JAL-2228 removed FeatureCounterI in favour of FeatureSetCounterI with

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

diff --git a/examples/groovy/featuresCounter.groovy b/examples/groovy/featuresCounter.groovy
new file mode 100644 (file)
index 0000000..ccbb830
--- /dev/null
+++ b/examples/groovy/featuresCounter.groovy
@@ -0,0 +1,48 @@
+import jalview.workers.AlignmentAnnotationFactory;
+import jalview.workers.FeatureSetCounterI;
+
+/*
+ * 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.
+ */
+def annotator = 
+    [
+     getNames: { ['Phosphorylation', 'Turn'] as String[] }, 
+     getDescriptions:  { ['Count of Phosphorylation features', 'Count of Turn features'] as String[] },
+     getMinColour: { [0, 255, 255] as int[] }, // cyan
+     getMaxColour: { [0, 0, 255] as int[] }, // blue
+     count: 
+         { res, feats -> 
+                int phos
+                int turn
+                for (sf in feats)
+                {
+                         /*
+                          * Here we inspect the type of the sequence feature.
+                          * You can also test sf.description, sf.score, sf.featureGroup,
+                          * sf.strand, sf.phase, sf.begin, sf.end
+                          * or sf.getValue(attributeName) for GFF 'column 9' properties
+                          */
+                          if (sf.type.contains('TURN'))
+                   {
+                      turn++
+                   }
+                   if (sf.type.contains('PHOSPHORYLATION'))
+                   {
+                      phos++
+                   }
+                }
+                [phos, turn] as int[]
+         }
+     ] as FeatureSetCounterI
+    
+/*
+ * Register the annotation calculator with Jalview
+ */
+AlignmentAnnotationFactory.newCalculator(annotator)