ajcod.c

Section: Codon Constructors

All constructors return a new object by pointer. It is the responsibility of the user to first destroy any previous object. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions: ajCodNew ajCodNewCodenum ajCodNewCod

Function ajCodNew

Default constructor for empty AJAX codon objects.

Synopsis

Prototype

AjPCod ajCodNew (
      void
);

Type Name Read/Write Description

AjPCod RETURN Pointer to an codon object

Type	Name	Read/Write	Description
AjPCod		RETURN	Pointer to an codon object

Returns

AjPCod:

Pointer to an codon object

Description

Default constructor for empty AJAX codon objects.

Availability

In release 6.4.0

Function ajCodNewCodenum

Default constructor for empty AJAX codon usage objects, with the amino acid assignments taken from a standard genetic code.

Synopsis

Prototype

AjPCod ajCodNewCodenum (
      ajint code
);

Type Name Read/Write Description

ajint code Input Genetic code number

AjPCod RETURN Pointer to an codon object

Type	Name	Read/Write	Description
ajint	code	Input	Genetic code number
AjPCod		RETURN	Pointer to an codon object

Input

code:

(Input)

Genetic code number

Returns

AjPCod:

Pointer to an codon object

Description

Default constructor for empty AJAX codon usage objects, with the amino acid assignments taken from a standard genetic code.

Availability

In release 6.4.0

Function ajCodNewCod

Duplicate a codon object

Synopsis

Prototype

AjPCod ajCodNewCod (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon to duplicate

AjPCod RETURN Pointer to an codon object

Type	Name	Read/Write	Description
const AjPCod	thys	Input	Codon to duplicate
AjPCod		RETURN	Pointer to an codon object

Input

thys:

(Input)

Codon to duplicate

Returns

AjPCod:

Pointer to an codon object

Description

Duplicate a codon object

Availability

In release 6.4.0

Section: Codon Destructors

Destructor(s) for AjPCod objects

Functions: ajCodDel

Function ajCodDel

Default destructor for AJAX codon objects.

Synopsis

Prototype

void ajCodDel (
      AjPCod* pthys
);

Type Name Read/Write Description

AjPCod* pthys Output codon usage structure

void RETURN

Type	Name	Read/Write	Description
AjPCod*	pthys	Output	codon usage structure
void		RETURN

Output

pthys:

(Output)

codon usage structure

Returns

void:

No return value

Description

Default destructor for AJAX codon objects.

Availability

In release 6.4.0

Section: Codon Functions

Function(s) for AjPCod objects

Functions: ajCodBacktranslate ajCodBacktranslateAmbig ajCodBase ajCodClear ajCodClearData ajCodSetTripletsS ajCodIndex ajCodIndexC ajCodRead ajCodSetBacktranslate ajCodTriplet ajCodWriteOut ajCodWrite ajCodComp ajCodCalcCaiCod ajCodCalcCaiSeq ajCodCalcGribskov ajCodCalcNc ajCodCalcUsage ajCodGetName ajCodGetNameC ajCodGetDesc ajCodGetDescC ajCodGetSpecies ajCodGetSpeciesC ajCodGetDivision ajCodGetDivisionC ajCodGetRelease ajCodGetReleaseC ajCodGetNumcodon ajCodGetNumcds ajCodGetCode ajCodSetCodenum ajCodSetDescC ajCodSetDescS ajCodSetDivisionC ajCodSetDivisionS ajCodSetNameC ajCodSetNameS ajCodSetNumcds ajCodSetNumcodons ajCodSetReleaseC ajCodSetReleaseS ajCodSetSpeciesC ajCodSetSpeciesS ajCodoutformatFind ajCodPrintFormat ajCodGetCodonlist ajCodExit

Function ajCodBacktranslate

Back translate a string

Synopsis

Prototype

void ajCodBacktranslate (
      AjPStr* b,
      const AjPStr a,
      const AjPCod thys
);

Type Name Read/Write Description

AjPStr* b Output back translated sequence

const AjPStr a Input sequence

const AjPCod thys Input codon usage object

void RETURN

Type	Name	Read/Write	Description
AjPStr*	b	Output	back translated sequence
const AjPStr	a	Input	sequence
const AjPCod	thys	Input	codon usage object
void		RETURN

Input

a:	(Input)	sequence
thys:	(Input)	codon usage object

Output

(Output)

back translated sequence

Returns

void:

No return value

Description

Back translate a string

Availability

In release 6.4.0

Function ajCodBacktranslateAmbig

Back translate a string to a fully ambiguous nucleotide sequence as a string

Synopsis

Prototype

void ajCodBacktranslateAmbig (
      AjPStr* b,
      const AjPStr a,
      const AjPCod thys
);

Type Name Read/Write Description

AjPStr* b Output back translated sequence

const AjPStr a Input sequence

const AjPCod thys Input codon usage object

void RETURN

Type	Name	Read/Write	Description
AjPStr*	b	Output	back translated sequence
const AjPStr	a	Input	sequence
const AjPCod	thys	Input	codon usage object
void		RETURN

Input

a:	(Input)	sequence
thys:	(Input)	codon usage object

Output

(Output)

back translated sequence

Returns

void:

No return value

Description

Back translate a string to a fully ambiguous nucleotide sequence as a string

Availability

In release 6.4.0

Function ajCodBase

Return one codon value given a possibly ambiguous base

Synopsis

Prototype

ajint ajCodBase (
      ajint c
);

ajintcInputbase ajint RETURNsingle base value

Input

(Input)

base

Returns

ajint:

single base value

Description

Return one codon value given a possibly ambiguous base

Availability

In release 6.4.0

Function ajCodClear

Zero all entries

To retain the genetics code (the amino acids for each codon) use ajCodClearData instead.

Synopsis

Prototype

void ajCodClear (
      AjPCod thys
);

Type Name Read/Write Description

AjPCod thys Output codon usage structure

void RETURN

Type	Name	Read/Write	Description
AjPCod	thys	Output	codon usage structure
void		RETURN

Output

thys:

(Output)

codon usage structure

Returns

void:

No return value

Description

Zero all entries

To retain the genetics code (the amino acids for each codon) use ajCodClearData instead.

Availability

In release 6.4.0

Function ajCodClearData

Zero the name, number count and fraction codon entries

Synopsis

Prototype

void ajCodClearData (
      AjPCod thys
);

Type Name Read/Write Description

AjPCod thys Output codon usage structure

void RETURN

Type	Name	Read/Write	Description
AjPCod	thys	Output	codon usage structure
void		RETURN

Output

thys:

(Output)

codon usage structure

Returns

void:

No return value

Description

Zero the name, number count and fraction codon entries

Availability

In release 6.4.0

Function ajCodSetTripletsS

Load the num array of a codon structure

Used for creating a codon usage table

Skips triplets with ambiguity codes and any incomplete triplet at the end.

Synopsis

Prototype

void ajCodSetTripletsS (
      AjPCod thys,
      const AjPStr s,
      ajint* c
);

Type Name Read/Write Description

AjPCod thys Output Codon object

const AjPStr s Input dna sequence

ajint* c Output triplet count

void RETURN

Type	Name	Read/Write	Description
AjPCod	thys	Output	Codon object
const AjPStr	s	Input	dna sequence
ajint*	c	Output	triplet count
void		RETURN

Input

(Input)

dna sequence

Output

thys:	(Output)	Codon object
c:	(Output)	triplet count

Returns

void:

No return value

Description

Load the num array of a codon structure

Used for creating a codon usage table

Skips triplets with ambiguity codes and any incomplete triplet at the end.

Availability

In release 6.4.0

Function ajCodIndex

Return a codon index given a three character codon

Can be called with any coding sequence of 3 or more bases, and will use only the first 3 bases of the input.

Synopsis

Prototype

ajint ajCodIndex (
      const AjPStr s
);

Type Name Read/Write Description

const AjPStr s Input Codon

ajint RETURN Codon index AAA=0 TTT=3f

Type	Name	Read/Write	Description
const AjPStr	s	Input	Codon
ajint		RETURN	Codon index AAA=0 TTT=3f

Input

(Input)

Codon

Returns

ajint:

Codon index AAA=0 TTT=3f

Description

Return a codon index given a three character codon

Can be called with any coding sequence of 3 or more bases, and will use only the first 3 bases of the input.

Availability

In release 6.4.0

Function ajCodIndexC

Return a codon index given a three character codon

Can be called with any coding sequence of 3 or more bases, and will use only the first 3 bases of the input.

Synopsis

Prototype

ajint ajCodIndexC (
      const char* codon
);

Type Name Read/Write Description

const char* codon Input Codon pointer

ajint RETURN codon index AAA=0 TTT=3f

Type	Name	Read/Write	Description
const char*	codon	Input	Codon pointer
ajint		RETURN	codon index AAA=0 TTT=3f

Input

codon:

(Input)

Codon pointer

Returns

ajint:

codon index AAA=0 TTT=3f

Description

Return a codon index given a three character codon

Can be called with any coding sequence of 3 or more bases, and will use only the first 3 bases of the input.

Availability

In release 6.4.0

Function ajCodRead

Read a codon index from a filename using a specified format.

The format can be in the format argument, as a prefix format:: to the filename, or empty to allow all known formats to be tried.

Synopsis

Prototype

AjBool ajCodRead (
      AjPCod thys,
      const AjPStr fn,
      const AjPStr format
);

Type Name Read/Write Description

AjPCod thys Output Codon object

const AjPStr fn Input filename

const AjPStr format Input format

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
AjPCod	thys	Output	Codon object
const AjPStr	fn	Input	filename
const AjPStr	format	Input	format
AjBool		RETURN	ajTrue on success

Input

fn:	(Input)	filename
format:	(Input)	format

Output

thys:

(Output)

Codon object

Returns

AjBool:

ajTrue on success

Description

Read a codon index from a filename using a specified format.

The format can be in the format argument, as a prefix format:: to the filename, or empty to allow all known formats to be tried.

Availability

In release 6.4.0

Function ajCodSetBacktranslate

Fill the codon usage object "back" element with the most commonly used triplet index for the amino acids

Synopsis

Prototype

void ajCodSetBacktranslate (
      AjPCod thys
);

Type Name Read/Write Description

AjPCod thys Modify codon usage structure

void RETURN

Type	Name	Read/Write	Description
AjPCod	thys	Modify	codon usage structure
void		RETURN

Input & Output

thys:

(Modify)

codon usage structure

Returns

void:

No return value

Description

Fill the codon usage object "back" element with the most commonly used triplet index for the amino acids

Availability

In release 6.4.0

Function ajCodTriplet

Convert triplet index to triple

Synopsis

Prototype

char* ajCodTriplet (
      ajint idx
);

Type Name Read/Write Description

ajint idx Input triplet index

char* RETURN Triplet

Type	Name	Read/Write	Description
ajint	idx	Input	triplet index
char*		RETURN	Triplet

Input

idx:

(Input)

triplet index

Returns

char*:

Triplet

Description

Convert triplet index to triple

Availability

In release 6.4.0

Function ajCodWriteOut

Write codon structure to output file

Synopsis

Prototype

void ajCodWriteOut (
      const AjPCod thys,
      AjPOutfile outf
);

Type Name Read/Write Description

const AjPCod thys Input codon usage

AjPOutfile outf Modify output file

void RETURN

Type	Name	Read/Write	Description
const AjPCod	thys	Input	codon usage
AjPOutfile	outf	Modify	output file
void		RETURN

Input

thys:

(Input)

codon usage

Input & Output

outf:

(Modify)

output file

Returns

void:

No return value

Description

Write codon structure to output file

Availability

In release 6.4.0

Function ajCodWrite

Write codon structure to output file

Synopsis

Prototype

void ajCodWrite (
      AjPCod thys,
      AjPFile outf
);

Type Name Read/Write Description

AjPCod thys Modify codon usage

AjPFile outf Modify output file

void RETURN

Input & Output

thys:	(Modify)	codon usage
outf:	(Modify)	output file

Returns

void:

No return value

Description

Write codon structure to output file

Availability

In release 6.4.0

Function ajCodComp

Calculate sequence composition

Synopsis

Prototype

void ajCodComp (
      ajint* NA,
      ajint* NC,
      ajint* NG,
      ajint* NT,
      const char* str
);

Type Name Read/Write Description

ajint* NA Output number of A's

ajint* NC Output number of C's

ajint* NG Output number of G's

ajint* NT Output number of T'

const char* str Input sequence

void RETURN

Input

str:

(Input)

sequence

Output

NA:	(Output)	number of A's
NC:	(Output)	number of C's
NG:	(Output)	number of G's
NT:	(Output)	number of T'

Returns

void:

No return value

Description

Calculate sequence composition

Availability

In release 6.4.0

Function ajCodCalcCaiCod

Calculate codon adaptive index using overall codon usage data only.

See equation 8 in NAR 15:1281-1295

Synopsis

Prototype

double ajCodCalcCaiCod (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input codon usage

double RETURN CAI

Input

thys:

(Input)

codon usage

Returns

double:

CAI

Description

Calculate codon adaptive index using overall codon usage data only.

See equation 8 in NAR 15:1281-1295

Availability

In release 6.4.0

Function ajCodCalcCaiSeq

Calculate codon adaptive index for a coding sequence

See equation 7 in NAR 15:1281-1295

Synopsis

Prototype

double ajCodCalcCaiSeq (
      const AjPCod thys,
      const AjPStr str
);

Type Name Read/Write Description

const AjPCod thys Input codon usage

const AjPStr str Input sequence

double RETURN CAI

Input

thys:	(Input)	codon usage
str:	(Input)	sequence

Returns

double:

CAI

Description

Calculate codon adaptive index for a coding sequence

See equation 7 in NAR 15:1281-1295

Availability

In release 6.4.0

Function ajCodCalcGribskov

Calculate Gribskov statistic (count per thousand) in AjPCod internals

Synopsis

Prototype

void ajCodCalcGribskov (
      AjPCod thys,
      const AjPStr s
);

Type Name Read/Write Description

AjPCod thys Modify codon usage for sequence

const AjPStr s Input sequence

void RETURN

Input

(Input)

sequence

Input & Output

thys:

(Modify)

codon usage for sequence

Returns

void:

No return value

Description

Calculate Gribskov statistic (count per thousand) in AjPCod internals

Availability

In release 6.4.0

Function ajCodCalcNc

Calculate effective number of codons Wright, F. (1990) Gene 87:23-29

Synopsis

Prototype

double ajCodCalcNc (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input codon usage

double RETURN Nc

Input

thys:

(Input)

codon usage

Returns

double:

Description

Calculate effective number of codons Wright, F. (1990) Gene 87:23-29

Availability

In release 6.4.0

Function ajCodCalcUsage

Calculate fractional and thousand elements of a codon object Used for creating a codon usage table

If no counts are stored, warns of need to first run ajCodSetTriplets

Synopsis

Prototype

void ajCodCalcUsage (
      AjPCod thys,
      ajint c
);

Type Name Read/Write Description

AjPCod thys Modify Codon object

ajint c Input triplet count

void RETURN

Input

(Input)

triplet count

Input & Output

thys:

(Modify)

Codon object

Returns

void:

No return value

Description

Calculate fractional and thousand elements of a codon object Used for creating a codon usage table

If no counts are stored, warns of need to first run ajCodSetTriplets

Availability

In release 6.4.0

Function ajCodGetName

Returns the name of a codon table

Synopsis

Prototype

const AjPStr ajCodGetName (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const AjPStr RETURN Original filename

Input

thys:

(Input)

Codon usage object

Returns

const AjPStr:

Original filename

Description

Returns the name of a codon table

Availability

In release 6.4.0

Function ajCodGetNameC

Returns the name of a codon table

Synopsis

Prototype

const char* ajCodGetNameC (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const char* RETURN Original filename

Input

thys:

(Input)

Codon usage object

Returns

const char*:

Original filename

Description

Returns the name of a codon table

Availability

In release 6.4.0

Function ajCodGetDesc

Returns the description of a codon table

Synopsis

Prototype

const AjPStr ajCodGetDesc (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const AjPStr RETURN Original filename

Input

thys:

(Input)

Codon usage object

Returns

const AjPStr:

Original filename

Description

Returns the description of a codon table

Availability

In release 6.4.0

Function ajCodGetDescC

Returns the description of a codon table

Synopsis

Prototype

const char* ajCodGetDescC (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const char* RETURN Original filename

Input

thys:

(Input)

Codon usage object

Returns

const char*:

Original filename

Description

Returns the description of a codon table

Availability

In release 6.4.0

Function ajCodGetSpecies

Returns the species of a codon table

Synopsis

Prototype

const AjPStr ajCodGetSpecies (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const AjPStr RETURN Species

Input

thys:

(Input)

Codon usage object

Returns

const AjPStr:

Species

Description

Returns the species of a codon table

Availability

In release 6.4.0

Function ajCodGetSpeciesC

Returns the species of a codon table

Synopsis

Prototype

const char* ajCodGetSpeciesC (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const char* RETURN Species

Input

thys:

(Input)

Codon usage object

Returns

const char*:

Species

Description

Returns the species of a codon table

Availability

In release 6.4.0

Function ajCodGetDivision

Returns the division of a codon table

Synopsis

Prototype

const AjPStr ajCodGetDivision (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const AjPStr RETURN Division

Input

thys:

(Input)

Codon usage object

Returns

const AjPStr:

Division

Description

Returns the division of a codon table

Availability

In release 6.4.0

Function ajCodGetDivisionC

Returns the division of a codon table

Synopsis

Prototype

const char* ajCodGetDivisionC (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const char* RETURN Division

Input

thys:

(Input)

Codon usage object

Returns

const char*:

Division

Description

Returns the division of a codon table

Availability

In release 6.4.0

Function ajCodGetRelease

Returns the release of a codon table

Synopsis

Prototype

const AjPStr ajCodGetRelease (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const AjPStr RETURN Release

Input

thys:

(Input)

Codon usage object

Returns

const AjPStr:

Release

Description

Returns the release of a codon table

Availability

In release 6.4.0

Function ajCodGetReleaseC

Returns the release of a codon table

Synopsis

Prototype

const char* ajCodGetReleaseC (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

const char* RETURN Release

Input

thys:

(Input)

Codon usage object

Returns

const char*:

Release

Description

Returns the release of a codon table

Availability

In release 6.4.0

Function ajCodGetNumcodon

Returns the number of codons in a codon table

Synopsis

Prototype

ajint ajCodGetNumcodon (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

ajint RETURN Number of codons

Input

thys:

(Input)

Codon usage object

Returns

ajint:

Number of codons

Description

Returns the number of codons in a codon table

Availability

In release 6.4.0

Function ajCodGetNumcds

Returns the numbers of CDSs in a codon table

Synopsis

Prototype

ajint ajCodGetNumcds (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

ajint RETURN Number of CDSs

Input

thys:

(Input)

Codon usage object

Returns

ajint:

Number of CDSs

Description

Returns the numbers of CDSs in a codon table

Availability

In release 6.4.0

Function ajCodGetCode

Returns the genetic code of a codon table

Synopsis

Prototype

ajint ajCodGetCode (
      const AjPCod thys
);

Type Name Read/Write Description

const AjPCod thys Input Codon usage object

ajint RETURN Number of CDSs

Input

thys:

(Input)

Codon usage object

Returns

ajint:

Number of CDSs

Description

Returns the genetic code of a codon table

Availability

In release 6.4.0

Function ajCodSetCodenum

Assigns the genetic code in a codon table

Synopsis

Prototype

void ajCodSetCodenum (
      AjPCod thys,
      ajint geneticcode
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

ajint geneticcode Input Genetic code

void RETURN

Input

geneticcode:

(Input)

Genetic code

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the genetic code in a codon table

Availability

In release 6.4.0

Function ajCodSetDescC

Assigns the description of a codon table

Synopsis

Prototype

void ajCodSetDescC (
      AjPCod thys,
      const char* desc
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const char* desc Input Description

void RETURN

Input

desc:

(Input)

Description

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the description of a codon table

Availability

In release 6.4.0

Function ajCodSetDescS

Assigns the description of a codon table

Synopsis

Prototype

void ajCodSetDescS (
      AjPCod thys,
      const AjPStr desc
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const AjPStr desc Input Description

void RETURN

Input

desc:

(Input)

Description

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the description of a codon table

Availability

In release 6.4.0

Function ajCodSetDivisionC

Assigns the division of a codon table

Synopsis

Prototype

void ajCodSetDivisionC (
      AjPCod thys,
      const char* division
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const char* division Input Division

void RETURN

Input

division:

(Input)

Division

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the division of a codon table

Availability

In release 6.4.0

Function ajCodSetDivisionS

Assigns the division of a codon table

Synopsis

Prototype

void ajCodSetDivisionS (
      AjPCod thys,
      const AjPStr division
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const AjPStr division Input Division

void RETURN

Input

division:

(Input)

Division

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the division of a codon table

Availability

In release 6.4.0

Function ajCodSetNameC

Assigns the name of a codon table

Synopsis

Prototype

void ajCodSetNameC (
      AjPCod thys,
      const char* name
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const char* name Input Name

void RETURN

Input

name:

(Input)

Name

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the name of a codon table

Availability

In release 6.4.0

Function ajCodSetNameS

Assigns the name of a codon table

Synopsis

Prototype

void ajCodSetNameS (
      AjPCod thys,
      const AjPStr name
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const AjPStr name Input Name

void RETURN

Input

name:

(Input)

Name

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the name of a codon table

Availability

In release 6.4.0

Function ajCodSetNumcds

Assigns the number of CDSs in a codon table

Synopsis

Prototype

void ajCodSetNumcds (
      AjPCod thys,
      ajint numcds
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

ajint numcds Input Number of codons

void RETURN

Input

numcds:

(Input)

Number of codons

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the number of CDSs in a codon table

Availability

In release 6.4.0

Function ajCodSetNumcodons

Assigns the number of codons in a codon table

Synopsis

Prototype

void ajCodSetNumcodons (
      AjPCod thys,
      ajint numcodon
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

ajint numcodon Input Number of codons

void RETURN

Input

numcodon:

(Input)

Number of codons

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the number of codons in a codon table

Availability

In release 6.4.0

Function ajCodSetReleaseC

Assigns the of a codon table

Synopsis

Prototype

void ajCodSetReleaseC (
      AjPCod thys,
      const char* release
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const char* release Input Release

void RETURN

Input

release:

(Input)

Release

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the of a codon table

Availability

In release 6.4.0

Function ajCodSetReleaseS

Assigns the release of a codon table

Synopsis

Prototype

void ajCodSetReleaseS (
      AjPCod thys,
      const AjPStr release
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const AjPStr release Input Release

void RETURN

Input

release:

(Input)

Release

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the release of a codon table

Availability

In release 6.4.0

Function ajCodSetSpeciesC

Assigns the species of a codon table

Synopsis

Prototype

void ajCodSetSpeciesC (
      AjPCod thys,
      const char* species
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const char* species Input Species

void RETURN

Input

species:

(Input)

Species

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the species of a codon table

Availability

In release 6.4.0

Function ajCodSetSpeciesS

Assigns the species of a codon table

Synopsis

Prototype

void ajCodSetSpeciesS (
      AjPCod thys,
      const AjPStr species
);

Type Name Read/Write Description

AjPCod thys Modify Codon usage object

const AjPStr species Input Species

void RETURN

Input

species:

(Input)

Species

Input & Output

thys:

(Modify)

Codon usage object

Returns

void:

No return value

Description

Assigns the species of a codon table

Availability

In release 6.4.0

Function ajCodoutformatFind

Tests the output format for an outcodon ACD type

Synopsis

Prototype

AjBool ajCodoutformatFind (
      const AjPStr name,
      ajint* iformat
);

Type Name Read/Write Description

const AjPStr name Input Format name

ajint* iformat Output Internal format index

AjBool RETURN True on success

Input

name:

(Input)

Format name

Output

iformat:

(Output)

Internal format index

Returns

AjBool:

True on success

Description

Tests the output format for an outcodon ACD type

Availability

In release 6.4.0

Function ajCodPrintFormat

Reports the internal data structures

Synopsis

Prototype

void ajCodPrintFormat (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full report, currently no extra details printed

void RETURN

Input

full:

(Input)

Full report, currently no extra details printed

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the internal data structures

Availability

In release 6.4.0

Function ajCodGetCodonlist

Writes codon triplets to a string list

Synopsis

Prototype

void ajCodGetCodonlist (
      const AjPCod cod,
      AjPList list
);

Type Name Read/Write Description

const AjPCod cod Input Cusp file

AjPList list Output List with character distributions

void RETURN

Input

cod:

(Input)

Cusp file

Output

list:

(Output)

List with character distributions

Returns

void:

No return value

Description

Writes codon triplets to a string list

Availability

In release 6.4.0

Function ajCodExit

Cleans up codon usage processing internal memory

Synopsis

Prototype

void ajCodExit (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Cleans up codon usage processing internal memory

Availability

In release 6.4.0

Type	Name	Read/Write	Description
AjPFile	outf	Modify	Output file
AjBool	full	Input	Full report, currently no extra details printed
void		RETURN

ajcod.c

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