|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
pal.substmodel.WAG
public class WAG
WAG model of amino acid evolution (S. Whelan and N. Goldman 2000)
Nested Class Summary |
---|
Nested classes/interfaces inherited from interface pal.misc.Parameterized |
---|
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Field Summary |
---|
Fields inherited from class pal.substmodel.AbstractRateMatrix |
---|
format |
Constructor Summary | |
---|---|
WAG(double[] f)
constructor |
Method Summary | |
---|---|
int |
getModelID()
get numerical code describing the model type |
static double[] |
getOriginalFrequencies()
|
static void |
getOriginalFrequencies(double[] f)
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix |
java.lang.String |
getUniqueName()
|
protected void |
rebuildRateMatrix(double[][] rate,
double[] parameters)
|
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
Methods inherited from class pal.substmodel.AminoAcidModel |
---|
getDefaultValue, getInstance, getLowerLimit, getNumParameters, getParameterName, getSuitableModelID, getUpperLimit, printFrequencies, setParameterSE |
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, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale |
Methods inherited from interface pal.misc.Parameterized |
---|
getParameter, setParameter |
Constructor Detail |
---|
public WAG(double[] f)
f
- amino acid frequenciesMethod Detail |
---|
public int getModelID()
AbstractRateMatrix
getModelID
in interface RateMatrix
getModelID
in class AbstractRateMatrix
public void report(java.io.PrintWriter out)
Report
report
in interface Report
report
in class AminoAcidModel
out
- output streampublic static void getOriginalFrequencies(double[] f)
f
- array where amino acid frequencies will be storedpublic static double[] getOriginalFrequencies()
public java.lang.String getUniqueName()
getUniqueName
in interface RateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters)
rebuildRateMatrix
in class AbstractRateMatrix
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |