void
CBlastScopeSource::AddDataLoaders(CRef<objects::CScope> scope)
{
const int blastdb_loader_priority =
kBlastDbLoaderPriority + (s_CountBlastDbDataLoaders() - 1);
// Note that these priorities are needed so that the CScope::AddXXX methods
// don't need a specific priority (the default will be fine).
if (!m_BlastDbLoaderName.empty()) {
_TRACE("Adding " << m_BlastDbLoaderName << " at priority " <<
blastdb_loader_priority);
scope->AddDataLoader(m_BlastDbLoaderName, blastdb_loader_priority);
}
if (!m_GbLoaderName.empty()) {
_TRACE("Adding " << m_GbLoaderName << " at priority " <<
(int)CBlastScopeSource::kGenbankLoaderPriority);
scope->AddDataLoader(m_GbLoaderName, kGenbankLoaderPriority);
}
}
void
InitializeSubject(CRef<blast::CBlastDatabaseArgs> db_args,
CRef<blast::CBlastOptionsHandle> opts_hndl,
bool is_remote_search,
CRef<blast::CLocalDbAdapter>& db_adapter,
CRef<objects::CScope>& scope)
{
db_adapter.Reset();
_ASSERT(db_args.NotEmpty());
CRef<CSearchDatabase> search_db = db_args->GetSearchDatabase();
// Initialize the scope...
if (is_remote_search) {
const bool is_protein =
Blast_SubjectIsProtein(opts_hndl->GetOptions().GetProgramType())
? true : false;
SDataLoaderConfig config(is_protein);
if (search_db.NotEmpty() && search_db->GetDatabaseName() != "n/a") {
config.m_BlastDbName = search_db->GetDatabaseName();
}
CBlastScopeSource scope_src(config);
// configure scope to fetch sequences remotely for formatting
if (scope.NotEmpty()) {
scope_src.AddDataLoaders(scope);
} else {
scope = scope_src.NewScope();
}
} else {
if (scope.Empty()) {
scope.Reset(new CScope(*CObjectManager::GetInstance()));
}
}
_ASSERT(scope.NotEmpty());
// ... and then the subjects
CRef<IQueryFactory> subjects;
if ( (subjects = db_args->GetSubjects(scope)) ) {
_ASSERT(search_db.Empty());
db_adapter.Reset(new CLocalDbAdapter(subjects, opts_hndl));
} else {
_ASSERT(search_db.NotEmpty());
try {
// Try to open the BLAST database even for remote searches, as if
// it is available locally, it will be better to fetch the
// sequence data for formatting from this (local) source
CRef<CSeqDB> seqdb = search_db->GetSeqDb();
db_adapter.Reset(new CLocalDbAdapter(*search_db));
scope->AddDataLoader(RegisterOMDataLoader(seqdb));
} catch (const CSeqDBException&) {
// The BLAST database couldn't be found, report this for local
// searches, but for remote searches go on.
if (is_remote_search ) {
db_adapter.Reset(new CLocalDbAdapter(*search_db));
} else {
throw;
}
}
}
/// Set the BLASTDB data loader as the default data loader (if applicable)
if (search_db.NotEmpty()) {
string dbloader_name =
s_FindBlastDbDataLoaderName(search_db->GetDatabaseName(),
search_db->IsProtein());
if ( !dbloader_name.empty() ) {
// FIXME: will this work with multiple BLAST DBs?
scope->AddDataLoader(dbloader_name,
CBlastDatabaseArgs::kSubjectsDataLoaderPriority);
_TRACE("Setting " << dbloader_name << " priority to "
<< (int)CBlastDatabaseArgs::kSubjectsDataLoaderPriority
<< " for subjects");
}
}
}
