bool CSeq_id_Handle::operator==(const CSeq_id& id) const
{
if ( IsGi() ) {
return id.IsGi() && id.GetGi() == m_Packed;
}
return *this == GetMapper().GetHandle(id);
}
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;
}
static string s_IdLabel(const CSeq_id& cxx_id, EIDLabelType type)
{
string label;
CSeq_id::ELabelType gl_type = CSeq_id::eContent;
CSeq_id::TLabelFlags flags = (CSeq_id::fLabel_Version |
CSeq_id::fLabel_GeneralDbIsContent);
switch (type) {
case eFastaShort: gl_type = CSeq_id::eFasta; break;
case eTextAccOnly: flags &= ~CSeq_id::fLabel_Version; break;
case eReport: flags &= ~CSeq_id::fLabel_GeneralDbIsContent; break;
default: break;
}
cxx_id.GetLabel(&label, gl_type, flags);
return label;
}
bool CFastaDeflineReader::x_IsValidLocalID(const CSeq_id& id, TFastaFlags fasta_flags)
{
string id_label;
id.GetLabel(&id_label, 0, CSeq_id::eContent);
return x_IsValidLocalID(id_label, fasta_flags);
}
CBioseq_Handle CSimpleOM::GetBioseqHandle(TGi gi)
{
CSeq_id id;
id.SetGi(gi);
return GetBioseqHandle(id);
}
