X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=9a6e0606f2bc37fd4a4b775aa8103a08454aff46;hb=00386d5511d779b555e93dbf71f33675937e1570;hp=28109d5ae002e3c48df53f11a395009272d0214d;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 28109d5..9a6e060 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -106,9 +106,7 @@ public class FastaFile extends AlignFile {
       if (gaps) {
         seq = s[i].getSequence();
       } else {
-        seq = AlignSeq.extractGaps(s[i].getSequence(),"-");
-        seq = AlignSeq.extractGaps(seq,".");
-        seq = AlignSeq.extractGaps(seq," ");
+        seq = AlignSeq.extractGaps("-. ",s[i].getSequence());
       }
 
       out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n");