X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredThread.java;fp=src%2Fjalview%2Fws%2FJPredThread.java;h=ba114f2068bf23015a9038d37781eabe7f908596;hb=aa9a4b5f3c7b97646d7ca7164f4211ab651c0862;hp=c2305e6cb21b5ca6a6c20dd67c1fe62605e5d9c4;hpb=825a9e8fcb05f794dc082ce84656c477cfff4918;p=jalview.git

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index c2305e6..ba114f2 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -88,7 +88,7 @@ class JPredThread
           if (predMap != null)
           {
             Object[] alandcolsel = input.getAlignmentAndColumnSelection(
-                alignFrame.getViewport().getGapCharacter());
+                getGapChar());
             sqs = (SequenceI[]) alandcolsel[0];
             al = new Alignment(sqs);
             alcsel = (ColumnSelection) alandcolsel[1];
@@ -131,7 +131,7 @@ class JPredThread
         FirstSeq = prediction.getQuerySeqPosition();
         if (predMap != null)
         {
-          char gc = alignFrame.getViewport().getGapCharacter();
+          char gc = getGapChar();
           SequenceI[] sqs = (SequenceI[]) ( (java.lang.Object[]) input.
                                            getAlignmentAndColumnSelection(gc))[
               0];
@@ -146,8 +146,7 @@ class JPredThread
           new jalview.commands.RemoveGapsCommand("Remove Gaps",
                                                  new SequenceI[]
                                                  {sqs[msaIndex]},
-                                                 alignFrame.getCurrentView().
-                                                 getAlignment());
+                                                 currentView);
 
           SequenceI profileseq = al.getSequenceAt(FirstSeq);
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());