jbrowse-plugin-graphgenomeviewer 4.2.0 → 4.4.0

package/src/GraphGenomeView/model.ts

@@ -40,6 +40,11 @@ import {
 } from '@jbrowse/bandage-core/layout/walkRowDraw'
 import { walkRowsExtent } from '@jbrowse/bandage-core/layout/walkRowLayout'
 import { walkRows } from '@jbrowse/bandage-core/layout/walkRows'
+import {
+  segmentAt,
+  stripMarks,
+  walkStripFrame,
+} from '@jbrowse/bandage-core/layout/walkStrip'
 import {
   LAYOUT_MODES,
   LAYOUT_MODE_VALUES,
@@ -298,6 +303,22 @@ const VIEWPORT_PANES_BUILT = 1
 // How many walk rows read their haplotype's genes, the first rows down
 const WALK_GENE_ROWS = 40
 
+// The rows a sample filter keeps, in the order it names them
+function filterSamples<R extends { sample: string; label: string }>(
+  rows: R[],
+  samples: string[] | undefined,
+) {
+  return samples
+    ? rows
+        .filter(r => samples.includes(r.sample))
+        .sort(
+          (a, b) =>
+            samples.indexOf(a.sample) - samples.indexOf(b.sample) ||
+            a.label.localeCompare(b.label),
+        )
+    : rows
+}
+
 // What the canvas draws under the tube map, whose ink is all TubeMapOverlay's
 const EMPTY_BATCH: RenderBatch = {
   nodeStrokes: [],
@@ -494,7 +515,7 @@ export function GraphPaneMixin() {
         // with a label that opens it. Off by default: on a base-level cut
         // every SNP's halo is a blob.
         showBubbles: types.optional(types.boolean, false),
-        showDeletionEdges: types.optional(types.boolean, false),
+        showDeletionEdges: types.optional(types.boolean, true),
         // The session's genes drawn onto the backbone: exons along the nodes
         // that carry them, names pinned at their midpoints. See genes/.
         showGenes: types.optional(types.boolean, true),
@@ -517,6 +538,9 @@ export function GraphPaneMixin() {
         // Samples whose walks the walk rows show, by the name before the
         // haplotype number; undefined shows every walk the cut holds.
         walkRowSamples: types.maybe(types.frozen<string[]>()),
+        // Walk rows in a strip under a layout that draws nodes, linked to the
+        // drawing: a node's passes tick each bar, a bar's point lights its node
+        walkStrip: types.optional(types.boolean, false),
         // Walks lifted out of the drawing, each a layer with a lane of its own
         // and the rest fading, coloured by the encoding it states or by the
         // default one. See walkEncoding.ts. Empty lifts none.
@@ -622,6 +646,8 @@ export function GraphPaneMixin() {
       // whether the pointer is over this pane, whose own hit test then says
       // what it is on
       pointerInPane: false,
+      // the strip point the pointer is over, which lights its node above
+      stripHover: null as { row: string; offset: number } | null,
       hoveredEdge: null as number | null,
       selectedNode: null as string | null,
       viewportDirty: 0,
@@ -966,6 +992,9 @@ export function GraphPaneMixin() {
       get alleleDeletions() {
         return self.layoutResult?.alleleDeletions ?? []
       },
+      get deletionRoutes() {
+        return self.layoutResult?.deletionRoutes
+      },
       // Whether the current layout states y in screen px rather than in the same
       // units as x (LayoutResult.pixelRows). Everything that has to put the two
       // axes in one expression reads this through scaleX/scaleY.
@@ -1157,16 +1186,7 @@ export function GraphPaneMixin() {
         if (!bars) {
           return undefined
         }
-        const samples = self.walkRowSamples
-        const rows = samples
-          ? bars.rows
-              .filter(r => samples.includes(r.sample))
-              .sort(
-                (a, b) =>
-                  samples.indexOf(a.sample) - samples.indexOf(b.sample) ||
-                  a.label.localeCompare(b.label),
-              )
-          : bars.rows
+        const rows = filterSamples(bars.rows, self.walkRowSamples)
         const [reference, ...paired] = withCalls(
           [bars.reference, ...rows],
           repeat?.calls,
@@ -1527,12 +1547,163 @@ export function GraphPaneMixin() {
       },
     }))
     .views(self => ({
-      // The gene reads walk rows need: for each row whose haplotype
+      // The contributors a view can actually be opened on: those naming an
+      // assembly this session has loaded. Every strain of an E. coli pangenome
+      // demo is its own assembly, so all of them resolve; an HPRC graph names
+      // hundreds of haplotypes that no session loads, so only the reference
+      // does.
+      get launchableAssemblies() {
+        return resolveContributors(
+          withReferenceRegion(self.contributingAssemblies, self.graphRegion),
+          self.assemblyResolver,
+        )
+      },
+      // Whether there is a linear view this graph may draw a highlight into —
+      // the paired one, or the session's only one on the reference assembly.
+      // Read by the node menu, which offers the item only when it would land
+      // somewhere.
+      get canHighlightInLinearView() {
+        const region = self.graphRegion
+        return (
+          region !== undefined &&
+          linearViewTarget({
+            views: [...getSession(self).views],
+            connectedViewId: self.connectedViewId,
+            assemblyName: region.assemblyName,
+          }) !== undefined
+        )
+      },
+      // Where one node can be opened: on its own assembly, and on the reference
+      // the graph was cut against. Both are padded to a readable window — a
+      // base-level allele is a few bp, and a linear view framed on exactly that
+      // shows no context at all.
+      nodeLaunchTargets(nodeId: string) {
+        const node = self.nodeById?.get(nodeId)
+        const own = node ? nodeOwnLocation(node) : undefined
+        const ownAssembly = own
+          ? resolveLocationAssembly(self.assemblyResolver, own)
+          : undefined
+        const region = self.graphRegion
+        const nodeById = self.nodeById
+        const neighbors = self.nodeNeighbors
+        const span =
+          region && nodeById && neighbors
+            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })
+            : undefined
+        const onReference =
+          region && span
+            ? {
+                sample: region.assemblyName,
+                haplotype: undefined,
+                refName: region.refName,
+                ...span,
+              }
+            : undefined
+        return {
+          own:
+            own && ownAssembly
+              ? { location: paddedLocation(own), assembly: ownAssembly }
+              : undefined,
+          reference:
+            region && onReference
+              ? {
+                  location: paddedLocation(onReference),
+                  assembly: region.assemblyName,
+                }
+              : undefined,
+          // Unpadded: a mark is of the node, the same span its hover band
+          // draws. The padding above is room to read a view opened on it.
+          highlight:
+            region && onReference
+              ? { location: onReference, assembly: region.assemblyName }
+              : undefined,
+        }
+      },
+    }))
+    .views(self => ({
+      // The linear view this pane draws inside, when a display hosts it: x is
+      // that view's window and the cut is re-made when the window leaves it.
+      // A pane that is a view of its own has none.
+      get host(): LinearHost | undefined {
+        let view: unknown
+        try {
+          view = getContainingView(self)
+        } catch {
+          return undefined
+        }
+        return isLinearHost(view) ? view : undefined
+      },
+    }))
+    .views(self => ({
+      // Whether the strip of walk rows sits under the drawing: asked for, on a
+      // standalone view whose layout draws nodes, for a graph with walks, and
+      // not while a bubble is popped
+      get walkStripShown() {
+        return (
+          self.walkStrip &&
+          !self.host &&
+          self.modeDrawsNodes &&
+          !self.layoutResult?.tubeMap &&
+          !self.walkRowBars &&
+          self.popStack.length === 0 &&
+          (self.graph?.paths?.length ?? 0) > 1
+        )
+      },
+      // The strip's rows: the cut's, with the sample filter and no repeat
+      // pick, which the Repeat menu only offers in walk rows
+      get walkStripRows() {
+        const graph = self.graph
+        const bars =
+          graph && this.walkStripShown
+            ? walkRows(graph, self.graphRegion)
+            : undefined
+        return bars
+          ? { ...bars, rows: filterSamples(bars.rows, self.walkRowSamples) }
+          : undefined
+      },
+      get walkStripFrame() {
+        const bars = this.walkStripRows
+        if (!bars) {
+          return undefined
+        }
+        return walkStripFrame(bars, { width: self.paneWidth })
+      },
+      // Whether a cut must follow every snarl a walk leaves the window by, so
+      // walks come back whole: walk rows measure them, and so does the strip
+      get cutsWholeWalks() {
+        return (
+          layoutModeByValue(self.chosenLayoutMode).wholeWalks ||
+          (self.walkStrip && !self.host)
+        )
+      },
+      // Where each walk passes the hovered node, or the selected one
+      get walkStripMarks() {
+        const bars = this.walkStripRows
+        const id = self.hoveredNode ?? self.selectedNode
+        const node = id === null ? undefined : self.nodeById?.get(id)
+        return bars && node && self.graph
+          ? stripMarks(self.graph, [bars.reference, ...bars.rows], node)
+          : []
+      },
+      // Where the drawing has the node a strip point lights, for the ring
+      // that finds it in a hairball
+      get walkStripLocator() {
+        const id = self.stripHover ? self.hoveredNode : null
+        return id === null
+          ? undefined
+          : nodeAnchor(self.nodePositions?.[id], p => ({
+              x: p.x * self.scaleX + self.translateX,
+              y: p.y * self.scaleY + self.translateY,
+            }))
+      },
+    }))
+    .views(self => ({
+      // The gene reads walk rows need, as the layout or the strip: for each row whose haplotype
       // (`HG00097#1`) names an assembly with a gene track, that track over the
       // span of its own contig the row's bar covers. The first WALK_GENE_ROWS
       // such rows are read, and the rest counted for the key.
       get walkGeneReads() {
-        const bars = self.walkRowBars
+        const bars = self.walkRowBars ?? self.walkStripRows
         if (!bars || !self.showGenes) {
           return undefined
         }
@@ -1608,8 +1779,7 @@ export function GraphPaneMixin() {
       // open: the span of its contig the bar covers, on the session assembly
       // its haplotype names (the cut's own assembly for the reference row).
       // The label names the haplotype when no assembly is loaded for it.
-      walkRowLaunchTarget(index: number) {
-        const bars = self.walkRowBars
+      walkRowLaunchTarget(index: number, bars = self.walkRowBars) {
         const row = bars ? [bars.reference, ...bars.rows][index] : undefined
         if (!row?.axis) {
           return undefined
@@ -1639,7 +1809,7 @@ export function GraphPaneMixin() {
       // Each row's genes as offsets along its bar: the reference row's from
       // the backbone's gene track, every other row's from its own assembly
       get walkRowGenes() {
-        const bars = self.walkRowBars
+        const bars = self.walkRowBars ?? self.walkStripRows
         if (!bars || !self.showGenes) {
           return undefined
         }
@@ -1652,94 +1822,6 @@ export function GraphPaneMixin() {
           : undefined
       },
     }))
-    .views(self => ({
-      // The contributors a view can actually be opened on: those naming an
-      // assembly this session has loaded. Every strain of an E. coli pangenome
-      // demo is its own assembly, so all of them resolve; an HPRC graph names
-      // hundreds of haplotypes that no session loads, so only the reference
-      // does.
-      get launchableAssemblies() {
-        return resolveContributors(
-          withReferenceRegion(self.contributingAssemblies, self.graphRegion),
-          self.assemblyResolver,
-        )
-      },
-      // Whether there is a linear view this graph may draw a highlight into —
-      // the paired one, or the session's only one on the reference assembly.
-      // Read by the node menu, which offers the item only when it would land
-      // somewhere.
-      get canHighlightInLinearView() {
-        const region = self.graphRegion
-        return (
-          region !== undefined &&
-          linearViewTarget({
-            views: [...getSession(self).views],
-            connectedViewId: self.connectedViewId,
-            assemblyName: region.assemblyName,
-          }) !== undefined
-        )
-      },
-      // Where one node can be opened: on its own assembly, and on the reference
-      // the graph was cut against. Both are padded to a readable window — a
-      // base-level allele is a few bp, and a linear view framed on exactly that
-      // shows no context at all.
-      nodeLaunchTargets(nodeId: string) {
-        const node = self.nodeById?.get(nodeId)
-        const own = node ? nodeOwnLocation(node) : undefined
-        const ownAssembly = own
-          ? resolveLocationAssembly(self.assemblyResolver, own)
-          : undefined
-        const region = self.graphRegion
-        const nodeById = self.nodeById
-        const neighbors = self.nodeNeighbors
-        const span =
-          region && nodeById && neighbors
-            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })
-            : undefined
-        const onReference =
-          region && span
-            ? {
-                sample: region.assemblyName,
-                haplotype: undefined,
-                refName: region.refName,
-                ...span,
-              }
-            : undefined
-        return {
-          own:
-            own && ownAssembly
-              ? { location: paddedLocation(own), assembly: ownAssembly }
-              : undefined,
-          reference:
-            region && onReference
-              ? {
-                  location: paddedLocation(onReference),
-                  assembly: region.assemblyName,
-                }
-              : undefined,
-          // Unpadded: a mark is of the node, the same span its hover band
-          // draws. The padding above is room to read a view opened on it.
-          highlight:
-            region && onReference
-              ? { location: onReference, assembly: region.assemblyName }
-              : undefined,
-        }
-      },
-    }))
-    .views(self => ({
-      // The linear view this pane draws inside, when a display hosts it: x is
-      // that view's window and the cut is re-made when the window leaves it.
-      // A pane that is a view of its own has none.
-      get host(): LinearHost | undefined {
-        let view: unknown
-        try {
-          view = getContainingView(self)
-        } catch {
-          return undefined
-        }
-        return isLinearHost(view) ? view : undefined
-      },
-    }))
     .views(self => ({
       // Whether the drawing's x is reference bp a host can place. Walk rows
       // put the backbone at its bp too, but their bars are lengths, so the
@@ -2212,6 +2294,7 @@ export function GraphPaneMixin() {
           // `deletions` is and for the same reason — see `referenceRamp`.
           referenceRamp: self.referenceRamp,
           deletions: self.deletionEdgeIndexes,
+          deletionRoutes: self.deletionRoutes,
           hiddenEdges: self.hiddenEdgeIndexes,
           // passed so the shared edge-curve cache can tell a drag from a pan
           version: self.positionsVersion,
@@ -2301,6 +2384,7 @@ export function GraphPaneMixin() {
               ? self.walkLayers.map(l => (l.color ? l : l.walk))
               : undefined,
             facet: self.walkLayers.length > 1 ? self.facetSpec : undefined,
+            walkStrip: self.walkStripShown || undefined,
             width: self.paneWidth,
             height: self.paneCeiling,
             colorScheme: self.chosenColorScheme,
@@ -2319,7 +2403,7 @@ export function GraphPaneMixin() {
             : `${layoutModeByValue(self.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`
       },
       // The drawing as a standalone SVG, fitted, with its genes, its lifted
-      // walks' keys and facet panels; see figureSvg
+      // walks' keys, facet panels and the strip of walk rows; see figureSvg
       figure() {
         const { graph, layoutResult } = self
         return graph && layoutResult && !this.figureUnavailable
@@ -2340,6 +2424,11 @@ export function GraphPaneMixin() {
               walkRows: self.walkRowBars,
               rowGenes: self.walkRowGenes,
               rowGeneGaps: self.walkRowGeneGaps,
+              walkStrip: self.walkStripRows && {
+                rows: self.walkStripRows,
+                rowGenes: self.walkRowGenes,
+                rowGeneGaps: self.walkRowGeneGaps,
+              },
               spec: this.figureSpec(),
             })
           : undefined
@@ -2598,6 +2687,26 @@ export function GraphPaneMixin() {
       setPointerInPane(inside: boolean) {
         self.pointerInPane = inside
       },
+      setWalkStrip(show: boolean) {
+        self.walkStrip = show
+        self.stripHover = null
+      },
+      // The pointer over the strip: the node under it becomes the hovered
+      // node, so the drawing, the tooltip and a linked linear view follow
+      setStripHover(hover: { row: string; offset: number } | null) {
+        self.stripHover = hover
+        const bars = self.walkStripRows
+        const frame = self.walkStripFrame
+        const row =
+          hover && bars
+            ? [bars.reference, ...bars.rows].find(r => r.name === hover.row)
+            : undefined
+        const node =
+          row && frame && self.graph
+            ? segmentAt(self.graph, row, hover!.offset, frame.scaleX)
+            : undefined
+        self.hoveredNode = node ?? null
+      },
       setLegendSize(size: { width: number; height: number }) {
         self.legendSize = size
       },
@@ -4039,6 +4148,18 @@ export function GraphPaneMixin() {
               self.setShowGenes(!self.showGenes)
             },
           },
+          ...(self.modeDrawsNodes && (self.graph?.paths?.length ?? 0) > 1
+            ? [
+                {
+                  type: 'checkbox' as const,
+                  label: 'Walk rows under the graph',
+                  checked: self.walkStrip,
+                  onClick: () => {
+                    self.setWalkStrip(!self.walkStrip)
+                  },
+                },
+              ]
+            : []),
           ...(self.referenceStripApplies
             ? [
                 {

package/src/GraphGenomeView/viewModel.ts

@@ -2,7 +2,8 @@ import { layoutModeByValue } from '@jbrowse/bandage-core/layoutModes'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { getSession } from '@jbrowse/core/util'
-import { types } from '@jbrowse/mobx-state-tree'
+import { addDisposer, types } from '@jbrowse/mobx-state-tree'
+import { reaction } from 'mobx'
 
 import { GraphPaneMixin, MAX_GRAPH_REGION_BP, formatSpanBp } from './model'
 import {
@@ -134,7 +135,7 @@ export default function stateModelFactory() {
             return self.cutSubgraph(readConfObject(track, 'adapter'), region, {
               hops: self.subgraphContext,
               haplotypes: self.subgraphHaplotypes,
-              ...(layoutModeByValue(self.chosenLayoutMode).wholeWalks
+              ...(self.cutsWholeWalks
                 ? { snarls: 'overlapping' as const }
                 : {}),
             })
@@ -147,13 +148,14 @@ export default function stateModelFactory() {
       retryLoad() {
         void self.load()
       },
-      // walk rows measures whole walks, which a GBZ cut only follows when
-      // asked, so entering or leaving it cuts the track again
+      // walk rows, and the strip of them under a node layout, measure whole
+      // walks, which a GBZ cut only follows when asked, so a change in whether
+      // the drawing needs them cuts the track again; the strip's toggle does
+      // the same (afterAttach)
       switchLayout(mode: LayoutModeValue) {
-        const from = layoutModeByValue(self.chosenLayoutMode)
+        const before = self.cutsWholeWalks
         self.setLayoutMode(mode)
-        return self.loadedTrackId &&
-          layoutModeByValue(mode).wholeWalks !== from.wholeWalks
+        return self.loadedTrackId && self.cutsWholeWalks !== before
           ? self.load()
           : self.recomputeLayout()
       },
@@ -164,6 +166,20 @@ export default function stateModelFactory() {
         if (!self.graph) {
           void self.load()
         }
+        addDisposer(
+          self,
+          reaction(
+            () => self.walkStrip,
+            () => {
+              if (
+                self.loadedTrackId &&
+                !layoutModeByValue(self.chosenLayoutMode).wholeWalks
+              ) {
+                void self.load()
+              }
+            },
+          ),
+        )
       },
     }))
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.2.0'
+export const version = '4.4.0'

package/dist/chunks/chunk-ECKLYJWP.js

@@ -1,2 +0,0 @@
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