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

JBrowse 2 linear genome view

import { getConf } from '@jbrowse/core/configuration';
import { getSession } from '@jbrowse/core/util';
export async function fetchSequence(model, regions) {
    const session = getSession(model);
    const { leftOffset, rightOffset } = model;
    if (!leftOffset || !rightOffset) {
        throw new Error('no offsets on model to use for range');
    }
    const assemblyNames = new Set(regions.map(r => r.assemblyName));
    if (assemblyNames.size > 1) {
        throw new Error('not able to fetch sequences from multiple assemblies currently');
    }
    const { rpcManager, assemblyManager } = session;
    const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';
    const assembly = assemblyManager.get(assemblyName);
    if (!assembly) {
        throw new Error(`assembly ${assemblyName} not found`);
    }
    const adapterConfig = getConf(assembly, ['sequence', 'adapter']);
    const sessionId = 'getSequence';
    return rpcManager.call(sessionId, 'CoreGetFeatures', {
        adapterConfig,
        regions,
        sessionId,
    });
}