taxonomy_writer.cpp

Go to the documentation of this file.

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 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/taxonomy_writer.hpp"
 
#include "genesis/taxonomy/iterator/preorder.hpp"
#include "genesis/taxonomy/taxon.hpp"
#include "genesis/taxonomy/taxonomy.hpp"
#include "genesis/taxonomy/taxonomy.hpp"
#include "genesis/taxonomy/taxopath.hpp"
 
#include <iostream>
 
namespace genesis {
namespace taxonomy {
 
// =================================================================================================
//     Writing
// =================================================================================================
 
void TaxonomyWriter::write( Taxonomy const& tax, std::shared_ptr<utils::BaseOutputTarget> target ) const
{
    auto& os = target->ostream();
    for( auto const& tit : preorder( tax )) {
        os << tax_gen_.to_string( tit.taxon() );
 
        if( write_ids_ ) {
            os << "\t" << tit.taxon().id();
        }
        if( write_ranks_ ) {
            os << "\t" << tit.taxon().rank();
        }
 
        os << "\n";
    }
}
 
} // namespace taxonomy
} // namespace genesis