X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=185674be113698cd248ebf1081bb2ba358336855;hb=16342ec2ab61d371ee70f61ac0294f2716fab638;hp=1e1b8bf3fb03f1afc9117466ccd0845a2f9c33fb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 1e1b8bf..185674b 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -304,10 +304,10 @@ public class JPredFile extends AlignFile
 
       seqs.addElement(newSeq);
     }
-    if (seqs.size() > 0)
+    if (seqs.size() > 0 && QuerySeqPosition>-1)
     {
       // try to make annotation for a prediction only input (default if no
-      // alignment is given)
+      // alignment is given and prediction contains a QUERY or align;sequence_id line)
       Alignment tal = new Alignment(this.getSeqsAsArray());
       try
       {
@@ -319,6 +319,7 @@ public class JPredFile extends AlignFile
         IOException ex = new IOException(
                 "Couldn't parse concise annotation for prediction profile.\n"
                         + e);
+        e.printStackTrace(); // java 1.1 does not have : ex.setStackTrace(e.getStackTrace());
         throw ex;
       }
       this.annotations = new Vector();