jbrowse-plugin-graphgenomeviewer 4.0.2 → 4.0.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "4.0.2",
+  "version": "4.0.4",
   "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": {

package/src/GraphAddTrackWorkflow/buildTrackConfig.test.ts

@@ -23,6 +23,10 @@ describe('buildTrackConfig', () => {
       trackId: 'hprc',
       name: 'HPRC graph',
       assemblyNames: ['hg38'],
+      displays: [
+        { type: 'LinearGraphDisplay', displayId: 'hprc-LinearGraphDisplay' },
+        { type: 'LinearBasicDisplay', displayId: 'hprc-LinearBasicDisplay' },
+      ],
       adapter: {
         type: 'RgfaTabixAdapter',
         segmentsLocation: segs,

package/src/GraphAddTrackWorkflow/buildTrackConfig.ts

@@ -108,7 +108,19 @@ export function buildTrackConfig(args: {
     assemblyNames: [assembly],
     adapter: buildAdapterConfig(args),
     ...(choice === 'RgfaTabixAdapter'
-      ? { displayDefaults: { showLabels: 'none' } }
+      ? {
+          displays: [
+            {
+              type: 'LinearGraphDisplay',
+              displayId: `${trackId}-LinearGraphDisplay`,
+            },
+            {
+              type: 'LinearBasicDisplay',
+              displayId: `${trackId}-LinearBasicDisplay`,
+            },
+          ],
+          displayDefaults: { showLabels: 'none' },
+        }
       : {}),
   }
 }

package/src/GraphGenomeView/host.ts

@@ -105,9 +105,15 @@ export function hostWindow(view: LinearHost): HostWindow | undefined {
 
 // The window plus one window-width each side, clamped to the displayed
 // region, with the margins narrowed until the whole cut fits under `capBp`.
-export function hostCut(window: HostWindow, capBp: number): SubgraphRegion {
+export function hostCut(
+  window: HostWindow,
+  capBp: number,
+  margins = true,
+): SubgraphRegion {
   const visible = window.end - window.start
-  const margin = Math.max(0, Math.min(window.span, (capBp - visible) / 2))
+  const margin = margins
+    ? Math.max(0, Math.min(window.span, (capBp - visible) / 2))
+    : 0
   return {
     refName: window.refName,
     assemblyName: window.assemblyName,
@@ -116,11 +122,24 @@ export function hostCut(window: HostWindow, capBp: number): SubgraphRegion {
   }
 }
 
-export function cutHolds(cut: SubgraphRegion | undefined, window: HostWindow) {
+// With margins, a cut holds while the window is inside it; without, only the
+// window itself does, since the drawing is the window.
+export function cutHolds(
+  cut: SubgraphRegion | undefined,
+  window: HostWindow,
+  margins = true,
+) {
+  if (
+    cut?.refName !== window.refName ||
+    cut.assemblyName !== window.assemblyName
+  ) {
+    return false
+  }
+  if (margins) {
+    return cut.start <= window.start && window.end <= cut.end
+  }
+  const exact = hostCut(window, Infinity, false)
   return (
-    cut?.refName === window.refName &&
-    cut.assemblyName === window.assemblyName &&
-    cut.start <= window.start &&
-    window.end <= cut.end
+    Math.abs(cut.start - exact.start) < 1 && Math.abs(cut.end - exact.end) < 1
   )
 }

package/src/GraphGenomeView/layoutModes.ts

@@ -39,6 +39,10 @@ export interface LayoutMode {
   // rest rather than hiding them, so the reason a mode is unavailable stays
   // visible instead of the menu silently changing shape between graphs
   available: (graph: Graph) => boolean
+  // whether the drawing puts reference bp on x, so a host places it and a cut
+  // carries margins to pan over. A mode without one draws its own picture of
+  // the window, so its cut is the window alone.
+  referenceAxis: boolean
   // whether `run` draws this graph itself, as opposed to handing off to the
   // engine. Not the same question as `available` and not derivable from it:
   // 'force' is available for every graph and draws none of them itself. The two
@@ -63,6 +67,7 @@ export const LAYOUT_MODES = [
     description:
       'x is reference bp, one row per stable rank. Needs rGFA tags or a reference path.',
     run: anchoredLayout,
+    referenceAxis: true,
     available: hasBackbone,
     drawsLocally: hasBackbone,
   },
@@ -72,6 +77,7 @@ export const LAYOUT_MODES = [
     description:
       'x is reference bp, one row per contributing assembly. Needs rGFA tags or a reference path.',
     run: sampleRowLayout,
+    referenceAxis: true,
     available: hasAlleles,
     drawsLocally: hasAlleles,
   },
@@ -81,6 +87,7 @@ export const LAYOUT_MODES = [
     description:
       "x is each walk's own bp: one bar per haplotype, sequence the reference also carries in blue and sequence it does not in purple, so a repeat expansion reads as bar length. Needs W or P lines.",
     run: walkRowLayout,
+    referenceAxis: true,
     available: hasWalks,
     drawsLocally: hasWalks,
   },
@@ -90,6 +97,7 @@ export const LAYOUT_MODES = [
     description:
       'x is reference order, not bp: every node gets room, bubbles read as lenses. Needs rGFA tags or a reference path.',
     run: orderedLayout,
+    referenceAxis: false,
     available: hasBackbone,
     drawsLocally: hasBackbone,
   },
@@ -99,6 +107,7 @@ export const LAYOUT_MODES = [
     description:
       'The reference as a line with one typed glyph per bubble, from the bubble index or from the graph itself: SNP, indel, deletion, inversion, repeat array. Click a glyph to open the graph inside it.',
     run: variantMapLayout,
+    referenceAxis: true,
     available: hasBackbone,
     drawsLocally: hasBackbone,
   },
@@ -107,6 +116,7 @@ export const LAYOUT_MODES = [
     label: FORCE_LAYOUT_LABEL,
     description: 'OGDF FMMM, via the external Bandage engine.',
     run: () => undefined,
+    referenceAxis: false,
     available: () => true,
     drawsLocally: () => false,
   },

package/src/GraphGenomeView/model.ts

@@ -2504,7 +2504,11 @@ export default function stateModelFactory() {
       // its edge re-cuts the window plus a window-width each side, on the tier
       // the zoom asks for. Overlapping re-cuts are ordered by doSubgraphLoad's
       // liveLoad, so the latest window wins.
+      // Returns whether it re-cut. A layout that draws its own picture of the
+      // window is cut to the window alone; one the host places carries
+      // margins to pan over.
       settleOn(seen: HostWindow) {
+        const margins = layoutModeByValue(self.layoutMode).referenceAxis
         const above = self.coarseAboveBpPerPx
         const tier =
           above !== undefined && seen.bpPerPx > above ? 'coarse' : 'fine'
@@ -2516,14 +2520,15 @@ export default function stateModelFactory() {
             : undefined
         if (
           self.cutNote !== undefined ||
-          (tier === self.cutTier && cutHolds(self.loadedRegion, seen))
+          (tier === self.cutTier && cutHolds(self.loadedRegion, seen, margins))
         ) {
-          return
+          return false
         }
         self.coarseCut = tier === 'coarse'
-        self.loadedRegion = hostCut(seen, cap)
+        self.loadedRegion = hostCut(seen, cap, margins)
         self.recuts++
         void self.reloadSubgraph()
+        return true
       },
     }))
     .actions(self => ({
@@ -2832,7 +2837,13 @@ export default function stateModelFactory() {
       // A layout picked from a menu: the mode, then the drawing it makes.
       switchLayout(mode: LayoutModeValue) {
         self.setLayoutMode(mode)
-        return self.recomputeLayout()
+        const { host } = self
+        const seen = host ? hostWindow(host) : undefined
+        // A cut the new mode would make differently is made again, and that
+        // reload lays the graph out; otherwise the layout alone is redone.
+        return seen && self.settleOn(seen)
+          ? Promise.resolve()
+          : self.recomputeLayout()
       },
       retryLoad() {
         if (self.loadedTrackId && self.loadedRegion) {

package/src/LinearGraphDisplay/LinearGraphDisplay.test.ts

@@ -13,6 +13,7 @@ import { types } from '@jbrowse/mobx-state-tree'
 import { linearGenomeViewStateModelFactory } from '@jbrowse/plugin-linear-genome-view'
 
 import LinearGraphDisplayF from './index'
+import GbzBaseSyntenyAdapterF from '../GbzBaseSyntenyAdapter/index'
 import RgfaTabixAdapterF from '../RgfaTabixAdapter/index'
 
 import type { LinearGraphDisplayModel } from './model'
@@ -97,25 +98,28 @@ function createEnvironment({ tiered = true } = {}) {
   console.warn = vi.fn()
   const pluginManager = new PluginManager()
   RgfaTabixAdapterF(pluginManager)
-  pluginManager.addTrackType(() => {
-    const trackConfigSchema = ConfigurationSchema(
-      'FeatureTrack',
-      {},
-      {
-        baseConfiguration: createBaseTrackConfig(pluginManager),
-        explicitIdentifier: 'trackId',
-      },
-    )
-    return new TrackType({
-      name: 'FeatureTrack',
-      configSchema: trackConfigSchema,
-      stateModel: createBaseTrackModel(
-        pluginManager,
-        'FeatureTrack',
-        trackConfigSchema,
-      ),
+  GbzBaseSyntenyAdapterF(pluginManager)
+  for (const name of ['FeatureTrack', 'SyntenyTrack']) {
+    pluginManager.addTrackType(() => {
+      const trackConfigSchema = ConfigurationSchema(
+        name,
+        {},
+        {
+          baseConfiguration: createBaseTrackConfig(pluginManager),
+          explicitIdentifier: 'trackId',
+        },
+      )
+      return new TrackType({
+        name,
+        configSchema: trackConfigSchema,
+        stateModel: createBaseTrackModel(
+          pluginManager,
+          name,
+          trackConfigSchema,
+        ),
+      })
     })
-  })
+  }
   LinearGraphDisplayF(pluginManager)
   pluginManager.addViewType(
     () =>
@@ -155,7 +159,20 @@ function createEnvironment({ tiered = true } = {}) {
     },
     { pluginManager },
   )
-  const trackConfigs = [trackConfig]
+  const gbzTrackConfig = trackSchema.create(
+    {
+      type: 'SyntenyTrack',
+      trackId: 'walks',
+      name: 'walks',
+      assemblyNames: [ASM, 'HG1.1', 'HG2.1'],
+      adapter: { type: 'GbzBaseSyntenyAdapter', assemblyNames: [ASM] },
+      displays: [
+        { type: 'LinearGraphDisplay', displayId: 'walks-LinearGraphDisplay' },
+      ],
+    },
+    { pluginManager },
+  )
+  const trackConfigs = [trackConfig, gbzTrackConfig]
 
   const assemblyRegions = [
     { refName: REF, start: 0, end: CONTIG, assemblyName: ASM },
@@ -321,19 +338,44 @@ test('with no coarse tier the margins narrow to the cap, and past it the last cu
   expect(pane.cutNote).toMatch(/Holding the last cut/)
 })
 
-test('a layout whose x is not reference bp draws its own viewport, and still re-cuts', async () => {
+test('a layout whose x is not reference bp draws its own viewport of the window alone, and still re-cuts', async () => {
   const { view, pane, cuts } = await shownGraph()
   await pane.switchLayout('force')
+  await wait(SETTLE_MS)
   expect(pane.hostPlacesX).toBe(false)
   expect(pane.viewportOwner).not.toBe('host')
+  expect(cuts).toHaveLength(2)
+  expect(cuts[1]!.region).toMatchObject({ start: 1_000_000, end: 1_060_000 })
   view.scrollTo(2_000_000 / view.bpPerPx)
   await wait(SETTLE_MS)
-  expect(cuts).toHaveLength(2)
+  expect(cuts).toHaveLength(3)
+  expect(cuts[2]!.region.start).toBe(2_000_000)
+  expect(Math.abs(cuts[2]!.region.end - 2_060_000)).toBeLessThanOrEqual(1)
   await pane.switchLayout('auto')
+  await wait(SETTLE_MS)
   expect(pane.hostPlacesX).toBe(true)
   expect(graphX(pane, 2_030_000)).toBeCloseTo(lgvX(view, 2_030_000), 6)
 })
 
+test('a launch in the force layout cuts the window alone', async () => {
+  const { view, cuts } = createEnvironment()
+  view.zoomTo(60_000 / WIDTH_PX)
+  view.scrollTo(1_000_000 / view.bpPerPx)
+  view.showTrack(
+    'graph',
+    {},
+    {
+      type: 'LinearGraphDisplay',
+      pane: { layoutMode: 'force' },
+    },
+  )
+  const display = view.tracks[0]!.displays[0] as LinearGraphDisplayModel
+  display.pane.startRenderingBackend(fakeRenderer())
+  await wait(SETTLE_MS)
+  expect(cuts).toHaveLength(1)
+  expect(cuts[0]!.region).toMatchObject({ start: 1_000_000, end: 1_060_000 })
+})
+
 test('the track is as tall as its rows, up to the configured height', async () => {
   const { display, pane } = await shownGraph()
   expect(display.height).toBe(pane.canvasHeight)
@@ -385,6 +427,16 @@ test('a launch that states one pane prop takes the rest from the config', async
   expect(display.pane.hostPlacesX).toBe(true)
 })
 
+test('a GBZ track cuts for the lanes it names', async () => {
+  const { view } = createEnvironment()
+  view.zoomTo(60_000 / WIDTH_PX)
+  view.scrollTo(1_000_000 / view.bpPerPx)
+  view.showTrack('walks')
+  const display = view.tracks[0]!.displays[0] as LinearGraphDisplayModel
+  expect(display.type).toBe('LinearGraphDisplay')
+  expect(display.pane.subgraphHaplotypes).toEqual(['HG1.1', 'HG2.1'])
+})
+
 test('the track menu offers the layouts, colours and the settings dialog', async () => {
   const { display } = await shownGraph()
   const labels = display

package/src/LinearGraphDisplay/components/LinearGraphDisplay.tsx

@@ -29,6 +29,7 @@ const LinearGraphDisplay = observer(function LinearGraphDisplay({
       data-cut-tier={pane.cutTier}
       data-recuts={pane.recuts}
       data-node-count={pane.hasGraph ? pane.nodeCount : undefined}
+      data-loading={pane.isLoading ? '' : undefined}
       style={{
         position: 'relative',
         width: pane.width,

package/src/LinearGraphDisplay/model.ts

@@ -12,6 +12,7 @@ import { COLOR_SCHEMES } from '../GraphGenomeView/colorSchemes'
 import { isLinearHost } from '../GraphGenomeView/host'
 import { LAYOUT_MODES } from '../GraphGenomeView/layoutModes'
 import paneModelFactory from '../GraphGenomeView/model'
+import { trackLanes } from '../launchSubgraph/subgraphTracks'
 
 import type { LinearGraphDisplayConfigModel } from './configSchema'
 import type { MenuItem } from '@jbrowse/core/ui'
@@ -141,6 +142,31 @@ export function stateModelFactory(configSchema: LinearGraphDisplayConfigModel) {
                   },
                 ]
               : []),
+            ...(pane.layoutMode === 'walkrows' && pane.repeatChoices.length > 0
+              ? [
+                  {
+                    label: 'Repeat',
+                    subMenu: [
+                      {
+                        type: 'radio' as const,
+                        label: 'Whole window',
+                        checked: pane.repeatKey === '',
+                        onClick: () => {
+                          pane.setRepeatKey('')
+                        },
+                      },
+                      ...pane.repeatChoices.map(({ key, name, unit }) => ({
+                        type: 'radio' as const,
+                        label: `${name} · ${unit.toLocaleString()} bp unit`,
+                        checked: pane.repeatKey === key,
+                        onClick: () => {
+                          pane.setRepeatKey(key)
+                        },
+                      })),
+                    ],
+                  },
+                ]
+              : []),
             ...(pane.hostPlacesX
               ? []
               : [
@@ -233,6 +259,16 @@ export function stateModelFactory(configSchema: LinearGraphDisplayConfigModel) {
           const { pane } = self
           self.applyConfig()
           pane.adoptTrack(self.trackId)
+          // A GBZ track cuts for the lanes it names, as its lanes display
+          // draws them, unless a launch or a reader picked others.
+          if (
+            pane.subgraphHaplotypes === undefined &&
+            self.adapterConfig.type === 'GbzBaseSyntenyAdapter'
+          ) {
+            pane.setSubgraphHaplotypes(
+              trackLanes(self.parentTrack.configuration),
+            )
+          }
           pane.startHosting()
           addDisposer(
             self,

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.0.2'
+export const version = '4.0.4'

package/dist/chunks/AddTrackWorkflow-TPCKXM2H.js

@@ -1,2 +0,0 @@
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n=[...t.entries()].sort(([a,i],[l,f])=>Tt(i,f)||K(a,l)).map(([a])=>a),o=n.length;for(let a of n){let i=t.get(a);for(let l of e.get(a)??[])t.has(l)||(t.set(l,{at:i.at,side:1,hops:i.hops+1}),n.push(l))}let r=new Set(n.slice(o)),s=new Set;for(let a of r){if(s.has(a))continue;let{at:i}=t.get(a),l=[a];s.add(a);let f=!0;for(let d of l){let{hops:u}=t.get(d),c=!0,m=!1;for(let p of e.get(d)??[]){let h=t.get(p);h.at===i&&r.has(p)?(c&&=h.hops<=u,s.has(p)||(s.add(p),l.push(p))):h.at!==i&&(m||=h.at<i,f&&=h.at<i)}f&&=!c||m}if(f)for(let d of l){let u=t.get(d);t.set(d,{...u,side:-1,hops:-u.hops})}}}function lo(e){let t=new Set(e.nodes.map(s=>s.id)),n=new Map;for(let s of e.edges)!t.has(s.from)||!t.has(s.to)||((n.get(s.from)??n.set(s.from,[]).get(s.from)).push(s.to),(n.get(s.to)??n.set(s.to,[]).get(s.to)).push(s.from));let o=e.nodes.filter(S).sort((s,a)=>K(s.stable.start,a.stable.start)||K(s.name,a.name)),r=new Map;return io(e,o).forEach((s,a)=>{r.set(s,{at:a,side:0,hops:0})}),co(n,r),r}function 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