@jbrowse/plugin-linear-genome-view/esm/LaunchLinearGenomeView/index.js

JBrowse 2 linear genome view

import { parseLocString, when } from '@jbrowse/core/util';
import { handleSelectedRegion } from '../searchUtils';
export default function LaunchLinearGenomeViewF(pluginManager) {
    pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', async ({ session, assembly, loc, tracks = [], tracklist, nav, highlight, }) => {
        try {
            const { assemblyManager } = session;
            const view = session.addView('LinearGenomeView', {});
            await when(() => !!view.volatileWidth);
            if (!assembly) {
                throw new Error('No assembly provided when launching linear genome view');
            }
            const asm = await assemblyManager.waitForAssembly(assembly);
            if (!asm) {
                throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
            }
            if (tracklist) {
                view.activateTrackSelector();
            }
            if (nav !== undefined) {
                view.setHideHeader(!nav);
            }
            if (highlight !== undefined) {
                for (const h of highlight) {
                    const p = parseLocString(h, refName => assemblyManager.isValidRefName(refName, assembly));
                    const { start, end } = p;
                    if (start !== undefined && end !== undefined) {
                        view.addToHighlights({
                            ...p,
                            start,
                            end,
                            assemblyName: assembly,
                        });
                    }
                }
            }
            await handleSelectedRegion({
                input: loc,
                model: view,
                assembly: asm,
            });
            const idsNotFound = [];
            for (const track of tracks) {
                tryTrack(view, track, idsNotFound);
            }
            if (idsNotFound.length) {
                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
            }
        }
        catch (e) {
            session.notifyError(`${e}`, e);
            throw e;
        }
    });
}
function tryTrack(model, trackId, idsNotFound) {
    try {
        model.showTrack(trackId);
    }
    catch (e) {
        if (/Could not resolve identifier/.exec(`${e}`)) {
            idsNotFound.push(trackId);
        }
        else {
            throw e;
        }
    }
}