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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Synopsis

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.

Input

codes:	(Input)	Matrix labels, e.g. valid sequence character codes
n:	(Input)	Number of labels
filename:	(Input)	Matrix filename

Returns

AjPMatrix:

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

Description

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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Availability

In release 6.4.0

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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Synopsis

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.

Input

codes:	(Input)	Matrix column labels, e.g. valid sequence character codes
n:	(Input)	Number of column labels
rcodes:	(Input)	Matrix row labels, e.g. valid sequence character codes
rn:	(Input)	Number of row labels
filename:	(Input)	Matrix filename

Returns

AjPMatrix:

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

Description

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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Availability

In release 6.4.0

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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Synopsis

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.

Input

codes:	(Input)	Matrix labels, e.g. valid sequence char codes
n:	(Input)	Number of labels
filename:	(Input)	Matrix filename

Returns

AjPMatrixf:

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

Description

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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Availability

In release 6.4.0

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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Synopsis

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.

Input

codes:	(Input)	Matrix labels, e.g. valid sequence char codes
n:	(Input)	Number of labels
rcodes:	(Input)	Matrix row labels, e.g. valid sequence character codes.
rn:	(Input)	Number of row labels
filename:	(Input)	Matrix filename

Returns

AjPMatrixf:

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

Description

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.

The matrix comparison value table Matrix is created and initialised with zeroes.

Availability

In release 6.4.0

Function ajMatrixfDel

Delete a float matrix

Synopsis

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

Output

thys:

(Output)

Matrix to delete

Returns

void:

No return value

Description

Delete a float matrix

Availability

In release 6.4.0

Function ajMatrixDel

Delete an integer matrix

Synopsis

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

Output

thys:

(Output)

Matrix to delete

Returns

void:

No return value

Description

Delete an integer matrix

Availability

In release 6.4.0

Function ajMatrixNewFile

Constructs a comparison matrix from a given local data file

Synopsis

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

Input

filename:

(Input)

Input filename

Returns

AjPMatrix:

Matrix object

Description

Constructs a comparison matrix from a given local data file

Availability

In release 6.4.0

Function ajMatrixfNewFile

Constructs a comparison matrix from a given local data file

Synopsis

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

Input

filename:

(Input)

Input filename

Returns

AjPMatrixf:

Float matrix object

Description

Constructs a comparison matrix from a given local data file

Availability

In release 6.4.0

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.

Synopsis

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.

Input

thys:	(Input)	Matrix object
seq:	(Input)	Sequence object

Output

numseq:

(Output)

Index code version of the sequence

Returns

AjBool:

ajTrue on success.

Description

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

Availability

In release 6.4.0

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.

Synopsis

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.

Input

thys:	(Input)	Float Matrix object
seq:	(Input)	Sequence object

Output

numseq:

(Output)

Index code version of the sequence

Returns

AjBool:

ajTrue on success.

Description

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

Availability

In release 6.4.0

Function ajMatrixGetCodes

Returns the character codes for each offset in the matrix

Synopsis

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

Input

thys:

(Input)

Matrix object

Returns

AjPStr:

Matrix codes

Description

Returns the character codes for each offset in the matrix

Availability

In release 6.4.0

Function ajMatrixfGetCodes

Returns the character codes for each offset in the matrix

Synopsis

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

Input

thys:

(Input)

Matrix object

Returns

AjPStr:

Matrix codes

Description

Returns the character codes for each offset in the matrix

Availability

In release 6.4.0

Function ajMatrixGetMatrix

Returns the matrix values array in the matrix

Synopsis

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

Input

thys:

(Input)

Matrix object

Returns

AjIntArray*:

Matrix values array

Description

Returns the matrix values array in the matrix

Availability

In release 6.4.0

Function ajMatrixfGetMatrix

Returns the matrix values array in the matrix

Synopsis

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

Input

thys:

(Input)

Matrix object

Returns

AjFloatArray*:

Matrix values array

Description

Returns the matrix values array in the matrix

Availability

In release 6.4.0

Function ajMatrixGetRows

Returns the comparison matrix row size.

Synopsis

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	.

Input

thys:

(Input)

Matrix object

Returns

ajuint:

Description

Returns the comparison matrix row size.

Availability

In release 6.4.0

Function ajMatrixGetSize

Returns the comparison matrix size.

Synopsis

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	.

Input

thys:

(Input)

Matrix object

Returns

ajuint:

Description

Returns the comparison matrix size.

Availability

In release 6.4.0

Function ajMatrixfGetRows

Returns the comparison matrix row size.

Synopsis

Prototype

ajuint ajMatrixfGetRows (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

ajuint RETURN .

Input

thys:

(Input)

Matrix object

Returns

ajuint:

Description

Returns the comparison matrix row size.

Availability

In release 6.4.0

Function ajMatrixfGetSize

Returns the comparison matrix size.

Synopsis

Prototype

ajuint ajMatrixfGetSize (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

ajuint RETURN .

Input

thys:

(Input)

Matrix object

Returns

ajuint:

Description

Returns the comparison matrix size.

Availability

In release 6.4.0

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.

Synopsis

Prototype

AjPSeqCvt ajMatrixGetCvt (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

AjPSeqCvt RETURN sequence character conversion table

Input

thys:

(Input)

Matrix object

Returns

AjPSeqCvt:

sequence character conversion table

Description

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.

Availability

In release 6.4.0

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.

Synopsis

Prototype

AjPSeqCvt ajMatrixfGetCvt (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Float Matrix object

AjPSeqCvt RETURN sequence character conversion table

Input

thys:

(Input)

Float Matrix object

Returns

AjPSeqCvt:

sequence character conversion table

Description

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.

Availability

In release 6.4.0

Function ajMatrixGetLabelNum

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

Synopsis

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

Input

thys:	(Input)	Matrix object
i:	(Input)	Character index

Returns

const AjPStr:

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

Description

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

Availability

In release 6.4.0

Function ajMatrixfGetLabelNum

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

Synopsis

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

Input

thys:	(Input)	Matrix object
i:	(Input)	Character index

Returns

const AjPStr:

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

Description

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

Availability

In release 6.4.0

Function ajMatrixGetName

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

Synopsis

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.

Input

thys:

(Input)

Matrix object

Returns

const AjPStr:

The name, a pointer to the internal name.

Description

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

Availability

In release 6.4.0

Function ajMatrixfGetName

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

Synopsis

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.

Input

thys:

(Input)

Matrix object

Returns

const AjPStr:

The name, a pointer to the internal name.

Description

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

Availability

In release 6.4.0

Function ajMatrixExit

Cleans matrix processing internals

Synopsis

Prototype

void ajMatrixExit (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Cleans matrix processing internals

Availability

In release 6.4.0

ajmatrices.c

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