CRef<SInternalData>
SplitQuery_CreateChunkData(CRef<IQueryFactory> qf,
CRef<CBlastOptions> options,
CRef<SInternalData> full_data,
bool is_multi_threaded /* = false */)
{
BlastSeqSrc* seqsrc =
BlastSeqSrcCopy(full_data->m_SeqSrc->GetPointer());
CRef<SBlastSetupData> setup_data =
BlastSetupPreliminarySearchEx(
qf, options,
CRef<objects::CPssmWithParameters>(),
seqsrc, is_multi_threaded);
BlastSeqSrcResetChunkIterator(seqsrc);
setup_data->m_InternalData->m_SeqSrc.Reset(new TBlastSeqSrc(seqsrc,
BlastSeqSrcFree));
_ASSERT(setup_data->m_QuerySplitter->IsQuerySplit() == false);
if (full_data->m_ProgressMonitor->Get()) {
setup_data->m_InternalData->m_FnInterrupt = full_data->m_FnInterrupt;
SBlastProgress* bp =
SBlastProgressNew(full_data->m_ProgressMonitor->Get()->user_data);
setup_data->m_InternalData->m_ProgressMonitor.Reset(new CSBlastProgress(bp));
}
return setup_data->m_InternalData;
}
CPrelimSearchThread(SInternalData& internal_data,
const CBlastOptionsMemento* opts_memento)
: m_InternalData(internal_data), m_OptsMemento(opts_memento)
{
// The following fields need to be copied to ensure MT-safety
BlastSeqSrc* seqsrc =
BlastSeqSrcCopy(m_InternalData.m_SeqSrc->GetPointer());
m_InternalData.m_SeqSrc.Reset(new TBlastSeqSrc(seqsrc,
BlastSeqSrcFree));
// The progress field must be copied to ensure MT-safety
if (m_InternalData.m_ProgressMonitor->Get()) {
SBlastProgress* bp =
SBlastProgressNew(m_InternalData.m_ProgressMonitor->Get()->user_data);
m_InternalData.m_ProgressMonitor.Reset(new CSBlastProgress(bp));
}
}
Int2 SThreadLocalDataArraySetup(SThreadLocalDataArray* array,
EBlastProgramType program,
const BlastScoringOptions* score_options,
const BlastEffectiveLengthsOptions* eff_len_options,
const BlastExtensionOptions* ext_options,
const BlastHitSavingOptions* hit_options,
BlastQueryInfo* query_info,
BlastScoreBlk* sbp,
const BlastSeqSrc* seqsrc)
{
Uint4 i;
Int2 status = 0;
if (!array)
return BLASTERR_INVALIDPARAM;
for (i = 0; i < array->num_elems; i++) {
status =
BLAST_GapAlignSetUp(program, seqsrc, score_options, eff_len_options,
ext_options, hit_options, query_info, sbp,
&array->tld[i]->score_params,
&array->tld[i]->ext_params,
&array->tld[i]->hit_params,
&array->tld[i]->eff_len_params,
&array->tld[i]->gap_align);
if (status)
return status;
if ( !(array->tld[i]->query_info = BlastQueryInfoDup(query_info)) ) {
return BLASTERR_MEMORY;
}
if ( !(array->tld[i]->seqsrc = BlastSeqSrcCopy(seqsrc)) ) {
return BLASTERR_MEMORY;
}
if ( !(array->tld[i]->results = Blast_HSPResultsNew(query_info->num_queries)) ) {
return BLASTERR_MEMORY;
}
}
return 0;
}
