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 "genesis/utils/io/input_source.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 read( std::shared_ptr<utils::BaseInputSource> source, Taxonomy& target ) const;
 
    Taxonomy read( std::shared_ptr<utils::BaseInputSource> source ) 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