JAL-2473 removed unused fields in JalviewDialog

[jalview.git] / src / jalview / ws / jws1 / JPredThread.java

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 86bb56f..e685d00 100644 (file)
--- 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));
         }
       }
     }