Extending Jalview with Groovy - A customisable feature counter
The groovy script below shows how to add a new calculation track to a Jalview alignment window.

As currently written, it will add two tracks to a protein alignment view which count Pfam features in each column, and ones where a charge residue also occur.

To try it for yourself:

1. Copy and paste it into the groovy script console
2. Load the example Feredoxin project (the one that opens by default when you first launched Jalview)
3. Select Calculations→Execute Groovy Script from the alignment window's menu bar to run the script on the current view.

Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.
https://www.jalview.org/examples/groovy/featuresCounter.groovy - rendered with hilite.me

    /*
     * Jalview - A Sequence Alignment Editor and Viewer (2.11.1.3)
     * Copyright (C) 2020 The Jalview Authors
     *
     * This file is part of Jalview.
     *
     * Jalview is free software: you can redistribute it and/or
     * modify it under the terms of the GNU General Public License
     * as published by the Free Software Foundation, either version 3
     * of the License, or (at your option) any later version.
     *
     * Jalview is distributed in the hope that it will be useful, but
     * WITHOUT ANY WARRANTY; without even the implied warranty
     * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     * PURPOSE.  See the GNU General Public License for more details.
     *
     * You should have received a copy of the GNU General Public License
     * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
     * The Jalview Authors are detailed in the 'AUTHORS' file.
     */

    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.
     *
     * Note: The feature api provided by 2.10.2 is not compatible with scripts
     * that worked with earlier Jalview versions. Apologies for the inconvenience.
     */

    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)