void CExportStrategy::x_Process_SearchDb(CRef<CSearchDatabase> & db)
{
if (db.Empty())
{
NCBI_THROW(CBlastException, eInvalidArgument,
"Empty reference for CSearchDatabase.");
}
if (db->GetDatabaseName().empty())
{
NCBI_THROW(CBlastException, eInvalidArgument,
"Error: No database specified");
}
// Set database Name
CRef<CBlast4_subject> subject_p(new CBlast4_subject);
subject_p->SetDatabase(db->GetDatabaseName());
m_QueueSearchRequest->SetSubject(*subject_p);
// Set Entrez Query Limitation
string entrez_query_limit = db->GetEntrezQueryLimitation();
if(!entrez_query_limit.empty())
{
CRef<CBlast4_parameter> p(new CBlast4_parameter);
p->SetName(CBlast4Field::GetName(eBlastOpt_EntrezQuery));
CRef<CBlast4_value> v(new CBlast4_value);
v->SetString().assign(entrez_query_limit);
p->SetValue(*v);
_ASSERT(CBlast4Field::Get(eBlastOpt_EntrezQuery).Match(*p));
m_QueueSearchRequest->SetProgram_options().Set().push_back(p);
}
// Set the GI List Limitation
const CSearchDatabase::TGiList& gi_list_limit = db->GetGiListLimitation();
if (!gi_list_limit.empty())
{
x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_GiList), gi_list_limit);
}
// Set the negative GI list
const CSearchDatabase::TGiList& neg_gi_list = db->GetNegativeGiListLimitation();
if (!neg_gi_list.empty())
{
x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_NegativeGiList), neg_gi_list);
}
// Set the filtering algorithms
int algo_id = db->GetFilteringAlgorithm();
if (algo_id != -1)
{
x_AddParameterToProgramOptions(CBlast4Field::Get(eBlastOpt_DbFilteringAlgorithmId), algo_id);
}
}
void CExportStrategy::x_Process_SearchDb(CRef<CSearchDatabase> & db)
{
if (db.Empty())
{
NCBI_THROW(CBlastException, eInvalidArgument,
"Empty reference for CSearchDatabase.");
}
if (db->GetDatabaseName().empty())
{
NCBI_THROW(CBlastException, eInvalidArgument,
"Error: No database specified");
}
// Set database Name
CRef<CBlast4_subject> subject_p(new CBlast4_subject);
subject_p->SetDatabase(db->GetDatabaseName());
m_QueueSearchRequest->SetSubject(*subject_p);
// Set Entrez Query Limitation
string entrez_query_limit = db->GetEntrezQueryLimitation();
if(!entrez_query_limit.empty())
{
CRef<CBlast4_parameter> p(new CBlast4_parameter);
p->SetName(CBlast4Field::GetName(eBlastOpt_EntrezQuery));
CRef<CBlast4_value> v(new CBlast4_value);
v->SetString().assign(entrez_query_limit);
p->SetValue(*v);
_ASSERT(CBlast4Field::Get(eBlastOpt_EntrezQuery).Match(*p));
m_QueueSearchRequest->SetProgram_options().Set().push_back(p);
}
// Set the GI List Limitation
const CSearchDatabase::TGiList& gi_list_limit = db->GetGiListLimitation();
if (!gi_list_limit.empty())
{
#ifdef NCBI_STRICT_GI
vector<int> int_gi_list;
ITERATE ( vector<TGi>, it, gi_list_limit ) {
int_gi_list.push_back(GI_TO( int, *it));
}