align.h File Reference

Pairwise alignment oriented functions header. More...

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

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Functions
void	alignPair (Alignment **alignment, int type, Chain *query, Chain *target, Scorer *scorer, int *cards, int cardsLen, Thread *thread)
	Pairwise alignment function. More...
void	alignScoredPair (Alignment **alignment, int type, Chain *query, Chain *target, Scorer *scorer, int score, int *cards, int cardsLen, Thread *thread)
	Pairwise alignment function. More...
void	alignBest (Alignment **alignment, int type, Chain **queries, int queriesLen, Chain *target, Scorer *scorer, int *cards, int cardsLen, Thread *thread)
	Best scored pair alignment function. More...
void	scorePair (int *score, int type, Chain *query, Chain *target, Scorer *scorer, int *cards, int cardsLen, Thread *thread)
	Pairwise scoring function. More...

Detailed Description

Pairwise alignment oriented functions header.

Function Documentation

void alignBest	(	Alignment **	alignment,
		int	type,
		Chain **	queries,
		int	queriesLen,
		Chain *	target,
		Scorer *	scorer,
		int *	cards,
		int	cardsLen,
		Thread *	thread
	)

Best scored pair alignment function.

Function aligns queries and the target chain with the scorer object. Only the best scored pair is aligned and returned. If needed function utilzes provided CUDA cards.

Parameters

alignment	output alignment object
type	aligning type, can be SW_ALIGN, NW_ALIGN, HW_ALIGN or OV_ALIGN
queries	query chains array
queriesLen	query chains array length
target	target chain
scorer	scorer object used for alignment
cards	cuda cards index array
cardsLen	cuda cards index array length
thread	thread on which the function will be executed, if NULL function is executed on the current thread

void alignPair	(	Alignment **	alignment,
		int	type,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer,
		int *	cards,
		int	cardsLen,
		Thread *	thread
	)

Pairwise alignment function.

Function aligns query and the target chain with the scorer object. If needed function utilzes provided CUDA cards.

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
cards	cuda cards index array
cardsLen	cuda cards index array length
thread	thread on which the function will be executed, if NULL function is executed on the current thread

void alignScoredPair	(	Alignment **	alignment,
		int	type,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer,
		int	score,
		int *	cards,
		int	cardsLen,
		Thread *	thread
	)

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 scorePair function. If needed function utilzes provided CUDA cards.

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
cards	cuda cards index array
cardsLen	cuda cards index array length
thread	thread on which the function will be executed, if NULL function is executed on the current thread

void scorePair	(	int *	score,
		int	type,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer,
		int *	cards,
		int	cardsLen,
		Thread *	thread
	)

Pairwise scoring function.

Function only returns the score of the alignment. If needed function utilzes provided CUDA cards.

Parameters

score	output score
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
cards	cuda cards index array
cardsLen	cuda cards index array length
thread	thread on which the function will be executed, if NULL function is executed on the current thread