@jbrowse/plugin-linear-genome-view/esm/LinearGenomeView/afterAttach.js

JBrowse 2 linear genome view

import { getSession, localStorageSetItem, parseLocString, } from '@jbrowse/core/util';
import { addDisposer } from '@jbrowse/mobx-state-tree';
import { autorun, when } from 'mobx';
function tryParseJson(s) {
    try {
        const v = JSON.parse(s);
        return v && typeof v === 'object'
            ? v
            : undefined;
    }
    catch {
        return undefined;
    }
}
export function setupInitAutorun(self) {
    addDisposer(self, autorun(async function initAutorun() {
        const { init, initialized } = self;
        if (!initialized) {
            return;
        }
        if (init) {
            const session = getSession(self);
            const { assemblyManager } = session;
            if (init.tracklist) {
                self.activateTrackSelector();
                const currentWidth = self.volatileWidth;
                await when(() => self.volatileWidth !== currentWidth, {
                    timeout: 500,
                }).catch(() => {
                });
            }
            try {
                if (init.loc) {
                    const asm = await assemblyManager.waitForAssembly(init.assembly);
                    if (!asm) {
                        throw new Error('Assembly not found');
                    }
                    await self.navToSearchString({
                        input: init.loc,
                        assembly: asm,
                    });
                }
                else {
                    self.showAllRegionsInAssembly(init.assembly);
                }
            }
            catch (e) {
                console.error(init, e);
                session.notifyError(`${e}`, e);
            }
            if (init.tracks) {
                const idsNotFound = [];
                for (const t of init.tracks) {
                    try {
                        if (typeof t === 'string') {
                            self.showTrack(t);
                        }
                        else {
                            self.showTrack(t.trackId, t.trackSnapshot ?? {}, t.displaySnapshot ?? {});
                        }
                    }
                    catch (e) {
                        const trackId = typeof t === 'string' ? t : t.trackId;
                        if (/Could not resolve identifier/.exec(`${e}`)) {
                            idsNotFound.push(trackId);
                        }
                        else {
                            throw e;
                        }
                    }
                }
                if (idsNotFound.length) {
                    session.notifyError(`Could not resolve identifiers: ${idsNotFound.join(',')}`, new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`));
                }
            }
            if (init.nav !== undefined) {
                self.setHideHeader(!init.nav);
            }
            if (self.highlight.length) {
                const fallback = self.assemblyNames[0];
                if (fallback) {
                    const normalized = self.highlight.map(h => h.assemblyName ? h : { ...h, assemblyName: fallback });
                    if (normalized.some((h, i) => h !== self.highlight[i])) {
                        self.setHighlight(normalized);
                    }
                }
            }
            if (init.highlight) {
                for (const h of init.highlight) {
                    const json = h.trim().startsWith('{') && tryParseJson(h);
                    if (json &&
                        typeof json.refName === 'string' &&
                        typeof json.start === 'number' &&
                        typeof json.end === 'number') {
                        self.addToHighlights({
                            refName: json.refName,
                            start: json.start,
                            end: json.end,
                            assemblyName: typeof json.assemblyName === 'string'
                                ? json.assemblyName
                                : init.assembly,
                            color: typeof json.color === 'string' ? json.color : undefined,
                            label: typeof json.label === 'string' ? json.label : undefined,
                        });
                    }
                    else {
                        const p = parseLocString(h, refName => assemblyManager.isValidRefName(refName, init.assembly));
                        const { start, end } = p;
                        if (start !== undefined && end !== undefined) {
                            self.addToHighlights({
                                ...p,
                                start,
                                end,
                                assemblyName: init.assembly,
                            });
                        }
                    }
                }
            }
            self.setInit(undefined);
        }
    }, { name: 'LGVInit' }));
}
export function setupCoarseDynamicBlocksAutorun(self) {
    addDisposer(self, autorun(function coarseDynamicBlocksAutorun() {
        if (self.initialized) {
            self.setCoarseDynamicBlocks(self.dynamicBlocks);
        }
    }, { delay: 500, name: 'LGVCoarseDynamicBlocks' }));
}
export function setupLocalStorageAutorun(self) {
    addDisposer(self, autorun(function localStorageAutorun() {
        const s = (s) => JSON.stringify(s);
        const { showCytobandsSetting, showCenterLine, colorByCDS, showTrackOutlines, trackLabels, } = self;
        localStorageSetItem('lgv-showCytobands', s(showCytobandsSetting));
        localStorageSetItem('lgv-showCenterLine', s(showCenterLine));
        localStorageSetItem('lgv-colorByCDS', s(colorByCDS));
        localStorageSetItem('lgv-showTrackOutlines', s(showTrackOutlines));
        localStorageSetItem('lgv-trackLabels', trackLabels);
    }, { name: 'LGVLocalStorage' }));
}
export function doAfterAttach(self) {
    setupInitAutorun(self);
    setupCoarseDynamicBlocksAutorun(self);
    setupLocalStorageAutorun(self);
}