Merge branch 'develop' into features/JAL-2228_efficient_featurecounts

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

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 68c2295..b0392d4 100644 (file)
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,5 +1,26 @@
+/*
+ * 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 jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
@@ -48,6 +69,8 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(AnnotationProviderI calculator)
   {
+    // TODO need an interface for AlignFrame by which to access
+    // its AlignViewportI and AlignmentViewPanel
     AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
     if (currentAlignFrame != null)
     {
@@ -62,6 +85,20 @@ public class AlignmentAnnotationFactory
   }
 
   /**
+   * 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