pal.substmodel
public abstract class AminoAcidModel extends AbstractRateMatrix implements RateMatrix
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
format
Modifier | Constructor and Description |
---|---|
protected |
AminoAcidModel(double[] f) |
Modifier and Type | Method and Description |
---|---|
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) |
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 |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter
|
addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getModelID, getOrthogonalHints, getParameter, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, parameterChanged, rebuild, rebuildRateMatrix, removePalObjectListener, scale, setDataType, setDistance, setDistanceTranspose, setFrequencies, setParameter, setParameters, setParametersNoScale, updateMatrixExp
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
getParameter, setParameter
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
public 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 numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter numberpublic java.lang.String getParameterName(int i)
getParameterName
in interface NamedParameterized
protected void printFrequencies(java.io.PrintWriter out)
printFrequencies
in class AbstractRateMatrix