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

JBrowse 2 config utilities

import { readConfObject } from '@jbrowse/core/configuration';
import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
import { makeFeatures } from '../FromConfigAdapter/FromConfigAdapter';
export default class FromConfigRegionsAdapter extends BaseAdapter {
    constructor(config, getSubAdapter, pluginManager) {
        super(config, getSubAdapter, pluginManager);
        const f = readConfObject(config, 'features');
        this.features = makeFeatures(f);
    }
    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);
            }
        }
        regions.sort((a, b) => a.refName.localeCompare(b.refName));
        return regions;
    }
}