CodonUsageTable
in package
Holds raw codon observation counts from a reference gene set (typically the highly expressed genes of a host organism), keyed by codon in DNA notation. This is deliberately just a validated data carrier : it knows nothing about which codons are synonymous with each other, since that grouping comes from the genetic code, not from this table, and is CodonAdaptationIndexCalculator's concern.
A codon absent from the table is treated as observed zero times by getCount(), not as an error, since a real reference set - especially a small one - can legitimately never have used some codon. Class CodonUsageTable
Tags
Table of Contents
Properties
- $counts : array<string, int>
Methods
- __construct() : mixed
- CodonUsageTable constructor.
- getCodons() : array<string|int, string>
- getCount() : int
Properties
$counts
private
array<string, int>
$counts
Methods
__construct()
CodonUsageTable constructor.
public
__construct(array<string, int> $aCodonCounts) : mixed
Parameters
- $aCodonCounts : array<string, int>
-
Codon (3 letters, A/C/G/T, case insensitive) => a non-negative observation count
getCodons()
public
getCodons() : array<string|int, string>
Return values
array<string|int, string> —The codons this table has an explicit observation count for
getCount()
public
getCount(string $sCodon) : int
Parameters
- $sCodon : string
-
3 letters, A/C/G/T, case insensitive
Return values
int —0 when the codon was never observed in this table