From 60083c09e41c5685e7afea332b58dbca2cdd61a7 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 7 Aug 2016 16:51:11 +0100
Subject: [PATCH] JAL-2068 add the worker to the currently displayed alignment
 panel and viewport

---
 src/jalview/workers/AlignmentAnnotationFactory.java |    6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index f804a19..2b7d9e1 100644
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -32,11 +32,11 @@ public class AlignmentAnnotationFactory
   {
     // TODO need an interface for AlignFrame by which to access
     // its AlignViewportI and AlignmentViewPanel
-    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame() ;
+    AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
     if (currentAlignFrame != null)
     {
-      newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
-              .getAlignPanels().get(0), counter);
+      newCalculator(currentAlignFrame.getAlignViewport(),
+              currentAlignFrame, counter);
     }
     else
     {
-- 
1.7.10.2