tree/function/manipulation.hpp

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#ifndef GENESIS_TREE_FUNCTION_MANIPULATION_H_
#define GENESIS_TREE_FUNCTION_MANIPULATION_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 <cstddef> // size_t
#include <functional>
 
#include "genesis/tree/tree.hpp"
#include "genesis/tree/common_tree/tree.hpp"
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
class Tree;
class TreeNode;
class TreeEdge;
class TreeLink;
class Subtree;
 
// =================================================================================================
//     Minimal Tree
// =================================================================================================
 
Tree minimal_tree_topology();
 
template< class NodeDataType = CommonNodeData, class EdgeDataType = CommonEdgeData >
Tree minimal_tree()
{
    auto tree = minimal_tree_topology();
    for( size_t i = 0; i < tree.node_count(); ++i ) {
        tree.node_at(i).reset_data( NodeDataType::create() );
    }
    for( size_t i = 0; i < tree.edge_count(); ++i ) {
        tree.edge_at(i).reset_data( EdgeDataType::create() );
    }
    return tree;
}
 
// =================================================================================================
//     Add Nodes
// =================================================================================================
 
TreeNode& add_new_node( Tree& tree, TreeNode& target_node );
 
TreeNode& add_new_node(
    Tree& tree,
    TreeEdge& target_edge,
    std::function<void( TreeEdge& target_edge, TreeEdge& new_edge )> adjust_edges = {}
);
 
TreeNode& add_new_leaf_node(
    Tree& tree,
    TreeEdge& target_edge,
    std::function<void( TreeEdge& target_edge, TreeEdge& new_edge )> adjust_edges = {}
);
 
// =================================================================================================
//     Delete Nodes
// =================================================================================================
 
void delete_node( Tree& tree, TreeNode& target_node );
 
void delete_leaf_node( Tree& tree, TreeNode& target_node );
 
void delete_linear_node(
    Tree& tree,
    TreeNode& target_node,
    std::function<void( TreeEdge& remaining_edge, TreeEdge& deleted_edge )> adjust_edges = {}
);
 
void delete_subtree( Tree& tree, Subtree const& subtree );
 
void delete_edge(
    Tree& tree,
    TreeEdge& target_edge,
    std::function<void( TreeNode& remaining_node, TreeNode& deleted_node )> adjust_nodes = {}
);
 
void delete_zero_branch_length_edges( Tree& tree, bool include_leaf_edges = false );
 
// =================================================================================================
//     Rooting, Rerooting, Unrooting
// =================================================================================================
 
TreeNode& make_rooted(
    Tree& tree,
    TreeEdge& target_edge,
    std::function<void( TreeEdge& target_edge, TreeEdge& new_edge )> adjust_edges = {}
);
 
TreeNode& make_rooted(
    Tree& tree,
    std::function<void( TreeEdge& target_edge, TreeEdge& new_edge )> adjust_edges = {}
);
 
void make_unrooted(
    Tree& tree,
    std::function<void( TreeEdge& remaining_edge, TreeEdge& deleted_edge )> adjust_edges = {}
);
 
void change_rooting( Tree& tree, TreeLink& at_link );
 
void change_rooting( Tree& tree, TreeNode& at_node );
 
// =================================================================================================
//     Ladderize
// =================================================================================================
 
enum class LadderizeOrder
{
    kSmallFirst,
    kLargeFirst
};
 
void ladderize( Tree& tree, LadderizeOrder order = LadderizeOrder::kSmallFirst );
 
} // namespace tree
} // namespace genesis
 
#endif // include guard