edu.uconn.mcb.lineageevolver
Class JTT

java.lang.Object
  edu.uconn.mcb.lineageevolver.JTT

All Implemented Interfaces:

SubstitutionMatrix

public class JTT

extends java.lang.Object

implements SubstitutionMatrix

JTT Substitution Matrix.

Author:

Hasan Khalil, Lina Pezzella

Field Summary

private static double[][]

rate The actual matrix data.

Constructor Summary

JTT()
Default constructor for objects of type JTT.

Method Summary

Substitutable

getSubstitution(Substitutable s) Returns a suitable substitution for the provided substitutable according to this substitution matrix.

Methods inherited from class java.lang.Object

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

Field Detail

rate

private static double[][] rate

The actual matrix data.

Constructor Detail

JTT

public JTT()

Default constructor for objects of type JTT. Fills in the values for the matrix. Only half of the matrix is specified. The symmetric property of the JTT matrix is used to fill the rest programmatically rather than manually.

Method Detail

getSubstitution

public Substitutable getSubstitution(Substitutable s)

Description copied from interface: SubstitutionMatrix

Returns a suitable substitution for the provided substitutable according to this substitution matrix. Choices should be made in a randomized fashion, weighted according to the values in the substitution matrix. The return and parameter types must match.

Specified by:

getSubstitution in interface SubstitutionMatrix

Parameters:

s - the substitutable for which a substitution must be generated.

Returns:

a substitution suitable for the provided substitutable.

See Also:

SubstitutionMatrix.getSubstitution(edu.uconn.mcb.lineageevolver.Substitutable)