From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 10 May 2016 14:04:26 +0000 (+0100)
Subject: JAL-2103 reinstate legacy behaviour (when full_MSA not available)

X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2fa368f637a366a6549116bfb40dee39f77b76cd;p=jalview.git

JAL-2103 reinstate legacy behaviour (when full_MSA not available)

---

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 7176163..bb09af3 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -222,12 +222,12 @@ class JPredThread extends JWS1Thread implements WSClientI
           }
           if (fullAlignment == null)
           {
-            // ///
+            // //
             // Uses RemoveGapsCommand
-            // ///
-            // new jalview.commands.RemoveGapsCommand(
-            // MessageManager.getString("label.remove_gaps"),
-            // new SequenceI[] { sqs[msaIndex] }, currentView);
+            // //
+            new jalview.commands.RemoveGapsCommand(
+                    MessageManager.getString("label.remove_gaps"),
+                    new SequenceI[] { sqs[msaIndex] }, currentView);
 
             SequenceI profileseq = al.getSequenceAt(FirstSeq);
             profileseq.setSequence(sqs[msaIndex].getSequenceAsString());