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

Constructors
Modifier Constructor Description

protected AminoAcidModel(double[] f)

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 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 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

- 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

Class AminoAcidModel

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Field Summary

Fields inherited from class pal.substmodel.AbstractRateMatrix

Constructor Summary

Method Summary

Methods inherited from class pal.substmodel.AbstractRateMatrix

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.Parameterized

Methods inherited from interface pal.substmodel.RateMatrix

Constructor Detail

AminoAcidModel

Method Detail

getInstance

getSuitableModelID

report

getNumParameters

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue

getParameterName

printFrequencies