JAL-838 ScoreMatrix now respects SimilarityParams!

[jalview.git] / src / jalview / analysis / scoremodels / PIDModel.java

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index 24e9a1c..50c4a71 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -124,7 +124,7 @@ public class PIDModel implements SimilarityScoreModelI,
         {
           break;
         }
-        if (options.denominatorIncludesGaps())
+        if (options.includesGaps())
         {
           divideBy++;
         }
@@ -159,7 +159,7 @@ public class PIDModel implements SimilarityScoreModelI,
          * gap-residue: include if options say so, 
          * count as match if options say so
          */
-        if (options.denominatorIncludesGaps())
+        if (options.includesGaps())
         {
           divideBy++;
         }