pal.substmodel
Class AminoAcidModel

java.lang.Object
  pal.substmodel.AbstractRateMatrix
      pal.substmodel.AminoAcidModel

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix

Direct Known Subclasses:

BLOSUM62, CPREV, Dayhoff, JTT, MTREV24, VT, WAG

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

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

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
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

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

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, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale

Methods inherited from interface pal.misc.Parameterized

getParameter, setParameter

Constructor Detail

AminoAcidModel

protected AminoAcidModel(double[] f)

Method Detail

getInstance

public static AminoAcidModel getInstance(int modelID,
                                         double[] freq)

Create amino acid model according to model type

Parameters:

modelID - model code

freq - model frequencies

Returns:

amino acid rate matrix

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

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)

Specified by:

report in interface Report

Parameters:

out - output stream

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

setParameterSE

public void setParameterSE(double paramSE,
                           int n)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Parameters:

paramSE - standard error of parameter value

n - parameter number

getLowerLimit

public double getLowerLimit(int n)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

lower bound

getUpperLimit

public double getUpperLimit(int n)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

upper bound

getDefaultValue

public double getDefaultValue(int n)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

n - parameter number

Returns:

default value

getParameterName

public java.lang.String getParameterName(int i)

Specified by:

getParameterName in interface NamedParameterized

Returns:

a short identifier for this parameter type. Should be the same for all instances of a given class!

printFrequencies

protected void printFrequencies(java.io.PrintWriter out)

Overrides:

printFrequencies in class AbstractRateMatrix