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
);

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 3.0.0

Function ajMatrixNewAsym

Creates a new, zero assymetrical 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
);

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 assymetrical 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 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.

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

Synopsis

Prototype

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

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 3.0.0

Function ajMatrixfNewAsym

Creates a new, zero assymetrical 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
);

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 assymetrical 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 3.0.0

Function ajMatrixfDel

Delete a float matrix

Synopsis

Prototype

void ajMatrixfDel (
      AjPMatrixf* thys
);

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 3.0.0

Function ajMatrixDel

Delete an integer matrix

Synopsis

Prototype

void ajMatrixDel (
      AjPMatrix* thys
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Function ajMatrixSize

Returns the comparison matrix size.

Synopsis

Prototype

ajint ajMatrixSize (
      const AjPMatrix thys
);

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 3.0.0

Function ajMatrixfSize

Returns the comparison matrix size.

Synopsis

Prototype

ajint ajMatrixfSize (
      const AjPMatrixf thys
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Function ajMatrixRead

Constructs a comparison matrix from a given local data file

Synopsis

Prototype

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

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 3.0.0

Function ajMatrixfRead

Constructs a comparison matrix from a given local data file

Synopsis

Prototype

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

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Function ajMatrixGetCodes

Returns the character codes for each offset in the matrix

Synopsis

Prototype

AjPStr ajMatrixGetCodes (
      const AjPMatrix thys
);

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 3.0.0

Function ajMatrixfGetCodes

Returns the character codes for each offset in the matrix

Synopsis

Prototype

AjPStr ajMatrixfGetCodes (
      const AjPMatrixf thys
);

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 3.0.0

ajmatrices.c

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