TranslatesUnderGeneticCode
Shared by the services that read codons (ORF search, CAI, codon optimization) : the standard code (table 1) goes through SequenceInterface::translateCodon(), as they always did, and any other NCBI table through AlternateGeneticCodeTranslator. The class using it holds the SequenceInterface in $this->sequenceManager.
Table of Contents
Properties
Methods
- assertSupportedGeneticCode() : void
- translateUnder() : string
Properties
$geneticCodeTranslator
private
AlternateGeneticCodeTranslator|null
$geneticCodeTranslator
= null
Methods
assertSupportedGeneticCode()
private
assertSupportedGeneticCode(int $iGeneticCode) : void
Parameters
- $iGeneticCode : int
-
An NCBI table id (see GeneticCodeTable::SUPPORTED_TABLES)
Tags
translateUnder()
private
translateUnder(string $sCodon, int $iGeneticCode) : string
Parameters
- $sCodon : string
- $iGeneticCode : int
Return values
string —The amino acid, "*" for a stop, "X" for an ambiguous codon