X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FJPredFile.java;h=a038cacb4746d9e8e3e3b62a0eba851a3e12fa08;hb=057425f8881d0e8986e9e7a8004b709e42334f34;hp=1e1b8bf3fb03f1afc9117466ccd0845a2f9c33fb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 1e1b8bf..a038cac 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);
+        e.printStackTrace(); // java 1.1 does not have : ex.setStackTrace(e.getStackTrace());
         throw ex;
       }
       this.annotations = new Vector();