org.biojava3.phylo
Class ScoreMatrix

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

public class ScoreMatrix
extends Object


Method Summary
 int[][] getMatrix()
           
 int getPairwiseScore(char c, char d)
           
 int getPairwiseScore(String A1, 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(String A1,
                            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)