C++ (Cpp) subject_p Examples

Example #1

File: search_strategy.cpp Project: timothyjlaurent/nacl_blast

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);
    }
}

Example #2

File: search_strategy.cpp Project: DmitrySigaev/ncbi

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));
       		}