Seq_align.hpp File Reference

#include <objects/seqalign/Seq_align_.hpp>
#include <objects/seqloc/Na_strand.hpp>
#include <util/range_coll.hpp>

Include dependency graph for Seq_align.hpp:

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Classes
class	CSeq_align
struct	CSeq_align::SIndel
struct	CSeq_align::SSeqIdChooser
	Create a Dense-seg from a Std-seg Used by AlnMgr to handle nucl2prot alignments. More...

Functions
CRef< CSeq_align >	RemapAlignToLoc (const CSeq_align &align, CSeq_align::TDim row, const CSeq_loc &loc)
	Remap seq-align row to the seq-loc. More...

Function Documentation

RemapAlignToLoc()

CRef<CSeq_align> RemapAlignToLoc	(	const CSeq_align &	align,
		CSeq_align::TDim	row,
		const CSeq_loc &	loc
	)

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.

Parameters

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.

Returns

Reference to the new seq-align with the mapped row.

Definition at line 1401 of file Seq_align.cpp.

References copy(), eNa_strand_unknown, CSeq_loc::GetId(), CSeq_loc::GetStrand(), CSeq_loc_Base::IsWhole(), len, CSeq_loc_Mapper_Base::Map(), NCBI_THROW, row, and CSeq_loc::SetStrand().

Referenced by s_RemapToSubjectLoc().