scorer.h File Reference

Provides object used for alignment scoring. More...

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Typedefs
typedef struct Scorer	Scorer
	Scorer object used for alignment scoring. More...

Functions
Scorer *	scorerCreate (const char *name, int *scores, char maxCode, int gapOpen, int gapExtend)
	Scorer constructor. More...
void	scorerDelete (Scorer *scorer)
	Scorer destructor. More...
int	scorerGetGapExtend (Scorer *scorer)
	Gap extend penalty getter. More...
int	scorerGetGapOpen (Scorer *scorer)
	Gap open penalty getter. More...
char	scorerGetMaxCode (Scorer *scorer)
	Max code getter. More...
int	scorerGetMaxScore (Scorer *scorer)
	Max score getter. More...
const char *	scorerGetName (Scorer *scorer)
	Name getter. More...
int	scorerIsScalar (Scorer *scorer)
	Scalar getter. More...
int	scorerScore (Scorer *scorer, char a, char b)
	Scores two codes. More...
Scorer *	scorerDeserialize (char *bytes)
	Scorer deserialization method. More...
void	scorerSerialize (char **bytes, int *bytesLen, Scorer *scorer)
	Scorer serialization method. More...
char	scorerDecode (char c)
	Scorer static decoding method. More...
char	scorerEncode (char c)
	Scorer static encoding method. More...

Detailed Description

Provides object used for alignment scoring.

Typedef Documentation

typedef struct Scorer Scorer

Scorer object used for alignment scoring.

Scorer is organized as a similarity table with additional gap penalties. Affine gap penalty model is used. Scorer codes are defined as characters. Scorer works only on input characters coded with the scorerEncode(char) method.

Function Documentation

Scorer* scorerCreate	(	const char *	name,
		int *	scores,
		char	maxCode,
		int	gapOpen,
		int	gapExtend
	)

Scorer constructor.

Input scores table must be an array which length is equal to maxCode * maxCode. Input scores table must be organized so that columns and rows correspond to the codes shown in scorerEncode(char).

Parameters

name	scorer name, copy is made
scores	similarity table, copy is made
maxCode	maximum code that scorer should work with
gapOpen	gap open penalty given as a positive integer
gapExtend	gap extend penalty given as a positive integer

Returns

scorer object

char scorerDecode

(

char

c

)

Scorer static decoding method.

Function is exact inverse of scorerEncode(char).

Parameters

c	input character

Returns

decoded character

void scorerDelete

(

Scorer *

scorer

)

Scorer destructor.

Parameters

scorer

scorer object

Scorer* scorerDeserialize

(

char *

bytes

)

Scorer deserialization method.

Method deserializes scorer object from a byte buffer.

Parameters

bytes

byte buffer

Returns

scorer object

char scorerEncode

(

char

c

)

Scorer static encoding method.

Encoding method is case insensitive. Function returns character code which is grater or equal to zero or if the codes are not available -1.

Encoding is done in the following way:

• characters 'A'-'Z' are encoded to 0-25
• characters 'a'-'z' are encoded to 0-25
• characters '0'-'9' are encoded to 26-35
• all other input characters cannot be encoded

Parameters

c	input character

Returns

encoded character or -1 if coding isn't available

int scorerGetGapExtend

(

Scorer *

scorer

)

Gap extend penalty getter.

Gap extend penalty is defined as a positive integer.

Parameters

scorer

scorer object

Returns

gap extend penalty

int scorerGetGapOpen

(

Scorer *

scorer

)

Gap open penalty getter.

Gap open penalty is defined as a positive integer.

Parameters

scorer

scorer object

Returns

gap open penalty

char scorerGetMaxCode

(

Scorer *

scorer

)

Max code getter.

Max code is defined as the highest code scorer can work with.

Parameters

scorer

scorer object

Returns

max code

int scorerGetMaxScore

(

Scorer *

scorer

)

Max score getter.

Max score is defined as the highest score two codes can be scored.

Parameters

scorer

scorer object

Returns

max score

const char* scorerGetName

(

Scorer *

scorer

)

Name getter.

Scorer name usually coresponds to similarity matrix names.

Parameters

scorer

scorer object

Returns

name

int scorerIsScalar

(

Scorer *

scorer

)

Scalar getter.

Getter for scalar property. Scorer is scalar if the similarity matrix can be reduced to match, mismatch scorer. In other words scorer is scalar if every two equal codes are scored equaly and every two unequal codes are scored equaly.

Parameters

scorer

scorer object

Returns

1 if scorer if scalar 0 otherwise

int scorerScore	(	Scorer *	scorer,
		char	a,
		char	b
	)

Scores two codes.

Given scorer scores two given codes. Both codes should be greater or equal to 0 and less than maxCode.

Parameters

scorer	scorer object
a	first code
b	second code

Returns

similarity score of a and b

void scorerSerialize	(	char **	bytes,
		int *	bytesLen,
		Scorer *	scorer
	)

Scorer serialization method.

Method serializes scorer object to a byte buffer.

Parameters

bytes	output byte buffer
bytesLen	output byte buffer length
scorer	scorer object