parsimony.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_parsimony_
#define _biomcmc_parsimony_

#include "topology_distance.h"

typedef struct binary_parsimony_datamatrix_struct* binary_parsimony_datamatrix; 
typedef struct binary_parsimony_struct* binary_parsimony;

struct binary_parsimony_datamatrix_struct {
  int ntax, nchar, i;  
  bool **s;            
  int *freq, freq_sum; 
  int *occupancy;      
  uint32_t *col_hash;  
  int ref_counter;     
};

struct binary_parsimony_struct {
  int *score;      
  binary_parsimony_datamatrix external, internal; 
  double costs[4];
  int ref_counter; 
};

binary_parsimony_datamatrix new_binary_parsimony_datamatrix (int n_sequences);
binary_parsimony_datamatrix new_binary_parsimony_datamatrix_fixed_length (int n_sequences, int n_sites);
void del_binary_parsimony_datamatrix (binary_parsimony_datamatrix mrp);
binary_parsimony new_binary_parsimony (int n_sequences);
binary_parsimony new_binary_parsimony_fixed_length (int n_sequences, int n_sites);
void del_binary_parsimony (binary_parsimony pars);
void update_binary_parsimony_from_topology (binary_parsimony pars, topology t, int *map, int n_species);
int binary_parsimony_score_of_topology (binary_parsimony pars, topology t);
void pairwise_distances_from_binary_parsimony_datamatrix (binary_parsimony_datamatrix mrp, double **dist, int n_dist);

#endif