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DNA_seq_indexer API

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This commit is contained in:
Celine Mercier
2016-04-12 16:38:47 +02:00
parent 04e3a7b5a9
commit be05c889e2
16 changed files with 200 additions and 97 deletions
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20
src/obidmscolumn_seq.c
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@ -18,7 +18,7 @@
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
#include "obiblob_indexer.h"
#include "dna_seq_indexer.h"
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
@ -33,7 +33,6 @@
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
{
Obi_blob_p value_b;
index_t idx;
// Check that the line number is not greater than the maximum allowed
@ -56,21 +55,13 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
// Encode the value on a byte array with a header // TODO make function
value_b = obi_seq_to_blob(value);
if (value_b == NULL)
return -1;
// Add in the indexer
idx = obi_indexer_add(column->indexer, value_b);
idx = obi_index_dna_seq(column->indexer, value);
if (idx == -1)
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;
free(value_b);
return 0;
}
@ -114,8 +105,7 @@ int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p c
const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
index_t idx;
Obi_blob_p value_b;
index_t idx;
if ((line_nb+1) > ((column->header)->line_count))
{
@ -130,9 +120,7 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
if (idx == OBIIdx_NA)
return OBISeq_NA;
value_b = obi_indexer_get(column->indexer, idx);
return obi_blob_to_seq(value_b);
return obi_retrieve_dna_seq(column->indexer, idx);
}