topology_space.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_topology_space_h_
#define _biomcmc_topology_space_h_

#include "newick_space.h" 

typedef struct topology_space_struct* topology_space;

struct topology_space_struct 
{
  int ntrees, ndistinct; 
  topology *tree, *distinct; 
  double *freq;              
  char_vector taxlabel;      
  hashtable taxlabel_hash;   
  bool is_rooted;            
  char *filename;            
};

void add_string_with_size_to_topology_space (topology_space *tsp_address, char *long_string, size_t string_size, bool use_root_location);
void add_topology_to_topology_space_if_distinct (topology topol, topology_space tsp, double tree_weight, bool use_root_location);

topology_space read_topology_space_from_file (char *seqfilename, hashtable external_taxhash, bool use_root_location);
topology_space read_topology_space_from_file_with_burnin_thin (char *seqfilename, hashtable external_taxhash, int burnin, int thin, bool use_root_location);
void merge_topology_spaces (topology_space ts1, topology_space ts2, double weight_ts1, bool use_root_location);
void  sort_topology_space_by_frequency(topology_space tsp, double *external_freqs) ; // INCOMPLETE

void save_topology_space_to_trprobs_file (topology_space tsp, char *filename, double credible);
int estimate_treesize_from_file (char *seqfilename);

topology_space new_topology_space (void);
void del_topology_space (topology_space tsp);

#endif