From c865a01627208f07db46ae7d28c06f39d83924ee Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sat, 15 Jan 2005 15:05:23 +0000
Subject: [PATCH] bugfix for writing fasta file without gap characters.

---
 src/jalview/io/FastaFile.java |    4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

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");
-- 
1.7.10.2