org.biojava3.phylo
Class ScoreMatrix

java.lang.Object
  org.biojava3.phylo.ScoreMatrix

public class ScoreMatrix
extends java.lang.Object

Method Summary

int[][]	getMatrix()
int	getPairwiseScore(char c, char d)
int	getPairwiseScore(java.lang.String A1, java.lang.String A2)
boolean	isDNA()
boolean	isProtein()

Methods inherited from class java.lang.Object

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

Method Detail

isDNA

public boolean isDNA()

isProtein

public boolean isProtein()

getMatrix

public int[][] getMatrix()

getPairwiseScore

public int getPairwiseScore(java.lang.String A1,
                            java.lang.String A2)

Parameters:

A1 -

A2 -

Returns:

score for substituting first char in A1 with first char in A2

getPairwiseScore

public int getPairwiseScore(char c,
                            char d)