factored out reference to parent alignFrame (so all views can be closed whilst a...

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

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