199 lines
6.4 KiB
C
199 lines
6.4 KiB
C
/****************************************************************************
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* Header file for utility functions *
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****************************************************************************/
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/**
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* @file utils.h
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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* @date 29 March 2016
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* @brief Header file for utility functions.
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*/
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#ifndef UTILS_H_
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#define UTILS_H_
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#include <stdio.h>
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#include <sys/stat.h>
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#include "obidms.h"
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#include "obitypes.h"
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#define FORMATTED_TIME_LENGTH (1024) /**< The length allocated for the character string containing a formatted date.
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*/
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#define ONE_IF_ZERO(x) (((x)==0)?1:(x)) /**< If x is equal to 0, x takes the value 1.
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*/
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#define DNA_ALPHA "acgtbdefhijklmnopqrsuvwxyz#![]" /**< DNA alphabet (IUPAC).
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//"ABCDEFGHIJKLMNOPQRSTUVWXYZ#![]" */
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#define CDNA_ALPHA "tgcavhefdijmlknopqysabwxrz#!][" /**< Complementary DNA alphabet (IUPAC).
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//"TVGHEFCDIJMLKNOPQYSAABWXRZ#!][" */
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/**
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* @brief Copy the content of a file into another file.
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*
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* @param src_file_path The path to the source file to copy.
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* @param dest_file_path The path to the destination file.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since July 2017
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int copy_file(const char* src_file_path, const char* dest_file_path);
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/**
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* @brief Counts the number of digits of a number.
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*
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* @param i The number.
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*
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* @returns The number of digits of the number.
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*
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* @since July 2017
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int digit_count(index_t i);
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/**
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* @brief Builds a word from a prefix and an index, with the form prefix_index.
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*
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* @warning The returned pointer has to be freed by the caller.
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*
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* @param prefix The prefix for the word.
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* @param idx The index to use as suffix.
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*
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* @returns The built word.
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*
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* @since July 2017
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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char* build_word_with_idx(const char* prefix, index_t idx);
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/**
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* @brief Counts the number of files and directories in a directory.
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*
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* @param dir_path The absolute path of the directory.
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*
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* @returns The number of files and directories in the directory.
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*
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* @since April 2016
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int count_dir(char* dir_path);
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/**
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* @brief Formats a date in a way that is easy to read.
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*
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* @warning The pointer returned must be freed by the caller.
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*
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* @param date A date.
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*
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* @returns The date formatted in a way that is easy to read.
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*
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* @since October 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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char* obi_format_date(time_t date);
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/**
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* @brief Allocates a chunk of memory aligned on 16 bytes boundary.
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*
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* @warning The pointer returned must be freed by the caller.
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* @warning The memory chunk pointed at by the returned pointer can be
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* smaller than the size asked for, since the address is shifted
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* to be aligned.
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*
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* @param size The size in bytes of the memory chunk to be allocated.
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* Ideally the closest multiple of 16 greater than the wanted size.
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* @param shift A pointer on an integer corresponding to the shift made to align
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* the address. Used to free the memory chunk.
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*
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* @returns The pointer on the aligned memory.
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*
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* @since May 2016
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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void* obi_get_memory_aligned_on_16(int size, int* shift);
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/**
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* @brief Version of quick sort modified to allow the user to provide an
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* additional pointer sent to the comparison function.
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*
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* @param key This is the pointer to the object that serves as key for the search, type-casted as a void*.
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* @param base This is the pointer to the first object of the array where the search is performed, type-casted as a void*.
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* @param num This is the number of elements in the array pointed by base.
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* @param size This is the size in bytes of each element in the array.
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* @param user_data This is an additional pointer passed to the comparison function.
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* @param cmp This is the function that compares two elements, eventually with an additional pointer.
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*
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* @returns A pointer to an entry in the array that matches the search key.
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* @retval NULL if key is not found.
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*
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* @since January 2017
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* @author original code modified by Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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void* bsearch_user_data(const void* key, const void* base, size_t num, size_t size, const void* user_data,
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int (*cmp)(const void *key, const void *elt, const void* user_data));
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/**
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* @brief Version of quick sort modified to allow the user to provide an
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* additional pointer sent to the comparison function.
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*
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* @param aa This is the pointer to the first element of the array to be sorted.
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* @param n This is the number of elements in the array pointed by base.
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* @param es This is the size in bytes of each element in the array.
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* @param user_data This is an additional pointer passed to the comparison function.
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* @param cmp This is the function that compares two elements, eventually with an additional pointer.
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*
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* @since January 2017
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* @author original code modified by Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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void qsort_user_data(void *aa, size_t n, size_t es, const void *user_data, int (*cmp)(const void *, const void *, const void *));
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/**
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* Function returning the reverse complement of a nucleotide sequence.
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*
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* @warning The sequence must be in lower case.
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* @warning The sequence will be replaced by its reverse complement without being copied.
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*
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* @param nucAcSeq The nucleotide sequence.
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*
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* @returns The reverse complemented sequence.
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*
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* @since December 2016
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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* @note Copied from ecoPCR source code
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*/
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char* reverse_complement_sequence(char* nucAcSeq);
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/**
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* Function returning the reverse complement of a pattern.
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*
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* @warning The pattern must be in lower case.
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* @warning The pattern will be replaced by its reverse complement without being copied.
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*
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* @param nucAcSeq The pattern.
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*
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* @returns The reverse complemented pattern.
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*
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* @since December 2016
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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* @note Copied from ecoPCR source code
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*/
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char* reverse_complement_pattern(char* nucAcSeq);
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#endif /* UTILS_H_ */
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