Database alignment oriented functions header. More...

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

Include dependency graph for database.h:

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

Typedefs
typedef struct ChainDatabase	ChainDatabase
	Ddatabase scoring object. More...

typedef void(*	ValueFunction )(double values, int scores, Chain query, Chain database, int databaseLen, void param)

Functions
ChainDatabase *	chainDatabaseCreate (Chain *database, int databaseStart, int databaseLen, int cards, int cardsLen)
	ChainDatabase constructor. More...

void	chainDatabaseDelete (ChainDatabase *chainDatabase)
	ChainDatabase destructor. More...

void	alignDatabase (DbAlignment **dbAlignments, int dbAlignmentsLen, int type, Chain query, ChainDatabase chainDatabase, Scorer scorer, int maxAlignments, ValueFunction valueFunction, void valueFunctionParam, double valueThreshold, int indexes, int indexesLen, int cards, int cardsLen, Thread *thread)
	Database aligning function. More...

void	shotgunDatabase (DbAlignment **dbAlignments, int dbAlignmentsLen, int type, Chain *queries, int queriesLen, ChainDatabase chainDatabase, Scorer scorer, int maxAlignments, ValueFunction valueFunction, void valueFunctionParam, double valueThreshold, int indexes, int indexesLen, int cards, int cardsLen, Thread *thread)
	Shotgun aligning function. More...

Detailed Description

Database alignment oriented functions header.

Typedef Documentation

typedef struct ChainDatabase ChainDatabase

Ddatabase scoring object.

In the database aligning, queries are often changed and the database is fairly static. ChainDatabase is the chain database prepared for both CPU and GPU usage to reduce the preperation time in repetitive aligning.

typedef void(* ValueFunction)(double *values, int *scores, Chain *query, Chain **database, int databaseLen, void *param)

Database alignments are often scored by other methods than the alignment score. ValueFunction defines function type for valueing the align scores between a query and the database. Function should calculate the values and store them in the values array which has length equal to databaseLen. Better alignment scores should have smaller value.

Parameters

values	output, values of the align scores
scores	scores between the query and targets in the database
query	query chain
database	target chain array
databaseLen	target chain array length
param	additional parameters for the value function

Function Documentation

void alignDatabase	(	DbAlignment ***	dbAlignments,
		int *	dbAlignmentsLen,
		int	type,
		Chain *	query,
		ChainDatabase *	chainDatabase,
		Scorer *	scorer,
		int	maxAlignments,
		ValueFunction	valueFunction,
		void *	valueFunctionParam,
		double	valueThreshold,
		int *	indexes,
		int	indexesLen,
		int *	cards,
		int	cardsLen,
		Thread *	thread
	)

Database aligning function.

Function scores the query with every target in the chainDatabase, in other words with every chain in the database array with witch the chainDatabase was created. After the scoring function values the scores with the valueFunction and every pair with value over the valueThreshold is discarded. If there is more than maxAlignments pairs left only the best maxAlignments pairs are aligned and returned. If the indexes array is given only the targets with given indexes will be considered, other will be ignored.

Parameters

dbAlignments	output dbAlignments array, new array is created
dbAlignmentsLen	output, length of the output dbAlignments array
type	aligning type, can be SW_ALIGN, NW_ALIGN, HW_ALIGN or OV_ALIGN
query	query chain
chainDatabase	chain database object
scorer	scorer object used for alignment
maxAlignments	maximum number of alignments to return, if negative number of alignments wont be limited
valueFunction	function for valueing the alignment scores
valueThreshold	maximum value of returned alignments
valueFunctionParam	additional parameters for the value function
indexes	array of indexes of which chains from the database to score, if NULL all are solved
indexesLen	indexes array length
cards	cuda cards index array
cardsLen	cuda cards index array length, greater or equal to 1
thread	thread on which the function will be executed, if NULL function is executed on the current thread

ChainDatabase* chainDatabaseCreate	(	Chain **	database,
		int	databaseStart,
		int	databaseLen,
		int *	cards,
		int	cardsLen
	)

ChainDatabase constructor.

Parameters

database	chain array
databaseStart	index of the first chain to solve
databaseLen	length offset from databaseStart to last chain that needs to be solved
cards	cuda cards index array which the database will be available on
cardsLen	cuda cards index array length, greater or equal to 1

Returns: chainDatabase object

void chainDatabaseDelete ( ChainDatabase * chainDatabase )

ChainDatabase destructor.

Parameters

chainDatabase chainDatabase object

void shotgunDatabase	(	DbAlignment ****	dbAlignments,
		int **	dbAlignmentsLen,
		int	type,
		Chain **	queries,
		int	queriesLen,
		ChainDatabase *	chainDatabase,
		Scorer *	scorer,
		int	maxAlignments,
		ValueFunction	valueFunction,
		void *	valueFunctionParam,
		double	valueThreshold,
		int *	indexes,
		int	indexesLen,
		int *	cards,
		int	cardsLen,
		Thread *	thread
	)

Shotgun aligning function.

Function is the same as the alignDatabase() but it works on the array of queries. As result of the an array of arrays of alignments is outputed as well as the array of coresponding lengths. This function is faster than calling alignDatabase() for every query separately.

Parameters

dbAlignments	output dbAlignments array of arrays, one for each query, new array of arrays is created
dbAlignmentsLen	output, lengths of the output dbAlignments arrays, one for each query, new array is created
type	aligning type, can be SW_ALIGN, NW_ALIGN, HW_ALIGN or OV_ALIGN
queries	query chains array
queriesLen	query chains array length
chainDatabase	chain database object
scorer	scorer object used for alignment
maxAlignments	maximum number of alignments to return, if negative number of alignments wont be limited
valueFunction	function for valueing the alignment scores
valueThreshold	maximum value of returned alignments
valueFunctionParam	additional parameters for the value function
indexes	array of indexes of which chains from the database to score, if NULL all are solved
indexesLen	indexes array length
cards	cuda cards index array
cardsLen	cuda cards index array length, greater or equal to 1
thread	thread on which the function will be executed, if NULL function is executed on the current thread

Typedefs

Functions

Detailed Description

Typedef Documentation

Function Documentation