phyloxml_writer.hpp

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#ifndef GENESIS_TREE_COMMON_TREE_PHYLOXML_WRITER_H_
#define GENESIS_TREE_COMMON_TREE_PHYLOXML_WRITER_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/tree/common_tree/tree.hpp"
#include "genesis/tree/formats/phyloxml/writer.hpp"
#include "genesis/utils/formats/xml/document.hpp"
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Common Tree Phyloxml Writer Plugin
// =================================================================================================
 
class CommonTreePhyloxmlWriterPlugin
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------------
 
    CommonTreePhyloxmlWriterPlugin() = default;
    virtual ~CommonTreePhyloxmlWriterPlugin() = default;
 
    CommonTreePhyloxmlWriterPlugin(CommonTreePhyloxmlWriterPlugin const&) = default;
    CommonTreePhyloxmlWriterPlugin(CommonTreePhyloxmlWriterPlugin&&)      = default;
 
    CommonTreePhyloxmlWriterPlugin& operator= (CommonTreePhyloxmlWriterPlugin const&) = default;
    CommonTreePhyloxmlWriterPlugin& operator= (CommonTreePhyloxmlWriterPlugin&&)      = default;
 
    // -------------------------------------------------------------------------
    //     Plugin Functions
    // -------------------------------------------------------------------------
 
    void node_to_element( TreeNode const& node, utils::XmlElement& element ) const
    {
        set_name_(element, node.data<CommonNodeData>().name);
    }
 
    void edge_to_element( TreeEdge const& edge, utils::XmlElement& element ) const
    {
        set_branch_length_(element, edge.data<CommonEdgeData>().branch_length);
    }
 
    void register_with( PhyloxmlWriter& writer ) const
    {
        writer.node_to_element_plugins.push_back(
            [&]( TreeNode const& node, utils::XmlElement& element ) {
                node_to_element( node, element );
            }
        );
        writer.edge_to_element_plugins.push_back(
            [&]( TreeEdge const& edge, utils::XmlElement& element ) {
                edge_to_element( edge, element );
            }
        );
    }
 
    // -------------------------------------------------------------------------
    //     Member Functions
    // -------------------------------------------------------------------------
 
private:
 
    void set_name_( utils::XmlElement& element, const std::string& name ) const
    {
        // TODO do not create new element if there is already one!
        auto name_e = utils::make_unique< utils::XmlElement >( "name" );
        name_e->append_markup(name);
        element.content.push_back(std::move(name_e));
    }
 
    void set_branch_length_( utils::XmlElement& element, double length ) const
    {
        // TODO do not create new element if there is already one!
        auto bl_e = utils::make_unique< utils::XmlElement >( "branch_length" );
        bl_e->append_markup(std::to_string(length));
        element.content.push_back(std::move(bl_e));
    }
 
};
 
// =================================================================================================
//     Common Tree Phyloxml Writer
// =================================================================================================
 
class CommonTreePhyloxmlWriter
    : public PhyloxmlWriter
    , public CommonTreePhyloxmlWriterPlugin
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------------
 
    CommonTreePhyloxmlWriter()
    {
        register_with( *this );
    }
};
 
} // namespace tree
} // namespace genesis
 
#endif // include guard