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/**
* PLL (version 1.0.0) a software library for phylogenetic inference
* Copyright (C) 2013 Tomas Flouri and Alexandros Stamatakis
*
* Derived from
* RAxML-HPC, a program for sequential and parallel estimation of phylogenetic
* trees by Alexandros Stamatakis
*
* 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/>.
*
* For any other enquiries send an Email to Tomas Flouri
* Tomas.Flouri@h-its.org
*
* When publishing work that uses PLL please cite PLL
*
* @file newick.h
*/
#ifndef __pll_NEWICK__
#define __pll_NEWICK__
#include "stack.h"
/** @brief Intermediate structure for storing a newick tree
Holds the structure of a parsed newick tree. The number of inner nodes is stored in \a nodes
*/
typedef struct
{
int nodes; /**< @brief Total number of nodes in the tree == 2*tips - 1 for rooted and 2*tips -2 for unrooted */
int tips; /**< @brief Number of leaves (tips) in the tree */
pllStack * tree; /**< @brief Parsed tree represented as elements of a stack. Corresponds to placing the postorder traversal of a rooted tree in a pushdown store */
} pllNewickTree;
/** @brief Information describing the parsed newick tree nodes
This structure is placed in the ::pllNewickTree LIFO element pllNewickTree::tree
and described each node of the parsed tree.
@todo Rename this to something more proper
*/
typedef struct
{
int depth; /**< @brief Distance of node from root */
char * name; /**< @brief Name of the taxon represented by the node (in case it is a leaf) */
char * branch; /**< @brief Length of branch that leads to its parent */
int leaf; /**< @brief \b PLL_TRUE if the node is a leaf, otherwise \b PLL_FALSE */
int rank; /**< @brief Rank of the node, i.e. how many children it has */
} pllNewickNodeInfo;
#endif
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