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java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
pal.substmodel.GTR
public class GTR
GTR (general time reversible) model of nucleotide evolution Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.
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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Fields inherited from class pal.substmodel.AbstractRateMatrix |
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format |
Constructor Summary | |
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GTR(double[] params,
double[] freq)
constructor 2 |
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GTR(double a,
double b,
double c,
double d,
double e,
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()
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double |
getUpperLimit(int n)
get upper parameter limit |
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) |
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 |
Constructor Detail |
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public GTR(double a, double b, double c, double d, double e, double[] freq)
a
- entry in rate matrixb
- entry in rate matrixc
- entry in rate matrixd
- entry in rate matrixe
- entry in rate matrixfreq
- nucleotide frequenciespublic GTR(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 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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