read_newick_trees.h

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/* 
 * This file is part of biomcmc-lib, a low-level library for phylogenomic analysis.
 * Copyright (C) 2019-today  Leonardo de Oliveira Martins [ leomrtns at gmail.com;  http://www.leomartins.org ]
 *
 * biomcmc 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 2 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 (file "COPYING" or http://www.gnu.org/copyleft/gpl.html).
 */

#ifndef _biomcmc_read_newick_trees_h
#define _biomcmc_read_newick_trees_h

#include "topology_distance.h" 
#include "nexus_common.h" 

typedef struct newick_node_struct* newick_node;
typedef struct newick_tree_struct* newick_tree; 
struct newick_node_struct
{
  newick_node up, right, left; 
  int id;               
  double branch_length; 
  char *taxlabel;       
};

struct newick_tree_struct
{
  newick_node *nodelist; 
  newick_node *leaflist; 
  newick_node root;      
  int nnodes, nleaves;   
};

newick_tree new_newick_tree (int nleaves);
void del_newick_tree (newick_tree T);
void copy_topology_from_newick_tree (topology tree, newick_tree nwk_tree, bool create_tree_taxlabel);
newick_tree new_newick_tree_from_string (char *external_string);
newick_node subtree_newick_tree (newick_tree tree, char *lsptr, char *rsptr, int *node_id, newick_node up);
int number_of_leaves_in_newick (char **string, int *number_branches);

#endif