JAL-2446 merged to spike branch

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

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index f804a19..b0392d4 100644 (file)
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -28,35 +48,17 @@ public class AlignmentAnnotationFactory
    * @param counter
    *          provider of feature counts per alignment position
    */
-  public static void newCalculator(FeatureCounterI counter)
+  public static void newCalculator(FeatureSetCounterI counter)
   {
-    // TODO need an interface for AlignFrame by which to access
-    // its AlignViewportI and AlignmentViewPanel
-    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame() ;
-    if (currentAlignFrame != null)
-    {
-      newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
-              .getAlignPanels().get(0), counter);
-    }
-    else
+    AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
+    if (currentAlignFrame == null)
     {
       System.err
               .println("Can't register calculator as no alignment window has focus");
+      return;
     }
-  }
-
-  /**
-   * Constructs and registers a new alignment annotation worker
-   * 
-   * @param viewport
-   * @param panel
-   * @param counter
-   *          provider of feature counts per alignment position
-   */
-  public static void newCalculator(AlignViewportI viewport,
-          AlignmentViewPanel panel, FeatureCounterI counter)
-  {
-    new ColumnCounterWorker(viewport, panel, counter);
+    new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
+            currentAlignFrame, counter);
   }
 
   /**
@@ -69,11 +71,11 @@ public class AlignmentAnnotationFactory
   {
     // TODO need an interface for AlignFrame by which to access
     // its AlignViewportI and AlignmentViewPanel
-    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame() ;
+    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
     if (currentAlignFrame != null)
     {
-      newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
-              .getAlignPanels().get(0), calculator);
+      new AnnotationWorker(currentAlignFrame.getViewport(),
+              currentAlignFrame.getAlignPanels().get(0), calculator);
     }
     else
     {
@@ -91,8 +93,7 @@ public class AlignmentAnnotationFactory
    *          provider of AlignmentAnnotation for the alignment
    */
   public static void newCalculator(AlignViewportI viewport,
-          AlignmentViewPanel panel,
-          AnnotationProviderI calculator)
+          AlignmentViewPanel panel, AnnotationProviderI calculator)
   {
     new AnnotationWorker(viewport, panel, calculator);
   }