JAL-2416 tidy up after switch from ' ' to '-' in score matrices

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index b904432..f7da9f3 100644 (file)
--- 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);
   }

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index c12f544..85f619b 100644 (file)
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -60,7 +60,7 @@ public class AlignSeqTest
     AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
             "s2", "ACGT"), AlignSeq.DNA);
     int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
-        7, 7, 8, 8, 9, 9, 10, -1, 11, -1 };
+        7, 7, 8, 8, 9, 9, -1, -1, 10, -1 };
     String s = "aAcCgGtTuUiIxXrRyYnN .-?";
     assertArrayEquals(expected, as.indexEncode(s));
   }
@@ -70,8 +70,8 @@ public class AlignSeqTest
   {
     AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
             "s2", "RQW"), AlignSeq.PEP);
-    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, 23, 24,
-        -1, -1, -1 };
+    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 24,
+        -1, 23, -1 };
     String s = "aArRnNzZxX *.-?";
     assertArrayEquals(expected, as.indexEncode(s));
   }