bool CSeqAnnotFromFasta::PurgeNonAlphaFromSequence(CBioseq& bioseq) {
bool result = false;
CSeq_inst::TLength newLength;
string originalSequence;
// CRef< CBioseq > bioseq;
// if (cd.GetBioseqForIndex(index, bioseq)) {
if (bioseq.GetInst().IsSetSeq_data()) {
CSeq_data& seqData = bioseq.SetInst().SetSeq_data();
if (seqData.IsNcbieaa()) {
originalSequence = seqData.SetNcbieaa().Set();
} else if (seqData.IsIupacaa()) {
originalSequence = seqData.SetIupacaa().Set();
} else if (seqData.IsNcbistdaa()) {
std::vector < char >& vec = seqData.SetNcbistdaa().Set();
NcbistdaaToNcbieaaString(vec, &originalSequence);
}
if (PurgeNonAlpha(originalSequence)) {
// if (originalSequence.length() > 0 && find_if(originalSequence.begin(), originalSequence.end(), isNotAlpha) != originalSequence.end()) {
// originalSequence.erase(remove_if(originalSequence.begin(), originalSequence.end(), isNotAlpha), originalSequence.end());
// _TRACE("after remove non-alpha: \n" << originalSequence);
seqData.Select(CSeq_data::e_Ncbieaa);
seqData.SetNcbieaa().Set(originalSequence);
result = true;
}
newLength = originalSequence.length();
bioseq.SetInst().SetLength(newLength);
}
// }
return result;
}
//
// CreateConsensus()
//
// compute a consensus sequence given a particular alignment
// the rules for a consensus are:
// - a segment is consensus gap if > 50% of the sequences are gap at this
// segment. 50% exactly is counted as sequence
// - for a segment counted as sequence, for each position, the most
// frequently occurring base is counted as consensus. in the case of
// a tie, the consensus is considered muddied, and the consensus is
// so marked
//
CRef<CDense_seg>
CAlnVec::CreateConsensus(int& consensus_row, CBioseq& consensus_seq,
const CSeq_id& consensus_id) const
{
consensus_seq.Reset();
if ( !m_DS || m_NumRows < 1) {
return CRef<CDense_seg>();
}
bool isNucleotide = GetBioseqHandle(0).IsNucleotide();
size_t i;
size_t j;
// temporary storage for our consensus
vector<string> consens(m_NumSegs);
CreateConsensus(consens);
//
// now, create a new CDense_seg
// we create a new CBioseq for our data and
// copy the contents of the CDense_seg
//
string data;
TSignedSeqPos total_bases = 0;
CRef<CDense_seg> new_ds(new CDense_seg());
new_ds->SetDim(m_NumRows + 1);
new_ds->SetNumseg(m_NumSegs);
new_ds->SetLens() = m_Lens;
new_ds->SetStarts().reserve(m_Starts.size() + m_NumSegs);
if ( !m_Strands.empty() ) {
new_ds->SetStrands().reserve(m_Strands.size() +
m_NumSegs);
}
for (i = 0; i < consens.size(); ++i) {
// copy the old entries
for (j = 0; j < (size_t)m_NumRows; ++j) {
int idx = i * m_NumRows + j;
new_ds->SetStarts().push_back(m_Starts[idx]);
if ( !m_Strands.empty() ) {
new_ds->SetStrands().push_back(m_Strands[idx]);
}
}
// add our new entry
// this places the consensus as the last sequence
// it should preferably be the first, but this would mean adjusting
// the bioseq handle and seqvector caches, and all row numbers would
// shift
if (consens[i].length() != 0) {
new_ds->SetStarts().push_back(total_bases);
} else {
new_ds->SetStarts().push_back(-1);
}
if ( !m_Strands.empty() ) {
new_ds->SetStrands().push_back(eNa_strand_unknown);
}
total_bases += consens[i].length();
data += consens[i];
}
// copy our IDs
for (i = 0; i < m_Ids.size(); ++i) {
new_ds->SetIds().push_back(m_Ids[i]);
}
// now, we construct a new Bioseq
{{
// sequence ID
CRef<CSeq_id> id(new CSeq_id());
id->Assign(consensus_id);
consensus_seq.SetId().push_back(id);
new_ds->SetIds().push_back(id);
// add a description for this sequence
CSeq_descr& desc = consensus_seq.SetDescr();
CRef<CSeqdesc> d(new CSeqdesc);
desc.Set().push_back(d);
d->SetComment("This is a generated consensus sequence");
// the main one: Seq-inst
CSeq_inst& inst = consensus_seq.SetInst();
inst.SetRepr(CSeq_inst::eRepr_raw);
inst.SetMol(isNucleotide ? CSeq_inst::eMol_na : CSeq_inst::eMol_aa);
inst.SetLength(data.length());
CSeq_data& seq_data = inst.SetSeq_data();
if (isNucleotide) {
CIUPACna& na = seq_data.SetIupacna();
na = CIUPACna(data);
} else {
CIUPACaa& aa = seq_data.SetIupacaa();
aa = CIUPACaa(data);
}
}}
consensus_row = new_ds->GetIds().size() - 1;
return new_ds;
}
