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 ajCodNewCode ajCodDup

Function ajCodNew

Default constructor for empty AJAX codon objects.

Synopsis

Prototype
AjPCod ajCodNew (
      void
);

TypeNameRead/WriteDescription
AjPCod RETURNPointer to an codon object

Returns
AjPCod:Pointer to an codon object

Description

Default constructor for empty AJAX codon objects.

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 5.0.0

Function ajCodNewCode

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

Synopsis

Prototype
AjPCod ajCodNewCode (
      ajint code
);

TypeNameRead/WriteDescription
ajintcodeInputGenetic code number
AjPCod RETURNPointer 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.

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 5.0.0

Function ajCodDup

Duplicate a codon object

Synopsis

Prototype
AjPCod ajCodDup (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon to duplicate
AjPCod RETURNPointer to an codon object

Input
thys:(Input)Codon to duplicate
Returns
AjPCod:Pointer to an codon object

Description

Duplicate a codon object

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 5.0.0

Section: Codon Destructors

Desctuctor(s) for AjPCod objects

Functions: ajCodDel

Function ajCodDel

Default destructor for AJAX codon objects.

Synopsis

Prototype
void ajCodDel (
      AjPCod* pthys
);

TypeNameRead/WriteDescription
AjPCod*pthysOutputcodon usage structure
void RETURN

Output
pthys:(Output)codon usage structure
Returns
void:No return value

Description

Default destructor for AJAX codon objects.

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 5.0.0

Section: Codon Functions

Function(s) for AjPCod objects

Functions: ajCodBacktranslate ajCodBacktranslateAmbig ajCodBase ajCodCalcGribskov ajCodCalcNc ajCodCalculateUsage ajCodClear ajCodClearData ajCodCountTriplets ajCodIndex ajCodIndexC ajCodRead ajCodSetBacktranslate ajCodTriplet ajCodWriteOut ajCodWrite ajCodComp ajCodCalcCai ajCodCaiW ajCodCai ajCodGetName ajCodGetNameC ajCodGetDesc ajCodGetDescC ajCodGetSpecies ajCodGetSpeciesC ajCodGetDivision ajCodGetDivisionC ajCodGetRelease ajCodGetReleaseC ajCodGetNumcodon ajCodGetNumcds ajCodGetCode ajCodAssName ajCodAssNameC ajCodAssDesc ajCodAssDescC ajCodAssSpecies ajCodAssSpeciesC ajCodAssRelease ajCodAssReleaseC ajCodAssDivision ajCodAssDivisionC ajCodAssNumcodon ajCodAssNumcds ajCodAssCode ajCodOutFormat ajCodPrintFormat ajCodGetCodonlist ajCodExit

Function ajCodBacktranslate

Backtranslate a string

Synopsis

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

TypeNameRead/WriteDescription
AjPStr*bOutputbacktranslated sequence
const AjPStraInputsequence
const AjPCodthysInputcodon usage object
void RETURN

Input
a:(Input)sequence
thys:(Input)codon usage object
Output
b:(Output)backtranslated sequence
Returns
void:No return value

Description

Backtranslate a string

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 5.0.0

Function ajCodBacktranslateAmbig

Backtranslate a string to a fully ambiguous nucleotide sequence as a string

Synopsis

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

TypeNameRead/WriteDescription
AjPStr*bOutputbacktranslated sequence
const AjPStraInputsequence
const AjPCodthysInputcodon usage object
void RETURN

Input
a:(Input)sequence
thys:(Input)codon usage object
Output
b:(Output)backtranslated sequence
Returns
void:No return value

Description

Backtranslate a string to a fully ambiguous nucleotide sequence as a string

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 5.0.0

Function ajCodBase

Return one codon value given a possibly ambiguous base

Synopsis

Prototype
ajint ajCodBase (
      ajint c
);
ajintcInputbase ajint RETURNsingle base value

Input
c:(Input)base
Returns
ajint:single base value

Description

Return one codon value given a possibly ambiguous base

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 5.0.0

Function ajCodCalcGribskov

Calculate Gribskov statistic (count per thousand) in AjPCod internals

Synopsis

Prototype
void ajCodCalcGribskov (
      AjPCod thys,
      const AjPStr s
);

TypeNameRead/WriteDescription
AjPCodthysModifycodon usage for sequence
const AjPStrsInputsequence
void RETURN

Input
s:(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

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 5.0.0

Function ajCodCalcNc

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

Synopsis

Prototype
double ajCodCalcNc (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputcodon usage
double RETURNNc

Input
thys:(Input)codon usage
Returns
double:Nc

Description

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

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 5.0.0

Function ajCodCalculateUsage

Calculate fractional and thousand elements of a codon object Used for creating a codon usage table Requires pre-running of ajCodCountTriplets

Synopsis

Prototype
void ajCodCalculateUsage (
      AjPCod thys,
      ajint c
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon object
ajintcInputtriplet count
void RETURN

Input
c:(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 Requires pre-running of ajCodCountTriplets

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 5.0.0

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
);

TypeNameRead/WriteDescription
AjPCodthysOutputcodon 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.

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 5.0.0

Function ajCodClearData

Zero the name, number count and fraction codon entries

Synopsis

Prototype
void ajCodClearData (
      AjPCod thys
);

TypeNameRead/WriteDescription
AjPCodthysOutputcodon 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

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 5.0.0

Function ajCodCountTriplets

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

TypeNameRead/WriteDescription
AjPCodthysOutputCodon object
const AjPStrsInputdna sequence
ajint*cOutputtriplet count
void RETURN

Input
s:(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.

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 5.0.0

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
);

TypeNameRead/WriteDescription
const AjPStrsInputCodon
ajint RETURNCodon index AAA=0 TTT=3f

Input
s:(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.

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 5.0.0

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
);

TypeNameRead/WriteDescription
const char*codonInputCodon pointer
ajint RETURNcodon 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.

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 5.0.0

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
);

TypeNameRead/WriteDescription
AjPCodthysOutputCodon object
const AjPStrfnInputfilename
const AjPStrformatInputformat
AjBool RETURNajTrue 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.

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 5.0.0

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
);

TypeNameRead/WriteDescription
AjPCod*thysModifycodon 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

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 5.0.0

Function ajCodTriplet

Convert triplet index to triple

Synopsis

Prototype
char* ajCodTriplet (
      ajint idx
);

TypeNameRead/WriteDescription
ajintidxInputtriplet index
char* RETURNTriplet

Input
idx:(Input)triplet index
Returns
char*:Triplet

Description

Convert triplet index to triple

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 5.0.0

Function ajCodWriteOut

Write codon structure to output file

Synopsis

Prototype
void ajCodWriteOut (
      const AjPCod thys,
      AjPOutfile outf
);

TypeNameRead/WriteDescription
const AjPCodthysInputcodon usage
AjPOutfileoutfModifyoutput 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

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 5.0.0

Function ajCodWrite

Write codon structure to output file

Synopsis

Prototype
void ajCodWrite (
      AjPCod thys,
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPCodthysModifycodon usage
AjPFileoutfModifyoutput 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

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 5.0.0

Function ajCodComp

Calculate sequence composition

Synopsis

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

TypeNameRead/WriteDescription
ajint*NAOutputnumber of A's
ajint*NCOutputnumber of C's
ajint*NGOutputnumber of G's
ajint*NTOutputnumber of T'
const char*strInputsequence
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

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 5.0.0

Function ajCodCalcCai

Calculate codon adaptive index using equation 8 NAR 15:1281-1295

Synopsis

Prototype
double ajCodCalcCai (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputcodon usage
double RETURNCAI

Input
thys:(Input)codon usage
Returns
double:CAI

Description

Calculate codon adaptive index using equation 8 NAR 15:1281-1295

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 5.0.0

Function ajCodCaiW

Calculate codon adaptive index W values NAR 15:1281-1295

Synopsis

Prototype
double* ajCodCaiW (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputcodon usage
double* RETURNw value array

Input
thys:(Input)codon usage
Returns
double*:w value array

Description

Calculate codon adaptive index W values NAR 15:1281-1295

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 5.0.0

Function ajCodCai

Calculate codon adaptive index using equation 7 NAR 15:1281-1295

Synopsis

Prototype
double ajCodCai (
      const AjPCod thys,
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPCodthysInputcodon usage
const AjPStrstrInputsequence
double RETURNCAI

Input
thys:(Input)codon usage
str:(Input)sequence
Returns
double:CAI

Description

Calculate codon adaptive index using equation 7 NAR 15:1281-1295

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 5.0.0

Function ajCodGetName

Returns the name of a codon table

Synopsis

Prototype
const AjPStr ajCodGetName (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const AjPStr RETURNOriginal filename

Input
thys:(Input)Codon usage object
Returns
const AjPStr:Original filename

Description

Returns the name of a codon table

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 5.0.0

Function ajCodGetNameC

Returns the name of a codon table

Synopsis

Prototype
const char* ajCodGetNameC (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const char* RETURNOriginal filename

Input
thys:(Input)Codon usage object
Returns
const char*:Original filename

Description

Returns the name of a codon table

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 5.0.0

Function ajCodGetDesc

Returns the description of a codon table

Synopsis

Prototype
const AjPStr ajCodGetDesc (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const AjPStr RETURNOriginal filename

Input
thys:(Input)Codon usage object
Returns
const AjPStr:Original filename

Description

Returns the description of a codon table

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 5.0.0

Function ajCodGetDescC

Returns the description of a codon table

Synopsis

Prototype
const char* ajCodGetDescC (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usgage object
const char* RETURNOriginal filename

Input
thys:(Input)Codon usgage object
Returns
const char*:Original filename

Description

Returns the description of a codon table

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 5.0.0

Function ajCodGetSpecies

Returns the species of a codon table

Synopsis

Prototype
const AjPStr ajCodGetSpecies (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const AjPStr RETURNSpecies

Input
thys:(Input)Codon usage object
Returns
const AjPStr:Species

Description

Returns the species of a codon table

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 5.0.0

Function ajCodGetSpeciesC

Returns the species of a codon table

Synopsis

Prototype
const char* ajCodGetSpeciesC (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const char* RETURNSpecies

Input
thys:(Input)Codon usage object
Returns
const char*:Species

Description

Returns the species of a codon table

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 5.0.0

Function ajCodGetDivision

Returns the division of a codon table

Synopsis

Prototype
const AjPStr ajCodGetDivision (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const AjPStr RETURNDivision

Input
thys:(Input)Codon usage object
Returns
const AjPStr:Division

Description

Returns the division of a codon table

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 5.0.0

Function ajCodGetDivisionC

Returns the division of a codon table

Synopsis

Prototype
const char* ajCodGetDivisionC (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const char* RETURNDivision

Input
thys:(Input)Codon usage object
Returns
const char*:Division

Description

Returns the division of a codon table

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 5.0.0

Function ajCodGetRelease

Returns the release of a codon table

Synopsis

Prototype
const AjPStr ajCodGetRelease (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const AjPStr RETURNRelease

Input
thys:(Input)Codon usage object
Returns
const AjPStr:Release

Description

Returns the release of a codon table

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 5.0.0

Function ajCodGetReleaseC

Returns the release of a codon table

Synopsis

Prototype
const char* ajCodGetReleaseC (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
const char* RETURNRelease

Input
thys:(Input)Codon usage object
Returns
const char*:Release

Description

Returns the release of a codon table

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 5.0.0

Function ajCodGetNumcodon

Returns the number of codons in a codon table

Synopsis

Prototype
ajint ajCodGetNumcodon (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
ajint RETURNNumber of codons

Input
thys:(Input)Codon usage object
Returns
ajint:Number of codons

Description

Returns the number of codons in a codon table

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 5.0.0

Function ajCodGetNumcds

Returns the numbers od CDSs in a codon table

Synopsis

Prototype
ajint ajCodGetNumcds (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
ajint RETURNNumber of CDSs

Input
thys:(Input)Codon usage object
Returns
ajint:Number of CDSs

Description

Returns the numbers od CDSs in a codon table

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 5.0.0

Function ajCodGetCode

Returns the genetic code of a codon table

Synopsis

Prototype
ajint ajCodGetCode (
      const AjPCod thys
);

TypeNameRead/WriteDescription
const AjPCodthysInputCodon usage object
ajint RETURNNumber of CDSs

Input
thys:(Input)Codon usage object
Returns
ajint:Number of CDSs

Description

Returns the genetic code of a codon table

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 5.0.0

Function ajCodAssName

Assigns the name of a codon table

Synopsis

Prototype
void ajCodAssName (
      AjPCod thys,
      const AjPStr name
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const AjPStrnameInputName
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

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 5.0.0

Function ajCodAssNameC

Assigns the name of a codon table

Synopsis

Prototype
void ajCodAssNameC (
      AjPCod thys,
      const char* name
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const char*nameInputName
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

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 5.0.0

Function ajCodAssDesc

Assigns the description of a codon table

Synopsis

Prototype
void ajCodAssDesc (
      AjPCod thys,
      const AjPStr desc
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const AjPStrdescInputDescription
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

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 5.0.0

Function ajCodAssDescC

Assigns the description of a codon table

Synopsis

Prototype
void ajCodAssDescC (
      AjPCod thys,
      const char* desc
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const char*descInputDescription
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

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 5.0.0

Function ajCodAssSpecies

Assigns the species of a codon table

Synopsis

Prototype
void ajCodAssSpecies (
      AjPCod thys,
      const AjPStr species
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const AjPStrspeciesInputSpecies
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

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 5.0.0

Function ajCodAssSpeciesC

Assigns the species of a codon table

Synopsis

Prototype
void ajCodAssSpeciesC (
      AjPCod thys,
      const char* species
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const char*speciesInputSpecies
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

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 5.0.0

Function ajCodAssRelease

Assigns the release of a codon table

Synopsis

Prototype
void ajCodAssRelease (
      AjPCod thys,
      const AjPStr release
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const AjPStrreleaseInputRelease
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

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 5.0.0

Function ajCodAssReleaseC

Assigns the of a codon table

Synopsis

Prototype
void ajCodAssReleaseC (
      AjPCod thys,
      const char* release
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const char*releaseInputRelease
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

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 5.0.0

Function ajCodAssDivision

Assigns the division of a codon table

Synopsis

Prototype
void ajCodAssDivision (
      AjPCod thys,
      const AjPStr division
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const AjPStrdivisionInputDivision
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

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 5.0.0

Function ajCodAssDivisionC

Assigns the division of a codon table

Synopsis

Prototype
void ajCodAssDivisionC (
      AjPCod thys,
      const char* division
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
const char*divisionInputDivision
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

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 5.0.0

Function ajCodAssNumcodon

Assigns the number of codons in a codon table

Synopsis

Prototype
void ajCodAssNumcodon (
      AjPCod thys,
      ajint numcodon
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
ajintnumcodonInputNumber 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

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 5.0.0

Function ajCodAssNumcds

Assigns the number of CDSs in a codon table

Synopsis

Prototype
void ajCodAssNumcds (
      AjPCod thys,
      ajint numcds
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
ajintnumcdsInputNumber 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

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 5.0.0

Function ajCodAssCode

Assigns the genetic code in a codon table

Synopsis

Prototype
void ajCodAssCode (
      AjPCod thys,
      ajint geneticcode
);

TypeNameRead/WriteDescription
AjPCodthysModifyCodon usage object
ajintgeneticcodeInputGenetic 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

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 5.0.0

Function ajCodOutFormat

Tests the output format for an outcodon ACD type

Synopsis

Prototype
ajint ajCodOutFormat (
      const AjPStr name
);

TypeNameRead/WriteDescription
const AjPStrnameInputFormat name
ajint RETURNInternal format index, of -1 if not found

Input
name:(Input)Format name
Returns
ajint:Internal format index, of -1 if not found

Description

Tests the output format for an outcodon ACD type

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 5.0.0

Function ajCodPrintFormat

Reports the internal data structures

Synopsis

Prototype
void ajCodPrintFormat (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull 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

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 5.0.0

Function ajCodGetCodonlist

Writes codon triplets to a string list

Synopsis

Prototype
void ajCodGetCodonlist (
      const AjPCod cod,
      AjPList list
);

TypeNameRead/WriteDescription
const AjPCodcodInputCusp file
AjPListlistOutputList 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

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 5.0.0

Function ajCodExit

Cleans up codon usage processing internal memory

Synopsis

Prototype
void ajCodExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up codon usage 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 5.0.0