JAL-2664 Updates following review

[jalview.git] / src / jalview / api / analysis / SimilarityParamsI.java

diff --git a/src/jalview/api/analysis/SimilarityParamsI.java b/src/jalview/api/analysis/SimilarityParamsI.java
index 9ec2151..581449f 100644 (file)
--- a/src/jalview/api/analysis/SimilarityParamsI.java
+++ b/src/jalview/api/analysis/SimilarityParamsI.java
@@ -19,17 +19,19 @@ public interface SimilarityParamsI
    * 
    * @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 includeGaps();
 
   /**
    * Answers true if only the shortest sequence length is used to divide the