statalign.model.score
Class SubstitutionScore

java.lang.Object
  statalign.model.score.SubstitutionScore

Direct Known Subclasses:

Blosum62, DNAScore

public abstract class SubstitutionScore
extends java.lang.Object

The ancestral class of substitution scores

Author:

novak

Field Summary

int[][]	dist The distance matrix for subtitutions.
int[][]	which This array tells the mapping between characters and indices in the distance array.

Constructor Summary

SubstitutionScore()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

dist

public int[][] dist

The distance matrix for subtitutions. It is a distance and not a similarity matrix! Distances are used to construct a NJ tree as initial tree.

which

public int[][] which

This array tells the mapping between characters and indices in the distance array. For details, see the Blosum62.java and DNAscore.java, how to fill in this array in implemented subclasses. It is a two dimensional array to allow ambiguous characters in DNA and RNA sequences.

Constructor Detail

SubstitutionScore

public SubstitutionScore()