DIAlign::Alignment Namespace Reference

Contains some of the core alignment functions for non-affine alignment. More...

Functions
AlignObj	doAlignment (SimMatrix s, double gap, bool OverlapAlignment)
	This function performs dynamic programming and calculates AlignObj::M and Traceback. More...
void	getAlignedIndices (AlignObj &alignObj)
	This tracebacks along the highest scoring path, preparing list of scores and aligned indices. More...

Detailed Description

Contains some of the core alignment functions for non-affine alignment.

See doAlignment() and getAlignedIndices().

Function Documentation

AlignObj DIAlign::Alignment::doAlignment	(	SimMatrix	s,
		double	gap,
		bool	OverlapAlignment
	)

This function performs dynamic programming and calculates AlignObj::M and Traceback.

Traceback matrix keeps record of the path as we fill matrix M.

void DIAlign::Alignment::getAlignedIndices

(

AlignObj &

alignObj

)

This tracebacks along the highest scoring path, preparing list of scores and aligned indices.

It calculates row and column index pair associated with the highest scoring path through similarity matrix. Output is a list of row-column index pairs of all highest scoring traceback paths.