156 lines
4.7 KiB
C
Executable File
156 lines
4.7 KiB
C
Executable File
/****************************************************************************
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* Header file for OBITypes *
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****************************************************************************/
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/**
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* @file obitypes.h
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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* @date 18 May 2015
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* @brief Header file for the handling of OBITypes.
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*/
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#ifndef OBITYPES_H_
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#define OBITYPES_H_
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#include <stdio.h>
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#include <unistd.h>
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#include <stdint.h>
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#define OBIInt_NA (INT32_MIN) /**< NA value for the type OBI_INT */
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#define OBIIdx_NA (INT64_MIN) /**< NA value for indices */
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#define OBIFloat_NA (float_NA()) /**< NA value for the type OBI_FLOAT */
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#define OBIChar_NA (0) /**< NA value for the type OBI_CHAR */ // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
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#define OBISeq_NA (NULL) /**< NA value for the type OBI_SEQ */ // TODO discuss
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#define OBIStr_NA (NULL) /**< NA value for the type OBI_STR */ // TODO discuss
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#define OBIBlob_NA (NULL) /**< NA value for the type Obiblobs */ // TODO discuss
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#define OBIQual_char_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in character string format */
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#define OBIQual_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */
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#define OBITuple_NA (NULL) /**< NA value for tuples of any type */
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/**
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* @brief enum for the boolean OBIType.
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*/
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typedef enum OBIBool {
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OBIFalse = 0,
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OBITrue = 1,
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OBIBool_NA = 2
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} obibool_t, *obibool_p; /**< a boolean true/false value */ // TODO check name convention?
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/**
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* @brief enum OBITypes for the data type of the OBIDMS columns.
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*/
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typedef enum OBIType {
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OBI_VOID = 0, /**< data type not specified */
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OBI_INT, /**< a signed integer value (C type : int32_t) */
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OBI_FLOAT, /**< a floating value (C type : double) */
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OBI_BOOL, /**< a boolean true/false value, see obibool_t enum */
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OBI_CHAR, /**< a character (C type : char) */
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OBI_QUAL, /**< an index in a data structure (C type : int64_t) referring to a quality score array */
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OBI_STR, /**< an index in a data structure (C type : int64_t) referring to a character string */
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OBI_SEQ, /**< an index in a data structure (C type : int64_t) referring to a DNA sequence */
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OBI_IDX /**< an index referring to a line in another column (C type : int64_t) */
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} OBIType_t, *OBIType_p;
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/**
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* Typedefs for the OBITypes.
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*/
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typedef int32_t obiint_t;
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typedef double obifloat_t;
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typedef char obichar_t;
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typedef int64_t index_t;
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typedef char byte_t; /**< Defining byte type.
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*/
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typedef int32_t obiversion_t; /**< Defining type for version numbers.
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*/
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/**
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* @brief Union used to compute the NA value of the OBI_FLOAT OBIType.
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*/
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typedef union
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{
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double value;
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unsigned int word[2];
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} ieee_double;
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/**
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* @brief Returns the NA value of the OBI_FLOAT OBIType.
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* This value corresponds to the float NA value as defined in R.
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*/
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static double float_NA(void)
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{
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volatile ieee_double x;
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x.word[0] = 0x7ff00000;
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x.word[1] = 1954;
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return x.value;
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}
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/**
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* @brief Trick to suppress compilation warnings about unused
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* float_NA function actually called in macro.
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*/
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static inline void suppress_warning(void) {
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(void)float_NA;
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(void)suppress_warning;
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}
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/**
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* @brief Returns the memory size in bytes of an OBIType.
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*
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* @param type The OBIType code used as query.
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*
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* @returns The size in bytes of the type.
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* @retval 0 if an error occurred (unknown type).
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*
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* @since May 2015
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* @author Eric Coissac (eric.coissac@metabarcoding.org)
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*/
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size_t obi_sizeof(OBIType_t type);
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/**
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* @brief Returns the size required to store an array of elements with an OBIType.
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*
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* The returned size is large enough to store an array large enough
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* to store all the elements but rounded at a multiple of the memory page size.
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*
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* @param data_type The OBIType of the elements.
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* @param nb_lines The number of lines to be stored.
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* @param nb_elements_per_line The number of elements per line.
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*
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* @returns The size in bytes of the array.
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* @retval 0 if an error occurred (unknown type).
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*
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* @since May 2015
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* @author Eric Coissac (eric.coissac@metabarcoding.org)
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*/
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size_t obi_array_sizeof(OBIType_t data_type, index_t nb_lines, index_t nb_elements_per_line);
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/**
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* @brief Returns the name in the form of a character string of an OBIType.
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*
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*
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* @param data_type The OBIType code used as query.
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*
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* @returns The name of the OBIType.
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* @retval NULL if an error occurred (unknown type or error allocating the memory for the character string).
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*
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* @since August 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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char* name_data_type(int data_type);
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#endif /* OBITYPES_H_ */
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