Package pal.substmodel
Class AminoAcidModel
- java.lang.Object
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- pal.substmodel.AbstractRateMatrix
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- pal.substmodel.AminoAcidModel
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
public abstract class AminoAcidModel extends AbstractRateMatrix implements 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:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
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Fields inherited from class pal.substmodel.AbstractRateMatrix
format
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Constructor Summary
Constructors Modifier Constructor Description protected
AminoAcidModel(double[] f)
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description double
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
getNumParameters()
get number of parametersjava.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 setdouble
getUpperLimit(int n)
get upper parameter limitprotected 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-
Methods 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
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface pal.misc.Parameterized
getParameter, setParameter
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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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Method Detail
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getInstance
public static AminoAcidModel getInstance(int modelID, double[] freq)
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
public abstract void report(java.io.PrintWriter out)
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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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
public java.lang.String getParameterName(int i)
- 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
protected void printFrequencies(java.io.PrintWriter out)
- Overrides:
printFrequencies
in classAbstractRateMatrix
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