examples/groovy/featuresCounter.groovy

   1 import jalview.workers.AlignmentAnnotationFactory;
   2 import jalview.workers.FeatureSetCounterI;
   3
   4 /*
   5  * Example script to compute two alignment annotations
   6  * - count of Phosphorylation features
   7  * - count of Turn features
   8  * To try this, first load example file uniref50.fa and load on features file
   9  * exampleFeatures.txt, before running this script
  10  *
  11  * The script only needs to be run once - it will be registered by Jalview
  12  * and recalculated automatically when the alignment changes.
  13  */
  14 def annotator =
  15     [
  16      getNames: { ['Phosphorylation', 'Turn'] as String[] },
  17      getDescriptions:  { ['Count of Phosphorylation features', 'Count of Turn features'] as String[] },
  18      getMinColour: { [0, 255, 255] as int[] }, // cyan
  19      getMaxColour: { [0, 0, 255] as int[] }, // blue
  20      count:
  21          { res, feats ->
  22                 int phos
  23                 int turn
  24                 for (sf in feats)
  25                 {
  26                           /*
  27                            * Here we inspect the type of the sequence feature.
  28                            * You can also test sf.description, sf.score, sf.featureGroup,
  29                            * sf.strand, sf.phase, sf.begin, sf.end
  30                            * or sf.getValue(attributeName) for GFF 'column 9' properties
  31                            */
  32                            if (sf.type.contains('TURN'))
  33                    {
  34                       turn++
  35                    }
  36                    if (sf.type.contains('PHOSPHORYLATION'))
  37                    {
  38                       phos++
  39                    }
  40                 }
  41                 [phos, turn] as int[]
  42          }
  43      ] as FeatureSetCounterI
  44
  45 /*
  46  * Register the annotation calculator with Jalview
  47  */
  48 AlignmentAnnotationFactory.newCalculator(annotator)