First version of quality handling (not working yet) and now it is

checked that a column is writable before enlarging it

src/obidmscolumn_qual.c

@@ -0,0 +1,115 @@
+/****************************************************************************
+ * 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);
+}
+