char_vector.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_char_vector_h_
#define _biomcmc_char_vector_h_

#include "lowlevel.h"
#include "prob_distribution.h"

typedef struct char_vector_struct* char_vector;

struct char_vector_struct
{
  char **string;  
  int nstrings;   
  size_t *alloc;  
  size_t *nchars; 
  int ref_counter;
  int next_avail; 
};

char_vector new_char_vector (int nstrings);
char_vector new_char_vector_big (int nstrings);
char_vector new_char_vector_from_valid_strings_char_vector (char_vector vec, int *valid, int n_valid); 
char_vector new_char_vector_fixed_length (int nstrings, int nchars);

void del_char_vector (char_vector vec);

void char_vector_link_string_at_position (char_vector vec, const char *string, int position);

void char_vector_add_string_at_position (char_vector vec, const char *string, int position);

void char_vector_add_string (char_vector vec, const char *string);

void char_vector_append_string_at_position (char_vector vec, const char *string, int position);
void char_vector_append_string (char_vector vec, const char *string);

void char_vector_append_string_big_at_position (char_vector vec, const char *string, int position);
void char_vector_append_string_big (char_vector vec, const char *string);
void char_vector_finalise_big (char_vector vec);

void char_vector_expand_nstrings (char_vector vec, int new_size);

void char_vector_reorder_strings_from_external_order (char_vector vec, int *order);

int char_vector_remove_empty_strings (char_vector vec);
int char_vector_remove_duplicate_strings (char_vector vec);
void char_vector_reduce_to_valid_strings (char_vector vec, int *valid, int n_valid);

void char_vector_reorder_by_size_or_lexicographically (char_vector vec, bool lexico, int *order);
bool char_vector_link_address_if_identical (char_vector *v1, char_vector *v2);
void index_species_gene_char_vectors (char_vector species, char_vector gene, int *sp_idx_in_gene, int *order_external);
void update_species_count_from_gene_char_vector (char_vector species, char_vector gene, int *sp_count);

#endif