X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=8b5240ca5fbf56edf9693a086cafedccb92b858a;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=b0392d43dcba33e116a609df29fdd3c84f8f95d1;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index b0392d4..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;
@@ -27,15 +29,15 @@ 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. <br>
+ * such as Groovy) to 'register and forget' an alignment annotation calculator.
+ * <br>
  * Currently supports two flavours of calculator:
  * <ul>
  * <li>a simple 'feature counter' which counts any desired score derivable from
- * residue value and any sequence features at each position of the alignment</li>
+ * residue value and any sequence features at each position of the
+ * alignment</li>
  * <li>a 'general purpose' calculator which computes one or more complete
  * AlignmentAnnotation objects</li>
  * </ul>
@@ -50,11 +52,12 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(FeatureSetCounterI counter)
   {
-    AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
+    AlignmentViewPanel currentAlignFrame = Jalview.getInstance()
+            .getCurrentAlignFrame().alignPanel;
     if (currentAlignFrame == null)
     {
-      System.err
-              .println("Can't register calculator as no alignment window has focus");
+      jalview.bin.Console.errPrintln(
+              "Can't register calculator as no alignment window has focus");
       return;
     }
     new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
@@ -71,7 +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(),
@@ -79,8 +83,8 @@ public class AlignmentAnnotationFactory
     }
     else
     {
-      System.err
-              .println("Can't register calculator as no alignment window has focus");
+      jalview.bin.Console.errPrintln(
+              "Can't register calculator as no alignment window has focus");
     }
   }
 
@@ -111,7 +115,8 @@ public class AlignmentAnnotationFactory
   public static Annotation newAnnotation(String displayChar, String desc,
           char secondaryStructure, float val, Color color)
   {
-    return new Annotation(displayChar, desc, secondaryStructure, val, color);
+    return new Annotation(displayChar, desc, secondaryStructure, val,
+            color);
   }
 
   /**