TGi CAsnCache_DataLoader::GetGi(const CSeq_id_Handle& idh)
{
SCacheInfo& index = x_GetIndex();
CFastMutexGuard LOCK(index.cache_mtx);
CAsnIndex::TGi gi = 0;
time_t timestamp = 0;
if (index.cache->GetIdInfo(idh, gi, timestamp)) {
//LOG_POST(Error << "CAsnCache_DataLoader::GetGi(): " << idh << " -> " << gi);
return GI_FROM(CAsnIndex::TGi, gi);
}
return ZERO_GI;
}
/// not yet in SC-6.0...
void CAsnCache_DataLoader::GetGis(const TIds& ids, TLoaded& loaded, TIds& ret)
{
SCacheInfo& index = x_GetIndex();
CFastMutexGuard LOCK(index.cache_mtx);
ret.clear();
ret.resize(ids.size());
loaded.clear();
loaded.resize(ids.size());
for (size_t i = 0; i < ids.size(); ++i) {
CAsnIndex::TGi gi = 0;
time_t timestamp = 0;
if (index.cache->GetIdInfo(ids[i], gi, timestamp)) {
ret[i] = CSeq_id_Handle::GetHandle(GI_FROM(CAsnIndex::TGi, gi));
loaded[i] = true;
}
}
}
void CSeqTableLocColumns::ParseDefaults(void)
{
if ( !m_Is_set ) {
return;
}
if ( m_Loc ) {
m_Is_real_loc = true;
if ( m_Id || m_Gi || m_From || m_To || m_Strand ||
!m_ExtraColumns.empty() ) {
NCBI_THROW_FMT(CAnnotException, eBadLocation,
"Conflicting "<<m_FieldName<<" columns");
}
return;
}
if ( !m_Id && !m_Gi ) {
NCBI_THROW_FMT(CAnnotException, eBadLocation,
"No "<<m_FieldName<<".id column");
}
if ( m_Id && m_Gi ) {
NCBI_THROW_FMT(CAnnotException, eBadLocation,
"Conflicting "<<m_FieldName<<" columns");
}
if ( m_Id ) {
if ( m_Id->IsSetDefault() ) {
m_DefaultIdHandle =
CSeq_id_Handle::GetHandle(m_Id->GetDefault().GetId());
}
}
if ( m_Gi ) {
if ( m_Gi->IsSetDefault() ) {
m_DefaultIdHandle =
CSeq_id_Handle::GetGiHandle(
GI_FROM(CSeqTable_single_data::TInt, m_Gi->GetDefault().GetInt()));
}
}
if ( m_To ) {
// interval
if ( !m_From ) {
NCBI_THROW_FMT(CAnnotException, eBadLocation,
"column "<<m_FieldName<<".to without "<<
m_FieldName<<".from");
}
m_Is_simple_interval = true;
}
else if ( m_From ) {
// point
m_Is_simple_point = true;
}
else {
// whole
if ( m_Strand || !m_ExtraColumns.empty() ) {
NCBI_THROW_FMT(CAnnotException, eBadLocation,
"extra columns in whole "<<m_FieldName);
}
m_Is_simple_whole = true;
}
if ( m_ExtraColumns.empty() ) {
m_Is_simple = true;
}
else {
m_Is_probably_simple = true;
}
}