ranks.cpp

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/*
    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/taxonomy/functions/ranks.hpp"

#include "genesis/utils/text/string.hpp"

#include <unordered_map>

namespace genesis {
namespace taxonomy {

// =================================================================================================
//     Ranks
// =================================================================================================

static const std::unordered_map<char, std::string> rank_abbreviations = {
    { 'd', "Domain" },
    { 'k', "Kingdom" },
    { 'p', "Phylum" },
    { 'c', "Class" },
    { 'o', "Order" },
    { 'f', "Family" },
    { 'g', "Genus" },
    { 's', "Species" }
};

std::string rank_from_abbreviation( char r )
{
    char const c = static_cast<char>( std::tolower( static_cast<unsigned char>( r )));
    if( rank_abbreviations.count( c ) > 0 ) {
        return rank_abbreviations.at( c );
    } else {
        return "";
    }
}

std::string rank_to_abbreviation( std::string const& rank )
{
    auto r = utils::to_lower( rank );
    for( auto const& p : rank_abbreviations ) {
        if( utils::to_lower( p.second ) == r ) {
            return std::string( 1, p.first );
        }
    }
    return "";
}

std::pair< std::string, std::string > resolve_rank_abbreviation( std::string const& entry )
{
    std::string rank = "";
    std::string name = entry;

    // Check whether the name is of the form "X_something".
    // If so, use it to split off the rank name and resolve the abbreviation.
    if( entry.size() >= 2 && entry[1] == '_' ) {
        rank = rank_from_abbreviation( entry[0] );
    }

    // If the previous step was successful and yielded a valid rank name,
    // shorten the actual name accordingly.
    if( rank != "" ) {
        size_t pos = entry.find_first_not_of( "_", 1 );
        name = entry.substr( pos );
    }

    return { rank, name };
}

} // namespace taxonomy
} // namespace genesis