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java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
pal.substmodel.JTT
public class JTT
JTT model of amino acid evolution Jones, D. T., Taylor, W. R. and Thornton, J. M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci., 8, 275-282.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Field Summary |
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Fields inherited from class pal.substmodel.AbstractRateMatrix |
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format |
Constructor Summary | |
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JTT(double[] f)
constructor |
Method Summary | |
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int |
getModelID()
get numerical code describing the model type |
static double[] |
getOriginalFrequencies()
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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()
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protected void |
rebuildRateMatrix(double[][] rate,
double[] parameters)
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void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
Methods inherited from class pal.substmodel.AminoAcidModel |
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getDefaultValue, getInstance, getLowerLimit, getNumParameters, getParameterName, getSuitableModelID, getUpperLimit, printFrequencies, setParameterSE |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface pal.substmodel.RateMatrix |
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addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale |
Methods inherited from interface pal.misc.Parameterized |
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getParameter, setParameter |
Constructor Detail |
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public JTT(double[] f)
f
- amino acid frequenciesMethod Detail |
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public int getModelID()
AbstractRateMatrix
getModelID
in interface RateMatrix
getModelID
in class AbstractRateMatrix
public void report(java.io.PrintWriter out)
Report
report
in interface Report
report
in class AminoAcidModel
out
- output streampublic static void getOriginalFrequencies(double[] f)
f
- array where amino acid frequencies will be storedpublic static double[] getOriginalFrequencies()
public java.lang.String getUniqueName()
getUniqueName
in interface RateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters)
rebuildRateMatrix
in class AbstractRateMatrix
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