bool CBasicFastaWrapper::ReadAsSeqEntry(CNcbiIstream& iStream, CRef< CSeq_entry >& seqEntry)
{
bool result = ReadFile(iStream);
if (result) {
seqEntry->Assign(*m_seqEntry);
}
return result;
}
CRef< COrg_ref > GetCommonTax(CCdCore* cd, bool useRootWhenNoTaxInfo)
{
int comTax = 0;
CRef< COrg_ref > orgRef;
CTaxon1 taxServer;
if (!taxServer.Init())
return orgRef;
bool is_species;
bool is_uncultured;
string blast_name;
int num = cd->GetNumRows();
for (int i = 0; i < num; i++)
{
TGi gi = INVALID_GI;
cd->GetGI(i,gi,false);
int taxid = 0;
if (gi > ZERO_GI)
taxServer.GetTaxId4GI(gi, taxid);
if (taxid == 0)
{
CRef< CBioseq > bioseq;
if (cd->GetBioseqForRow(i, bioseq))
{
taxid = GetTaxIdInBioseq(*bioseq);
}
}
if (taxid > 0)
{
if (comTax == 0)
comTax = taxid;
else
{
int joined = taxServer.Join(comTax, taxid);
if (joined == 0)
{
LOG_POST("Failed to join two taxids:"<<comTax<<" and "<<taxid<<". The latter one is ignored.");
}
else
comTax = joined;
}
}
if (comTax == 1) //reach root
break;
}
// The condition 'comTax == 0' is true only if no row satisfied (taxid > 0) above.
// Use root tax node as common tax node unless told not to.
if (comTax == 0 && useRootWhenNoTaxInfo)
comTax = 1;
orgRef = new COrg_ref;
if (comTax > 0) {
orgRef->Assign(*taxServer.GetOrgRef(comTax, is_species, is_uncultured, blast_name));
} else {
orgRef.Reset();
}
return orgRef;
}
CRef<CSeq_feat> CFeatTrim::Apply(const CSeq_feat& feat,
const CRange<TSeqPos>& range)
{
CRef<CSeq_loc> loc = Ref(new CSeq_loc());
loc->Assign(feat.GetLocation());
const TSeqPos from = range.GetFrom();
const TSeqPos to = range.GetTo();
const bool set_partial = true;
x_TrimLocation(from, to, set_partial, loc);
if (loc->IsNull()) {
return Ref(new CSeq_feat());
}
// Create a new seq-feat with the trimmed location
CRef<CSeq_feat> new_sf(new CSeq_feat());
new_sf->Assign(feat);
new_sf->SetLocation(*loc);
if (!loc->IsNull() &&
(loc->IsPartialStart(eExtreme_Biological) ||
loc->IsPartialStop(eExtreme_Biological))) {
new_sf->SetPartial(true);
}
// If Cdregion need to consider changes in frameshift
if (new_sf->GetData().IsCdregion()) {
const TSeqPos offset = x_GetStartOffset(feat, from, to);
x_UpdateFrame(offset, new_sf->SetData().SetCdregion());
if (new_sf->SetData().SetCdregion().IsSetCode_break()) {
// iterate over code breaks and remove if they fall outside the range
list<CRef<CCode_break>>& code_breaks = new_sf->SetData().SetCdregion().SetCode_break();
code_breaks.remove_if(SOutsideRange(from,to));
if (code_breaks.empty()) {
new_sf->SetData().SetCdregion().ResetCode_break();
}
else {
const auto strand = loc->GetStrand();
// Trim the 3' end
if (strand != eNa_strand_minus) {
for (auto code_break : code_breaks) {
const TSeqPos cb_to = code_break->GetLoc().GetTotalRange().GetTo();
if (cb_to > to) {
x_TrimCodeBreak(from, to, *code_break);
}
}
}
else { // strand == eNa_strand_minus
for (auto code_break : code_breaks) {
const TSeqPos cb_from = code_break->GetLoc().GetTotalRange().GetFrom();
if (cb_from < from) {
x_TrimCodeBreak(from, to, *code_break);
}
}
}
}
}
}
else
if (new_sf->GetData().GetSubtype() == CSeqFeatData::eSubtype_tRNA) {
auto& rna = new_sf->SetData().SetRna();
if (rna.IsSetExt() && rna.GetExt().IsTRNA()) {
x_TrimTrnaExt(from, to, rna.SetExt().SetTRNA());
}
}
return new_sf;
}