void Application::processContigs(const BOOM::String &contigsFile,
BOOM::Map<BOOM::String,TranscriptList*> &transcriptMap)
{
BOOM::FastaReader fastaReader(contigsFile);
BOOM::String def, seq;
while(fastaReader.nextSequence(def,seq))
{
BOOM::String substrate=BOOM::FastaReader::getId(def);
if(transcriptMap.isDefined(substrate))
{
TranscriptList &transcripts=*transcriptMap[substrate];
int n=transcripts.size();
for(int i=0 ; i<n ; ++i)
{
BOOM::GffTranscript *feature=transcripts[i];
switch(feature->getStrand())
{
case '+':
processForwardFeature(feature->getEnd(),seq);
break;
case '-':
processReverseFeature(feature->getBegin(),seq);
break;
default:
continue;
}
}
}
}
}
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;
}
