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java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
pal.substmodel.HKY
public class HKY
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitchondrial DNA. J. Mol. Evol. 22:160-174.
Parameters
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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static int |
KAPPA_PARAMETER_INDEX
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Fields inherited from class pal.substmodel.AbstractRateMatrix |
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format |
Constructor Summary | |
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HKY(double[] params,
double[] freq)
Constructor 2 |
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HKY(double kappa,
double[] freq)
Constructor 1 |
Method Summary | |
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java.lang.Object |
clone()
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double |
getDefaultValue(int n)
get default value of parameter |
double |
getLowerLimit(int n)
get lower parameter limit |
int |
getModelID()
get numerical code describing the model type |
int |
getNumParameters()
get number of parameters |
java.lang.String |
getParameterName(int i)
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java.lang.String |
getUniqueName()
|
double |
getUpperLimit(int n)
get upper parameter limit |
protected void |
rebuildRateMatrix(double[][] rate,
double[] parameters)
|
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
Methods inherited from class pal.substmodel.NucleotideModel |
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getInstance, printFrequencies, printRatios |
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, 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 |
Field Detail |
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public static final int KAPPA_PARAMETER_INDEX
Constructor Detail |
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public HKY(double kappa, double[] freq)
kappa
- transition/transversion rate ratiofreq
- nucleotide frequenciespublic HKY(double[] params, double[] freq)
params
- parameter listfreq
- nucleotide frequenciesMethod Detail |
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public java.lang.Object clone()
clone
in interface RateMatrix
clone
in class AbstractRateMatrix
public int getModelID()
AbstractRateMatrix
getModelID
in interface RateMatrix
getModelID
in class AbstractRateMatrix
public void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output streampublic int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
n
- parameter number
public double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter number
public double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter number
public java.lang.String getParameterName(int i)
getParameterName
in interface NamedParameterized
public java.lang.String getUniqueName()
getUniqueName
in interface RateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters)
rebuildRateMatrix
in class AbstractRateMatrix
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