tree/function/functions.hpp

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#ifndef GENESIS_TREE_FUNCTION_FUNCTIONS_H_
#define GENESIS_TREE_FUNCTION_FUNCTIONS_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/utils/containers/matrix.hpp"
 
#include <cstddef> // size_t
#include <vector>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
class Tree;
class TreeNode;
class TreeEdge;
class TreeLink;
 
// =================================================================================================
//     Node Properties
// =================================================================================================
 
bool is_leaf( TreeLink const& link );
 
bool is_leaf( TreeNode const& node );
 
bool is_leaf( TreeEdge const& edge );
 
bool is_inner( TreeLink const& link );
 
bool is_inner( TreeNode const& node );
 
bool is_inner( TreeEdge const& edge );
 
bool is_root( TreeLink const& link );
 
bool is_root( TreeNode const& node );
 
size_t degree( TreeLink const& link );
 
size_t degree( TreeNode const& node );
 
// =================================================================================================
//     Node Count Properties
// =================================================================================================
 
// TODO add other interesting member functions: http://en.wikipedia.org/wiki/Tree_%28data_structure%29
 
size_t max_degree( Tree const& tree );
 
bool is_bifurcating( Tree const& tree, bool loose = false );
 
bool is_binary( Tree const& tree, bool loose = false );
 
bool is_rooted( Tree const& tree );
 
size_t leaf_node_count(  Tree const& tree );
 
size_t inner_node_count( Tree const& tree );
 
size_t node_count( Tree const& tree );
 
size_t leaf_edge_count(  Tree const& tree );
 
size_t inner_edge_count( Tree const& tree );
 
size_t edge_count( Tree const& tree );
 
std::vector<size_t> inner_edge_indices( Tree const& tree );
 
std::vector<size_t> leaf_edge_indices( Tree const& tree );
 
std::vector<size_t> inner_node_indices( Tree const& tree );
 
std::vector<size_t> leaf_node_indices( Tree const& tree );
 
// =================================================================================================
//     Tree Sides
// =================================================================================================
 
utils::Matrix<signed char> edge_sides( Tree const& tree );
 
utils::Matrix<signed char> node_root_direction_matrix( Tree const& tree );
 
// TODO the naming convention of the above two functions is really off!
 
// =================================================================================================
//     Subtrees
// =================================================================================================
 
size_t subtree_size( Tree const& tree, TreeLink const& link );
 
std::vector<size_t> subtree_sizes( Tree const& tree, TreeNode const& node );
 
std::vector<size_t> subtree_sizes( Tree const& tree );
 
size_t subtree_max_path_height( Tree const& tree, TreeLink const& link );
 
std::vector<size_t> subtree_max_path_heights( Tree const& tree, TreeNode const& node );
std::vector<size_t> subtree_max_path_heights( Tree const& tree );
 
utils::Matrix<signed char> sign_matrix( Tree const& tree, bool compressed = false );
 
// =================================================================================================
//     Misc
// =================================================================================================
 
std::vector< TreeLink const* > path_to_root( TreeNode const& node );
 
TreeNode const& lowest_common_ancestor( TreeNode const& node_a, TreeNode const& node_b );
 
TreeNode&       lowest_common_ancestor( TreeNode& node_a,       TreeNode& node_b );
 
utils::Matrix<size_t> lowest_common_ancestors( Tree const& tree );
 
} // namespace tree
} // namespace genesis
 
#endif // include guard