obitools3/src/obiblob.h

/****************************************************************************
 * Obiblob header file	                                                    *
 ****************************************************************************/

/**
 * @file obiblob.h
 * @author Celine Mercier
 * @date November 18th 2015
 * @brief Header file for handling Obi_blob structures.
 */


#ifndef OBIBLOB_H_
#define OBIBLOB_H_


#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>

#include "obitypes.h"


#define ELEMENT_SIZE_STR (8)								/**< The size of an element from a value of type character string.
                              	  	 	 	 	 	 	 	 */
#define ELEMENT_SIZE_SEQ_2 (2)								/**< The size of an element from a value of type DNA sequence encoded on 2 bits.
                              	  	 	 	 	 	 	 	 */
#define ELEMENT_SIZE_SEQ_4 (4)								/**< The size of an element from a value of type DNA sequence encoded on 4 bits.
                              	  	 	 	 	 	 	 	 */


/**
 * @brief Blob structure.
 *  TODO
 */
typedef struct Obi_blob {
	uint8_t  element_size;		 	/**< Size in bits of one element from the value.
	 	 	 	 	 	 	 	 	 */
	int32_t  length_encoded_value;	/**< Length in bytes of the encoded value.
	 	 	 	 	 	 	 	 	 */
	int32_t  length_decoded_value;	/**< Length in bytes of the decoded value.
	 	 	 	 	 	 	 	 	 */
	byte_t   value[];				/**< Encoded value.
	 	 	 	 	 	 	 	 	 */
} Obi_blob_t, *Obi_blob_p;


/**
 * @brief Converts a character string to a blob.
 *
 * @warning The blob must be freed by the caller.
 *
 * @param value The character string to convert.
 *
 * @returns A pointer to the blob created.
 * @retval NULL if an error occurred.
 *
 * @since October 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
Obi_blob_p obi_str_to_blob(char* value);


/**
 * @brief Converts a blob to a character string.
 *
 * @param value_b The blob to convert.
 *
 * @returns A pointer to the character string contained in the blob.
 *
 * @since October 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
const char* obi_blob_to_str(Obi_blob_p value_b);


/**
 * @brief Converts a DNA sequence to a blob with a header.
 *
 * @warning The blob must be freed by the caller.
 *
 * @param value The DNA sequence to convert.
 *
 * @returns A pointer to the blob created.
 * @retval NULL if an error occurred.
 *
 * @since November 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
Obi_blob_p obi_seq_to_blob(char* seq);


/**
 * @brief Converts a blob to a DNA sequence.
 *
 * @param value_b The blob to convert.
 *
 * @returns A pointer to the DNA sequence contained in the blob.
 * @retval NULL if an error occurred.
 *
 * @since November 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
const char* obi_blob_to_seq(Obi_blob_p value_b);		// TODO move to encode source files


#endif /* OBIBLOB_H_ */