DIAlign::ConstrainMatrix Namespace Reference

Namespace for constraing similarity score matrix. More...

Functions
void	calcNoBeefMask (SimMatrix &MASK, double A1, double A2, double B1, double B2, double B1p, double B2p, int noBeef, bool hardConstrain)
	Fill a diagonal strip with one through the matrix MASK. More...
void	constrainSimilarity (SimMatrix &s, const SimMatrix &MASK, double constrainVal)
	Applies the mask from calcNoBeefMask() on the similarity matrix. More...

Detailed Description

Namespace for constraing similarity score matrix.

Function Documentation

void DIAlign::ConstrainMatrix::calcNoBeefMask	(	SimMatrix &	MASK,
		double	A1,
		double	A2,
		double	B1,
		double	B2,
		double	B1p,
		double	B2p,
		int	noBeef,
		bool	hardConstrain
	)

Fill a diagonal strip with one through the matrix MASK.

A1 and A2 are end-coordinates of signal A, similarly, B1 and B2 are end-coordinates for signal B. B1P and B2p are mapping of A1 and A2 calculated through some external mapper. The function fits a line between (A1, B1p) and (A2, B2p). It further sets every value as 0 for the cells that are within distance noBeef from the line. Other cells are either set as 1.0 (hardConstrain = true) or their distance from the line (hardConstrain = false). In the given example below noBeef = 1, value = 0.0 is represented as X, non-zero values are represented as whitespace. Only the region between (A1, B1) and (A2, B2) is in the MASK matrix.

*     |             XX| B2p
*     |            XXX|
*     |           XXX |
*  B2 +---------------+
*     |       XXX     |
*     |      XXX      |
*     |     XXX       |
*     |    XXX        |
*     |   XXX         |
*     |  XXX          |
*     | XXX           |
*     |XX             | B1p
* B1  +---------------+
*    A1              A2
* 

void DIAlign::ConstrainMatrix::constrainSimilarity	(	SimMatrix &	s,
		const SimMatrix &	MASK,
		double	constrainVal
	)

Applies the mask from calcNoBeefMask() on the similarity matrix.

MASK and s must be of the same size. constrainVal is a penalizing factor for the MASK.