void x_LoadSequences(const string& filename, bool parse_id)
{
CNcbiIfstream instream(filename.c_str());
BOOST_REQUIRE(instream);
CStreamLineReader line_reader(instream);
CFastaReader::TFlags flags = 0;
if (!parse_id) {
flags |= CFastaReader::fNoParseID;
}
CFastaReader fasta_reader(line_reader, flags);
fasta_reader.IgnoreProblem(
ILineError::eProblem_ModifierFoundButNoneExpected);
while (!line_reader.AtEOF()) {
CRef<CSeq_entry> entry = fasta_reader.ReadOneSeq();
if (entry == 0) {
NCBI_THROW(CObjReaderException, eInvalid,
"Could not retrieve seq entry");
}
m_Scope->AddTopLevelSeqEntry(*entry);
CTypeConstIterator<CBioseq> itr(ConstBegin(*entry));
}
}
// --------------------------------------------------------------------------
bool CAsn2FastaApp::HandleSeqEntry(CRef<CSeq_entry>& se)
// --------------------------------------------------------------------------
{
CSeq_entry_Handle seh = m_Scope->AddTopLevelSeqEntry(*se);
bool ret = HandleSeqEntry(seh);
m_Scope->RemoveTopLevelSeqEntry(seh);
return ret;
}
// --------------------------------------------------------------------------
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();
}
int ReadFastaQueries(const string& filename,
vector< CRef<objects::CSeq_loc> >& seqs,
CRef<objects::CScope>& scope,
bool parse_deflines /* = false*/,
objects::CSeqIdGenerator* id_generator /* = NULL*/)
{
seqs.clear();
CNcbiIfstream instream(filename.c_str());
if (!instream) {
return -1;
}
CStreamLineReader line_reader(instream);
CFastaReader::TFlags flags = CFastaReader::fAssumeProt |
CFastaReader::fForceType;
if (!parse_deflines) {
flags |= CFastaReader::fNoParseID;
}
CFastaReader fasta_reader(line_reader, flags);
if (id_generator) {
fasta_reader.SetIDGenerator(*id_generator);
}
scope->AddDefaults();
while (!line_reader.AtEOF()) {
CRef<CSeq_entry> entry = fasta_reader.ReadOneSeq();
if (entry == 0) {
return -1;
}
scope->AddTopLevelSeqEntry(*entry);
CTypeConstIterator<CBioseq> itr(ConstBegin(*entry));
CRef<CSeq_loc> seqloc(new CSeq_loc());
seqloc->SetWhole().Assign(*itr->GetId().front());
seqs.push_back(seqloc);
}
return 0;
}
int ReadMsa(const string& filename, CRef<CSeq_align>& align,
CRef<CScope> scope, bool parse_deflines /* = false*/,
objects::CSeqIdGenerator* id_generator /* = NULL*/)
{
if (scope.Empty()) {
return -1;
}
CNcbiIfstream instream(filename.c_str());
if (!instream) {
return -1;
}
CStreamLineReader line_reader(instream);
CFastaReader::TFlags flags = CFastaReader::fAssumeProt |
CFastaReader::fForceType | CFastaReader::fValidate;
if (!parse_deflines) {
flags |= CFastaReader::fNoParseID;
}
CFastaReader fasta_reader(line_reader, flags);
if (id_generator) {
fasta_reader.SetIDGenerator(*id_generator);
}
CRef<CSeq_entry> entry = fasta_reader.ReadAlignedSet(-1);
if (entry.Empty()) {
return -1;
}
scope->AddTopLevelSeqEntry(*entry);
// notify of a problem if the whole file was not read
if (!line_reader.AtEOF()) {
return -1;
}
align = entry->GetAnnot().front()->GetData().GetAlign().front();
return 0;
}
// --------------------------------------------------------------------------
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();
}