#include "types.h"
Functions | |
void | get_sequences (sequence_array *array_of_seqs) |
Function used to retrieve sequences contained in the fasta file and reference file. | |
void | destroy_sequence (p_sequence s) |
Function used to destroy a p_sequence structure. | |
int | is_present_array_sequence (char *seq_name_to_find, sequence_array *array_of_seqs) |
Function used to retrieve the index of a sequence according to its name. | |
void | get_real_length_sequence (p_sequence seq) |
Function used to calculate the real length of a sequence. | |
char | get_complementary_base (char nucleotide) |
Function used to get the complementary nucleotide. | |
void | complete_sequences_attributes (sequence_array *array_of_seqs) |
Function used to complete some missing attributes in the sequence array. |
void complete_sequences_attributes | ( | sequence_array * | array_of_seqs | ) |
Function used to complete some missing attributes in the sequence array.
[in,out] | array_of_seqs | : the array containing all sequences and that will be updated |
[in,out] | : | array_of_seqs : the array containing all sequences and that will be updated |
References DESTROY, sequence_array::nb_seqs, NEW, RENEW, and sequence_array::seqs.
Referenced by main().
void destroy_sequence | ( | p_sequence | s | ) |
Function used to destroy a p_sequence structure.
[in,out] | s | : the p_sequence to destroy |
References DESTROY.
Referenced by destroy_main_structure().
char get_complementary_base | ( | char | nucleotide | ) |
Function used to get the complementary nucleotide.
[in] | nucleotide | : the nucleotide to get its complementary |
[in] | nucleotide | : the nucleotide to get its complementary |
References _ERROR, and ERROR_.
Referenced by complete_set_sequences().
void get_real_length_sequence | ( | p_sequence | seq | ) |
Function used to calculate the real length of a sequence.
[in,out] | seq | : the reference sequence |
Referenced by get_sequences().
void get_sequences | ( | sequence_array * | array_of_seqs | ) |
Function used to retrieve sequences contained in the fasta file and reference file.
Function used to retrieve sequences contained in the fasta file.
[in,out] | array_of_seqs | : the array of sequences that will be updated with sequences contained in the fasta file |
References _ERROR, char_array::chars, DESTROY, ERROR_, free_flex_mem(), get_real_length_sequence(), char_array::nb_chars, sequence_array::nb_seqs, NEW, OPTS_file, OPTS_file_array, OPTS_ref_file, RENEW, sequence_array::seqs, sequence_file_name, sequence_nb_errors, sequence_result, sequenceparse(), and sequencerestart().
Referenced by main().
int is_present_array_sequence | ( | char * | seq_name_to_find, | |
sequence_array * | array_of_seqs | |||
) |
Function used to retrieve the index of a sequence according to its name.
[in] | seq_name_to_find | : the name to search for |
[in] | array_of_seqs | : the array of sequences |
References sequence_array::nb_seqs, and sequence_array::seqs.
Referenced by complete_alignments_attributes().