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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.substmodel.AbstractRateMatrix | +--pal.substmodel.AminoAcidModel
base class of rate matrices for amino acids
Fields inherited from class pal.substmodel.AbstractRateMatrix |
dataType, dimension, format, frequency, rate |
Constructor Summary | |
protected |
AminoAcidModel(double[] f)
|
Method Summary | |
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 |
double |
getParameter(int n)
get model parameter |
java.lang.String |
getParameterName(int i)
|
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)
|
abstract void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface pal.substmodel.RateMatrix |
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, setDistance |
Constructor Detail |
protected AminoAcidModel(double[] f)
Method Detail |
public static AminoAcidModel getInstance(int modelID, double[] freq)
modelID
- model codefreq
- model frequenciespublic static int getSuitableModelID(double[] freq)
freq
- amino acid frequencies of the data setpublic abstract void report(java.io.PrintWriter out)
Report
report
in interface Report
pal.misc.Report
out
- output streampublic int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
pal.misc.Parameterized
public void setParameter(double param, int n)
Parameterized
setParameter
in interface Parameterized
pal.misc.Parameterized
param
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
getParameter
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
pal.misc.Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic java.lang.String getParameterName(int i)
getParameterName
in interface NamedParameterized
pal.misc.NamedParameterized
protected void printFrequencies(java.io.PrintWriter out)
printFrequencies
in class AbstractRateMatrix
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