develop merge

[jalview.git] / examples / groovy / multipleFeatureAnnotations.groovy

diff --git a/examples/groovy/multipleFeatureAnnotations.groovy b/examples/groovy/multipleFeatureAnnotations.groovy
new file mode 100644 (file)
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+++ b/examples/groovy/multipleFeatureAnnotations.groovy
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+import jalview.workers.AlignmentAnnotationFactory;
+import jalview.workers.AnnotationProviderI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
+import java.awt.Color;
+
+/*
+ * Example script to compute two alignment annotations
+ * - count of Phosphorylation features
+ * - count of Turn features
+ * To try this, first load example file uniref50.fa and load on features file
+ * exampleFeatures.txt, before running this script
+ *
+ * The script only needs to be run once - it will be registered by Jalview
+ * and recalculated automatically when the alignment changes.
+ */
+
+/*
+ * A closure that returns true if value includes "PHOSPHORYLATION"
+ */
+def phosCounter = { type ->    type.contains("PHOSPHORYLATION") }
+
+/*
+ * A closure that returns true if value includes "TURN"
+ */
+def turnCounter = { type ->    type.contains("TURN") }
+
+/*
+ * A closure that computes and returns an array of Annotation values,
+ * one for each column of the alignment
+ */
+def getAnnotations(al, fr, counter) 
+{
+    def width = al.width
+    def counts = new int[width] 
+    def max = 0
+    
+    /*
+     * count features in each column, record the maximum value
+     */
+    for (col = 0 ; col < width ; col++)
+    {
+        def count = 0
+        for (row = 0 ; row < al.height ; row++)
+        {
+            seq = al.getSequenceAt(row)
+            if (seq != null && col < seq.getLength())
+            {
+                def res = seq.getCharAt(col)
+                if (!Comparison.isGap(res))
+                {
+                    pos = seq.findPosition(col)
+                    features = fr.findFeaturesAtRes(seq, pos)
+                    for (feature in features)
+                    {
+                        if (counter.call(feature.type))
+                        {
+                            count++
+                        }
+                    }
+                }
+            }
+        }
+        counts[col] = count
+        if (count > max)
+        {
+            max = count
+        }
+    }
+    
+    /*
+     * make the Annotation objects, with a graduated colour scale 
+     * (from min value to max value) for the histogram bars 
+     */
+    def zero = '0' as char
+    def anns = new Annotation[width] 
+    for (col = 0 ; col < width ; col++)
+    {
+        def c = counts[col]
+        if (c > 0)
+        {
+            Color color = ColorUtils.getGraduatedColour(c, 0, Color.cyan,
+                max, Color.blue)
+            anns[col] = AlignmentAnnotationFactory.newAnnotation(String.valueOf(c),
+                String.valueOf(c), zero, c, color)
+        }
+    }
+    anns
+}
+
+/*
+ * Define the method that performs the calculations, and builds two
+ * AlignmentAnnotation objects
+ */
+def annotator = 
+    [ calculateAnnotation: { al, fr ->
+        def phosAnns = getAnnotations(al, fr, phosCounter)
+        def ann1 = AlignmentAnnotationFactory.newAlignmentAnnotation("Phosphorylation", "Count of Phosphorylation features", phosAnns)
+        def turnAnns = getAnnotations(al, fr, turnCounter)
+        def ann2 = AlignmentAnnotationFactory.newAlignmentAnnotation("Turn", "Count of Turn features", turnAnns)
+        return [ann1, ann2]
+      } 
+    ] as AnnotationProviderI
+    
+/*
+ * Register the annotation calculator with Jalview
+ */
+AlignmentAnnotationFactory.newCalculator(annotator)