int CTitleTester::Run(void)
{
const CArgs& args = GetArgs();
CRef<CObjectManager> objmgr = CObjectManager::GetInstance();
CScope scope(*objmgr);
CSeq_id id;
CGBDataLoader::RegisterInObjectManager(*objmgr);
scope.AddDefaults();
CDeflineGenerator gen;
CDeflineGenerator::TUserFlags flags = 0;
if (args["reconstruct"]) {
flags |= CDeflineGenerator::fIgnoreExisting;
}
if (args["allproteins"]) {
flags |= CDeflineGenerator::fAllProteinNames;
}
if (args["localannots"]) {
flags |= CDeflineGenerator::fLocalAnnotsOnly;
}
if (args["gi"]) {
id.SetGi(args["gi"].AsInteger());
CBioseq_Handle handle = scope.GetBioseqHandle(id);
NcbiCout << gen.GenerateDefline(handle, flags) << NcbiEndl;
} else {
CNcbiIstream& in(args["in"].AsInputFile());
while (in >> id.SetGi()) {
string s;
try {
CBioseq_Handle handle = scope.GetBioseqHandle(id);
s = gen.GenerateDefline(handle, flags);
} catch (exception& e) {
s = e.what();
}
NcbiCout << id.GetGi() << ": " << s << NcbiEndl;
}
}
return 0;
}
CBioseq_Handle CSimpleOM::GetBioseqHandle(TGi gi)
{
CSeq_id id;
id.SetGi(gi);
return GetBioseqHandle(id);
}