------------------------------
 
private:
 
    void read_(
        std::shared_ptr< utils::BaseInputSource > source,
        std::function<void( GenomeRegion const& region )> callback
    ) const;
 
    // -------------------------------------------------------------------------
    //     Member Variables
    // -------------------------------------------------------------------------
 
    bool zero_based_ = false;
    bool end_exclusive_ = false;
};
 
} // namespace population
} // namespace genesis
 
#endif // include guard