JAL-2416 use '-' not space for gap in score matrices

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

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index a4b8343..6a74dfc 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -33,6 +33,8 @@ import java.util.Arrays;
 public class ScoreMatrix implements SimilarityScoreModelI,
         PairwiseScoreModelI
 {
+  private static final char GAP_CHARACTER = Comparison.GAP_DASH;
+
   /*
    * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
    * for pairwise scoring; 2.10.2 uses gap score (last column) in
@@ -350,7 +352,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   public MatrixI findSimilarities(AlignmentView seqstrings,
           SimilarityParamsI options)
   {
-    char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X') : ' ';
+    char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
+            : Comparison.GAP_DASH;
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
     return findSimilarities(seqs, options);
   }
@@ -408,9 +411,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
           break;
         }
       }
-      // Change GAP_SPACE to GAP_DASH if we adopt - for gap in matrices
-      char c1 = i >= len1 ? Comparison.GAP_SPACE : seq1.charAt(i);
-      char c2 = i >= len2 ? Comparison.GAP_SPACE : seq2.charAt(i);
+
+      char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
+      char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
       boolean gap1 = Comparison.isGap(c1);
       boolean gap2 = Comparison.isGap(c2);