obitools3/src/obidmscolumn_qual.h

/****************************************************************************
 * OBIDMS_column_qual header file                                           *
 ****************************************************************************/

/**
 * @file obidsmcolumn_qual.h
 * @author Celine Mercier
 * @date May 4th 2016
 * @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to sequence quality arrays.
 */


#ifndef OBIDMSCOLUMN_QUAL_H_
#define OBIDMSCOLUMN_QUAL_H_


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

#include "obidmscolumn.h"
#include "obitypes.h"


/**
 * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function is for qualities in the character string format.
 *
 * @warning Pointers returned by obi_open_column() don't allow writing.
 *
 * @param column A pointer as returned by obi_create_column() or obi_clone_column().
 * @param line_nb The number of the line where the value should be set.
 * @param element_idx The index of the element that should be set in the line.
 * @param value The value that should be set, in the character string format.
 *
 * @returns An integer value indicating the success of the operation.
 * @retval 0 on success.
 * @retval -1 if an error occurred.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);


/**
 * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function is for qualities in the integer format.
 *
 * @warning Pointers returned by obi_open_column() don't allow writing.
 *
 * @param column A pointer as returned by obi_create_column() or obi_clone_column().
 * @param line_nb The number of the line where the value should be set.
 * @param element_idx The index of the element that should be set in the line.
 * @param value The value that should be set, in the integer format.
 *
 * @returns An integer value indicating the success of the operation.
 * @retval 0 on success.
 * @retval -1 if an error occurred.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, uint8_t* value);


/**
 * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function returns quality scores in the character string format.
 *
 * @param column A pointer as returned by obi_create_column().
 * @param line_nb The number of the line where the value should be recovered.
 * @param element_idx The index of the element that should be recovered in the line.
 *
 * @returns The recovered value, in the character string format.
 * @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);


/**
 * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function returns quality scores in the integer format.
 *
 * @param column A pointer as returned by obi_create_column().
 * @param line_nb The number of the line where the value should be recovered.
 * @param element_idx The index of the element that should be recovered in the line.
 *
 * @returns The recovered value, in the integer format.
 * @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);


/**
 * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function is for quality scores in the character string format.
 *
 * @warning Pointers returned by obi_open_column() don't allow writing.
 *
 * @param column A pointer as returned by obi_create_column() or obi_clone_column().
 * @param line_nb The number of the line where the value should be set.
 * @param element_name The name of the element that should be set in the line.
 * @param value The value that should be set, in the character string format.
 *
 * @returns An integer value indicating the success of the operation.
 * @retval 0 on success.
 * @retval -1 if an error occurred.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);


/**
 * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function is for quality scores in the integer format.
 *
 * @warning Pointers returned by obi_open_column() don't allow writing.
 *
 * @param column A pointer as returned by obi_create_column() or obi_clone_column().
 * @param line_nb The number of the line where the value should be set.
 * @param element_name The name of the element that should be set in the line.
 * @param value The value that should be set, in the integer format.
 *
 * @returns An integer value indicating the success of the operation.
 * @retval 0 on success.
 * @retval -1 if an error occurred.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, uint8_t* value);


/**
 * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function returns quality scores in the character string format.
 *
 * @param column A pointer as returned by obi_create_column() or obi_clone_column().
 * @param line_nb The number of the line where the value should be recovered.
 * @param element_name The name of the element that should be recovered in the line.
 *
 * @returns The recovered value, in the character string format.
 * @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);


/**
 * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
 * to sequence qualities handled by an indexer, and using the index of the element in the column's line.
 *
 * This function returns quality scores in the integer format.
 *
 * @param column A pointer as returned by obi_create_column() or obi_clone_column().
 * @param line_nb The number of the line where the value should be recovered.
 * @param element_name The name of the element that should be recovered in the line.
 *
 * @returns The recovered value, in the integer format.
 * @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
 *
 * @since May 2016
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
utin8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);


#endif /* OBIDMSCOLUMN_QUAL_H_ */