Database sequnce alignment result storage header. More...

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

Include dependency graph for db_alignment.h:

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

Typedefs
typedef struct DbAlignment	DbAlignment
	Database sequnce alignment result storage object. More...

Functions
DbAlignment *	dbAlignmentCreate (Chain query, int queryStart, int queryEnd, int queryIdx, Chain target, int targetStart, int targetEnd, int targetIdx, double value, int score, Scorer scorer, char path, int pathLen)
	DbAlignment object constructor. More...

void	dbAlignmentDelete (DbAlignment *dbAlignment)
	DbAlignment destructor. More...

char	dbAlignmentGetMove (DbAlignment *dbAlignment, int index)
	Move getter. More...

int	dbAlignmentGetPathLen (DbAlignment *dbAlignment)
	Path length getter. More...

Chain *	dbAlignmentGetQuery (DbAlignment *dbAlignment)
	Query getter. More...

int	dbAlignmentGetQueryEnd (DbAlignment *dbAlignment)
	Query end getter. More...

int	dbAlignmentGetQueryIdx (DbAlignment *dbAlignment)
	Query index getter. More...

int	dbAlignmentGetQueryStart (DbAlignment *dbAlignment)
	Query start getter. More...

int	dbAlignmentGetScore (DbAlignment *dbAlignment)
	Score getter. More...

Scorer *	dbAlignmentGetScorer (DbAlignment *dbAlignment)
	Scorer getter. More...

Chain *	dbAlignmentGetTarget (DbAlignment *dbAlignment)
	Target getter. More...

int	dbAlignmentGetTargetEnd (DbAlignment *dbAlignment)
	Target end getter. More...

int	dbAlignmentGetTargetIdx (DbAlignment *dbAlignment)
	Target index getter. More...

int	dbAlignmentGetTargetStart (DbAlignment *dbAlignment)
	Target start getter. More...

double	dbAlignmentGetValue (DbAlignment *dbAlignment)
	Value getter. More...

void	dbAlignmentCopyPath (DbAlignment dbAlignment, char dest)
	Copies path to the destination buffer. More...

Alignment *	dbAlignmentToAlignment (DbAlignment *dbAlignment)
	Creates alignment object from the dbAlignment object. More...

Detailed Description

Database sequnce alignment result storage header.

Typedef Documentation

typedef struct DbAlignment DbAlignment

Database sequnce alignment result storage object.

Database alignment object is fairly similiar to Alignment object. In addition it stores query index in the query database and the target index in the target database. Also database alignments are often scored by other methods than the alignment score, database alignment value is also stored. Database alignment value representation is user defined.

Function Documentation

void dbAlignmentCopyPath	(	DbAlignment *	dbAlignment,
		char *	dest
	)

Copies path to the destination buffer.

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

Parameters

dbAlignment	dbAlignment object
dest	destination buffer

DbAlignment* dbAlignmentCreate	(	Chain *	query,
		int	queryStart,
		int	queryEnd,
		int	queryIdx,
		Chain *	target,
		int	targetStart,
		int	targetEnd,
		int	targetIdx,
		double	value,
		int	score,
		Scorer *	scorer,
		char *	path,
		int	pathLen
	)

DbAlignment 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
queryIdx	query index
target	target sequnce
targetStart	target start position
targetEnd	target end position, inclusive
targetIdx	target index
value	alignment value
score	alignment score
scorer	scorer object used for alignment
path	alignment path
pathLen	alignment path length

Returns: alignment object

void dbAlignmentDelete ( DbAlignment * dbAlignment )

DbAlignment destructor.

Parameters

dbAlignment dbAlignment object

char dbAlignmentGetMove	(	DbAlignment *	dbAlignment,
		int	index
	)

Move getter.

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

Parameters

dbAlignment	dbAlignment object
index	path move index

Returns: path move

int dbAlignmentGetPathLen ( DbAlignment * dbAlignment )

Path length getter.

Parameters

dbAlignment dbAlignment object

Returns: path length

Chain* dbAlignmentGetQuery ( DbAlignment * dbAlignment )

Query getter.

Parameters

dbAlignment dbAlignment object

Returns: query

int dbAlignmentGetQueryEnd ( DbAlignment * dbAlignment )

Query end getter.

Parameters

dbAlignment dbAlignment object

Returns: query end

int dbAlignmentGetQueryIdx ( DbAlignment * dbAlignment )

Query index getter.

Parameters

dbAlignment dbAlignment object

Returns: query index

int dbAlignmentGetQueryStart ( DbAlignment * dbAlignment )

Query start getter.

Parameters

dbAlignment dbAlignment object

Returns: query start

int dbAlignmentGetScore ( DbAlignment * dbAlignment )

Score getter.

Parameters

dbAlignment dbAlignment object

Returns: score

Scorer* dbAlignmentGetScorer ( DbAlignment * dbAlignment )

Scorer getter.

Parameters

dbAlignment dbAlignment object

Returns: scorer

Chain* dbAlignmentGetTarget ( DbAlignment * dbAlignment )

Target getter.

Parameters

dbAlignment dbAlignment object

Returns: target

int dbAlignmentGetTargetEnd ( DbAlignment * dbAlignment )

Target end getter.

Parameters

dbAlignment dbAlignment object

Returns: target end

int dbAlignmentGetTargetIdx ( DbAlignment * dbAlignment )

Target index getter.

Parameters

dbAlignment dbAlignment object

Returns: target index

int dbAlignmentGetTargetStart ( DbAlignment * dbAlignment )

Target start getter.

Parameters

dbAlignment dbAlignment object

Returns: target start

double dbAlignmentGetValue ( DbAlignment * dbAlignment )

Value getter.

Parameters

dbAlignment dbAlignment object

Returns: value

Alignment* dbAlignmentToAlignment ( DbAlignment * dbAlignment )

Creates alignment object from the dbAlignment object.

Parameters

dbAlignment dbAlignment object

Returns: alignment object

Typedefs

Functions

Detailed Description

Typedef Documentation

Function Documentation