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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixArray

Returns the comparison matrix as an array of integer arrays. Sequence characters are indexed in this array using the internal Sequence Conversion table in the matrix (see ajMatrixCvt)

Synopsis

Prototype

AjIntArray* ajMatrixArray (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

AjIntArray* RETURN array of integer arrays for comparison values.

Type	Name	Read/Write	Description
const AjPMatrix	thys	Input	Matrix object
AjIntArray*		RETURN	array of integer arrays for comparison values.

Input

thys:

(Input)

Matrix object

Returns

AjIntArray*:

array of integer arrays for comparison values.

Description

Returns the comparison matrix as an array of integer arrays. Sequence characters are indexed in this array using the internal Sequence Conversion table in the matrix (see ajMatrixCvt)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixfArray

Returns the comparison matrix as an array of float arrays. Sequence characters are indexed in this array using the internal Sequence Conversion table in the matrix (see ajMatrixCvt)

Synopsis

Prototype

AjFloatArray* ajMatrixfArray (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Float Matrix object

AjFloatArray* RETURN array of float arrays for comparison values.

Type	Name	Read/Write	Description
const AjPMatrixf	thys	Input	Float Matrix object
AjFloatArray*		RETURN	array of float arrays for comparison values.

Input

thys:

(Input)

Float Matrix object

Returns

AjFloatArray*:

array of float arrays for comparison values.

Description

Returns the comparison matrix as an array of float arrays. Sequence characters are indexed in this array using the internal Sequence Conversion table in the matrix (see ajMatrixCvt)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixSize

Returns the comparison matrix size.

Synopsis

Prototype

ajint ajMatrixSize (
      const AjPMatrix thys
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

ajint RETURN .

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

Input

thys:

(Input)

Matrix object

Returns

ajint:

Description

Returns the comparison matrix size.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixfSize

Returns the comparison matrix size.

Synopsis

Prototype

ajint ajMatrixfSize (
      const AjPMatrixf thys
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

ajint RETURN .

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

Input

thys:

(Input)

Matrix object

Returns

ajint:

Description

Returns the comparison matrix size.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixCvt

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 ajMatrixCvt (
      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

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixfCvt

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 ajMatrixfCvt (
      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

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixChar

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

Synopsis

Prototype

void ajMatrixChar (
      const AjPMatrix thys,
      ajint i,
      AjPStr* label
);

Type Name Read/Write Description

const AjPMatrix thys Input Matrix object

ajint i Input Character index

AjPStr* label Output Matrix label, e.g. sequence character code

void RETURN

Type	Name	Read/Write	Description
const AjPMatrix	thys	Input	Matrix object
ajint	i	Input	Character index
AjPStr*	label	Output	Matrix label, e.g. sequence character code
void		RETURN

Input

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

Output

label:

(Output)

Matrix label, e.g. sequence character code

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixfChar

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

void ajMatrixfChar (
      const AjPMatrixf thys,
      ajint i,
      AjPStr* label
);

Type Name Read/Write Description

const AjPMatrixf thys Input Matrix object

ajint i Input Character index

AjPStr* label Output Matrix label, e.g. sequence character code

void RETURN

Type	Name	Read/Write	Description
const AjPMatrixf	thys	Input	Matrix object
ajint	i	Input	Character index
AjPStr*	label	Output	Matrix label, e.g. sequence character code
void		RETURN

Input

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

Output

label:

(Output)

Matrix label, e.g. sequence character code

Returns

void:

No return value

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixName

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

Synopsis

Prototype

const AjPStr ajMatrixName (
      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.

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixfName

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

Synopsis

Prototype

const AjPStr ajMatrixfName (
      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.

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixRead

Constructs a comparison matrix from a given local data file

Synopsis

Prototype

AjBool ajMatrixRead (
      AjPMatrix* pthis,
      const AjPStr filename
);

Type Name Read/Write Description

AjPMatrix* pthis Output New Matrix object.

const AjPStr filename Input Input filename

AjBool RETURN ajTrue on success.

Input

filename:

(Input)

Input filename

Output

pthis:

(Output)

New Matrix object.

Returns

AjBool:

ajTrue on success.

Description

Constructs a comparison matrix from a given local data file

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixfRead

Constructs a comparison matrix from a given local data file

Synopsis

Prototype

AjBool ajMatrixfRead (
      AjPMatrixf* pthis,
      const AjPStr filename
);

Type Name Read/Write Description

AjPMatrixf* pthis Output New Float Matrix object.

const AjPStr filename Input Input filename

AjBool RETURN ajTrue on success.

Input

filename:

(Input)

Input filename

Output

pthis:

(Output)

New Float Matrix object.

Returns

AjBool:

ajTrue on success.

Description

Constructs a comparison matrix from a given local data file

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixSeqNum

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

Synopsis

Prototype

AjBool ajMatrixSeqNum (
      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.

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajMatrixfSeqNum

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 ajMatrixfSeqNum (
      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.

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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

Input

thys:

(Input)

Matrix object

Returns

AjPStr:

Matrix codes

Description

Returns the character codes for each offset in the matrix

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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

Input

thys:

(Input)

Matrix object

Returns

AjPStr:

Matrix codes

Description

Returns the character codes for each offset in the matrix

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Type	Name	Read/Write	Description
AjPMatrix*	pthis	Output	New Matrix object.
const AjPStr	filename	Input	Input filename
AjBool		RETURN	ajTrue on success.

ajmatrices.c

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