X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=00fbad5af0c96c23c20dd82dcc27d187017a15c9;hb=4756b29312ca78d0975248c65e50157399e6ce39;hp=885305ace8fe46c8cce1139cf914a9663dcddb45;hpb=3d558ed2093c9d85699945ff70271f0be119b434;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 {