ajtranslate


Data type AjPTrn

Ajax Sequence translation object.

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

Constructor(s)

NameDescription
ajTrnNewDefault constructor
ajTrnNewIDefault constructor
ajTrnNewCDefault constructor

Destructor(s)

NameDescription
ajTrnDelDefault destructor

Input

NameDescription
ajTrnReadFileReads a Genetic Code file

Operator(s)

NameDescription
ajTrnCodonTranslating a codon from an AjPStr
ajTrnRevCodonReverse complement translating a codon from an AjPStr
ajTrnCodonCTranslating a codon from a char* text
ajTrnRevCodonCTranslating a codon from a char* text
ajTrnCodonKTranslating a codon from a char* to a char
ajTrnRevCodonKReverse complement translating a codon from a char* to a char
ajTrnCTranslating a sequence from a char* text
ajTrnRevCReverse complement translating a sequence from a char* text
ajTrnAltRevC(Alt) Reverse complement translating a sequence from a char* text
ajTrnStrTranslating a sequence from a AjPStr
ajTrnRevStrReverse complement translating a sequence from a AjPStr
ajTrnAltRevStr(Alt) Reverse complement translating a sequence from a AjPStr
ajTrnSeqTranslating a sequence from a AjPSeq
ajTrnRevSeqReverse complement translating a sequence from a AjPSeq
ajTrnAltRevSeqReverse complement translating a sequence from a AjPSeq
ajTrnCFrameTranslating a sequence from a char* in a frame
ajTrnStrFrameTranslating a sequence from a AjPStr in a frame
ajTrnSeqFrameTranslating a sequence from a AjPSeq in a frame
ajTrnSeqFramePepTranslating a sequence from a AjPSeq in a frame and returns a new peptide
ajTrnDangleCTranslates the last 1 or two bases of a sequence in a char* text
ajTrnDangleSTranslates the last 1 or two bases of a sequence in a AjStr
ajTrnSeqOrigTranslating a sequence

Cast(s)

NameDescription
ajTrnGetTitleReturns description of the translation table
ajTrnGetFilenameReturns file name the translation table was read from

Operator(s)

NameDescription
ajTrnCodonstrTypeSChecks whether the input codon is a Start codon, a Stop codon or something else
ajTrnCodonstrTypeCChecks whether a const char* codon is a Start codon, a Stop codon or something else

Attributes

NameTypeDescription
FileNameAjPStrname of file that held the data
TitleAjPStrtitle of data read from file
GCchar[16][16][16]genetic codon table
Startschar[16][16][16]initiation site table

Alias name(s)

Name
AjSTrn
AjOTrn