replace space

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b3cf890..817472a 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -506,6 +506,7 @@ public class Alignment implements AlignmentI {
             Sequence seq = (Sequence) sequences.elementAt(i);\r
             seq.sequence = seq.sequence.replace('.', gc);\r
             seq.sequence = seq.sequence.replace('-', gc);\r
+            seq.sequence = seq.sequence.replace(' ', gc);\r
         }\r
     }\r
 \r