X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fanalysis%2FSimilarityParamsI.java;h=581449fb617332f21c2e7be7ecba3fe3b7caf70e;hb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;hp=9ec215120f07dc6dd50ee4b99e958488a152774f;hpb=a4015623cfd1057095d5d54043de462d9163af4b;p=jalview.git

diff --git a/src/jalview/api/analysis/SimilarityParamsI.java b/src/jalview/api/analysis/SimilarityParamsI.java
index 9ec2151..581449f 100644
--- 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