Commit 4ead37ee by Celine Mercier

Finished moving obiblob functions to obiblob files and documentation for

obiblob functions
parent bce360bb
......@@ -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
......
......@@ -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));
}
......@@ -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_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_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_4 (4) /**< The size of an element from a value of type DNA sequence encoded on 4 bits.
*/
/**
* @brief Blob structure.
* TODO
* @brief Blob structure, for handling encoded values.
*/
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_ */
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