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:
/* * Jalview - A Sequence Alignment Editor and Viewer (2.11.3.3) * Copyright (C) 2024 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)