PairwiseDistance

java.lang.Object
- pal.distance.PairwiseDistance

All Implemented Interfaces:

java.io.Serializable
```
public class PairwiseDistance
extends java.lang.Object
implements java.io.Serializable
```
determines the (observed and ML) distance between a pair of sequences

Version:

$Id: PairwiseDistance.java,v 1.10 2002/09/08 03:47:01 matt Exp $

Author:

Korbinian Strimmer

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field Description

double distance
last estimated distance

double distanceSE
last estimate standard error of a distance

Fields
Modifier and Type	Field	Description
`double`	`distance`	last estimated distance
`double`	`distanceSE`	last estimate standard error of a distance

Constructor Summary

Constructors
Constructor	Description
`PairwiseDistance(SitePattern sp)`	Constructor 1 (estimate observed distances only)
`PairwiseDistance(SitePattern sp, SubstitutionModel m)`	Constructor 2 (uses evolutionary model)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`getDistance(byte[] s1, byte[] s2)`	compute distance between two sequences (not necessarly in the given alignment but with the same weights in the site pattern)
`double`	`getDistance(int s1, int s2)`	compute distance between 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

- Field Detail
  - distance
```
public double distance
```
    last estimated distance
  - distanceSE
```
public double distanceSE
```
    last estimate standard error of a distance
- Constructor Detail
  - PairwiseDistance
```
public PairwiseDistance(SitePattern sp)
```
    Constructor 1 (estimate observed distances only)
    
    Parameters:
    
    sp - site pattern
  - PairwiseDistance
```
public PairwiseDistance(SitePattern sp,
                        SubstitutionModel m)
```
    Constructor 2 (uses evolutionary model)
    
    Parameters:
    
    sp - site pattern
    
    m - evolutionary model
- 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
  - getDistance
```
public double getDistance(int s1,
                          int s2)
```
    compute distance between two sequences in the given alignment
    
    Parameters:
    
    s1 - number of first sequence
    
    s2 - number of second sequence
    
    Returns:
    
    estimated distance (observed or ML, depending on constructor used)
  - getDistance
```
public double getDistance(byte[] s1,
                          byte[] s2)
```
    compute distance between two sequences (not necessarly 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
    
    Returns:
    
    estimated distance (observed or ML, depending on constructor used)

Class PairwiseDistance

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

distance

distanceSE

Constructor Detail

PairwiseDistance

PairwiseDistance

Method Detail

updateModel

updateSitePattern

getDistance

getDistance