X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=4d73aa6e96d83183693b07e5127c8517d69941d0;hb=a7bec763a3e4f17a549115f8f9f19ee4c742c26b;hp=4268353fb37e3d585a97f778ac9e8ec8c78f3199;hpb=1f705b7d5fb0920573037631b810aac3262ee190;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4268353..4d73aa6 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -400,7 +400,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
       if (dseqs[0]==null) {
         dseqs[0] = new Sequence(sq);
-        dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sq.getSequence()));
+        dseqs[0].setSequence(
+            jalview.analysis.AlignSeq.extractGaps(
+                jalview.util.Comparison.GapChars,
+                sq.getSequenceAsString()));
+
         sq.setDatasetSequence(dseqs[0]);
       }
       Alignment ds=new Alignment(dseqs);