ajbase.c

Function ajBaseCodes

Returns a string of matching base codes

Synopsis

Prototype

const AjPStr ajBaseCodes (
      ajint ibase
);

Input

ibase:(Input)Original base code

Returns

const AjPStr:Base codes

Description

Returns a string of matching base codes

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajAZToInt

Returns A=0 to Z=25 or 27 otherwise

Synopsis

Prototype

ajint ajAZToInt (
      ajint c
);

Input

c:(Input)character to convert

Returns

ajint:A=0 to Z=25 or 27 if unknown

Description

Returns A=0 to Z=25 or 27 otherwise

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajIntToAZ

Returns 'A' for 0 to 'Z' for 25

Synopsis

Prototype

ajint ajIntToAZ (
      ajint n
);

Input

n:(Input)character to convert

Returns

ajint:0 as 'A' up to 25 as 'Z'

Description

Returns 'A' for 0 to 'Z' for 25

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajBinToAZ

Converts a binary OR'd representation of an IUB base where A=1, C=2, G=4 and T=8 into an ambiguous DNA base code (uses T rather than U).

Uses the base table set up by ajBaseInit

Synopsis

Prototype

char ajBinToAZ (
      ajint c
);

Input

c:(Input)character to convert

Returns

char:Ambiguous DNA base code

Description

Converts a binary OR'd representation of an IUB base where A=1, C=2, G=4 and T=8 into an ambiguous DNA base code (uses T rather than U).

Uses the base table set up by ajBaseInit

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajAZToBin

Returns a binary OR'd representation of an IUB base where A=1, C=2, G=4 and T=8 Uses the base table set up by ajBaseInit

Synopsis

Prototype

ajint ajAZToBin (
      ajint c
);

Input

c:(Input)character to convert

Returns

ajint:Binary OR'd representation

Description

Returns a binary OR'd representation of an IUB base where A=1, C=2, G=4 and T=8 Uses the base table set up by ajBaseInit

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajAZToBinC

Returns a binary OR'd representation of an IUB base where A=1, C=2, G=4 and T=8 Uses the base table set up by ajBaseInit

Synopsis

Prototype

char ajAZToBinC (
      char c
);

Input

c:(Input)character to convert

Returns

char:Binary OR'd representation

Description

Returns a binary OR'd representation of an IUB base where A=1, C=2, G=4 and T=8 Uses the base table set up by ajBaseInit

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajBaseInit

Sets up binary OR'd representation of an IUB bases in a table aj_base_table where A=1, C=2, G=4 and T=8 Also sets up a match probability array aj_base_prob holding the probability of one IUB base matching any other. Uses the Ebases.iub file Is initialised if necessary from other AJAX functions.

Synopsis

Prototype

AjBool ajBaseInit (
      void
);

Returns

AjBool:True on success

Description

Sets up binary OR'd representation of an IUB bases in a table aj_base_table where A=1, C=2, G=4 and T=8 Also sets up a match probability array aj_base_prob holding the probability of one IUB base matching any other. Uses the Ebases.iub file Is initialised if necessary from other AJAX functions.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajBaseAa1ToAa3

Writes an AjPStr with an amino acid 3 letter code

Synopsis

Prototype

AjBool ajBaseAa1ToAa3 (
      char aa1,
      AjPStr* aa3
);

Input

aa1:(Input)Single letter identifier of amino acid

Output

aa3:(Output)AjPStr object

Returns

AjBool:True on succcess

Description

Writes an AjPStr with an amino acid 3 letter code

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajBaseProb

Returns an element of the base match probability array

Synopsis

Prototype

float ajBaseProb (
      ajint base1,
      ajint base2
);

Input

base1:(Input)First base offset
base2:(Input)Second base offset

Returns

float:Base probability value

Description

Returns an element of the base match probability array

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajBaseExit

Cleans up sequence base processing internal memory

Synopsis

Prototype

void ajBaseExit (
      void
);

Returns

void:No return value

Description

Cleans up sequence base processing internal memory

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0