Uses of Interface
pal.datatype.CodonTable

Packages that use CodonTable

pal.alignment	Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.
pal.datatype	Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
pal.substmodel	Classes describing substitution models, i.e.

Uses of CodonTable in pal.alignment

Methods in pal.alignment with parameters of type CodonTable

static void

AlignmentUtils.getPositionMisalignmentInfo(Alignment a, java.io.PrintWriter out, int startingCodonPosition, CodonTable translator, boolean removeIncompleteCodons)

Uses of CodonTable in pal.datatype

Methods in pal.datatype that return CodonTable

static CodonTable	CodonTableFactory.createTranslator(int type) Creates a translator of a given types
static CodonTable	CodonTableFactory.createUniversalTranslator()

Methods in pal.datatype with parameters of type CodonTable

static char[]	CodonTableUtils.convertNucleotideToAminoAcid(char[] nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequence
static java.lang.String	CodonTableUtils.convertNucleotideToAminoAcid(java.lang.String nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequence

Constructors in pal.datatype with parameters of type CodonTable

GapBalanced(CodonTable translationTable)

SpecificAminoAcids(CodonTable translationTable)

Uses of CodonTable in pal.substmodel

Constructors in pal.substmodel with parameters of type CodonTable

NeutralSelectionRateMatrixGroup(MutableDouble kappaStore, double[] freqs, CodonTable table)

PositiveSelectionRateMatrixGroup(MutableDouble kappaStore, MutableDouble omegaStore, double[] freqs, CodonTable table)

YangCodonModel.SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa)

YangCodonModel.SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double proportionZero)

YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega)

YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1)

YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1, double p2)

YangCodonModel(double[] params, double[] freq, CodonTable codonTable)
constructor 3

YangCodonModel(double omega, double kappa, double[] freq, CodonTable codonTable)
constructor 1