Launch a linear genome view

Open a linear genome view imperatively via the LaunchView extension point.

Most view types are declared up front in defaultSession.views. For views that should appear in response to runtime conditions instead (a button click, a search hit, a backend event), use the LaunchView-* extension points. This example boots an empty session and then launches a LinearGenomeView after mount:

import { getEnv } from '@jbrowse/core/util'

const { pluginManager } = getEnv(state)

await pluginManager.evaluateAsyncExtensionPoint('LaunchView-LinearGenomeView', {
  session: state.session,
  assembly: 'hg38',
  loc: 'chr10:1-100000',
  tracks: ['my_track'],
})
// also: LaunchView-LinearSyntenyView, LaunchView-DotplotView

This is the same machinery the import wizard uses internally, so anything the user can launch from the UI you can launch from code. State actions like showTrack/hideTrack and navToLocString are documented per view under docs/models.

View source

import { useEffect, useState } from 'react'

import { ErrorMessage } from '@jbrowse/core/ui'
import { getEnv } from '@jbrowse/core/util'
import { JBrowseApp, createViewState } from '@jbrowse/react-app2'

export default function WithLaunchLinearGenomeView() {
  const [viewState, setViewState] =
    useState<ReturnType<typeof createViewState>>()
  const [error, setError] = useState<unknown>()

  useEffect(() => {
    // eslint-disable-next-line @typescript-eslint/no-floating-promises
    ;(async () => {
      try {
        const state = createViewState({
          config: {
            assemblies: [
              {
                name: 'GRCh38',
                aliases: ['hg38'],
                sequence: {
                  type: 'ReferenceSequenceTrack',
                  trackId: 'GRCh38-ReferenceSequenceTrack',
                  adapter: {
                    type: 'BgzipFastaAdapter',
                    uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
                  },
                },
                refNameAliases: {
                  adapter: {
                    type: 'RefNameAliasAdapter',
                    uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt',
                  },
                },
              },
            ],
            tracks: [
              {
                type: 'QuantitativeTrack',
                trackId: 'hg38.100way.phyloP100way',
                name: 'hg38.100way.phyloP100way',
                category: ['Conservation'],
                assemblyNames: ['hg38'],
                adapter: {
                  type: 'BigWigAdapter',
                  uri: 'https://hgdownload.soe.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw',
                },
              },
            ],
          },
        })
        const { pluginManager } = getEnv(state)

        setViewState(state)
        await pluginManager.evaluateAsyncExtensionPoint(
          'LaunchView-LinearGenomeView',
          {
            tracks: ['hg38.100way.phyloP100way'],
            loc: 'chr10:1-100000',
            assembly: 'hg38',
            session: state.session,
          },
        )
      } catch (e) {
        console.error(e)
        setError(e)
      }
    })()
  }, [])

  return viewState ? (
    <>
      {error ? <ErrorMessage error={error} /> : null}
      <JBrowseApp viewState={viewState} />
    </>
  ) : null
}