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