alignment.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_alignment_h_
#define _biomcmc_alignment_h_

#include "distance_matrix.h"
#include "nexus_common.h"

typedef struct alignment_struct* alignment;

struct alignment_struct
{
  int ntax, nchar, npat;   
  char_vector character;   
  char_vector taxlabel;    
  char_vector taxshort;    
  hashtable taxlabel_hash; 
  int n_charset;                    
  int *charset_start, *charset_end; 
  bool is_aligned;         
  int *site_pattern;       
  int *pattern_freq;       
  char *filename;          
  int ref_counter;
};

alignment read_alignment_from_file (char *seqfilename);
alignment read_fasta_alignment_from_file (char *seqfilename);
alignment read_nexus_alignment_from_file (char *seqfilename);
void print_alignment_in_fasta_format (alignment align, FILE *stream);
void del_alignment (alignment align);

distance_matrix new_distance_matrix_from_valid_matrix_elems (distance_matrix original, int *valid, int n_valid);
distance_matrix new_distance_matrix_from_alignment (alignment align);

void store_likelihood_info_at_leaf (double **l, char *align, int n_pat, int n_state);

#endif