#include <getopt.h>
#include "options.h"
#include "macros.h"
#include "io.h"
Functions | |
void | usage () |
Function that defines the software options. | |
int | parse_params (int argc, char **argv) |
Function used to parse user parameters. | |
int | check_parameters_validity () |
Function used to check parameters entered by the user. | |
void | destroy_options () |
Function used to destroyed allocated options. | |
Variables | |
char * | OPTS_ref_file = NULL |
char * | OPTS_file |
char_array * | OPTS_file_array = NULL |
char * | OPTS_output_dir = "./" |
int | OPTS_output_format = 1 |
int | OPTS_verbose = 0 |
int | OPTS_lambda = 1 |
char_array * | OPTS_alignments = NULL |
int | OPTS_min_length_region = 30 |
int | OPTS_max_length_region = 500 |
int | OPTS_filter_species = 0 |
int | OPTS_min_id = 50 |
int | OPTS_max_id = 100 |
int | OPTS_nb_seqs_set = -1 |
int | OPTS_selecting_mode = 0 |
int | OPTS_max_species_repet = -1 |
int | OPTS_carnac = 0 |
int check_parameters_validity | ( | ) |
Function used to check parameters entered by the user.
References _ERROR, char_array::chars, DESTROY, ERROR_, char_array::nb_chars, NEW, OPTS_carnac, OPTS_file, OPTS_max_id, OPTS_max_length_region, OPTS_min_id, OPTS_min_length_region, OPTS_output_dir, OPTS_ref_file, and RENEW.
Referenced by main().
void destroy_options | ( | ) |
Function used to destroyed allocated options.
This function will destroy the allocated options : the reference name, the array of alignments files and the location of the file in fasta or in GFF3 format
References char_array::chars, DESTROY, char_array::nb_chars, OPTS_file, OPTS_output_dir, and OPTS_ref_file.
Referenced by main().
int parse_params | ( | int | argc, | |
char ** | argv | |||
) |
Function used to parse user parameters.
[in] | argc | : number of parameters |
[in] | argv | : the parameters |
References _ERROR, char_array::chars, ERROR_, char_array::nb_chars, NEW, OPTS_carnac, OPTS_file, OPTS_filter_species, OPTS_lambda, OPTS_max_id, OPTS_max_length_region, OPTS_max_species_repet, OPTS_min_id, OPTS_min_length_region, OPTS_nb_seqs_set, OPTS_output_dir, OPTS_output_format, OPTS_ref_file, OPTS_selecting_mode, OPTS_verbose, and RENEW.
Referenced by main().
void usage | ( | ) |
Function that defines the software options.
This function will be printed on the screen to help users deal with options. It will be printed also when user's options are not correct
References DISPLAY_ERR.
Referenced by main().
char_array* OPTS_alignments = NULL |
Array of alignments file
Referenced by print_verbose_start_alignments(), and read_alignments_files().
int OPTS_carnac = 0 |
Carnac selected parameter
Referenced by check_parameters_validity(), compare_all_against_ref(), destroy_main_structure(), maxi_clique_search(), parse_params(), print_verbose_start_compare_ref(), print_verbose_start_search_naive_clique(), and search_naive_clique().
char* OPTS_file |
Other species file(s)
Referenced by check_parameters_validity(), destroy_options(), get_sequences(), and parse_params().
char_array* OPTS_file_array = NULL |
Array of file(s) containing sequences
Referenced by get_sequences().
int OPTS_filter_species = 0 |
Filter on species
Referenced by calculate_nb_al_function(), and parse_params().
int OPTS_lambda = 1 |
Score lambda parameter
Referenced by calculate_score_function(), parse_params(), print_verbose_start_score(), and score_function().
int OPTS_max_id = 100 |
Minimum identity threshold
Referenced by check_parameters_validity(), compare_all_against_ref(), maxi_clique_search(), parse_params(), print_verbose_start_compare_ref(), print_verbose_start_search_naive_clique(), search_naive_clique(), and small_in_large().
int OPTS_max_length_region = 500 |
Maximal length of a region
Referenced by check_parameters_validity(), get_interesting_regions(), parse_params(), and print_verbose_start_conserved_regions().
int OPTS_max_species_repet = -1 |
Maximum number of repetitions by species
Referenced by check_species_repetitions(), main(), parse_params(), and print_verbose_start_check_repetitions().
int OPTS_min_id = 50 |
Minimum identity threshold
Referenced by check_parameters_validity(), compare_all_against_ref(), maxi_clique_search(), parse_params(), print_verbose_start_compare_ref(), print_verbose_start_search_naive_clique(), search_naive_clique(), and small_in_large().
int OPTS_min_length_region = 30 |
Minimal length of a region
Referenced by check_parameters_validity(), get_interesting_regions(), parse_params(), and print_verbose_start_conserved_regions().
int OPTS_nb_seqs_set = -1 |
Number of sequences wanted by set
Referenced by maxi_clique_search(), parse_params(), print_verbose_start_search_naive_clique(), print_verbose_start_write_GFF3(), print_verbose_start_write_multifasta(), recursive_search_maxi_clique(), search_naive_clique(), write_GFF3(), and write_multifasta().
char* OPTS_output_dir = "./" |
Output directory
Referenced by check_parameters_validity(), destroy_options(), parse_params(), print_verbose_start_write_GFF3(), print_verbose_start_write_multifasta(), write_GFF3(), and write_multifasta().
int OPTS_output_format = 1 |
Output format
Referenced by main(), and parse_params().
char* OPTS_ref_file = NULL |
Reference file
Referenced by check_parameters_validity(), destroy_options(), get_sequences(), parse_params(), and print_verbose_start_sequences().
int OPTS_selecting_mode = 0 |
Selecting mode
Referenced by main(), parse_params(), write_GFF3(), and write_multifasta().
int OPTS_verbose = 0 |
Verbose option
Referenced by check_species_repetitions(), compare_all_against_ref(), main(), maxi_clique_search(), parse_params(), read_alignments_files(), and search_naive_clique().