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) 2014-2019 Lucas Czech and HITS gGmbH

    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/utils/tools/char_lookup.hpp"
#include "genesis/utils/io/input_source.hpp"

#include <iosfwd>
#include <memory>
#include <string>

namespace genesis {

// =================================================================================================
//     Forward Declarations
// =================================================================================================

namespace utils {
    class InputStream;
}

namespace sequence {
    class SequenceSet;
    class Sequence;
}

// =================================================================================================
//     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;

    // ---------------------------------------------------------------------
    //     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();

    // ---------------------------------------------------------------------
    //     Members
    // ---------------------------------------------------------------------

private:

    ParsingMethod           parsing_method_ = ParsingMethod::kDefault;

    SiteCasing              site_casing_      = SiteCasing::kToUpper;
    bool                    guess_abundances_ = false;
    bool                    use_validation_   = false;
    utils::CharLookup<bool> lookup_;

};

} // namespace sequence
} // namespace genesis

#endif // include guard