taxonomy_reader.hpp

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#ifndef GENESIS_TAXONOMY_FORMATS_TAXONOMY_READER_H_
#define GENESIS_TAXONOMY_FORMATS_TAXONOMY_READER_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2018 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/taxonomy/formats/taxopath_parser.hpp"
#include "genesis/utils/formats/csv/reader.hpp"

#include <string>

namespace genesis {

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

namespace utils {

    class InputStream;

} // namespace utils

namespace taxonomy {

    class Taxonomy;

// =================================================================================================
//     Taxonomy Reader
// =================================================================================================

class TaxonomyReader
{
public:

    // ---------------------------------------------------------------------
    //     Enums and Structs
    // ---------------------------------------------------------------------

    struct Line
    {
        std::string name;
        std::string rank;
        std::string id;
    };

    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------

    TaxonomyReader();
    ~TaxonomyReader() = default;

    TaxonomyReader( TaxonomyReader const& ) = default;
    TaxonomyReader( TaxonomyReader&& )      = default;

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

    // ---------------------------------------------------------------------
    //     Reading
    // ---------------------------------------------------------------------

    void from_stream( std::istream&      is, Taxonomy& tax ) const;

    void from_file  ( std::string const& fn, Taxonomy& tax ) const;

    void from_string( std::string const& is, Taxonomy& tax ) const;

    Taxonomy from_stream( std::istream&      is ) const;

    Taxonomy from_file  ( std::string const& fn ) const;

    Taxonomy from_string( std::string const& is ) const;

    // ---------------------------------------------------------------------
    //     Parsing
    // ---------------------------------------------------------------------

    void parse_document(
        utils::InputStream& it,
        Taxonomy&           tax
    ) const;

    Line parse_line(
        utils::InputStream& it
    ) const;

    // ---------------------------------------------------------------------
    //     Properties
    // ---------------------------------------------------------------------

    utils::CsvReader&  csv_reader();

    TaxopathParser& taxopath_parser();

    TaxonomyReader& name_field_position( int value );

    int             name_field_position() const;

    TaxonomyReader& rank_field_position( int value );

    int             rank_field_position() const;

    TaxonomyReader& id_field_position( int value );

    int             id_field_position() const;

    TaxonomyReader& expect_strict_order( bool value );

    bool            expect_strict_order() const;

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

private:

    utils::CsvReader  csv_reader_;
    TaxopathParser taxopath_parser_;

    int  name_field_position_ =  0;
    int  rank_field_position_ = -1;
    int  id_field_position_   = -1;
    bool expect_strict_order_ = false;

};

} // namespace taxonomy
} // namespace genesis

#endif // include guard