develop merge

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

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
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+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
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+package jalview.workers;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+
+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>
+ * 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
+ * AlignmentAnnotation objects</li>
+ * </ul>
+ */
+public class AlignmentAnnotationFactory
+{
+  /**
+   * Constructs and registers a new alignment annotation worker
+   * 
+   * @param counter
+   *          provider of feature counts per alignment position
+   */
+  public static void newCalculator(FeatureCounterI counter)
+  {
+    if (Desktop.getCurrentAlignFrame() != null)
+    {
+      newCalculator(Desktop.getCurrentAlignFrame(), counter);
+    }
+    else
+    {
+      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 counter
+   *          provider of feature counts per alignment position
+   */
+  public static void newCalculator(AlignFrame af, FeatureCounterI counter)
+  {
+    new ColumnCounterWorker(af, counter);
+  }
+
+  /**
+   * Constructs and registers a new alignment annotation worker
+   * 
+   * @param calculator
+   *          provider of AlignmentAnnotation for the alignment
+   */
+  public static void newCalculator(AnnotationProviderI calculator)
+  {
+    if (Desktop.getCurrentAlignFrame() != null)
+    {
+      newCalculator(Desktop.getCurrentAlignFrame(), calculator);
+    }
+    else
+    {
+      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 calculator
+   *          provider of AlignmentAnnotation for the alignment
+   */
+  public static void newCalculator(AlignFrame af,
+          AnnotationProviderI calculator)
+  {
+    new AnnotationWorker(af, calculator);
+  }
+
+  /**
+   * Factory method to construct an Annotation object
+   * 
+   * @param displayChar
+   * @param desc
+   * @param secondaryStructure
+   * @param val
+   * @param color
+   * @return
+   */
+  public static Annotation newAnnotation(String displayChar, String desc,
+          char secondaryStructure, float val, Color color)
+  {
+    return new Annotation(displayChar, desc, secondaryStructure, val, color);
+  }
+
+  /**
+   * Factory method to construct an AlignmentAnnotation object
+   * 
+   * @param name
+   * @param desc
+   * @param anns
+   * @return
+   */
+  public static AlignmentAnnotation newAlignmentAnnotation(String name,
+          String desc, Annotation[] anns)
+  {
+    return new AlignmentAnnotation(name, desc, anns);
+  }
+}