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Packages that use CodonTable | |
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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 |
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Methods in pal.alignment with parameters of type CodonTable | |
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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 |
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Methods in pal.datatype that return CodonTable | |
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static CodonTable |
CodonTableFactory.createTranslator(int type)
Creates a translator of a given types |
static CodonTable |
CodonTableFactory.createUniversalTranslator()
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Methods in pal.datatype with parameters of type CodonTable | |
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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 | |
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GapBalanced(CodonTable translationTable)
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SpecificAminoAcids(CodonTable translationTable)
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Uses of CodonTable in pal.substmodel |
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Constructors in pal.substmodel with parameters of type CodonTable | |
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NeutralSelectionRateMatrixGroup(MutableDouble kappaStore,
double[] freqs,
CodonTable table)
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PositiveSelectionRateMatrixGroup(MutableDouble kappaStore,
MutableDouble omegaStore,
double[] freqs,
CodonTable table)
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YangCodonModel.SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa)
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YangCodonModel.SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double proportionZero)
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YangCodonModel.SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega)
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YangCodonModel.SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega,
double p0,
double p1)
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YangCodonModel.SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega,
double p0,
double p1,
double p2)
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YangCodonModel(double[] params,
double[] freq,
CodonTable codonTable)
constructor 3 |
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YangCodonModel(double omega,
double kappa,
double[] freq,
CodonTable codonTable)
constructor 1 |
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