}
/**
- * Returns the pairwise score for substituting c with d, or zero if c or d is
- * an unscored or unexpected character
+ * Returns the pairwise score for substituting c with d. If either c or d is
+ * an unexpected character, returns 1 for identity (c == d), else the minimum
+ * score value in the matrix.
*/
@Override
public float getPairwiseScore(char c, char d)
/*
* one or both symbols not found in the matrix
- * note: a possible strategy here would be to return the minimum
- * matrix value if c != d
*/
- return 0;
+ return c == d ? 1 : getMinimumScore();
}
/**