SequencePairLikelihood

java.lang.Object
- pal.distance.SequencePairLikelihood

All Implemented Interfaces:

java.io.Serializable, UnivariateFunction
```
public class SequencePairLikelihood
extends java.lang.Object
implements UnivariateFunction, java.io.Serializable
```
computation of the (negative) log-likelihood for a pair of sequences

Version:

$Id: SequencePairLikelihood.java,v 1.11 2002/12/05 04:27:28 matt Exp $

Author:

Korbinian Strimmer

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

SequencePairLikelihood(SitePattern sp, SubstitutionModel m)
initialisation

Constructors
Constructor	Description
`SequencePairLikelihood(SitePattern sp, SubstitutionModel m)`	initialisation

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`evaluate(double arc)`	compute function value
`double`	`getLowerBound()`	get lower bound of argument
`double`	`getUpperBound()`	get upper bound of argument
`void`	`setSequences(byte[] s1, byte[] s2)`	specification of two sequences (not necessarily in the given alignment but with the same weights in the site pattern)
`void`	`setSequences(int s1, int s2)`	specification of two sequences in the given alignment
`void`	`updateModel(SubstitutionModel m)`	update model of substitution
`void`	`updateSitePattern(SitePattern sp)`	update site pattern

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SequencePairLikelihood
```
public SequencePairLikelihood(SitePattern sp,
                              SubstitutionModel m)
```
    initialisation
    
    Parameters:
    
    sp - site pattern
    
    m - model of substitution
- Method Detail
  - updateModel
```
public void updateModel(SubstitutionModel m)
```
    update model of substitution
    
    Parameters:
    
    model - of substitution
  - updateSitePattern
```
public void updateSitePattern(SitePattern sp)
```
    update site pattern
    
    Parameters:
    
    site - pattern
  - setSequences
```
public void setSequences(int s1,
                         int s2)
```
    specification of two sequences in the given alignment
    
    Parameters:
    
    s1 - number of first sequence
    
    s2 - number of second sequence
  - setSequences
```
public void setSequences(byte[] s1,
                         byte[] s2)
```
    specification of two sequences (not necessarily in the given alignment but with the same weights in the site pattern)
    
    Parameters:
    
    s1 - site pattern of first sequence
    
    s2 - site pattern of second sequence
  - evaluate
```
public final double evaluate(double arc)
```
    Description copied from interface: UnivariateFunction
    
    compute function value
    
    Specified by:
    
    evaluate in interface UnivariateFunction
    
    Returns:
    
    function value
  - getLowerBound
```
public double getLowerBound()
```
    Description copied from interface: UnivariateFunction
    
    get lower bound of argument
    
    Specified by:
    
    getLowerBound in interface UnivariateFunction
    
    Returns:
    
    lower bound
  - getUpperBound
```
public double getUpperBound()
```
    Description copied from interface: UnivariateFunction
    
    get upper bound of argument
    
    Specified by:
    
    getUpperBound in interface UnivariateFunction
    
    Returns:
    
    upper bound

Class SequencePairLikelihood

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SequencePairLikelihood

Method Detail

updateModel

updateSitePattern

setSequences

setSequences

evaluate

getLowerBound

getUpperBound