phylo_factor_colors.hpp

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#ifndef GENESIS_TREE_MASS_TREE_PHYLO_FACTOR_COLORS_H_
#define GENESIS_TREE_MASS_TREE_PHYLO_FACTOR_COLORS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2023 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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/tree/mass_tree/phylo_factor.hpp"
#include "genesis/utils/color/color.hpp"
#include "genesis/utils/color/list_qualitative.hpp"
 
#include <functional>
#include <limits>
#include <unordered_set>
#include <vector>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
class Subtree;
class Tree;
using MassTree = Tree;
 
// =================================================================================================
//     Helper Functions
// =================================================================================================
 
std::vector<size_t> phylo_factor_edge_indices(
    std::vector<PhyloFactor> const& factors,
    size_t max_factor = std::numeric_limits<std::size_t>::max()
);
 
// =================================================================================================
//     Single Factor Coloring
// =================================================================================================
 
struct PhyloFactorSingleColors
{
    utils::Color factor_edge = utils::Color( 0.0, 0.0, 0.0 );
 
    utils::Color primary_edges = utils::Color( 0.529411765, 0.439215686, 0.670588235 );
 
    utils::Color secondary_edges = utils::Color( 0.352941176, 0.682352941, 0.380392157 );
 
    utils::Color previous_factors = utils::Color( 0.0, 0.0, 0.0 );
 
    utils::Color neutral_edges = utils::Color( 0.8, 0.8, 0.8 );
};
 
std::vector<utils::Color> phylo_factor_single_factor_colors(
    Tree const& tree,
    std::vector<PhyloFactor> const& factors,
    size_t factor_index,
    PhyloFactorSingleColors colors = {}
);
 
// =================================================================================================
//     Factor Clade Coloring
// =================================================================================================
 
struct PhyloFactorCladeColors
{
    utils::Color factor_edges = utils::Color( 0.0, 0.0, 0.0 );
 
    utils::Color base_edges = utils::Color( 0.8, 0.8, 0.8 );
 
    std::vector<utils::Color> clade_colors = utils::color_list_set1();
};
 
std::vector<utils::Color> phylo_factor_clade_colors(
    Tree const& tree,
    std::vector<PhyloFactor> const& factors,
    size_t num_factors = 0,
    PhyloFactorCladeColors colors = {}
);
 
} // namespace tree
} // namespace genesis
 
#endif // include guard