fastq_input_iterator.hpp

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#ifndef GENESIS_SEQUENCE_FORMATS_FASTQ_INPUT_ITERATOR_H_
#define GENESIS_SEQUENCE_FORMATS_FASTQ_INPUT_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/formats/fastq_reader.hpp"
#include "genesis/sequence/sequence.hpp"
#include "genesis/utils/core/std.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/io/input_stream.hpp"
 
#include <cstddef>
#include <iterator>
#include <memory>
#include <sstream>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Fastq Input Iterator
// =================================================================================================
 
class FastqInputIterator
{
public:
 
    // -------------------------------------------------------------------------
    //     Member Types
    // -------------------------------------------------------------------------
 
    using self_type         = FastqInputIterator;
    using value_type        = Sequence;
    using pointer           = value_type*;
    using reference         = value_type&;
    using difference_type   = std::ptrdiff_t;
    using iterator_category = std::input_iterator_tag;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    FastqInputIterator()
        : input_stream_( nullptr )
        , sequence_()
        , reader_()
    {}
 
    explicit FastqInputIterator( std::shared_ptr<utils::BaseInputSource> source )
        : input_stream_( std::make_shared<utils::InputStream>( source ))
        , sequence_()
        , reader_()
    {
        increment();
    }
 
    FastqInputIterator( std::shared_ptr<utils::BaseInputSource> source, FastqReader const& settings )
        : input_stream_( std::make_shared<utils::InputStream>( source ))
        , sequence_()
        , reader_( settings )
    {
        increment();
    }
 
    ~FastqInputIterator() = default;
 
    FastqInputIterator( self_type const& ) = default;
    FastqInputIterator( self_type&& )      = default;
 
    self_type& operator= ( self_type const& ) = default;
    self_type& operator= ( self_type&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Comparators
    // -------------------------------------------------------------------------
 
    bool operator == ( self_type const& other ) const
    {
        return input_stream_ == other.input_stream_;
    }
 
    bool operator != ( self_type const& other ) const
    {
        return !( *this == other );
    }
 
    explicit operator bool() const
    {
        return good_;
    }
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    value_type const& operator * () const
    {
        return sequence_;
    }
 
    value_type const* operator -> () const
    {
        return &sequence_;
    }
 
    value_type const& dereference() const
    {
        return sequence_;
    }
 
    // -------------------------------------------------------------------------
    //     Iteration
    // -------------------------------------------------------------------------
 
    self_type& begin()
    {
        return *this;
    }
 
    self_type end()
    {
        return FastqInputIterator();
    }
 
    self_type& operator ++ ()
    {
        increment();
        return *this;
    }
 
    self_type operator ++(int)
    {
        auto r = *this;
        increment();
        return r;
    }
 
    void increment()
    {
        // Check whether the input stream is good (not end-of-stream) and can be read from.
        // If not, we reached its end, so we stop reading in the next iteration.
        if( ! input_stream_ || ! *input_stream_ ) {
            good_ = false;
            input_stream_ = nullptr;
            sequence_ = Sequence();
            return;
        }
 
        reader_.parse_sequence( *input_stream_, sequence_ );
    }
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    bool good_ = true;
    std::shared_ptr<utils::InputStream> input_stream_;
 
    Sequence    sequence_;
    FastqReader reader_;
};
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard