fastx_output_stream.hpp

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#ifndef GENESIS_SEQUENCE_FORMATS_FASTX_OUTPUT_STREAM_H_
#define GENESIS_SEQUENCE_FORMATS_FASTX_OUTPUT_STREAM_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 <lucas.czech@sund.ku.dk>
    University of Copenhagen, Globe Institute, Section for GeoGenetics
    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark
*/
 
#include "genesis/sequence/sequence.hpp"
#include "genesis/sequence/formats/fasta_writer.hpp"
#include "genesis/sequence/formats/fastq_writer.hpp"
 
#include "genesis/utils/io/output_target.hpp"
 
#include <iterator>
#include <iostream>
 
#if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
 
    #include <string_view>
 
#endif
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forward declarations and typedefs
// =================================================================================================
 
template<class Writer>
class FastxOutputStream;
 
using FastaOutputStream = FastxOutputStream<FastaWriter>;
using FastqOutputStream = FastxOutputStream<FastqWriter>;
 
// =================================================================================================
//     Fasta and Fastq Output Stream
// =================================================================================================
 
template<class Writer>
class FastxOutputStream
{
public:
 
    // -------------------------------------------------------------------------
    //     Member Types
    // -------------------------------------------------------------------------
 
    using self_type = FastxOutputStream;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    FastxOutputStream() = delete;
 
    explicit FastxOutputStream(
        std::shared_ptr<utils::BaseOutputTarget> target
    )
        : target_( target )
        , writer_()
    {}
 
    FastxOutputStream(
        std::shared_ptr<utils::BaseOutputTarget> target,
        Writer const& writer
    )
        : target_( target )
        , writer_( writer )
    {}
 
    ~FastxOutputStream() = default;
 
    FastxOutputStream( self_type const& ) = default;
    FastxOutputStream( self_type&& )      = default;
 
    self_type& operator= ( self_type const& ) = default;
    self_type& operator= ( self_type&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    self_type const& operator<< ( Sequence const& sequence ) const
    {
        writer_.write( sequence, target_ );
        return *this;
    }
 
    self_type const& write( Sequence const& sequence ) const
    {
        writer_.write( sequence, target_ );
        return *this;
    }
 
    template<
        typename T = Writer,
        typename std::enable_if< std::is_same<T, FastqWriter>::value >::type* = nullptr
    >
    self_type const& write( Sequence const& sequence, std::string const& quality_string ) const
    {
        writer_.write( sequence, quality_string, target_ );
        return *this;
    }
 
    #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
 
    template<
        typename T = Writer,
        typename std::enable_if< std::is_same<T, FastqWriter>::value >::type* = nullptr
    >
    self_type const& write(
        std::string_view const& label,
        std::string_view const& sites,
        std::string_view const& quality
    ) const {
        writer_.write( label, sites, quality, target_ );
        return *this;
    }
 
    #endif
 
    // -------------------------------------------------------------------------
    //     Settings
    // -------------------------------------------------------------------------
 
    std::shared_ptr<utils::BaseOutputTarget> output_target() const
    {
        return target_;
    }
 
    Writer& writer()
    {
        return writer_;
    }
 
    Writer const& writer() const
    {
        return writer_;
    }
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    std::shared_ptr<utils::BaseOutputTarget> target_;
    Writer writer_;
};
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard