Finished moving obiblob functions to obiblob files and documentation for

obiblob functions

src/obiavl.c

@@ -951,7 +951,7 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
 
 int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value)
 {
-	return (bloom_check(&((avl->header)->bloom_filter), value, blob_sizeof(value)));
+	return (bloom_check(&((avl->header)->bloom_filter), value, obi_blob_sizeof(value)));
 }
 
 
@@ -963,7 +963,7 @@ index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_blob_p value)
 	value_idx = ((avl->data)->header)->data_size_used;
 
 	// Grow the data if needed
-	value_size = blob_sizeof(value);
+	value_size = obi_blob_sizeof(value);
 	while (((avl->data)->header)->data_size_max < (value_idx + value_size))
 	{
 		if (grow_avl_data(avl->data) < 0)
@@ -1978,7 +1978,7 @@ index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value)
 
 	n = 0;
 	depth = 0;
-	crc = crc64((byte_t*)value, blob_sizeof(value));
+	crc = crc64((byte_t*)value, obi_blob_sizeof(value));
 
 	// Check if first node
 	if (!((avl->header)->nb_items))
@@ -2025,7 +2025,7 @@ index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value)
 		if (comp == 0)
 		{ // check if really same value
 			to_compare = obi_avl_get(avl, current_node->value);
-			comp = blob_compare(to_compare, value);
+			comp = obi_blob_compare(to_compare, value);
 		}
 
 		if (comp > 0)
@@ -2107,7 +2107,7 @@ index_t obi_avl_find(OBIDMS_avl_p avl, Obi_blob_p value)
 	AVL_node_p       current_node;
 	uint64_t         crc;
 
-	crc = crc64((byte_t*)value, blob_sizeof(value));
+	crc = crc64((byte_t*)value, obi_blob_sizeof(value));
 
 	next = (avl->header)->root_idx;
 	while (next != -1)
@@ -2120,7 +2120,7 @@ index_t obi_avl_find(OBIDMS_avl_p avl, Obi_blob_p value)
 		if (comp == 0)
 		{ // Check if really same value
 			to_compare = obi_avl_get(avl, current_node->value);
-			comp = blob_compare(to_compare, value);
+			comp = obi_blob_compare(to_compare, value);
 		}
 
 		if (comp > 0)
@@ -2205,7 +2205,7 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
 	}
 
 	// Add in the current AVL
-	bloom_add(&((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->bloom_filter), value, blob_sizeof(value));
+	bloom_add(&((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->bloom_filter), value, obi_blob_sizeof(value));
 	index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->current_avl_idx], value);
 
 	// Build the index containing the AVL index

src/obiblob.c

@@ -55,3 +55,37 @@ Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_
 	return blob;
 }
 
+
+int obi_blob_compare(Obi_blob_p value_1, Obi_blob_p value_2)
+{
+	int 	comp;
+	int32_t b;
+
+	if (value_1->element_size != value_2->element_size)
+		return (value_1->element_size - value_2->element_size);
+
+	if (value_1->length_encoded_value != value_2->length_encoded_value)
+		return (value_1->length_encoded_value - value_2->length_encoded_value);
+
+	if (value_1->element_size != ELEMENT_SIZE_STR) // because if so, length_decoded_value == length_encoded_value
+	{
+		if (value_1->length_decoded_value != value_2->length_decoded_value)
+			return (value_1->length_decoded_value - value_2->length_decoded_value);
+	}
+
+	b = 0;
+	comp = 0;
+	while (!comp && (b < value_1->length_encoded_value))
+	{
+		comp = *((value_1->value)+b) - *((value_2->value)+b);
+		b++;
+	}
+	return comp;
+}
+
+
+int obi_blob_sizeof(Obi_blob_p value)
+{
+	return (sizeof(Obi_blob_t) + (value->length_encoded_value));
+}
+

src/obiblob.h

@@ -21,20 +21,19 @@
 #include "obitypes.h"
 
 
-#define ELEMENT_SIZE_STR (8)								/**< The size of an element from a value of type character string.
+#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_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.
+#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.
+ * @brief Blob structure, for handling encoded values.
- *  TODO
  */
 typedef struct Obi_blob {
-	uint8_t  element_size;		 	/**< Size in bits of one element from the value.
+	uint8_t  element_size;		 	/**< Size in bits of one element from the encoded value.
 	 	 	 	 	 	 	 	 	 */
 	int32_t  length_encoded_value;	/**< Length in bytes of the encoded value.
 	 	 	 	 	 	 	 	 	 */
@@ -46,9 +45,54 @@ typedef struct Obi_blob {
 
 
 
-// TODO doc
+/**
+ * @brief Function building a blob structure.
+ *
+ * @param encoded_value A pointer to the encoded value that will be stored in the blob.
+ * @param element_size The size in bits of one element from the encoded value.
+ * @param length_encoded_value The length in bytes of the encoded value.
+ * @param length_decoded_value The length in bytes of the decoded value.
+ *
+ * @returns A pointer to the created blob structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
 Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value);
 
 
+/**
+ * @brief Function comparing two blobs.
+ *
+ * The encoding is compared first, then the length of the
+ * values, then the values themselves.
+ *
+ * @param value_1 A pointer to the first blob structure.
+ * @param value_2 A pointer to the second blob structure.
+ *
+ * @returns A value < 0 if value_1 < value_2,
+ * 			a value > 0 if value_1 > value_2,
+ * 			and 0 if value_1 == value_2.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_blob_compare(Obi_blob_p value_1, Obi_blob_p value_2);
+
+
+/**
+ * @brief Function calculating the size in bytes of a blob.
+ *
+ * @param value A pointer to the blob structure.
+ *
+ * @returns The size of the blob in bytes.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_blob_sizeof(Obi_blob_p value);
+
+
 #endif /* OBIBLOB_H_ */