pre_proc.h File Reference

Preprocessing utilities header. More...

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

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Functions
Chain *	createChainComplement (Chain *chain)
	Creates chain complement. More...
void	readFastaChain (Chain **chain, const char *path)
	Fasta chain reading function. More...
void	readFastaChains (Chain ***chains, int *chainsLen, const char *path)
	Fasta chain reading function. More...
void	scorerCreateScalar (Scorer **scorer, int match, int mismatch, int gapOpen, int gapExtend)
	Scalar scorer creation utility functions. More...
void	scorerCreateMatrix (Scorer **scorer, char *name, int gapOpen, int gapExtend)
	Nonscalar scorer creation utility functions. More...

Detailed Description

Preprocessing utilities header.

Function Documentation

Chain* createChainComplement

(

Chain *

chain

)

Creates chain complement.

Function persumes the characters in the chain are nucleotides. Every 'A' is turned into 'T', every 'C' to 'G' and vice versa. Any other characters are left intact. Also the complement chain is in the reverse order of the original.

Parameters

chain

chain object

Returns

chain complement

void readFastaChain	(	Chain **	chain,
		const char *	path
	)

Fasta chain reading function.

Function reads file from the given path, which should be in the fasta format. More on fasta format http://en.wikipedia.org/wiki/FASTA_format. Function persumes only one chain is in the file. Function persumes that the fasta chain name is no more than 1000 characters long.

Parameters

chain	output chain object
path	file path

void readFastaChains	(	Chain ***	chains,
		int *	chainsLen,
		const char *	path
	)

Fasta chain reading function.

Function works in the same way as the readFastaChain() but does not persume only one chain is in the file.

Parameters

chains	output chain array object
chainsLen	output chain array length
path	file path

void scorerCreateMatrix	(	Scorer **	scorer,
		char *	name,
		int	gapOpen,
		int	gapExtend
	)

Nonscalar scorer creation utility functions.

Scorer is created with the max score equal to 26. Observing the scorerEncode() method it means this scorer only accepts alphabet characters and it must not be used with no other characters. This function is used for creating the scorer with the most common standard similarity matrices.

Parameters

scorer	output scorer object
name	name can be one of the "BLOSUM_62", "BLOSUM_45", "BLOSUM_50", "BLOSUM_80", "BLOSUM_90", "PAM_30", "PAM_70" or "PAM_250"
gapOpen	affine gap open penalty, defined as positive integer
gapExtend	affine gap extend penalty, defined as positive integer

void scorerCreateScalar	(	Scorer **	scorer,
		int	match,
		int	mismatch,
		int	gapOpen,
		int	gapExtend
	)

Scalar scorer creation utility functions.

Scorer is created with the max score equal to 26. Observing the scorerEncode() method it means this scorer only accepts alphabet characters and it must not be used with no other characters. This scorer is scalar, see scorerIsScalar().

Parameters

scorer	output scorer object
match	match score for every two equal codes, defined as positive integer
mismatch	mismatch penalty for every two unequal codes, defined as negative integer
gapOpen	affine gap open penalty, defined as positive integer
gapExtend	affine gap extend penalty, defined as positive integer