From: jprocter <Jim Procter>
Date: Tue, 18 Jul 2006 14:12:45 +0000 (+0000)
Subject: use of GapChars
X-Git-Tag: Release_2_1~281
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3896a79ee3a374979a32d68edd1dac8def7e15b7;p=jalview.git

use of GapChars
---

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