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java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
pal.substmodel.F84
public class F84
Felsenstein 1984 (PHYLIP) model of nucleotide evolution
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 |
EXPECTED_TS_TV_PARAMETER_INDEX
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Fields inherited from class pal.substmodel.AbstractRateMatrix |
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format |
Constructor Summary | |
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F84(double[] params,
double[] freq)
Constructor 2 |
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F84(double expectedTsTv,
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)
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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 |
java.lang.String |
toString()
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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, 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 EXPECTED_TS_TV_PARAMETER_INDEX
Constructor Detail |
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public F84(double expectedTsTv, double[] freq)
expectedTsTv
- expected transition-transversion ratiofreq
- nucleotide frequenciespublic F84(double[] params, double[] freq)
params
- parameter listfreq
- nucleotide 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
public java.lang.String toString()
toString
in class java.lang.Object
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