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

JBrowse 2 config utilities

import { ObservableCreate } from '@jbrowse/core/util/rxjs';
import SimpleFeature from '@jbrowse/core/util/simpleFeature';
import { firstValueFrom } from 'rxjs';
import { toArray } from 'rxjs/operators';
import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter';
export default class FromConfigSequenceAdapter extends FromConfigAdapter {
    getFeatures(region) {
        return ObservableCreate(async (observer) => {
            const feats = await firstValueFrom(super.getFeatures(region).pipe(toArray()));
            const feat = feats[0];
            observer.next(new SimpleFeature({
                ...feat.toJSON(),
                uniqueId: `${feat.id()}:${region.start}-${region.end}`,
                end: region.end,
                start: region.start,
                seq: feat
                    .get('seq')
                    .slice(Math.max(region.start - feat.get('start'), 0), Math.max(region.end - feat.get('start'), 0)),
            }));
            observer.complete();
        });
    }
    async getRegions() {
        const regions = [];
        for (const [refName, features] of this.features) {
            let currentRegion;
            for (const feature of features) {
                if (currentRegion &&
                    currentRegion.end >= feature.get('start') &&
                    currentRegion.start <= feature.get('end')) {
                    currentRegion.end = feature.get('end');
                }
                else {
                    if (currentRegion) {
                        regions.push(currentRegion);
                    }
                    currentRegion = {
                        refName,
                        start: feature.get('start'),
                        end: feature.get('end'),
                    };
                }
            }
            if (currentRegion) {
                regions.push(currentRegion);
            }
        }
        return regions;
    }
}