NCBI C++ ToolKit
Seq-align utilities
+ Collaboration diagram for Seq-align utilities:

Seq-align mapping

Seq-align mapping

CRef< CSeq_alignRemapAlignToLoc (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...
 

Detailed Description

Function Documentation

◆ GetProductString()

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().

◆ RemapAlignToLoc()

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.

Treats the given row as being relative to the location, maps it to the sequence(s) referenced by this location.

Parameters
alignThe seq-align object to be mapped (the object will be modified!).
rowRow to be mapped.
locSeq-loc to which the row should be mapped.
scopeOptional scope may be required by CSeq_loc_Mapper to process some locations (e.g. whole locations).
Returns
Reference to the new seq-align with the mapped row.

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().

Modified on Thu Mar 28 17:09:31 2024 by modify_doxy.py rev. 669887