fasta_reader.hpp

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#ifndef GENESIS_SEQUENCE_FORMATS_FASTA_READER_H_
#define GENESIS_SEQUENCE_FORMATS_FASTA_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/sequence/reference_genome.hpp"
#include "genesis/sequence/sequence_dict.hpp"
#include "genesis/sequence/sequence_set.hpp"
#include "genesis/sequence/sequence.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/tools/char_lookup.hpp"
 
#include <iosfwd>
#include <memory>
#include <string>
 
namespace genesis {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace utils {
    class InputStream;
}
 
// =================================================================================================
//     Fasta Reader
// =================================================================================================
 
namespace sequence {
 
class FastaReader
{
public:
 
    // ---------------------------------------------------------------------
    //     Typedefs and Enums
    // ---------------------------------------------------------------------
 
    enum class ParsingMethod
    {
        kDefault,
 
        kPedantic
    };
 
    enum class SiteCasing
    {
        kUnchanged,
 
        kToUpper,
 
        kToLower
    };
 
    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------
 
    FastaReader();
    ~FastaReader() = default;
 
    FastaReader( FastaReader const& ) = default;
    FastaReader( FastaReader&& )      = default;
 
    FastaReader& operator= ( FastaReader const& ) = default;
    FastaReader& operator= ( FastaReader&& )      = default;
 
    // ---------------------------------------------------------------------
    //     Reading
    // ---------------------------------------------------------------------
 
    SequenceSet read( std::shared_ptr< utils::BaseInputSource > source ) const;
 
    void read( std::shared_ptr< utils::BaseInputSource > source, SequenceSet& sequence_set ) const;
 
    SequenceDict read_dict( std::shared_ptr<utils::BaseInputSource> source ) const;
 
    ReferenceGenome read_reference_genome(
        std::shared_ptr<utils::BaseInputSource> source,
        bool also_look_up_first_word = true
    ) const;
 
    // ---------------------------------------------------------------------
    //     Parsing
    // ---------------------------------------------------------------------
 
    void parse_document(
        utils::InputStream& input_stream,
        SequenceSet&        sequence_set
    ) const;
 
    bool parse_sequence(
        utils::InputStream& input_stream,
        Sequence&           sequence
    ) const;
 
    bool parse_sequence_pedantic(
        utils::InputStream& input_stream,
        Sequence&           sequence
    ) const;
 
    // ---------------------------------------------------------------------
    //     Properties
    // ---------------------------------------------------------------------
 
    FastaReader&  parsing_method( ParsingMethod value );
 
    ParsingMethod parsing_method() const;
 
    FastaReader& site_casing( SiteCasing value );
 
    SiteCasing site_casing() const;
 
    FastaReader& guess_abundances( bool value );
 
    bool guess_abundances() const;
 
    FastaReader& valid_chars( std::string const& chars );
 
    std::string  valid_chars() const;
 
    utils::CharLookup<bool>& valid_char_lookup();
 
    // ---------------------------------------------------------------------
    //     Helper Functions
    // ---------------------------------------------------------------------
 
private:
 
    template<class R, typename... A>
    void parse_document_( utils::InputStream& input_stream, R& result, A... args ) const
    {
        Sequence seq;
        if( parsing_method_ == ParsingMethod::kDefault ) {
            while( parse_sequence( input_stream, seq ) ) {
                result.add( std::move(seq), args... );
            }
        } else if( parsing_method_ == ParsingMethod::kPedantic ) {
            while( parse_sequence_pedantic( input_stream, seq ) ) {
                result.add( std::move(seq), args... );
            }
        } else {
            // There are no other methods currently implemented.
            assert( false );
        }
    }
 
    // ---------------------------------------------------------------------
    //     Members
    // ---------------------------------------------------------------------
 
private:
 
    ParsingMethod           parsing_method_ = ParsingMethod::kDefault;
 
    SiteCasing              site_casing_      = SiteCasing::kUnchanged;
    bool                    guess_abundances_ = false;
    bool                    use_validation_   = false;
    utils::CharLookup<bool> lookup_;
 
    // Internal reading buffer
    mutable std::string buffer_;
};
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard