X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=f7da9f3f8845db6fc737532a85f34aaa68299621;hb=81f1e29b00bc98403d45d2258da71ac19c425c57;hp=b904432d6652d41c15f802f13aed860ac0dd1c49;hpb=adca107ff292173bc844ad4a5c6c7eba958ad24a;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index b904432..f7da9f3 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -394,7 +394,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
           SimilarityParamsI options)
   {
     char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
-            : Comparison.GAP_DASH;
+            : gapCharacter;
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
     return findSimilarities(seqs, options);
   }