Major update: New column type to store sequence qualities. Closes #41

src/obidmscolumn_qual.c

@@ -6,7 +6,7 @@
  * @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.
+ * @brief Functions handling OBIColumns containing data in the form of indices referring to sequence qualities.
  */
 
 
@@ -14,9 +14,10 @@
 #include <stdio.h>
 #include <stdint.h>
 
+#include "obidmscolumn_qual.h"
 #include "obidmscolumn.h"
 #include "obitypes.h"
-#include "obidmscolumn_str.c"
+#include "uint8_indexer.h"
 
 
 /**********************************************************************
@@ -26,38 +27,83 @@
  **********************************************************************/
 
 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);
+{
+	uint8_t* int_value;
+	int      int_value_length;
+	int 	 i;
+	int		 ret_value;
+
+	int_value_length = strlen(value);
+	int_value = (uint8_t*) malloc(int_value_length * sizeof(uint8_t));
+
+	// Convert in uint8_t array to index in that format
+	for (i=0; i<int_value_length; i++)
+		int_value[i] = ((uint8_t)(value[i])) - QUALITY_ASCII_BASE;
+
+	ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, int_value, int_value_length);
+
+	free(int_value);
+
+	return ret_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)
+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, int value_length)
 {
-	char* value_char;
+	index_t idx;
+	char*   new_indexer_name;
 
-	// Transform the int array into a char array
-	// Length??
-	//value_char = ;
+	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
+		return -1;
 
-	obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value_char)
+	// Add the value in the indexer
+	idx = obi_index_uint8(column->indexer, value, value_length);
+	if (idx == -1)	// An error occurred
+	{
+		if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
+		{
+			// If the error is that the indexer is read-only, clone it
+			new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
+			if (new_indexer_name == NULL)
+				return -1;
+			column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
+			// Add the value in the new indexer
+			idx = obi_index_uint8(column->indexer, value, value_length);
+			if (idx == -1)
+				return -1;
+		}
+		else
+			return -1;
+	}
+	// Add the value's index in the column
+	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
 
 	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;
+{
+	char* 		   value;
+	const uint8_t* int_value;
+	int			   int_value_length;
+	int			   i;
 
-	value = obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
-	if (strcmp(value, OBIStr_NA) == 0)
-		return OBIQual_char_NA;
+	int_value = obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, &int_value_length);
+
+	value = (char*) malloc((int_value_length + 1) * sizeof(char));
+
+	// Encode int quality to char quality
+	for (i=0; i<int_value_length; i++)
+		value[i] = (char)(int_value[i] + QUALITY_ASCII_BASE);
+
+	value[i] = '\0';
 
 	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)
+const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, int* value_length)
 {
 	index_t idx;
 
@@ -70,7 +116,7 @@ uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t
 	if (idx == OBIIdx_NA)
 		return OBIQual_int_NA;
 
-	return obi_retrieve_quality_int(column->indexer, idx);
+	return obi_retrieve_uint8(column->indexer, idx, value_length);
 }
 
 
@@ -84,13 +130,13 @@ int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t li
 }
 
 
-int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, uint8_t* value)
+int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const uint8_t* value, int value_length)
 {
 	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);
+	return obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, value, value_length);
 }
 
 
@@ -104,12 +150,12 @@ char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t
 }
 
 
-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)
+const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, int* value_length)
 {
 	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);
+	return obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, value_length);
 }