From: jprocter <Jim Procter>
Date: Tue, 13 Oct 2009 15:24:07 +0000 (+0000)
Subject: fix for pfam files with empty annotation or sequence entries
X-Git-Tag: Release_2_5~180
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0ac591e7fec4cea76833f4b6ec8ed1f7dcd1f8b5;p=jalview.git

fix for pfam files with empty annotation or sequence entries
---

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());
+            }
           }
         }
       }