JAL-2738 copy to spikes/mungo

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

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 520b232..2507bb5 100644 (file)
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,5 +1,27 @@
+/*
+ * 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;
 import jalview.datamodel.Annotation;
@@ -9,12 +31,14 @@ 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 'feature counter' which can count any desired property derivable from
- * residue value and any sequence features at each position of the alignment</li>
- * <li>a 'general purpose' calculator which computes one more complete
+ * <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>
+ * <li>a 'general purpose' calculator which computes one or more complete
  * AlignmentAnnotation objects</li>
  * </ul>
  */
@@ -26,30 +50,18 @@ public class AlignmentAnnotationFactory
    * @param counter
    *          provider of feature counts per alignment position
    */
-  public static void newCalculator(FeatureCounterI counter)
+  public static void newCalculator(FeatureSetCounterI counter)
   {
-    if (Jalview.getCurrentAlignFrame() != null)
-    {
-      newCalculator(Jalview.getCurrentAlignFrame(), counter);
-    }
-    else
+    AlignmentViewPanel currentAlignFrame = Jalview
+            .getCurrentAlignFrame().alignPanel;
+    if (currentAlignFrame == null)
     {
-      System.err
-              .println("Can't register calculator as no alignment window has focus");
+      System.err.println(
+              "Can't register calculator as no alignment window has focus");
+      return;
     }
-  }
-
-  /**
-   * Constructs and registers a new alignment annotation worker
-   * 
-   * @param af
-   *          the AlignFrame for which the annotation is to be calculated
-   * @param counter
-   *          provider of feature counts per alignment position
-   */
-  public static void newCalculator(AlignFrame af, FeatureCounterI counter)
-  {
-    new ColumnCounterWorker(af, counter);
+    new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
+            currentAlignFrame, counter);
   }
 
   /**
@@ -60,29 +72,33 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(AnnotationProviderI calculator)
   {
-    if (Jalview.getCurrentAlignFrame() != null)
+    // TODO need an interface for AlignFrame by which to access
+    // its AlignViewportI and AlignmentViewPanel
+    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
+    if (currentAlignFrame != null)
     {
-      newCalculator(Jalview.getCurrentAlignFrame(), calculator);
+      new AnnotationWorker(currentAlignFrame.getViewport(),
+              currentAlignFrame.getAlignPanels().get(0), calculator);
     }
     else
     {
-      System.err
-              .println("Can't register calculator as no alignment window has focus");
+      System.err.println(
+              "Can't register calculator as no alignment window has focus");
     }
   }
 
   /**
    * Constructs and registers a new alignment annotation worker
    * 
-   * @param af
-   *          the AlignFrame for which the annotation is to be calculated
+   * @param viewport
+   * @param panel
    * @param calculator
    *          provider of AlignmentAnnotation for the alignment
    */
-  public static void newCalculator(AlignFrame af,
-          AnnotationProviderI calculator)
+  public static void newCalculator(AlignViewportI viewport,
+          AlignmentViewPanel panel, AnnotationProviderI calculator)
   {
-    new AnnotationWorker(af, calculator);
+    new AnnotationWorker(viewport, panel, calculator);
   }
 
   /**
@@ -98,7 +114,8 @@ 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);
   }
 
   /**