Uses of Interface
pal.datatype.CodonTable
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Packages that use CodonTable Package Description 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. -
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Uses of CodonTable in pal.alignment
Methods in pal.alignment with parameters of type CodonTable Modifier and Type Method Description static void
AlignmentUtils. getPositionMisalignmentInfo(Alignment a, java.io.PrintWriter out, int startingCodonPosition, CodonTable translator, boolean removeIncompleteCodons)
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Uses of CodonTable in pal.datatype
Methods in pal.datatype that return CodonTable Modifier and Type Method Description static CodonTable
CodonTableFactory. createTranslator(int type)
Creates a translator of a given typesstatic CodonTable
CodonTableFactory. createUniversalTranslator()
Methods in pal.datatype with parameters of type CodonTable Modifier and Type Method Description static char[]
CodonTableUtils. convertNucleotideToAminoAcid(char[] nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator)
Translates a Nucleotide sequence into a Amino Acid sequencestatic 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 sequenceConstructors in pal.datatype with parameters of type CodonTable Constructor Description GapBalanced(CodonTable translationTable)
SpecificAminoAcids(CodonTable translationTable)
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Uses of CodonTable in pal.substmodel
Constructors in pal.substmodel with parameters of type CodonTable Constructor Description NeutralSelectionRateMatrixGroup(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
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