apparent bug in JpredFile parser where annotation was not being removed from alignmen...

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 30cd181..dabd47a 100755 (executable)
--- 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();