X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=8b5240ca5fbf56edf9693a086cafedccb92b858a;hb=c1f3a352a553ccd40063b14336b27e5a2a7329cf;hp=2507bb58a9b0aee05356da7f2b371cca35f220ed;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 2507bb5..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.
@@ -52,11 +52,11 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(FeatureSetCounterI counter)
   {
-    AlignmentViewPanel currentAlignFrame = Jalview
+    AlignmentViewPanel currentAlignFrame = Jalview.getInstance()
             .getCurrentAlignFrame().alignPanel;
     if (currentAlignFrame == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Can't register calculator as no alignment window has focus");
       return;
     }
@@ -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(),
@@ -82,7 +83,7 @@ public class AlignmentAnnotationFactory
     }
     else
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Can't register calculator as no alignment window has focus");
     }
   }