X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=62566cf7ffe7bb07e17d946dce18be977d21d459;hb=5bd245162908974e3c96329da6a803598341bae1;hp=72274de5071effd17232818cd38e854358e8bfce;hpb=9967bbf3d9c8e015662f09f5ec1b363333f0b117;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 72274de..62566cf 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
@@ -103,7 +104,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       {
         return null;
       }
-      Alignment al = null;
+      AlignmentI al = null;
       ColumnSelection alcsel = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
@@ -231,7 +232,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (alant.sequenceRef != null)
         {
           replaceAnnotationOnAlignmentWith(alant, alant.label,
-                  "jalview.jws1.Jpred", alant.sequenceRef);
+                  "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
+                  alant.sequenceRef);
         }
       }
       return new Object[]
@@ -278,7 +280,7 @@ class JPredThread extends JWS1Thread implements WSClientI
      * @param al
      * @param profileseq
      */
-    private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+    private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
     {
       char gc = al.getGapCharacter();
       int[] gapMap = profileseq.gapMap();