Package pal.substmodel
Class AminoAcidModel
java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
- All Implemented Interfaces:
Serializable
,Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
base class of rate matrices for amino acids
- Version:
- $Id: AminoAcidModel.java,v 1.8 2003/11/13 04:05:39 matt Exp $
- Author:
- Korbinian Strimmer
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
Fields inherited from class pal.substmodel.AbstractRateMatrix
format
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
getDefaultValue
(int n) get default value of parameterstatic AminoAcidModel
getInstance
(int modelID, double[] freq) Create amino acid model according to model typedouble
getLowerLimit
(int n) get lower parameter limitint
get number of parametersgetParameterName
(int i) static int
getSuitableModelID
(double[] freq) get numerical code of amino acid model that would probably be suitable for a given sequence data setdouble
getUpperLimit
(int n) get upper parameter limitprotected void
abstract void
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)void
setParameterSE
(double paramSE, int n) set standard errors for model parameterMethods inherited from class pal.substmodel.AbstractRateMatrix
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
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface pal.misc.Parameterized
getParameter, setParameter
Methods inherited from interface pal.substmodel.RateMatrix
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
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Constructor Details
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AminoAcidModel
protected AminoAcidModel(double[] f)
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Method Details
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getInstance
Create amino acid model according to model type- Parameters:
modelID
- model codefreq
- model frequencies- Returns:
- amino acid rate matrix
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getSuitableModelID
public static int getSuitableModelID(double[] freq) get numerical code of amino acid model that would probably be suitable for a given sequence data set- Parameters:
freq
- amino acid frequencies of the data set- Returns:
- numerical code of suitable AminoAcidModel
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model) -
getNumParameters
public int getNumParameters()Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Returns:
- number of parameters
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setParameterSE
public void setParameterSE(double paramSE, int n) Description copied from interface:Parameterized
set standard errors for model parameter- Specified by:
setParameterSE
in interfaceParameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
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getLowerLimit
public double getLowerLimit(int n) Description copied from interface:Parameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:Parameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n) Description copied from interface:Parameterized
get default value of parameter- Specified by:
getDefaultValue
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- default value
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getParameterName
- Specified by:
getParameterName
in interfaceNamedParameterized
- Returns:
- a short identifier for this parameter type. Should be the same for all instances of a given class!
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printFrequencies
- Overrides:
printFrequencies
in classAbstractRateMatrix
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