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;
}
bool
ReadWaypointFile(struct zzip_dir *dir, const char *path,
WaypointFileType file_type, Waypoints &way_points,
WaypointFactory factory, OperationEnvironment &operation)
{
auto *reader = CreateWaypointReader(file_type, factory);
if (reader == nullptr)
return false;
bool success = false;
ZipLineReader line_reader(dir, path, IgnoreError(), Charset::AUTO);
if (!line_reader.error()) {
reader->Parse(way_points, line_reader, operation);
success = true;
}
delete reader;
return success;
}
