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java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
pal.substmodel.TN
public class TN
Tamura-Nei model of nucleotide evolution Tamura, K. and M. Nei. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Bio. Evol. 10:512-526.
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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static int |
R_PARAMETER_INDEX
|
Fields inherited from class pal.substmodel.AbstractRateMatrix |
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format |
Constructor Summary | |
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TN(double[] params,
double[] freq)
constructor 2 |
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TN(double kappa,
double r,
double[] freq)
constructor 1 |
Method Summary | |
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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)
|
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, 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 |
Field Detail |
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public static final int KAPPA_PARAMETER_INDEX
public static final int R_PARAMETER_INDEX
Constructor Detail |
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public TN(double kappa, double r, double[] freq)
kappa
- transition/transversion rate ratior
- pyrimidine/purin transition rate ratiofreq
- nucleotide frequenciespublic TN(double[] params, double[] freq)
params
- parameter listfreq
- nucleotode 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
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 getUniqueName()
getUniqueName
in interface RateMatrix
public java.lang.String getParameterName(int i)
getParameterName
in interface NamedParameterized
protected void rebuildRateMatrix(double[][] rate, double[] parameters)
rebuildRateMatrix
in class AbstractRateMatrix
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