jbrowse-plugin-graphgenomeviewer 7.4.2 → 7.4.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "7.4.2",
+  "version": "7.4.4",
   "description": "JBrowse 2 graph genome (pangenome) view: rGFA reference-anchored layouts, the Bandage force-directed engine, and haplotype lanes read from a gbz-base database",
   "license": "GPL-3.0-or-later",
   "repository": {
@@ -32,7 +32,7 @@
     "@jbrowse/core": "5.0.0-beta.11",
     "@jbrowse/display-kit": "5.0.0-beta.11",
     "@jbrowse/display-ui": "5.0.0-beta.11",
-    "@jbrowse/graph-walks": "^4.0.0",
+    "@jbrowse/graph-walks": "^4.2.0",
     "@jbrowse/render-core": "5.0.0-beta.11",
     "@jbrowse/synteny-core": "5.0.0-beta.11"
   },
@@ -40,7 +40,7 @@
     "@emotion/react": "^11.14.0",
     "@emotion/styled": "^11.14.1",
     "@eslint/js": "^10.0.1",
-    "@jbrowse/bandage-core": "^11.7.1",
+    "@jbrowse/bandage-core": "^11.9.0",
     "@jbrowse/cli": "^4.3.0",
     "@jbrowse/mobx-state-tree": "^6.9.0",
     "@jbrowse/plugin-linear-genome-view": "5.0.0-beta.11",

package/src/GraphGenomeView/model.test.ts

@@ -874,27 +874,7 @@ describe('loadGFAFromLocation', () => {
     expect(model.graphRegion).toEqual(TEST_REGION)
   })
 
-  test('a graph read from a url gives the figure spec that reads it again', async () => {
-    rpcRespond()
-    mockReadFile.mockResolvedValue(SIMPLE_GFA)
-    const model = stateModelFactory().create({
-      type: 'GraphGenomeView',
-      gfaLocation: location,
-      loadedRegion: TEST_REGION,
-      layoutMode: 'auto',
-    })
-    await model.load()
-    expect(model.figureSpec()).toMatchObject({
-      gfa: location.uri,
-      region: 'chr1:1000-5000',
-      layout: 'auto',
-    })
-    expect(model.figure()).toContain(
-      '"gfa":"https://example.com/graphs/small.gfa"',
-    )
-  })
-
-  test('a gene track in tabix shorthand gives the figure spec its index', async () => {
+  test('a gene track in tabix shorthand turns genes on', async () => {
     rpcRespond()
     mockReadFile.mockResolvedValue(SIMPLE_GFA)
     mockSession.tracks = [
@@ -916,11 +896,7 @@ describe('loadGFAFromLocation', () => {
     })
     await model.load()
     expect(model.showGenes).toBe(true)
-    expect(model.figureSpec()?.genes).toEqual({
-      file: 'https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz',
-      index: 'https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz.csi',
-      format: 'gff3',
-    })
+    expect(model.geneTrack?.trackId).toBe('ncbiRefSeq')
     mockSession.tracks = []
   })
 
@@ -3413,89 +3389,6 @@ describe('walk rows', () => {
     expect(svg).toContain("'s path")
   })
 
-  test("the figure spec keeps the strip's sample filter", async () => {
-    rpcRespond()
-    mockReadFile.mockResolvedValue(WALKS_GFA)
-    const model = stateModelFactory().create({
-      type: 'GraphGenomeView',
-      gfaLocation: {
-        uri: 'https://example.com/graphs/walks.gfa',
-        locationType: 'UriLocation',
-      },
-      loadedRegion: TEST_REGION,
-      layoutMode: 'ordered',
-      layers: { walkStrip: true },
-      rows: { kept: ['B'] },
-    })
-    await model.load()
-    expect(model.walkStripRows!.rows.map(r => r.label)).toEqual(['B#1'])
-    expect(model.figureSpec()).toMatchObject({
-      walkStrip: true,
-      walkRowSamples: ['B'],
-    })
-    model.setWalkStrip(false)
-    expect(model.figureSpec()?.walkRowSamples).toBeUndefined()
-  })
-
-  // bandage-figure shows deletion edges unless a spec says otherwise
-  test('the figure spec states deletion edges only when they are off', async () => {
-    rpcRespond()
-    mockReadFile.mockResolvedValue(WALKS_GFA)
-    const model = stateModelFactory().create({
-      type: 'GraphGenomeView',
-      gfaLocation: {
-        uri: 'https://example.com/graphs/walks.gfa',
-        locationType: 'UriLocation',
-      },
-      loadedRegion: TEST_REGION,
-      layoutMode: 'ordered',
-    })
-    await model.load()
-    expect(model.figureSpec()).not.toHaveProperty('showDeletionEdges')
-    model.setLayer('deletions', false)
-    expect(model.figureSpec()?.showDeletionEdges).toBe(false)
-  })
-
-  // bandage-figure laid a linear layout out as an ordinary one, and drew its
-  // own line widths, while the spec said nothing about either
-  test('the figure spec carries the settings that change the picture', async () => {
-    rpcRespond()
-    mockReadFile.mockResolvedValue(WALKS_GFA)
-    const model = stateModelFactory().create({
-      type: 'GraphGenomeView',
-      gfaLocation: {
-        uri: 'https://example.com/graphs/walks.gfa',
-        locationType: 'UriLocation',
-      },
-      loadedRegion: TEST_REGION,
-      layoutMode: 'ordered',
-      size: 9,
-    })
-    await model.load()
-    expect(model.figureSpec()).toMatchObject({ contigThickness: 9 })
-    expect(model.figureSpec()).not.toHaveProperty('connectorThickness')
-    expect(model.figureSpec()).not.toHaveProperty('linearLayout')
-    model.setLinearLayout(true)
-    expect(model.figureSpec()?.linearLayout).toBe(true)
-  })
-
-  test('walk rows offer no figure spec, since bandage-figure draws no walk rows', async () => {
-    rpcRespond()
-    mockReadFile.mockResolvedValue(WALKS_GFA)
-    const model = stateModelFactory().create({
-      type: 'GraphGenomeView',
-      gfaLocation: {
-        uri: 'https://example.com/graphs/walks.gfa',
-        locationType: 'UriLocation',
-      },
-      loadedRegion: TEST_REGION,
-      layoutMode: 'walkrows',
-    })
-    await model.load()
-    expect(model.walkRowBars).toBeDefined()
-    expect(model.figureSpecUnavailable).toMatch(/^bandage-figure draws no /)
-  })
-
   test("a picker's set keeps lifted walks this cut does not hold", async () => {
     rpcRespond()
     const model = stateModelFactory().create({

package/src/GraphGenomeView/pane/fitViews.ts

@@ -5,7 +5,6 @@ import {
   facetGrid,
 } from '@jbrowse/bandage-core/facetGrid'
 import { figureSvg } from '@jbrowse/bandage-core/figure'
-import { figureSpecSettings } from '@jbrowse/bandage-core/figureSettings'
 import { rowLabelBox } from '@jbrowse/bandage-core/graphLabels'
 import {
   LEGEND_INSET_PX,
@@ -34,10 +33,6 @@ import {
 } from '@jbrowse/bandage-core/tubeMap/genes'
 import { padded } from '@jbrowse/bandage-core/viewport'
 import { walkPosition } from '@jbrowse/bandage-core/walkKey'
-import {
-  expandTabixShorthand,
-  readConfObject,
-} from '@jbrowse/core/configuration'
 import { untracked } from 'mobx'
 
 import { SECTION_HEADER_PX, sectionPlacement } from '../walkRowGroups'
@@ -52,7 +47,6 @@ import {
   VIEWPORT_PANES_BUILT,
   dependOn,
   paneViewportOf,
-  uriOf,
 } from './paneBase'
 import { trackedDpr } from '../trackedDpr'
 
@@ -63,7 +57,6 @@ import type {
 } from '@jbrowse/bandage-core/layout/walkRowDraw'
 import type { Renderer } from '@jbrowse/bandage-core/renderer/types'
 import type { LiftedWalk, WalkLift } from '@jbrowse/bandage-core/walkHighlight'
-import type { FileLocation } from '@jbrowse/core/util/types'
 
 export const TOOLTIP_INSET_PX = 8
 export const FACET_KEY_ROW_PX = 19
@@ -557,96 +550,6 @@ export const withFitViews = withHostViews
         ? (walkPosition(walk, node.id, node.length) ?? 'not on this walk')
         : undefined
     },
-    // The spec bandage-figure makes this drawing from with no browser, or
-    // undefined for a graph it cannot read again: one cut from a gbz-base
-    // track or read from a GFA url, with the genes of a GFF3 tabix track
-    figureSpec() {
-      const region = self.graphRegion
-      const adapter = self.sourceAdapter
-      const panSN = adapter?.assemblyNameToPanSN as
-        Record<string, string> | undefined
-      const window = region && `${region.refName}:${region.start}-${region.end}`
-      const gfa = uriOf(self.sourceGfaLocation)
-      const db =
-        adapter?.type === 'GbzBaseSyntenyAdapter'
-          ? uriOf(adapter.gbzDbLocation as FileLocation)
-          : undefined
-      const source = gfa
-        ? { gfa, region: window }
-        : db && region && window
-          ? {
-              gbz: {
-                db,
-                index: uriOf(adapter!.haplotypeIndexLocation as FileLocation),
-                region: window,
-                // the adapter cuts a lane by its PanSN prefix
-                haplotypes: self.cutHaplotypes?.map(
-                  lane => panSN?.[lane] ?? lane,
-                ),
-                referenceSample:
-                  (adapter!.referenceSample as string | undefined) ||
-                  panSN?.[region.assemblyName] ||
-                  region.assemblyName,
-                context: adapter!.context as number | undefined,
-                snarls: self.cutsWholeWalks
-                  ? 'overlapping'
-                  : (adapter!.subgraphSnarls as string | undefined),
-              },
-            }
-          : undefined
-      if (!source) {
-        return undefined
-      }
-      const geneTrack = self.showGenes ? self.geneTrack : undefined
-      const geneConf = geneTrack
-        ? self.sessionTrack(geneTrack.trackId)
-        : undefined
-      const geneAdapter = geneConf
-        ? expandTabixShorthand(
-            readConfObject(geneConf, 'adapter') as Record<string, unknown>,
-            'gffGzLocation',
-          )
-        : undefined
-      const genes =
-        geneAdapter?.type === 'Gff3TabixAdapter'
-          ? {
-              file: uriOf(geneAdapter.gffGzLocation as FileLocation),
-              index: uriOf(
-                (geneAdapter.index as { location?: FileLocation } | undefined)
-                  ?.location,
-              ),
-              format: 'gff3',
-            }
-          : undefined
-      return JSON.parse(
-        JSON.stringify({
-          ...source,
-          genes: genes?.file && genes.index ? genes : undefined,
-          referencePath: self.referencePath || undefined,
-          layout: self.chosenLayoutMode,
-          ...figureSpecSettings({
-            engine: self.layoutEngine,
-            quality: self.layoutQuality,
-            linearLayout: self.linearLayout,
-            bubbleSpread: self.bubbleSpread,
-            showDeletionEdges: self.showDeletionEdges,
-            colorScheme: self.chosenColorScheme,
-            nodeWidth: self.nodeWidth,
-            contigThickness: self.contigThickness,
-            connectorThickness: self.connectorThickness,
-            colorDomain: self.statedColorDomain,
-          }),
-          walks: self.walkLayers.length
-            ? self.walkLayers.map(l => (l.color ? l : l.walk))
-            : undefined,
-          facet: self.walkLayers.length > 1 ? self.facetSpec : undefined,
-          walkStrip: self.walkStripShown || undefined,
-          walkRowSamples: self.walkStripShown ? self.walkRowSamples : undefined,
-          width: self.paneWidth,
-          height: self.paneCeiling,
-        }),
-      ) as Record<string, unknown>
-    },
     // Why the drawing cannot be written as SVG, which draws the canvas's
     // nodes, or walk rows' bars
     get figureUnavailable() {
@@ -658,15 +561,6 @@ export const withFitViews = withHostViews
             ? undefined
             : `${layoutModeByValue(self.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`
     },
-    // Why bandage-figure can't make this drawing again: it draws only
-    // layouts with nodes, from a graph it can read for itself
-    get figureSpecUnavailable() {
-      return !self.drawsNodes
-        ? `bandage-figure draws no ${layoutModeByValue(self.chosenLayoutMode).label} layout`
-        : this.figureSpec()
-          ? undefined
-          : 'bandage-figure reads a graph cut from a gbz-base track or a GFA url'
-    },
     // The drawing as a standalone SVG, fitted, with its genes, its lifted
     // walks' keys, facet panels and the strip of walk rows; see figureSvg
     figure() {
@@ -695,9 +589,6 @@ export const withFitViews = withHostViews
               rowGenes: self.walkRowGenes,
               rowGeneGaps: self.walkRowGeneGaps,
             },
-            // the SVG carries the spec only where the spec draws this same
-            // picture: one of nodes (figureSpecUnavailable)
-            spec: self.drawsNodes ? this.figureSpec() : undefined,
           })
         : undefined
     },

package/src/GraphGenomeView/pane/graphViews.ts

@@ -666,10 +666,6 @@ export const withGraphViews = paneBase
     get cutHaplotypes(): string[] | undefined {
       return undefined
     },
-    // the GFA the graph on screen was read from, where a host says
-    get sourceGfaLocation(): FileLocation | undefined {
-      return undefined
-    },
     get sourceAdapter() {
       const track = self.sourceTrack
       return track ? trackAdapterConfig(self, track) : undefined

package/src/GraphGenomeView/pane/launchActions.ts

@@ -5,7 +5,6 @@ import {
   layoutModeByValue,
 } from '@jbrowse/bandage-core/layoutModes'
 import { getSession } from '@jbrowse/core/util'
-import ContentCopyIcon from '@mui/icons-material/ContentCopy'
 import HubIcon from '@mui/icons-material/Hub'
 import PaletteIcon from '@mui/icons-material/Palette'
 import PhotoCameraIcon from '@mui/icons-material/PhotoCamera'
@@ -338,27 +337,6 @@ export const withLaunchActions = withRenderingActions
             }
           },
         },
-        {
-          label: 'Copy figure spec',
-          icon: ContentCopyIcon,
-          disabled: self.figureSpecUnavailable !== undefined,
-          disabledHelpText: self.figureSpecUnavailable,
-          onClick: () => {
-            const spec = self.figureSpec()
-            const session = getSession(self)
-            navigator.clipboard
-              .writeText(`${JSON.stringify(spec, null, 2)}\n`)
-              .then(() => {
-                session.notify(
-                  'Figure spec copied. Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg',
-                  'info',
-                )
-              })
-              .catch((e: unknown) => {
-                session.notify(`Could not copy the figure spec: ${String(e)}`)
-              })
-          },
-        },
       ]
     },
     // `picks` false where a toolbar already picks the walks, leaving what is

package/src/GraphGenomeView/pane/loadActions.ts

@@ -349,7 +349,7 @@ export const withLoadActions = withEngineSettings.actions(self => {
         : parsed
     const folded =
       foldBelowBp > 0 && !readsOf
-        ? foldVariants(anchored, foldBelowBp)
+        ? foldVariants(anchored, foldBelowBp, { cut: true })
         : anchored
     const graph =
       region && folded !== anchored

package/src/GraphGenomeView/pane/paneBase.ts

@@ -177,13 +177,6 @@ export function fileName(location: FileLocation) {
   return path.split(/[\\/]/).at(-1) ?? ''
 }
 
-// A url bandage-figure can read again, or undefined for a local file
-export function uriOf(location: FileLocation | undefined) {
-  return location && 'uri' in location && location.uri
-    ? new URL(location.uri, location.baseUri ?? window.location.href).href
-    : undefined
-}
-
 type ViewportOwner = 'fit' | 'user' | 'host'
 
 interface BuiltViewport {

package/src/GraphGenomeView/viewModel.ts

@@ -93,9 +93,6 @@ export default function stateModelFactory() {
       get paneMeasured() {
         return self.widthMeasured
       },
-      get sourceGfaLocation() {
-        return self.gfaLocation
-      },
       get sourceTrack(): AnyConfigurationModel | undefined {
         return self.loadedTrackId
           ? self.sessionTrack(self.loadedTrackId)

package/src/RgfaTabixAdapter/configSchema.ts

@@ -30,8 +30,8 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * `walksUri` takes the prefix of a walk file in place of `uri`, and resolves
  * `<walksUri>.walks.bed.gz` and its `.tbi`. `gfa-to-tabix --walks -o <prefix>`
  * writes one per reference sample, so a track names one as
- * `<prefix>.<sample>`. The adapter reads walk format 4, which gfa-to-tabix
- * writes from 1.2, through @jbrowse/graph-walks. Such a graph's cut carries
+ * `<prefix>.<sample>`. The adapter reads walk format 5, which gfa-to-tabix
+ * writes from 1.4, through @jbrowse/graph-walks. Such a graph's cut carries
  * the haplotypes' walks, and `defaultHaplotypes` names the ones it is cut for
  * until the user picks others.
  *
@@ -152,7 +152,7 @@ const RgfaTabixAdapter = ConfigurationSchema(
     ),
     /**
      * #slot
-     * a `gfa-to-tabix --walks` file in walk format 4: per reference chunk,
+     * a `gfa-to-tabix --walks` file in walk format 5: per reference chunk,
      * the reference's path, the ways haplotypes leave it and each haplotype's
      * piece. Unset means the graph has no walks.
      */

package/src/RgfaTabixAdapter/walkFiles.test.ts

@@ -35,27 +35,27 @@ const fixture = (name: string) =>
 //   W HG002   1 chr1 >1>2>7>4>5>6   7 replaces 3
 //   W HG002   2 chr1 >1>2>3>4>8>6   8 replaces 5
 //   W HG00097 1 chr1 >1>2>3>4>5>6
-const headerPrefix = fixture('walks4_header')
+const headerPrefix = fixture('walks5_header')
 
-// walks4_header's walks with the reference named as pggb names a P-line,
+// walks5_header's walks with the reference named as pggb names a P-line,
 // GRCh38#chr1
-const twoPartPrefix = fixture('walks4_twopart')
+const twoPartPrefix = fixture('walks5_twopart')
 
 // An unchopped graph, node 1 spanning 0-2600 and filed under chunk 0 alone:
 //   W GRCh38 0 chr1 >1>2>4
 //   W HG002  1 chr1 >1>3>4   3 replaces 2
-const maxNodePrefix = fixture('walks4_maxnode')
+const maxNodePrefix = fixture('walks5_maxnode')
 
 // Twelve 500 bp reference nodes over chr1:0-6000 in one 10 kb chunk:
 //   W GRCh38  0 chr1 >1>2>3>4>5>6>7>8>9>10>11>12
 //   W HG002   1 chr1 >1>2>3>20>21>9>10>11>12   20 and 21, 2 kb each, replace 4-8
 //   W HG002   2 chr1 >1>2>3>4>5>6>7>8>9>10>11>12
 //   W HG003   1 chr1 >1>2>3>22                 the contig ends on 22, 300 bp
-const rejoinPrefix = fixture('walks4_rejoin')
+const rejoinPrefix = fixture('walks5_rejoin')
 
 // The same graph in 1 kb chunks, whose rows name the chunks their path goes on
 // in: HG002#1 leaves chunk 1000 for 20 and 21 and rejoins at 9, in chunk 4000
-const followPrefix = fixture('walks4_follow')
+const followPrefix = fixture('walks5_follow')
 
 function makeAdapter(prefix: string, slots = {}) {
   const local = (path: string) => ({

package/src/WalkFormsAdapter/WalkFormsAdapter.test.ts

@@ -0,0 +1,204 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { ExpansionTooLargeError, formsCut } from '@jbrowse/graph-walks'
+import { firstValueFrom } from 'rxjs'
+import { toArray } from 'rxjs/operators'
+
+import Adapter from './WalkFormsAdapter.ts'
+import configSchema from './configSchema.ts'
+import WalkFormsAdapterF from './index.ts'
+
+import type * as GraphWalks from '@jbrowse/graph-walks'
+
+vi.mock('@jbrowse/graph-walks', async importOriginal => {
+  const actual = await importOriginal<typeof GraphWalks>()
+  return { ...actual, formsCut: vi.fn(actual.formsCut) }
+})
+
+// Four walks over a 3.6 kb reference of six 600 bp nodes, in 1 kb chunks
+// (RgfaTabixAdapter/walkFiles.test.ts builds on the same file):
+//   W GRCh38  0 chr1 >1>2>3>4>5>6
+//   W HG002   1 chr1 >1>2>7>4>5>6   7 (550 bp) replaces 3
+//   W HG002   2 chr1 >1>2>3>4>8>6   8 (20 bp) replaces 5
+//   W HG00097 1 chr1 >1>2>3>4>5>6
+const walks =
+  require.resolve('../RgfaTabixAdapter/test_data/walks5_header.GRCh38.walks.bed.gz')
+
+const local = (path: string) => ({
+  localPath: path,
+  locationType: 'LocalPathLocation',
+})
+
+// Each test pins its own window, since the cut cache outlives an adapter
+function makeAdapter(slots: Record<string, unknown>) {
+  return new Adapter(
+    configSchema.create({
+      walksLocation: local(walks),
+      walksIndex: { location: local(`${walks}.tbi`) },
+      ...slots,
+    }),
+  )
+}
+
+const pinned = (start: number) => ({ refName: 'chr1', start, end: 3600 })
+
+const region = (start: number, end: number, refName = 'chr1') => ({
+  refName,
+  assemblyName: 'hg38',
+  start,
+  end,
+})
+
+const featuresOf = (adapter: Adapter, query = region(0, 3600)) =>
+  firstValueFrom(adapter.getFeatures(query).pipe(toArray()))
+
+const placeholders = (features: Awaited<ReturnType<typeof featuresOf>>) =>
+  features
+    .filter(f => f.id().startsWith('forms-reference-'))
+    .map(f => ({
+      start: f.get('start'),
+      end: f.get('end'),
+      genotypes: f.get('genotypes'),
+    }))
+
+test('registers the adapter type', () => {
+  const pm = new PluginManager()
+  WalkFormsAdapterF(pm)
+  pm.createPluggableElements()
+  expect(pm.getAdapterType('WalkFormsAdapter').name).toBe('WalkFormsAdapter')
+})
+
+test('names the reference sample contigs as the assembly does', async () => {
+  expect(await makeAdapter({ pinned: pinned(0) }).getRefNames()).toEqual([
+    'chr1',
+  ])
+})
+
+test('one source per form, labelled by share and change', async () => {
+  const adapter = makeAdapter({ pinned: pinned(1) })
+  expect(await adapter.getSourcesAndWarnings()).toEqual({
+    sources: [
+      { name: 'F1', label: '33% · ref', haplotypes: 1, forms: 1 },
+      {
+        name: 'F2',
+        label: '33% · repl 600bp->550bp',
+        haplotypes: 1,
+        forms: 1,
+      },
+      { name: 'F3', label: '33% · del 580bp', haplotypes: 1, forms: 1 },
+    ],
+    warnings: [],
+  })
+})
+
+test('features are the pinned window changes, with a genotype per form', async () => {
+  const features = await featuresOf(makeAdapter({ pinned: pinned(2) }))
+  expect(
+    features.map(f => ({
+      start: f.get('start'),
+      end: f.get('end'),
+      consequence: f.get('consequence'),
+      svType: f.get('svType'),
+      type: f.get('type'),
+      genotypes: f.get('genotypes'),
+    })),
+  ).toEqual([
+    {
+      start: 1200,
+      end: 1800,
+      consequence: 'loss',
+      svType: 'CPX',
+      type: 'complex_substitution',
+      genotypes: { F1: '0', F2: '1', F3: '0' },
+    },
+    {
+      start: 2400,
+      end: 3000,
+      consequence: 'loss',
+      svType: 'DEL',
+      type: 'deletion',
+      genotypes: { F1: '0', F2: '0', F3: '1' },
+    },
+  ])
+})
+
+test('a query with no change gives one reference placeholder', async () => {
+  const adapter = makeAdapter({ pinned: pinned(3) })
+  expect(placeholders(await featuresOf(adapter, region(1900, 2300)))).toEqual([
+    { start: 1900, end: 1901, genotypes: { F1: '0', F2: '0', F3: '0' } },
+  ])
+  expect(
+    placeholders(await featuresOf(adapter, region(0, 3600, 'chr2'))),
+  ).toHaveLength(1)
+  expect(
+    placeholders(await featuresOf(adapter, region(2900, 3600))),
+  ).toHaveLength(0)
+})
+
+test('a floor change regroups the cut without cutting again', async () => {
+  vi.mocked(formsCut).mockClear()
+  const fine = makeAdapter({ pinned: pinned(4), floorBp: 50 })
+  const coarse = makeAdapter({ pinned: pinned(4), floorBp: 1000 })
+  expect((await fine.getSourcesAndWarnings()).sources).toHaveLength(3)
+  expect((await coarse.getSourcesAndWarnings()).sources).toEqual([
+    { name: 'F1', label: '100% · ref', haplotypes: 3, forms: 1 },
+  ])
+  expect(placeholders(await featuresOf(coarse))).toEqual([
+    { start: 0, end: 1, genotypes: { F1: '0' } },
+  ])
+  expect(formsCut).toHaveBeenCalledTimes(1)
+})
+
+test('exclude leaves samples out of every form', async () => {
+  const adapter = makeAdapter({ pinned: pinned(5), exclude: ['HG002'] })
+  expect((await adapter.getSourcesAndWarnings()).sources).toEqual([
+    { name: 'F1', label: '100% · ref', haplotypes: 1, forms: 1 },
+  ])
+})
+
+test('maxForms gives the smaller forms one empty row', async () => {
+  const adapter = makeAdapter({ pinned: pinned(6), maxForms: 1 })
+  const { sources, warnings } = await adapter.getSourcesAndWarnings()
+  expect(sources.map(s => s.label)).toEqual(['33% · ref', 'other forms · 67%'])
+  expect(warnings).toEqual([
+    expect.stringMatching(/^Forms of chr1:7-3,600: 2 smaller forms/),
+  ])
+  expect(placeholders(await featuresOf(adapter))).toEqual([
+    { start: 0, end: 1, genotypes: { F1: '0' } },
+  ])
+})
+
+test('a pinned window past walkByteBudget says so, without a zoom-in notice', async () => {
+  const error = await makeAdapter({ pinned: pinned(7), walkByteBudget: 1 })
+    .getSourcesAndWarnings()
+    .catch((e: unknown) => e)
+  expect(error).toBeInstanceOf(Error)
+  expect(error).not.toHaveProperty('regionTooLarge')
+  expect(`${error}`).toMatch(
+    /^Error: The pinned window chr1:8-3,600 is too large to cut for structural forms: .*walkByteBudget, 0\.0 MB\. .*Raise walkByteBudget$/,
+  )
+})
+
+test('a window whose walks are too many to read in full says so', async () => {
+  vi.mocked(formsCut).mockClear()
+  vi.mocked(formsCut).mockRejectedValueOnce(
+    new ExpansionTooLargeError(24_000_000, 16_000_000, 3592),
+  )
+  const error = await makeAdapter({ pinned: pinned(9) })
+    .getSourcesAndWarnings()
+    .catch((e: unknown) => e)
+  expect(formsCut).toHaveBeenCalledWith(
+    expect.anything(),
+    expect.anything(),
+    expect.objectContaining({ partial: false }),
+  )
+  expect(error).not.toHaveProperty('regionTooLarge')
+  expect(`${error}`).toBe(
+    'Error: The pinned window chr1:10-3,600 is too large to read every walk in full for structural forms: its walks take 24.0 M steps, over the 16.0 M step budget, and about 2.39Kbp of it fits. Pin a narrower window',
+  )
+})
+
+test('an adapter with no pinned window says so', async () => {
+  await expect(makeAdapter({}).getSourcesAndWarnings()).rejects.toThrow(
+    /needs `pinned`/,
+  )
+})