void
SplitQuery_SetEffectiveSearchSpace(CRef<CBlastOptions> options,
CRef<IQueryFactory> full_query_fact,
CRef<SInternalData> full_data)
{
_ASSERT(full_data);
_ASSERT(full_data->m_SeqSrc);
// If the effective search options have been set, we don't need to
// recompute those...
if (options->GetEffectiveSearchSpace() != 0) {
return;
}
const BlastSeqSrc* seqsrc = full_data->m_SeqSrc->GetPointer();
Int8 total_length = BlastSeqSrcGetTotLenStats(seqsrc);
if (total_length <= 0)
total_length = BlastSeqSrcGetTotLen(seqsrc);
Int4 num_seqs = BlastSeqSrcGetNumSeqsStats(seqsrc);
if (num_seqs <= 0)
num_seqs = BlastSeqSrcGetNumSeqs(seqsrc);
CEffectiveSearchSpaceCalculator calc(full_query_fact, *options,
num_seqs, total_length,
full_data->m_ScoreBlk->GetPointer());
BlastQueryInfo* qinfo = full_data->m_QueryInfo;
_ASSERT(qinfo);
vector<Int8> eff_searchsp;
for (size_t index = 0; index <= (size_t)qinfo->last_context; index++) {
eff_searchsp.push_back(calc.GetEffSearchSpaceForContext(index));
}
options->SetEffectiveSearchSpace(eff_searchsp);
}
Int2
Blast_DatabaseSearch(SeqLoc* query_seqloc,
Blast_PsiCheckpointLoc * psi_checkpoint,
char* db_name,
SeqLoc* masking_locs,
const SBlastOptions* options,
BlastTabularFormatData* tf_data,
SBlastSeqalignArray* *seqalign_arr,
SeqLoc** filter_out,
Blast_SummaryReturn* extra_returns)
{
BlastSeqSrc *seq_src = NULL;
Boolean db_is_prot;
Int2 status = 0;
BlastHSPResults* results = NULL;
ReadDBFILE* rdfp = NULL;
if (!options || !query_seqloc || !db_name || !extra_returns)
return -1;
db_is_prot =
(options->program == eBlastTypeBlastp ||
options->program == eBlastTypeBlastx ||
options->program == eBlastTypeRpsBlast ||
options->program == eBlastTypeRpsTblastn);
rdfp = readdb_new(db_name, db_is_prot);
seq_src = ReaddbBlastSeqSrcAttach(rdfp);
if (seq_src == NULL) {
SBlastMessageWrite(&extra_returns->error, SEV_WARNING,
"Initialization of subject sequences source failed",
NULL, options->believe_query);
} else if (BlastSeqSrcGetNumSeqs(seq_src) == 0) {
SBlastMessageWrite(&extra_returns->error, SEV_WARNING,
"Database is empty", NULL, options->believe_query);
} else {
char* error_str = BlastSeqSrcGetInitError(seq_src);
if (error_str)
SBlastMessageWrite(&extra_returns->error, SEV_WARNING, error_str, NULL, options->believe_query);
}
/* If there was an error initializing the sequence source, return without
doing the search. */
if (extra_returns->error)
return -1;
status =
Blast_RunSearch(query_seqloc, psi_checkpoint, seq_src,
masking_locs, options, tf_data, &results,
filter_out, extra_returns);
/* The ReadDBFILE structure will not be destroyed here, because the
initialising function used readdb_attach */
BlastSeqSrcFree(seq_src);
if (!status && !tf_data) {
status =
BLAST_ResultsToSeqAlign(options->program, &results,
query_seqloc, rdfp, NULL,
options->score_options->gapped_calculation,
options->score_options->is_ooframe,
seqalign_arr);
}
readdb_destruct(rdfp);
if (status)
return status;
return status;
}
