Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / workers / AlignmentAnnotationFactory.java

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 2507bb5..8b5240c 100644 (file)
--- 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");
     }
   }