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;
}
