int CSeq_id_Handle::CompareOrdered(const CSeq_id_Handle& id) const
{
// small optimization to avoid creation of temporary CSeq_id objects
if ( int diff = Which() - id.Which() ) {
return diff;
}
if ( IsGi() && id.IsGi() ) {
return GetGi() - id.GetGi();
}
return GetSeqId()->CompareOrdered(*id.GetSeqId());
}
Int8 CLDS2_Database::x_GetLdsSeqId(const CSeq_id_Handle& id)
{
CSQLITE_Statement* st = NULL;
if ( id.IsGi() ) {
// Try to use integer index
st = &x_GetStatement(eSt_GetLdsSeqIdForIntId);
st->Bind(1, id.GetGi());
}
else {
// Use text index
st = &x_GetStatement(eSt_GetLdsSeqIdForTxtId);
st->Bind(1, id.AsString());
}
if ( st->Step() ) {
Int8 ret = st->GetInt8(0);
st->Reset();
return ret;
}
// Id not in the database yet -- add new entry.
st = &x_GetStatement(eSt_AddLdsSeqId);
st->Bind(1, id.AsString());
if ( id.IsGi() ) {
st->Bind(2, id.GetGi());
}
else {
// HACK: reset GI to null if not available.
st->Bind(2, (void*)NULL, 0);
}
CNcbiOstrstream out;
out << MSerial_AsnBinary << *id.GetSeqId();
string buf = CNcbiOstrstreamToString(out);
st->Bind(3, buf.size());
st->Bind(4, buf.data(), buf.size());
st->Execute();
Int8 ret = st->GetLastInsertedRowid();
st->Reset();
return ret;
}
int
CLocalBlastDbAdapter::GetTaxId(const CSeq_id_Handle& idh)
{
int retval = static_cast<int>(kInvalidSeqPos);
CConstRef<CSeq_id> id = idh.GetSeqId();
if (id.NotEmpty()) {
int oid = 0;
if (SeqidToOid(*id, oid)) {
map<int, int> gi_to_taxid;
m_SeqDB->GetTaxIDs(oid, gi_to_taxid);
if (idh.IsGi()) {
retval = gi_to_taxid[GI_TO(int, idh.GetGi())];
} else {