edu.uconn.mcb.lineageevolver
Interface SubstitutionMatrix

All Known Implementing Classes:
JTT

public interface SubstitutionMatrix

Common interface for all substitution matrices.

Author:
Hasan Khalil, Lina Pezzella

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

Method Detail

getSubstitution

public Substitutable getSubstitution(Substitutable s)
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.

Parameters:
s - the substitutable for which a substitution must be generated.
Returns:
a substitution suitable for the provided substitutable.