X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=8b5240ca5fbf56edf9693a086cafedccb92b858a;hb=9bfda76754fb426a471e1c12c9f0ca0c4c1784bc;hp=c4e4b04af7e0efbe49a14e2df9d0fa607f3522f7;hpb=c932f0e85a8852824cdd8ce790af68682732c85c;p=jalview.git

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index c4e4b04..8b5240c 100644
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -20,6 +20,8 @@
  */
 package jalview.workers;
 
+import java.awt.Color;
+
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Jalview;
@@ -27,8 +29,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
 
-import java.awt.Color;
-
 /**
  * Factory class with methods which allow clients (including external scripts
  * such as Groovy) to 'register and forget' an alignment annotation calculator.
@@ -52,7 +52,7 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(FeatureSetCounterI counter)
   {
-    AlignmentViewPanel currentAlignFrame = Jalview
+    AlignmentViewPanel currentAlignFrame = Jalview.getInstance()
             .getCurrentAlignFrame().alignPanel;
     if (currentAlignFrame == null)
     {
@@ -74,7 +74,8 @@ public class AlignmentAnnotationFactory
   {
     // TODO need an interface for AlignFrame by which to access
     // its AlignViewportI and AlignmentViewPanel
-    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
+    AlignFrame currentAlignFrame = Jalview.getInstance()
+            .getCurrentAlignFrame();
     if (currentAlignFrame != null)
     {
       new AnnotationWorker(currentAlignFrame.getViewport(),