X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=00fbad5af0c96c23c20dd82dcc27d187017a15c9;hb=6c4bc68ae8b1c5005e79661bb2d8246515cb787d;hp=885305ace8fe46c8cce1139cf914a9663dcddb45;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 885305a..00fbad5 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -204,7 +204,10 @@ public class SeqsetUtils
       boolean ungapped[] = new boolean[sequences.length];
       int msflen=0;
       for (int i=0,j=sequences.length; i<j;i++) {
-        String tempseq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequences[i].getSequence());
+        String tempseq = jalview.analysis.AlignSeq.extractGaps(
+            jalview.util.Comparison.GapChars,
+            sequences[i].getSequenceAsString());
+
         if (tempseq.length()==0)
           ungapped[i]=false;
         else {