From 0ac591e7fec4cea76833f4b6ec8ed1f7dcd1f8b5 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 13 Oct 2009 15:24:07 +0000 Subject: [PATCH] fix for pfam files with empty annotation or sequence entries --- src/jalview/io/PfamFile.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 7e0a976..5e9df60 100755 --- a/src/jalview/io/PfamFile.java +++ b/src/jalview/io/PfamFile.java @@ -60,6 +60,7 @@ public class PfamFile extends AlignFile { if (line.indexOf("#") != 0) { + // TODO: verify pfam format requires spaces and not tab characters - if not upgrade to use stevesoft regex and look for whitespace. StringTokenizer str = new StringTokenizer(line, " "); String id = ""; @@ -83,8 +84,10 @@ public class PfamFile extends AlignFile { headers.addElement(id); } - - tempseq.append(str.nextToken()); + if (str.hasMoreTokens()) + { + tempseq.append(str.nextToken()); + } } } } -- 1.7.10.2