Init & persistence

import { LinearGenomeView } from '@jbrowse/react-linear-genome-view2'

export default function WithInitAdvanced() {
  return (
    <LinearGenomeView
      assembly={{
        name: 'hg38',
        uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
        refNameAliases: {
          uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt',
        },
        geneticCodes: { chrM: 2 },
      }}
      tracks={[
        {
          type: 'FeatureTrack',
          trackId: 'ncbi-refseq-genes',
          name: 'NCBI RefSeq Genes',
          assemblyNames: ['hg38'],
          adapter: {
            type: 'Gff3TabixAdapter',
            uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz',
          },
        },
      ]}
      init={{
        loc: 'chr1:11,106,077-11,261,675',
        tracklist: true,
        nav: true,
        tracks: [
          { trackId: 'ncbi-refseq-genes', displaySnapshot: { height: 200 } },
        ],
        highlight: ['chr1:11,170,000-11,190,000'],
      }}
    />
  )
}

import {
  JBrowseLinearGenomeView,
  useCreateViewState,
} from '@jbrowse/react-linear-genome-view2'

export default function WithSessionHighlights() {
  const state = useCreateViewState({
    assembly: {
      name: 'hg38',
      aliases: ['GRCh38'],
      uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
      refNameAliases: {
        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt',
      },
      geneticCodes: { chrM: 2 },
    },
    tracks: [
      {
        type: 'FeatureTrack',
        trackId: 'ncbi-refseq-genes',
        name: 'NCBI RefSeq Genes',
        assemblyNames: ['hg38'],
        adapter: {
          type: 'Gff3TabixAdapter',
          uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz',
        },
      },
    ],
    defaultSession: {
      name: 'Session highlights',
      view: {
        type: 'LinearGenomeView',
        highlight: [
          {
            assemblyName: 'hg38',
            refName: 'chr1',
            start: 11_130_000,
            end: 11_145_000,
            color: 'rgba(255, 0, 0, 0.25)',
            label: 'Region of interest',
          },
          {
            assemblyName: 'hg38',
            refName: 'chr1',
            start: 11_200_000,
            end: 11_220_000,
            color: 'rgba(0, 128, 255, 0.25)',
            label: 'Promoter',
          },
        ],
        loc: 'chr1:11,106,077-11,261,675',
        assembly: 'hg38',
        tracks: [
          {
            trackId: 'ncbi-refseq-genes',
            displaySnapshot: { height: 200 },
          },
        ],
      },
    },
  })
  return state ? <JBrowseLinearGenomeView viewState={state} /> : null
}

import { useEffect } from 'react'

import { useCreateOnceAsync } from '@jbrowse/core/util/hooks'
import { getSnapshot, onSnapshot } from '@jbrowse/mobx-state-tree'
import {
  JBrowseLinearGenomeView,
  createViewStateAsync,
} from '@jbrowse/react-linear-genome-view2'

const STORAGE_KEY = 'jbrowse-lgv-example-session'

const assembly = {
  name: 'volvox',
  uri: 'https://jbrowse.org/genomes/volvox/volvox.2bit',
}

const tracks = [
  {
    type: 'FeatureTrack',
    trackId: 'volvox_gff3',
    name: 'Volvox genes',
    assemblyNames: ['volvox'],
    adapter: {
      type: 'Gff3TabixAdapter',
      uri: 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.sort.gff3.gz',
    },
  },
]

const freshSession = {
  name: 'Persisted session',
  view: {
    type: 'LinearGenomeView',
    assembly: 'volvox',
    loc: 'ctgA:1105..1221',
    tracks: ['volvox_gff3'],
  },
}

async function build() {
  const saved = localStorage.getItem(STORAGE_KEY)
  localStorage.removeItem(STORAGE_KEY)
  try {
    return await createViewStateAsync({
      assembly,
      tracks,
      session: saved ? JSON.parse(saved) : undefined,
      defaultSession: freshSession,
    })
  } catch (e) {
    console.error(e)
    return createViewStateAsync({
      assembly,
      tracks,
      defaultSession: freshSession,
    })
  }
}

export default function WithSessionPersistence() {
  const state = useCreateOnceAsync(build)

  useEffect(() => {
    if (state) {
      const save = (snap: unknown) => {
        localStorage.setItem(STORAGE_KEY, JSON.stringify(snap))
      }
      save(getSnapshot(state.session))
      return onSnapshot(state.session, save)
    }
    return undefined
  }, [state])

  return state ? (
    <div>
      <p>
        Pan, zoom, or toggle tracks, then reload the page — the view comes back
        where you left it.{' '}
        <button
          onClick={() => {
            localStorage.removeItem(STORAGE_KEY)
            location.reload()
          }}
        >
          Reset saved session
        </button>
      </p>
      <JBrowseLinearGenomeView viewState={state} />
    </div>
  ) : null
}

import { useEffect, useState } from 'react'

import {
  JBrowseLinearGenomeView,
  createViewStateAsync,
  decodeSession,
  destroyViewState,
  encodeSession,
} from '@jbrowse/react-linear-genome-view2'

import type {
  SessionSnapshot,
  ViewModel,
} from '@jbrowse/react-linear-genome-view2'

const assembly = {
  name: 'volvox',
  uri: 'https://jbrowse.org/genomes/volvox/volvox.2bit',
}

const tracks = [
  {
    type: 'FeatureTrack',
    trackId: 'volvox_gff3',
    name: 'Volvox genes',
    assemblyNames: ['volvox'],
    adapter: {
      type: 'Gff3TabixAdapter',
      uri: 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.sort.gff3.gz',
    },
  },
]

const freshSession = {
  name: 'Session in URL',
  view: {
    type: 'LinearGenomeView',
    assembly: 'volvox',
    loc: 'ctgA:1..50000',
    tracks: ['volvox_gff3'],
  },
}

function readSessionParam() {
  return (
    new URLSearchParams(window.location.hash.slice(1)).get('session') ??
    undefined
  )
}

function writeSessionParam(value: string) {
  const params = new URLSearchParams(window.location.hash.slice(1))
  params.set('session', value)
  window.history.replaceState(null, '', `#${params.toString()}`)
}

function build(session?: SessionSnapshot) {
  return createViewStateAsync({
    assembly,
    tracks,
    session,
    defaultSession: session ? undefined : freshSession,
  })
}

export default function SessionInUrl() {
  const [state, setState] = useState<ViewModel | undefined>(undefined)
  const [status, setStatus] = useState('')

  useEffect(() => {
    const mount = {
      unmounted: false,
      engine: undefined as ViewModel | undefined,
    }
    const open = (session?: SessionSnapshot) =>
      build(session).then(
        engine => {
          if (mount.unmounted) {
            destroyViewState(engine)
          } else {
            mount.engine = engine
            setState(engine)
          }
        },
        (e: unknown) => {
          console.error(e)
          setStatus(`could not open the view: ${e}`)
        },
      )
    const param = readSessionParam()
    if (param) {
      decodeSession(param)
        .then(session =>
          open(session).then(() => {
            setStatus(`restored "${session.name}" from the URL`)
          }),
        )
        .catch((e: unknown) => {
          console.error(e)
          void open()
          setStatus(`could not restore the session in the URL: ${e}`)
        })
    } else {
      void open()
    }
    return () => {
      mount.unmounted = true
      if (mount.engine) {
        destroyViewState(mount.engine)
      }
    }
  }, [])

  return state ? (
    <div>
      <div style={{ padding: 8, fontSize: 13, background: '#8881' }}>
        <button
          type="button"
          onClick={() => {
            void encodeSession(state)
              .then(encoded => {
                writeSessionParam(encoded)
                setStatus(
                  `saved to the URL (${encoded.length} chars) — copy the address bar, or reload to restore it`,
                )
              })
              .catch((e: unknown) => {
                console.error(e)
                setStatus(`could not save the session to the URL: ${e}`)
              })
          }}
        >
          Save this view to the URL
        </button>{' '}
        {status || 'navigate or toggle a track, then save'}
      </div>
      <JBrowseLinearGenomeView viewState={state} />
    </div>
  ) : null
}