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 (executable)
--- 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());
+            }
           }
         }
       }