bugfix for writing fasta file without gap characters.

[jalview.git] / src / jalview / io / FastaFile.java

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