utils/formats/nexus/writer.cpp

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/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 Lucas Czech
 
    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/formats/nexus/writer.hpp"
 
#include "genesis/utils/core/fs.hpp"
#include "genesis/utils/formats/nexus/document.hpp"
#include "genesis/utils/io/output_stream.hpp"
 
#include <stdexcept>
#include <fstream>
#include <ostream>
#include <sstream>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Nexus Writer
// =================================================================================================
 
void NexusWriter::write( NexusDocument const& document, std::shared_ptr<utils::BaseOutputTarget> target ) const
{
    auto& os = target->ostream();
    os << "#NEXUS\n";
 
    for(auto& block : document) {
        os << "\nBEGIN " << block->block_name() << ";\n";
        os << *block;
        os << "END;\n";
    }
}
 
std::string NexusWriter::to_string( NexusDocument const& document ) const
{
    std::stringstream sstr;
    write( document, utils::to_stream( sstr ));
    return sstr.str();
}
 
} // namespace utils
} // namespace genesis