From 712d1fca4bfa7e91d667e9931fb67fbc99a5f369 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 10 May 2007 13:59:37 +0000
Subject: [PATCH] apparent bug in JpredFile parser where annotation was not
 being removed from alignment profile when reading in a
 concise file as an alignment.

---
 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 30cd181..dabd47a 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -237,8 +237,9 @@ public class JPredFile
             name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
           }
 
+          if (QuerySeqPosition==-1)
+            QuerySeqPosition = ids.size();
           ids.addElement(name);
-
           noSeqs++;
         }
         else
@@ -278,7 +279,7 @@ public class JPredFile
                               ") has an unexpected number of columns");
       }
 
-      if (newSeq.getName().startsWith("QUERY") &&
+      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName().startsWith("align;"))&&
           (QuerySeqPosition == -1))
       {
         QuerySeqPosition = seqs.size();
-- 
1.7.10.2