Merge branch 'develop' into features/filetypeEnum

[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 bb4fc37..4e5cadc 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -365,7 +365,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         {
           msa = new vamsas.objects.simple.Msfalignment();
           PileUpfile pileup = new PileUpfile();
-          msa.setMsf(pileup.print(msf));
+          msa.setMsf(pileup.print(msf, true));
         }
       }
     }