ChaosGameRepresentationInterface
in
Interface ChaosGameRepresentationInterface - the computation behind a CGR and an FCGR image, with no drawing : the points of the chaos game, and the counts of the oligonucleotides on their grid.
Tags
Table of Contents
Methods
- cell() : array{0: int, 1: int}
- frequencyMatrix() : array<string|int, array<string|int, int>>
- oligoCounts() : array<string, int>
- points() : array<int, array{0: float, 1: float}>
Methods
cell()
public
cell(string $sOligo) : array{0: int, 1: int}
Parameters
- $sOligo : string
-
A, C, G and T only, 1 to 8 of them
Return values
array{0: int, 1: int} —[column, row] of the oligonucleotide on the 2^k x 2^k grid
frequencyMatrix()
public
frequencyMatrix(DnaSequence $oSequence, int $iOligoLength[, bool $bBothStrands = false ]) : array<string|int, array<string|int, int>>
Parameters
- $oSequence : DnaSequence
- $iOligoLength : int
-
1 to 8
- $bBothStrands : bool = false
Return values
array<string|int, array<string|int, int>> —Row by row, the count of the oligonucleotide in each cell of the grid
oligoCounts()
public
oligoCounts(DnaSequence $oSequence, int $iOligoLength[, bool $bBothStrands = false ]) : array<string, int>
Parameters
- $oSequence : DnaSequence
- $iOligoLength : int
-
1 to 8
- $bBothStrands : bool = false
-
Count the reverse complement too
Return values
array<string, int> —Every oligonucleotide of that length, 0 included, to its count
points()
public
points(DnaSequence $oSequence) : array<int, array{0: float, 1: float}>
Parameters
- $oSequence : DnaSequence
Return values
array<int, array{0: float, 1: float}> —One [x, y] per A, C, G or T, in [0, 1[