cpu_module.h File Reference

CPU implementations of common functions. More...

#include "alignment.h"
#include "chain.h"
#include "scorer.h"

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Functions
void	alignPairCpu (Alignment **alignment, int type, Chain *query, Chain *target, Scorer *scorer)
	Pairwise alignment function. More...
void	alignScoredPairCpu (Alignment **alignment, int type, Chain *query, Chain *target, Scorer *scorer, int score)
	Pairwise alignment function. More...
void	nwFindScoreCpu (int *queryStart, int *targetStart, Chain *query, Chain *target, Scorer *scorer, int score)
	Score finding function. More...
void	nwReconstructCpu (char **path, int *pathLen, int *outScore, Chain *query, int queryFrontGap, int queryBackGap, Chain *target, int targetFrontGap, int targetBackGap, Scorer *scorer, int score)
	Needleman-Wunsch reconstruction implementation. More...
void	ovFindScoreCpu (int *queryStart, int *targetStart, Chain *query, Chain *target, Scorer *scorer, int score)
	Implementation of score finding function. More...
int	scorePairCpu (int type, Chain *query, Chain *target, Scorer *scorer)
	Pairwise scoring function. More...

Detailed Description

CPU implementations of common functions.

Function Documentation

void alignPairCpu	(	Alignment **	alignment,
		int	type,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer
	)

Pairwise alignment function.

Function aligns query and the target chain with the scorer object.

Parameters

alignment	output alignment object
query	query chain
target	target chain
scorer	scorer object used for alignment
type	aligning type, can be SW_ALIGN, NW_ALIGN, HW_ALIGN or OV_ALIGN

void alignScoredPairCpu	(	Alignment **	alignment,
		int	type,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer,
		int	score
	)

Pairwise alignment function.

Function aligns previously score query and the target chain with the scorer object. If the score isn't valid for the produced alignment an error will occur. Function is primaraly provided to get alignments after calling scorePairCpu function.

Parameters

alignment	output alignment object
type	aligning type, can be SW_ALIGN, NW_ALIGN, HW_ALIGN or OV_ALIGN
query	query chain
target	target chain
scorer	scorer object used for alignment
score	alignment score

void nwFindScoreCpu	(	int *	queryStart,
		int *	targetStart,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer,
		int	score
	)

Score finding function.

Method uses Needleman-Wunsch algorithm with all of the start conditions set to infinity. This assures path contains the first cell and does not start with gaps. If the score is found it return the coordinates of the cell with the provided score, (-1, -1) otherwise.

Parameters

queryStart	output, if found query index of found cell, -1 otherwise
targetStart	output, if found target index of found cell, -1 otherwise
query	query chain
target	target chain
scorer	scorer object used for alignment
score	input alignment score

void nwReconstructCpu	(	char **	path,
		int *	pathLen,
		int *	outScore,
		Chain *	query,
		int	queryFrontGap,
		int	queryBackGap,
		Chain *	target,
		int	targetFrontGap,
		int	targetBackGap,
		Scorer *	scorer,
		int	score
	)

Needleman-Wunsch reconstruction implementation.

If the score is provided function uses Ukkonen's banded optimization. QueryFrontGap and targetFrontGap arguments can't both be not equal to 0. QueryBackGap and targetBackGap arguments can't both be not equal to 0. For path format see Alignment.

Parameters

path	output path
pathLen	output path length
outScore	output score
query	query chain
queryFrontGap	if not equal to 0, force that path starts in MOVE_UP
queryBackGap	if not equal to 0, force that path ends in MOVE_UP
target	target chain
targetFrontGap	if not equal to 0, force that path starts in MOVE_LEFT
targetBackGap	if not equal to 0, force that path ends in MOVE_LEFT
scorer	scorer object used for alignment
score	input alignment score if known, otherwise NO_SCORE

void ovFindScoreCpu	(	int *	queryStart,
		int *	targetStart,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer,
		int	score
	)

Implementation of score finding function.

Method uses Needleman-Wunsch algorithm. If the score is found and the indicies of the coresponding cell are on the border of the solving matrix, functions returns the coordinates of the cell with the provided score, (-1, -1) otherwise.

Parameters

queryStart	output, if found query index of found cell, -1 otherwise
targetStart	output, if found target index of found cell, -1 otherwise
query	query chain
target	target chain
scorer	scorer object used for alignment
score	input alignment score

int scorePairCpu	(	int	type,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer
	)

Pairwise scoring function.

Function provides only the alignment score without any other information. Scoring types are equivalent to aligning types.

Parameters

type	scoring type, can be SW_ALIGN, NW_ALIGN, HW_ALIGN or OV_ALIGN
query	query chain
target	target chain
scorer	scorer object used for alignment