use of GapChars

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 0e52ea7..615f670 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -445,7 +445,7 @@ public class Sequence implements SequenceI
     public int[] gapMap()\r
     {\r
         // Returns an int array giving the position of each residue in the sequence in the alignment\r
-        String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);\r
+        String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);\r
         int[] map = new int[seq.length()];\r
         int j = 0;\r
         int p = 0;\r