#include "types.h"
Functions | |
float | score_function (float score_pos_i_minus_1, int nb_al_pos_i, float mean_al, float epsilon, int lambda) |
Defines the score function for the position i. | |
void | destroy_main_structure (p_matt_ygraph m) |
Function used to destroy all structures allocated. | |
int | is_present_int_array (int num, int *array, int length) |
Function used to check if a number is present in an array of integers. | |
int | is_present_char_array (char *string, char_array *array) |
Function used to check if a string is present in a char_array. | |
void | copy_interval_query (p_interval_query interval_1, p_interval_query interval_2) |
Function used to copy two interval queries. | |
void | calculate_nb_al_function (p_matt_ygraph m) |
Function used to calculate the number of alignments by position. | |
void | calculate_score_function (p_matt_ygraph m) |
Function used to calculate the score function. | |
void | get_interesting_regions (p_matt_ygraph m) |
Function used to determine interesting regions on the reference. | |
void | determine_pos_query (p_matt_ygraph m, int index_interval, int index_aln) |
Function used to determine the positions on the query sequence for the conserved region on the reference. | |
void | complete_set_sequences (p_matt_ygraph m) |
Function used to determine the sequences of the reference sequence and all query sequences of all sets. | |
void | get_sets_of_sequences (p_matt_ygraph m) |
Function used to determine the sets of sequences of conserved regions. | |
void | eliminate_redundancy_set (p_matt_ygraph m, int index_set) |
Function used to eliminate redundant sequences inside the current set. | |
void | compare_all_against_ref (p_matt_ygraph m) |
Function used to compare all sequences against the reference for all sets of sequences. | |
void | sort_identity_ref (p_matt_ygraph m) |
Function used to sort all queries in each set by reference identity. | |
void | check_species_repetitions (p_matt_ygraph m) |
Function used to check species repetitions. | |
void | search_naive_clique (p_matt_ygraph m) |
Function used to serach the naive clique for all sets. | |
void | recursive_search_maxi_clique (p_set_of_seqs set, p_clique temp_clique, int index) |
Function used to search recursively the maxi clique in the current set. | |
void | maxi_clique_search (p_matt_ygraph m) |
Function used to search the maxi clique for all sets. |
void calculate_nb_al_function | ( | p_matt_ygraph | m | ) |
Function used to calculate the number of alignments by position.
[in,out] | m | : the main structure containing all needed information |
References alignment_info_array::al_info, DESTROY, destroy_alignment(), eliminate_redundancy_species(), alignment_info_array::nb_al_info, NEW, and OPTS_filter_species.
Referenced by main().
void calculate_score_function | ( | p_matt_ygraph | m | ) |
Function used to calculate the score function.
[in,out] | m | : the main structure containing information |
[in,out] | m | : the main structure to destroy |
References OPTS_lambda, and score_function().
Referenced by main().
void check_species_repetitions | ( | p_matt_ygraph | m | ) |
Function used to check species repetitions.
[in,out] | m | : the main structure containing information and that will be updated |
References char_array::chars, DESTROY, is_present_char_array(), char_array::nb_chars, NEW, OPTS_max_species_repet, OPTS_verbose, print_verbose_end_checking_repetitions_set(), print_verbose_start_checking_repetitions_set(), and RENEW.
Referenced by main().
void compare_all_against_ref | ( | p_matt_ygraph | m | ) |
Function used to compare all sequences against the reference for all sets of sequences.
[in,out] | m | : the main structure containing information and that will be updated |
References copy_interval_query(), DESTROY, eliminate_redundancy_set(), NEW, OPTS_carnac, OPTS_max_id, OPTS_min_id, OPTS_verbose, print_verbose_end_compare_ref_set(), print_verbose_start_compare_ref_set(), RENEW, and small_in_large().
Referenced by main().
void complete_set_sequences | ( | p_matt_ygraph | m | ) |
Function used to determine the sequences of the reference sequence and all query sequences of all sets.
[in,out] | m | : the main structure containing all sets |
[in,out] | m | : main structure containing all sets |
References get_complementary_base(), and NEW.
Referenced by get_sets_of_sequences().
void copy_interval_query | ( | p_interval_query | interval_1, | |
p_interval_query | interval_2 | |||
) |
Function used to copy two interval queries.
[in,out] | interval_1 | : the interval to copy in |
[in] | interval_2 | : the interval to copy |
References NEW.
Referenced by compare_all_against_ref(), and eliminate_redundancy_set().
void destroy_main_structure | ( | p_matt_ygraph | m | ) |
Function used to destroy all structures allocated.
[in,out] | m | : the main structure to destroy |
References DESTROY, destroy_alignment(), destroy_sequence(), and OPTS_carnac.
Referenced by main().
void determine_pos_query | ( | p_matt_ygraph | m, | |
int | index_interval, | |||
int | index_al | |||
) |
Function used to determine the positions on the query sequence for the conserved region on the reference.
[in,out] | m | : the main structure containing information and that will be updated |
[in] | index_interval | : index of the reference interval in the array of conserved region |
[in] | index_al | : index of the alignment concerned |
Referenced by get_sets_of_sequences().
void eliminate_redundancy_set | ( | p_matt_ygraph | m, | |
int | index_set | |||
) |
Function used to eliminate redundant sequences inside the current set.
[in,out] | m | : the main structure containing information and that will be updated |
[in] | index_set | : the index of the set to process |
References copy_interval_query(), DESTROY, is_present_int_array(), NEW, and RENEW.
Referenced by compare_all_against_ref().
void get_interesting_regions | ( | p_matt_ygraph | m | ) |
Function used to determine interesting regions on the reference.
[in,out] | m | : the main structure containing information and that will be updated with defined regions |
References NEW, OPTS_max_length_region, OPTS_min_length_region, and RENEW.
Referenced by main().
void get_sets_of_sequences | ( | p_matt_ygraph | m | ) |
Function used to determine the sets of sequences of conserved regions.
[in,out] | m | : the main structure containing information and that will be updated with the sets |
References complete_set_sequences(), DESTROY, determine_pos_query(), get_length_ref_intersect(), is_ref_intersect(), NEW, and RENEW.
Referenced by main().
int is_present_char_array | ( | char * | string, | |
char_array * | array | |||
) |
Function used to check if a string is present in a char_array.
[in] | string | : the string to search for |
[in] | array | : the char_array |
References char_array::chars, and char_array::nb_chars.
Referenced by check_species_repetitions().
int is_present_int_array | ( | int | num, | |
int * | array, | |||
int | length | |||
) |
Function used to check if a number is present in an array of integers.
[in] | num | : the number to search for |
[in] | array | : the array of integers |
[in] | length | : length of the array |
Referenced by eliminate_redundancy_set(), and recursive_search_maxi_clique().
void maxi_clique_search | ( | p_matt_ygraph | m | ) |
Function used to search the maxi clique for all sets.
[in,out] | m | : the main structure containing information and that will be updated |
[in,out] | m | : the main structure containing information and that will be updated |
References aln(), DESTROY, NEW, OPTS_carnac, OPTS_max_id, OPTS_min_id, OPTS_nb_seqs_set, OPTS_verbose, print_verbose_end_maxi_clique_set(), print_verbose_start_maxi_clique_set(), recursive_search_maxi_clique(), and RENEW.
Referenced by main().
void recursive_search_maxi_clique | ( | p_set_of_seqs | set, | |
p_clique | temp_clique, | |||
int | index | |||
) |
Function used to search recursively the maxi clique in the current set.
[in,out] | set | : the current set |
[in,out] | temp_clique | : the temporary maxi clique |
[in] | index | : the index in the query array of the sequence to add |
References DESTROY, is_present_int_array(), NEW, OPTS_nb_seqs_set, recursive_search_maxi_clique(), and RENEW.
Referenced by maxi_clique_search(), and recursive_search_maxi_clique().
float score_function | ( | float | score_pos_i_minus_1, | |
int | nb_al_pos_i, | |||
float | mean_al, | |||
float | epsilon, | |||
int | lambda | |||
) |
Defines the score function for the position i.
[in] | score_pos_i_minus_1 | : the score at position i - 1 |
[in] | nb_al_pos_i | : number of alignments at position i |
[in] | mean_al | : mean number of alignments by position |
[in] | epsilon | : float to add at the nb_al_i parameter to avoid log(0) |
[in] | lambda | : parameter threshold |
References MAX, and OPTS_lambda.
Referenced by calculate_score_function().
void search_naive_clique | ( | p_matt_ygraph | m | ) |
Function used to serach the naive clique for all sets.
Function used to search the naive clique for all sets.
[in,out] | m | : the main structure containing information and that will be updated |
References aln(), DESTROY, NEW, OPTS_carnac, OPTS_max_id, OPTS_min_id, OPTS_nb_seqs_set, OPTS_verbose, print_verbose_end_naive_clique_set(), print_verbose_no_connect(), print_verbose_start_naive_clique_set(), and RENEW.
Referenced by main().
void sort_identity_ref | ( | p_matt_ygraph | m | ) |
Function used to sort all queries in each set by reference identity.
[in,out] | m | : the main structure containing information and that will be updated |
References compare_sort_id().
Referenced by main().