Uses of Interface
pal.datatype.CodonTable
Packages that use CodonTable
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
Classes describing substitution models, i.e.
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Uses of CodonTable in pal.alignment
Methods in pal.alignment with parameters of type CodonTableModifier and TypeMethodDescriptionstatic void
AlignmentUtils.getPositionMisalignmentInfo
(Alignment a, PrintWriter out, int startingCodonPosition, CodonTable translator, boolean removeIncompleteCodons) -
Uses of CodonTable in pal.datatype
Methods in pal.datatype that return CodonTableModifier and TypeMethodDescriptionstatic CodonTable
CodonTableFactory.createTranslator
(int type) Creates a translator of a given typesstatic final CodonTable
CodonTableFactory.createUniversalTranslator()
Methods in pal.datatype with parameters of type CodonTableModifier and TypeMethodDescriptionstatic final char[]
CodonTableUtils.convertNucleotideToAminoAcid
(char[] nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequencestatic final String
CodonTableUtils.convertNucleotideToAminoAcid
(String nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequenceConstructors in pal.datatype with parameters of type CodonTableModifierConstructorDescriptionGapBalanced
(CodonTable translationTable) SpecificAminoAcids
(CodonTable translationTable) -
Uses of CodonTable in pal.substmodel
Constructors in pal.substmodel with parameters of type CodonTableModifierConstructorDescriptionNeutralSelectionRateMatrixGroup
(MutableDouble kappaStore, double[] freqs, CodonTable table) PositiveSelectionRateMatrixGroup
(MutableDouble kappaStore, MutableDouble omegaStore, double[] freqs, CodonTable table) SimpleNeutralSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa) SimpleNeutralSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa, double proportionZero) SimplePositiveSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega) SimplePositiveSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1) SimplePositiveSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1, double p2) YangCodonModel
(double[] params, double[] freq, CodonTable codonTable) constructor 3YangCodonModel
(double omega, double kappa, double[] freq, CodonTable codonTable) constructor 1