//==========================================================================
void GeometryTools::splitSurfaceIntoPatches(const SplineSurface& sf,
vector<SplineSurface>& pat)
//==========================================================================
{
SplineSurface orig = sf;
orig.makeBernsteinKnotsU();
orig.makeBernsteinKnotsV();
int num_u = orig.numCoefs_u();
int num_v = orig.numCoefs_v();
int order_u = orig.order_u();
int order_v = orig.order_v();
int numpat_u = num_u / order_u;
int numpat_v = num_v / order_v;
pat.resize(numpat_u * numpat_v);
typedef vector<double>::const_iterator const_iter;
const_iter itu = orig.basis_u().begin();
const_iter itv;
for (int i = 0; i < numpat_u; ++i) {
itv = orig.basis_v().begin();
for (int j = 0; j < numpat_v; ++j) {
shared_ptr<SplineSurface>
new_sf(orig.subSurface(*itu, *itv,
*(itu+order_u), *(itv+order_v)));
pat[numpat_u*j + i] = *new_sf;
itv += order_v;
}
itu += order_u;
}
return;
}
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;
}