From 3e59c98d7a3a8edec93ef35e4e6bdc7c5479c0ef Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 16 Sep 2008 09:10:07 +0000
Subject: [PATCH] fix exception raised when JNet concise files with no
 sequence content are parsed (c.f. TarO Jnet concise files)

---
 src/jalview/io/JPredFile.java |    5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 1e1b8bf..ec4a89e 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -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);
+        ex.setStackTrace(e.getStackTrace());
         throw ex;
       }
       this.annotations = new Vector();
-- 
1.7.10.2