///////////////////////////////////////////////////////
///
/// Read a string from a stream. The string is following
/// by its size
///
inline string ReadStringFromStream(CNcbiIstream& is)
{
string str;
if (!is.good() || is.eof())
return str;
size_t size;
is >> size;
if (!is.good() || is.eof())
return str;
vector<char> buf(size+1, 0);
is.read(&*buf.begin(), size+1);
size_t count = is.gcount();
if (count > 0)
str.append((&*buf.begin())+1, count-1);
return str;
}
bool CBasicFastaWrapper::ReadFile(CNcbiIstream& iStream)
{
bool result = (iStream.good());
if (!result) {
m_error = "Read Error: invalid stream.\n";
} else {
CNcbiOstrstream oss;
oss << iStream.rdbuf();
iStream.seekg(0);
m_activeFastaString = CNcbiOstrstreamToString(oss);
if (m_cacheRawFasta) m_rawFastaString = m_activeFastaString;
// temporarily turn off warning messages (in case of '.' in *.a2m files)
EDiagSev originalDiagSev = SetDiagPostLevel(eDiag_Error);
try{
CStreamLineReader lineReader(iStream);
CFastaReader fastaReader(lineReader, m_readFastaFlags);
//CCounterManager counterMgr(reader.SetIDGenerator(), NULL);
m_seqEntry = fastaReader.ReadSet();
// If there is only one sequence in the fasta, the Seq-entry returned is a Bioseq and not a Bioseq-set.
// In that case, change the Bioseq to a Bioseq-set so caller doesn't have to manage multiple Seq-entry choices.
if (m_seqEntry->IsSeq() && m_useBioseqSet) {
CRef<CSeq_entry> bioseqFromFasta(new CSeq_entry);
bioseqFromFasta->Assign(*m_seqEntry);
m_seqEntry->Select(CSeq_entry::e_Set);
m_seqEntry->SetSet().SetSeq_set().push_back(bioseqFromFasta);
}
} catch (...) {
result = false;
m_seqEntry.Reset();
}
if (m_seqEntry.Empty()) {
result = false;
m_error = "Read Error: empty seq entry.\n";
}
SetDiagPostLevel(originalDiagSev);
}
return result;
}