obitools3/src/obidmscolumn_qual.c

/****************************************************************************
 * OBIDMS_column_qual functions                                             *
 ****************************************************************************/

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


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

#include "obidmscolumn.h"
#include "obitypes.h"
#include "obidmscolumn_str.c"


/**********************************************************************
 *
 * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
 *
 **********************************************************************/

int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
{	// TODO discuss
	return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
}


int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const uint8_t* value)
{
	char* value_char;

	// Transform the int array into a char array
	// Length??
	//value_char = ;

	obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value_char)

	return 0;
}


char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{	// TODO discuss
	char* value;

	value = obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
	if (strcmp(value, OBIStr_NA) == 0)
		return OBIQual_char_NA;

	return value;
}


uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)	// TODO const? (mapped)
{
	index_t idx;

	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
		return OBIQual_int_NA;

	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);

	// Check NA
	if (idx == OBIIdx_NA)
		return OBIQual_int_NA;

	return obi_retrieve_quality_int(column->indexer, idx);
}


int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;

	return obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value);
}


int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, uint8_t* value)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return -1;

	return obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, value);
}


char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBIQual_char_NA;

	return obi_column_get_obiqual_char_with_elt_idx(column, line_nb, element_idx);
}


uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)	// TODO const? (mapped)
{
	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
	if (element_idx == OBIIdx_NA)
		return OBIQual_int_NA;

	return obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx);
}