*
* @return
*/
+ // TODO is this specific to a PID score only?
+ // score matrix will compute whatever is configured for gap-residue
boolean matchGaps();
/**
- * Answers true if the demoninator (normalisation factor) of the score count
- * includes gap-residue positions, false if it only includes residue-residue
- * aligned positions. Gap-gap positions are included if this and
- * includeGappedColumns both answer true.
+ * Answers true if gaps are included in the calculation. This may affect the
+ * calculated score, the denominator (normalisation factor) of the score, or
+ * both. Gap-gap positions are included if this and includeGappedColumns both
+ * answer true.
*
* @return
*/
- boolean denominatorIncludesGaps();
+ boolean includesGaps();
/**
* Answers true if only the shortest sequence length is used to divide the