Pairwise sequnce alignment result storage header. More...

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

Include dependency graph for alignment.h:

This graph shows which files directly or indirectly include this file:

Macros
#define	MOVE_STOP 0
	Stop move. More...

#define	MOVE_LEFT 2
	Path insertion move. More...

#define	MOVE_UP 3
	Path deletion move. More...

#define	MOVE_DIAG 1
	Path alignment move. More...

Typedefs
typedef struct Alignment	Alignment
	Pairwise sequnce alignment result storage object. More...

Functions
Alignment *	alignmentCreate (Chain query, int queryStart, int queryEnd, Chain target, int targetStart, int targetEnd, int score, Scorer scorer, char path, int pathLen)
	Alignment object constructor. More...

void	alignmentDelete (Alignment *alignment)
	Alignment destructor. More...

char	alignmentGetMove (Alignment *alignment, int index)
	Move getter. More...

int	alignmentGetPathLen (Alignment *alignment)
	Path len getter. More...

Chain *	alignmentGetQuery (Alignment *alignment)
	Query getter. More...

int	alignmentGetQueryEnd (Alignment *alignment)
	Query end getter. More...

int	alignmentGetQueryStart (Alignment *alignment)
	Query start getter. More...

int	alignmentGetScore (Alignment *alignment)
	Score getter. More...

Scorer *	alignmentGetScorer (Alignment *alignment)
	Scorer getter. More...

Chain *	alignmentGetTarget (Alignment *alignment)
	Target getter. More...

int	alignmentGetTargetEnd (Alignment *alignment)
	Target end getter. More...

int	alignmentGetTargetStart (Alignment *alignment)
	Target start getter. More...

void	alignmentCopyPath (Alignment alignment, char dest)
	Copies path to the destination buffer. More...

Alignment *	alignmentDeserialize (char *bytes)
	Alignment deserialization method. More...

void	alignmentSerialize (char *bytes, int bytesLen, Alignment *alignment)
	Alignment serialization method. More...

Detailed Description

Pairwise sequnce alignment result storage header.

Macro Definition Documentation

#define MOVE_DIAG 1

Path alignment move.

Named diagonal move because of the diagonal move in matrix done while backtracking.

#define MOVE_LEFT 2

Path insertion move.

Named diagonal move because of the up move in matrix done while backtracking.

#define MOVE_STOP 0

Stop move.

Stop move is not used in alignment path. However it is used internaly in sequnce alignment algorithms.

#define MOVE_UP 3

Path deletion move.

Named diagonal move because of the up move in matrix done while backtracking.

Typedef Documentation

typedef struct Alignment Alignment

Pairwise sequnce alignment result storage object.

All off the pairwise sequnce alignment algorithms produce a similiar result. Input query and target sequences are stored as Chain object. Algorithm scoring system is stored as Scorer object. Alignment stores the query and target start and endpoints as well as the alignment score. Alignment path is stored as a character array. Every character represents one move and can be MOVE_LEFT, MOVE_UP or MOVE_DIAG. Alignment path is stored in format convinient for backtracking, in other words the moves are named by the matrix movement while backtracking.

Function Documentation

void alignmentCopyPath	(	Alignment *	alignment,
		char *	dest
	)

Copies path to the destination buffer.

Method copies path to the destination buffer which should be at least long as the alignment path length.

Parameters

alignment	alignment object
dest	destination buffer

Alignment* alignmentCreate	(	Chain *	query,
		int	queryStart,
		int	queryEnd,
		Chain *	target,
		int	targetStart,
		int	targetEnd,
		int	score,
		Scorer *	scorer,
		char *	path,
		int	pathLen
	)

Alignment object constructor.

Alignment object is constructed from the query and target sequence aligned and their coresponding start and stop positions, alignment score, scorer which was used for alignment and the alignment path. None of the input objects are copied via the constructor.

Parameters

query	query sequnce
queryStart	query start position
queryEnd	query end position, inclusive
target	target sequnce
targetStart	target start position
targetEnd	target end position, inclusive
score	alignment score
scorer	scorer object used for alignment
path	alignment path
pathLen	alignment path length

Returns: alignment object

void alignmentDelete ( Alignment * alignment )

Alignment destructor.

Parameters

alignment alignment object

Alignment* alignmentDeserialize ( char * bytes )

Alignment deserialization method.

Method deserializes alignment object from a byte buffer.

Parameters

bytes byte buffer

Returns: alignment object

char alignmentGetMove	(	Alignment *	alignment,
		int	index
	)

Move getter.

Given index must be greater or equal to zero and less than alignment path length.

Parameters

alignment	alignment object
index	path move index

Returns: path move

int alignmentGetPathLen ( Alignment * alignment )

Path len getter.

Parameters

alignment alignment object

Returns: path len

Chain* alignmentGetQuery ( Alignment * alignment )

Query getter.

Parameters

alignment alignment object

Returns: query

int alignmentGetQueryEnd ( Alignment * alignment )

Query end getter.

Parameters

alignment alignment object

Returns: query end

int alignmentGetQueryStart ( Alignment * alignment )

Query start getter.

Parameters

alignment alignment object

Returns: query start

int alignmentGetScore ( Alignment * alignment )

Score getter.

Parameters

alignment alignment object

Returns: score

Scorer* alignmentGetScorer ( Alignment * alignment )

Scorer getter.

Parameters

alignment alignment object

Returns: scorer

Chain* alignmentGetTarget ( Alignment * alignment )

Target getter.

Parameters

alignment alignment object

Returns: target

int alignmentGetTargetEnd ( Alignment * alignment )

Target end getter.

Parameters

alignment alignment object

Returns: target end

int alignmentGetTargetStart ( Alignment * alignment )

Target start getter.

Parameters

alignment alignment object

Returns: target start

void alignmentSerialize	(	char **	bytes,
		int *	bytesLen,
		Alignment *	alignment
	)

Alignment serialization method.

Method serializes alignment object to a byte buffer.

Parameters

bytes	output byte buffer
bytesLen	output byte buffer length
alignment	alignment object

Macros

Typedefs

Functions

Detailed Description

Macro Definition Documentation

Typedef Documentation

Function Documentation