jbrowse-plugin-graphgenomeviewer 4.0.4 → 4.0.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "4.0.4",
+  "version": "4.0.6",
   "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/GraphGenomeView/host.test.ts

@@ -0,0 +1,41 @@
+import { cutHolds, hostCut } from './host'
+
+import type { HostWindow } from './host'
+
+const window: HostWindow = {
+  refName: 'chr1',
+  assemblyName: 'hg38',
+  start: 1_000_000.4,
+  end: 1_060_000.4,
+  bpPerPx: 60,
+  span: 60_000,
+  regionStart: 0,
+  regionEnd: 10_000_000,
+}
+
+test('a cut with margins is the window plus a window-width each side, under the cap', () => {
+  expect(hostCut(window, Infinity)).toEqual({
+    refName: 'chr1',
+    assemblyName: 'hg38',
+    start: 940_000,
+    end: 1_120_001,
+  })
+  const capped = hostCut(window, 66_000)
+  expect(capped.end - capped.start).toBeLessThanOrEqual(66_000)
+  expect(cutHolds(capped, window)).toBe(true)
+})
+
+test('a cut without margins is the window alone, and holds for that window only', () => {
+  const cut = hostCut(window, Infinity, false)
+  expect(cut).toMatchObject({ start: 1_000_000, end: 1_060_001 })
+  expect(cutHolds(cut, window, false)).toBe(true)
+  expect(
+    cutHolds(cut, { ...window, start: 1_010_000, end: 1_070_000 }, false),
+  ).toBe(false)
+})
+
+test('a cut trimmed to a cap the window fills still holds that window', () => {
+  const cut = hostCut(window, 60_000)
+  expect(cut.end - cut.start).toBeLessThanOrEqual(60_000)
+  expect(cutHolds(cut, window)).toBe(true)
+})

package/src/GraphGenomeView/host.ts

@@ -114,11 +114,20 @@ export function hostCut(
   const margin = margins
     ? Math.max(0, Math.min(window.span, (capBp - visible) / 2))
     : 0
+  let start = Math.max(window.regionStart, Math.floor(window.start - margin))
+  let end = Math.min(window.regionEnd, Math.ceil(window.end + margin))
+  // Rounding outward can put a cut a base or two past the cap, which the load
+  // refuses whole; trim it back rather than lose the cut.
+  const over = end - start - capBp
+  if (over > 0) {
+    start += Math.floor(over / 2)
+    end -= Math.ceil(over / 2)
+  }
   return {
     refName: window.refName,
     assemblyName: window.assemblyName,
-    start: Math.max(window.regionStart, Math.floor(window.start - margin)),
-    end: Math.min(window.regionEnd, Math.ceil(window.end + margin)),
+    start,
+    end,
   }
 }
 
@@ -135,8 +144,9 @@ export function cutHolds(
   ) {
     return false
   }
+  // to the base, since a cut trimmed to its cap can end a base inside the window
   if (margins) {
-    return cut.start <= window.start && window.end <= cut.end
+    return cut.start <= window.start + 1 && window.end <= cut.end + 1
   }
   const exact = hostCut(window, Infinity, false)
   return (

package/src/GraphGenomeView/layoutModes.ts

@@ -39,10 +39,11 @@ 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 a cut for this mode carries a window-width margin each side, to
+  // pan over before the next cut. A mode that draws a picture of the window
+  // — force, ordered, and walk rows, whose bars are lengths through it — is
+  // cut to the window alone.
+  cutMargins: 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
@@ -67,7 +68,7 @@ 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,
+    cutMargins: true,
     available: hasBackbone,
     drawsLocally: hasBackbone,
   },
@@ -77,7 +78,7 @@ 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,
+    cutMargins: true,
     available: hasAlleles,
     drawsLocally: hasAlleles,
   },
@@ -87,7 +88,7 @@ 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,
+    cutMargins: false,
     available: hasWalks,
     drawsLocally: hasWalks,
   },
@@ -97,7 +98,7 @@ 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,
+    cutMargins: false,
     available: hasBackbone,
     drawsLocally: hasBackbone,
   },
@@ -107,7 +108,7 @@ 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,
+    cutMargins: true,
     available: hasBackbone,
     drawsLocally: hasBackbone,
   },
@@ -116,7 +117,7 @@ export const LAYOUT_MODES = [
     label: FORCE_LAYOUT_LABEL,
     description: 'OGDF FMMM, via the external Bandage engine.',
     run: () => undefined,
-    referenceAxis: false,
+    cutMargins: false,
     available: () => true,
     drawsLocally: () => false,
   },

package/src/GraphGenomeView/model.ts

@@ -2508,7 +2508,7 @@ export default function stateModelFactory() {
       // 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 margins = layoutModeByValue(self.layoutMode).cutMargins
         const above = self.coarseAboveBpPerPx
         const tier =
           above !== undefined && seen.bpPerPx > above ? 'coarse' : 'fine'

package/src/hoverSync/graphViewHighlights.test.ts

@@ -22,6 +22,27 @@ test('a graph view launched from this linear view contributes its highlight', ()
 
 const linearView = (id: string) => ({ id, type: 'LinearGenomeView' })
 
+test("a graph pane inside this linear view's own track contributes its highlight", () => {
+  const view = {
+    ...linearView('lgv1'),
+    tracks: [
+      {
+        displays: [
+          {
+            id: 'display1',
+            type: 'LinearGraphDisplay',
+            pane: { type: 'GraphGenomeView', hoverHighlight: HIGHLIGHT },
+          },
+        ],
+      },
+    ],
+  }
+  expect(graphViewHighlights([view], 'lgv1')).toEqual([
+    { key: 'display1', region: HIGHLIGHT },
+  ])
+  expect(graphViewHighlights([view], 'lgv2')).toEqual([])
+})
+
 test('a graph view launched from a different linear view is ignored', () => {
   expect(
     graphViewHighlights(

package/src/hoverSync/graphViewHighlights.ts

@@ -89,6 +89,21 @@ function isOnAssembly(
 // The highlights a linear view should draw for the graph views connected to it.
 // Reads `session.views` structurally: the members it needs are declared by
 // GraphGenomeView, not by the AbstractViewModel the session array is typed as.
+// The graph panes inside a linear view's own tracks, connected to it by where
+// they sit.
+function trackPanes(view: Record<string, unknown>) {
+  const tracks = Array.isArray(view.tracks) ? view.tracks : []
+  return tracks.flatMap((track: unknown) => {
+    const displays =
+      isRecord(track) && Array.isArray(track.displays) ? track.displays : []
+    return displays.flatMap((display: unknown) =>
+      isRecord(display) && isRecord(display.pane)
+        ? [{ key: display.id, pane: display.pane }]
+        : [],
+    )
+  })
+}
+
 export function graphViewHighlights(
   views: unknown[],
   linearViewId: string,
@@ -101,6 +116,17 @@ export function graphViewHighlights(
     withRows(views).map(view => (isRecord(view) ? view.id : undefined)),
   )
   for (const view of views) {
+    if (isRecord(view) && view.id === linearViewId) {
+      for (const { key, pane } of trackPanes(view)) {
+        const region = readRegion(pane.hoverHighlight)
+        if (region && isOnAssembly(region, linearAssemblyNames)) {
+          highlights.push({
+            key: typeof key === 'string' ? key : 'graph-track',
+            region,
+          })
+        }
+      }
+    }
     if (
       isRecord(view) &&
       view.type === 'GraphGenomeView' &&

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.0.4'
+export const version = '4.0.6'