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java.lang.Object | +--pal.substmodel.AbstractRateMatrix | +--pal.substmodel.AminoAcidModel | +--pal.substmodel.JTT
JTT model of amino acid evolution
Fields inherited from class pal.substmodel.AbstractRateMatrix |
dataType, dimension, format, frequency, rate |
Fields inherited from interface pal.util.XMLConstants |
A_TO_C, A_TO_G, A_TO_T, ALIGNMENT, ALPHA, ANCESTRAL_MU_RATE, ANCESTRAL_POP_SIZE, ATTRIBUTE, BACKWARDS, BLOSUM62, C_TO_G, C_TO_T, COALESCENT, CONST_EXP_GROWTH, CONSTANT_MUTATION_RATE, CONSTANT_POPULATION, CPREV, DATA_TYPE, DATA_TYPE_ID, DAYHOFF, DAYS, DEMOGRAPHIC_MODEL, DIRECTION, EDGE, EXPONENTIAL_GROWTH, F81, F84, FREQUENCIES, G_TO_T, GENERATIONS, GROWTH_RATE, GTR, HEIGHT, HKY, ID, JC, JTT, KAPPA, LENGTH, MISSING, MODEL, MONTHS, MTREV24, MU_STEP_TIME, MUTATION_RATE, MUTATION_RATE_MODEL, MUTATIONS, NAME, NODE, OMEGA, ORIGIN, PARAMETER, POPULATION_SIZE, PYRIMIDINE_PURINE_RATIO, RATE_MATRIX, SEQUENCE, SPACES_PER_LEVEL, STEPPED_MUTATION_RATE, TIME, TIME_DATA, TN, TREE, TS_TV_RATIO, TWO_STATE, TYPE, UNIFORM, UNITS, UNKNOWN, VALUE, VT, WAG, YANG_CODON_MODEL, YEARS |
Constructor Summary | |
JTT(double[] f)
constructor |
Method Summary | |
int |
getModelID()
get numerical code describing the model type |
static void |
getOriginalFrequencies(double[] f)
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix |
java.lang.String |
getUniqueName()
|
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
Methods inherited from class pal.substmodel.AminoAcidModel |
getDefaultValue, getInstance, getLowerLimit, getNumParameters, getParameter, getParameterName, getSuitableModelID, getUpperLimit, printFrequencies, setParameter, setParameterSE |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface pal.substmodel.RateMatrix |
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, setDistance |
Constructor Detail |
public JTT(double[] f)
f
- amino acid frequenciesMethod Detail |
public int getModelID()
RateMatrix
getModelID
in class AbstractRateMatrix
pal.substmodel.RateMatrix
public void report(java.io.PrintWriter out)
Report
report
in class AminoAcidModel
pal.misc.Report
out
- output streampublic static void getOriginalFrequencies(double[] f)
f
- array where amino acid frequencies will be storedpublic java.lang.String getUniqueName()
pal.substmodel.RateMatrix
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