ajmatrices.c

Function ajMatrixNew

Creates a new, zero matrix from an array of strings and a matrix name. If the matrix is a residue substitution matrix then each string would be a defined sequence character.

Prototype

AjPMatrix ajMatrixNew (
      const AjPPStr codes,
      ajint n,
      const AjPStr filename
);

Type Name Read/Write Description

const AjPPStr codes Input Matrix labels, e.g. valid sequence character codes

ajint n Input Number of labels

const AjPStr filename Input Matrix filename

AjPMatrix RETURN New matrix, or NULL if codes, n or filename are 0.

Type	Name	Read/Write	Description
`const AjPPStr`	`codes`	Input	Matrix labels, e.g. valid sequence character codes
`ajint`	`n`	Input	Number of labels
`const AjPStr`	`filename`	Input	Matrix filename
`AjPMatrix`		RETURN	New matrix, or NULL if codes, n or filename are 0.

From EMBOSS 1.0.0

Function ajMatrixNewAsym

Creates a new, zero asymmetrical matrix from two array of strings and a matrix name. If the matrix is a substitution matrix then each string would be a defined code, e.g. sequence character.

Prototype

AjPMatrix ajMatrixNewAsym (
      const AjPPStr codes,
      ajint n,
      const AjPPStr rcodes,
      ajint rn,
      const AjPStr filename
);

Type Name Read/Write Description

const AjPPStr codes Input Matrix column labels, e.g. valid sequence character codes

ajint n Input Number of column labels

const AjPPStr rcodes Input Matrix row labels, e.g. valid sequence character codes

ajint rn Input Number of row labels

const AjPStr filename Input Matrix filename

AjPMatrix RETURN New matrix, or NULL if codes, n or filename are 0.

Type	Name	Read/Write	Description
`const AjPPStr`	`codes`	Input	Matrix column labels, e.g. valid sequence character codes
`ajint`	`n`	Input	Number of column labels
`const AjPPStr`	`rcodes`	Input	Matrix row labels, e.g. valid sequence character codes
`ajint`	`rn`	Input	Number of row labels
`const AjPStr`	`filename`	Input	Matrix filename
`AjPMatrix`		RETURN	New matrix, or NULL if codes, n or filename are 0.

From EMBOSS 3.0.0

Function ajMatrixfNew

Creates a new, zero matrix from an array of strings and a matrix name. If the matrix is a residue substitution matrix then each string would be a defined sequence character.

Prototype

AjPMatrixf ajMatrixfNew (
      const AjPPStr codes,
      ajint n,
      const AjPStr filename
);

Type Name Read/Write Description

const AjPPStr codes Input Matrix labels, e.g. valid sequence char codes

ajint n Input Number of labels

const AjPStr filename Input Matrix filename

AjPMatrixf RETURN New matrix, or NULL if codes, n or filename are 0.

Type	Name	Read/Write	Description
`const AjPPStr`	`codes`	Input	Matrix labels, e.g. valid sequence char codes
`ajint`	`n`	Input	Number of labels
`const AjPStr`	`filename`	Input	Matrix filename
`AjPMatrixf`		RETURN	New matrix, or NULL if codes, n or filename are 0.

From EMBOSS 1.0.0

Function ajMatrixfNewAsym

Creates a new, zero asymmetrical matrix from an array of strings and a matrix name. If the matrix is a residue substitution matrix then each string would be a defined sequence character.

Prototype

AjPMatrixf ajMatrixfNewAsym (
      const AjPPStr codes,
      ajint n,
      const AjPPStr rcodes,
      ajint rn,
      const AjPStr filename
);

Type Name Read/Write Description

const AjPPStr codes Input Matrix labels, e.g. valid sequence char codes

ajint n Input Number of labels

const AjPPStr rcodes Input Matrix row labels, e.g. valid sequence character codes.

ajint rn Input Number of row labels

const AjPStr filename Input Matrix filename

AjPMatrixf RETURN New matrix, or NULL if codes, n or filename are 0.

Type	Name	Read/Write	Description
`const AjPPStr`	`codes`	Input	Matrix labels, e.g. valid sequence char codes
`ajint`	`n`	Input	Number of labels
`const AjPPStr`	`rcodes`	Input	Matrix row labels, e.g. valid sequence character codes.
`ajint`	`rn`	Input	Number of row labels
`const AjPStr`	`filename`	Input	Matrix filename
`AjPMatrixf`		RETURN	New matrix, or NULL if codes, n or filename are 0.

From EMBOSS 3.0.0

Function ajMatrixfDel

Delete a float matrix

Prototype

void ajMatrixfDel (
      AjPMatrixf* thys
);

Type Name Read/Write Description

AjPMatrixf* thys Output Matrix to delete

void RETURN

Type	Name	Read/Write	Description
`AjPMatrixf*`	`thys`	Output	Matrix to delete
`void`		RETURN

From EMBOSS 1.6.1

Function ajMatrixDel

Delete an integer matrix

Prototype

void ajMatrixDel (
      AjPMatrix* thys
);

Type Name Read/Write Description

AjPMatrix* thys Output Matrix to delete

void RETURN

Type	Name	Read/Write	Description
`AjPMatrix*`	`thys`	Output	Matrix to delete
`void`		RETURN

From EMBOSS 2.1.0

Function ajMatrixNewFile

Constructs a comparison matrix from a given local data file

Prototype

AjPMatrix ajMatrixNewFile (
      const AjPStr filename
);

Type Name Read/Write Description

const AjPStr filename Input Input filename

AjPMatrix RETURN Matrix object

Type	Name	Read/Write	Description
`const AjPStr`	`filename`	Input	Input filename
`AjPMatrix`		RETURN	Matrix object

From EMBOSS 6.2.0

Function ajMatrixfNewFile

Constructs a comparison matrix from a given local data file

Prototype

AjPMatrixf ajMatrixfNewFile (
      const AjPStr filename
);

Type Name Read/Write Description

const AjPStr filename Input Input filename

AjPMatrixf RETURN Float matrix object

Type	Name	Read/Write	Description
`const AjPStr`	`filename`	Input	Input filename
`AjPMatrixf`		RETURN	Float matrix object

From EMBOSS 6.2.0

Function ajMatrixSeqIndex

Converts a sequence to index numbers using the matrix's internal conversion table. Sequence characters not defined in the matrix are converted to zero.

Prototype

AjBool ajMatrixSeqIndex (
      const AjPMatrix thys,
      const AjPSeq seq,
      AjPStr* numseq
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

const AjPSeq seq Input Sequence object

AjPStr* numseq Output Index code version of the sequence

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`const AjPSeq`	`seq`	Input	Sequence object
`AjPStr*`	`numseq`	Output	Index code version of the sequence
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 6.2.0

Function ajMatrixfSeqIndex

Converts a sequence to index numbers using the matrix's internal conversion table. Sequence characters not defined in the matrix are converted to zero.

Prototype

AjBool ajMatrixfSeqIndex (
      const AjPMatrixf thys,
      const AjPSeq seq,
      AjPStr* numseq
);

Type Name Read/Write Description

const AjPMatrixf thys Input Float Matrix object

const AjPSeq seq Input Sequence object

AjPStr* numseq Output Index code version of the sequence

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Float Matrix object
`const AjPSeq`	`seq`	Input	Sequence object
`AjPStr*`	`numseq`	Output	Index code version of the sequence
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 6.2.0

Function ajMatrixGetCodes

Returns the character codes for each offset in the matrix

Prototype

AjPStr ajMatrixGetCodes (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

AjPStr RETURN Matrix codes

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`AjPStr`		RETURN	Matrix codes

From EMBOSS 4.0.0

Function ajMatrixfGetCodes

Returns the character codes for each offset in the matrix

Prototype

AjPStr ajMatrixfGetCodes (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

AjPStr RETURN Matrix codes

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Matrix object
`AjPStr`		RETURN	Matrix codes

From EMBOSS 4.0.0

Function ajMatrixGetMatrix

Returns the matrix values array in the matrix

Prototype

AjIntArray* ajMatrixGetMatrix (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

AjIntArray* RETURN Matrix values array

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`AjIntArray*`		RETURN	Matrix values array

From EMBOSS 6.2.0

Function ajMatrixfGetMatrix

Returns the matrix values array in the matrix

Prototype

AjFloatArray* ajMatrixfGetMatrix (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

AjFloatArray* RETURN Matrix values array

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Matrix object
`AjFloatArray*`		RETURN	Matrix values array

From EMBOSS 6.2.0

Function ajMatrixGetRows

Returns the comparison matrix row size.

Prototype

ajuint ajMatrixGetRows (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

ajuint RETURN .

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`ajuint`		RETURN	.

From EMBOSS 6.3.0

Function ajMatrixGetSize

Returns the comparison matrix size.

Prototype

ajuint ajMatrixGetSize (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

ajuint RETURN .

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`ajuint`		RETURN	.

From EMBOSS 6.2.0

Function ajMatrixfGetRows

Returns the comparison matrix row size.

Prototype

ajuint ajMatrixfGetRows (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

ajuint RETURN .

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Matrix object
`ajuint`		RETURN	.

From EMBOSS 6.3.0

Function ajMatrixfGetSize

Returns the comparison matrix size.

Prototype

ajuint ajMatrixfGetSize (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

ajuint RETURN .

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Matrix object
`ajuint`		RETURN	.

From EMBOSS 6.2.0

Function ajMatrixGetCvt

Returns the sequence character conversion table for a matrix. This table converts any character defined in the matrix to a positive integer, and any other character is converted to zero.

Prototype

AjPSeqCvt ajMatrixGetCvt (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

AjPSeqCvt RETURN sequence character conversion table

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`AjPSeqCvt`		RETURN	sequence character conversion table

From EMBOSS 6.2.0

Function ajMatrixfGetCvt

Returns the sequence character conversion table for a matrix. This table converts any character defined in the matrix to a positive integer, and any other character is converted to zero.

Prototype

AjPSeqCvt ajMatrixfGetCvt (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Float Matrix object

AjPSeqCvt RETURN sequence character conversion table

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Float Matrix object
`AjPSeqCvt`		RETURN	sequence character conversion table

From EMBOSS 6.2.0

Function ajMatrixGetLabelNum

Returns the sequence character (or asymmetric matrix label) for a matrix column.

Prototype

const AjPStr ajMatrixGetLabelNum (
      const AjPMatrix thys,
      ajint i
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

ajint i Input Character index

const AjPStr RETURN Matrix label, e.g. sequence character code or '?' if not found

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`ajint`	`i`	Input	Character index
`const AjPStr`		RETURN	Matrix label, e.g. sequence character code or '?' if not found

From EMBOSS 6.2.0

Function ajMatrixfGetLabelNum

Returns the sequence character (or asymmetric matrix label) for a matrix column.

Prototype

const AjPStr ajMatrixfGetLabelNum (
      const AjPMatrixf thys,
      ajint i
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

ajint i Input Character index

const AjPStr RETURN Matrix label, e.g. sequence character code or '?' if not found

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Matrix object
`ajint`	`i`	Input	Character index
`const AjPStr`		RETURN	Matrix label, e.g. sequence character code or '?' if not found

From EMBOSS 6.2.0

Function ajMatrixGetName

Returns the name of a matrix object, usually the filename from which it was read.

Prototype

const AjPStr ajMatrixGetName (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

const AjPStr RETURN The name, a pointer to the internal name.

Type	Name	Read/Write	Description
`const AjPMatrix`	`thys`	Input	Matrix object
`const AjPStr`		RETURN	The name, a pointer to the internal name.

From EMBOSS 6.2.0

Function ajMatrixfGetName

Returns the name of a matrix object, usually the filename from which it was read.

Prototype

const AjPStr ajMatrixfGetName (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

const AjPStr RETURN The name, a pointer to the internal name.

Type	Name	Read/Write	Description
`const AjPMatrixf`	`thys`	Input	Matrix object
`const AjPStr`		RETURN	The name, a pointer to the internal name.

From EMBOSS 6.2.0

Function ajMatrixExit

Cleans matrix processing internals

Prototype

void ajMatrixExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.2.0