SearchWorker::SearchWorker(Options* opts,
QueryInfo* qi,
FMIndex* index,
DbInfo* di,
CSymDustMasker* csdm,
CSeqMasker* win_m,
int tid)
{
ASSERT(opts != NULL);
global_queries = qi;
options = opts;
fmindex = index;
dbinfo = di;
results = new OutputFormat(options->output_options, options->hit_options, dbinfo);
dust_masker = csdm;
window_masker = win_m;
thread_id = tid;
word_params = NULL;
ext_params = NULL;
hit_params = NULL;
eff_params = NULL;
score_params = NULL;
sbp = NULL;
gapped_aligner = NULL;
eff_options = BlastEffectiveLengthsOptionsNew();
}
Int2 BLAST_InitDefaultOptions(EBlastProgramType program_number,
LookupTableOptions** lookup_options,
QuerySetUpOptions** query_setup_options,
BlastInitialWordOptions** word_options,
BlastExtensionOptions** ext_options,
BlastHitSavingOptions** hit_options,
BlastScoringOptions** score_options,
BlastEffectiveLengthsOptions** eff_len_options,
PSIBlastOptions** psi_options,
BlastDatabaseOptions** db_options)
{
Int2 status;
if ((status = LookupTableOptionsNew(program_number, lookup_options)))
return status;
if ((status=BlastQuerySetUpOptionsNew(query_setup_options)))
return status;
if ((status=BlastInitialWordOptionsNew(program_number, word_options)))
return status;
if ((status=BlastScoringOptionsNew(program_number, score_options)))
return status;
if ((status = BlastExtensionOptionsNew(program_number, ext_options,
(*score_options)->gapped_calculation)))
return status;
if ((status=BlastHitSavingOptionsNew(program_number, hit_options,
(*score_options)->gapped_calculation)))
return status;
if ((status=BlastEffectiveLengthsOptionsNew(eff_len_options)))
return status;
if ((status=PSIBlastOptionsNew(psi_options)))
return status;
if ((status=BlastDatabaseOptionsNew(db_options)))
return status;
return 0;
}
/// Parametrized constructor
/// @param options the BLAST options [in]
CEffectiveSearchSpacesMemento(CBlastOptions* options)
: m_Options(options), m_EffLenOrig(0), m_EffLenReplace(0)
{
_ASSERT(options);
if (options->m_Local) {
m_EffLenOrig = options->m_Local->m_EffLenOpts.Release();
BlastEffectiveLengthsOptionsNew(&m_EffLenReplace);
memcpy((void*) m_EffLenReplace,
(void*) m_EffLenOrig,
sizeof(*m_EffLenOrig));
m_EffLenReplace->searchsp_eff =
(Int8*)malloc(sizeof(Int8) * m_EffLenOrig->num_searchspaces);
memcpy((void*) m_EffLenReplace->searchsp_eff,
(void*) m_EffLenOrig->searchsp_eff,
sizeof(Int8) * m_EffLenOrig->num_searchspaces);
options->m_Local->m_EffLenOpts.Reset(m_EffLenReplace);
}
}