X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=e685d00297e3a10a8bf2a10560fcf622ee36237b;hb=aa2c6fc3fbfa5a5a60ffd3bfeb6321f1d5e4a2f2;hp=86bb56f85a836ebd230f02ff4dc26b8506c946c4;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 86bb56f..e685d00 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -38,6 +38,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JPredFile;
 import jalview.io.JnetAnnotationMaker;
+import jalview.io.PileUpfile;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
@@ -179,8 +180,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         else
         {
           throw (new Exception(MessageManager.formatMessage(
-                  "exception.unknown_format_for_file", new String[] {
-                      format.toString(), result.getAligfile() })));
+                  "exception.unknown_format_for_file", new String[] { "",
+                      result.getAligfile() })));
         }
       }
       else
@@ -363,8 +364,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (msf.length > 1)
         {
           msa = new vamsas.objects.simple.Msfalignment();
-          jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
-          msa.setMsf(pileup.print(msf));
+          PileUpfile pileup = new PileUpfile();
+          msa.setMsf(pileup.print(msf, true));
         }
       }
     }