@jbrowse/plugin-config/esm/FromConfigAdapter/FromConfigAdapter.js

JBrowse 2 config utilities

import { readConfObject } from '@jbrowse/core/configuration';
import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
import SimpleFeature from '@jbrowse/core/util/simpleFeature';
export function makeFeatures(fdata) {
    const features = new Map();
    for (const entry of fdata) {
        const f = new SimpleFeature(entry);
        const refName = f.get('refName');
        let bucket = features.get(refName);
        if (!bucket) {
            bucket = [];
            features.set(refName, bucket);
        }
        bucket.push(f);
    }
    for (const refFeatures of features.values()) {
        refFeatures.sort((a, b) => a.get('start') - b.get('start'));
    }
    return features;
}
export default class FromConfigAdapter extends BaseFeatureDataAdapter {
    constructor(conf, getSubAdapter, pluginManager) {
        super(conf, getSubAdapter, pluginManager);
        const feats = readConfObject(conf, 'features');
        this.features = makeFeatures(feats);
    }
    async getRefNames() {
        return [...this.features.keys()];
    }
    async getRefNameAliases() {
        return [...this.features.values()].map(featureArray => ({
            refName: featureArray[0].get('refName'),
            aliases: featureArray[0].get('aliases'),
        }));
    }
    getFeatures(region) {
        const { refName, start, end } = region;
        return ObservableCreate(async (observer) => {
            const features = this.features.get(refName) || [];
            for (const f of features) {
                if (f.get('end') > start && f.get('start') < end) {
                    observer.next(f);
                }
            }
            observer.complete();
        });
    }
}