com.hfg.bio.phylogeny

Class JukesCantorModel

java.lang.Object

com.hfg.bio.phylogeny.JukesCantorModel

All Implemented Interfaces:

DistanceMatrixModel

public class JukesCantorModel
extends Object
implements DistanceMatrixModel

Implementation of the Jukes-Cantor distance matrix calculation model. It assumes that all changes are equally likely.

Jukes, T.H., Cantor, C.R. (1969). "Evolution of protein molecules". In Munro, H.N.. Mammalian protein metabolism. New York: Academic Press. pp. 21-123.

For a quick overview, see http://en.wikipedia.org/wiki/Jukes-Cantor_model

Constructor Summary

Constructors

Constructor and Description
JukesCantorModel()

Method Summary

Modifier and Type	Method and Description
float	calculateDistance(BioSequence inSeq1, BioSequence inSeq2) Calculates the Jukes-Cantor distance score for a pair of sequences.
String	name() Returns the model name as required by the DistanceMatrixModel interface.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

JukesCantorModel

public JukesCantorModel()

Method Detail

name

public String name()

Returns the model name as required by the DistanceMatrixModel interface.

Specified by:

name in interface DistanceMatrixModel

calculateDistance

public float calculateDistance(BioSequence inSeq1,
                               BioSequence inSeq2)

Calculates the Jukes-Cantor distance score for a pair of sequences. The sequences must be aligned to be the same length.

Specified by:

calculateDistance in interface DistanceMatrixModel