From: jprocter <Jim Procter>
Date: Sat, 15 Jan 2005 15:05:23 +0000 (+0000)
Subject: bugfix for writing fasta file without gap characters.
X-Git-Tag: Release_2_0~762
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c865a01627208f07db46ae7d28c06f39d83924ee;p=jalview.git

bugfix for writing fasta file without gap characters.
---

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");