X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=8b5240ca5fbf56edf9693a086cafedccb92b858a;hb=5e17ddc59003daff5f9933cf5710889bcdb9e856;hp=68c229581db3af2b68751e240b5347026a3c6c76;hpb=e811386cfe6d7ab7d73db56a31ac83732e185861;p=jalview.git

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 68c2295..8b5240c 100644
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,20 +1,43 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
+import java.awt.Color;
+
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Jalview;
 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>
@@ -29,11 +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(),
@@ -48,7 +72,10 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(AnnotationProviderI calculator)
   {
-    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
+    // TODO need an interface for AlignFrame by which to access
+    // its AlignViewportI and AlignmentViewPanel
+    AlignFrame currentAlignFrame = Jalview.getInstance()
+            .getCurrentAlignFrame();
     if (currentAlignFrame != null)
     {
       new AnnotationWorker(currentAlignFrame.getViewport(),
@@ -56,12 +83,26 @@ 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");
     }
   }
 
   /**
+   * Constructs and registers a new alignment annotation worker
+   * 
+   * @param viewport
+   * @param panel
+   * @param calculator
+   *          provider of AlignmentAnnotation for the alignment
+   */
+  public static void newCalculator(AlignViewportI viewport,
+          AlignmentViewPanel panel, AnnotationProviderI calculator)
+  {
+    new AnnotationWorker(viewport, panel, calculator);
+  }
+
+  /**
    * Factory method to construct an Annotation object
    * 
    * @param displayChar
@@ -74,7 +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);
   }
 
   /**