jbrowse-plugin-graphgenomeviewer 7.4.4 → 7.5.0

package/src/launchFromGraph/launchTracks.test.ts

@@ -1,95 +0,0 @@
-import { expect, test } from 'vitest'
-
-import { launchTracks } from './launchTracks'
-
-// Plain objects rather than config models: readConfObject returns a non-MST
-// object's own fields unchanged, so this exercises the same read path.
-function track(props: Record<string, unknown>) {
-  return props as never
-}
-
-const TRACKS = [
-  track({
-    type: 'FeatureTrack',
-    trackId: 'K12_genes',
-    assemblyNames: ['K12'],
-  }),
-  track({
-    type: 'FeatureTrack',
-    trackId: 'CFT073_genes',
-    assemblyNames: ['CFT073'],
-  }),
-  track({
-    type: 'FeatureTrack',
-    trackId: 'ecoli_minigraph_segments',
-    assemblyNames: ['K12'],
-  }),
-  track({
-    type: 'SyntenyTrack',
-    trackId: 'ecoli_pggb_ava',
-    assemblyNames: ['K12', 'CFT073'],
-  }),
-  track({
-    type: 'AlignmentsTrack',
-    trackId: 'K12_reads',
-    assemblyNames: ['K12'],
-  }),
-]
-
-const session = { tracks: TRACKS, assemblies: [] }
-
-// The bug this exists for: the graph's own track is configured for the
-// reference alone, so a per-strain launch carrying only that landed on
-// `No tracks active`.
-test("a non-reference launch gets that strain's own annotation", () => {
-  expect(launchTracks({ session, assemblyName: 'CFT073' })).toEqual([
-    'CFT073_genes',
-  ])
-})
-
-test("the graph's own track leads a launch on the reference", () => {
-  expect(
-    launchTracks({
-      session,
-      assemblyName: 'K12',
-      first: 'ecoli_minigraph_segments',
-    }),
-  ).toEqual(['ecoli_minigraph_segments', 'K12_genes'])
-})
-
-// A launch is a jump to a locus, not a session restore: an alignments track
-// turned on behind the user fetches data nobody asked for, and a synteny track
-// is what the launch beside this one opens as a view of its own.
-test('only annotation tracks are carried', () => {
-  expect(launchTracks({ session, assemblyName: 'K12' })).toEqual([
-    'K12_genes',
-    'ecoli_minigraph_segments',
-  ])
-})
-
-test('an assembly the session has no annotation for gets none', () => {
-  expect(launchTracks({ session, assemblyName: 'IAI39' })).toEqual([])
-})
-
-test('a track naming the assembly by an alias is carried', () => {
-  const aliased = {
-    tracks: [
-      track({
-        type: 'FeatureTrack',
-        trackId: 'ncbi_genes',
-        assemblyNames: ['GRCh38'],
-      }),
-    ],
-    assemblies: [],
-    assemblyManager: {
-      has: (name: string) => name === 'GRCh38' || name === 'hg38',
-      get: () => ({ name: 'hg38' }),
-    },
-  }
-  expect(launchTracks({ session: aliased, assemblyName: 'hg38' })).toEqual([
-    'ncbi_genes',
-  ])
-  expect(launchTracks({ session: aliased, assemblyName: 'GRCh38' })).toEqual([
-    'ncbi_genes',
-  ])
-})

package/src/launchFromGraph/launchTracks.ts

@@ -1,49 +0,0 @@
-import { readConfObject } from '@jbrowse/core/configuration'
-
-import { canonicalAssemblyName, trackAssemblies } from './launchFromGraph'
-
-import type { TrackScanSession } from './launchFromGraph'
-
-const ANNOTATION_TRACK_TYPE = 'FeatureTrack'
-
-// What to turn on in a linear view the graph opens on `assemblyName`.
-//
-// A launch used to carry the graph's own track and nothing else, and that track
-// is configured for the reference alone — so `Launch view` → `CFT073 chr:…`
-// landed on `No tracks active`, which answers "where is this strain's sequence?"
-// with an empty pane. What the session does hold for a contributing assembly is
-// that assembly's own annotation, and on a pangenome config that is one track
-// per strain (`CFT073_genes`), which is exactly what makes the landing readable.
-//
-// Annotation tracks only, not everything configured for the assembly. A launch
-// is a jump to a locus, and an alignments or coverage track turned on behind the
-// user's back fetches data nobody asked for; a FeatureTrack at a 50 kb window is
-// a tabix range query.
-//
-// `first` is the graph's own track when the launch is on the reference, so the
-// segments the graph drew sit at the top of the view rather than wherever config
-// order puts them.
-export function launchTracks({
-  session,
-  assemblyName,
-  first,
-}: {
-  session: TrackScanSession
-  assemblyName: string
-  first?: string
-}) {
-  const wanted = canonicalAssemblyName(session, assemblyName)
-  const found: string[] = []
-  for (const track of session.tracks) {
-    const trackId: unknown = readConfObject(track, 'trackId')
-    if (
-      readConfObject(track, 'type') === ANNOTATION_TRACK_TYPE &&
-      typeof trackId === 'string' &&
-      trackId !== first &&
-      trackAssemblies(session, track).includes(wanted)
-    ) {
-      found.push(trackId)
-    }
-  }
-  return first ? [first, ...found] : found
-}