ajbase.c

Datatypes:

none Base

Datatype: none

Function is for manipulating nucleotide base codes

Sections:

character conversion Casts

Complement General use

binary conversion Casts

query General use

retrieval General use

Doublet names Casts

exit Miscellaneous

Section: character conversion

Functions converting binary forms of base codes

Functions:

ajBaseAlphaCompare Returns an element of the base match probability array

ajBaseAlphaToBin 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 daseInit

Function ajBaseAlphaCompare

Returns an element of the base match probability array

Prototype

float ajBaseAlphaCompare (
      ajint base,
      ajint base2
);

Type Name Read/Write Description

ajint base Input First base offset

ajint base2 Input Second base offset

float RETURN Base probability value

Type	Name	Read/Write	Description
`ajint`	`base`	Input	First base offset
`ajint`	`base2`	Input	Second base offset
`float`		RETURN	Base probability value

From EMBOSS 6.0.0

Function ajBaseAlphaToBin

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 daseInit

Prototype

ajint ajBaseAlphaToBin (
      ajint base
);

Type Name Read/Write Description

ajint base Input character to convert

ajint RETURN Binary OR'd representation

Type	Name	Read/Write	Description
`ajint`	`base`	Input	character to convert
`ajint`		RETURN	Binary OR'd representation

From EMBOSS 6.0.0

Function ajBaseAlphacharCompare

Check ambiguity codes (IUB) to estimate the distance score.

Prototype

float ajBaseAlphacharCompare (
      char c,
      char c2
);

Type Name Read/Write Description

char c Input First base to compare

char c2 Input Second base to compare

float RETURN estimated match

Type	Name	Read/Write	Description
`char`	`c`	Input	First base to compare
`char`	`c2`	Input	Second base to compare
`float`		RETURN	estimated match

From EMBOSS 6.0.0

Function ajBaseAlphacharToBin

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 baseInit

Prototype

char ajBaseAlphacharToBin (
      char c
);

Type Name Read/Write Description

char c Input character to convert

char RETURN Binary OR'd representation

Type	Name	Read/Write	Description
`char`	`c`	Input	character to convert
`char`		RETURN	Binary OR'd representation

From EMBOSS 6.0.0

Section: Complement

Functions complementing nucleotide base codes

Functions:

ajBaseAlphacharComp Complements a nucleotide base.

Function ajBaseAlphacharComp

Complements a nucleotide base.

Prototype

char ajBaseAlphacharComp (
      char c
);

Type Name Read/Write Description

char c Input Base character.

char RETURN Complementary base.

Type	Name	Read/Write	Description
`char`	`c`	Input	Base character.
`char`		RETURN	Complementary base.

From EMBOSS 6.0.0

Section: binary conversion

Functions converting binary forms of base codes

Functions:

ajBaseBinToAlpha 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).

Function ajBaseBinToAlpha

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).

Prototype

char ajBaseBinToAlpha (
      ajint c
);

Type Name Read/Write Description

ajint c Input character to convert

char RETURN Ambiguous DNA base code

Type	Name	Read/Write	Description
`ajint`	`c`	Input	character to convert
`char`		RETURN	Ambiguous DNA base code

From EMBOSS 6.0.0

Section: query

Functions

Functions:

ajBaseExistsBin Tests whether a base code exists

ajBaseExistsChar Tests whether a base code exists

Function ajBaseExistsBin

Tests whether a base code exists

Prototype

AjBool ajBaseExistsBin (
      ajint base
);

Type Name Read/Write Description

ajint base Input Base code in range 0 to 31

AjBool RETURN True if base code is known

Type	Name	Read/Write	Description
`ajint`	`base`	Input	Base code in range 0 to 31
`AjBool`		RETURN	True if base code is known

From EMBOSS 6.0.0

Function ajBaseExistsChar

Tests whether a base code exists

Prototype

AjBool ajBaseExistsChar (
      char c
);

Type Name Read/Write Description

char c Input Base character

AjBool RETURN True if base code is known

Type	Name	Read/Write	Description
`char`	`c`	Input	Base character
`AjBool`		RETURN	True if base code is known

From EMBOSS 6.0.0

Section: retrieval

Functions

Functions:

ajBaseGetCodes Returns a string of matching base codes

ajBaseGetMnemonic Returns a string of matching base codes

Function ajBaseGetCodes

Returns a string of matching base codes

Prototype

const AjPStr ajBaseGetCodes (
      ajint base
);

Type Name Read/Write Description

ajint base Input Original base code

const AjPStr RETURN Base codes

Type	Name	Read/Write	Description
`ajint`	`base`	Input	Original base code
`const AjPStr`		RETURN	Base codes

From EMBOSS 6.0.0

Function ajBaseGetMnemonic

Returns a string of matching base codes

Prototype

const AjPStr ajBaseGetMnemonic (
      ajint base
);

Type Name Read/Write Description

ajint base Input Original base code

const AjPStr RETURN Base codes

Type	Name	Read/Write	Description
`ajint`	`base`	Input	Original base code
`const AjPStr`		RETURN	Base codes

From EMBOSS 6.0.0

Section: Doublet names

Functions exchanging residue codes with PDB two letter codes

Functions:

ajBaseFromDoublet Takes a 2 character PDB base code and writes a char with the corresponding single letter code.

Function ajBaseFromDoublet

Takes a 2 character PDB base code and writes a char with the corresponding single letter code.

Prototype

AjBool ajBaseFromDoublet (
      const AjPStr nuc2,
      char* Pc
);

Type Name Read/Write Description

const AjPStr nuc2 Input AjPStr object (2 letter code)

char* Pc Output Resulting residue code

AjBool RETURN True on success, false if doublet is not recognised

Type	Name	Read/Write	Description
`const AjPStr`	`nuc2`	Input	AjPStr object (2 letter code)
`char*`	`Pc`	Output	Resulting residue code
`AjBool`		RETURN	True on success, false if doublet is not recognised

From EMBOSS 6.1.0

Section: exit

Functions called on exit from the program by ajExit to do any necessary cleanup and to report internal statistics to the debug file

Functions:

ajBaseExit Cleans up sequence base and residue processing internal memory

Function ajBaseExit

Cleans up sequence base and residue processing internal memory

Prototype

void ajBaseExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.0.0

Section: character conversion

Functions converting binary forms of amino acid residue codes

Functions:

ajResidueAlphaToBin Returns a binary OR'd representation of an IUB residue where A=1, C=2, Uses the base table set up by residueInit

Function ajResidueAlphaToBin

Returns a binary OR'd representation of an IUB residue where A=1, C=2, Uses the base table set up by residueInit

Prototype

ajint ajResidueAlphaToBin (
      ajint base
);

Type Name Read/Write Description

ajint base Input character to convert

ajint RETURN Binary OR'd representation

Type	Name	Read/Write	Description
`ajint`	`base`	Input	character to convert
`ajint`		RETURN	Binary OR'd representation

From EMBOSS 6.0.0

Section: binary conversion

Functions converting binary forms of base codes

Functions:

ajResidueBinToAlpha Converts a binary OR'd representation of an IUB residue where A=1, C=2, etc into an ambiguous protein code

Function ajResidueBinToAlpha

Converts a binary OR'd representation of an IUB residue where A=1, C=2, etc into an ambiguous protein code

Prototype

char ajResidueBinToAlpha (
      ajint c
);

Type Name Read/Write Description

ajint c Input character to convert

char RETURN Ambiguous residue code

Type	Name	Read/Write	Description
`ajint`	`c`	Input	character to convert
`char`		RETURN	Ambiguous residue code

From EMBOSS 6.0.0

Section: query

Functions

Functions:

ajResidueExistsBin Tests whether a residue code exists

ajResidueExistsChar Tests whether a residue code exists

Function ajResidueExistsBin

Tests whether a residue code exists

Prototype

AjBool ajResidueExistsBin (
      ajint base
);

Type Name Read/Write Description

ajint base Input Base code in range 0 to 31

AjBool RETURN True if base code is known

Type	Name	Read/Write	Description
`ajint`	`base`	Input	Base code in range 0 to 31
`AjBool`		RETURN	True if base code is known

From EMBOSS 6.0.0

Function ajResidueExistsChar

Tests whether a residue code exists

Prototype

AjBool ajResidueExistsChar (
      char c
);

Type Name Read/Write Description

char c Input Base character

AjBool RETURN True if base code is known

Type	Name	Read/Write	Description
`char`	`c`	Input	Base character
`AjBool`		RETURN	True if base code is known

From EMBOSS 6.0.0

Section: retrieval

Functions

Functions:

ajResidueGetCodes Returns a string of matching amino acid residue codes

ajResidueGetMnemonic Returns a string of matching amino acid residue codes

Function ajResidueGetCodes

Returns a string of matching amino acid residue codes

Prototype

const AjPStr ajResidueGetCodes (
      ajint base
);

Type Name Read/Write Description

ajint base Input Original base code

const AjPStr RETURN Base codes

Type	Name	Read/Write	Description
`ajint`	`base`	Input	Original base code
`const AjPStr`		RETURN	Base codes

From EMBOSS 6.0.0

Function ajResidueGetMnemonic

Returns a string of matching amino acid residue codes

Prototype

const AjPStr ajResidueGetMnemonic (
      ajint base
);

Type Name Read/Write Description

ajint base Input Original base code

const AjPStr RETURN Base codes

Type	Name	Read/Write	Description
`ajint`	`base`	Input	Original base code
`const AjPStr`		RETURN	Base codes

From EMBOSS 6.0.0

Section: Triplet names

Functions exchanging residue codes with three letter codes

Functions:

ajResidueFromTriplet Takes a 3 character amino acid code and writes a char with the corresponding single letter code.

ajResidueToTriplet Writes an AjPStr with an amino acid 3 letter code

Function ajResidueFromTriplet

Takes a 3 character amino acid code and writes a char with the corresponding single letter code.

Prototype

AjBool ajResidueFromTriplet (
      const AjPStr aa3,
      char* Pc
);

Type Name Read/Write Description

const AjPStr aa3 Input AjPStr object (3 letter code)

char* Pc Output Resulting residue code

AjBool RETURN True on success, false if triplet is not recognised

Type	Name	Read/Write	Description
`const AjPStr`	`aa3`	Input	AjPStr object (3 letter code)
`char*`	`Pc`	Output	Resulting residue code
`AjBool`		RETURN	True on success, false if triplet is not recognised

From EMBOSS 6.0.0

Function ajResidueToTriplet

Writes an AjPStr with an amino acid 3 letter code

Prototype

AjBool ajResidueToTriplet (
      char c,
      AjPStr* Paa3
);

Type Name Read/Write Description

char c Input Single letter identifier of amino acid

AjPStr* Paa3 Output AjPStr object

AjBool RETURN True on success

Type	Name	Read/Write	Description
`char`	`c`	Input	Single letter identifier of amino acid
`AjPStr*`	`Paa3`	Output	AjPStr object
`AjBool`		RETURN	True on success

From EMBOSS 6.0.0

Section: Conversion

Functions:

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

ajBasecodeToInt Returns A=0 to Z=25 or 27 otherwise

Function ajBasecodeFromInt

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

Prototype

ajint ajBasecodeFromInt (
      ajint n
);

Type Name Read/Write Description

ajint n Input character to convert

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

Type	Name	Read/Write	Description
`ajint`	`n`	Input	character to convert
`ajint`		RETURN	0 as 'A' up to 25 as 'Z'

From EMBOSS 6.0.0

Function ajBasecodeToInt

Returns A=0 to Z=25 or 27 otherwise

Prototype

ajint ajBasecodeToInt (
      ajint c
);

Type Name Read/Write Description

ajint c Input character to convert

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

Type	Name	Read/Write	Description
`ajint`	`c`	Input	character to convert
`ajint`		RETURN	A=0 to Z=25 or 27 if unknown

From EMBOSS 6.0.0

character conversion	Casts
Complement	General use
binary conversion	Casts
query	General use
retrieval	General use
Doublet names	Casts
exit	Miscellaneous

ajBaseAlphaCompare	Returns an element of the base match probability array
ajBaseAlphaToBin	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 daseInit

ajBaseExistsBin	Tests whether a base code exists
ajBaseExistsChar	Tests whether a base code exists

ajBaseGetCodes	Returns a string of matching base codes
ajBaseGetMnemonic	Returns a string of matching base codes

ajResidueExistsBin	Tests whether a residue code exists
ajResidueExistsChar	Tests whether a residue code exists

ajResidueGetCodes	Returns a string of matching amino acid residue codes
ajResidueGetMnemonic	Returns a string of matching amino acid residue codes

ajResidueFromTriplet	Takes a 3 character amino acid code and writes a char with the corresponding single letter code.
ajResidueToTriplet	Writes an AjPStr with an amino acid 3 letter code

ajBasecodeFromInt	Returns 'A' for 0 to 'Z' for 25
ajBasecodeToInt	Returns A=0 to Z=25 or 27 otherwise