@jbrowse/core/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js

JBrowse 2 core libraries used by plugins

import { firstValueFrom, merge } from 'rxjs';
import { toArray } from 'rxjs/operators';
import { BaseAdapter } from "./BaseAdapter.js";
import { aggregateQuantitativeStats, calculateFeatureDensityStats, } from "./stats.js";
import { ObservableCreate } from "../../util/rxjs.js";
import { blankStats, scoresToStats } from "../../util/stats.js";
export class BaseFeatureDataAdapter extends BaseAdapter {
    async getHeader(_opts) {
        return null;
    }
    async getMetadata(_opts) {
        return null;
    }
    getFeaturesInRegion(region, opts = {}) {
        return ObservableCreate(async (observer) => {
            const hasData = await this.hasDataForRefName(region.refName, opts);
            if (!hasData) {
                observer.complete();
            }
            else {
                this.getFeatures(region, opts).subscribe(observer);
            }
        });
    }
    getFeaturesInMultipleRegions(regions, opts = {}) {
        return merge(...regions.map(region => this.getFeaturesInRegion(region, opts)));
    }
    async hasDataForRefName(refName, opts = {}) {
        const refNames = await this.getRefNames(opts);
        return refNames.includes(refName);
    }
    async getRegionQuantitativeStats(region, opts) {
        const feats = this.getFeatures(region, {
            ...opts,
            statsEstimationMode: true,
        });
        return scoresToStats(region, feats);
    }
    async getMultiRegionQuantitativeStats(regions = [], opts) {
        if (!regions.length) {
            return blankStats();
        }
        const stats = await Promise.all(regions.map(region => this.getRegionQuantitativeStats(region, opts)));
        return aggregateQuantitativeStats(stats);
    }
    getRegionFeatureDensityStats(region, opts) {
        return calculateFeatureDensityStats(region, (region2, opts2) => this.getFeatures(region2, opts2), opts);
    }
    async getMultiRegionFeatureDensityStats(regions, opts) {
        if (!regions.length) {
            throw new Error('No regions supplied');
        }
        return this.getRegionFeatureDensityStats(regions[0], opts);
    }
    async getSources(regions) {
        const features = await firstValueFrom(this.getFeaturesInMultipleRegions(regions).pipe(toArray()));
        const sources = new Set();
        for (const f of features) {
            sources.add(f.get('source'));
        }
        return [...sources].map(source => ({
            name: source,
        }));
    }
    async getExportData(_regions, _formatType, _opts) {
        return undefined;
    }
}