#include "io.h"
#include "macros.h"
#include "options.h"
Functions | |
void | read_file (FILE *fd, char **content) |
Function used to read a file and get its content. | |
void | get_size_number (int num, int *size) |
Function used to get the number of chars taken to represent an integer into a string. | |
int | write_GFF3 (p_matt_ygraph m) |
Function used to write GFF3 files. | |
int | write_multifasta (p_matt_ygraph m) |
Function used to write multifasta files. | |
void | print_verbose_start_process () |
Function used to print starting message on screen. | |
void | print_verbose_start_sequences () |
Function used to print the starting message on screen concerning the parsing of the sequences. | |
void | print_verbose_end_sequences (sequence_array *array_of_seqs) |
Function used to print the ending message on screen concerning the parsing of the sequences. | |
void | print_verbose_start_alignments () |
Function used to print the starting message on screen concerning the parsing of the alignments. | |
void | print_verbose_start_alignments_file (char *filename) |
Function used to print the starting message on screen concerning the parsing of the alignments in the current file. | |
void | print_verbose_end_alignments_file (int nb_al) |
Function used to print the starting message on screen concerning the parsing of the alignments in the current file. | |
void | print_verbose_end_alignments (int nb_al) |
Function used to print the ending message on screen concerning the parsing of the alignments. | |
void | print_verbose_start_score () |
Function used to print the starting message on screen concerning the score calculation. | |
void | print_verbose_end_score (float mean) |
Function used to print the ending message on screen concerning the score calculation. | |
void | print_verbose_start_conserved_regions () |
Function used to print the starting message on screen concerning the searching for conserved regions. | |
void | print_verbose_end_conserved_regions (int nb_sets) |
Function used to print the ending message on screen concerning the searching for conserved regions. | |
void | print_verbose_start_build_sets () |
Function used to print the starting message on screen concerning the building sets step. | |
void | print_verbose_end_build_sets (int nb_sets) |
Function used to print the ending message on screen concerning the building sets step. | |
void | print_verbose_start_compare_ref () |
Function used to print the starting message on screen concerning the comparison step of all queries against the reference. | |
void | print_verbose_start_compare_ref_set (int nb_set, int nb_seqs) |
Function used to print the starting message on screen concerning the comparison step of all queries against the reference for the current set. | |
void | print_verbose_end_compare_ref_set (int nb_seqs) |
Function used to print the ending message on screen concerning the comparison step of all queries against the reference for the current set. | |
void | print_verbose_sort_identity_ref () |
Function used to print the message on screen concerning the sorting of queries by identities. | |
void | print_verbose_end_compare_ref () |
Function used to print the ending message on screen concerning the comparison step of all queries against the reference. | |
void | print_verbose_start_check_repetitions () |
Function used to print the message on screen concerning the checking of species repetitions. | |
void | print_verbose_start_checking_repetitions_set (int nb_set, int nb_seqs) |
Function used to print the starting message on screen concerning the species repetitions for the current set. | |
void | print_verbose_end_checking_repetitions_set (int nb_seqs) |
Function used to print the ending message on screen concerning the species repetitions for the current set. | |
void | print_verbose_end_check_repetitions () |
Function used to print the ending message on screen concerning the checking of species repetitions. | |
void | print_verbose_start_search_naive_clique () |
Function used to print the starting message on screen concerning the comparison step of the naive clique search. | |
void | print_verbose_start_naive_clique_set (int nb_set, int nb_seqs) |
Function used to print the starting message on screen concerning the comparison step of searching the naive clique for the current set. | |
void | print_verbose_end_naive_clique_set (int nb_seqs) |
Function used to print the ending message on screen concerning the comparison step of searching the naive clique for the current set. | |
void | print_verbose_end_search_naive_clique () |
Function used to print the ending message on screen concerning the comparison step of the naive clique search. | |
void | print_verbose_no_connect (int nb) |
Function used to print the the message when a set of sequences has no connected sequence. | |
void | print_verbose_start_maxi_clique_set (int nb_set, int nb_seqs) |
Function used to print the starting message on screen concerning the comparison step of searching the maxi clique for the current set. | |
void | print_verbose_end_maxi_clique_set (int nb_seqs) |
Function used to print the ending message on screen concerning the comparison step of searching the maxi clique for the current set. | |
void | print_verbose_start_write_GFF3 () |
Function used to print the starting message on screen concerning the writing of result GFF3 files. | |
void | print_verbose_end_write_GFF3 (int nb_files) |
Function used to print the ending message on screen concerning the writing of result GFF3 files. | |
void | print_verbose_start_write_multifasta () |
Function used to print the starting message on screen concerning the writing of result multifasta files. | |
void | print_verbose_end_write_multifasta (int nb_files) |
Function used to print the ending message on screen concerning the writing of result multifasta files. | |
void | print_verbose_end_process (long execution_time) |
Function used to print the ending message. |
void get_size_number | ( | int | num, | |
int * | size | |||
) |
Function used to get the number of chars taken to represent an integer into a string.
[in] | num | : the number to consider |
[in,out] | size | : the calculated size |
Referenced by write_GFF3(), and write_multifasta().
void print_verbose_end_alignments | ( | int | nb_al | ) |
Function used to print the ending message on screen concerning the parsing of the alignments.
[in] | nb_al | : the number of alignments found |
References _PRINT, LINE, and PRINT_.
Referenced by main().
void print_verbose_end_alignments_file | ( | int | nb_al | ) |
Function used to print the starting message on screen concerning the parsing of the alignments in the current file.
[in] | nb_al | : number of alignment found in the current file |
References _PRINT, and PRINT_.
Referenced by read_alignments_files().
void print_verbose_end_build_sets | ( | int | nb_sets | ) |
Function used to print the ending message on screen concerning the building sets step.
[in] | nb_sets | : the number of sets built |
References _PRINT, LINE, and PRINT_.
Referenced by main().
void print_verbose_end_check_repetitions | ( | ) |
void print_verbose_end_checking_repetitions_set | ( | int | nb_seqs | ) |
Function used to print the ending message on screen concerning the species repetitions for the current set.
[in] | nb_seqs | : the number of sequences in the set (ref + queries) |
References _PRINT, and PRINT_.
Referenced by check_species_repetitions().
void print_verbose_end_compare_ref | ( | ) |
Function used to print the ending message on screen concerning the comparison step of all queries against the reference.
This function will print the ending message on screen concerning the comparison step of all queries against the reference
References _PRINT, LINE, and PRINT_.
Referenced by main().
void print_verbose_end_compare_ref_set | ( | int | nb_seqs | ) |
Function used to print the ending message on screen concerning the comparison step of all queries against the reference for the current set.
[in] | nb_seqs | : the number of seqs in the set after the comparison (ref + query) |
References _PRINT, and PRINT_.
Referenced by compare_all_against_ref().
void print_verbose_end_conserved_regions | ( | int | nb_sets | ) |
Function used to print the ending message on screen concerning the searching for conserved regions.
[in] | nb_sets | : the number of conserved regions found |
References _PRINT, LINE, and PRINT_.
Referenced by main().
void print_verbose_end_maxi_clique_set | ( | int | nb_seqs | ) |
Function used to print the ending message on screen concerning the comparison step of searching the maxi clique for the current set.
[in] | nb_seqs | : the number of seqs in the set after the maxi clique serach (ref + query) |
References PRINT_.
Referenced by maxi_clique_search().
void print_verbose_end_naive_clique_set | ( | int | nb_seqs | ) |
Function used to print the ending message on screen concerning the comparison step of searching the naive clique for the current set.
[in] | nb_seqs | : the number of seqs in the set after the naive clique serach (ref + query) |
References _PRINT, and PRINT_.
Referenced by search_naive_clique().
void print_verbose_end_process | ( | long | execution_time | ) |
void print_verbose_end_score | ( | float | mean | ) |
Function used to print the ending message on screen concerning the score calculation.
[in] | mean | : the mean number of alignments found by position |
References _PRINT, LINE, and PRINT_.
Referenced by main().
void print_verbose_end_search_naive_clique | ( | ) |
Function used to print the ending message on screen concerning the comparison step of the naive clique search.
Function used to print the ending message on screen concerning the comparison step of the maxi clique search.
This function will print the ending message on screen concerning the comparison step of of the naive clique search
This function will print the ending message on screen concerning the comparison step of of the maxi clique search
References _PRINT, LINE, and PRINT_.
Referenced by main().
void print_verbose_end_sequences | ( | sequence_array * | array_of_seqs | ) |
Function used to print the ending message on screen concerning the parsing of the sequences.
This function will print the ending message on screen concerning the parsing of the sequences (number of sequences, their name and length)
[in] | array_of_seqs | : the array of extracted sequences |
References _PRINT, LINE, sequence_array::nb_seqs, PRINT_, and sequence_array::seqs.
Referenced by main().
void print_verbose_end_write_GFF3 | ( | int | nb_files | ) |
Function used to print the ending message on screen concerning the writing of result GFF3 files.
[in] | nb_files | : the number of GFF3 files written |
Referenced by main().
void print_verbose_end_write_multifasta | ( | int | nb_files | ) |
Function used to print the ending message on screen concerning the writing of result multifasta files.
[in] | nb_files | : the number of multifasta files written |
Referenced by main().
void print_verbose_no_connect | ( | int | nb | ) |
Function used to print the the message when a set of sequences has no connected sequence.
nb | : the number of the set concerned |
References _PRINT, and PRINT_.
Referenced by search_naive_clique().
void print_verbose_sort_identity_ref | ( | ) |
void print_verbose_start_alignments | ( | ) |
Function used to print the starting message on screen concerning the parsing of the alignments.
This function will print the starting message on screen concerning the parsing of the alignments
References _PRINT, char_array::nb_chars, OPTS_alignments, and PRINT_.
Referenced by main().
void print_verbose_start_alignments_file | ( | char * | filename | ) |
Function used to print the starting message on screen concerning the parsing of the alignments in the current file.
[in] | filename | : the name of the current alignment file |
References _PRINT, and PRINT_.
Referenced by read_alignments_files().
void print_verbose_start_build_sets | ( | ) |
void print_verbose_start_check_repetitions | ( | ) |
Function used to print the message on screen concerning the checking of species repetitions.
This function will print the message on screen concerning the checking of species repetitions
References _PRINT, OPTS_max_species_repet, and PRINT_.
Referenced by main().
void print_verbose_start_checking_repetitions_set | ( | int | nb_set, | |
int | nb_seqs | |||
) |
Function used to print the starting message on screen concerning the species repetitions for the current set.
[in] | nb_set | : the number of set processed |
[in] | nb_seqs | : the number of sequences in the set (ref + queries) |
References _PRINT, and PRINT_.
Referenced by check_species_repetitions().
void print_verbose_start_compare_ref | ( | ) |
Function used to print the starting message on screen concerning the comparison step of all queries against the reference.
This function will print the starting message on screen concerning the comparison step of all queries against the reference
References _PRINT, OPTS_carnac, OPTS_max_id, OPTS_min_id, and PRINT_.
Referenced by main().
void print_verbose_start_compare_ref_set | ( | int | nb_set, | |
int | nb_seqs | |||
) |
Function used to print the starting message on screen concerning the comparison step of all queries against the reference for the current set.
[in] | nb_set | : the number of set processed |
[in] | nb_seqs | : the number of sequences in the set (ref + queries) |
References _PRINT, and PRINT_.
Referenced by compare_all_against_ref().
void print_verbose_start_conserved_regions | ( | ) |
Function used to print the starting message on screen concerning the searching for conserved regions.
This function will print the starting message on screen concerning the searching of the conserved regions
References _PRINT, OPTS_max_length_region, OPTS_min_length_region, and PRINT_.
Referenced by main().
void print_verbose_start_maxi_clique_set | ( | int | nb_set, | |
int | nb_seqs | |||
) |
Function used to print the starting message on screen concerning the comparison step of searching the maxi clique for the current set.
[in] | nb_set | : the number of set processed |
[in] | nb_seqs | : the number of sequences in the set (ref + queries) |
References PRINT_.
Referenced by maxi_clique_search().
void print_verbose_start_naive_clique_set | ( | int | nb_set, | |
int | nb_seqs | |||
) |
Function used to print the starting message on screen concerning the comparison step of searching the naive clique for the current set.
[in] | nb_set | : the number of set processed |
[in] | nb_seqs | : the number of sequences in the set (ref + queries) |
References _PRINT, and PRINT_.
Referenced by search_naive_clique().
void print_verbose_start_process | ( | ) |
void print_verbose_start_score | ( | ) |
Function used to print the starting message on screen concerning the score calculation.
This function will print the starting message on screen concerning the score calculation
References _PRINT, OPTS_lambda, and PRINT_.
Referenced by main().
void print_verbose_start_search_naive_clique | ( | ) |
Function used to print the starting message on screen concerning the comparison step of the naive clique search.
Function used to print the starting message on screen concerning the comparison step of the maxi clique search.
This function will print the starting message on screen concerning the comparison step of of the naive clique search
This function will print the starting message on screen concerning the comparison step of of the maxi clique search
References _PRINT, OPTS_carnac, OPTS_max_id, OPTS_min_id, OPTS_nb_seqs_set, and PRINT_.
Referenced by main().
void print_verbose_start_sequences | ( | ) |
Function used to print the starting message on screen concerning the parsing of the sequences.
This function will print the starting message on screen concerning the parsing of the sequences
References _PRINT, OPTS_ref_file, and PRINT_.
Referenced by main().
void print_verbose_start_write_GFF3 | ( | ) |
Function used to print the starting message on screen concerning the writing of result GFF3 files.
This function will print the starting message on screen concerning the writing of result GFF3 files
References OPTS_nb_seqs_set, OPTS_output_dir, and PRINT_.
Referenced by main().
void print_verbose_start_write_multifasta | ( | ) |
Function used to print the starting message on screen concerning the writing of result multifasta files.
This function will print the starting message on screen concerning the writing of result multifasta files
References OPTS_nb_seqs_set, OPTS_output_dir, and PRINT_.
Referenced by main().
void read_file | ( | FILE * | fd, | |
char ** | content | |||
) |
Function used to read a file and get its content.
[in] | fd | : the file descriptor of the reading file |
[out] | content | : the string representation of the file content |
[in] | fd | : the file descriptor of the reading file |
[out] | content | : the string representation of the file content |
References NEW.
Referenced by carnac_individual_energy().
int write_GFF3 | ( | p_matt_ygraph | m | ) |
Function used to write GFF3 files.
[in] | m | : the main structure containing all info needed |
References _ERROR, DESTROY, ERROR_, get_size_number(), NEW, OPTS_nb_seqs_set, OPTS_output_dir, and OPTS_selecting_mode.
Referenced by main().
int write_multifasta | ( | p_matt_ygraph | m | ) |
Function used to write multifasta files.
[in] | m | : the main structure containing all info needed |
References _ERROR, DESTROY, ERROR_, get_size_number(), NEW, OPTS_nb_seqs_set, OPTS_output_dir, and OPTS_selecting_mode.
Referenced by main().