- * 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.