#include <sys/time.h>
#include "io.h"
#include "types.h"
#include "macros.h"
#include "options.h"
#include "sequence.h"
#include "alignment.h"
#include "matt_ygraph.h"
Functions | |
int | main (int argc, char **argv) |
Main function. |
int main | ( | int | argc, | |
char ** | argv | |||
) |
Main function.
[in] | argc | : number of parameters |
[in] | argv | : the parameters |
References calculate_nb_al_function(), calculate_score_function(), check_parameters_validity(), check_species_repetitions(), compare_all_against_ref(), complete_alignments_attributes(), complete_sequences_attributes(), DESTROY, destroy_main_structure(), destroy_options(), get_interesting_regions(), get_sequences(), get_sets_of_sequences(), maxi_clique_search(), NEW, OPTS_max_species_repet, OPTS_output_format, OPTS_selecting_mode, OPTS_verbose, parse_params(), print_verbose_end_alignments(), print_verbose_end_build_sets(), print_verbose_end_check_repetitions(), print_verbose_end_compare_ref(), print_verbose_end_conserved_regions(), print_verbose_end_process(), print_verbose_end_score(), print_verbose_end_search_naive_clique(), print_verbose_end_sequences(), print_verbose_end_write_GFF3(), print_verbose_end_write_multifasta(), print_verbose_sort_identity_ref(), print_verbose_start_alignments(), print_verbose_start_build_sets(), print_verbose_start_check_repetitions(), print_verbose_start_compare_ref(), print_verbose_start_conserved_regions(), print_verbose_start_process(), print_verbose_start_score(), print_verbose_start_search_naive_clique(), print_verbose_start_sequences(), print_verbose_start_write_GFF3(), print_verbose_start_write_multifasta(), read_alignments_files(), search_naive_clique(), sort_identity_ref(), usage(), write_GFF3(), and write_multifasta().