fastq_output_iterator.hpp

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#ifndef GENESIS_SEQUENCE_FORMATS_FASTQ_OUTPUT_ITERATOR_H_
#define GENESIS_SEQUENCE_FORMATS_FASTQ_OUTPUT_ITERATOR_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 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@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/

#include "genesis/sequence/sequence.hpp"
#include "genesis/sequence/formats/fastq_writer.hpp"

#include "genesis/utils/io/output_target.hpp"

#include <iterator>
#include <iostream>

namespace genesis {
namespace sequence {

// =================================================================================================
//     Fastq Output Iterator
// =================================================================================================

class FastqOutputIterator
{
public:

    // -------------------------------------------------------------------------
    //     Member Types
    // -------------------------------------------------------------------------

    using self_type = FastqOutputIterator;

    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------

    FastqOutputIterator() = delete;

    explicit FastqOutputIterator( std::shared_ptr<utils::BaseOutputTarget> target )
        : target_( target )
        , writer_()
    {}

    FastqOutputIterator( std::shared_ptr<utils::BaseOutputTarget> target, FastqWriter const& writer )
        : target_( target )
        , writer_( writer )
    {}

    ~FastqOutputIterator() = default;

    FastqOutputIterator( self_type const& ) = default;
    FastqOutputIterator( self_type&& )      = default;

    self_type& operator= ( self_type const& ) = default;
    self_type& operator= ( self_type&& )      = default;

    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------

    self_type& operator<< ( Sequence const& seq )
    {
        writer_.write( seq, target_ );
        return *this;
    }

    FastqWriter& writer()
    {
        return writer_;
    }

    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------

private:

    std::shared_ptr<utils::BaseOutputTarget> target_;
    FastqWriter writer_;
};

} // namespace sequence
} // namespace genesis

#endif // include guard