obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Fixed bug with retrieval of values from AVLs (bad cast in byte array

Browse Source 
structure)
This commit is contained in:
Celine Mercier
2016-04-11 17:07:22 +02:00
parent 966b1325ed
commit c225cfd8b6
1 changed files with 4 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files

25
src/obiavl.c
View File

@ -310,7 +310,7 @@ int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2);
* @since October 2015 * @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
*/ */
int32_t byte_array_sizeof(Obi_byte_array_p value); int byte_array_sizeof(Obi_byte_array_p value);
/** /**
@ -1006,7 +1006,6 @@ int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2)
comp = 0; comp = 0;
while (!comp && (b < value_1->length_encoded_value)) while (!comp && (b < value_1->length_encoded_value))
{ {
//fprintf(stderr, "\ncomparing %c and %c", *((value_1->value)+b), *((value_2->value)+b));
comp = *((value_1->value)+b) - *((value_2->value)+b); comp = *((value_1->value)+b) - *((value_2->value)+b);
b++; b++;
} }
@ -1014,7 +1013,7 @@ int byte_array_compare(Obi_byte_array_p value_1, Obi_byte_array_p value_2)
} }
int32_t byte_array_sizeof(Obi_byte_array_p value) int byte_array_sizeof(Obi_byte_array_p value)
{ {
return (sizeof(Obi_byte_array_t) + (value->length_encoded_value)); return (sizeof(Obi_byte_array_t) + (value->length_encoded_value));
} }
@ -1023,7 +1022,7 @@ int32_t byte_array_sizeof(Obi_byte_array_p 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_byte_array_p value)
{ {
index_t value_idx; index_t value_idx;
int32_t value_size; int value_size;
value_idx = ((avl->data)->header)->data_size_used; value_idx = ((avl->data)->header)->data_size_used;
@ -2050,8 +2049,7 @@ 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_byte_array_p obi_avl_get(OBIDMS_avl_p avl, index_t idx)
{ {
obidebug(1, "\ngetting >%s", ((Obi_byte_array_p)((avl->data)->data)+idx)->value); return ((Obi_byte_array_p)(((avl->data)->data)+idx));
return ((Obi_byte_array_p)((avl->data)->data)+idx);
} }
@ -2211,11 +2209,8 @@ index_t obi_avl_find(OBIDMS_avl_p avl, Obi_byte_array_p value)
if (comp == 0) if (comp == 0)
{ // Check if really same value { // Check if really same value
//fprintf(stderr, "\ngonna get\n");
to_compare = obi_avl_get(avl, current_node->value); to_compare = obi_avl_get(avl, current_node->value);
//fprintf(stderr, "\ngot, gonna compare\n");
comp = byte_array_compare(to_compare, value); comp = byte_array_compare(to_compare, value);
//fprintf(stderr, "\ncompared\n");
} }
if (comp > 0) if (comp > 0)
@ -2239,14 +2234,9 @@ Obi_byte_array_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx)
int32_t avl_idx; int32_t avl_idx;
index_t idx_in_avl; index_t idx_in_avl;
//fprintf(stderr, "\noriginal index = %lld", idx);
avl_idx = (int32_t) (idx >> 32); avl_idx = (int32_t) (idx >> 32);
idx_in_avl = idx & 0x00000000FFFFFFFF; idx_in_avl = idx & 0x00000000FFFFFFFF;
//fprintf(stderr, "\navl index = %d", avl_idx);
//fprintf(stderr, "\nindex in avl = %lld", idx_in_avl);
return obi_avl_get((avl_group->sub_avls)[avl_idx], idx_in_avl); return obi_avl_get((avl_group->sub_avls)[avl_idx], idx_in_avl);
} }
@ -2257,13 +2247,9 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_byte_array_p value)
index_t index_with_avl; index_t index_with_avl;
int i; int i;
//fprintf(stderr, "\nAdding %s", value->value);
if (maybe_in_avl((avl_group->sub_avls)[avl_group->current_avl_idx], value)) if (maybe_in_avl((avl_group->sub_avls)[avl_group->current_avl_idx], value))
{ {
//fprintf(stderr, "\nmaybe in current AVL");
index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->current_avl_idx], value); index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->current_avl_idx], value);
//fprintf(stderr, "\nfind went fine\n");
if (index_in_avl >= 0) if (index_in_avl >= 0)
{ {
index_with_avl = avl_group->current_avl_idx; index_with_avl = avl_group->current_avl_idx;
@ -2276,7 +2262,6 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_byte_array_p value)
{ {
if (maybe_in_avl((avl_group->sub_avls)[i], value)) if (maybe_in_avl((avl_group->sub_avls)[i], value))
{ {
//fprintf(stderr, "\nmaybe in AVL %d", i);
if (remap_an_avl((avl_group->sub_avls)[i]) < 0) if (remap_an_avl((avl_group->sub_avls)[i]) < 0)
return -1; return -1;
index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[i], value); index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[i], value);
@ -2300,8 +2285,6 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_byte_array_p value)
return -1; return -1;
} }
//fprintf(stderr, "\nAdding in current AVL");
// Add in the current AVL // 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, byte_array_sizeof(value));
index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->current_avl_idx], value); index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->current_avl_idx], value);