Example #1
0
//==========================================================================
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;
}
Example #2
0
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;
}