void
BlastSetUp_MaskQuery(BLAST_SequenceBlk* query_blk,
const BlastQueryInfo* query_info,
const BlastMaskLoc *filter_maskloc,
EBlastProgramType program_number)
{
const Boolean kIsNucl = (program_number == eBlastTypeBlastn);
Int4 context; /* loop variable. */
ASSERT(query_blk);
ASSERT(query_info);
ASSERT(filter_maskloc);
for (context = query_info->first_context;
context <= query_info->last_context; ++context) {
Int4 query_length = 0;
Int4 context_offset = 0;
Uint1 *buffer = NULL; /* holds sequence */
if (query_info->contexts[context].is_valid == FALSE) {
continue;
}
query_length = query_info->contexts[context].query_length;
context_offset = query_info->contexts[context].query_offset;
buffer = &query_blk->sequence[context_offset];
ASSERT(buffer);
Blast_MaskTheResidues(buffer, query_length, kIsNucl,
filter_maskloc->seqloc_array[context],
BlastIsReverseStrand(kIsNucl, context), 0);
}
}
void
BlastSetUp_MaskQuery(BLAST_SequenceBlk* query_blk,
const BlastQueryInfo* query_info,
const BlastMaskLoc *filter_maskloc,
EBlastProgramType program_number)
{
const Boolean kIsNucl = (program_number == eBlastTypeBlastn);
Int4 context; /* loop variable. */
Int4 total_length;
Boolean has_mask = FALSE; /* Check for whether filter_maskloc is empty. */
Int4 index; /* loop variable. */
ASSERT(query_blk);
ASSERT(query_info);
ASSERT(filter_maskloc);
for (index=0; index<filter_maskloc->total_size; index++)
{
if (filter_maskloc->seqloc_array[index])
{
has_mask = TRUE;
break;
}
}
if (has_mask == FALSE)
return;
total_length = query_info->contexts[query_info->last_context].query_offset
+ query_info->contexts[query_info->last_context].query_length + 2;
query_blk->sequence_start_nomask = BlastMemDup(query_blk->sequence_start, total_length);
query_blk->sequence_nomask = query_blk->sequence_start_nomask + 1;
query_blk->nomask_allocated = TRUE;
for (context = query_info->first_context;
context <= query_info->last_context; ++context) {
Int4 query_length = 0;
Int4 context_offset = 0;
Uint1 *buffer = NULL; /* holds sequence */
if (query_info->contexts[context].is_valid == FALSE) {
continue;
}
query_length = query_info->contexts[context].query_length;
context_offset = query_info->contexts[context].query_offset;
buffer = &query_blk->sequence[context_offset];
ASSERT(buffer);
Blast_MaskTheResidues(buffer, query_length, kIsNucl,
filter_maskloc->seqloc_array[context],
BlastIsReverseStrand(kIsNucl, context), 0);
}
}
