// --------------------------------------------------------------------------
CSeq_entry_Handle CAsn2FastaApp::ObtainSeqEntryFromBioseqSet(
CObjectIStream& is)
// --------------------------------------------------------------------------
{
try {
CRef<CSeq_entry> entry(new CSeq_entry);
is >> entry->SetSet();
return m_Scope->AddTopLevelSeqEntry(*entry);
}
catch (CException& e) {
if (! (is.GetFailFlags() & is.eEOF)) {
ERR_POST(Error << e);
}
}
return CSeq_entry_Handle();
}
// --------------------------------------------------------------------------
CSeq_entry_Handle CAsn2FastaApp::ObtainSeqEntryFromBioseq(
CObjectIStream& is)
// --------------------------------------------------------------------------
{
try {
CRef<CBioseq> bs(new CBioseq);
is >> *bs;
CBioseq_Handle bsh = m_Scope->AddBioseq(*bs);
return bsh.GetTopLevelEntry();
}
catch (CException& e) {
if (! (is.GetFailFlags() & is.eEOF)) {
ERR_POST(Error << e);
}
}
return CSeq_entry_Handle();
}
// --------------------------------------------------------------------------
CSeq_entry_Handle CAsn2FastaApp::ObtainSeqEntryFromSeqEntry(
CObjectIStream& is)
// --------------------------------------------------------------------------
{
try {
CRef<CSeq_entry> se(new CSeq_entry);
is >> *se;
if (se->Which() == CSeq_entry::e_not_set) {
NCBI_THROW(CException, eUnknown,
"provided Seq-entry is empty");
}
return m_Scope->AddTopLevelSeqEntry(*se);
}
catch (CException& e) {
if (! (is.GetFailFlags() & is.eEOF)) {
ERR_POST(Error << e);
}
}
return CSeq_entry_Handle();
}
