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 8a86ce0..2507bb5 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;
@@ -8,15 +28,16 @@ import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
 
 import java.awt.Color;
-import java.lang.reflect.Method;
 
 /**
  * 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>
@@ -29,83 +50,18 @@ public class AlignmentAnnotationFactory
    * @param counter
    *          provider of feature counts per alignment position
    */
-  public static void newCalculator(ColumnCounterI counter)
+  public static void newCalculator(FeatureSetCounterI counter)
   {
-    // TODO need an interface for AlignFrame by which to access
-    // its AlignViewportI and AlignmentViewPanel
-    AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
-    if (currentAlignFrame != null)
-    {
-      Method newCalcMethod = null;
-      try
-      {
-        for (Method m : AlignmentAnnotationFactory.class.getMethods())
-        {
-          if (m.getName().equals("newCalculator"))
-          {
-            if (m.getParameterCount() == 3
-                    && m.getParameterTypes()[2].isInstance(counter))
-            {
-              newCalcMethod = m;
-              break;
-            }
-          }
-        }
-      } catch (Exception q)
-      {
-      }
-      if (newCalcMethod == null)
-      {
-
-        System.err
-                .println("Couldn't find a newCalculator method for ColumnCounterI type "
-                        + counter.getClass().getName());
-      }
-      try
-      {
-        newCalcMethod.invoke(null, currentAlignFrame.getAlignViewport(),
-                currentAlignFrame, counter);
-      } catch (Exception ie)
-      {
-        System.err
-                .println("Exception when reporting newCalculator method for ColumnCounterI type "
-                        + counter.getClass().getName());
-      }
-    }
-    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 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);
-  }
-
-  /**
-   * Constructs and registers a new alignment annotation worker for a set of
-   * column counters
-   * 
-   * @param viewport
-   * @param panel
-   * @param counter
-   *          provider of feature counts per alignment position
-   */
-  public static void newCalculator(AlignViewportI viewport,
-          AlignmentViewPanel panel, FeatureSetCounterI counter)
-  {
-    new ColumnCounterSetWorker(viewport, panel, counter);
+    new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
+            currentAlignFrame, counter);
   }
 
   /**
@@ -121,13 +77,13 @@ public class AlignmentAnnotationFactory
     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
     {
-      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");
     }
   }
 
@@ -158,7 +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);
   }
 
   /**