phyloxml/color_writer_plugin.hpp

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#ifndef GENESIS_TREE_FORMATS_PHYLOXML_COLOR_WRITER_PLUGIN_H_
#define GENESIS_TREE_FORMATS_PHYLOXML_COLOR_WRITER_PLUGIN_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 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/tree/formats/color_writer_plugin.hpp"
#include "genesis/tree/formats/phyloxml/writer.hpp"
#include "genesis/tree/tree.hpp"
#include "genesis/utils/formats/xml/document.hpp"
 
#include <cassert>
#include <stdexcept>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Phyloxml Color Writer Plugin
// =================================================================================================
 
class PhyloxmlColorWriterPlugin : public ColorWriterPlugin
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------------
 
    PhyloxmlColorWriterPlugin() = default;
    virtual ~PhyloxmlColorWriterPlugin() override = default;
 
    PhyloxmlColorWriterPlugin(PhyloxmlColorWriterPlugin const&) = default;
    PhyloxmlColorWriterPlugin(PhyloxmlColorWriterPlugin&&)      = default;
 
    PhyloxmlColorWriterPlugin& operator= (PhyloxmlColorWriterPlugin const&) = default;
    PhyloxmlColorWriterPlugin& operator= (PhyloxmlColorWriterPlugin&&)      = default;
 
    // -------------------------------------------------------------------------
    //      Plugin Functions
    // -------------------------------------------------------------------------
 
    void prepare_writing( Tree const& tree, utils::XmlDocument& xml ) const
    {
        (void) xml;
 
        if (!ColorWriterPlugin::enable_color()) {
            return;
        }
 
        // If an edge color vector was set, it needs to match the tree's edge count.
        if (
            ColorWriterPlugin::edge_colors().size() > 0 &&
            ColorWriterPlugin::edge_colors().size() != tree.edge_count()
        ) {
            throw std::length_error(
                "Color vector does not have as many elements as the tree has edges."
            );
        }
    }
 
    void edge_to_element( TreeEdge const& edge, utils::XmlElement& element ) const
    {
        if (!ColorWriterPlugin::enable_color()) {
            return;
        }
 
        // If an edge color vector was set, use it.
        if (ColorWriterPlugin::edge_colors().size() > 0) {
            assert( edge.index() <= ColorWriterPlugin::edge_colors().size() );
            set_color_(element, ColorWriterPlugin::edge_colors()[edge.index()]);
        }
    }
 
    void register_with( PhyloxmlWriter& writer ) const
    {
        writer.prepare_writing_plugins.push_back(
            [&]( Tree const& tree, utils::XmlDocument& xml ) {
                prepare_writing( tree, xml );
            }
        );
        writer.edge_to_element_plugins.push_back(
            [&]( TreeEdge const& edge, utils::XmlElement& element ) {
                edge_to_element( edge, element );
            }
        );
    }
 
    // -------------------------------------------------------------------------
    //     Member Functions
    // -------------------------------------------------------------------------
 
private:
 
    void set_color_( utils::XmlElement& element, unsigned char r, unsigned char g, unsigned char b ) const
    {
        if(
            ColorWriterPlugin::use_ignored_color() &&
            utils::Color(r, g, b) == ColorWriterPlugin::ignored_color()
        ) {
            return;
        }
 
        // TODO do not create new element if there is already one!
        auto re = utils::make_unique< utils::XmlElement >("red");
        re->append_markup(std::to_string(r));
 
        auto ge = utils::make_unique< utils::XmlElement >("green");
        ge->append_markup(std::to_string(g));
 
        auto be = utils::make_unique< utils::XmlElement >("blue");
        be->append_markup(std::to_string(b));
 
        auto color = utils::make_unique< utils::XmlElement >("color");
        color->content.push_back(std::move(re));
        color->content.push_back(std::move(ge));
        color->content.push_back(std::move(be));
 
        element.content.push_back(std::move(color));
    }
 
    void set_color_( utils::XmlElement& element, utils::Color color ) const
    {
        set_color_( element, color.r_byte(), color.g_byte(), color.b_byte() );
    }
 
};
 
} // namespace tree
} // namespace genesis
 
#endif // include guard