ajtranslate

Data type AjPTrn

Holds the Genetic Code specification and information needed to translate the sequence and find initiation sites.

Constructor(s)

Name	Description
ajTrnNew	Default constructor
ajTrnNewI	Default constructor
ajTrnNewC	Default constructor

Destructor(s)

Name	Description
ajTrnDel	Default destructor

Input

Name	Description
ajTrnReadFile	Reads a Genetic Code file

Operator(s)

Name	Description
ajTrnCodon	Translating a codon from an AjPStr
ajTrnRevCodon	Reverse complement translating a codon from an AjPStr
ajTrnCodonC	Translating a codon from a char* text
ajTrnRevCodonC	Translating a codon from a char* text
ajTrnCodonK	Translating a codon from a char* to a char
ajTrnRevCodonK	Reverse complement translating a codon from a char* to a char
ajTrnC	Translating a sequence from a char* text
ajTrnRevC	Reverse complement translating a sequence from a char* text
ajTrnAltRevC	(Alt) Reverse complement translating a sequence from a char* text
ajTrnStr	Translating a sequence from a AjPStr
ajTrnRevStr	Reverse complement translating a sequence from a AjPStr
ajTrnAltRevStr	(Alt) Reverse complement translating a sequence from a AjPStr
ajTrnSeq	Translating a sequence from a AjPSeq
ajTrnRevSeq	Reverse complement translating a sequence from a AjPSeq
ajTrnAltRevSeq	Reverse complement translating a sequence from a AjPSeq
ajTrnCFrame	Translating a sequence from a char* in a frame
ajTrnStrFrame	Translating a sequence from a AjPStr in a frame
ajTrnSeqFrame	Translating a sequence from a AjPSeq in a frame
ajTrnSeqFramePep	Translating a sequence from a AjPSeq in a frame and returns a new peptide
ajTrnDangleC	Translates the last 1 or two bases of a sequence in a char* text
ajTrnDangleS	Translates the last 1 or two bases of a sequence in a AjStr
ajTrnSeqOrig	Translating a sequence

Cast(s)

Name	Description
ajTrnGetTitle	Returns description of the translation table
ajTrnGetFilename	Returns file name the translation table was read from

Operator(s)

Name	Description
ajTrnCodonstrTypeS	Checks whether the input codon is a Start codon, a Stop codon or something else
ajTrnCodonstrTypeC	Checks whether a const char* codon is a Start codon, a Stop codon or something else

Attributes

Name	Type	Description
FileName	AjPStr	name of file that held the data
Title	AjPStr	title of data read from file
GC	char[16][16][16]	genetic codon table
Starts	char[16][16][16]	initiation site table

Alias name(s)

Name
AjSTrn
AjOTrn