NCBI C++ ToolKit
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Seq-align mapping | |
CRef< CSeq_align > | RemapAlignToLoc (const CSeq_align &align, CSeq_align::TDim row, const CSeq_loc &loc, CScope *scope=NULL) |
Remap seq-align row to the seq-loc. More... | |
string | GetProductString (const CSeq_align &align, CScope &scope) |
Given a spliced-seg alignment with MismatchedBases user object, compose product sequence data. More... | |
string GetProductString | ( | const CSeq_align & | align, |
CScope & | scope | ||
) |
Given a spliced-seg alignment with MismatchedBases user object, compose product sequence data.
Return empty string if the alignment is not a spliced-seg or if it does not contain MismatchedBases.
Definition at line 282 of file seq_align_util.cpp.
References CProductStringBuilder::GetProductString().
CRef<CSeq_align> RemapAlignToLoc | ( | const CSeq_align & | align, |
CSeq_align::TDim | row, | ||
const CSeq_loc & | loc, | ||
CScope * | scope = NULL |
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) |
Remap seq-align row to the seq-loc.
Treats the given row as being relative to the location, maps it to the sequence(s) referenced by this location.
align | The seq-align object to be mapped (the object will be modified!). |
row | Row to be mapped. |
loc | Seq-loc to which the row should be mapped. |
scope | Optional scope may be required by CSeq_loc_Mapper to process some locations (e.g. whole locations). |
Definition at line 52 of file seq_align_util.cpp.
References copy(), eNa_strand_unknown, GetLength(), CSeq_loc_Mapper_Base::Map(), NCBI_THROW, and CSeq_loc::SetStrand().