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java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
public abstract class AminoAcidModel
base class of rate matrices for amino acids
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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protected |
AminoAcidModel(double[] f)
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Method Summary | |
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double |
getDefaultValue(int n)
get default value of parameter |
static AminoAcidModel |
getInstance(int modelID,
double[] freq)
Create amino acid model according to model type |
double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumParameters()
get number of parameters |
java.lang.String |
getParameterName(int i)
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static int |
getSuitableModelID(double[] freq)
get numerical code of amino acid model that would probably be suitable for a given sequence data set |
double |
getUpperLimit(int n)
get upper parameter limit |
protected void |
printFrequencies(java.io.PrintWriter out)
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abstract 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 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, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale |
Methods inherited from interface pal.misc.Parameterized |
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getParameter, setParameter |
Constructor Detail |
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protected AminoAcidModel(double[] f)
Method Detail |
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public static AminoAcidModel getInstance(int modelID, double[] freq)
modelID
- model codefreq
- model frequencies
public static int getSuitableModelID(double[] freq)
freq
- amino acid frequencies of the data set
public abstract 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
protected void printFrequencies(java.io.PrintWriter out)
printFrequencies
in class AbstractRateMatrix
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