From c2dd5464538291087fffb47809c108ace0b236cc Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 26 Feb 2014 16:14:31 +0000 Subject: [PATCH] fix for JAL-686 - don't trim spaces before creating annotation --- src/jalview/io/FastaFile.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index 9cc3b55..f866928 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -76,14 +76,14 @@ public class FastaFile extends AlignFile StringBuffer sb = new StringBuffer(); boolean firstLine = true; - String line; + String line,uline; Sequence seq = null; boolean annotation = false; - while ((line = nextLine()) != null) + while ((uline = nextLine()) != null) { - line = line.trim(); + line = uline.trim(); if (line.length() > 0) { if (line.charAt(0) == '>') @@ -132,7 +132,7 @@ public class FastaFile extends AlignFile } else { - sb.append(line); + sb.append(annotation ? uline : line); } } } -- 1.7.10.2