tree/formats/phyloxml/writer.hpp

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#ifndef GENESIS_TREE_FORMATS_PHYLOXML_WRITER_H_
#define GENESIS_TREE_FORMATS_PHYLOXML_WRITER_H_
 
/*
    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/utils/io/output_target.hpp"
 
#include <functional>
#include <string>
#include <vector>
 
namespace genesis {
 
// =================================================================================================
//     Forward declarations
// =================================================================================================
 
namespace utils {
    class XmlDocument;
    class XmlElement;
}
 
namespace tree {
 
class  Tree;
class  TreeNode;
class  TreeEdge;
class  TreeSet;
 
// =================================================================================================
//     Phyloxml Writer
// =================================================================================================
 
class PhyloxmlWriter
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    using prepare_writing_function = std::function< void(
        Tree const& tree, utils::XmlDocument& xml
    ) >;
 
    using finish_writing_function = std::function< void(
        Tree const& tree, utils::XmlDocument& xml
    ) >;
 
    using node_to_element_function = std::function< void(
        TreeNode const& node, utils::XmlElement&  element
    ) >;
 
    using edge_to_element_function = std::function< void(
        TreeEdge const& edge, utils::XmlElement&  element
    ) >;
 
    // -------------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------------
 
    PhyloxmlWriter() = default;
    virtual ~PhyloxmlWriter() = default;
 
    PhyloxmlWriter(PhyloxmlWriter const&) = default;
    PhyloxmlWriter(PhyloxmlWriter&&)      = default;
 
    PhyloxmlWriter& operator= (PhyloxmlWriter const&) = default;
    PhyloxmlWriter& operator= (PhyloxmlWriter&&)      = default;
 
    // ---------------------------------------------------------------------
    //     Writing
    // ---------------------------------------------------------------------
 
    void write( Tree const& tree, std::shared_ptr<utils::BaseOutputTarget> target ) const;
 
    void to_document ( Tree const& tree, utils::XmlDocument& xml) const;
 
    // -------------------------------------------------------------------------
    //     Plugin Functions
    // -------------------------------------------------------------------------
 
    std::vector<prepare_writing_function> prepare_writing_plugins;
 
    std::vector<finish_writing_function>  finish_writing_plugins;
 
    std::vector<node_to_element_function> node_to_element_plugins;
 
    std::vector<edge_to_element_function> edge_to_element_plugins;
 
};
 
} // namespace tree
} // namespace genesis
 
#endif // include guard