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)