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Renamed "Obi_byte_arrays" to "Obiblobs" and moved Obiblob functions to

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separate obiblob.c and obiblob.h files
This commit is contained in:
Celine Mercier
2016-04-12 11:21:14 +02:00
parent c225cfd8b6
commit 375bfcce8a
8 changed files with 304 additions and 249 deletions
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67
src/obiavl.c
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@ -22,6 +22,7 @@
#include "bloom.h"
#include "crc64.h"
#include "obiavl.h"
#include "obiblob.h"
#include "obierrno.h"
#include "obitypes.h"
#include "obidebug.h"
@ -270,7 +271,7 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group);
* The function checks a bloom filter. No false negatives, possible false positives.
*
* @param avl A pointer to the AVL tree structure.
* @param value A pointer to the byte array structure.
* @param value A pointer to the blob structure.
*
* @retval 0 if the value is definitely not already stored in the AVL tree.
* @retval 1 if the value might already be stored in the AVL tree.
@ -278,17 +279,17 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group);
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int maybe_in_avl(OBIDMS_avl_p avl, Obi_byte_array_p value);
int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value);
/**
* @brief Internal function comparing two byte arrays.
* @brief Internal 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 byte array structure.
* @param value_2 A pointer to the second byte array structure.
* @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,
@ -297,27 +298,27 @@ int maybe_in_avl(OBIDMS_avl_p avl, Obi_byte_array_p value);
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2);
int blob_compare(Obi_blob_p value_1, Obi_blob_p value_2);
/**
* @brief Internal function calculating the size in bytes of a byte array.
* @brief Internal function calculating the size in bytes of a blob.
*
* @param value A pointer to the byte array structure.
* @param value A pointer to the blob structure.
*
* @returns The size of the byte array in bytes.
* @returns The size of the blob in bytes.
*
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int byte_array_sizeof(Obi_byte_array_p value);
int blob_sizeof(Obi_blob_p value);
/**
* @brief Internal function storing a value (byte array) in the data array referred to by an AVL tree.
* @brief Internal function storing a value (blob) in the data array referred to by an AVL tree.
*
* @param avl A pointer to the AVL tree structure.
* @param value A pointer to the value (byte array structure).
* @param value A pointer to the value (blob structure).
*
* @returns The index of the stored value.
* @retval -1 if an error occurred.
@ -325,7 +326,7 @@ int byte_array_sizeof(Obi_byte_array_p value);
* @since December 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_byte_array_p value);
index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_blob_p value);
/**
@ -979,13 +980,13 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
}
int maybe_in_avl(OBIDMS_avl_p avl, Obi_byte_array_p value)
int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value)
{
return (bloom_check(&((avl->header)->bloom_filter), value, byte_array_sizeof(value)));
return (bloom_check(&((avl->header)->bloom_filter), value, blob_sizeof(value)));
}
int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2)
int blob_compare(Obi_blob_p value_1, Obi_blob_p value_2)
{
int comp;
int32_t b;
@ -1013,13 +1014,13 @@ int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2)
}
int byte_array_sizeof(Obi_byte_array_p value)
int blob_sizeof(Obi_blob_p value)
{
return (sizeof(Obi_byte_array_t) + (value->length_encoded_value));
return (sizeof(Obi_blob_t) + (value->length_encoded_value));
}
index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_byte_array_p value)
index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_blob_p value)
{
index_t value_idx;
int value_size;
@ -1027,7 +1028,7 @@ index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, Obi_byte_array_p value)
value_idx = ((avl->data)->header)->data_size_used;
// Grow the data if needed
value_size = byte_array_sizeof(value);
value_size = blob_sizeof(value);
while (((avl->data)->header)->data_size_max < (value_idx + value_size))
{
if (grow_avl_data(avl->data) < 0)
@ -2047,20 +2048,20 @@ int obi_close_avl_group(OBIDMS_avl_group_p avl_group)
}
Obi_byte_array_p obi_avl_get(OBIDMS_avl_p avl, index_t idx)
Obi_blob_p obi_avl_get(OBIDMS_avl_p avl, index_t idx)
{
return ((Obi_byte_array_p)(((avl->data)->data)+idx));
return ((Obi_blob_p)(((avl->data)->data)+idx));
}
index_t obi_avl_add(OBIDMS_avl_p avl, Obi_byte_array_p value)
index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value)
{
AVL_node_p node_to_add = NULL;
AVL_node_p current_node;
index_t next, parent;
index_t value_data_idx;
index_t node_idx;
Obi_byte_array_p to_compare;
Obi_blob_p to_compare;
int comp;
int n;
int depth;
@ -2068,7 +2069,7 @@ index_t obi_avl_add(OBIDMS_avl_p avl, Obi_byte_array_p value)
n = 0;
depth = 0;
crc = crc64((byte_t*)value, byte_array_sizeof(value));
crc = crc64((byte_t*)value, blob_sizeof(value));
// Check if first node
if (!((avl->header)->nb_items))
@ -2115,7 +2116,7 @@ index_t obi_avl_add(OBIDMS_avl_p avl, Obi_byte_array_p value)
if (comp == 0)
{ // check if really same value
to_compare = obi_avl_get(avl, current_node->value);
comp = byte_array_compare(to_compare, value);
comp = blob_compare(to_compare, value);
}
if (comp > 0)
@ -2189,15 +2190,15 @@ index_t obi_avl_add(OBIDMS_avl_p avl, Obi_byte_array_p value)
// Find if a value is already in an AVL tree
index_t obi_avl_find(OBIDMS_avl_p avl, Obi_byte_array_p value)
index_t obi_avl_find(OBIDMS_avl_p avl, Obi_blob_p value)
{
int comp;
index_t next;
Obi_byte_array_p to_compare;
Obi_blob_p to_compare;
AVL_node_p current_node;
uint64_t crc;
crc = crc64((byte_t*)value, byte_array_sizeof(value));
crc = crc64((byte_t*)value, blob_sizeof(value));
next = (avl->header)->root_idx;
while (next != -1)
@ -2210,7 +2211,7 @@ index_t obi_avl_find(OBIDMS_avl_p avl, Obi_byte_array_p value)
if (comp == 0)
{ // Check if really same value
to_compare = obi_avl_get(avl, current_node->value);
comp = byte_array_compare(to_compare, value);
comp = blob_compare(to_compare, value);
}
if (comp > 0)
@ -2229,7 +2230,7 @@ index_t obi_avl_find(OBIDMS_avl_p avl, Obi_byte_array_p value)
}
Obi_byte_array_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx)
Obi_blob_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx)
{
int32_t avl_idx;
index_t idx_in_avl;
@ -2241,7 +2242,7 @@ Obi_byte_array_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx)
}
index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_byte_array_p value)
index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
{
int32_t index_in_avl;
index_t index_with_avl;
@ -2286,7 +2287,7 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_byte_array_p value)
}
// Add in the current AVL
bloom_add(&((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->bloom_filter), value, byte_array_sizeof(value));
bloom_add(&((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->bloom_filter), value, 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