/// Overloaded method to attempt to read non-FASTA input types
virtual CRef<CSeq_entry> ReadOneSeq(ILineErrorListener * pMessageListener) {
const string line = NStr::TruncateSpaces_Unsafe(*++GetLineReader());
if ( !line.empty() && isalnum(line.data()[0]&0xff) ) {
try {
CRef<CSeq_id> id(new CSeq_id(line, (CSeq_id::fParse_AnyRaw |
CSeq_id::fParse_ValidLocal)));
if (id->IsLocal() && !NStr::StartsWith(line, "lcl|") ) {
// Expected to throw an exception.
id.Reset(new CSeq_id(line));
}
CRef<CBioseq> bioseq(x_CreateBioseq(id));
CRef<CSeq_entry> retval(new CSeq_entry());
retval->SetSeq(*bioseq);
return retval;
} catch (const CSeqIdException& e) {
if (NStr::Find(e.GetMsg(), "Malformatted ID") != NPOS) {
// This is probably just plain fasta, so just
// defer to CFastaReader
} else {
throw;
}
} catch (const exception&) {
throw;
} catch (...) {
// in case of other exceptions, just defer to CFastaReader
}
} // end if ( !line.empty() ...
// If all fails, fall back to parent's implementation
GetLineReader().UngetLine();
return CFastaReader::ReadOneSeq(pMessageListener);
}
CRef<CDense_seg> CAlnVec::CreateConsensus(int& consensus_row,
const CSeq_id& consensus_id) const
{
CRef<CBioseq> bioseq(new CBioseq);
CRef<CDense_seg> ds = CreateConsensus(consensus_row,
*bioseq, consensus_id);
// add bioseq to the scope
CRef<CSeq_entry> entry(new CSeq_entry());
entry->SetSeq(*bioseq);
GetScope().AddTopLevelSeqEntry(*entry);
return ds;
}
void SequenceTable::addSequences(CSeq_entry& seqEntry)
{
if (seqEntry.IsSet())
{
list< CRef< CSeq_entry > >& seqSet = seqEntry.SetSet().SetSeq_set();
list< CRef< CSeq_entry > >::iterator it = seqSet.begin();
for (; it != seqSet.end(); it++)
addSequences(*(*it));
}
else
{
CRef< CBioseq > bioseq(&(seqEntry.SetSeq()));
addSequence(bioseq);
}
}
