jbrowse-plugin-graphgenomeviewer 4.0.21 → 4.0.22

package/dist/chunks/chunk-JXSDDOKD.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/core/data_adapters/dataAdapterCache", "global-externals:@jbrowse/core/pluggableElementTypes", "global-externals:@mui/material/SvgIcon", "global-externals:@jbrowse/core/configuration", "global-externals:@jbrowse/core/util/colorBits", "global-externals:mobx", "global-externals:@jbrowse/render-core/canvas2dUtils", "global-externals:@jbrowse/render-core/RenderLifecycleMixin", "../../src/GetGraphReads.ts", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/utils/createSvgIcon.mjs", "../../packages/core/src/util/geometry.ts", "../../packages/core/src/deletionEdges.ts", "../../packages/core/src/layout/mergeRuns.ts", "../../packages/core/src/overlayLabels.ts", "../../packages/core/src/graphLabels.ts", "../../packages/core/src/labelLayout.ts", "../../packages/core/src/walkEncoding.ts", "../../packages/core/src/renderer/GeometryBuilder.ts", "../../packages/core/src/renderer/colorBits.ts", "../../packages/core/src/referenceSpan.ts", "../../packages/core/src/util/edgeCurves.ts", "../../src/launchFromGraph/contributors.ts", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/CompareArrows.mjs", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/HighlightAlt.mjs", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/LineStyle.mjs", "../../src/launchFromGraph/graphMenuItems.ts", "../../packages/core/src/tubeMap/reads.ts", "../../packages/core/src/alleleProjection/projectAlleles.ts", "../../packages/core/src/layout/placeOffReference.ts", "../../packages/core/src/layout/anchoredLayout.ts", "../../packages/core/src/layout/orderedLayout.ts", "../../packages/core/src/layout/sampleRowLayout.ts", "../../node_modules/.pnpm/@gmod+tubemap-core@0.1.0/node_modules/@gmod/tubemap-core/dist/types.js", "../../node_modules/.pnpm/@gmod+tubemap-core@0.1.0/node_modules/@gmod/tubemap-core/dist/layout.js", "../../node_modules/.pnpm/@gmod+tubemap-core@0.1.0/node_modules/@gmod/tubemap-core/dist/geometry.js", "../../packages/core/src/layout/tubeMapLayout.ts", "../../packages/core/src/layout/walkRows.ts", "../../packages/core/src/layout/walkRowLayout.ts", "../../packages/core/src/layoutModes.ts", "../../packages/core/src/bubbles/classifyBubble.ts", "../../packages/core/src/gfa-core/gfaParser.ts", "../../packages/core/src/gfa/gfaConverter.ts", "../../packages/core/src/layout/orientToReference.ts", "../../packages/core/src/layout/referenceSeeds.ts", "../../packages/core/src/pipeline.ts", "../../packages/core/src/referenceStrip.ts", "../../packages/core/src/tubeMap/axis.ts", "../../packages/core/src/tubeMap/connectors.ts", "../../packages/core/src/tubeMap/deviations.ts", "../../packages/core/src/tubeMap/mismatches.ts", "../../packages/core/src/tubeMap/draw.ts", "../../packages/core/src/tubeMap/genes.ts", "../../packages/core/src/viewport.ts", "../../src/GraphGenomeView/host.ts", "../../src/GraphGenomeView/repeats/walkCalls.ts", "../../packages/core/src/bubbles/bubbleHalos.ts", "../../packages/core/src/bubbles/bubblesFromGraph.ts", "../../packages/core/src/bubbles/popBubble.ts", "../../packages/core/src/genes/genePins.ts", "../../packages/core/src/layout/trimToWindow.ts", "../../packages/core/src/tubeMap/coarsen.ts", "../../packages/core/src/tubeMap/warp.ts", "../../packages/core/src/tubeMap/frame.ts", "../../packages/core/src/walkHighlight.ts", "../../src/GraphGenomeView/model.ts", "../../src/GraphGenomeView/genes/geneFeatures.ts", "../../src/GraphGenomeView/lenientEnum.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../src/hoverSync/lgvHover.ts", "../../src/launchFromGraph/launchFromGraph.ts", "../../src/launchFromGraph/linearViewTarget.ts", "../../src/launchFromGraph/launchTracks.ts", "../../src/launchFromGraph/syntenyTracks.ts", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/Settings.mjs"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/data_adapters/dataAdapterCache\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes\"];", "module.exports = JBrowseExports[\"@mui/material/SvgIcon\"];", "module.exports = JBrowseExports[\"@jbrowse/core/configuration\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util/colorBits\"];", "module.exports = JBrowseExports[\"mobx\"];", "module.exports = JBrowseExports[\"@jbrowse/render-core/canvas2dUtils\"];", "module.exports = JBrowseExports[\"@jbrowse/render-core/RenderLifecycleMixin\"];", "import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport { RpcMethodType } from '@jbrowse/core/pluggableElementTypes'\n\nimport type { GafReads } from './gaf/gafFile'\nimport type { RpcExecuteArgs } from '@jbrowse/core/rpc/RpcRegistry'\n\n// The reads aligned over a cut's segments, from an adapter whose config names\n// a GAF (GbzBaseSyntenyAdapter's `readsLocation`). Asked after the cut is\n// parsed, because the segment names are what a GAF index is keyed by.\n\nexport interface GetGraphReadsArgs {\n  adapterConfig: Record<string, unknown>\n  nodeNames: string[]\n}\n\ndeclare module '@jbrowse/core/rpc/RpcRegistry' {\n  interface RpcRegistry {\n    GetGraphReads: {\n      args: GetGraphReadsArgs\n      return: GafReads\n    }\n  }\n}\n\ninterface ReadsAdapter {\n  getReads(\n    nodeNames: string[],\n    opts: { signal?: AbortSignal },\n  ): Promise<GafReads>\n}\n\nfunction isReadsAdapter(adapter: object): adapter is ReadsAdapter {\n  return (\n    'getReads' in adapter &&\n    typeof (adapter as ReadsAdapter).getReads === 'function'\n  )\n}\n\nconst isNamed = (location: unknown) =>\n  typeof location === 'object' &&\n  location !== null &&\n  Object.entries(location).some(\n    ([key, value]) =>\n      ['uri', 'localPath', 'blobId'].includes(key) &&\n      typeof value === 'string' &&\n      value !== '',\n  )\n\n// Whether an adapter config as written names reads, so a graph without them\n// makes no round trip to ask\nexport function namesReads(adapterConfig: Record<string, unknown>) {\n  return (\n    (typeof adapterConfig.reads === 'string' && adapterConfig.reads !== '') ||\n    isNamed(adapterConfig.readsLocation)\n  )\n}\n\nexport default class GetGraphReads extends RpcMethodType<'GetGraphReads'> {\n  name = 'GetGraphReads' as const\n\n  async execute(args: RpcExecuteArgs<'GetGraphReads'>) {\n    const { adapterConfig, nodeNames, sessionId, signal } = args\n    const { dataAdapter } = await getAdapter(\n      this.pluginManager,\n      sessionId,\n      adapterConfig,\n    )\n    return isReadsAdapter(dataAdapter)\n      ? dataAdapter.getReads(nodeNames, { signal })\n      : { records: [], total: 0 }\n  }\n}\n", "'use client';\n\nexport { createSvgIcon as default } from '@mui/material/SvgIcon';", "import { ROW_HEIGHT_PX } from '../layout/rowSpacing'\n\nimport type { GraphEdge, NodeSegment } from '../types'\n\n// An SVG path along a polyline, rounded to two decimals.\nexport function svgPath(points: NodeSegment[]) {\n  const round = (v: number) => Math.round(v * 100) / 100\n  return points\n    .map((p, i) => `${i ? 'L' : 'M'}${round(p.x)},${round(p.y)}`)\n    .join('')\n}\n\nexport function projectLine(\n  x1: number,\n  y1: number,\n  x2: number,\n  y2: number,\n  distance: number,\n): [number, number] {\n  const d = Math.hypot(y2 - y1, x2 - x1)\n  if (d === 0) {\n    return [x2, y2]\n  }\n  const vx = (x2 - x1) / d\n  const vy = (y2 - y1) / d\n  return [x2 + distance * vx, y2 + distance * vy]\n}\n\nexport interface BezierCurve {\n  x0: number\n  y0: number\n  cx0: number\n  cy0: number\n  cx1: number\n  cy1: number\n  x1: number\n  y1: number\n}\n\n// The cubic's own point at t, by de Casteljau. Used to place a label ON a curve\n// rather than at a position derived from what the curve was supposed to be: an\n// apex recomputed from the bulge and the endpoints agrees with the drawing only\n// as long as both derive it the same way, and they did not.\nexport function curvePointAt(c: BezierCurve, t: number) {\n  const u = 1 - t\n  const a = u * u * u\n  const b = 3 * u * u * t\n  const d = 3 * u * t * t\n  const e = t * t * t\n  return {\n    x: a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1,\n    y: a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1,\n  }\n}\n\n// Halfway along a run of curves, measured in curves rather than in arc length: a\n// run is one cubic for every edge this is used on (computeEdgeCurves returns a\n// single curve except for self-loops), so the two agree where it matters and the\n// cheap version cannot be wrong by more than a curve.\nexport function curveMidpoint(curves: BezierCurve[]) {\n  const mid = curves[Math.floor(curves.length / 2)]\n  return mid ? curvePointAt(mid, 0.5) : undefined\n}\n\n// Control-polygon bounds, which contain the curve. Used to ask how big a drawn\n// edge is on screen, where the answer has to hold under any layout: a bulge\n// alone is in whatever units the layout works in.\nexport function curveBounds(curves: BezierCurve[]) {\n  let minX = Infinity\n  let minY = Infinity\n  let maxX = -Infinity\n  let maxY = -Infinity\n  for (const c of curves) {\n    minX = Math.min(minX, c.x0, c.cx0, c.cx1, c.x1)\n    maxX = Math.max(maxX, c.x0, c.cx0, c.cx1, c.x1)\n    minY = Math.min(minY, c.y0, c.cy0, c.cy1, c.y1)\n    maxY = Math.max(maxY, c.y0, c.cy0, c.cy1, c.y1)\n  }\n  return { minX, minY, maxX, maxY }\n}\n\n// The sub-curve over [t0, t1], exact rather than sampled: de Casteljau twice,\n// which is what keeps a dashed curve on the same path as the solid one.\nfunction subCurve(c: BezierCurve, t0: number, t1: number): BezierCurve {\n  const p0 = curvePointAt(c, t0)\n  const p1 = curvePointAt(c, t1)\n  // The Hermite tangents of the whole cubic at t0/t1, scaled by the sub-span,\n  // are the sub-curve's control-point offsets.\n  const dt = (t1 - t0) / 3\n  const d0 = curveTangentAt(c, t0)\n  const d1 = curveTangentAt(c, t1)\n  return {\n    x0: p0.x,\n    y0: p0.y,\n    cx0: p0.x + d0.x * dt,\n    cy0: p0.y + d0.y * dt,\n    cx1: p1.x - d1.x * dt,\n    cy1: p1.y - d1.y * dt,\n    x1: p1.x,\n    y1: p1.y,\n  }\n}\n\nfunction curveTangentAt(c: BezierCurve, t: number) {\n  const u = 1 - t\n  const a = 3 * u * u\n  const b = 6 * u * t\n  const d = 3 * t * t\n  return {\n    x: a * (c.cx0 - c.x0) + b * (c.cx1 - c.cx0) + d * (c.x1 - c.cx1),\n    y: a * (c.cy0 - c.y0) + b * (c.cy1 - c.cy0) + d * (c.y1 - c.cy1),\n  }\n}\n\n// A curve chopped into dashes, each its own run so a renderer strokes them as\n// separate paths. Dashing is geometry here rather than a stroke style because\n// the two backends do not share one: Canvas2D has setLineDash, a GPU backend\n// tessellating these curves does not, and a dash pattern that only exists in one\n// of them is a figure that changes with the renderer.\n//\n// `dashWorld` is the period in layout units, so a caller passing screen px over\n// the current scale gets dashes of a constant on-screen size.\nexport function dashCurves(\n  curves: BezierCurve[],\n  dashWorld: number,\n): BezierCurve[][] {\n  const out: BezierCurve[][] = []\n  for (const c of curves) {\n    // Control-polygon length overestimates the arc, which errs toward more\n    // dashes rather than toward a curve that reads as solid.\n    const polyLen =\n      Math.hypot(c.cx0 - c.x0, c.cy0 - c.y0) +\n      Math.hypot(c.cx1 - c.cx0, c.cy1 - c.cy0) +\n      Math.hypot(c.x1 - c.cx1, c.y1 - c.cy1)\n    // Odd, so a dash sits at each end of the curve and the arc reads as\n    // attached to both nodes rather than floating between them.\n    const spans = Math.max(3, Math.round(polyLen / dashWorld) | 1)\n    for (let i = 0; i < spans; i += 2) {\n      out.push([subCurve(c, i / spans, (i + 1) / spans)])\n    }\n  }\n  return out\n}\n\nexport function translateCurves(\n  curves: BezierCurve[],\n  dx: number,\n  dy: number,\n): BezierCurve[] {\n  const out: BezierCurve[] = new Array(curves.length)\n  for (let i = 0; i < curves.length; i++) {\n    const c = curves[i]!\n    out[i] = {\n      x0: c.x0 + dx,\n      y0: c.y0 + dy,\n      cx0: c.cx0 + dx,\n      cy0: c.cy0 + dy,\n      cx1: c.cx1 + dx,\n      cy1: c.cy1 + dy,\n      x1: c.x1 + dx,\n      y1: c.y1 + dy,\n    }\n  }\n  return out\n}\n\ntype Side = 'start' | 'end'\n\n// The attachment point, and the point just inside the node from it \u2014 which is\n// what gives the outward tangent, so a curve leaves along the node it leaves\n// rather than straight at its partner.\nfunction attachment(segments: NodeSegment[], side: Side) {\n  const last = segments.length - 1\n  return side === 'end'\n    ? { at: segments[last]!, inward: segments[last - 1] }\n    : { at: segments[0]!, inward: segments[1] }\n}\n\n// Ceilings on how far a control point runs along its own node's direction: a\n// fraction of the separation the curve has to cover, so endpoints that nearly\n// touch cannot fold the cubic back over itself, and an absolute cap so a\n// graph-wide edge does not sprout a huge hook.\nconst TANGENT_SPAN_FACTOR = 0.5\nconst MAX_TANGENT = 80\n\n// Which drawn end of each node the edge joins.\n//\n// A link states the orientation it reads each segment in, but a node is drawn\n// in whatever direction its layout placed it \u2014 reference-forward on the\n// anchored rows, run-sweep order off them, arbitrary under FMMM \u2014 and nothing\n// records that direction, so the strands cannot be turned into drawn ends. What\n// the drawing itself says is which ends face each other, so that is what is\n// read: each node attaches at whichever of its two ends is nearer the OTHER\n// node's drawn span, with the forward reading (leave the from-node's end, enter\n// the to-node's start) winning a tie.\n//\n// Nearer to the span, not to the other attachment point. A bubble's two nodes\n// usually overlap in x, and there the distances to a point differ by a hair\n// that says nothing \u2014 enough to hang a node's entry and exit edges off the same\n// end, which draws them crossed. Overlapping spans give both ends distance 0,\n// i.e. a tie, and the tie is what keeps such a bubble forward. What survives is\n// the case the rule is for: `L s381 - s2087 +` then `L s2087 + s378 -` is\n// NCTC86 crossing its locus right to left, and joining last-point to\n// first-point regardless drew the second link 7 kb backwards across the segment\n// it rejoins \u2014 the long X in pangenome/rgfa_subgraph_launch. There the spans do\n// not overlap and the far end loses by 7 kb. Pinned by bubbleCrossing.test.ts.\nfunction spanOf(segments: NodeSegment[]) {\n  let min = Infinity\n  let max = -Infinity\n  for (const s of segments) {\n    min = Math.min(min, s.x)\n    max = Math.max(max, s.x)\n  }\n  return { min, max }\n}\n\nfunction distanceToSpan(x: number, span: { min: number; max: number }) {\n  return Math.max(0, span.min - x, x - span.max)\n}\n\nfunction facingSide(\n  segments: NodeSegment[],\n  other: { min: number; max: number },\n  tieBreak: Side,\n): Side {\n  const startGap = distanceToSpan(segments[0]!.x, other)\n  const endGap = distanceToSpan(segments[segments.length - 1]!.x, other)\n  return startGap === endGap ? tieBreak : startGap < endGap ? 'start' : 'end'\n}\n\nfunction facingSides(fromSegments: NodeSegment[], toSegments: NodeSegment[]) {\n  return {\n    from: facingSide(fromSegments, spanOf(toSegments), 'end'),\n    to: facingSide(toSegments, spanOf(fromSegments), 'start'),\n  }\n}\n\n// A cubic whose two control points both sit `b` off the chord reaches 3b/4 at\n// its midpoint: (P0 + 3C0 + 3C1 + P1)/8 with the endpoints on the chord.\nconst APEX_FRACTION = 0.75\n// How far past the run the apex goes, so the arc reads as passing AROUND the\n// reference it skips rather than through it.\nconst BOW_CLEARANCE = 1.15\n\n// How far, and which way, to bow an arc so that it encloses the run of nodes it\n// bypasses -- the deletion case. Both come from where that run actually lies\n// relative to this edge's own chord, which is the only thing that can answer\n// either question.\n//\n// It used to be a magnitude alone, `0.35 * the summed drawn length of the\n// bypassed nodes`, bowed to a hardcoded side. Both halves were wrong, and the\n// amylase 94.2 kb arc showed each: summed path length is not spatial reach, so a\n// chain that snakes (as an FMMM chain does) sizes an arc far past where its own\n// nodes are; and the fixed sign is a coin flip on which side those nodes fell.\n// Measured on that figure, the bypassed run reached 739 units to one side of a\n// 16-unit chord while the arc bowed 719 units to the other -- a balloon in empty\n// space, enclosing nothing, beside the run it was supposed to name. The two arcs\n// in the same figure that read correctly were the two whose runs happened to\n// fall on the hardcoded side.\n//\n// Sign comes from the FARTHEST point rather than the mean, because the arc has\n// to clear the whole run, not most of it.\n//\n// The magnitude needs two terms, and the perpendicular one alone is not enough:\n// in an anchored layout the backbone is a straight line, so a bypassed run lies\n// exactly ON the chord, reaches nowhere off it, and an arc sized by clearance\n// alone collapses back into the stub at a joint this exists to prevent. That is\n// every anchored figure, and it is what the unit tests caught. So the run's\n// extent ALONG the chord carries the collinear case, at the same 0.35 the old\n// rule used, which is what keeps those figures where they are; clearance takes\n// over exactly when the run has gone somewhere the arc would otherwise miss.\nconst ALONG_FRACTION = 0.35\n// The most bow a deletion gets in a ROW layout, in screen px, which is what y\n// already is there.\n//\n// A cap rather than a smaller fraction, because the fraction is the part that is\n// wrong: `span * ALONG_FRACTION` scales the bow with the amount of reference\n// skipped, and in a row layout the arc's own SPAN states that exactly \u2014 its two\n// feet are the deletion's two coordinates on the backbone \u2014 while the label\n// prints it in bp. So the bow carries no information there, and letting it grow\n// with the event turns a big deletion into a loop enclosing a dozen unrelated\n// nodes and edges while a small one stays the flat tie under the backbone that\n// reads correctly. Reported as \"the dashed lines frankly look weird for the\n// 'deletion'\" on `pangenome/hprc_cfhr_deletion`, whose 84.7 kb arc dived 5.5\n// rows into the rank rows while its 28.6 kb and 11.2 kb neighbours sat just\n// under the reference row: four deletions in one frame, drawn as four different\n// kinds of mark.\n//\n// Three rows: enough to clear the reference row's own tube and to read as an arc\n// across several hundred px of backbone, not enough to reach the second rank\n// row. The isotropic layout is NOT capped \u2014 there the run the arc bows around is\n// scattered rather than collinear, so the bow is what makes the bubble's two\n// arms comparable, which is the clearance term's whole job.\nconst MAX_ROW_BOW_PX = 3 * ROW_HEIGHT_PX\n\nexport function bowAround(\n  p1x: number,\n  p1y: number,\n  p2x: number,\n  p2y: number,\n  toward: NodeSegment[],\n  // Ceiling on the returned magnitude, in the units this function is working in.\n  // Undefined leaves the bow uncapped; see MAX_ROW_BOW_PX.\n  maxBow?: number,\n) {\n  const chord = Math.hypot(p2x - p1x, p2y - p1y)\n  const ux = chord === 0 ? 1 : (p2x - p1x) / chord\n  const uy = chord === 0 ? 0 : (p2y - p1y) / chord\n  let reach = 0\n  let minAlong = Infinity\n  let maxAlong = -Infinity\n  for (const p of toward) {\n    const dx = p.x - p1x\n    const dy = p.y - p1y\n    const perp = dx * -uy + dy * ux\n    if (Math.abs(perp) > Math.abs(reach)) {\n      reach = perp\n    }\n    const along = dx * ux + dy * uy\n    minAlong = Math.min(minAlong, along)\n    maxAlong = Math.max(maxAlong, along)\n  }\n  const span = toward.length ? maxAlong - minAlong : 0\n  const uncapped = Math.max(\n    (Math.abs(reach) * BOW_CLEARANCE) / APEX_FRACTION,\n    span * ALONG_FRACTION,\n  )\n  const size = maxBow === undefined ? uncapped : Math.min(uncapped, maxBow)\n  // A run that sits on the chord has no side of its own; the arc keeps the one\n  // it has always taken there, so a collinear layout draws exactly as before.\n  return reach < 0 ? -size : size\n}\n\n// How the drawing maps layout units to screen pixels, both axes together.\n//\n// **One object rather than two arguments, and that is the point of it.** Every\n// measurement in this file \u2014 a chord length, a tangent projection, a bow \u2014 mixes\n// x and y in one `hypot`, so it needs both. On a row layout they differ: x is\n// reference bp and y is a row pitch in screen px (LayoutResult.pixelRows), and\n// the same drop of 20 is a fifth of a pane one way and twenty bases the other.\n// Passing them separately meant a caller could pass one and default the other,\n// which compiles, draws a wrong picture, and reports nothing. Three callers\n// build these curves \u2014 the drawing, the hit index, and the label that rides them\n// \u2014 and they have to agree; a pair that cannot be half-passed is what makes that\n// structural instead of remembered.\n//\n// The two numbers are the model's own `scaleX`/`scaleY`, handed over unchanged\n// rather than pre-divided, so nothing downstream can combine an x scale from one\n// moment with a y scale from another.\nexport interface AxisScale {\n  scaleX: number\n  scaleY: number\n  // Whether the layout's y is already SCREEN PIXELS \u2014 true for the two row\n  // layouts, false for the isotropic simulation (see rowSpacing.ts and the\n  // model's axisScaleOf). It rides here rather than being threaded to each\n  // caller because the three functions that build a deletion's curve \u2014 the\n  // drawing, the hit index and the label that rides it \u2014 all take an `axis` and\n  // all three have to agree about the bow; a fourth parameter only some of them\n  // passed is how a label and its arc end up in different corners of the\n  // drawing, which has happened here before.\n  //\n  // NOT derivable as `scaleY !== scaleX`: on a row layout scaleY is pinned to 1\n  // and scaleX is the zoom, so the two coincide at one zoom level and anything\n  // keyed on the difference would silently stop applying there.\n  pixelRows?: boolean\n}\n\n// y in x units: what makes the two axes comparable. 1 on an isotropic layout\n// (FMMM), where every number below is exactly what it was.\nexport function yToXOf({ scaleX, scaleY }: AxisScale) {\n  return scaleY / scaleX\n}\n\n// How far apart two adjacent path ribbons run, in world x units.\nexport const PATH_RIBBON_SPACING = 3\n\n// A polyline's overall direction in DRAWN space, or undefined when it has none.\nfunction drawnDirection(\n  a: { x: number; y: number },\n  b: { x: number; y: number },\n  yToX: number,\n) {\n  const dx = b.x - a.x\n  const dy = (b.y - a.y) * yToX\n  const len = Math.hypot(dx, dy)\n  return len === 0 ? undefined : { x: dx / len, y: dy / len }\n}\n\n// Where each of an edge's path ribbons is drawn, as an offset from the edge\n// itself, in world units \u2014 the one derivation of it, because three callers need\n// the same answer: the geometry that draws the ribbons, the spatial index that\n// bounds them and the hit test that measures against them. Two of those already\n// held their own copy of these four lines.\n//\n// The fan runs perpendicular to the edge, and the perpendicular is taken in\n// DRAWN space: on a row layout x is bp and y is screen px, so a perpendicular\n// taken from the raw coordinates is perpendicular to nothing on screen. `yToX`\n// converts before the direction is measured and the y component is converted\n// back, the same round trip `pointNormalsOf` makes for a node's own outline. On\n// an isotropic layout `yToX` is 1 and this is the arithmetic it always did.\n//\n// **Two abutting nodes have no chord to be perpendicular to, and in an anchored\n// layout that is every backbone link rather than a corner case**: consecutive\n// segments meet at exactly one point, so the chord is zero-length. Both callers\n// used to give up there, which left the whole backbone chain with no edge\n// geometry at all whenever `drawPaths` was on \u2014 no curve, no arrowhead, nothing\n// to hover \u2014 and the abutting nodes hid it. A node's own drawn direction answers\n// what the chord cannot, and for a backbone running along x it fans the ribbons\n// across the row, which is where they belong.\nexport function pathRibbonOffsets(\n  fromSegments: NodeSegment[],\n  toSegments: NodeSegment[],\n  count: number,\n  axis: AxisScale,\n  spacing = PATH_RIBBON_SPACING,\n) {\n  const yToX = yToXOf(axis)\n  const dir = drawnDirection(\n    fromSegments[fromSegments.length - 1]!,\n    toSegments[0]!,\n    yToX,\n  ) ??\n    drawnDirection(fromSegments[0]!, fromSegments.at(-1)!, yToX) ??\n    drawnDirection(toSegments[0]!, toSegments.at(-1)!, yToX) ?? { x: 1, y: 0 }\n  const offsets: { x: number; y: number }[] = []\n  for (let i = 0; i < count; i++) {\n    const distance = (i - (count - 1) / 2) * spacing\n    offsets.push({ x: -dir.y * distance, y: (dir.x * distance) / yToX })\n  }\n  return offsets\n}\n\nfunction scaleYOf(points: NodeSegment[], yToX: number) {\n  return points.map(p => ({ x: p.x, y: p.y * yToX }))\n}\n\nfunction unscaleYOf(curves: BezierCurve[], yToX: number) {\n  for (const c of curves) {\n    c.y0 /= yToX\n    c.cy0 /= yToX\n    c.cy1 /= yToX\n    c.y1 /= yToX\n  }\n  return curves\n}\n\n// How far a self-loop or hairpin reaches off its node, in layout units: half\n// the node's drawn length, held between two screen sizes. Bandage uses a fixed\n// `edgeLength` in scene units, which fits one layout's units and no other's: a\n// fixed 50 units was 50 kb of drawing under the engine (1 unit per kb) and 50\n// bp on an anchored row, and under the engine it drew a 100 px oval around a\n// node a tenth that long.\nconst SELF_LOOP_MIN_PX = 12\nconst SELF_LOOP_MAX_PX = 40\n\nfunction selfLoopReach(segments: NodeSegment[], scale: number) {\n  let length = 0\n  for (let i = 1; i < segments.length; i++) {\n    length += Math.hypot(\n      segments[i]!.x - segments[i - 1]!.x,\n      segments[i]!.y - segments[i - 1]!.y,\n    )\n  }\n  const nodePx = length * scale\n  const reachPx = Math.min(\n    SELF_LOOP_MAX_PX,\n    Math.max(SELF_LOOP_MIN_PX, nodePx / 2),\n  )\n  return reachPx / Math.max(scale, Number.EPSILON)\n}\n\n// How an edge joins a node to itself: `true` is a loop from the end back\n// round to the start, a Side is a hairpin that leaves that end and returns to\n// it, and `false` is an edge between two nodes.\nexport type SelfLink = boolean | Side\n\n// `L a + a -` leaves a's end and arrives at the start of a read backwards,\n// which is a's end again, and `L a - a +` is the same at its start. Drawn end\n// to start like a cycle it named the wrong ends, which is the difference\n// between an inverted repeat and a tandem one. Bandage draws the same case\n// with its own path (makeSpecialPathConnectingNodeToReverseComplement).\nexport function selfLinkOf(edge: GraphEdge): SelfLink {\n  if (edge.from !== edge.to) {\n    return false\n  }\n  return edge.fromStrand && edge.toStrand && edge.fromStrand !== edge.toStrand\n    ? edge.fromStrand === '+'\n      ? 'end'\n      : 'start'\n    : true\n}\n\n// A teardrop off one end, after Bandage's: it leaves along the node, turns at\n// the apex and comes back in on itself.\nfunction hairpinCurves(\n  attach: { at: NodeSegment; inward: NodeSegment | undefined },\n  reach: number,\n  offsetX: number,\n  offsetY: number,\n): BezierCurve[] {\n  const { at, inward } = attach\n  const dx = inward ? at.x - inward.x : 1\n  const dy = inward ? at.y - inward.y : 0\n  const len = Math.hypot(dx, dy) || 1\n  const ux = dx / len\n  const uy = dy / len\n  const px = at.x + offsetX\n  const py = at.y + offsetY\n  const nearX = px + (ux * reach) / 3\n  const nearY = py + (uy * reach) / 3\n  const apexX = px + ux * reach\n  const apexY = py + uy * reach\n  const sideX = (-uy * reach) / 2\n  const sideY = (ux * reach) / 2\n  return [\n    {\n      x0: px,\n      y0: py,\n      cx0: nearX,\n      cy0: nearY,\n      cx1: apexX + sideX,\n      cy1: apexY + sideY,\n      x1: apexX,\n      y1: apexY,\n    },\n    {\n      x0: apexX,\n      y0: apexY,\n      cx0: apexX - sideX,\n      cy0: apexY - sideY,\n      cx1: nearX,\n      cy1: nearY,\n      x1: px,\n      y1: py,\n    },\n  ]\n}\n\nexport function computeEdgeCurves(\n  fromSegments: NodeSegment[],\n  toSegments: NodeSegment[],\n  selfLink: SelfLink,\n  offsetX: number,\n  offsetY: number,\n  axis: AxisScale,\n  // The nodes this edge bypasses, for a deletion; empty for every other edge.\n  // Given them, the curve bows around them.\n  //\n  // Topologically a deletion is a bubble whose reference arm is a run of long\n  // nodes and whose own arm is a bare link, so at the engine's 5-unit edge\n  // length it collapses into a stub at a joint and the one event a graph shows\n  // better than a linear view is invisible. Bowing it around that run is what\n  // makes the two arms comparable, which is what a reader has to see to read it\n  // as an alternative route.\n  //\n  // Taken as nodes rather than as a precomputed number because the chord is\n  // needed to turn them into one, and only this function knows the chord -- it\n  // picks the attachment ends. Three callers build this curve (the drawing, the\n  // hit index and the label that rides it) and a second derivation of it is a\n  // second thing to keep in step; that is exactly how the label and the arc once\n  // came out in different corners of the drawing.\n  bypassed: NodeSegment[] = [],\n  // Only the recursion below passes this: the cap belongs to the layout, so it\n  // is read off `axis` at the top level and handed down already converted into\n  // the isotropic body's units.\n  maxBowIn?: number,\n): BezierCurve[] {\n  const scale = axis.scaleX\n  const yToX = yToXOf(axis)\n  const maxBow = maxBowIn ?? (axis.pixelRows ? MAX_ROW_BOW_PX : undefined)\n  if (yToX !== 1) {\n    // Recur once with y already in x units, then put the answer back. The\n    // isotropic body below is the only implementation, so an anisotropic\n    // drawing cannot drift from the one every force-directed figure uses.\n    //\n    // It costs three small arrays per edge, which was worth measuring before\n    // being clever about: over 8,000 deletion-bearing edges \u2014 the top of the\n    // range this view draws at all \u2014 the whole pass is 1.9 ms isotropic against\n    // 2.8 ms here, once per debounced rebuild, against the ~9 ms of geometry the\n    // toolbar already reports. Inlining the conversion would buy 0.9 ms and cost\n    // the single implementation, so it is not done.\n    return unscaleYOf(\n      computeEdgeCurves(\n        scaleYOf(fromSegments, yToX),\n        scaleYOf(toSegments, yToX),\n        selfLink,\n        offsetX,\n        offsetY * yToX,\n        { scaleX: scale, scaleY: scale },\n        scaleYOf(bypassed, yToX),\n        // the cap is a y measure and the body works in x units, so it converts\n        // with everything else that crosses this boundary\n        maxBow === undefined ? undefined : maxBow * yToX,\n      ),\n      yToX,\n    )\n  }\n  if (typeof selfLink === 'string') {\n    return hairpinCurves(\n      attachment(fromSegments, selfLink),\n      selfLoopReach(fromSegments, scale),\n      offsetX,\n      offsetY,\n    )\n  }\n  const sides = selfLink\n    ? { from: 'end' as Side, to: 'start' as Side }\n    : facingSides(fromSegments, toSegments)\n  const fromAttach = attachment(fromSegments, sides.from)\n  const toAttach = attachment(toSegments, sides.to)\n  const fromEnd = fromAttach.at\n  const toStart = toAttach.at\n\n  const p1x = fromEnd.x + offsetX\n  const p1y = fromEnd.y + offsetY\n  const p2x = toStart.x + offsetX\n  const p2y = toStart.y + offsetY\n\n  if (selfLink) {\n    let segDirX = 1\n    let segDirY = 0\n    if (fromAttach.inward) {\n      const dx = fromEnd.x - fromAttach.inward.x\n      const dy = fromEnd.y - fromAttach.inward.y\n      const len = Math.hypot(dx, dy)\n      if (len > 0) {\n        segDirX = dx / len\n        segDirY = dy / len\n      }\n    }\n\n    const ext = selfLoopReach(fromSegments, scale)\n    const perpX = -segDirY\n    const perpY = segDirX\n    const midX = (fromEnd.x + toStart.x) / 2 + offsetX + perpX * ext\n    const midY = (fromEnd.y + toStart.y) / 2 + offsetY + perpY * ext\n    const cp1x = p1x + segDirX * ext\n    const cp1y = p1y + segDirY * ext\n    const cp2x = p2x - segDirX * ext\n    const cp2y = p2y - segDirY * ext\n\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cp1x,\n        cy0: cp1y,\n        cx1: cp1x + perpX * ext,\n        cy1: cp1y + perpY * ext,\n        x1: midX,\n        y1: midY,\n      },\n      {\n        x0: midX,\n        y0: midY,\n        cx0: cp2x + perpX * ext,\n        cy0: cp2y + perpY * ext,\n        cx1: cp2x,\n        cy1: cp2y,\n        x1: p2x,\n        y1: p2y,\n      },\n    ]\n  } else {\n    // The point just inside each node from where the edge attaches, so\n    // projectLine extends OUTWARD from the node. A node drawn as a single point\n    // has no direction of its own; mirroring the chord through the attachment\n    // leaves it pointing at its partner, i.e. a straight leader.\n    const fromPrev = fromAttach.inward ?? {\n      x: fromEnd.x - (toStart.x - fromEnd.x),\n      y: fromEnd.y - (toStart.y - fromEnd.y),\n    }\n    const toNext = toAttach.inward ?? {\n      x: toStart.x - (fromEnd.x - toStart.x),\n      y: toStart.y - (fromEnd.y - toStart.y),\n    }\n\n    const dist = Math.hypot(p2x - p1x, p2y - p1y)\n    // Each control point leaves along its OWN node's direction, so the tangent\n    // extension may only run as far as the other endpoint actually lies in that\n    // direction. Sizing it by the whole separation instead cannot work on an\n    // anchored layout, where the separation is mostly the row drop: both edges\n    // of a bubble then leave sideways and come back, and the pair draws as a\n    // crossed bowtie rather than as a bubble (pinned by bubbleCrossing.test.ts,\n    // which fails on 17 of the pggb subgraph's alleles under a flat\n    // `dist * 0.35`). Projecting the separation onto the tangent is rotation\n    // invariant, so a force-directed layout, whose edges do run along their\n    // nodes, is unchanged; and it is clamped at 0, so an edge that doubles back\n    // gets a straight leader instead of a loop.\n    const tangentProj = (\n      prev: { x: number; y: number },\n      at: { x: number; y: number },\n      towardX: number,\n      towardY: number,\n    ) => {\n      const dx = at.x - prev.x\n      const dy = at.y - prev.y\n      const len = Math.hypot(dx, dy)\n      const along = len === 0 ? 0 : (towardX * dx + towardY * dy) / len\n      return Math.max(\n        0,\n        Math.min(dist * TANGENT_SPAN_FACTOR, MAX_TANGENT, along * 0.5),\n      )\n    }\n    const towardToX = toStart.x - fromEnd.x\n    const towardToY = toStart.y - fromEnd.y\n    const [cx1, cy1] = projectLine(\n      fromPrev.x,\n      fromPrev.y,\n      fromEnd.x,\n      fromEnd.y,\n      tangentProj(fromPrev, fromEnd, towardToX, towardToY),\n    )\n    const [cx2, cy2] = projectLine(\n      toNext.x,\n      toNext.y,\n      toStart.x,\n      toStart.y,\n      tangentProj(toNext, toStart, -towardToX, -towardToY),\n    )\n\n    // Perpendicular to the chord, so the bow is symmetric about it, and spread\n    // the two control points APART along it. Perpendicular alone draws a hairpin\n    // whenever the bulge exceeds the chord \u2014 which is the normal case for a\n    // deletion, whose endpoints the simulation leaves adjacent however much\n    // reference it skips \u2014 and a hairpin reads as a stray line rather than as a\n    // route. The along-chord spread opens it into an arch.\n    //\n    // The spread takes the MAGNITUDE, not the signed bulge: it decides how open\n    // the arch is, not which way it faces, and letting it flip swaps the two\n    // control points past each other and folds the cubic into a cusp.\n    const bulge = bypassed.length\n      ? bowAround(p1x, p1y, p2x, p2y, bypassed, maxBow)\n      : 0\n    const chordLen = dist === 0 ? 1 : dist\n    const ux = (p2x - p1x) / chordLen\n    const uy = (p2y - p1y) / chordLen\n    const bulgeX = -uy * bulge\n    const bulgeY = ux * bulge\n    const spreadX = ux * Math.abs(bulge)\n    const spreadY = uy * Math.abs(bulge)\n\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cx1 + offsetX + bulgeX - spreadX,\n        cy0: cy1 + offsetY + bulgeY - spreadY,\n        cx1: cx2 + offsetX + bulgeX + spreadX,\n        cy1: cy2 + offsetY + bulgeY + spreadY,\n        x1: p2x,\n        y1: p2y,\n      },\n    ]\n  }\n}\n", "import { firstNodeAtOrAfter, isBackbone } from './anchoredNodes'\nimport { computeEdgeCurves } from './util/geometry'\n\nimport type { AnchoredNode } from './anchoredNodes'\nimport type { Graph, GraphEdge } from './types'\nimport type { AxisScale } from './util/geometry'\n\n// A deletion is the one kind of variation this view could not draw, and the\n// reason is structural rather than cosmetic: extra sequence is a *node*, so it\n// gets a tube, a colour and a hover. Missing sequence is an **edge** \u2014 a link\n// from one backbone segment to another that is not its neighbour \u2014 and every\n// edge in the drawing was painted the same grey, so the graph said nothing about\n// the events a linear view is worst at.\n//\n// It needs no new data. Both endpoints of such an edge carry rGFA coordinates on\n// the same stable sequence, so the bp the haplotype skips is the gap between\n// them, and the whole classification is arithmetic on SN/SO plus the segment\n// lengths already parsed. `agent-docs/reference/PANGENOME_GRAPHS.md` in\n// jbrowse-components measured what this finds on the hosted HPRC graph: 8\n// deletions in the 200 kb MHC class II window against 78 attributed alleles, 1\n// in the 70 kb C4 window.\n//\n// Two things this deliberately does not do:\n//\n//   - it does not attribute the deletion to a haplotype. A backbone-to-backbone\n//     skip has GRCh38 at both ends, so there is no `SN` naming a donor, and the\n//     same reference note records why: a deletion only carries a donor when it\n//     also carries novel sequence, and then it is not a clean deletion any more.\n//   - it does not treat a same-position link as a deletion. Adjacent backbone\n//     segments abut (gap 0) and a substitution's flanks can overlap by the\n//     aligned bases, so only a positive gap counts.\n\n// A skip has to clear this to be drawn as a deletion. minigraph's SV-resolution\n// graph does not record anything smaller than tens of bp, so this is not a\n// biological threshold but a guard against calling a rounding artifact a\n// deletion \u2014 abutting segments are the common case and they must not light up.\nconst MIN_DELETION_BP = 1\n\nexport interface DeletionEdge {\n  // index into graph.edges, which is what the renderer keys its curve ranges by\n  edgeIndex: number\n  // the edge's own endpoints, so anything that needs the arc as it is DRAWN can\n  // rebuild it (deletionArcCurves) instead of approximating it from `bypassed`\n  from: string\n  to: string\n  refName: string\n  start: number\n  end: number\n  bp: number\n  // Backbone node ids whose reference interval lies inside the skipped span:\n  // the route a haplotype taking this edge does NOT take. A drawing sizes the\n  // deletion's arc off their drawn length so the two arms of the bubble are\n  // comparable; nothing else can supply that, because in a force layout the\n  // edge's own endpoints are wherever the simulation put them.\n  bypassed: string[]\n}\n\n// Where the backbone this deletion bypasses is drawn, as points. `bowAround`\n// turns them into how far and which way the arc bows; this only has to say which\n// points they are, and is shared so the geometry that draws the arc, the index\n// that hit-tests it and the overlay that labels it all bow around the same run.\nexport function bypassedPoints(\n  nodePositions: Record<string, { x: number; y: number }[]>,\n  bypassed: string[],\n) {\n  return bypassed.flatMap(id => nodePositions[id] ?? [])\n}\n\n// The deletion's arc exactly as the renderer draws it, for anything that has to\n// agree with the drawing: the label that rides it, and hit detection.\n//\n// This exists because the label used to be placed at an apex derived from the\n// BYPASSED nodes while the curve was drawn between the EDGE's endpoints. In an\n// anchored layout the bypassed run lies between the endpoints, so the two agreed\n// and the divergence was invisible; under FMMM the endpoints are wherever the\n// simulation left them and the bypassed run is elsewhere, so the words and the\n// arc they named came out in different corners of the drawing\n// (`pangenome/hprc_cfhr_deletion`, reviewed 2026-07-31). One function is the fix:\n// a second derivation of the same curve is a second thing to keep in step.\nexport function deletionArcCurves(\n  nodePositions: Record<string, { x: number; y: number }[]>,\n  deletion: DeletionEdge,\n  axis: AxisScale,\n) {\n  const from = nodePositions[deletion.from]\n  const to = nodePositions[deletion.to]\n  return from?.length && to?.length\n    ? computeEdgeCurves(\n        from,\n        to,\n        deletion.from === deletion.to,\n        0,\n        0,\n        axis,\n        bypassedPoints(nodePositions, deletion.bypassed),\n      )\n    : undefined\n}\n\n// The backbone by stable sequence, each sorted by start, so the run a deletion\n// bypasses is a slice rather than a scan. Filtering the whole backbone per\n// candidate edge is O(edges x backbone), which at the node budget this view\n// accepts (20,000) is hundreds of millions of comparisons for a pass that runs\n// once per graph.\nfunction backboneBySequence(graph: Graph) {\n  const bySequence = new Map<string, AnchoredNode[]>()\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const list = bySequence.get(node.stable.refName)\n      if (list) {\n        list.push(node)\n      } else {\n        bySequence.set(node.stable.refName, [node])\n      }\n    }\n  }\n  for (const list of bySequence.values()) {\n    list.sort((a, b) => a.stable.start - b.stable.start)\n  }\n  return bySequence\n}\n\n// Backbone nodes lying wholly inside [start, end) on `refName`. Sorted by\n// start, so the candidates are one contiguous run and the walk stops at the\n// first node starting past the end; only the upper bound still needs testing\n// per node, since a long node can start inside and finish outside.\nfunction bypassedNodes(\n  nodes: AnchoredNode[] | undefined,\n  start: number,\n  end: number,\n) {\n  const bypassed: string[] = []\n  if (nodes) {\n    for (let i = firstNodeAtOrAfter(nodes, start); i < nodes.length; i++) {\n      const node = nodes[i]!\n      if (node.stable.start >= end) {\n        break\n      }\n      if (node.stable.start + node.length <= end) {\n        bypassed.push(node.id)\n      }\n    }\n  }\n  return bypassed\n}\n\n// A link leaves the END of `from` as it reads it and arrives at the START of\n// `to`. Read the way the reference reads a node, its end is its right side, so\n// a link leaves `from` on the right when the two readings agree and arrives at\n// `to` on the left when they do.\n//\n// A deletion joins the right side of the left node to the left side of the\n// right one, from whichever strand the file states it: `L 1 + 3 +`, or the\n// same link as `L 3 - 1 -`. `L 3 + 1 +` joins the right side of the RIGHT node\n// to the left side of the left one, sequence read again, a duplication. A link\n// with one reading against the reference lands on a node's far side, an\n// inversion. Neither skips anything. Coordinates alone could not tell them\n// from a deletion: each was drawn as one, and hidden with them by default.\n//\n// A link stating no strands is judged by its coordinates, as all once were.\nfunction skipsBetween(\n  edge: GraphEdge,\n  from: AnchoredNode,\n  to: AnchoredNode,\n  forwards: boolean,\n) {\n  const { fromStrand, toStrand } = edge\n  if (fromStrand === undefined || toStrand === undefined) {\n    return true\n  }\n  const leavesRight = fromStrand === (from.stable.strand ?? '+')\n  const arrivesLeft = toStrand === (to.stable.strand ?? '+')\n  return forwards ? leavesRight && arrivesLeft : !leavesRight && !arrivesLeft\n}\n\n// Every edge that skips reference sequence, in graph.edges order.\nexport function deletionEdges(graph: Graph): DeletionEdge[] {\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const backbone = backboneBySequence(graph)\n  const found: DeletionEdge[] = []\n  for (let edgeIndex = 0; edgeIndex < graph.edges.length; edgeIndex++) {\n    const edge = graph.edges[edgeIndex]!\n    const from = byId.get(edge.from)\n    const to = byId.get(edge.to)\n    if (\n      from !== undefined &&\n      to !== undefined &&\n      isBackbone(from) &&\n      isBackbone(to) &&\n      from.stable.refName === to.stable.refName\n    ) {\n      // Which endpoint is upstream comes from the coordinates, since a file\n      // may state a link from either strand. Whether it SKIPS what lies\n      // between comes from its sides: a deletion leaves the right side of the\n      // left node and arrives at the left side of the right one.\n      const forwards = from.stable.start <= to.stable.start\n      const [left, right] = forwards ? [from, to] : [to, from]\n      const start = left.stable.start + left.length\n      const end = right.stable.start\n      const bp = end - start\n      if (bp >= MIN_DELETION_BP && skipsBetween(edge, from, to, forwards)) {\n        const refName = left.stable.refName\n        found.push({\n          edgeIndex,\n          from: edge.from,\n          to: edge.to,\n          refName,\n          start,\n          end,\n          bp,\n          bypassed: bypassedNodes(backbone.get(refName), start, end),\n        })\n      }\n    }\n  }\n  return found\n}\n", "import { isBackbone } from '../anchoredNodes'\n\nimport type { Graph, GraphEdge, GraphNode, NodeSegment } from '../types'\n\n// A base-level graph chops its sequence into short nodes at every variant and\n// every kilobase, so a cut of it is thousands of nodes strung in unbranching\n// runs. FMMM only needs the runs: each becomes one node, laid out as one\n// chain, and its positions are split back onto the members afterwards, so the\n// drawing, the hit index and the labels never see the merged graph.\n//\n// A node joins the run before it when the run's end side and the node's start\n// side each hold exactly one link, and it is that link read forward. Sides, not\n// in- and out-edges: a graph holds one node per segment, so `L a + b -` joins\n// b's END, and counting it as an in-edge of b both merged across it and handed\n// the engine a link attached at the wrong end. A self loop keeps its node alone.\n\nexport interface MergedRuns {\n  graph: Graph\n  // merged node id to the member ids in chain order; a run of one is absent\n  runs: Map<string, string[]>\n}\n\ntype Side = 'start' | 'end'\n\n// The strand a node's id carries, which is the one its drawn chain reads.\nfunction ownStrand(id: string) {\n  return id.endsWith('-') ? '-' : '+'\n}\n\nfunction flip(strand: '+' | '-') {\n  return strand === '+' ? '-' : '+'\n}\n\nfunction sidesOf(edge: GraphEdge) {\n  const from: Side =\n    (edge.fromStrand ?? ownStrand(edge.from)) === ownStrand(edge.from)\n      ? 'end'\n      : 'start'\n  const to: Side =\n    (edge.toStrand ?? ownStrand(edge.to)) === ownStrand(edge.to)\n      ? 'start'\n      : 'end'\n  return { from, to }\n}\n\nexport function mergeRuns(graph: Graph): MergedRuns {\n  const sides = graph.edges.map(sidesOf)\n  // node side -> indexes of the edges attached there\n  const at = new Map<string, number[]>()\n  const attach = (id: string, side: Side, ei: number) => {\n    const key = `${id}|${side}`\n    const list = at.get(key)\n    if (list) {\n      list.push(ei)\n    } else {\n      at.set(key, [ei])\n    }\n  }\n  graph.edges.forEach((edge, ei) => {\n    attach(edge.from, sides[ei]!.from, ei)\n    attach(edge.to, sides[ei]!.to, ei)\n  })\n  // the edge that carries node `a`'s run on into the next node, if one does\n  const joinAfter = (a: string) => {\n    const out = at.get(`${a}|end`)\n    if (out?.length !== 1) {\n      return undefined\n    }\n    const ei = out[0]!\n    const edge = graph.edges[ei]!\n    return edge.from === a &&\n      edge.to !== a &&\n      sides[ei]!.from === 'end' &&\n      sides[ei]!.to === 'start' &&\n      at.get(`${edge.to}|start`)?.length === 1\n      ? ei\n      : undefined\n  }\n  const joined = new Set<number>()\n  const runOf = new Map<string, string>()\n  const runs = new Map<string, string[]>()\n  for (const node of graph.nodes) {\n    const into = at.get(`${node.id}|start`)\n    const pred = into?.length === 1 ? graph.edges[into[0]!]!.from : undefined\n    if (\n      runOf.has(node.id) ||\n      (pred !== undefined && joinAfter(pred) === into![0])\n    ) {\n      continue\n    }\n    const run = [node.id]\n    for (;;) {\n      const ei = joinAfter(run.at(-1)!)\n      const next = ei === undefined ? undefined : graph.edges[ei]!.to\n      if (next === undefined || runOf.has(next)) {\n        break\n      }\n      joined.add(ei!)\n      run.push(next)\n    }\n    for (const id of run) {\n      runOf.set(id, node.id)\n    }\n    if (run.length > 1) {\n      runs.set(node.id, run)\n    }\n  }\n  // a cycle with no branch has no run start; the loop above never reached it\n  for (const node of graph.nodes) {\n    if (!runOf.has(node.id)) {\n      runOf.set(node.id, node.id)\n    }\n  }\n\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const nodes: GraphNode[] = []\n  for (const node of graph.nodes) {\n    if (runOf.get(node.id) !== node.id) {\n      continue\n    }\n    const run = runs.get(node.id)\n    if (!run) {\n      nodes.push(node)\n      continue\n    }\n    const members = run.map(id => byId.get(id)!)\n    const backbone = members.filter(isBackbone)\n    const first = backbone.length\n      ? backbone.reduce((a, b) => (a.stable.start <= b.stable.start ? a : b))\n      : members[0]!\n    nodes.push({\n      id: node.id,\n      name: node.name,\n      length: members.reduce((sum, n) => sum + n.length, 0),\n      depth: node.depth,\n      stable: first.stable,\n    })\n  }\n  // A link can only reach a run at its free ends, the first member's start and\n  // the last's end, since every inner side holds exactly the join. So a\n  // member's side is the run's side, and a flipped one crosses over as the\n  // strand opposite the run's own.\n  const seen = new Set<string>()\n  const edges: GraphEdge[] = []\n  graph.edges.forEach((edge, ei) => {\n    const from = runOf.get(edge.from)!\n    const to = runOf.get(edge.to)!\n    const side = sides[ei]!\n    const key = `${from}|${side.from}>${to}|${side.to}`\n    if (joined.has(ei) || seen.has(key)) {\n      return\n    }\n    seen.add(key)\n    edges.push({\n      from,\n      to,\n      ...(side.from === 'start' ? { fromStrand: flip(ownStrand(from)) } : {}),\n      ...(side.to === 'end' ? { toStrand: flip(ownStrand(to)) } : {}),\n    })\n  })\n  return {\n    graph: { ...graph, nodes, edges, paths: undefined, pathVisits: undefined },\n    runs,\n  }\n}\n\n// Each member takes the stretch of its run's polyline its weight entitles it\n// to, in chain order, with the shared points interpolated so the members abut.\nexport function splitRuns(\n  positions: Record<string, NodeSegment[]>,\n  runs: Map<string, string[]>,\n  weightOf: (id: string) => number,\n) {\n  const out: Record<string, NodeSegment[]> = { ...positions }\n  for (const [id, members] of runs) {\n    const line = positions[id]\n    if (!line?.length) {\n      continue\n    }\n    delete out[id]\n    const arc = arcPrefix(line)\n    const total = arc.at(-1)!\n    const weights = members.map(m => Math.max(weightOf(m), 0))\n    const weightSum = weights.reduce((a, b) => a + b, 0) || members.length\n    let from = 0\n    members.forEach((member, k) => {\n      const share = weightSum\n        ? (weights[k]! / weightSum) * total\n        : total / members.length\n      const to = k === members.length - 1 ? total : from + share\n      out[member] = slice(line, arc, from, to)\n      from = to\n    })\n  }\n  return out\n}\n\n// The stretch of a polyline between two fractions of its arc length, with the\n// ends interpolated. What splitRuns cuts a run with, and what the gene pins cut\n// a backbone node with to place an exon.\nexport function polylineSlice(line: NodeSegment[], from: number, to: number) {\n  if (line.length === 0) {\n    return []\n  }\n  const arc = arcPrefix(line)\n  const total = arc.at(-1)!\n  return slice(line, arc, from * total, to * total)\n}\n\n// The point halfway along a polyline by arc length, where a node's label goes.\nexport function polylineMidpoint(line: NodeSegment[]): NodeSegment {\n  const arc = arcPrefix(line)\n  return pointAt(line, arc, arc.at(-1)! / 2)\n}\n\n// Cumulative distance to each point of a polyline, starting at 0.\nfunction arcPrefix(line: NodeSegment[]) {\n  const arc = [0]\n  for (let i = 1; i < line.length; i++) {\n    arc.push(\n      arc[i - 1]! +\n        Math.hypot(line[i]!.x - line[i - 1]!.x, line[i]!.y - line[i - 1]!.y),\n    )\n  }\n  return arc\n}\n\nfunction pointAt(line: NodeSegment[], arc: number[], s: number): NodeSegment {\n  if (s <= 0) {\n    return { ...line[0]! }\n  }\n  let i = 1\n  while (i < arc.length && arc[i]! < s) {\n    i++\n  }\n  if (i >= arc.length) {\n    return { ...line.at(-1)! }\n  }\n  const span = arc[i]! - arc[i - 1]!\n  const t = span > 0 ? (s - arc[i - 1]!) / span : 0\n  const a = line[i - 1]!\n  const b = line[i]!\n  return { x: a.x + (b.x - a.x) * t, y: a.y + (b.y - a.y) * t }\n}\n\nfunction slice(line: NodeSegment[], arc: number[], from: number, to: number) {\n  const points = [pointAt(line, arc, from)]\n  for (let i = 0; i < line.length; i++) {\n    if (arc[i]! > from && arc[i]! < to) {\n      points.push({ ...line[i]! })\n    }\n  }\n  points.push(pointAt(line, arc, to))\n  return points\n}\n", "// Every label drawn over the graph claims a box in screen px from one\n// occupancy, so a label that would land on one already placed, or off the pane,\n// is dropped whichever overlay it belongs to. Callers take in priority order.\n// A chip is drawn whole or not at all.\n\nexport interface Box {\n  x0: number\n  x1: number\n  y0: number\n  y1: number\n}\n\nexport const LABEL_PX = 11\nexport const LABEL_CHAR_PX = 6.2\nexport const LABEL_PAD = 4\n\nexport interface LabelCandidate<T> {\n  item: T\n  x: number\n  y: number\n  text: string\n  // how many rows down to try when the spot is taken, for a label that is\n  // worth a column beside its neighbours rather than dropping\n  stack?: number\n}\n\nexport interface PlacedLabel<T> extends LabelCandidate<T> {\n  w: number\n}\n\nexport type TakeBox = (box: Box) => boolean\n\nexport function labelWidth(text: string) {\n  return text.length * LABEL_CHAR_PX + LABEL_PAD * 2\n}\n\nexport function overlaps(a: Box, b: Box) {\n  return a.x0 < b.x1 && a.x1 > b.x0 && a.y0 < b.y1 && a.y1 > b.y0\n}\n\ninterface Frame {\n  width: number\n  height: number\n}\n\nfunction offFrame(box: Box, frame: Frame) {\n  return (\n    box.x1 <= 0 ||\n    box.x0 >= frame.width ||\n    box.y1 <= 0 ||\n    box.y0 >= frame.height\n  )\n}\n\nfunction insideFrame(box: Box, frame: Frame) {\n  return (\n    box.x0 >= 0 &&\n    box.x1 <= frame.width &&\n    box.y0 >= 0 &&\n    box.y1 <= frame.height\n  )\n}\n\nexport function occupancy(frame: Frame, reserved: Box[] = []): TakeBox {\n  const placed = [...reserved]\n  return box => {\n    if (offFrame(box, frame) || placed.some(p => overlaps(p, box))) {\n      return false\n    }\n    placed.push(box)\n    return true\n  }\n}\n\nexport function placeLabels<T>(\n  candidates: LabelCandidate<T>[],\n  frame: Frame,\n  take: TakeBox,\n): PlacedLabel<T>[] {\n  const out: PlacedLabel<T>[] = []\n  const row = LABEL_PX + LABEL_PAD * 2\n  for (const c of candidates) {\n    const w = labelWidth(c.text)\n    // a stack grows away from the nearer edge of the pane\n    const direction = c.y > frame.height / 2 ? -1 : 1\n    for (let tries = 0; tries <= (c.stack ?? 0); tries++) {\n      const y = c.y + direction * tries * row\n      const box = {\n        x0: c.x - w / 2,\n        x1: c.x + w / 2,\n        y0: y - LABEL_PX - LABEL_PAD,\n        y1: y + LABEL_PAD,\n      }\n      if (offFrame(box, frame)) {\n        break\n      }\n      if (insideFrame(box, frame) && take(box)) {\n        out.push({ ...c, y, w })\n        break\n      }\n    }\n  }\n  return out\n}\n", "import { deletionArcCurves } from './deletionEdges'\nimport { polylineMidpoint } from './layout/mergeRuns'\nimport { occupancy } from './overlayLabels'\nimport { curveBounds, curveMidpoint } from './util/geometry'\n\nimport type { DeletionEdge } from './deletionEdges'\nimport type { Box, TakeBox } from './overlayLabels'\nimport type { AlleleDeletion, NodeSegment } from './types'\nimport type { AxisScale, BezierCurve } from './util/geometry'\n\n// What to write on the drawing, and where. Bandage labels a node with its name,\n// its length or its depth; a segment id means nothing to a reader of a pangenome\n// (\"s462766\"), so the label here is the one fact that carries the story \u2014 how\n// much sequence the alternative is worth. A node says its length, a deletion arc\n// says what it skips.\n//\n// **Every length written here is positive, and a deletion says it is one.**\n// A deletion arc used to be labelled \"\u221294.2 kb\", and a review read that as the\n// node's sequence length being negative, which is the only thing a bare signed\n// number beside a graph can mean. \"skips 94.2 kb\" replaced it and left a reader\n// asking 94.2 kb of what; \"skips 94.2 kb of reference\" answered that and still\n// drew \"it is sort of unclear what 'skips X bp of reference' means. is there any\n// better wording?\" on a third round. So the label now names the event rather\n// than describing the arc's mechanics: \"94.2 kb del\" abbreviates the term a\n// reader already has for reference sequence a haplotype does not carry, and\n// against the reference is what a deletion is measured from by default.\n//\n// **Two rules decide which labels there are, and both are about the drawing\n// rather than about a threshold on the graph.**\n//\n// A label has to fit the node it names, within a factor of two: past that it is\n// a label with a node attached rather than a node with a label. The rule used to\n// be a flat minimum drawn length (46 screen px) regardless of how long the text\n// was, which reads as arbitrary from the outside \u2014 review asked why some nodes\n// state a length and others do not, and nothing in the picture could answer it.\n// Measured against the text, the answer is in the picture: the node is shorter\n// than the words.\n//\n// And a label is dropped when its box would overlap one already placed. Labels\n// go biggest-sequence-first, so what survives a crowd is the allele that\n// matters; this is also what fixes labels printing on top of each other (\"\u221210\n// kb3.2 kb\" in the amylase figure).\n//\n// Between them they hold at both ends of the scale a pangenome graph spans: 63\n// kb-scale nodes at the amylase locus nearly all carry a length, and a 154-node\n// base-level pggb graph of 1-100 bp segments carries almost none \u2014 where every\n// label would have said \"1 bp\" and covered the segment it named.\n//\n// Collision is measured in SCREEN pixels, because that is where the text has its\n// size: the same two labels clear each other zoomed in and collide zoomed out,\n// so a wide view sheds labels on its own. This is why there is no \"show labels\"\n// toggle \u2014 a control whose only job is to undo a bad default is a bad default.\n\n// A deletion is worth saying even when its arc is small, because the arc is the\n// only thing on screen that represents it; but not when it is a dot.\n//\n// Measured on the arc's DRAWN EXTENT (the larger side of its bounds, in screen\n// px), not on its bulge. Bulge is in whatever units the layout works in: under\n// FMMM it is a fraction of the bypassed nodes' drawn length at the engine's own\n// scale, and in an anchored layout it is a fraction of their length in bp. The\n// same deletion therefore cleared this in one layout and not the other, which is\n// how `pangenome/hprc_cfhr_deletion` lost the labels on its 2.2 kb and 9.3 kb\n// arcs by changing nothing but the layout. Extent is what a reader sees either\n// way, and it is the same quantity the node rule below uses.\nconst MIN_DELETION_LABEL_PX = 26\n\n// One node label per this much pane, and never fewer than a handful: at a\n// 1400 by 600 pane that is about twenty.\nconst PX_PER_NODE_LABEL = 40_000\nconst MIN_NODE_LABELS = 8\n\n// A deletion clearing that floor still need not be able to CARRY its label: the\n// text is a fixed 26 characters however small the event's arc is, so at the LPA\n// KIV-2 locus `skips 27.7 kb of reference` came out four times the width of the\n// arc it was centred on, reading as a caption dropped on the bubble beside it\n// rather than as that arc's name (`pangenome/hprc_lpa_kiv2`, reviewed\n// 2026-07-31).\n//\n// A node in the same position simply loses its label, and that is right for a\n// node \u2014 the tube is still drawn, still coloured, still hoverable, and the graph\n// is full of them. It is wrong for a deletion, which is one dashed curve\n// standing for sequence that is not in the picture at all: dropped, nothing\n// tells a reader the arc is an event rather than another link.\n//\n// So the label moves off the arc instead and takes a leader line with it. It is\n// displaced along the direction the arc bows \u2014 which is the side the bulge was\n// drawn INTO, so it is the open side by construction \u2014 far enough that its box\n// clears the curve, and the leader states the association the proximity no\n// longer does.\nconst LEADER_GAP_PX = 8\n\n// The label's own box, for collision. Mirrors GraphCanvas's nodeLabelStyle:\n// 10px text in 3px of horizontal padding, on a 13px line. Character width is an\n// average rather than a measurement \u2014 placement runs on every pan and zoom, and\n// a canvas text metric per candidate costs more than the occasional\n// half-character of slack is worth.\nconst LABEL_CHAR_PX = 5.7\nconst LABEL_PAD_PX = 6\nconst LABEL_HEIGHT_PX = 13\n// Breathing room, so two labels that merely touch still read as two.\nconst LABEL_GAP_PX = 3\n// How much wider than its node a label may be before it is the label that is\n// being drawn rather than the node.\nconst MAX_LABEL_OVERHANG = 2\n\n// Half the box a piece of label text occupies. Split out of `labelBox` because\n// the width is wanted before there is anywhere to put the box: a displaced\n// deletion label is clamped by its own half-width, and the node pass below\n// rejects on size before it has a position at all.\nfunction labelHalfWidth(text: string) {\n  return (text.length * LABEL_CHAR_PX + LABEL_PAD_PX + LABEL_GAP_PX) / 2\n}\n\n// Constant whatever the label says, so a candidate's vertical cull costs\n// nothing and can be taken before its text exists.\nconst LABEL_HALF_HEIGHT = (LABEL_HEIGHT_PX + LABEL_GAP_PX) / 2\n\n// The narrowest box `formatBp` can ask for, `1 bp`. A node drawn shorter than\n// this cannot carry ANY label, so the check happens before the length is\n// formatted: on a 7,499-node cut nearly every node fails it, and building a\n// string and a box per node only to discard both was most of this pass\n// (measured 37 ms per frame, and this pass runs on every pan).\nconst MIN_LABEL_HALF_WIDTH = labelHalfWidth('1 bp')\n\n// translate(-50%, -50%) in the style, so the anchor is the box's centre.\nfunction boxAt(halfW: number, x: number, y: number): Box {\n  return {\n    x0: x - halfW,\n    x1: x + halfW,\n    y0: y - LABEL_HALF_HEIGHT,\n    y1: y + LABEL_HALF_HEIGHT,\n  }\n}\n\n// The box a row label occupies, from the same metrics RowLabels renders with\n// (11px text, 4px of horizontal padding, a 16px line, centred on its row). Lives\n// here rather than in the component so the two halves of the collision test\n// cannot drift apart.\nexport function rowLabelBox(text: string, screenY: number): Box {\n  return {\n    x0: 6,\n    x1: 6 + text.length * 6.2 + 8 + LABEL_GAP_PX,\n    y0: screenY - 8 - LABEL_GAP_PX / 2,\n    y1: screenY + 8 + LABEL_GAP_PX / 2,\n  }\n}\n\n// Slide a value into [lo, hi], leaving it alone when the range is empty \u2014 a box\n// wider than the canvas has nowhere to fit, and pinning it to one edge is worse\n// than the overflow.\nfunction clamp(v: number, lo: number, hi: number) {\n  return hi < lo ? v : Math.min(Math.max(v, lo), hi)\n}\n\n// A displaced label's tether, in the same screen pixels the label is placed in.\n// Both ends are computed here rather than in the component, because the label's\n// end is the point where its own box meets the line \u2014 geometry the placement\n// already has and the painter would have to rederive. It stops at the box edge\n// rather than at the centre because the label's background is translucent, so a\n// line run under it shows through the text.\nexport interface Leader {\n  arcX: number\n  arcY: number\n  labelX: number\n  labelY: number\n}\n\nexport interface GraphLabel {\n  key: string\n  text: string\n  // screen pixels, already through the transform the canvas draws with: the\n  // collision test needs them anyway, and returning layout units would have the\n  // caller redo the arithmetic that decided which labels there are\n  x: number\n  y: number\n  kind: 'node' | 'deletion'\n  // present only on a label that had to move off the thing it names\n  leader?: Leader\n}\n\n// bp in the unit that reads. Deliberately coarse: a label is a glance, and\n// \"12,345 bp\" costs twice the width of \"12 kb\" to say the same thing at the\n// scale a pangenome allele lives at.\nexport function formatBp(bp: number) {\n  if (bp >= 1_000_000) {\n    return `${+(bp / 1_000_000).toFixed(1)} Mb`\n  }\n  return bp >= 1000 ? `${+(bp / 1000).toFixed(1)} kb` : `${bp} bp`\n}\n\nfunction deletionText(bp: number) {\n  return `${formatBp(bp)} del`\n}\n\n// Which way the arc bows, as a unit vector: its chord's midpoint towards its\n// apex. A deletion's bulge is perpendicular to the chord by construction, so\n// this points away from the backbone the arc leaves and rejoins \u2014 the side the\n// curve was opened into, and the side with room in it.\n//\n// Taken on SCREEN, which is where the label it aims has to clear the curve. That\n// used to be free \u2014 with one scale for both axes the transform is a similarity,\n// so a layout direction is a screen direction \u2014 and on a row layout it is not:\n// the two axes are bp and px and the arc leaves at a different angle in each.\nfunction arcOutward(\n  curves: BezierCurve[],\n  apex: { x: number; y: number },\n  scaleX: number,\n  scaleY: number,\n) {\n  const first = curves[0]!\n  const last = curves[curves.length - 1]!\n  const dx = (apex.x - (first.x0 + last.x1) / 2) * scaleX\n  const dy = (apex.y - (first.y0 + last.y1) / 2) * scaleY\n  const len = Math.hypot(dx, dy)\n  // A curve with no bow has no outward side; up is as good as any, and this is\n  // unreachable for a deletion, whose bulge is what gives it extent at all.\n  return len === 0 ? { x: 0, y: -1 } : { x: dx / len, y: dy / len }\n}\n\n// How far the box's own boundary is from its centre in a given direction \u2014 the\n// support function of an axis-aligned rectangle. Displacing a label by this plus\n// a gap puts its near EDGE that gap away from the point, whatever angle the\n// leader leaves at, which a single radius cannot do for a box six times wider\n// than it is tall.\nfunction boxSupport(box: Box, dir: { x: number; y: number }) {\n  return (\n    (Math.abs(dir.x) * (box.x1 - box.x0)) / 2 +\n    (Math.abs(dir.y) * (box.y1 - box.y0)) / 2\n  )\n}\n\n// Where a ray along `dir` through the box's centre crosses the box, again from\n// the centre \u2014 which is where a leader coming in along that ray has to stop.\n//\n// This is not `boxSupport`, and the difference is the whole leader: support is\n// the distance to the supporting line perpendicular to `dir`, which a box six\n// times wider than it is tall touches at a corner, so a diagonal approach hits\n// the box's real edge four or five times sooner. Stopping the line at the\n// support distance drew an 8px stub at the arc with 50px of white between it and\n// the text it was supposed to tie to.\nfunction boxRayCrossing(box: Box, dir: { x: number; y: number }) {\n  const halfW = (box.x1 - box.x0) / 2\n  const halfH = (box.y1 - box.y0) / 2\n  return Math.min(\n    dir.x === 0 ? Infinity : halfW / Math.abs(dir.x),\n    dir.y === 0 ? Infinity : halfH / Math.abs(dir.y),\n  )\n}\n\n// The node's own extent along its polyline, IN SCREEN PX \u2014 what the label has\n// to fit inside. Measured through the transform rather than in layout units and\n// scaled afterwards, because on a row layout the two axes are in different units\n// and there is no single number to scale a mixed length by.\nfunction drawnLength(segments: NodeSegment[], scaleX: number, scaleY: number) {\n  let total = 0\n  for (let i = 1; i < segments.length; i++) {\n    const a = segments[i - 1]!\n    const b = segments[i]!\n    total += Math.hypot((b.x - a.x) * scaleX, (b.y - a.y) * scaleY)\n  }\n  return total\n}\n\n// The extent of a run's drawn points, in layout units. One pass rather than\n// four `Math.min(...points.map(...))` spreads over the same array: those\n// allocate a mapped copy per axis, and a run long enough \u2014 a chain of alleles\n// across a whole-file import \u2014 overflows the argument limit and throws\n// RangeError instead of labelling anything. Same reason `backboneSpan` is a\n// fold.\nfunction runBounds(\n  nodeIds: string[],\n  nodePositions: Record<string, NodeSegment[]>,\n) {\n  let minX = Infinity\n  let minY = Infinity\n  let maxX = -Infinity\n  let maxY = -Infinity\n  for (const id of nodeIds) {\n    for (const p of nodePositions[id] ?? []) {\n      minX = Math.min(minX, p.x)\n      maxX = Math.max(maxX, p.x)\n      minY = Math.min(minY, p.y)\n      maxY = Math.max(maxY, p.y)\n    }\n  }\n  return minX === Infinity ? undefined : { minX, minY, maxX, maxY }\n}\n\n// Both caches below are keyed the way hit detection keys its spatial indexes: a\n// WeakMap on the positions object, so two graph views cannot evict each other\n// and an entry dies with the layout it describes, plus an explicit check of\n// everything the value actually depends on. A node drag mutates the positions\n// in place, so their identity cannot report that they moved \u2014 hence `version`,\n// which the model bumps on exactly that (`positionsVersion`).\n//\n// What makes the caching worth having is that this whole pass reruns on every\n// pan: the labels are placed in screen space, so a translate changes where they\n// go, and neither the order they are considered in nor the arcs they ride\n// depends on it.\n\n// Node label candidates in the order they are considered \u2014 biggest allele\n// first \u2014 which is a function of the sequence lengths alone.\nconst nodeOrderCache = new WeakMap<\n  Record<string, NodeSegment[]>,\n  {\n    nodeLengths: Map<string, number>\n    order: [string, NodeSegment[]][]\n  }\n>()\n\nfunction labelOrder(\n  nodePositions: Record<string, NodeSegment[]>,\n  nodeLengths: Map<string, number>,\n) {\n  const cached = nodeOrderCache.get(nodePositions)\n  if (cached?.nodeLengths === nodeLengths) {\n    return cached.order\n  }\n  const order = Object.entries(nodePositions)\n    .filter(([id, segments]) => segments.length > 0 && nodeLengths.has(id))\n    .sort(([a], [b]) => nodeLengths.get(b)! - nodeLengths.get(a)!)\n  nodeOrderCache.set(nodePositions, { nodeLengths, order })\n  return order\n}\n\n// One deletion arc as the renderer draws it, plus the two things placement\n// reads off it: where its apex is, and how big it is on screen.\ninterface ArcPlacement {\n  deletion: DeletionEdge\n  curves: BezierCurve[]\n  apex: { x: number; y: number }\n  extent: number\n}\n\nconst arcCache = new WeakMap<\n  Record<string, NodeSegment[]>,\n  {\n    deletions: DeletionEdge[]\n    scaleX: number\n    scaleY: number\n    version: number\n    arcs: ArcPlacement[]\n  }\n>()\n\n// Biggest deletion first, so an arc that survives a crowd is the one carrying\n// the most sequence.\nfunction arcPlacements(\n  nodePositions: Record<string, NodeSegment[]>,\n  deletions: DeletionEdge[],\n  axis: AxisScale,\n  version: number,\n) {\n  const { scaleX, scaleY } = axis\n  const cached = arcCache.get(nodePositions)\n  if (\n    cached?.deletions === deletions &&\n    cached.scaleX === scaleX &&\n    cached.scaleY === scaleY &&\n    cached.version === version\n  ) {\n    return cached.arcs\n  }\n  const arcs: ArcPlacement[] = []\n  for (const deletion of [...deletions].sort((a, b) => b.bp - a.bp)) {\n    const curves = deletionArcCurves(nodePositions, deletion, axis)\n    const apex = curves ? curveMidpoint(curves) : undefined\n    if (curves && apex) {\n      const { minX, minY, maxX, maxY } = curveBounds(curves)\n      arcs.push({\n        deletion,\n        curves,\n        apex,\n        // in screen px, so the two axes' units cannot be added by accident\n        extent: Math.max((maxX - minX) * scaleX, (maxY - minY) * scaleY),\n      })\n    }\n  }\n  arcCache.set(nodePositions, { deletions, scaleX, scaleY, version, arcs })\n  return arcs\n}\n\ninterface SizeLabelArgs {\n  nodePositions: Record<string, NodeSegment[]>\n  // bp per node id, so this module never has to know what a GraphNode is\n  nodeLengths: Map<string, number>\n  deletions: DeletionEdge[]\n  // Deletions the layout found that carry a segment, so `deletions` above\n  // cannot: empty under a layout drawn at sequence scale, where a node's own\n  // length IS what its drawn extent means. See AlleleDeletion.\n  alleleDeletions?: AlleleDeletion[]\n  // Screen px per layout unit, both axes. They are equal on an isotropic layout\n  // and differ on a row layout, whose y is already px (scaleY === 1). One value\n  // so a caller cannot pass one and default the other \u2014 see AxisScale.\n  axis: AxisScale\n  translateX: number\n  translateY: number\n  width: number\n  height: number\n  // Bumped whenever the layout's positions are mutated in place, i.e. by a node\n  // drag. Everything cached across frames here is keyed by it \u2014 see the caches\n  // above \u2014 and reading it is also what makes a dragged node's label follow it.\n  version?: number\n}\n\nexport interface SizeLabelCandidate {\n  label: GraphLabel\n  box: Box\n}\n\n// Deletions come first, so an arc keeps its label against the nodes around it:\n// the arc is the only thing in the drawing that represents sequence which is\n// not there, and a reader who cannot read it has no other route to it.\nexport function sizeLabelCandidates({\n  nodePositions,\n  nodeLengths,\n  deletions,\n  alleleDeletions,\n  axis,\n  translateX,\n  translateY,\n  width,\n  height,\n  version = 0,\n}: SizeLabelArgs) {\n  const { scaleX, scaleY } = axis\n  const deletionCandidates: SizeLabelCandidate[] = []\n  const nodeCandidates: SizeLabelCandidate[] = []\n  for (const { deletion, curves, apex, extent } of arcPlacements(\n    nodePositions,\n    deletions,\n    axis,\n    version,\n  )) {\n    if (extent >= MIN_DELETION_LABEL_PX) {\n      const text = deletionText(deletion.bp)\n      const halfW = labelHalfWidth(text)\n      const box = boxAt(halfW, 0, 0)\n      const arcX = apex.x * scaleX + translateX\n      const arcY = apex.y * scaleY + translateY\n      // The node rule, applied to an arc: a label wider than twice what it\n      // names is a label with an arc attached. Under it the label stays\n      // centred on the curve, which is what every arc big enough to hold its\n      // own name already does.\n      const fits = extent >= (halfW * 2) / MAX_LABEL_OVERHANG\n      // Displaced by the SUPPORT distance, so the whole box clears the arc\n      // whatever angle it leaves at, then the leader is stopped at the box's\n      // real edge along the same ray.\n      const bow = arcOutward(curves, apex, scaleX, scaleY)\n      const offset = boxSupport(box, bow) + LEADER_GAP_PX\n      // ...and then slid back into the frame if that put it outside one. A\n      // tethered label chooses where it goes, and the cull below keeps any box\n      // merely OVERLAPPING the canvas, so displacing blind is how the MHC force\n      // layout came out with a clipped `\u2026ips 1.5 kb of reference` against its\n      // left edge. Sliding beats dropping and beats picking the arc's other\n      // side: the leader is redrawn to wherever the words ended up, so it stays\n      // unambiguous however far along the edge they had to move.\n      const x = fits ? arcX : clamp(arcX + bow.x * offset, halfW, width - halfW)\n      const y = fits\n        ? arcY\n        : clamp(\n            arcY + bow.y * offset,\n            LABEL_HALF_HEIGHT,\n            height - LABEL_HALF_HEIGHT,\n          )\n      // From where the label actually sits, not from the bow, or the line\n      // points off at the position the label would have had.\n      const away = Math.hypot(x - arcX, y - arcY)\n      let leader\n      if (away > 0) {\n        const dir = { x: (x - arcX) / away, y: (y - arcY) / away }\n        const crossing = boxRayCrossing(box, dir)\n        leader = {\n          arcX,\n          arcY,\n          labelX: x - dir.x * crossing,\n          labelY: y - dir.y * crossing,\n        }\n      }\n      deletionCandidates.push({\n        label: {\n          key: `del:${deletion.edgeIndex}`,\n          text,\n          x,\n          y,\n          kind: 'deletion',\n          leader,\n        },\n        box: boxAt(halfW, x, y),\n      })\n    }\n  }\n\n  // Segment-carrying deletions, next: the arcs above and these are the same\n  // event and are said in the same words, so they queue together ahead of the\n  // node lengths and biggest-first among themselves.\n  //\n  // A run's label rides the middle of what the layout DREW for it, which is the\n  // reference the allele replaces, and it has to fit that extent by the same\n  // factor-of-two rule a node label does \u2014 so the sliver a 2 bp skip occupies in\n  // a base-level graph carries nothing, and the 7.1 kb one CFT073 leaves in the\n  // E. coli pggb graph carries `7 kb del`.\n  //\n  // The nodes it covers are then barred from labelling themselves. Their length\n  // is a true fact and the wrong one to print here: `93 bp` written across a bar\n  // drawn 7.1 kb wide is read as the bar's size, which is the misreading this\n  // whole label exists to fix. It stays in the tooltip and the details panel.\n  const labelledByDeletion = new Set<string>()\n  const alleleRuns = [...(alleleDeletions ?? [])].sort((a, b) => b.bp - a.bp)\n  for (const run of alleleRuns) {\n    const drawn = runBounds(run.nodeIds, nodePositions)\n    if (!drawn) {\n      continue\n    }\n    // ON SCREEN, not in layout units, and that is the whole subtlety here. A\n    // run drawn over the reference it replaces can be far wider than the window\n    // \u2014 the E. coli one starts 7 kb before the left edge \u2014 so its true midpoint\n    // is nowhere, and a label placed there is culled for being off-canvas and\n    // the bar goes unnamed. The visible slice is what a reader has, so the\n    // label rides the middle of that, and the fit test asks whether the words\n    // fit what is SHOWN rather than what is drawn.\n    const shownLeft = Math.max(drawn.minX * scaleX + translateX, 0)\n    const shownRight = Math.min(drawn.maxX * scaleX + translateX, width)\n    const shownTop = Math.max(drawn.minY * scaleY + translateY, 0)\n    const shownBottom = Math.min(drawn.maxY * scaleY + translateY, height)\n    if (shownRight < shownLeft || shownBottom < shownTop) {\n      continue\n    }\n    const extent = Math.max(shownRight - shownLeft, shownBottom - shownTop)\n    const text = deletionText(run.bp)\n    const halfW = labelHalfWidth(text)\n    if (extent >= (halfW * 2) / MAX_LABEL_OVERHANG) {\n      for (const id of run.nodeIds) {\n        labelledByDeletion.add(id)\n      }\n      const x = clamp((shownLeft + shownRight) / 2, halfW, width - halfW)\n      const y = clamp(\n        (shownTop + shownBottom) / 2,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT,\n      )\n      deletionCandidates.push({\n        label: {\n          key: `alleledel:${run.nodeIds.join(',')}`,\n          text,\n          x,\n          y,\n          kind: 'deletion',\n        },\n        box: boxAt(halfW, x, y),\n      })\n    }\n  }\n\n  // Biggest allele first: in a crowd, the label that survives should be the one\n  // carrying the most sequence, not whichever node the layout happened to emit\n  // first. The order is `labelOrder`'s, cached across frames; the three rejects\n  // below are what a frame actually decides, cheapest first \u2014 a node barred by\n  // a run's label, then one whose row is off the pane (the box's height is a\n  // constant, so this needs no text), then one too short to hold the shortest\n  // label there is.\n  for (const [id, segments] of labelOrder(nodePositions, nodeLengths)) {\n    if (labelledByDeletion.has(id)) {\n      continue\n    }\n    const { x, y } = polylineMidpoint(segments)\n    const screenY = y * scaleY + translateY\n    if (\n      screenY + LABEL_HALF_HEIGHT <= 0 ||\n      screenY - LABEL_HALF_HEIGHT >= height\n    ) {\n      continue\n    }\n    const drawn = drawnLength(segments, scaleX, scaleY)\n    // The same comparison the real fit test makes, against the narrowest box\n    // any label can have \u2014 so nothing that would have passed is rejected here.\n    if (drawn < (MIN_LABEL_HALF_WIDTH * 2) / MAX_LABEL_OVERHANG) {\n      continue\n    }\n    const text = formatBp(nodeLengths.get(id)!)\n    const halfW = labelHalfWidth(text)\n    if (drawn >= (halfW * 2) / MAX_LABEL_OVERHANG) {\n      const screenX = x * scaleX + translateX\n      nodeCandidates.push({\n        label: {\n          key: `node:${id}`,\n          text,\n          x: screenX,\n          y: screenY,\n          kind: 'node',\n        },\n        box: boxAt(halfW, screenX, screenY),\n      })\n    }\n  }\n\n  return { deletions: deletionCandidates, nodes: nodeCandidates }\n}\n\n// Node labels are rationed to the pane's area: a base-level cut of hundreds of\n// short nodes fits a length on most of them at a moderate zoom, and a drawing\n// where every node states its length is a table with a graph under it. Biggest\n// first, so the ration goes to the alleles that carry sequence; zooming in\n// gives more area to fewer nodes and the labels come back.\nexport function nodeLabelBudget(width: number, height: number) {\n  return Math.max(\n    MIN_NODE_LABELS,\n    Math.floor((width * height) / PX_PER_NODE_LABEL),\n  )\n}\n\nexport function placeSizeLabels(\n  candidates: SizeLabelCandidate[],\n  take: TakeBox,\n  budget = Infinity,\n) {\n  const labels: GraphLabel[] = []\n  for (const { label, box } of candidates) {\n    if (labels.length >= budget) {\n      break\n    }\n    if (take(box)) {\n      labels.push(label)\n    }\n  }\n  return labels\n}\n\nexport function graphLabels({\n  reserved,\n  ...args\n}: SizeLabelArgs & { reserved?: Box[] }): GraphLabel[] {\n  const take = occupancy(args, reserved)\n  const { deletions, nodes } = sizeLabelCandidates(args)\n  return [\n    ...placeSizeLabels(deletions, take),\n    ...placeSizeLabels(nodes, take, nodeLabelBudget(args.width, args.height)),\n  ]\n}\n", "import {\n  nodeLabelBudget,\n  placeSizeLabels,\n  rowLabelBox,\n  sizeLabelCandidates,\n} from './graphLabels'\nimport {\n  LABEL_CHAR_PX,\n  LABEL_PAD,\n  LABEL_PX,\n  occupancy,\n  placeLabels,\n} from './overlayLabels'\n\nimport type { BubbleHalo, RouteLabel } from './bubbles/bubbleHalos'\nimport type { DeletionEdge } from './deletionEdges'\nimport type { GenePin } from './genes/genePins'\nimport type { GraphLabel } from './graphLabels'\nimport type { Box, PlacedLabel } from './overlayLabels'\nimport type { AlleleDeletion, NodeSegment } from './types'\nimport type { AxisScale } from './util/geometry'\n\nexport const HALO_FACTOR = 3.4\nexport const LEGEND_INSET_PX = 6\n// routes whose own stretches are drawn on top of each other stack their chips\nconst ROUTE_STACK = 8\nconst GENE_PIN_DROP_PX = 18\n// a gene's name drops a row or two rather than vanish under a bubble's\nconst GENE_STACK = 2\n// a chip's baseline this far down is the highest it sits whole in the pane\nconst TOPMOST_BASELINE = LABEL_PX + LABEL_PAD\n\nexport interface LabelLayoutSource {\n  paneWidth: number\n  canvasHeight: number\n  axisScale: AxisScale\n  translateX: number\n  translateY: number\n  contigThickness: number\n  legendSize: { width: number; height: number }\n  // the band along the top a reference strip draws in\n  referenceStripZonePx?: number\n  drawnRowLabels: { label: string; y: number }[]\n  bubbleHalos: BubbleHalo[]\n  genePins: GenePin[]\n  poppedFrom?: { label: string }\n  nodePositions?: Record<string, NodeSegment[]>\n  // false where the drawing is not the canvas's nodes (the tube map), so a\n  // length label would sit on a box's tubes rather than beside a node\n  labelsNodeSizes: boolean\n  nodeLengths: Map<string, number>\n  showDeletionEdges: boolean\n  deletions: DeletionEdge[]\n  alleleDeletions: AlleleDeletion[]\n  positionsVersion: number\n}\n\nexport interface LabelLayout {\n  bubbles: PlacedLabel<BubbleHalo>[]\n  genes: PlacedLabel<GenePin>[]\n  routes: PlacedLabel<{ halo: BubbleHalo; route: RouteLabel }>[]\n  sizes: GraphLabel[]\n}\n\nfunction byExtent<T>(items: T[], extent: (item: T) => number) {\n  return [...items].sort((a, b) => extent(b) - extent(a))\n}\n\n// The order is what survives a crowd: the bubble's name, then the gene's, then\n// what a deletion skips, then who takes each route, and a node's length last.\nexport function layoutLabels(m: LabelLayoutSource): LabelLayout {\n  const { paneWidth: width, canvasHeight: height, translateX, translateY } = m\n  const { scaleX, scaleY } = m.axisScale\n  const frame = { width, height }\n  const screen = (p: { x: number; y: number }) => ({\n    x: p.x * scaleX + translateX,\n    y: p.y * scaleY + translateY,\n  })\n  const reserved: Box[] = m.drawnRowLabels.map(({ label, y }) =>\n    rowLabelBox(label, y * scaleY + translateY),\n  )\n  const stripPx = m.referenceStripZonePx ?? 0\n  if (stripPx > 0) {\n    reserved.push({ x0: 0, x1: width, y0: 0, y1: stripPx })\n  }\n  if (m.legendSize.width > 0) {\n    reserved.push({\n      x0: width - LEGEND_INSET_PX - m.legendSize.width,\n      x1: width,\n      y0: 0,\n      y1: stripPx + LEGEND_INSET_PX + m.legendSize.height,\n    })\n  }\n  if (m.poppedFrom) {\n    reserved.push({\n      x0: 0,\n      x1: 60 + m.poppedFrom.label.length * LABEL_CHAR_PX * 1.2,\n      y0: 0,\n      y1: 44,\n    })\n  }\n  const take = occupancy(frame, reserved)\n\n  // On a row layout a bubble's name goes in the band above the top row, which\n  // is the reference it varies, and stays at the pane's top edge once that row\n  // scrolls out. Above its own nodes, a lower row's allele would put it on the\n  // reference line.\n  const onRows = m.drawnRowLabels.length > 0\n  const rowsTop = onRows\n    ? Math.min(...m.drawnRowLabels.map(r => r.y))\n    : Infinity\n  const halo = m.contigThickness * HALO_FACTOR\n  const byBubble = byExtent(m.bubbleHalos, h => h.members)\n  const bubbles = placeLabels(\n    byBubble.map(h => {\n      const { x, y } = screen({\n        x: h.labelAt.x,\n        y: Math.min(h.labelAt.y, rowsTop),\n      })\n      const baseline = y - halo / 2 - 6\n      return {\n        item: h,\n        x,\n        y: onRows ? Math.max(baseline, TOPMOST_BASELINE) : baseline,\n        text: h.label,\n      }\n    }),\n    frame,\n    take,\n  )\n\n  const genes = placeLabels(\n    byExtent(m.genePins, pin => pin.gene.end - pin.gene.start).map(pin => {\n      const { x, y } = screen(pin.at)\n      return {\n        item: pin,\n        x,\n        y: y + m.contigThickness + GENE_PIN_DROP_PX,\n        text: pin.covered < 0.98 ? `${pin.gene.name} \u2026` : pin.gene.name,\n        stack: GENE_STACK,\n      }\n    }),\n    frame,\n    take,\n  )\n  const sizeCandidates =\n    m.nodePositions && m.labelsNodeSizes\n      ? sizeLabelCandidates({\n          nodePositions: m.nodePositions,\n          nodeLengths: m.nodeLengths,\n          deletions: m.showDeletionEdges ? m.deletions : [],\n          alleleDeletions: m.alleleDeletions,\n          axis: m.axisScale,\n          translateX,\n          translateY,\n          width,\n          height,\n          version: m.positionsVersion,\n        })\n      : { deletions: [], nodes: [] }\n  const deletionLabels = placeSizeLabels(sizeCandidates.deletions, take)\n  const routes = placeLabels(\n    byBubble.flatMap(h =>\n      h.routes.map(route => {\n        const { x, y } = screen(route.at)\n        return {\n          item: { halo: h, route },\n          x,\n          y: y + 4,\n          text: route.text,\n          stack: ROUTE_STACK,\n        }\n      }),\n    ),\n    frame,\n    take,\n  )\n  const nodeLabels = placeSizeLabels(\n    sizeCandidates.nodes,\n    take,\n    nodeLabelBudget(width, height),\n  )\n  return {\n    bubbles,\n    genes,\n    routes,\n    sizes: [...deletionLabels, ...nodeLabels],\n  }\n}\n", "import { packAbgr } from '@jbrowse/core/util/colorBits'\n\nimport {\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  REFERENCE_RAMP_MAX_HUE,\n  hslToRgb,\n} from './renderer/GeometryBuilder'\n\n// How a lifted walk colours its lane, stated the way a grammar of graphics\n// states an encoding: a field, the quantity the walk has at each node it\n// visits, mapped through a scheme, the scale from that quantity to a colour.\n// Colour does one job at a time by default: a walk lifted alone shades light\n// to dark along itself, which follows it round a loop, and walks lifted\n// together each take one flat colour, which says which lane is which. The\n// reference takes grey, so no hue means anything but a haplotype.\n//\n// A session states it per walk, and leaves out whatever takes the default:\n//\n//   \"walkLayers\": [\n//     { \"walk\": \"GRCh38#0#chr6\" },\n//     { \"walk\": \"HG00133#1#CM090050.1\", \"color\": { \"scheme\": \"purple\" } }\n//   ]\n\nexport const WALK_FIELDS = [\n  {\n    value: 'progress',\n    label: 'Progress along the walk',\n    legend: 'light where each walk starts, dark where it ends',\n  },\n  { value: 'walk', label: 'One colour for the walk', legend: '' },\n  {\n    value: 'reference',\n    label: 'Reference position',\n    legend: 'along the reference left to right, charcoal off it',\n  },\n] as const\n\nexport type WalkField = (typeof WALK_FIELDS)[number]['value']\n\n// Each family runs from a light colour where the walk starts to a dark one of\n// another hue where it ends, so a walk reads in hue as well as lightness, and\n// no two families share a stretch of the colour wheel: one walk's gradient\n// never passes through another's colours. The reference takes grey to black, so\n// that no hue on a lane means anything but a haplotype. The rainbow is the\n// reference-position ramp, so it goes with that field only.\n//\n// A dichromat sees one axis, blue to yellow, so cyan to navy and yellow to red\n// stay apart for every reader and come first; pink and lime fold into them.\nexport const WALK_SCHEMES = [\n  { value: 'grey', label: 'Grey to black', ends: ['#a3a3a3', '#151515'] },\n  { value: 'blue', label: 'Cyan to navy', ends: ['#6ee0f0', '#0b2c7a'] },\n  { value: 'red', label: 'Yellow to red', ends: ['#ffd24a', '#b3121b'] },\n  { value: 'purple', label: 'Pink to plum', ends: ['#f5a3d8', '#5e1a6e'] },\n  { value: 'green', label: 'Lime to forest', ends: ['#b6e36c', '#0b5d3b'] },\n  { value: 'rainbow', label: 'Rainbow' },\n] as const\n\nexport type WalkScheme = (typeof WALK_SCHEMES)[number]['value']\n\nexport interface WalkEncoding {\n  field: WalkField\n  scheme: WalkScheme\n}\n\nexport interface WalkLayer {\n  walk: string\n  color?: Partial<WalkEncoding>\n}\n\n// the families lifted haplotypes take by default, in the order they were picked\nconst FAMILIES: WalkScheme[] = ['blue', 'red', 'purple', 'green']\n\nconst isField = (v: unknown): v is WalkField =>\n  WALK_FIELDS.some(f => f.value === v)\nconst isScheme = (v: unknown): v is WalkScheme =>\n  WALK_SCHEMES.some(s => s.value === v)\n\n// A stated field or scheme this build does not have reads as unset\nexport function resolveEncoding(\n  layer: WalkLayer,\n  reference: boolean,\n  picked: number,\n  alone = true,\n): WalkEncoding {\n  const { field: askedField, scheme: askedScheme } = layer.color ?? {}\n  const field = isField(askedField) ? askedField : alone ? 'progress' : 'walk'\n  const family = reference ? 'grey' : FAMILIES[picked % FAMILIES.length]!\n  const scheme = isScheme(askedScheme)\n    ? askedScheme === 'rainbow' && field !== 'reference'\n      ? family\n      : askedScheme\n    : family\n  return { field, scheme }\n}\n\n// Where a flat lane sits on its family: halfway between its ends\nconst BASE_T = 0.5\n\nconst toLinear = (c: number) =>\n  c <= 0.04045 ? c / 12.92 : ((c + 0.055) / 1.055) ** 2.4\nconst toGamma = (c: number) =>\n  c <= 0.0031308 ? c * 12.92 : 1.055 * c ** (1 / 2.4) - 0.055\n\n// sRGB hex to OKLab, where a straight line between two colours changes\n// lightness evenly, so a family's steps read alike from end to end\nfunction oklab(hex: string) {\n  const [r, g, b] = [1, 3, 5].map(i =>\n    toLinear(Number.parseInt(hex.slice(i, i + 2), 16) / 255),\n  ) as [number, number, number]\n  const l = Math.cbrt(0.4122214708 * r + 0.5363325363 * g + 0.0514459929 * b)\n  const m = Math.cbrt(0.2119034982 * r + 0.6806995451 * g + 0.1073969566 * b)\n  const s = Math.cbrt(0.0883024619 * r + 0.2817188376 * g + 0.6299787005 * b)\n  return [\n    0.2104542553 * l + 0.793617785 * m - 0.0040720468 * s,\n    1.9779984951 * l - 2.428592205 * m + 0.4505937099 * s,\n    0.0259040371 * l + 0.7827717662 * m - 0.808675766 * s,\n  ]\n}\n\nfunction oklabToRgb([L, a, b]: number[]) {\n  const l = (L! + 0.3963377774 * a! + 0.2158037573 * b!) ** 3\n  const m = (L! - 0.1055613458 * a! - 0.0638541728 * b!) ** 3\n  const s = (L! - 0.0894841775 * a! - 1.291485548 * b!) ** 3\n  return [\n    4.0767416621 * l - 3.3077115913 * m + 0.2309699292 * s,\n    -1.2684380046 * l + 2.6097574011 * m - 0.3413193965 * s,\n    -0.0041960863 * l - 0.7034186147 * m + 1.707614701 * s,\n  ].map(c => toGamma(Math.max(0, Math.min(1, c))) * 255)\n}\n\n// A scheme at t in [0, 1] as rgb 0-255\nexport function schemeRgb(scheme: WalkScheme, t: number) {\n  const x = Math.max(0, Math.min(1, t))\n  const family = WALK_SCHEMES.find(s => s.value === scheme)\n  if (!family || !('ends' in family)) {\n    return hslToRgb(x * REFERENCE_RAMP_MAX_HUE, 0.7, 0.5).map(c => c * 255)\n  }\n  const from = oklab(family.ends[0])\n  const to = oklab(family.ends[1])\n  return oklabToRgb(from.map((v, i) => v + (to[i]! - v) * x))\n}\n\nexport function schemeCss(scheme: WalkScheme, t: number) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round)\n  return `rgb(${r}, ${g}, ${b})`\n}\n\nexport function schemeColor(scheme: WalkScheme, t: number) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round)\n  return packAbgr(r!, g!, b!, 255)\n}\n\n// A field's value at a node through the walk's scheme; `t` undefined is a node\n// the field has nothing to say about, off the reference for `reference`\nexport function encodedColor({ field, scheme }: WalkEncoding, t?: number) {\n  return field === 'walk'\n    ? schemeColor(scheme, BASE_T)\n    : t === undefined\n      ? NO_VALUE_COLOR\n      : schemeColor(scheme, t)\n}\n\nexport const NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR\nexport const NO_VALUE_CSS = REFERENCE_RAMP_ALT_CSS\n\n// A swatch for the legend: the walk's colour, or the scheme across the field\nexport function encodingSwatchCss({ field, scheme }: WalkEncoding) {\n  if (field === 'walk') {\n    return schemeCss(scheme, BASE_T)\n  }\n  const stops = Array.from({ length: 7 }, (_, i) => {\n    const t = i / 6\n    return `${schemeCss(scheme, t)} ${t * 100}%`\n  })\n  return `linear-gradient(to right, ${stops.join(', ')})`\n}\n\nexport function fieldLegend(field: WalkField) {\n  return WALK_FIELDS.find(f => f.value === field)!.legend\n}\n", "import { packAbgr } from '@jbrowse/core/util/colorBits'\n\nimport { fadeAbgr } from './colorBits'\nimport { meanDepth, nodeWidthPx } from '../nodeWidths'\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt,\n} from '../pathColors'\nimport { referenceMidpoints } from '../referenceSpan'\nimport { baseEdgeCurves } from '../util/edgeCurves'\nimport {\n  dashCurves,\n  pathRibbonOffsets,\n  translateCurves,\n  yToXOf,\n} from '../util/geometry'\n\nimport type { ResolvedColorScheme } from '../colorSchemes'\nimport type { NodeWidth } from '../nodeWidths'\nimport type { Graph, GraphNode, NodeSegment } from '../types'\nimport type { WalkLift } from '../walkHighlight'\nimport type {\n  Arrowhead,\n  EdgeCurveBatch,\n  NodeStroke,\n  RenderBatch,\n  Run,\n} from './types'\nimport type { AxisScale, BezierCurve } from '../util/geometry'\n\n// Colors flow through the geometry builder as ABGR-in-u32 (see colorBits.ts),\n// so a brighten or fade is integer arithmetic and a batch of a hundred thousand\n// strokes carries its colours in one number each.\nconst EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217) // rgb(119,119,119) ~ 0.467, alpha 0.85\nconst EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217) // ~0.533, alpha 0.85\n// An edge that skips reference sequence: the graph's own statement that some\n// haplotype does not carry what the backbone does. Drawn thicker than a plain\n// link, and unconditionally rather than under a colour scheme, because a\n// deletion has no node to colour \u2014 nothing else in the drawing can carry it, so\n// there is no scheme it could disagree with. See deletionEdges.ts.\n//\n// NEAR-BLACK, not red. The reference-position ramp runs hue 0 to 300 at 70%/50%,\n// and its hue-0 end is rgb(217,38,38) \u2014 the old rgb(214,39,40) was that colour\n// to within three points, so at the start of any region the deletion arc and the\n// backbone under it were the same red (review: \"the 'red' coloring is too close\n// to the rainbow\"). Nothing else in the drawing is near-black: nodes are ramp\n// hues or the off-reference charcoal, plain links are mid grey. Weight and\n// darkness carry it instead of a hue, which is what keeps hue meaning reference\n// position and only that.\nconst EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240)\nconst DELETION_THICKNESS_FACTOR = 2.2\n// A lifted walk's links keep their plain ink, since the walk's lanes in the\n// nodes carry it, and the rest fades. The alpha they fade to keeps every colour\n// scheme's hues, only dimmer, on any background.\nexport const LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255)\nexport const FADED_ALPHA = 0.18\n// Dash period in screen px, so a dashed arc looks the same at any zoom. Dashes\n// are geometry rather than a stroke style, because only one of the two backends\n// has one; see dashCurves.\nconst DELETION_DASH_PX = 11\n\n// A node drawn under `drawPaths` is split into one lengthwise stripe per path in\n// the graph, in the legend's own order, and a path that does not visit the node\n// leaves its slot empty. The slot is what makes carriage readable: an absence\n// lands in the same place on every node, so \"which sample skips this segment\"\n// is a gap at a fixed height rather than something to be counted.\n//\n// Only the edges used to carry this, and how many of a graph's paths resolved\n// there was a function of how long the edge happened to be DRAWN: a kilobase\n// deletion is one long edge and separates all five strokes, while a 1 bp SNP\n// bubble is an edge a few px long and shows a speck (review: \"only deletion\n// really shows paths clearly, the edges between nodes are too small to see the\n// paths ... even coloring the length of the nodes using the per-sample colors\").\n// A node is drawn at its own length, which is the one thing in the drawing that\n// does not shrink to a joint.\n//\n// How many paths is too many to colour at all is not decided here \u2014 it is one\n// rule over the stripes, the ribbons and the key, so the model resolves it and\n// hands down the answer as `drawPaths`. See MAX_PATH_COLORS.\n//\n// A stripe below this many screen px is not a color, it is aliasing between\n// neighbouring stripes. Under it the node keeps its own scheme colour.\n// `contigThickness` is itself in screen px, so this bites on the path COUNT\n// rather than on the zoom.\nconst MIN_PATH_STRIPE_PX = 1.2\n// A lifted walk's lane is never thinner than this, so a node carrying three\n// lifted walks widens rather than splitting into hairlines\nconst MIN_WALK_LANE_PX = 4\n// Guards the screen-px-to-world division below against a degenerate transform.\nconst MIN_SCALE_FOR_OFFSET = 1e-6\n\n// An arrowhead's size in SCREEN px, grown from the half-width of the edge it\n// ends: the renderer expands it after the transform (see TransformUniform), so\n// a head is the same size at every zoom. A fixed 12 px head was twice the width\n// of a default 6 px node and hid the 1 bp nodes it pointed at; this one is about\n// a node wide on a default edge and grows with a deletion's or a walk's weight.\nconst ARROW_LENGTH_BASE_PX = 7\nconst ARROW_LENGTH_PER_EDGE_PX = 3\nconst ARROW_HALF_WIDTH_BASE_PX = 3\nconst ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5\n// A head on an edge shorter than itself would overhang the node it leaves, so\n// it shrinks to fit, and below this fraction of its size it is dropped until a\n// zoom lengthens the edge. In a tight bubble the old heads, laid over every\n// 1 bp allele, were most of the ink.\nconst MIN_ARROW_FIT = 0.5\nconst MIN_ARROW_SCALE = 0.45\n\n// Steps per cubic when walking a curve back from its end, spaced by the square\n// of the step so they bunch where the head sits: the first is 1/144 of the\n// cubic, a few px on even a long edge.\nconst ARROW_CURVE_STEPS = 12\n// Below this an edge has no length, only the rounding of sampling one.\nconst ABUTTING_PX = 1e-6\n\n// Scratch for backFromEnd, reused across edges: this runs once per head per\n// rebuild, and objects per sample doubled the cost of a 16k-edge build.\nlet walkX = new Float64Array(64)\nlet walkY = new Float64Array(64)\nlet walkPx = new Float64Array(64)\n\n// A run of curves as points walked back from its end into the walk arrays,\n// each with its distance from the end in screen px, as far as `untilPx`.\n// Returns the point count.\nfunction backFromEnd(\n  curves: BezierCurve[],\n  scale: number,\n  yToX: number,\n  untilPx: number,\n) {\n  const most = curves.length * ARROW_CURVE_STEPS + 1\n  if (walkX.length < most) {\n    walkX = new Float64Array(most)\n    walkY = new Float64Array(most)\n    walkPx = new Float64Array(most)\n  }\n  const last = curves[curves.length - 1]!\n  walkX[0] = last.x1\n  walkY[0] = last.y1\n  walkPx[0] = 0\n  let n = 1\n  let px = 0\n  for (let ci = curves.length - 1; ci >= 0 && px < untilPx; ci--) {\n    const c = curves[ci]!\n    for (let k = 1; k <= ARROW_CURVE_STEPS && px < untilPx; k++) {\n      const t = 1 - (k / ARROW_CURVE_STEPS) ** 2\n      const u = 1 - t\n      const a = u * u * u\n      const b = 3 * u * u * t\n      const d = 3 * u * t * t\n      const e = t * t * t\n      const x = a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1\n      const y = a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1\n      px += Math.hypot(x - walkX[n - 1]!, (y - walkY[n - 1]!) * yToX) * scale\n      walkX[n] = x\n      walkY[n] = y\n      walkPx[n] = px\n      n++\n    }\n  }\n  return n\n}\n\nfunction walkPointAt(n: number, px: number) {\n  let i = 1\n  while (i < n - 1 && walkPx[i]! < px) {\n    i++\n  }\n  const from = walkPx[i - 1]!\n  const to = walkPx[i]!\n  const f = to > from ? Math.min(1, Math.max(0, (px - from) / (to - from))) : 0\n  return {\n    x: walkX[i - 1]! + (walkX[i]! - walkX[i - 1]!) * f,\n    y: walkY[i - 1]! + (walkY[i]! - walkY[i - 1]!) * f,\n  }\n}\n\n// Bandage's rule, from GraphicsItemNode::shape: a node's arrow is sized by the\n// node's own width. Here the head belongs to the edge, so the edge sets its\n// size, and the node it enters sets where the tip stops. The tip lands on that\n// node's outline, which a round cap puts `nodeHalfWidth` from the endpoint in\n// every direction; on the centreline it sank half a node deep and covered the\n// node's first few px. Only as far as the edge is long, so an abutting joint\n// keeps its head on the joint.\n//\n// A joint's head lies over the node the edge leaves, so that node's drawn\n// length is the room it fits to. A run of 1 bp nodes on a walk row otherwise\n// drew a head at every joint, a serration along the row.\n//\n// The head lies along the curve it ends, from the curve point a head-length\n// back to the tip. The end tangent alone runs along the entered node, and an\n// edge that turns in its last few px then drew a head pointing across its own\n// stroke.\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments,\n}: {\n  curves: BezierCurve[]\n  edgeHalfWidth: number\n  nodeHalfWidth: number\n  scale: number\n  yToX: number\n  color: number\n  fromSegments: NodeSegment[]\n  toSegments: NodeSegment[]\n}): Arrowhead | undefined {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth\n  const n = backFromEnd(curves, scale, yToX, nodeHalfWidth + length)\n  const lengthPx = walkPx[n - 1]!\n  const inset = Math.min(nodeHalfWidth, lengthPx)\n  const room =\n    lengthPx < ABUTTING_PX\n      ? polylinePx(fromSegments, scale, yToX)\n      : lengthPx - inset\n  const fit = Math.min(1, room / length)\n  if (fit < MIN_ARROW_FIT) {\n    return undefined\n  }\n  const tip = walkPointAt(n, inset)\n  const base = walkPointAt(n, inset + length * fit)\n  const dx = tip.x - base.x\n  const dy = (tip.y - base.y) * yToX\n  const last = curves[curves.length - 1]!\n  return {\n    x: tip.x,\n    y: tip.y,\n    angle:\n      Math.hypot(dx, dy) > 0\n        ? Math.atan2(dy, dx)\n        : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth:\n      (ARROW_HALF_WIDTH_BASE_PX +\n        ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) *\n      fit,\n    color,\n  }\n}\n\nfunction polylinePx(segments: NodeSegment[], scale: number, yToX: number) {\n  let length = 0\n  for (let i = 1; i < segments.length; i++) {\n    length += Math.hypot(\n      segments[i]!.x - segments[i - 1]!.x,\n      (segments[i]!.y - segments[i - 1]!.y) * yToX,\n    )\n  }\n  return length * scale\n}\n\n// The way into a node from the end an edge reaches it at: the direction an\n// abutting edge, which has no length of its own, points.\nfunction intoDirection(last: BezierCurve, toSegments: NodeSegment[]) {\n  if (toSegments.length < 2) {\n    return undefined\n  }\n  const first = toSegments[0]!\n  const final = toSegments[toSegments.length - 1]!\n  const atStart =\n    Math.hypot(last.x1 - first.x, last.y1 - first.y) <=\n    Math.hypot(last.x1 - final.x, last.y1 - final.y)\n  return atStart\n    ? { from: first, to: toSegments[1]! }\n    : { from: final, to: toSegments[toSegments.length - 2]! }\n}\n\n// Per-point unit normals of a polyline, mitred at the interior joints so a\n// stripe slid along them keeps a constant distance from the node's own outline\n// where it bends.\n//\n// `yToX` puts the two axes in comparable units first (see computeEdgeCurves), so\n// the normal is perpendicular to the polyline AS DRAWN rather than to its\n// coordinates. It is 1 on an isotropic layout, where the two are the same thing.\nfunction pointNormalsOf(rawPoints: { x: number; y: number }[], yToX = 1) {\n  const points =\n    yToX === 1 ? rawPoints : rawPoints.map(p => ({ x: p.x, y: p.y * yToX }))\n  const pointNormals: { nx: number; ny: number }[] = []\n  for (let i = 0; i < points.length; i++) {\n    let nx = 0\n    let ny = 0\n\n    if (i === 0) {\n      const dx = points[1]!.x - points[0]!.x\n      const dy = points[1]!.y - points[0]!.y\n      const len = Math.hypot(dx, dy)\n      if (len > 0) {\n        nx = -dy / len\n        ny = dx / len\n      }\n    } else if (i === points.length - 1) {\n      const dx = points[i]!.x - points[i - 1]!.x\n      const dy = points[i]!.y - points[i - 1]!.y\n      const len = Math.hypot(dx, dy)\n      if (len > 0) {\n        nx = -dy / len\n        ny = dx / len\n      }\n    } else {\n      const dx1 = points[i]!.x - points[i - 1]!.x\n      const dy1 = points[i]!.y - points[i - 1]!.y\n      const len1 = Math.hypot(dx1, dy1)\n      const dx2 = points[i + 1]!.x - points[i]!.x\n      const dy2 = points[i + 1]!.y - points[i]!.y\n      const len2 = Math.hypot(dx2, dy2)\n\n      if (len1 > 0 && len2 > 0) {\n        const nx1 = -dy1 / len1\n        const ny1 = dx1 / len1\n        const nx2 = -dy2 / len2\n        const ny2 = dx2 / len2\n        nx = (nx1 + nx2) / 2\n        ny = (ny1 + ny2) / 2\n        const dot = nx1 * nx + ny1 * ny\n        if (dot > 0.1) {\n          nx /= dot\n          ny /= dot\n        }\n      } else if (len1 > 0) {\n        nx = -dy1 / len1\n        ny = dx1 / len1\n      } else if (len2 > 0) {\n        nx = -dy2 / len2\n        ny = dx2 / len2\n      }\n    }\n    pointNormals.push({ nx, ny })\n  }\n  return pointNormals\n}\n\n// The polyline shifted `distance` world units along its own normals, which is\n// the node equivalent of the constant perpendicular offset the edge path\n// strokes already take. `distance` is in x units and the normal is the drawn\n// one (pointNormalsOf), so the y component comes back out of x units here.\nfunction offsetPolyline(\n  points: { x: number; y: number }[],\n  normals: { nx: number; ny: number }[],\n  distance: number,\n  yToX = 1,\n) {\n  return points.map((p, i) => ({\n    x: p.x + normals[i]!.nx * distance,\n    y: p.y + (normals[i]!.ny * distance) / yToX,\n  }))\n}\n\nfunction packNorm(r: number, g: number, b: number, a: number) {\n  return packAbgr(\n    Math.round(r * 255),\n    Math.round(g * 255),\n    Math.round(b * 255),\n    Math.round(a * 255),\n  )\n}\n\nexport interface BuildOptions {\n  nodePositions: Record<string, NodeSegment[]>\n  graph: Graph\n  nodeById: Map<string, GraphNode>\n  colorScheme: ResolvedColorScheme\n  contigThickness: number\n  connectorThickness: number\n  // Whether to paint per path \u2014 the RESOLVED answer, not the raw view prop.\n  // Past MAX_PATH_COLORS a graph's paths are not drawable as colours at all and\n  // the model hands over `false`, which is the one place that decides it for\n  // the stripes, the ribbons and the key together. Same contract as\n  // `colorScheme` above, which arrives with 'auto' already resolved.\n  drawPaths: boolean\n  // thicker by depth, or every node at `contigThickness`; see nodeWidths.ts\n  nodeWidth?: NodeWidth\n  // walks lifted out: each draws a lane of its own along the nodes it visits,\n  // their links draw dark and heavy, and everything else fades to a fraction\n  // of its alpha\n  highlight?: WalkLift\n  // Both scales together, and required. Every screen-metric constant here (dash\n  // period, stripe width, arrowhead angle) divides by scaleX, and everything\n  // that mixes the axes needs their ratio; taking them as one value is what\n  // keeps a caller from supplying an x scale and defaulting y, which draws a\n  // wrong picture and reports nothing. See AxisScale.\n  axis: AxisScale\n  linearLayout?: boolean\n  viewportBounds?: { minX: number; minY: number; maxX: number; maxY: number }\n  // What the 'reference-position' scheme paints from: each node's midpoint on\n  // the reference, and the interval the hue spans. Unused by every other\n  // scheme, and passed in rather than derived here for the reason `deletions`\n  // below is \u2014 it costs a neighbour walk per node, it is a fact about the\n  // graph, and this function runs on every pan. `computeReferenceRamp` is what\n  // builds one.\n  referenceRamp?: ReferenceRamp\n  // links that skip reference sequence (deletionEdges()), keyed by their index\n  // into graph.edges and carrying the backbone node ids they bypass. Passed in\n  // rather than derived here because the model can hold it against the graph,\n  // and because the same set names the hover text.\n  deletions?: Map<number, string[]>\n  hiddenEdges?: ReadonlySet<number>\n  // Bumped when a drag moves the positions in place, which their identity\n  // cannot report. Only the shared curve cache reads it; see baseEdgeCurves.\n  version?: number\n}\n\nexport function hslToRgb(\n  h: number,\n  s: number,\n  l: number,\n): [number, number, number] {\n  const c = (1 - Math.abs(2 * l - 1)) * s\n  const x = c * (1 - Math.abs(((h / 60) % 2) - 1))\n  const m = l - c / 2\n  let r = 0\n  let g = 0\n  let b = 0\n  if (h < 60) {\n    r = c\n    g = x\n  } else if (h < 120) {\n    r = x\n    g = c\n  } else if (h < 180) {\n    g = c\n    b = x\n  } else if (h < 240) {\n    g = x\n    b = c\n  } else if (h < 300) {\n    r = x\n    b = c\n  } else {\n    r = c\n    b = x\n  }\n  return [r + m, g + m, b + m]\n}\n\n// Evenly-spaced RGB gradient stops (0-255 per channel).\nconst DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37],\n] as const\n\n// ranks >= 1, i.e. everything off the reference backbone\nconst STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122],\n] as const\n\nconst NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220],\n] as const\n\n// Sample a piecewise-linear RGB gradient; t is clamped to [0,1].\nfunction sampleGradient(\n  stops: readonly (readonly [number, number, number])[],\n  t: number,\n) {\n  const pos = Math.max(0, Math.min(1, t)) * (stops.length - 1)\n  const i = Math.min(stops.length - 2, Math.floor(pos))\n  const f = pos - i\n  const a = stops[i]!\n  const b = stops[i + 1]!\n  return packAbgr(\n    Math.round(a[0] + (b[0] - a[0]) * f),\n    Math.round(a[1] + (b[1] - a[1]) * f),\n    Math.round(a[2] + (b[2] - a[2]) * f),\n    255,\n  )\n}\n\n// Deterministic color from a string (djb2-style hash \u2192 HSL hue), for the\n// `random` node scheme. The path ribbons do NOT use this \u2014 see pathHueAt.\nfunction hashColor(str: string, alpha: number) {\n  const [r, g, b] = hslToRgb(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS)\n  return packNorm(r, g, b, alpha)\n}\n\n// A hue ramp over reference coordinates, which is the one colouring a linear\n// track can reproduce exactly: it is a function of two stated numbers and a\n// node's reference midpoint, so `hsl(min(300,max(0,(mid-start)/span*300)),70%,50%)`\n// in a track's `color` slot paints a segment the colour the graph paints its\n// node. Stops at 300 rather than wrapping to 360, so the two ends of the window\n// are red and magenta rather than both red.\nexport const REFERENCE_RAMP_MAX_HUE = 300\nconst REFERENCE_RAMP_SATURATION = 0.7\nconst REFERENCE_RAMP_LIGHTNESS = 0.5\n// Off-reference segments come off the ramp entirely and paint one flat charcoal.\n//\n// They used to keep the hue of the reference they replace, paler and softer, on\n// the argument that the correspondence is the whole scheme. Two rounds of docs\n// review say otherwise: a pale hue is still a hue on the ramp, so an alternative\n// allele reads as reference sequence at that position rather than as sequence\n// the reference does not have \u2014 \"non-backbone parts of the bandage graph could\n// be coloured in a non-spectrum colouring\". Nothing is lost by dropping the hue,\n// because in both anchored layouts an allele's x already states which reference\n// position it attaches to, and in the force layout its position states nothing\n// to begin with.\n//\n// Distinct from the light grey a node with no reference coordinates at all gets:\n// this one is anchored and off-reference, that one is unplaceable.\nconst REFERENCE_RAMP_ALT_RGB = [60, 65, 72] as const\nexport const REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255)\nexport const REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(', ')})`\n\nexport interface ReferenceRamp {\n  start: number\n  span: number\n  midpoints: Map<string, number>\n}\n\nexport interface ColorSchemeRange {\n  minDepth: number\n  maxDepth: number\n  minLength: number\n  maxLength: number\n  maxRank: number\n  nodeCount: number\n  referenceRamp?: ReferenceRamp\n}\n\n// The domain is stated by the caller \u2014 the region the subgraph was cut from \u2014\n// rather than measured off the nodes, because a linear view has no way to know\n// what the cut reached: segments overrun the region at both edges, so a\n// measured domain would shift the hue of every node by an amount the other\n// panel cannot compute. With no region (a whole-file import) the drawn extent\n// is all there is, and the ramp is then only comparable to itself.\nexport function computeReferenceRamp(\n  graph: Graph,\n  domain: { start: number; end: number } | undefined,\n): ReferenceRamp {\n  const midpoints = referenceMidpoints(graph)\n  if (domain && domain.end > domain.start) {\n    return {\n      start: domain.start,\n      span: domain.end - domain.start,\n      midpoints,\n    }\n  }\n  let min = Infinity\n  let max = -Infinity\n  for (const mid of midpoints.values()) {\n    min = Math.min(min, mid)\n    max = Math.max(max, mid)\n  }\n  return {\n    start: min === Infinity ? 0 : min,\n    span: max > min ? max - min : 1,\n    midpoints,\n  }\n}\n\nexport function computeColorSchemeRange(graph: Graph) {\n  let minDepth = Infinity\n  let maxDepth = -Infinity\n  let minLength = Infinity\n  let maxLength = -Infinity\n  let maxRank = 0\n  for (const n of graph.nodes) {\n    if (n.stable !== undefined && n.stable.rank > maxRank) {\n      maxRank = n.stable.rank\n    }\n    if (n.depth < minDepth) {\n      minDepth = n.depth\n    }\n    if (n.depth > maxDepth) {\n      maxDepth = n.depth\n    }\n    if (n.length < minLength) {\n      minLength = n.length\n    }\n    if (n.length > maxLength) {\n      maxLength = n.length\n    }\n  }\n  return {\n    minDepth,\n    maxDepth,\n    minLength,\n    maxLength,\n    maxRank,\n    nodeCount: graph.nodes.length,\n  } satisfies ColorSchemeRange\n}\n\nexport function getNodeColor(\n  node: GraphNode,\n  nodeIndex: number,\n  colorScheme: ResolvedColorScheme,\n  range: ColorSchemeRange,\n) {\n  switch (colorScheme) {\n    case 'random':\n      return hashColor(node.id, 1)\n\n    case 'depth':\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth\n          ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth)\n          : 0.5,\n      )\n\n    case 'node-length':\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength\n          ? (node.length - range.minLength) /\n              (range.maxLength - range.minLength)\n          : 0.5,\n      )\n\n    // rGFA states the backbone rather than leaving it to be inferred: rank 0 is\n    // the reference, higher ranks are the sequence that diverges from it. A\n    // graph with no SR tags draws every node as unranked.\n    case 'stable-rank':\n      return node.stable === undefined\n        ? packAbgr(160, 160, 160, 255)\n        : node.stable.rank === 0\n          ? packAbgr(52, 152, 219, 255)\n          : sampleGradient(\n              STABLE_RANK_GRADIENT,\n              range.maxRank > 1\n                ? (node.stable.rank - 1) / (range.maxRank - 1)\n                : 0,\n            )\n\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state. A node with no reference position at\n    // all \u2014 nothing anchored, or an allele whose flanks fell outside the cut \u2014\n    // is grey rather than a hue it has not earned.\n    case 'reference-position': {\n      const ramp = range.referenceRamp\n      const mid = ramp?.midpoints.get(node.id)\n      if (ramp === undefined || mid === undefined) {\n        return packAbgr(160, 160, 160, 255)\n      }\n      if (node.stable !== undefined && node.stable.rank > 0) {\n        return REFERENCE_RAMP_ALT_COLOR\n      }\n      const frac = Math.max(0, Math.min(1, (mid - ramp.start) / ramp.span))\n      const [r, g, b] = hslToRgb(\n        frac * REFERENCE_RAMP_MAX_HUE,\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS,\n      )\n      return packNorm(r, g, b, 1)\n    }\n\n    case 'grey':\n      return packAbgr(160, 160, 160, 255)\n\n    case 'rainbow': {\n      const hue = range.nodeCount > 1 ? (nodeIndex / range.nodeCount) * 360 : 0\n      const [r, g, b] = hslToRgb(hue, 0.75, 0.5)\n      return packNorm(r, g, b, 1)\n    }\n\n    default:\n      return packAbgr(52, 152, 219, 255)\n  }\n}\n\n// The SCREEN angle an arrowhead points: a cubic's tangent at t=1, which runs\n// from its last control point to its endpoint, so no tessellation is needed.\n// The head is expanded from a screen-px size after the transform, so its\n// direction has to be the drawn one too, and `yToX` puts the y difference in x\n// units first.\n//\n// A control point on the endpoint states no direction there. The tangent's\n// limit as t -> 1 then runs from the FIRST control point, and failing that from\n// the start. An edge with no length at all, the abutting joint of an anchored\n// layout, has none of those, and `into` (the way into the node it enters) is\n// what is left; without it such a head pointed along +x whatever the node did.\nexport function endTangent(\n  c: BezierCurve,\n  yToX = 1,\n  into?: { from: NodeSegment; to: NodeSegment },\n) {\n  const candidates: [number, number][] = [\n    [c.cx1, c.cy1],\n    [c.cx0, c.cy0],\n    [c.x0, c.y0],\n  ]\n  for (const [x, y] of candidates) {\n    const dx = c.x1 - x\n    const dy = (c.y1 - y) * yToX\n    if (Math.hypot(dx, dy) > 0) {\n      return Math.atan2(dy, dx)\n    }\n  }\n  return into\n    ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x)\n    : 0\n}\n\n// Whether any part of a node's polyline falls inside the viewport. Testing the\n// *segments* rather than their endpoints is what makes a node wider than the\n// window visible: in the reference-anchored layouts x is in bp, so a backbone\n// segment routinely spans the whole viewport with both ends outside it, and\n// point containment culled exactly the segment the view exists to show.\n//\n// Segment bounding boxes, not exact line-rect intersection: culling only has to\n// avoid dropping something visible, and a diagonal kept by its bbox costs one\n// polyline.\nfunction isPolylineInBounds(\n  segments: NodeSegment[],\n  bounds: { minX: number; minY: number; maxX: number; maxY: number },\n) {\n  let hit = false\n  for (let i = 0; i < segments.length - 1 && !hit; i++) {\n    const a = segments[i]!\n    const b = segments[i + 1]!\n    hit =\n      Math.max(a.x, b.x) >= bounds.minX &&\n      Math.min(a.x, b.x) <= bounds.maxX &&\n      Math.max(a.y, b.y) >= bounds.minY &&\n      Math.min(a.y, b.y) <= bounds.maxY\n  }\n  return hit\n}\n\nfunction isBezierInBounds(\n  curves: BezierCurve[],\n  bounds: { minX: number; minY: number; maxX: number; maxY: number },\n) {\n  for (const c of curves) {\n    const cMinX = Math.min(c.x0, c.cx0, c.cx1, c.x1)\n    const cMaxX = Math.max(c.x0, c.cx0, c.cx1, c.x1)\n    const cMinY = Math.min(c.y0, c.cy0, c.cy1, c.y1)\n    const cMaxY = Math.max(c.y0, c.cy0, c.cy1, c.y1)\n    if (\n      cMaxX >= bounds.minX &&\n      cMinX <= bounds.maxX &&\n      cMaxY >= bounds.minY &&\n      cMinY <= bounds.maxY\n    ) {\n      return true\n    }\n  }\n  return false\n}\n\n// Per-graph derivations, cached on the graph: this function runs on every\n// debounced pan and zoom, and a walk over every path's every step is a fact\n// about the graph rather than about the frame.\n\n// By position in the path list, matching pathLegend's swatches exactly, so the\n// key beside the drawing names the strokes in it.\n//\n// One array plus a name lookup, rather than an array and a Map of the same\n// colours: two paths that share a name then draw the same colour on their\n// edges and on their nodes, instead of the Map keeping the last one written\n// while the array kept the first. `gfaConverter` no longer produces such a\n// pair, and this is what makes the drawing merely wrong rather than\n// inconsistent if anything ever does again.\nconst paletteCache = new WeakMap<\n  Graph,\n  { pathColorByIndex: number[]; pathIndexByName: Map<string, number> }\n>()\n\nfunction pathPaletteOf(graph: Graph) {\n  let palette = paletteCache.get(graph)\n  if (!palette) {\n    const pathColorByIndex: number[] = []\n    const pathIndexByName = new Map<string, number>()\n    const paths = graph.paths ?? []\n    for (let i = 0; i < paths.length; i++) {\n      const [r, g, b] = hslToRgb(\n        pathHueAt(i, paths.length),\n        PATH_SATURATION,\n        PATH_LIGHTNESS,\n      )\n      pathColorByIndex.push(packNorm(r, g, b, 0.85))\n      if (!pathIndexByName.has(paths[i]!.name)) {\n        pathIndexByName.set(paths[i]!.name, i)\n      }\n    }\n    palette = { pathColorByIndex, pathIndexByName }\n    paletteCache.set(graph, palette)\n  }\n  return palette\n}\n\n// nodeId -> the indices of the paths that visit it, i.e. which stripe slots\n// this node fills. Built from the paths themselves rather than read off the\n// node, because `GraphNode.samples` collapses a sample's haplotypes together\n// and the legend does not.\nconst slotsCache = new WeakMap<Graph, Map<string, number[]>>()\nconst NO_SLOTS: ReadonlyMap<string, number[]> = new Map()\n\nfunction pathSlotsOf(graph: Graph): ReadonlyMap<string, number[]> {\n  let slots = slotsCache.get(graph)\n  if (!slots) {\n    slots = new Map()\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        const visits = slots.get(nodeId)\n        if (visits) {\n          visits.push(pathIdx)\n        } else {\n          slots.set(nodeId, [pathIdx])\n        }\n      }\n    }\n    slotsCache.set(graph, slots)\n  }\n  return slots\n}\n\nexport function buildGeometry(options: BuildOptions): RenderBatch {\n  const {\n    nodePositions,\n    graph,\n    nodeById,\n    colorScheme,\n    contigThickness,\n    connectorThickness,\n    drawPaths,\n    nodeWidth = 'uniform',\n    highlight,\n    axis,\n    linearLayout,\n    viewportBounds,\n    referenceRamp,\n    deletions,\n    hiddenEdges,\n    version = 0,\n  } = options\n  const depthNorm = nodeWidth === 'depth' ? meanDepth(graph) : 0\n  const scale = axis.scaleX\n  const yToX = yToXOf(axis)\n  // The offset-zero curve of every edge, from the one place that derives it \u2014\n  // shared with the hit index, which draws its boxes from the same objects.\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n  )\n\n  const nodeStrokes: NodeStroke[] = []\n  const nodeStrokeRuns = new Map<string, Run>()\n  const arrows: Arrowhead[] = []\n  const arrowRuns = new Map<number, Run>()\n  const edgeCurves: EdgeCurveBatch[] = []\n  const edgeCurveRuns = new Map<number, Run>()\n\n  const colorRange = { ...computeColorSchemeRange(graph), referenceRamp }\n\n  const nodeIndexMap = new Map<string, number>()\n  if (colorScheme === 'rainbow') {\n    for (let i = 0; i < graph.nodes.length; i++) {\n      nodeIndexMap.set(graph.nodes[i]!.id, i)\n    }\n  }\n\n  const pathCount = graph.paths?.length ?? 0\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph)\n  const pathColorByName = (name: string) =>\n    pathColorByIndex[pathIndexByName.get(name) ?? -1] ??\n    EDGE_PATH_FALLBACK_COLOR\n  const nodePathSlots =\n    drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS\n\n  // An arrowhead at every joint of a few hundred short nodes is a serration\n  // along the whole drawing, so heads wait for a zoom where a node is longer\n  // than its head.\n  const showArrows = scale > (linearLayout ? 1 : MIN_ARROW_SCALE)\n\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei]!\n    const fromSegments = nodePositions[edge.from]\n    const toSegments = nodePositions[edge.to]\n    const baseCurves = sharedCurves.get(ei)\n    if (\n      !fromSegments?.length ||\n      !toSegments?.length ||\n      !baseCurves ||\n      hiddenEdges?.has(ei)\n    ) {\n      continue\n    }\n\n    const numPaths = edge.pathIds?.length ?? 0\n    const bypassed = deletions?.get(ei)\n    const isDeletion = bypassed !== undefined\n    const onWalk = highlight?.edgeIndexes.has(ei) ?? false\n    const edgeThickness =\n      (connectorThickness / 2) * (isDeletion ? DELETION_THICKNESS_FACTOR : 1)\n    // One stroke per path crossing the edge, fanned off it: the shared curve\n    // slid sideways, which is also what the hit index tests against. Rebuilding\n    // the curve at each offset was 40% of a striped build and differed from a\n    // translation only in a deletion's bow, by the offset's few px.\n    const ribbons = drawPaths && numPaths > 0\n\n    // An arrowhead states which way a LINK is read, which is a property of the\n    // edge and not of each path crossing it. Drawn per ribbon it says one thing\n    // once per haplotype: five stacked heads at a joint, in five colours, for a\n    // single fact about a single link. That is the \"coloured confetti at each\n    // joint\" that made `drawPaths` unusable on a force layout, and it reached\n    // the anchored layouts too the moment their abutting edges started drawing\n    // again. Measured on `ecoli_pggb_subgraph.gfa`: 72 arrowheads plain, 155\n    // with ribbons, over 72 links.\n    //\n    // So one head per edge, in the edge's own colour rather than a ribbon's,\n    // since choosing a ribbon's would privilege one haplotype for a fact that\n    // belongs to none of them. `undefined` means this call draws no head.\n    const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR\n    const edgeColor =\n      !highlight || onWalk\n        ? plainEdgeColor\n        : fadeAbgr(plainEdgeColor, FADED_ALPHA)\n    const toNode = nodeById.get(edge.to)\n    const intoHalfWidth =\n      (toNode\n        ? nodeWidthPx(toNode, contigThickness, nodeWidth, depthNorm)\n        : contigThickness) / 2\n    const buildSingleEdge = (\n      offsetX: number,\n      offsetY: number,\n      color: number,\n      arrowColor: number | undefined,\n    ) => {\n      const curves =\n        offsetX === 0 && offsetY === 0\n          ? baseCurves\n          : translateCurves(baseCurves, offsetX, offsetY)\n\n      if (viewportBounds && !isBezierInBounds(curves, viewportBounds)) {\n        return\n      }\n\n      // A deletion is drawn dashed, and that is the only thing in the drawing\n      // that is. Weight and darkness were carrying it alone, and they could not:\n      // an off-reference node is charcoal rgb(60,65,72) and the arc is near-black\n      // rgb(24,24,28), which is ~25 points a channel apart, so in a figure the\n      // two dark strokes read as the same ink and the arc is the rarer of them\n      // (measured on `pangenome/hprc_lpa_kiv2`: 7,411 px of charcoal node against\n      // ~5,000 px of arc). Hue cannot separate them either, since hue means\n      // reference position and charcoal means having none. A broken line is\n      // available, unused, and says what it draws: sequence that is not there.\n      if (isDeletion) {\n        for (const dash of dashCurves(curves, DELETION_DASH_PX / scale)) {\n          edgeCurves.push({ curves: dash, thickness: edgeThickness, color })\n        }\n      } else {\n        edgeCurves.push({ curves, thickness: edgeThickness, color })\n      }\n\n      const head =\n        showArrows && arrowColor !== undefined\n          ? arrowheadFor({\n              curves,\n              edgeHalfWidth: edgeThickness,\n              nodeHalfWidth: intoHalfWidth,\n              scale,\n              yToX,\n              color: arrowColor,\n              fromSegments,\n              toSegments,\n            })\n          : undefined\n      if (head) {\n        arrows.push(head)\n      }\n    }\n\n    const edgeCurveStart = edgeCurves.length\n    const arrowStart = arrows.length\n\n    // A lifted walk's link carries on its lane from the node it leaves, so a\n    // lane runs unbroken through the joints rather than beside a grey link\n    const laneWalks =\n      highlight && onWalk && !ribbons ? highlight.walks : undefined\n    if (laneWalks) {\n      const fromNode = nodeById.get(edge.from)\n      const width = fromNode\n        ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm)\n        : contigThickness\n      const laneWidth = Math.max(width / laneWalks.length, MIN_WALK_LANE_PX)\n      // the lanes' sideways direction where the link leaves its node, which\n      // is the end a '-' link leaves from the start of\n      const normals = pointNormalsOf(fromSegments, yToX)\n      const { nx, ny } = (edge.fromStrand === '-'\n        ? normals[0]\n        : normals.at(-1)) ?? {\n        nx: 0,\n        ny: 0,\n      }\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET)\n      laneWalks.forEach((walk, lane) => {\n        if (!walk.edgeIndexes.has(ei)) {\n          return\n        }\n        const offset =\n          (lane - (laneWalks.length - 1) / 2) * laneWidth * worldPerScreenPx\n        const curves =\n          offset === 0\n            ? baseCurves\n            : translateCurves(baseCurves, nx * offset, (ny * offset) / yToX)\n        if (viewportBounds && !isBezierInBounds(curves, viewportBounds)) {\n          return\n        }\n        edgeCurves.push({\n          curves,\n          thickness: laneWidth / 2,\n          color:\n            walk.colors.get(edge.from) ??\n            walk.colors.get(edge.to) ??\n            plainEdgeColor,\n        })\n      })\n    } else if (!ribbons) {\n      buildSingleEdge(0, 0, edgeColor, edgeColor)\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis,\n      )\n      // The middle ribbon carries the head, which at an odd path count is the\n      // one drawn at offset 0, i.e. on the edge's own line. At an even count it\n      // is half a spacing off, which beats a sixth `computeEdgeCurves` call to\n      // rebuild a curve the fan is already centred on.\n      const arrowRibbon = Math.floor((numPaths - 1) / 2)\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const offset = offsets[pathIdx]!\n        const ribbonColor = pathColorByName(edge.pathIds![pathIdx]!)\n        buildSingleEdge(\n          offset.x,\n          offset.y,\n          highlight && !highlight.names.has(edge.pathIds![pathIdx]!)\n            ? fadeAbgr(ribbonColor, FADED_ALPHA)\n            : ribbonColor,\n          pathIdx === arrowRibbon ? edgeColor : undefined,\n        )\n      }\n    }\n\n    const edgeCurveCount = edgeCurves.length - edgeCurveStart\n    if (edgeCurveCount > 0) {\n      edgeCurveRuns.set(ei, { start: edgeCurveStart, count: edgeCurveCount })\n    }\n    const arrowCount = arrows.length - arrowStart\n    if (arrowCount > 0) {\n      arrowRuns.set(ei, { start: arrowStart, count: arrowCount })\n    }\n  }\n\n  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId)\n    if (!node) {\n      continue\n    }\n\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue\n    }\n\n    const faded = highlight !== undefined && !highlight.nodeIds.has(nodeId)\n    // Under lifted walks the lanes carry every colour, so the rest fades in\n    // grey rather than in a scheme no lane is drawn in\n    const own = faded\n      ? LIFT_BACKDROP_COLOR\n      : getNodeColor(\n          node,\n          nodeIndexMap.get(nodeId) ?? 0,\n          colorScheme,\n          colorRange,\n        )\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : own\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm)\n    const nodeThickness = width / 2\n\n    const start = nodeStrokes.length\n    // The node's drawn width is the same either way: the stripes divide it\n    // rather than inflate it, so turning paths on does not re-weight the\n    // drawing against the edges and the layout underneath it.\n    //\n    // A thickness is SCREEN px and a point is world units. So the slot width is\n    // screen px and the sideways shift that places a stripe has to be taken\n    // back into world units, or the stripes fan apart as you zoom in and\n    // collapse into one as you zoom out.\n    const slots = nodePathSlots.get(nodeId)\n    const slotWidth = width / pathCount\n    const drawable = segments.length >= 2\n    // Each lifted walk keeps one lane across the whole drawing, so a lane\n    // missing from a node is a walk that does not visit it\n    const lanes =\n      highlight && !faded && !slots?.length ? highlight.walks : undefined\n    if (drawable && lanes) {\n      const laneWidth = Math.max(width / lanes.length, MIN_WALK_LANE_PX)\n      const normals = pointNormalsOf(segments, yToX)\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET)\n      lanes.forEach((walk, lane) => {\n        const laneColor = walk.colors.get(nodeId)\n        if (laneColor === undefined) {\n          return\n        }\n        const offset =\n          (lane - (lanes.length - 1) / 2) * laneWidth * worldPerScreenPx\n        nodeStrokes.push({\n          points:\n            lanes.length === 1\n              ? segments\n              : offsetPolyline(segments, normals, offset, yToX),\n          thickness: laneWidth / 2,\n          color: laneColor,\n        })\n      })\n    } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {\n      const normals = pointNormalsOf(segments, yToX)\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET)\n      for (const slot of slots) {\n        const offset =\n          (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx\n        const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR\n        nodeStrokes.push({\n          points: offsetPolyline(segments, normals, offset, yToX),\n          thickness: slotWidth / 2,\n          // a node off the lifted walk fades whichever way it is painted\n          color: faded ? fadeAbgr(stripe, FADED_ALPHA) : stripe,\n        })\n      }\n    } else if (drawable) {\n      nodeStrokes.push({ points: segments, thickness: nodeThickness, color })\n    }\n    const count = nodeStrokes.length - start\n    if (count > 0) {\n      nodeStrokeRuns.set(nodeId, { start, count })\n    }\n  }\n\n  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns,\n  }\n}\n", "import {\n  abgrAlpha,\n  abgrBlue,\n  abgrGreen,\n  abgrRed,\n  packAbgr,\n} from '@jbrowse/core/util/colorBits'\n\n// The one ABGR helper core does not have. Everything else the renderer needs \u2014\n// the packing, the channel accessors, both css formatters \u2014 comes straight from\n// `@jbrowse/core/util/colorBits`, which ReExports/list.ts now names, so the\n// plugin bundle binds it to the host's copy. The plugin targets the latest\n// JBrowse beta; 5.0.0-beta.4 serves that module without `packAbgr`, and the\n// plugin fails to install there.\n\n// Scale a packed color's channels, clamped at full brightness and leaving alpha\n// alone. factor === 1 returns the color unchanged.\n// The same colour at a fraction of its alpha, so a faded node reads as the\n// same ink through it on any background.\nexport function fadeAbgr(c: number, alpha: number) {\n  return packAbgr(\n    abgrRed(c),\n    abgrGreen(c),\n    abgrBlue(c),\n    Math.round(abgrAlpha(c) * alpha),\n  )\n}\n\nexport function brightenAbgr(c: number, factor: number) {\n  return packAbgr(\n    Math.min(255, Math.round(abgrRed(c) * factor)),\n    Math.min(255, Math.round(abgrGreen(c) * factor)),\n    Math.min(255, Math.round(abgrBlue(c) * factor)),\n    abgrAlpha(c),\n  )\n}\n", "import { isBackbone } from './anchoredNodes'\n\nimport type { Graph, GraphNode } from './types'\n\n// How long an allele chain can be and still be located from both ends. An\n// allele is a run of off-reference segments between two backbone flanks, so the\n// two flanks sit at *different* hop depths from any segment in the middle and\n// the walk has to keep going after it finds the first one. Minigraph alleles are\n// short runs, so this reaches both flanks throughout the fixtures; a longer run\n// degrades to the flanks it did reach rather than to nothing.\nconst MAX_BACKBONE_HOPS = 4\n\nexport interface ReferenceSpan {\n  start: number\n  end: number\n}\n\n// Undirected adjacency over node ids. Edges carry the topology in both\n// directions for this purpose: finding the backbone a node hangs off doesn't\n// care which way the L line was written.\nexport function buildNeighbors(graph: Graph) {\n  const neighbors = new Map<string, string[]>()\n  function add(from: string, to: string) {\n    const list = neighbors.get(from)\n    if (list) {\n      list.push(to)\n    } else {\n      neighbors.set(from, [to])\n    }\n  }\n  for (const edge of graph.edges) {\n    add(edge.from, edge.to)\n    add(edge.to, edge.from)\n  }\n  return neighbors\n}\n\n// The reference interval an allele branches into: between the end of the\n// backbone segment upstream of it and the start of the one downstream.\n// `[min(ends), max(starts)]` picks those two out of the reached flanks without\n// needing to know which is which, and it degrades usefully in both directions \u2014\n// a pure insertion, whose flanks abut, collapses to the single reference point\n// it is inserted at, and a bubble with only one flank inside the window yields\n// that flank's own span.\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors,\n}: {\n  nodeId: string\n  nodeById: Map<string, GraphNode>\n  neighbors: Map<string, string[]>\n}) {\n  const seen = new Set([nodeId])\n  let frontier = [nodeId]\n  let minEnd = Infinity\n  let maxStart = -Infinity\n\n  // Backbone nodes are terminal \u2014 they are collected, never queued \u2014 so the walk\n  // cannot cross the reference into a neighbouring bubble. It stays inside the\n  // allele it started in and stops on its own at the flanks.\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next: string[] = []\n    for (const id of frontier) {\n      const adjacent = neighbors.get(id)\n      if (adjacent) {\n        for (const neighborId of adjacent) {\n          if (!seen.has(neighborId)) {\n            seen.add(neighborId)\n            const neighbor = nodeById.get(neighborId)\n            if (neighbor && isBackbone(neighbor)) {\n              minEnd = Math.min(minEnd, neighbor.stable.start + neighbor.length)\n              maxStart = Math.max(maxStart, neighbor.stable.start)\n            } else {\n              next.push(neighborId)\n            }\n          }\n        }\n      }\n    }\n    frontier = next\n  }\n\n  return minEnd === Infinity\n    ? undefined\n    : {\n        start: Math.min(minEnd, maxStart),\n        end: Math.max(minEnd, maxStart),\n      }\n}\n\n// The reference interval to highlight for a node, in the coordinates of the\n// stable sequence the subgraph was cut from.\n//\n// A rank-0 node states its own, so the interval is exact. A rank>0 allele has\n// none: its SO is an offset on a *different* stable sequence and is not\n// comparable to the reference axis (see the axis note in\n// layout/anchoredLayout.ts), so it is located by the backbone it branches from\n// instead.\nexport function nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors,\n}: {\n  nodeId: string\n  nodeById: Map<string, GraphNode>\n  neighbors: Map<string, string[]>\n}): ReferenceSpan | undefined {\n  const node = nodeById.get(nodeId)\n  return node === undefined\n    ? undefined\n    : isBackbone(node)\n      ? { start: node.stable.start, end: node.stable.start + node.length }\n      : flankingSpan({ nodeId, nodeById, neighbors })\n}\n\n// Every node's midpoint on the reference, keyed by id: what a position-based\n// colour scheme ramps over. Alleles come through the same flanking walk hover\n// sync uses, so a bubble takes the colour of the reference interval it branches\n// from instead of dropping out of the ramp \u2014 which is the whole point, since an\n// allele is exactly what a linear view cannot draw at a position of its own.\nexport function referenceMidpoints(graph: Graph) {\n  const nodeById = new Map(graph.nodes.map(node => [node.id, node]))\n  const neighbors = buildNeighbors(graph)\n  const midpoints = new Map<string, number>()\n  for (const node of graph.nodes) {\n    const span = nodeReferenceSpan({ nodeId: node.id, nodeById, neighbors })\n    if (span) {\n      midpoints.set(node.id, (span.start + span.end) / 2)\n    }\n  }\n  return midpoints\n}\n", "import { bypassedPoints } from '../deletionEdges'\nimport { computeEdgeCurves, selfLinkOf } from './geometry'\n\nimport type { Graph, NodeSegment } from '../types'\nimport type { AxisScale, BezierCurve } from './geometry'\n\n// Every edge's curve as it is DRAWN, at offset zero, derived once for a layout\n// at a zoom.\n//\n// `computeEdgeCurves` already says why there must be one derivation of this\n// rather than several: the drawing, the hit index and the label that rides an\n// arc all have to agree on where the curve is, and a second derivation is a\n// second thing to keep in step. That was true of the CODE and not of the WORK \u2014\n// the geometry builder and the edge hit index called it with identical\n// arguments, per edge, and each paid in full. The index's whole build was 14 ms\n// on a 12k-edge cut and most of it was this, redone.\n//\n// So the answer is the same shape as the argument: one function, and everyone\n// who wants the offset-zero curve of edge `ei` asks it. A path ribbon is that\n// curve rebuilt at its own offset, which is the one variant that is not shared.\n//\n// Cached the way hit detection caches its indexes, and for the same reasons: a\n// WeakMap on the positions object so two graph views cannot evict each other and\n// an entry dies with the layout it describes, plus a check of everything the\n// curves actually depend on. `deletions` is in that list because it decides\n// which edges bow and around what; `version` is, because a node drag mutates the\n// positions in place and their identity cannot report it.\nexport type EdgeCurves = Map<number, BezierCurve[]>\n\nconst cache = new WeakMap<\n  Record<string, NodeSegment[]>,\n  {\n    graph: Graph\n    scaleX: number\n    scaleY: number\n    deletions: Map<number, string[]> | undefined\n    version: number\n    curves: EdgeCurves\n  }\n>()\n\nexport function baseEdgeCurves(\n  nodePositions: Record<string, NodeSegment[]>,\n  graph: Graph,\n  axis: AxisScale,\n  // bypassed backbone ids per deletion edge, i.e. `deletionEdges()` keyed by\n  // edge index. An edge named here bows around the run it skips.\n  deletions: Map<number, string[]> | undefined,\n  version: number,\n): EdgeCurves {\n  const { scaleX, scaleY } = axis\n  const cached = cache.get(nodePositions)\n  if (\n    cached?.graph === graph &&\n    cached.scaleX === scaleX &&\n    cached.scaleY === scaleY &&\n    cached.deletions === deletions &&\n    cached.version === version\n  ) {\n    return cached.curves\n  }\n  const curves: EdgeCurves = new Map()\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei]!\n    const from = nodePositions[edge.from]\n    const to = nodePositions[edge.to]\n    // An edge whose endpoints the layout did not place has no curve, and its\n    // absence here is the same \"skip it\" every consumer already applies.\n    if (from?.length && to?.length) {\n      const bypassed = deletions?.get(ei)\n      curves.set(\n        ei,\n        computeEdgeCurves(\n          from,\n          to,\n          selfLinkOf(edge),\n          0,\n          0,\n          axis,\n          bypassed ? bypassedPoints(nodePositions, bypassed) : [],\n        ),\n      )\n    }\n  }\n  cache.set(nodePositions, {\n    graph,\n    scaleX,\n    scaleY,\n    deletions,\n    version,\n    curves,\n  })\n  return curves\n}\n", "import { isAnchored } from '@jbrowse/bandage-core/anchoredNodes'\nimport {\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from '@jbrowse/bandage-core/pansn'\n\nimport type { AnchoredNode } from '@jbrowse/bandage-core/anchoredNodes'\nimport type { Graph, GraphNode } from '@jbrowse/bandage-core/types'\n\nexport interface GraphLocation {\n  // PanSN sample name off the node's own stable sequence. The assembly that\n  // contributed the sequence, which is a *name*, not a resolved assembly \u2014 see\n  // resolveContributors.\n  sample: string\n  // `sample#hap` where the stable name states a haplotype (HPRC release 2.1\n  // names every node `NA20809#2#CM094351.1`), so a sample loaded as two\n  // assemblies opens the right one; undefined where it states none\n  haplotype: string | undefined\n  refName: string\n  start: number\n  end: number\n}\n\n// Where a node's own sequence lives, in the coordinates of the assembly that\n// contributed it. rGFA states this on every segment: SN names the stable\n// sequence and SO the offset on it, so this is exact at every rank.\n//\n// It is the other question from nodeReferenceSpan, which asks where a node sits\n// on the *reference* axis and can only approximate that off the backbone. A\n// rank>0 node has an exact coordinate of its own; what it has no coordinate for\n// is the reference.\nexport function nodeOwnLocation(node: GraphNode): GraphLocation | undefined {\n  return isAnchored(node) ? anchoredNodeLocation(node) : undefined\n}\n\nfunction anchoredNodeLocation(node: AnchoredNode): GraphLocation {\n  return {\n    sample: panSNSample(node.stable.refName),\n    haplotype: panSNHaplotype(node.stable.refName),\n    refName: panSNContig(node.stable.refName),\n    start: node.stable.start,\n    end: node.stable.start + node.length,\n  }\n}\n\nexport interface Contributor extends GraphLocation {\n  // lowest rank this assembly holds here: 0 means it is the reference backbone\n  rank: number\n  nodeCount: number\n}\n\ninterface Span {\n  start: number\n  end: number\n}\n\n// The widest run of spans with no gap larger than `maxGap`, which is the locus\n// this assembly contributes *here*. A bare union of every span would be wrong\n// on a graph where a sample also contributes sequence from a distant\n// duplication: the union then reads as a multi-megabase locus, and a linear view\n// launched at it shows neither end.\nfunction widestCluster(spans: Span[], maxGap: number) {\n  const sorted = [...spans].sort((a, b) => a.start - b.start)\n  let best: Span | undefined\n  let current: Span | undefined\n  for (const span of sorted) {\n    current =\n      current && span.start - current.end <= maxGap\n        ? { start: current.start, end: Math.max(current.end, span.end) }\n        : { start: span.start, end: span.end }\n    if (!best || current.end - current.start > best.end - best.start) {\n      best = current\n    }\n  }\n  return best\n}\n\ninterface Group {\n  sample: string\n  haplotype: string | undefined\n  refName: string\n  rank: number\n  spans: Span[]\n}\n\nfunction groupKey(loc: GraphLocation) {\n  return `${loc.haplotype ?? loc.sample}\u0000${loc.refName}`\n}\n\n// Every assembly with a segment in this graph, and the locus each one covers on\n// its own coordinates.\n//\n// This is what makes a launch out of the graph possible at all: the graph names\n// its contributors in the data (rGFA's SN tag), so a node, a row and the graph\n// as a whole can each say which assembly they belong to without consulting an\n// alignment.\n//\n// Ordered reference-first, then by name, so the row order matches\n// sampleRowLayout's and neither reshuffles as the window moves.\nexport function contributingAssemblies(\n  graph: Graph,\n  { maxGap = Infinity }: { maxGap?: number } = {},\n): Contributor[] {\n  const groups = new Map<string, Group>()\n  for (const node of graph.nodes) {\n    if (isAnchored(node)) {\n      const loc = anchoredNodeLocation(node)\n      const key = groupKey(loc)\n      const group = groups.get(key)\n      if (group) {\n        group.spans.push({ start: loc.start, end: loc.end })\n        group.rank = Math.min(group.rank, node.stable.rank)\n      } else {\n        groups.set(key, {\n          sample: loc.sample,\n          haplotype: loc.haplotype,\n          refName: loc.refName,\n          rank: node.stable.rank,\n          spans: [{ start: loc.start, end: loc.end }],\n        })\n      }\n    }\n  }\n\n  // One entry per assembly (a haplotype where the names state one, else the\n  // sample): an assembly contributing on several contigs is launched at the\n  // contig it contributes most of, since a linear view opens on one region.\n  const bySample = new Map<string, Contributor>()\n  for (const group of groups.values()) {\n    const span = widestCluster(group.spans, maxGap)\n    if (span) {\n      const candidate = {\n        sample: group.sample,\n        haplotype: group.haplotype,\n        refName: group.refName,\n        start: span.start,\n        end: span.end,\n        rank: group.rank,\n        nodeCount: group.spans.length,\n      }\n      const key = group.haplotype ?? group.sample\n      const existing = bySample.get(key)\n      if (!existing || candidate.nodeCount > existing.nodeCount) {\n        bySample.set(key, candidate)\n      }\n    }\n  }\n\n  // Reference first, then by name: the same order sampleRowLayout gives its\n  // rows, so the menu lists the assemblies in the order they are stacked on\n  // screen. Sorting by rank instead would order them by minigraph's build\n  // order, which is not what the labels beside the drawing say.\n  return [...bySample.values()].sort(\n    (a, b) =>\n      Number(a.rank !== 0) - Number(b.rank !== 0) ||\n      a.sample.localeCompare(b.sample) ||\n      (a.haplotype ?? '').localeCompare(b.haplotype ?? ''),\n  )\n}\n\n// The assembly a location opens on: its haplotype's where the name states one\n// and the session holds it, else its sample's. A session holding both\n// haplotypes of a sample opens the right one; one holding a haplotype under\n// the bare sample name still opens it.\nexport function resolveLocationAssembly(\n  resolve: (sample: string) => string | undefined,\n  loc: Pick<GraphLocation, 'sample' | 'haplotype'>,\n) {\n  const byHaplotype =\n    loc.haplotype === undefined ? undefined : resolve(loc.haplotype)\n  return byHaplotype ?? resolve(loc.sample)\n}\n\n// Contributors that name an assembly this session has loaded, which are the\n// only ones a linear or synteny view can open on.\n//\n// The two cases this filters apart are both normal. An E. coli pangenome demo\n// loads every strain as its own assembly, so every contributor resolves and the\n// whole graph is navigable. An HPRC graph names hundreds of haplotypes that no\n// session would ever load as assemblies, so only the reference resolves \u2014\n// there the reference projection (nodeReferenceSpan) is the way back to a\n// coordinate, not this.\n//\n// `resolve` is a name lookup rather than a list of names, because a PanSN sample\n// is the *graph's* spelling and need not be the assembly's. HPRC's graph writes\n// `CHM13`, and the assembly holding that sequence is UCSC's `hs1`, with CHM13\n// among its aliases; matching on names alone leaves that donor unopenable unless\n// the reader renames their assembly after the graph. The resolved (canonical)\n// name replaces the sample, so a launch opens the assembly the session knows.\nexport function resolveContributors(\n  contributors: Contributor[],\n  resolve: (sample: string) => string | undefined,\n) {\n  return contributors.flatMap(c => {\n    const sample = resolveLocationAssembly(resolve, c)\n    return sample === undefined ? [] : [{ ...c, sample }]\n  })\n}\n\n// 1-based inclusive, which is what a locstring means. Unformatted digits: this\n// is parsed, not read. locLabel is the one people read.\nexport function locString(loc: GraphLocation) {\n  return `${loc.refName}:${loc.start + 1}-${loc.end}`\n}\n\nexport function locLabel(loc: { refName: string; start: number; end: number }) {\n  return `${loc.refName}:${(loc.start + 1).toLocaleString()}-${loc.end.toLocaleString()}`\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z\"\n}), 'CompareArrows');", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2\"\n}), 'HighlightAlt');", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z\"\n}), 'LineStyle');", "import CompareArrowsIcon from '@mui/icons-material/CompareArrows'\nimport HighlightAltIcon from '@mui/icons-material/HighlightAlt'\nimport LineStyleIcon from '@mui/icons-material/LineStyle'\n\nimport { locLabel } from './contributors'\n\nimport type { Contributor, GraphLocation } from './contributors'\nimport type { LaunchableSyntenyTrack } from './syntenyTracks'\nimport type { MenuItem } from '@jbrowse/core/ui'\n\nconst LINEAR_LABEL = 'Linear genome view'\nconst SYNTENY_LABEL = 'Linear synteny view'\nconst NO_SYNTENY_TRACK =\n  'No synteny track in this session aligns these assemblies'\n\nexport interface LinearTarget {\n  location: GraphLocation\n  assembly: string\n}\n\n// One flat item when there is one thing to open, a submenu when there is a\n// choice. Same shape as subgraphMenuItems uses in the other direction, so the\n// two ends of the graph <-> linear trip read the same way.\nfunction oneOrMany<T>({\n  label,\n  icon,\n  entries,\n  entryLabel,\n  onSelect,\n  disabledHelpText,\n  nameTheOnlyEntry = true,\n}: {\n  label: string\n  icon: React.ElementType\n  entries: T[]\n  entryLabel: (entry: T) => string\n  onSelect: (entry: T) => () => void\n  disabledHelpText?: string\n  // Whether a lone entry's name is worth appending to the item. It is when the\n  // entry is where you land (`GRCh38 chr6:31,980,000-32,050,000`) and not when\n  // it is the ingredient used to get there \u2014 a synteny track's name says\n  // nothing the item does not already say, and reading it costs the width of\n  // `pggb graph: all-vs-all synteny (wfmash)`.\n  nameTheOnlyEntry?: boolean\n}): MenuItem[] {\n  const [first] = entries\n  // Nothing to open: a *disabled* item with the reason in its tooltip, when\n  // there is a reason worth reading. An item that vanishes teaches nobody that\n  // the session is one synteny track short of a multi-genome view.\n  const empty: MenuItem[] = disabledHelpText\n    ? [{ label, icon, disabled: true, disabledHelpText, onClick: () => {} }]\n    : []\n  return entries.length === 0\n    ? empty\n    : entries.length === 1 && first\n      ? [\n          {\n            label: nameTheOnlyEntry ? `${label} \u2014 ${entryLabel(first)}` : label,\n            icon,\n            onClick: onSelect(first),\n          },\n        ]\n      : [\n          {\n            label,\n            icon,\n            type: 'subMenu',\n            subMenu: entries.map(entry => ({\n              label: entryLabel(entry),\n              onClick: onSelect(entry),\n            })),\n          },\n        ]\n}\n\n// The graph's way out: a linear view of any assembly the graph names here, and a\n// synteny view of all of them at once. Until this existed the triangle had two\n// edges \u2014 a linear view could open a graph or a synteny view of a locus, and the\n// graph could open nothing at all.\n//\n// `contributors` are already resolved against the session's assemblies. On an\n// E. coli pangenome every strain is its own assembly, so all of them appear and\n// the synteny item is the interesting one; on an HPRC graph the 400-odd\n// contributing haplotypes are not loaded assemblies and only the reference\n// appears, which is the honest answer rather than a missing feature.\nexport function graphLaunchMenuItems({\n  contributors,\n  syntenyTracks,\n  onShowLinear,\n  onShowSynteny,\n}: {\n  contributors: Contributor[]\n  syntenyTracks: LaunchableSyntenyTrack[]\n  onShowLinear: (target: LinearTarget) => void\n  onShowSynteny: (trackId: string) => void\n}): MenuItem[] {\n  // sorted widest first\n  const widest = syntenyTracks[0]?.coverage ?? contributors.length\n  return [\n    ...oneOrMany({\n      label: LINEAR_LABEL,\n      icon: LineStyleIcon,\n      entries: contributors,\n      entryLabel: c => `${c.sample} ${locLabel(c)}`,\n      onSelect: c => () => {\n        onShowLinear({ location: c, assembly: c.sample })\n      },\n    }),\n    ...(contributors.length >= 2\n      ? oneOrMany({\n          // the count the launch opens, which is what the widest track aligns\n          // and not always every contributor; see launchSyntenyView\n          label: `${SYNTENY_LABEL} (${widest} assemblies)`,\n          icon: CompareArrowsIcon,\n          entries: syntenyTracks,\n          entryLabel: track =>\n            track.coverage < widest\n              ? `${track.name} (${track.coverage} of ${widest})`\n              : track.name,\n          nameTheOnlyEntry: false,\n          disabledHelpText: NO_SYNTENY_TRACK,\n          onSelect: track => () => {\n            onShowSynteny(track.trackId)\n          },\n        })\n      : []),\n  ]\n}\n\n// A single node's way out, for the node context menu. Two different questions,\n// both worth offering:\n//\n//   - the node's own coordinates, on the assembly that contributed it. Exact,\n//     from the node's SN/SO, and available at every rank \u2014 but only openable\n//     when that assembly is loaded, which for an HPRC haplotype it is not.\n//   - where the node sits on the reference the graph was cut against. Always\n//     openable, and off the backbone it is the flanking projection rather than\n//     an exact span (see nodeReferenceSpan), so it is labelled as the region\n//     around the node rather than as the node.\n//\n// Labels are verbs. Review: \"the lineargenomeview menu item should say launch\n// if that is what it does\" \u2014 a bare `Linear genome view \u2014 hg38 chr6:\u2026` names a\n// place and leaves the reader to guess whether clicking scrolls the view beside\n// the graph or opens a new one. It does the first when there is one to scroll\n// (see showInLinearView), so \"Open in\" covers both without claiming a launch.\n//\n// Verb, assembly, and where \u2014 nothing else. Every word here is read inside a\n// menu opened on a node, so \"this node in the hg38 view\" and \"in linear view\"\n// restate the context they are already in; what a coordinate opens in is not in\n// question, and the assembly name is.\n//\n// Flat, not under a \"Launch view\" submenu: this menu is a handful of items and\n// every one is contextual to the node just clicked.\nexport function nodeLaunchMenuItems({\n  own,\n  reference,\n  highlight,\n  onShowLinear,\n  onHighlight,\n}: {\n  own: LinearTarget | undefined\n  reference: LinearTarget | undefined\n  // the node's exact reference span, where `reference` is padded to open on\n  highlight: LinearTarget | undefined\n  onShowLinear: (target: LinearTarget) => void\n  // absent when no linear view in the session is this graph's to mark\n  onHighlight?: (target: LinearTarget) => void\n}): MenuItem[] {\n  const entries = [\n    own\n      ? {\n          label: `Open in ${own.assembly} \u2014 ${locLabel(own.location)}`,\n          target: own,\n        }\n      : undefined,\n    // Only when it says something the item above doesn't. A backbone segment on\n    // a loaded reference answers both questions with the same assembly and\n    // nearly the same span, and offering that twice reads as two different\n    // places to go.\n    reference && reference.assembly !== own?.assembly\n      ? {\n          label: `Open in ${reference.assembly} \u2014 around this node`,\n          target: reference,\n        }\n      : undefined,\n  ].filter(entry => entry !== undefined)\n\n  // The reference projection, not the node's own coordinates: a highlight is\n  // drawn in the linear view already on screen, and that view is on the\n  // reference the subgraph was cut from.\n  return [\n    ...(onHighlight && highlight\n      ? [\n          {\n            label: `Highlight in ${highlight.assembly}`,\n            icon: HighlightAltIcon,\n            onClick: () => {\n              onHighlight(highlight)\n            },\n          },\n        ]\n      : []),\n    ...entries.map(({ label, target }) => ({\n      label,\n      icon: LineStyleIcon,\n      onClick: () => {\n        onShowLinear(target)\n      },\n    })),\n  ]\n}\n", "import { parseCs } from '../gaf/parseGaf'\n\nimport type { GafRecord } from '../gaf/parseGaf'\nimport type { Graph, GraphNode } from '../types'\nimport type { InputTrack, Mismatch } from '@gmod/tubemap-core'\n\n// GAF reads as tube map reads over a cut. A read keeps the steps whose\n// segments the cut holds, and its cs edits land on the node they fall in, at\n// a position in the direction the read walks it, as vg's GAM mappings state\n// theirs.\n\nexport function canonicalStrand(node: GraphNode) {\n  return node.id.endsWith('-') ? '-' : '+'\n}\n\n// A visit to a node as tubemap-core names it: `-` where the walk runs against\n// the strand the node is drawn in\nexport function stepName(node: GraphNode, strand: '+' | '-') {\n  return strand === canonicalStrand(node) ? node.id : `-${node.id}`\n}\n\n// Where each step starts on the walk, where that can be known: counted from\n// the walk's start up to the first segment outside the cut, and back from its\n// end down to the last. A step between two such segments has no start.\nfunction stepStarts(lengths: readonly (number | undefined)[], total: number) {\n  const starts: (number | undefined)[] = lengths.map(() => undefined)\n  let head = 0\n  let i = 0\n  for (; i < lengths.length && lengths[i] !== undefined; i++) {\n    starts[i] = head\n    head += lengths[i]!\n  }\n  let tail = total\n  for (let j = lengths.length - 1; j > i && lengths[j] !== undefined; j--) {\n    tail -= lengths[j]!\n    starts[j] = tail\n  }\n  return starts\n}\n\nfunction mismatchesByStep(\n  record: GafRecord,\n  lengths: readonly (number | undefined)[],\n) {\n  const byStep: Mismatch[][] = record.path.map(() => [])\n  if (record.cs === undefined) {\n    return byStep\n  }\n  const starts = stepStarts(lengths, record.pathLength)\n  // the step holding walk position `pos`, or for `atEnd` the one ending there\n  const stepAt = (pos: number, atEnd = false) => {\n    for (let s = 0; s < starts.length; s++) {\n      const start = starts[s]\n      const length = lengths[s]\n      if (\n        start !== undefined &&\n        length !== undefined &&\n        start <= pos &&\n        (pos < start + length || (atEnd && pos === start + length))\n      ) {\n        return { s, local: pos - start, room: start + length - pos }\n      }\n    }\n    return undefined\n  }\n  const add = (s: number, mismatch: Mismatch) => {\n    const list = byStep[s]!\n    const last = list.at(-1)\n    if (\n      mismatch.type === 'substitution' &&\n      last?.type === 'substitution' &&\n      last.pos + last.seq!.length === mismatch.pos\n    ) {\n      last.seq += mismatch.seq!\n    } else {\n      list.push(mismatch)\n    }\n  }\n  let pos = record.pathStart\n  for (const op of parseCs(record.cs)) {\n    if (op.op === 'match') {\n      pos += op.length\n    } else if (op.op === 'substitution') {\n      const at = stepAt(pos)\n      if (at) {\n        add(at.s, { type: 'substitution', pos: at.local, seq: op.seq })\n      }\n      pos += 1\n    } else if (op.op === 'insertion') {\n      const at = stepAt(pos, pos === record.pathEnd)\n      if (at) {\n        add(at.s, { type: 'insertion', pos: at.local, seq: op.seq })\n      }\n    } else {\n      let left = op.length\n      while (left > 0) {\n        const at = stepAt(pos)\n        const take = at ? Math.min(left, at.room) : left\n        if (at) {\n          add(at.s, { type: 'deletion', pos: at.local, length: take })\n        }\n        pos += take\n        left -= take\n      }\n    }\n  }\n  return byStep\n}\n\n// `firstId` follows the haplotype tracks' ids, which tubemap-core shares\n// between tracks and reads.\nexport function tubeMapReads(\n  graph: Graph,\n  records: readonly GafRecord[],\n  firstId: number,\n): InputTrack[] {\n  const nodeByName = new Map(graph.nodes.map(n => [n.name, n]))\n  const reads: InputTrack[] = []\n  for (const record of records) {\n    const nodes = record.path.map(step => nodeByName.get(step.name))\n    const kept = nodes.flatMap((node, i) => (node ? [i] : []))\n    const first = kept[0]\n    const last = kept.at(-1)\n    if (first !== undefined && last !== undefined) {\n      const mismatches = mismatchesByStep(\n        record,\n        nodes.map(n => n?.length),\n      )\n      const names = kept.map(i => stepName(nodes[i]!, record.path[i]!.strand))\n      const lastLength = nodes[last]!.length\n      reads.push({\n        id: firstId + reads.length,\n        name: record.name,\n        type: 'read',\n        sourceTrackID: 1,\n        sequence: names,\n        sequenceNew: kept.map((i, k) => ({\n          nodeName: names[k]!,\n          mismatches: mismatches[i]!,\n        })),\n        firstNodeOffset: first === 0 ? record.pathStart : 0,\n        finalNodeCoverLength:\n          last === record.path.length - 1\n            ? lastLength - (record.pathLength - record.pathEnd)\n            : lastLength,\n        mapping_quality:\n          record.mappingQuality === 255 ? 0 : record.mappingQuality,\n        is_secondary: record.secondary,\n        is_reverse: record.strand === '-',\n      })\n    }\n  }\n  return reads\n}\n\n// sequenceTubeMap's read palettes: blues forward, reds reverse, staggered by\n// read so neighbours differ\nexport const FORWARD_READ_COLORS = ['#6baed6', '#4292c6', '#2171b5', '#08519c']\nexport const REVERSE_READ_COLORS = ['#fb6a4a', '#ef3b2c', '#cb181d', '#a50f15']\n\nexport function readColor(read: { id: number; is_reverse?: boolean }) {\n  const colors = read.is_reverse ? REVERSE_READ_COLORS : FORWARD_READ_COLORS\n  return colors[read.id % colors.length]!\n}\n", "import { REFERENCE_RANK, isAnchored } from '../anchoredNodes'\nimport { buildNeighbors } from '../referenceSpan'\n\nimport type { AnchoredNode } from '../anchoredNodes'\nimport type { Graph } from '../types'\n\n// An rGFA subgraph's alleles on the reference axis, from the stable\n// coordinates and the L lines alone: an allele is a run of off-reference\n// segments, and the rank-0 segments it detaches from and reattaches to give it\n// a reference span. rGFA carries no W or P lines, so nothing here reads a walk.\n\nexport interface ProjectedAllele {\n  // reference bp the allele replaces, from the flanking rank-0 segments\n  start: number\n  refSpan: number\n  // the run's strand-suffixed node ids, ordered by `nodeOffsets`\n  nodeIds: string[]\n  // bp from the allele's entry to the start of each node, along the run's own\n  // edges, so a layout puts a node where it sits within the allele\n  nodeOffsets: number[]\n  // bp of the longest path through the run, the denominator for nodeOffsets:\n  // a bubble's branches are alternatives, so their sum is no assembly's length\n  pathLength: number\n}\n\n// PanSN is `sample#haplotype#contig`, but minigraph accepts a bare contig name\n// and the E. coli fixture is `K12#1#chr`, so this parses what is there.\nexport function parsePanSN(refName: string) {\n  const parts = refName.split('#')\n  const haplotype = parts.length >= 2 ? Number(parts[1]) : Number.NaN\n  return {\n    sample: parts[0] ?? refName,\n    haplotype: Number.isFinite(haplotype) ? haplotype : undefined,\n  }\n}\n\n// One connected run of off-reference segments and the rank-0 segments on its\n// boundary. Walked through anchored nodes only: everything reported about a\n// run is read off a stable coordinate.\nfunction collectRun(\n  seed: string,\n  byId: Map<string, AnchoredNode>,\n  adj: Map<string, string[]>,\n  claimed: Set<string>,\n) {\n  const members: AnchoredNode[] = []\n  const anchors: AnchoredNode[] = []\n  const queue = [seed]\n  claimed.add(seed)\n\n  while (queue.length > 0) {\n    const id = queue.pop()!\n    const node = byId.get(id)\n    if (node) {\n      members.push(node)\n      for (const neighborId of adj.get(id) ?? []) {\n        const neighbor = byId.get(neighborId)\n        if (neighbor) {\n          if (neighbor.stable.rank === REFERENCE_RANK) {\n            anchors.push(neighbor)\n          } else if (!claimed.has(neighborId)) {\n            claimed.add(neighborId)\n            queue.push(neighborId)\n          }\n        }\n      }\n    }\n  }\n  return { members, anchors }\n}\n\n// The reference interval an allele replaces: from the end of the last backbone\n// segment before it to the start of the first one after it. Anchors on two\n// stable sequences, or in an order that runs backwards (an inverted or\n// translocated attachment), state no span rather than a negative one.\nfunction anchorSpan(anchors: AnchoredNode[]) {\n  const refNames = new Set(anchors.map(a => a.stable.refName))\n  if (refNames.size !== 1 || anchors.length < 2) {\n    return undefined\n  }\n  const sorted = [...anchors].sort((a, b) => a.stable.start - b.stable.start)\n  const first = sorted[0]!\n  const last = sorted.at(-1)!\n  const start = first.stable.start + first.length\n  const end = last.stable.start\n  return end >= start ? { start, end, entry: first } : undefined\n}\n\n// Shortest-path bp from the upstream anchor to each member over the run's own\n// edges, which only orders the run. The edges are undirected (a GFA states a\n// reverse-complement link backwards and single-node mode collapses both\n// orientations), so there is no topological order and a longest-path\n// relaxation would not converge.\nfunction runDistances(\n  members: AnchoredNode[],\n  entry: AnchoredNode,\n  adj: Map<string, string[]>,\n) {\n  const byId = new Map(members.map(m => [m.id, m]))\n  const dist = new Map<string, number>()\n  const queue: string[] = []\n  for (const neighborId of adj.get(entry.id) ?? []) {\n    if (byId.has(neighborId)) {\n      dist.set(neighborId, 0)\n      queue.push(neighborId)\n    }\n  }\n  if (queue.length === 0) {\n    for (const member of members) {\n      dist.set(member.id, 0)\n      queue.push(member.id)\n    }\n  }\n  for (const id of queue) {\n    const reach = dist.get(id)! + byId.get(id)!.length\n    for (const neighborId of adj.get(id) ?? []) {\n      if (byId.has(neighborId)) {\n        const known = dist.get(neighborId)\n        if (known === undefined || reach < known) {\n          dist.set(neighborId, reach)\n          queue.push(neighborId)\n        }\n      }\n    }\n  }\n  return dist\n}\n\n// Where each member sits within the allele: ordered by distance from the entry\n// and swept forward, so a node starts where the last of its already-placed\n// neighbours ends. Offsets are then monotone along every edge in the run, which\n// is what keeps a bubble's entry and exit curves from crossing; where the two\n// branches differ in length the short one gets slack rather than the long one a\n// backwards edge.\nfunction runOffsets(\n  members: AnchoredNode[],\n  entry: AnchoredNode,\n  adj: Map<string, string[]>,\n) {\n  const dist = runDistances(members, entry, adj)\n  const ordered = [...members].sort((a, b) => dist.get(a.id)! - dist.get(b.id)!)\n  const rank = new Map(ordered.map((m, i) => [m.id, i]))\n  const byId = new Map(members.map(m => [m.id, m]))\n  const offsets = new Map<string, number>()\n  for (const [i, member] of ordered.entries()) {\n    let offset = 0\n    for (const neighborId of adj.get(member.id) ?? []) {\n      const neighbor = byId.get(neighborId)\n      if (neighbor && rank.get(neighborId)! < i) {\n        offset = Math.max(offset, offsets.get(neighborId)! + neighbor.length)\n      }\n    }\n    offsets.set(member.id, offset)\n  }\n  return { offsets, ordered }\n}\n\n// Every allele with a reference span, by start. A run that reaches the edge of\n// the cut has one anchor and no span, which is the ordinary case at a window\n// boundary; placeOffReference chains those off wherever they branch.\nexport function projectAlleles(graph: Graph): ProjectedAllele[] {\n  const byId = new Map(\n    graph.nodes.filter(isAnchored).map(n => [n.id, n] as const),\n  )\n  const adj = buildNeighbors(graph)\n  const claimed = new Set<string>()\n  const alleles: ProjectedAllele[] = []\n\n  for (const node of byId.values()) {\n    if (node.stable.rank !== REFERENCE_RANK && !claimed.has(node.id)) {\n      const { members, anchors } = collectRun(node.id, byId, adj, claimed)\n      const span = anchorSpan(anchors)\n      if (span) {\n        const { offsets, ordered } = runOffsets(members, span.entry, adj)\n        alleles.push({\n          start: span.start,\n          refSpan: span.end - span.start,\n          nodeIds: ordered.map(m => m.id),\n          nodeOffsets: ordered.map(m => offsets.get(m.id)!),\n          pathLength: ordered.reduce(\n            (max, m) => Math.max(max, offsets.get(m.id)! + m.length),\n            0,\n          ),\n        })\n      }\n    }\n  }\n\n  return alleles.sort((a, b) => a.start - b.start)\n}\n", "import { projectAlleles } from '../alleleProjection/projectAlleles'\nimport { buildNeighbors } from '../referenceSpan'\n\nimport type { AlleleDeletion, Graph, NodeSegment } from '../types'\n\n// Where off-reference segments go on a reference x axis. Shared by the two\n// row-structured layouts, which differ only in what a row means (stable rank\n// vs contributing assembly); how far along the reference a segment reaches is\n// the same question in both, and answering it twice is how they drifted.\n//\n// The rule: a segment occupies the reference its allele replaces, never its own\n// sequence length. x is reference bp \u2014 the axis the backbone declares and the\n// linear view beside it is drawn on \u2014 so an insertion, which consumes no\n// reference, must not advance along it. Both layouts used to advance by\n// sequence length, which made every off-reference x a false statement about\n// reference position and, on a 1 kb window holding a 100 kb allele, drew 101x\n// the window so that zoom-to-fit rendered the reference at 1% of the frame.\n//\n// Magnitude is the cost. An axis of reference coordinates has no way to state\n// how much sequence an insertion adds, so it is not stated here: it is in the\n// node tooltip, and drawn to scale in the allele-inventory track, where a CIGAR\n// gives the alignments display a channel for length that is not the x axis.\n\n// Reference bp an allele has to skip before the drawing calls it a deletion:\n// the 1 bp floor `deletionEdges` uses, a guard against abutting anchors' zero\n// gap rather than a biological threshold. Whether a small one is drawn is\n// decided by its label's fit in graphLabels.\nconst MIN_DELETION_BP = 1\n\n// Floor on an off-reference node's drawn span, as a fraction of the window.\n// Node thickness is a constant number of screen pixels, so a segment on a\n// sub-percent slice of the window draws wider than it is long and reads as a\n// dot on a stalk, and a pure insertion occupies no reference at all. Rank-0\n// nodes keep their exact offsets, so the reference axis is untouched.\nconst MIN_ALLELE_SPAN_FRACTION = 0.015\n\ninterface PlaceArgs {\n  graph: Graph\n  // the reference interval the drawing is scaled against (referenceSpan)\n  span: number\n  // y for a segment, which is the whole of what the two layouts disagree about\n  rowY: (node: Graph['nodes'][number]) => number\n  // the backbone, already placed at its declared offsets. Mutated in place, and\n  // read for the branch points the unanchored walk below starts from.\n  positions: Record<string, NodeSegment[]>\n}\n\nexport function placeOffReference({\n  graph,\n  span,\n  rowY,\n  positions,\n}: PlaceArgs): AlleleDeletion[] {\n  const minSpan = span * MIN_ALLELE_SPAN_FRACTION\n  const alleles = projectAlleles(graph)\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  // Alleles standing in for more reference than they carry. Collected here\n  // rather than derived by the label pass, because the reason they need saying\n  // is the placement done in this function: a run drawn over the reference it\n  // replaces has a width that is not its length, and nothing downstream can\n  // tell that from a node drawn at its own scale. Same measure the deletion\n  // arcs use \u2014 reference bp a haplotype does not carry \u2014 so the two kinds of\n  // deletion in a drawing are stated in the same units and the same words.\n  const alleleDeletions: AlleleDeletion[] = []\n\n  for (const allele of alleles) {\n    const skipped = allele.refSpan - allele.pathLength\n    if (skipped >= MIN_DELETION_BP) {\n      alleleDeletions.push({ nodeIds: allele.nodeIds, bp: skipped })\n    }\n    const drawn = Math.max(allele.refSpan, minSpan)\n    // A node sits where it sits *within* the allele: its bp offset from the\n    // entry, scaled so the run's longest path fills the reference the allele\n    // replaces. So a bubble path occupies the reference exactly once however\n    // many segments it is built from, and two parallel branches share the x\n    // range rather than queue up after each other \u2014 they are alternatives over\n    // the same interval, not consecutive sequence.\n    //\n    // Offsets are measured over the graph rather than over nodeIds' order (see\n    // runOffsets). Concatenating in traversal order put graph neighbours 26 kb\n    // apart on a 27 kb allele, and the edges spanning those gaps crossed as a\n    // long X. A run of all zero-length segments has no distances to scale by;\n    // splitting evenly beats 0/0, which wrote NaN into every position after it.\n    //\n    // Where the floor widens a run past the reference it replaces, the overhang\n    // hangs off the right, so the run can end past the rank-0 segment it\n    // rejoins and its exit edge runs backwards. That is handled where it shows,\n    // in computeEdgeCurves, which sizes each control point by how far the other\n    // endpoint lies along its own tangent \u2014 a backwards edge gets a straight\n    // leader rather than the loop that read as a crossed bowtie.\n    const scale = allele.pathLength > 0 ? drawn / allele.pathLength : 0\n    allele.nodeIds.forEach((nodeId, i) => {\n      const node = byId.get(nodeId)\n      if (node) {\n        const offset = allele.nodeOffsets[i]!\n        const even = drawn / allele.nodeIds.length\n        // both ends from the offset rather than start-plus-width, so two nodes\n        // the sweep placed end to end land on exactly the same x instead of on\n        // two roundings of it\n        const at = (bp: number) => allele.start + bp * scale\n        const y = rowY(node)\n        positions[nodeId] = scale\n          ? [\n              { x: at(offset), y },\n              { x: at(offset + node.length), y },\n            ]\n          : [\n              { x: allele.start + i * even, y },\n              { x: allele.start + (i + 1) * even, y },\n            ]\n      }\n    })\n  }\n\n  // A run that reaches the edge of the fetched subgraph has only one backbone\n  // anchor, so no reference span can be stated for it. That is the normal case\n  // at a window boundary, not an error, and dropping it is indistinguishable\n  // from the layout being broken \u2014 the sample-rows layout did drop them.\n  //\n  // They get the floor each, chained from wherever they branch: the only honest\n  // claim available is \"attaches here and continues past the edge\", and a floor\n  // keeps a chain of them bounded by the window instead of by their sequence.\n  // The same undirected adjacency the reference walk builds, from the one\n  // function that builds it. The copy here rebuilt each list with a spread per\n  // edge, which is quadratic in a node's degree and is the shape a collapsed\n  // repeat's hub node is worst at.\n  const neighbors = buildNeighbors(graph)\n  // Read forward while appending, so this is a BFS with an O(1) dequeue rather\n  // than a quadratic shift() over what ends up being every node in the run.\n  const queue = Object.keys(positions)\n  for (const fromId of queue) {\n    const fromEnd = positions[fromId]!.at(-1)!.x\n    for (const nextId of neighbors.get(fromId) ?? []) {\n      const next = byId.get(nextId)\n      if (next && !(nextId in positions)) {\n        const y = rowY(next)\n        positions[nextId] = [\n          { x: fromEnd, y },\n          { x: fromEnd + minSpan, y },\n        ]\n        queue.push(nextId)\n      }\n    }\n  }\n\n  return alleleDeletions\n}\n", "import { placeOffReference } from './placeOffReference'\nimport { ROW_HEIGHT_PX } from './rowSpacing'\nimport {\n  backboneNodes,\n  backbonePositions,\n  referenceSpan,\n} from '../anchoredNodes'\n\nimport type { Graph, LayoutResult, RowLabel } from '../types'\n\n// Layout for rGFA, where the graph states its own backbone instead of leaving a\n// force simulation to find one. Every segment carries SN/SO/SR (gfatools\n// doc/rGFA.md), so both axes come from the file:\n//\n//   x  reference bp, for every segment. Rank-0 segments sit at the offset they\n//      declare; an off-reference segment cannot use its own SO, which is an\n//      offset on a different stable sequence, so it takes the slice of the\n//      reference its allele replaces (placeOffReference).\n//   y  one row per stable rank *present in this subgraph*, the way lh3's own\n//      rGFA viewer (VRPG) does it: rank 0 is the reference line, higher ranks\n//      below it in order. In SCREEN PIXELS, not bp \u2014 see rowSpacing.ts, shared\n//      with the sample-row layout.\n\n// Rank is a property of the whole graph, not of the window being drawn: HPRC's\n// minigraph graph ranks up to 89, but an MHC window holds only ranks\n// 0/1/3/6/14/23. Indexing rows by raw rank would leave 17 of 24 rows empty and\n// zoom-to-fit would shrink the drawing to fit that void (measured: 0.3% scale).\n// So rows are the ranks actually present, in rank order \u2014 identical to the raw\n// rank whenever the window happens to hold a contiguous run from 0.\nfunction rankRows(graph: Graph) {\n  const present = new Set<number>()\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      present.add(node.stable.rank)\n    }\n  }\n  return new Map([...present].sort((a, b) => a - b).map((r, i) => [r, i]))\n}\n\nexport function anchoredLayout(\n  graph: Graph,\n  region?: { start: number; end: number },\n): LayoutResult | undefined {\n  const backbone = backboneNodes(graph)\n  if (backbone.length === 0) {\n    return undefined\n  }\n\n  const span = referenceSpan(backbone, region)\n  const rows = rankRows(graph)\n\n  // Row 0 by construction: a backbone exists, so rank 0 is present, and\n  // `rankRows` numbers the present ranks in ascending order.\n  const nodePositions = backbonePositions(backbone)\n\n  const alleleDeletions = placeOffReference({\n    graph,\n    span,\n    rowY: node =>\n      (node.stable ? (rows.get(node.stable.rank) ?? rows.size) : rows.size) *\n      ROW_HEIGHT_PX,\n    positions: nodePositions,\n  })\n\n  // Named from the same `rows` map that placed every node, so the axis and the\n  // drawing cannot disagree. Rank 0 is spelled out: \"the reference\" is what a\n  // reader needs, and \"Rank 0\" alone reads as an ordinal with no meaning.\n  const rowLabels: RowLabel[] = [...rows].map(([rank, row]) => ({\n    label: rank === 0 ? 'Reference (rank 0)' : `Rank ${rank}`,\n    y: row * ROW_HEIGHT_PX,\n  }))\n\n  return {\n    nodePositions,\n    rowLabels,\n    referenceAxis: true,\n    pixelRows: true,\n    alleleDeletions,\n  }\n}\n", "import { ROW_HEIGHT_PX } from './rowSpacing'\nimport { isBackbone } from '../anchoredNodes'\n\nimport type { AnchoredNode } from '../anchoredNodes'\nimport type { Graph, GraphNode, LayoutResult, NodeSegment } from '../types'\n\n// Reference-ordered layered layout: x is reference ORDER, not bp. Backbone\n// segments take increasing layers by stable offset, every other node the layer\n// between the anchors it hangs off, and a node is as wide as the log of its bp,\n// so a SNP allele gets the same room as a 10 kb segment and a bubble reads as a\n// lens rather than a bar under a line. y is a lane in screen px with the\n// reference pinned at lane 0 (ADR-042).\n\nconst GUTTER = 12\nconst LANE_PX = ROW_HEIGHT_PX\n\nfunction nodeWidth(node: GraphNode) {\n  return 10 + 8 * Math.log2(1 + node.length)\n}\n\nfunction compare<T extends string | number>(a: T, b: T) {\n  return a < b ? -1 : a > b ? 1 : 0\n}\n\n// Where a node sorts: `at` is the rank of a placed node, the backbone and what\n// the walks visit, and a node the search claims sorts before or after the one\n// that claimed it, by its steps from it. A tuple rather than an offset nudged\n// per step: on a base-level graph the backbone nodes are a bp apart, and a\n// chain a few nodes long nudged its keys past the ones that follow.\ninterface OrderKey {\n  at: number\n  side: -1 | 0 | 1\n  hops: number\n}\n\nfunction compareKeys(a: OrderKey, b: OrderKey) {\n  return (\n    compare(a.at, b.at) || compare(a.side, b.side) || compare(a.hops, b.hops)\n  )\n}\n\nconst UNREACHED: OrderKey = { at: Infinity, side: 0, hops: 0 }\n\n// Every node id in reference order: backbone by stable offset, every other node\n// beside a backbone node (orderKeys), nodes nothing reaches last. Name breaks\n// ties, so the order is a strict total order and the same graph always gets\n// the same one.\nexport function referenceOrder(graph: Graph) {\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const key = orderKeys(graph)\n  return graph.nodes\n    .map(n => n.id)\n    .sort(\n      (a, b) =>\n        compareKeys(key.get(a) ?? UNREACHED, key.get(b) ?? UNREACHED) ||\n        compare(byId.get(a)!.name, byId.get(b)!.name) ||\n        compare(a, b),\n    )\n}\n\n// A walk states where its nodes lie, which the links alone do not. Starting\n// from the backbone in offset order, each node a walk visits for the first time\n// goes into the order immediately after the node that walk came from, and the\n// nodes a walk visits before it meets a placed one go immediately before it.\n//\n// That keeps every true boundary. A walk's step joins two nodes on the same\n// side of a node every haplotype crosses once, unless one of them is that\n// node, so by induction the nodes between two such boundaries stay one\n// unbroken stretch of the order and no link among them reaches across. On the\n// eight-haplotype KIV-2 cut (15,808 nodes) the walks imply 28 bubbles and this\n// derives those 28, with 5 of 65,776 walk steps against the order. Placing\n// every node by the links alone derived 21, with 23,308 steps against it.\n//\n// A walk on the reverse strand is read end-first.\nfunction placeByWalks(graph: Graph, backbone: AnchoredNode[]) {\n  const isNode = new Set(graph.nodes.map(n => n.id))\n  const startOf = new Map(backbone.map(n => [n.id, n.stable.start]))\n  const next = new Map<string, string | undefined>()\n  const prev = new Map<string, string | undefined>()\n  backbone.forEach((n, i) => {\n    prev.set(n.id, backbone[i - 1]?.id)\n    next.set(n.id, backbone[i + 1]?.id)\n  })\n  let head = backbone[0]?.id\n  const insertAfter = (at: string, id: string) => {\n    const after = next.get(at)\n    next.set(at, id)\n    prev.set(id, at)\n    next.set(id, after)\n    if (after !== undefined) {\n      prev.set(after, id)\n    }\n  }\n  const insertBefore = (at: string, id: string) => {\n    const before = prev.get(at)\n    if (before === undefined) {\n      head = id\n      prev.set(id, undefined)\n      next.set(id, at)\n      prev.set(at, id)\n    } else {\n      insertAfter(before, id)\n    }\n  }\n\n  for (const path of graph.paths ?? []) {\n    let rising = 0\n    let falling = 0\n    let last: number | undefined\n    for (const id of path.nodeIds) {\n      const start = startOf.get(id)\n      if (start !== undefined) {\n        if (last !== undefined && start !== last) {\n          if (start > last) {\n            rising++\n          } else {\n            falling++\n          }\n        }\n        last = start\n      }\n    }\n    const ids = falling > rising ? [...path.nodeIds].reverse() : path.nodeIds\n    let from: string | undefined\n    const leading = new Set<string>()\n    for (const id of ids) {\n      if (next.has(id)) {\n        if (from === undefined) {\n          for (const lead of leading) {\n            insertBefore(id, lead)\n          }\n        }\n        from = id\n      } else if (isNode.has(id)) {\n        if (from === undefined) {\n          leading.add(id)\n        } else {\n          insertAfter(from, id)\n          from = id\n        }\n      }\n    }\n  }\n\n  const placed: string[] = []\n  for (let id = head; id !== undefined; id = next.get(id)) {\n    placed.push(id)\n  }\n  return placed\n}\n\n// The nodes no walk visits, which is every off-reference node of a graph with\n// no walks: each goes beside the nearest placed node that reaches it (BFS over\n// the links as undirected, seeded in order so a tie goes left).\n//\n// That search meets itself in the middle of an allele, so the far half of a\n// chain A>X1>X2>B is claimed from B, its RIGHT anchor. Placed after B, as every\n// claimed node once was, X2 sorted past the node it leads into, its link was\n// turned round, and the insertion stopped being a bubble. So a run of nodes\n// claimed from one placed node lies BEFORE it, farthest node first, when it is\n// such a far half: it touches nothing right of that node, and every dead end of\n// the search inside it is a place the search from the left arrived. Steps are\n// a position only along a chain. In a tangle the farthest node is a dead end\n// with nothing before it, and sorted first its links to its real neighbours\n// sweep across every boundary between, so any other run stays after.\nfunction placeBySearch(\n  adjacent: Map<string, string[]>,\n  key: Map<string, OrderKey>,\n) {\n  const queue = [...key.entries()]\n    .sort(([a, ka], [b, kb]) => compareKeys(ka, kb) || compare(a, b))\n    .map(([id]) => id)\n  const placed = queue.length\n  // the queue grows while the loop walks it, which for-of follows\n  for (const id of queue) {\n    const from = key.get(id)!\n    for (const nb of adjacent.get(id) ?? []) {\n      if (!key.has(nb)) {\n        key.set(nb, { at: from.at, side: 1, hops: from.hops + 1 })\n        queue.push(nb)\n      }\n    }\n  }\n\n  const searched = new Set(queue.slice(placed))\n  const sided = new Set<string>()\n  for (const seed of searched) {\n    if (sided.has(seed)) {\n      continue\n    }\n    const { at } = key.get(seed)!\n    const run = [seed]\n    sided.add(seed)\n    let farHalf = true\n    for (const id of run) {\n      const { hops } = key.get(id)!\n      let deadEnd = true\n      let touchesLeft = false\n      for (const nb of adjacent.get(id) ?? []) {\n        const other = key.get(nb)!\n        if (other.at === at && searched.has(nb)) {\n          deadEnd &&= other.hops <= hops\n          if (!sided.has(nb)) {\n            sided.add(nb)\n            run.push(nb)\n          }\n        } else if (other.at !== at) {\n          touchesLeft ||= other.at < at\n          farHalf &&= other.at < at\n        }\n      }\n      farHalf &&= !deadEnd || touchesLeft\n    }\n    if (farHalf) {\n      for (const id of run) {\n        const k = key.get(id)!\n        key.set(id, { ...k, side: -1, hops: -k.hops })\n      }\n    }\n  }\n}\n\nfunction orderKeys(graph: Graph) {\n  const ids = new Set(graph.nodes.map(n => n.id))\n  const adjacent = new Map<string, string[]>()\n  for (const e of graph.edges) {\n    if (!ids.has(e.from) || !ids.has(e.to)) {\n      continue\n    }\n    ;(adjacent.get(e.from) ?? adjacent.set(e.from, []).get(e.from)!).push(e.to)\n    ;(adjacent.get(e.to) ?? adjacent.set(e.to, []).get(e.to)!).push(e.from)\n  }\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort(\n      (a, b) =>\n        compare(a.stable.start, b.stable.start) || compare(a.name, b.name),\n    )\n  const key = new Map<string, OrderKey>()\n  placeByWalks(graph, backbone).forEach((id, rank) => {\n    key.set(id, { at: rank, side: 0, hops: 0 })\n  })\n  placeBySearch(adjacent, key)\n  return key\n}\n\nexport interface LayeredGraph {\n  layers: string[][]\n  layerOf: Map<string, number>\n  // predecessors in layer order, for the y sweep\n  preds: Map<string, string[]>\n}\n\n// The layered DAG the ordered layout draws and the bubble decomposition reads\n// (bubbles/bubblesFromGraph.ts), from one function so the two cannot disagree\n// about which nodes share a layer.\nexport function layerGraph(graph: Graph): LayeredGraph {\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const order = referenceOrder(graph)\n  const key = new Map(order.map((id, i) => [id, i]))\n  const isRef = (id: string) => isBackbone(byId.get(id)!)\n\n  // Every edge directed from lower reference key to higher, so the graph is\n  // acyclic by construction and no cycle-removal heuristic can misplace the\n  // reference.\n  const preds = new Map<string, string[]>(order.map(id => [id, []]))\n  const succs = new Map<string, string[]>(order.map(id => [id, []]))\n  const link = (a: string, b: string) => {\n    preds.get(b)!.push(a)\n    succs.get(a)!.push(b)\n  }\n  for (const e of graph.edges) {\n    if (e.from === e.to || !key.has(e.from) || !key.has(e.to)) {\n      continue\n    }\n    if (key.get(e.from)! < key.get(e.to)!) {\n      link(e.from, e.to)\n    } else {\n      link(e.to, e.from)\n    }\n  }\n  // The backbone chained by virtual edges, so the reference stays monotone even\n  // where adjacent segments are not linked inside the cut.\n  const backbone = order.filter(isRef)\n  for (let i = 1; i < backbone.length; i++) {\n    link(backbone[i - 1]!, backbone[i]!)\n  }\n\n  // Longest-path layering; the key order is a topological order of this DAG.\n  const layerOf = new Map<string, number>()\n  for (const id of order) {\n    let l = 0\n    for (const p of preds.get(id)!) {\n      l = Math.max(l, layerOf.get(p)! + 1)\n    }\n    layerOf.set(id, l)\n  }\n  // Then each allele slides right to centre between the layer its predecessors\n  // force and the one its successors allow, so a short allele sits in the\n  // middle of its bubble rather than hugging the left anchor.\n  for (let i = order.length - 1; i >= 0; i--) {\n    const id = order[i]!\n    const s = succs.get(id)!\n    if (isRef(id) || s.length === 0) {\n      continue\n    }\n    let minSucc = Infinity\n    for (const t of s) {\n      minSucc = Math.min(minSucc, layerOf.get(t)!)\n    }\n    const lo = layerOf.get(id)!\n    const hi = Math.max(lo, minSucc - 1)\n    layerOf.set(id, Math.floor((lo + hi) / 2))\n  }\n\n  const layers: string[][] = []\n  for (const id of order) {\n    ;(layers[layerOf.get(id)!] ??= []).push(id)\n  }\n  return { layers, layerOf, preds }\n}\n\nexport function orderedLayout(graph: Graph): LayoutResult | undefined {\n  if (!graph.nodes.some(isBackbone)) {\n    return undefined\n  }\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const isRef = (id: string) => isBackbone(byId.get(id)!)\n  const { layers, layerOf: layer, preds } = layerGraph(graph)\n\n  const layerWidth = layers.map(ids => {\n    let w = 0\n    for (const id of ids) {\n      w = Math.max(w, nodeWidth(byId.get(id)!))\n    }\n    return w\n  })\n  const layerX: number[] = []\n  let x = 0\n  for (let l = 0; l < layers.length; l++) {\n    layerX[l] = x\n    x += layerWidth[l]! + GUTTER\n  }\n\n  // y: sweep the layers left to right, each allele at the barycenter of its\n  // placed predecessors, then at the nearest FREE lane to it. Lane 0 is the\n  // reference line and stays reserved even in a layer with no backbone node,\n  // or an allele between two backbone segments reads as reference.\n  const y = new Map<string, number>()\n  for (const ids of layers) {\n    const free: { id: string; ideal: number }[] = []\n    for (const id of ids) {\n      if (isRef(id)) {\n        y.set(id, 0)\n        continue\n      }\n      const placed = preds.get(id)!.filter(p => y.has(p))\n      let ideal = 0\n      for (const p of placed) {\n        ideal += y.get(p)! / placed.length\n      }\n      // a node straight off the backbone wants to leave it, not sit on it\n      free.push({ id, ideal: ideal === 0 ? LANE_PX : ideal })\n    }\n    free.sort((a, b) => a.ideal - b.ideal)\n    const taken = new Set([0])\n    for (const { id, ideal } of free) {\n      let lane = Math.round(ideal / LANE_PX)\n      if (lane === 0) {\n        lane = ideal >= 0 ? 1 : -1\n      }\n      for (let d = 1; taken.has(lane); d++) {\n        if (!taken.has(lane + d)) {\n          lane += d\n        } else if (!taken.has(lane - d)) {\n          lane -= d\n        }\n      }\n      taken.add(lane)\n      y.set(id, lane * LANE_PX)\n    }\n  }\n\n  const nodePositions: Record<string, NodeSegment[]> = {}\n  for (const n of graph.nodes) {\n    const l = layer.get(n.id)!\n    const w = nodeWidth(n)\n    const cx = layerX[l]! + layerWidth[l]! / 2\n    const ny = y.get(n.id)!\n    nodePositions[n.id] = [\n      { x: cx - w / 2, y: ny },\n      { x: cx + w / 2, y: ny },\n    ]\n  }\n  return { nodePositions, referenceAxis: false, pixelRows: true }\n}\n", "import { placeOffReference } from './placeOffReference'\nimport { ROW_HEIGHT_PX } from './rowSpacing'\nimport { parsePanSN } from '../alleleProjection/projectAlleles'\nimport {\n  backboneNodes,\n  backbonePositions,\n  isOffReference,\n  referenceSpan,\n} from '../anchoredNodes'\n\nimport type { Graph, LayoutResult, RowLabel } from '../types'\n\n// One row per contributing assembly, x on the reference.\n//\n// The anchored layout rows by *rank*, which is a property of the graph's\n// construction order rather than of any sample: at an HPRC locus rank 1 holds\n// alleles from dozens of different haplotypes, so a row there means nothing\n// biological. This layout rows by the assembly each allele came from, so a row\n// is one sample and reading across it says what that sample does to the\n// reference: a deletion leaves the row empty across the span it removes, and an\n// insertion is a mark at the point it attaches. Insertion *size* is deliberately\n// not on this axis \u2014 see placeOffReference.\n//\n// Positions come from `projectAlleles`, which derives them from the stable\n// coordinates and the L-lines alone. rGFA has no W/P records to consult, so\n// anything requiring walks could not run on the format the graph tracks read.\n//\n// What a row means differs with where the coordinates came from, and the\n// difference is not cosmetic. On rGFA a segment's SN names the assembly that\n// *first contributed* it (SR is build order), so a row is first-seen\n// attribution. On a path-anchored graph it names an assembly that actually\n// carries the segment. Carriage is a set, though, and a row here is one node's\n// one position: where several assemblies carry a segment, it draws on the row\n// of the first path in the file that visits it, and `GraphNode.samples` holds\n// the rest. Drawing a segment once per carrier needs the layout to emit more\n// nodes than the graph has, which the renderer keys by node id and cannot do.\n\n// Every assembly with a segment in this subgraph, ordered by how much\n// off-reference sequence it contributes here, most first. Taken from the nodes\n// rather than from the projection's per-allele attribution: a bubble path can\n// mix assemblies, and a segment belongs on the row of the assembly its own\n// stable name gives it, not on the row of whichever contributor happens to\n// dominate the run it sits in.\n//\n// Read off the same field `rowY` places by, so every row that exists has nodes\n// on it and every node lands on a row that exists.\n//\n// **Sorted by content rather than by name**, which is the change and the\n// tradeoff. Alphabetical put `HG00099` above `HG00280` for no reason a reader\n// could see, so a row's neighbours said nothing and the stack had to be read one\n// row at a time. By contributed sequence it reads the way a sorted pileup does:\n// the haplotypes doing the most to the reference are together at the top, and\n// how far down the stack the marks stop IS how many samples carry anything.\n//\n// What that costs is comparing one window against another \u2014 the order is a fact\n// about the window, so a sample is not in the same place in two of them. That is\n// the case \u00A78's \"a row set cannot be requested\" is for, and an explicit sample\n// list is the right answer to it rather than an order nobody can read. A\n// follow's re-cut is the exception it can answer already: `keep` is the rows on\n// screen, those samples hold their order, and a sample new to the window goes\n// below them by content.\n//\n// Name breaks ties, so the order is still deterministic and a pan that changes\n// nothing about the content reshuffles nothing.\nfunction contributingSamples(graph: Graph, keep: readonly string[]) {\n  const carried = new Map<string, number>()\n  for (const node of graph.nodes) {\n    if (isOffReference(node)) {\n      const { sample } = parsePanSN(node.stable.refName)\n      carried.set(sample, (carried.get(sample) ?? 0) + node.length)\n    }\n  }\n  const held = new Map(keep.map((sample, row) => [sample, row]))\n  return [...carried.keys()].sort(\n    (a, b) =>\n      (held.get(a) ?? Infinity) - (held.get(b) ?? Infinity) ||\n      carried.get(b)! - carried.get(a)! ||\n      a.localeCompare(b),\n  )\n}\n\nexport function sampleRowLayout(\n  graph: Graph,\n  region?: { start: number; end: number },\n  keep: readonly string[] = [],\n): LayoutResult | undefined {\n  const backbone = backboneNodes(graph)\n  const samples = contributingSamples(graph, keep)\n  if (backbone.length === 0 || samples.length === 0) {\n    return undefined\n  }\n  const span = referenceSpan(backbone, region)\n\n  // The backbone keeps row 0 and every sample gets a row below it, in the\n  // order contributingSamples gives.\n  const rowOf = new Map(samples.map((s, i) => [s, i + 1]))\n  const nodePositions = backbonePositions(backbone)\n\n  // `placeOffReference` also reaches nodes with no coordinate at all: it walks\n  // out from what it placed to close a run that leaves the fetched window, and\n  // on a path-anchored graph a segment no P or W line visits never got a\n  // `stable` to begin with. That is legal GFA rather than a broken file, so\n  // asserting the coordinate here threw a bare \"cannot read properties of\n  // undefined\" out of the layout and left the view showing it instead of a\n  // graph. Such a node belongs on no sample's row, so it takes the spare row\n  // below the named ones, which is what the sibling layout does with an\n  // unrecognised rank.\n  const spareRow = samples.length + 1\n  const alleleDeletions = placeOffReference({\n    graph,\n    span,\n    rowY: node => {\n      const stable = node.stable\n      const row = stable\n        ? rowOf.get(parsePanSN(stable.refName).sample)\n        : undefined\n      return (row ?? spareRow) * ROW_HEIGHT_PX\n    },\n    positions: nodePositions,\n  })\n\n  // Built from the same `rowOf` map that placed the alleles, so a label cannot\n  // name a row the layout put somewhere else. Row 0 is the backbone, named for\n  // the assembly it comes from rather than \"reference\", because on this layout\n  // that name is one of the samples and reads as a peer of the rows below it.\n  const referenceSample = parsePanSN(backbone[0]!.stable.refName).sample\n  const rowLabels: RowLabel[] = [\n    { label: referenceSample, y: 0 },\n    ...samples.map(sample => ({\n      label: sample,\n      y: rowOf.get(sample)! * ROW_HEIGHT_PX,\n    })),\n  ]\n\n  return {\n    nodePositions,\n    rowLabels,\n    sampleRows: samples,\n    referenceAxis: true,\n    pixelRows: true,\n    alleleDeletions,\n  }\n}\n", "export function emptyTrackShapes() {\n    return {\n        rectangles: [],\n        curves: [],\n        corners: [],\n        verticalRectangles: [],\n        featureRectangles: [],\n    };\n}\n", "// The tube map layout, from input nodes and tracks to drawable shapes. Ported\n// from the original sequenceTubeMap JS, where it shared one module with the d3\n// drawing; the passes below still share module state, but layoutTubeMap resets\n// all of it on entry and runs synchronously, so no two calls see each other's.\nimport { emptyTrackShapes } from './types.js';\nconst DEBUG = false;\nconst DEFAULT_TRACK_COLORS = [\n    '#1f77b4',\n    '#ff7f0e',\n    '#2ca02c',\n    '#d62728',\n    '#9467bd',\n    '#8c564b',\n    '#e377c2',\n    '#7f7f7f',\n];\nfunction configFrom(options) {\n    return {\n        mergeNodesFlag: options.mergeNodes ?? true,\n        showReads: options.showReads ?? true,\n        coarsenedReadView: options.coarsenedReadView ?? false,\n        ignoreStrand: options.ignoreStrand ?? false,\n        nodeWidthOption: options.nodeWidthOption ?? 'normal',\n        charWidth: options.charWidth ?? 8.401,\n        trackWidth: options.trackWidth ?? 15,\n        mappingQualityCutoff: options.mappingQualityCutoff ?? 0,\n        focusReadNames: options.focusReadNames ?? null,\n        showExonsFlag: options.showExons ?? false,\n        trackColor: options.trackColor ??\n            (track => DEFAULT_TRACK_COLORS[track.id % DEFAULT_TRACK_COLORS.length]),\n        trackAlpha: options.trackAlpha ?? (() => 1),\n    };\n}\nlet config = configFrom({});\nlet bed = null;\nlet nodes = [];\n// Each track has a `path`, which is an array of Segment objects describing pieces of the path that need to be drawn, in order along the path.\nlet tracks = [];\n// Each read also has a `path` list of Segments, but reads are organized vertically using a different system than non-read tracks.\nlet reads = [];\nlet nodeMap = new Map();\nlet nodesPerOrder = [];\n// Scratch array used only during generateNodeOrder. Indexed by node index;\n// undefined = \"not yet assigned.\" Copied into node.order at end of layout.\nlet nodeOrders = [];\n// Lane assignment info for tracks, in one list per horizontal \"order\" slot.\n// Duplicates info in tracks' `path` lists but is organized by order. Reads do not use this.\nlet assignments = [];\nlet extraLeft = [];\nlet extraRight = [];\nlet maxOrder = -1; // horizontal order of the rightmost node\nlet shapes = emptyTrackShapes();\nlet imageBounds = { minX: 0, maxX: 0, minY: 0, maxY: 0 };\nlet trackForRuler;\nlet coarsenedEdgeMeta = new Map();\n// Lay out `inputNodes` and `inputTracks` (and `inputReads`, when\n// `showReads`), or return undefined when nothing visible is left to draw.\n// Neither input is modified. Track 0 is the reference the layout straightens.\nexport function layoutTubeMap(inputNodes, inputTracks, inputReads = [], options = {}) {\n    config = configFrom(options);\n    bed = options.bed ?? null;\n    shapes = emptyTrackShapes();\n    assignments = [];\n    extraLeft = [];\n    extraRight = [];\n    nodesPerOrder = [];\n    imageBounds = { minX: 0, maxX: 0, minY: 0, maxY: 0 };\n    trackForRuler = undefined;\n    coarsenedEdgeMeta = new Map();\n    if (inputNodes.length === 0 || inputTracks.length === 0) {\n        return undefined;\n    }\n    // Boundary promotion: layout passes below populate the Node/Track fields\n    // (width, order, x/y, path, indexSequence, etc.) before any reader runs.\n    const copies = deepCopy(inputNodes);\n    // Nodes are referenced in inputs by internal `name` attribute and not by\n    // index. Internally in e.g. a path's indexSequence we need to reference\n    // nodes by *signed* index, so index 0 can never be used: budge everything\n    // down and leave a hole (rather than an `undefined` entry) at 0, which we\n    // won't iterate over. Made after the copy, because not every structuredClone\n    // keeps a hole.\n    nodes = [];\n    copies.forEach((node, i) => {\n        nodes[i + 1] = node;\n    });\n    tracks = deepCopy(inputTracks);\n    // Whether any reads were loaded at all, distinct from `reads.length` below:\n    // a mapping-quality cutoff or focus-name filter can filter every read out,\n    // and that should not make the coarsened view fall back to bunching\n    // haplotypes instead \u2014 the graph does have reads, they're just all hidden.\n    const hadInputReads = inputReads.length > 0;\n    // Drop the reads we will never draw before cloning them \u2014 the deep copy of a\n    // large GAM is the single most expensive step in a redraw.\n    reads = deepCopy(filterReads(inputReads));\n    for (let i = tracks.length - 1; i >= 0; i -= 1) {\n        const t = tracks[i];\n        if (t.type === undefined) {\n            t.type = 'haplotype';\n        }\n        if (t.hidden === true) {\n            tracks.splice(i, 1);\n            continue;\n        }\n        if (t.indexOfFirstBase !== undefined) {\n            trackForRuler = t.name;\n        }\n    }\n    if (tracks.length === 0) {\n        return undefined;\n    }\n    // Run against the visible tracks only, so hiding the reference doesn't leave\n    // the layout straightened around a track that is no longer drawn.\n    straightenTrack(0);\n    nodeMap = generateNodeMap();\n    generateTrackIndexSequences(tracks);\n    if (config.showReads && reads.length > 0)\n        generateTrackIndexSequences(reads);\n    generateNodeWidth();\n    if (config.mergeNodesFlag) {\n        generateNodeSuccessors();\n        generateNodeOrder();\n        if (config.showReads && reads.length > 0)\n            reverseReversedReads();\n        mergeNodes();\n        nodeMap = generateNodeMap();\n        generateNodeWidth();\n        generateTrackIndexSequences(tracks);\n        if (config.showReads && reads.length > 0)\n            generateTrackIndexSequences(reads);\n    }\n    generateNodeSuccessors();\n    generateNodeDegree();\n    if (DEBUG)\n        console.log(`${nodes.length} nodes.`);\n    generateNodeOrder();\n    maxOrder = getMaxOrder();\n    // can cause problems when there is a reversed single track node\n    // OTOH, can solve problems with complex inversion patterns\n    switchNodeOrientation();\n    generateNodeOrder();\n    maxOrder = getMaxOrder();\n    // Coarsened (Sankey) mode normally collapses the *read* list into synthetic\n    // per-edge bands (below). A haplotype-only graph has no reads to coarsen,\n    // so a coarsened request there instead coarsens every haplotype but the\n    // reference: that one keeps its normal per-track lane (so it still carries\n    // the ruler) while the rest are pulled out of `tracks` here, before\n    // calculateTrackWidth/generateLaneAssignment ever see them, and rejoin the\n    // layout below through the same reads-style overlay used for coarsened\n    // reads.\n    const coarsenHaplotypes = config.showReads && config.coarsenedReadView && !hadInputReads;\n    if (coarsenHaplotypes) {\n        const rulerIndex = trackForRuler === undefined\n            ? -1\n            : tracks.findIndex(t => t.name === trackForRuler);\n        const refIndex = rulerIndex === -1 ? 0 : rulerIndex;\n        const altHaplotypes = tracks.filter((_, i) => i !== refIndex);\n        if (altHaplotypes.length > 0) {\n            const bands = buildCoarsenedSyntheticBands(altHaplotypes, 'haplotype');\n            // A haplotype that only ever visits one node produces no edge, so an\n            // all-single-node set of alts would otherwise leave `reads` empty and\n            // fall through to the no-overlay branch below, which never gives their\n            // nodes a y/contentHeight. Keep them off to the side instead of\n            // dropping them silently.\n            if (bands.length > 0) {\n                tracks = [tracks[refIndex]];\n                reads = bands;\n            }\n        }\n    }\n    calculateTrackWidth();\n    generateLaneAssignment();\n    if (config.showExonsFlag && bed !== null)\n        addTrackFeatures();\n    // Coarsened (Sankey) mode: collapse the read list (or, when coarsening\n    // haplotypes, the alt haplotypes pulled out above) to one synthetic \"read\"\n    // per (srcSigned \u2192 dstSigned) edge BEFORE the normal read placement runs.\n    // Each synthetic read traverses exactly two nodes, so the rest of the\n    // pipeline (placeReads, generateSVGShapesFromPath, curve drawing) handles\n    // it like any normal read: it gets a lane, picks up the \"right-down-left-\n    // up-right\" topology for loops automatically, and uses the same elegant\n    // bezier. Node heights end up proportional to *edge* count (typically\n    // tens) rather than *read* or *haplotype* count (potentially thousands).\n    const drawCoarsenedReads = config.showReads &&\n        config.coarsenedReadView &&\n        reads.length > 0 &&\n        !coarsenHaplotypes;\n    if (config.showReads && reads.length > 0) {\n        generateReadOnlyNodeAttributes();\n        reverseReversedReads();\n        generateTrackIndexSequences(reads);\n        if (drawCoarsenedReads) {\n            reads = buildCoarsenedSyntheticBands(reads, 'read');\n            reverseReversedReads();\n            generateTrackIndexSequences(reads);\n        }\n        placeReads();\n        tracks = tracks.concat(reads);\n    }\n    else {\n        nodes.forEach(node => {\n            if (node) {\n                node.incomingReads = [];\n                node.outgoingReads = [];\n                node.internalReads = [];\n            }\n        });\n    }\n    generateNodeXCoords();\n    generateSVGShapesFromPath();\n    if (DEBUG) {\n        console.log('Tracks:');\n        console.log(tracks);\n        console.log('Nodes:');\n        console.log(nodes);\n        console.log('Lane assignment:');\n        console.log(assignments);\n    }\n    getImageDimensions();\n    return {\n        nodes,\n        tracks,\n        reads,\n        nodeMap,\n        shapes,\n        bounds: imageBounds,\n        maxOrder,\n        trackForRuler,\n        coarsenedEdgeMeta,\n    };\n}\nfunction generateTrackColor(track, highlight = 'plain') {\n    return config.trackColor(track, highlight);\n}\nfunction generateTrackAlpha(track) {\n    return config.trackAlpha(track);\n}\n// structuredClone preserves sparse-array holes; JSON round-trip would fill them with null.\nfunction deepCopy(val) {\n    return structuredClone(val);\n}\n// Return true if the given name names a reverse strand node, and false otherwise.\nexport function isReverse(nodeName) {\n    const s = String(nodeName);\n    return s.length >= 1 && s.startsWith('-');\n}\n// Get the forward version of a node name, which may be either forward or backward (negative)\nexport function forward(nodeName) {\n    return isReverse(nodeName) ? String(nodeName).substring(1) : nodeName;\n}\n// Get the reverse version of a node name, which may be either forward or backward (negative)\nexport function reverse(nodeName) {\n    return isReverse(nodeName) ? nodeName : `-${nodeName}`;\n}\n// Get the opposite orientation node name for the given node.\nexport function flip(nodeName) {\n    return isReverse(nodeName) ? forward(nodeName) : reverse(nodeName);\n}\n// Signed-index orientation test. Uses 1/n to distinguish -0 from +0 since\n// indexSequence entries can be negative-zero for reverse-strand visits of node 0.\nexport function isForwardIndex(n) {\n    return (n || 1 / n) >= 0;\n}\n// straighten track given by index by inverting inverted nodes\n// only keep them inverted if this single track runs through them in both directions\n// Operates on the per-render `nodes`/`tracks` copies; inputs are left untouched.\nfunction straightenTrack(index) {\n    const nodesToInvert = new Set();\n    // find out which nodes should be inverted\n    let currentSequence = tracks[index].sequence;\n    for (let i = 0; i < currentSequence.length; i += 1) {\n        const cur = currentSequence[i];\n        if (isReverse(cur)) {\n            const nodeName = forward(cur);\n            const firstForwardIndex = currentSequence.indexOf(nodeName);\n            if (firstForwardIndex === -1 || firstForwardIndex > i) {\n                // only if this inverted node is no repeat\n                nodesToInvert.add(nodeName);\n            }\n        }\n    }\n    // invert nodes in the tracks' sequence\n    for (const track of tracks) {\n        currentSequence = track.sequence;\n        for (let j = 0; j < currentSequence.length; j += 1) {\n            const cur = currentSequence[j];\n            if (!isReverse(cur)) {\n                if (nodesToInvert.has(cur)) {\n                    currentSequence[j] = reverse(cur);\n                }\n            }\n            else if (nodesToInvert.has(forward(cur))) {\n                currentSequence[j] = forward(cur);\n            }\n        }\n    }\n    // invert the sequence within the nodes\n    nodes.forEach(node => {\n        if (node && nodesToInvert.has(node.name)) {\n            node.seq = node.seq.split('').reverse().join('');\n        }\n    });\n}\n// generates attributes (node.y, node.contentHeight) for nodes without tracks, only reads\nfunction generateReadOnlyNodeAttributes() {\n    nodesPerOrder = [];\n    for (let i = 0; i <= maxOrder; i += 1) {\n        nodesPerOrder[i] = [];\n    }\n    const orderY = new Map();\n    nodes.forEach(node => {\n        if (node.y !== undefined) {\n            setMapToMax(orderY, node.order, node.y + node.contentHeight);\n        }\n    });\n    // for order values where there is no node with haplotypes, orderY is calculated via tracks\n    tracks.forEach(track => {\n        if (track.type === 'haplotype') {\n            track.path.forEach(step => {\n                setMapToMax(orderY, step.order, (step.y ?? 0) + track.width);\n            });\n        }\n    });\n    nodes.forEach((node, i) => {\n        if (node.order >= 0 && node.y === undefined) {\n            node.y = (orderY.get(node.order) ?? 0) + 25;\n            node.contentHeight = 0;\n            nodesPerOrder[node.order].push(i);\n        }\n    });\n}\nfunction setMapToMax(map, key, value) {\n    const existing = map.get(key);\n    if (existing === undefined) {\n        map.set(key, value);\n    }\n    else {\n        map.set(key, Math.max(existing, value));\n    }\n}\nexport const READ_WIDTH = 7;\n// add info about reads to nodes (incoming, outgoing and internal reads)\nfunction assignReadsToNodes() {\n    nodes.forEach(node => {\n        if (node) {\n            node.incomingReads = [];\n            node.outgoingReads = [];\n            node.internalReads = [];\n        }\n    });\n    reads.forEach((read, idx) => {\n        // Honor a pre-set width (e.g. coarsened Sankey bands pre-size themselves\n        // by traversing-read count) \u2014 only fall back to the default for normal\n        // reads which leave width unset.\n        if (read.width === undefined || read.width === 0) {\n            read.width = READ_WIDTH;\n        }\n        if (read.path.length === 1) {\n            const firstNode = read.path[0].node;\n            if (firstNode !== null) {\n                nodes[firstNode].internalReads.push(idx);\n            }\n        }\n        else {\n            read.path.forEach((element, pathIdx) => {\n                if (pathIdx === 0) {\n                    const firstNode = read.path[0].node;\n                    if (firstNode !== null) {\n                        nodes[firstNode].outgoingReads.push([idx, pathIdx]);\n                    }\n                }\n                else {\n                    const elemNode = element.node;\n                    if (elemNode !== null) {\n                        nodes[elemNode].incomingReads.push([idx, pathIdx]);\n                    }\n                }\n            });\n        }\n    });\n}\n// calculate paths (incl. correct y coordinate) for all reads\nfunction placeReads() {\n    generateBasicPathsForReads();\n    assignReadsToNodes();\n    // sort nodes by order, then by y-coordinate\n    const sortedNodes = nodes.slice();\n    sortedNodes.sort(compareNodesByOrder);\n    // Organize read IDs by source track\n    const readsBySource = new Map();\n    for (let i = 0; i < reads.length; i++) {\n        const source = reads[i].sourceTrackID;\n        const bucket = readsBySource.get(source);\n        if (bucket === undefined) {\n            readsBySource.set(source, [i]);\n        }\n        else {\n            bucket.push(i);\n        }\n    }\n    const allSources = Array.from(readsBySource.keys()).sort((a, b) => a - b);\n    // Space out read tracks if multiple exist\n    const topMargin = allSources.length > 1 ? READ_WIDTH : 0;\n    sortedNodes.forEach(node => {\n        if (!node)\n            return;\n        // For each node\n        for (const source of allSources) {\n            // Go through all source tracks in order\n            // Place the reads from this source in this node.\n            // Use a margin to separate multiple read tracks if we have them.\n            placeReadSet(readsBySource.get(source), node, topMargin);\n        }\n    });\n    // place read segments which are without node\n    const bottomY = calculateBottomY();\n    const elementsWithoutNode = [];\n    reads.forEach((read, idx) => {\n        const len = read.path.length;\n        // For each path index, precompute the nearest preceding/following segment\n        // whose node is non-null and truthy. Falls back to the boundary segment when\n        // none qualifies, matching the original walking-loop semantics.\n        const prevSegment = new Array(len);\n        let lastValidPrev;\n        for (let i = 0; i < len; i++) {\n            if (i === 0) {\n                prevSegment[i] = undefined;\n            }\n            else {\n                prevSegment[i] = lastValidPrev ?? read.path[0];\n            }\n            const seg = read.path[i];\n            if (seg.node !== null && seg.node)\n                lastValidPrev = seg;\n        }\n        const nextSegment = new Array(len);\n        let firstValidNext;\n        for (let i = len - 1; i >= 0; i--) {\n            if (i === len - 1) {\n                nextSegment[i] = undefined;\n            }\n            else {\n                nextSegment[i] = firstValidNext ?? read.path[len - 1];\n            }\n            const seg = read.path[i];\n            if (seg.node !== null && seg.node)\n                firstValidNext = seg;\n        }\n        read.path.forEach((element, pathIdx) => {\n            if (element.y === undefined) {\n                const previousVisitToNode = prevSegment[pathIdx];\n                const nextVisitToNode = nextSegment[pathIdx];\n                // Specifically referring to segments between a cycle that's traversing from right to left\n                const betweenCycleReverseTraversal = Boolean(\n                // A segment can be between a cycle if it there are nodes on both sides\n                nextVisitToNode &&\n                    previousVisitToNode &&\n                    nextVisitToNode.isForward !== undefined &&\n                    previousVisitToNode.isForward !== undefined &&\n                    // A segment is between a cycle if the next node it visits is behind the previous node it visited\n                    (previousVisitToNode.order > nextVisitToNode.order ||\n                        // A segment can also be between a cycle if it's visiting the same node it just visited in the same direction\n                        (nextVisitToNode.order === previousVisitToNode.order &&\n                            nextVisitToNode.isForward === previousVisitToNode.isForward)));\n                element.betweenCycleReverseTraversal = betweenCycleReverseTraversal;\n                elementsWithoutNode.push({\n                    readIndex: idx,\n                    pathIndex: pathIdx,\n                    previousY: previousVisitToNode?.y,\n                    previousNode: previousVisitToNode?.node,\n                });\n            }\n        });\n    });\n    elementsWithoutNode.sort(compareNoNodeReads);\n    elementsWithoutNode.forEach(element => {\n        const read = reads[element.readIndex];\n        const segment = read.path[element.pathIndex];\n        segment.y = bottomY[segment.order];\n        bottomY[segment.order] += read.width;\n    });\n    if (DEBUG) {\n        console.log('Reads:');\n        console.log(reads);\n    }\n}\n// Place a particular collection of reads, identified by a list of read\n// numbers, into the given node at the right Y coordinates. All reads in all\n// nodes above it, and no reads in any nodes below it, are already placed.\n// Makes the given node bigger if needed and moves other nodes down if needed.\n// If topMargin is set, applies that amount of spacing down from whatever is above the reads.\nfunction placeReadSet(readIDs, node, topMargin) {\n    // Turn the read IDs into a set\n    const toPlace = new Set(readIDs);\n    // Get arrays of the read entry/exit/internal-ness records we want to work on\n    let incomingReads = node.incomingReads.filter(([readID]) => toPlace.has(readID));\n    const outgoingReads = node.outgoingReads.filter(([readID]) => toPlace.has(readID));\n    const internalReads = node.internalReads.filter(readID => toPlace.has(readID));\n    // Only actually use the top margin if we have any reads on the node.\n    if (incomingReads.length === 0 &&\n        outgoingReads.length === 0 &&\n        internalReads.length === 0) {\n        topMargin = 0;\n    }\n    // Determine where we start vertically in the node.\n    // TODO: Why do we have to double this to keep reads out of adjacent lanes???\n    const startY = node.y + node.contentHeight + topMargin * 2;\n    // sort incoming reads \u2014 decorate with a precomputed key so each compare is O(1).\n    // The original comparator walks pathIdx backwards in lockstep on both sides, picking\n    // the first step where either has a defined y (or reaches index 0). The walk's outcome\n    // for a single entry is fully captured by:\n    //   decisionStep: the smallest k>=1 where path[pathIdx-k].y is defined, or pathIdx+1\n    //                 if no preceding segment has a defined y (the \"reached 0\" case).\n    //   y:            the defined y at decisionStep, or undefined for \"reached 0\".\n    // Smaller decisionStep wins; ties put the \"reached 0\" entries first;\n    // otherwise compare y's.\n    const incomingKeys = incomingReads.map(entry => {\n        const [readID, pathIdx] = entry;\n        const path = reads[readID].path;\n        let decisionStep = pathIdx + 1;\n        let foundY;\n        for (let k = 1; k <= pathIdx; k++) {\n            const y = path[pathIdx - k]?.y;\n            if (y !== undefined) {\n                decisionStep = k;\n                foundY = y;\n                break;\n            }\n        }\n        return { entry, decisionStep, y: foundY };\n    });\n    incomingKeys.sort(compareIncomingReadKeys);\n    incomingReads = incomingKeys.map(k => k.entry);\n    // place incoming reads\n    let currentY = startY;\n    const occupiedUntil = new Map();\n    incomingReads.forEach(readElement => {\n        const read = reads[readElement[0]];\n        read.path[readElement[1]].y = currentY;\n        setOccupiedUntil(occupiedUntil, read, readElement[1], currentY, node);\n        currentY += read.width;\n    });\n    let maxY = currentY;\n    // sort outgoing reads\n    outgoingReads.sort(compareReadOutgoingSegmentsByGoingTo);\n    // place outgoing reads\n    const occupiedFrom = new Map();\n    currentY = startY;\n    outgoingReads.forEach(readElement => {\n        const read = reads[readElement[0]];\n        const firstNodeOffset = read.firstNodeOffset ?? 0;\n        // place in next lane\n        read.path[readElement[1]].y = currentY;\n        occupiedFrom.set(currentY, firstNodeOffset);\n        // if no conflicts. The original predicate was strict-less-than, which\n        // treats two reads that exactly touch (incoming ends at base K, outgoing\n        // starts at base K+1) as conflicting. They don't overlap, so they can\n        // share a lane \u2014 relax to <=. This also matters for coarsened Sankey\n        // bands at single-base nodes (e.g. a 1bp \"G\" node): with edge-only offsets\n        // the math becomes 0+1 < 1 (conflict, wrong) vs. 0+1 <= 1 (no conflict).\n        const occUntil = occupiedUntil.get(currentY);\n        if (occUntil === undefined || occUntil + 1 <= firstNodeOffset) {\n            currentY += read.width;\n            maxY = Math.max(maxY, currentY);\n        }\n        else {\n            // otherwise push down incoming reads to make place for outgoing Read\n            occupiedUntil.set(currentY, 0);\n            incomingReads.forEach(incReadElementIndices => {\n                const incRead = reads[incReadElementIndices[0]];\n                const incReadPathElement = incRead.path[incReadElementIndices[1]];\n                if (incReadPathElement.y !== undefined &&\n                    incReadPathElement.y >= currentY) {\n                    incReadPathElement.y += read.width;\n                    setOccupiedUntil(occupiedUntil, incRead, incReadElementIndices[1], incReadPathElement.y, node);\n                }\n            });\n            currentY += read.width;\n            maxY += read.width;\n        }\n    });\n    // sort internal reads\n    internalReads.sort(compareInternalReads);\n    // place internal reads\n    internalReads.forEach(readIdx => {\n        const currentRead = reads[readIdx];\n        const firstNodeOffset = currentRead.firstNodeOffset ?? 0;\n        const finalNodeCoverLength = currentRead.finalNodeCoverLength ?? 0;\n        currentY = startY;\n        while (firstNodeOffset < (occupiedUntil.get(currentY) ?? -Infinity) + 2 ||\n            finalNodeCoverLength > (occupiedFrom.get(currentY) ?? Infinity) - 3) {\n            currentY += currentRead.width || READ_WIDTH;\n        }\n        currentRead.path[0].y = currentY;\n        occupiedUntil.set(currentY, finalNodeCoverLength);\n        maxY = Math.max(maxY, currentY);\n    });\n    // adjust node height and move other nodes vertically down\n    const heightIncrease = maxY - node.y - node.contentHeight;\n    node.contentHeight += heightIncrease;\n    adjustVertically3(node, heightIncrease);\n}\n// Smaller decisionStep wins. On a tie, entries that walked off the front of the\n// path (no defined y) sort first and tie with each other; otherwise compare y.\nexport function compareIncomingReadKeys(a, b) {\n    if (a.decisionStep !== b.decisionStep) {\n        return a.decisionStep - b.decisionStep;\n    }\n    if (a.y === undefined || b.y === undefined) {\n        return (a.y === undefined ? 0 : 1) - (b.y === undefined ? 0 : 1);\n    }\n    return a.y - b.y;\n}\n// keeps track of where reads end within nodes\nfunction setOccupiedUntil(map, read, pathIndex, y, node) {\n    if (pathIndex === read.path.length - 1) {\n        // last node of current read\n        map.set(y, read.finalNodeCoverLength ?? 0);\n    }\n    else {\n        // read covers the whole node\n        map.set(y, node.sequenceLength);\n    }\n}\n// compare read segments which are outside of nodes to sort them in a good horizontal\n// and then vertical display order.\nfunction compareNoNodeReads(a, b) {\n    const readA = reads[a.readIndex];\n    const readB = reads[b.readIndex];\n    const segmentA = readA.path[a.pathIndex];\n    const segmentB = readB.path[b.pathIndex];\n    // Sort by order by segments\n    if (segmentA.order !== segmentB.order) {\n        return segmentA.order - segmentB.order;\n    }\n    // Sort by reads' source track\n    if (readA.sourceTrackID !== readB.sourceTrackID) {\n        return readA.sourceTrackID - readB.sourceTrackID;\n    }\n    // Sort by order of previous node\n    if (a.previousNode && b.previousNode) {\n        const prevNodeA = nodes[a.previousNode];\n        const prevNodeB = nodes[b.previousNode];\n        if (prevNodeA && prevNodeB && prevNodeA.order !== prevNodeB.order) {\n            return prevNodeA.order - prevNodeB.order;\n        }\n    }\n    // We want to sort in reverse order when the segment is along the reverse-going part of a cycle.\n    // This ensures a loop that starts on the outside, stays on the outside,\n    // and rolls up in order with other loops.\n    const aPrev = a.previousY ?? 0;\n    const bPrev = b.previousY ?? 0;\n    if (segmentA.betweenCycleReverseTraversal &&\n        segmentB.betweenCycleReverseTraversal) {\n        return bPrev - aPrev;\n    }\n    else {\n        return aPrev - bPrev;\n    }\n}\n// compare read segments by where they are going to\nfunction compareReadOutgoingSegmentsByGoingTo([readIndexA, pathIndexA], [readIndexB, pathIndexB]) {\n    // Expect two arrays both containing 2 integers.\n    // The first index of each array contains the read index\n    // The second index of each array contains the path index\n    // Segments are first sorted by the y value of their last node,\n    // then by the node they end on,\n    // then by length in final node\n    const readA = reads[readIndexA];\n    const readB = reads[readIndexB];\n    let previousValidYA;\n    let previousValidYB;\n    let lastPathIndexA = readA.path.length - 1;\n    let lastPathIndexB = readB.path.length - 1;\n    while (!previousValidYA && lastPathIndexA >= 0) {\n        previousValidYA = readA.path[lastPathIndexA]?.y;\n        lastPathIndexA -= 1;\n    }\n    while (!previousValidYB && lastPathIndexB >= 0) {\n        previousValidYB = readB.path[lastPathIndexB]?.y;\n        lastPathIndexB -= 1;\n    }\n    if (previousValidYA && previousValidYB) {\n        return previousValidYA - previousValidYB;\n    }\n    // Couldn't find a valid y value for at least one of the reads, sort by which node reads end on\n    const initialNodeA = readA.path[pathIndexA]?.node;\n    const initialNodeB = readB.path[pathIndexB]?.node;\n    let nodeA = initialNodeA != null ? nodes[initialNodeA] : null;\n    let nodeB = initialNodeB != null ? nodes[initialNodeB] : null;\n    // Follow the reads' paths until we find the node they diverge at\n    // Or, they go through all the same nodes and we do a tiebreaker at the end\n    while (nodeA != null && nodeB != null && nodeA === nodeB) {\n        if (pathIndexA < readA.path.length - 1) {\n            pathIndexA += 1;\n            while (readA.path[pathIndexA]?.node === null)\n                pathIndexA += 1; // skip null nodes in path\n            const nextNodeIdx = readA.path[pathIndexA]?.node;\n            nodeA = nextNodeIdx != null ? nodes[nextNodeIdx] : null;\n        }\n        else {\n            nodeA = null;\n        }\n        if (pathIndexB < readB.path.length - 1) {\n            pathIndexB += 1;\n            while (readB.path[pathIndexB]?.node === null)\n                pathIndexB += 1; // skip null nodes in path\n            const nextNodeIdx = readB.path[pathIndexB]?.node;\n            nodeB = nextNodeIdx != null ? nodes[nextNodeIdx] : null;\n        }\n        else {\n            nodeB = null;\n        }\n    }\n    if (nodeA != null) {\n        if (nodeB != null)\n            return compareNodesByOrder(nodeA, nodeB);\n        return 1; // nodeB is null, nodeA not null\n    }\n    if (nodeB != null)\n        return -1; // nodeB not null, nodeA null\n    // both nodes are null -> both end in the same node\n    const beginDiff = (readA.firstNodeOffset ?? 0) - (readB.firstNodeOffset ?? 0);\n    if (beginDiff !== 0)\n        return beginDiff;\n    // break tie: both reads cover the same nodes and begin at the same position\n    // One or both reads didn't have a previously valid Y value, compare by the endPosition of the read\n    return (readA.finalNodeCoverLength ?? 0) - (readB.finalNodeCoverLength ?? 0);\n}\n// Compare tracks based on ordering at their first convergence\nfunction compareTrackByInitialOrdering(trackA, trackB) {\n    // Find the first node where the two tracks converge, sort by layer.\n    // Tracks with no path sort first, and two of them tie.\n    if (trackA.path === undefined || trackB.path === undefined) {\n        return ((trackA.path === undefined ? 0 : 1) - (trackB.path === undefined ? 0 : 1));\n    }\n    const pathA = trackA.path;\n    const pathB = trackB.path;\n    let AIndex = 0;\n    let BIndex = 0;\n    while (AIndex < pathA.length && BIndex < pathB.length) {\n        const a = pathA[AIndex];\n        const b = pathB[BIndex];\n        const trackAOrder = a.order;\n        const trackBOrder = b.order;\n        if (trackAOrder === trackBOrder && a.node && b.node) {\n            return (b.y ?? 0) - (a.y ?? 0);\n        }\n        else if (trackAOrder < trackBOrder) {\n            AIndex += 1;\n        }\n        else if (trackAOrder > trackBOrder) {\n            BIndex += 1;\n        }\n        else {\n            // Orders are equal but are traversing out of nodes\n            AIndex += 1;\n            BIndex += 1;\n        }\n    }\n    // Tracks do not converge, keep the same ordering\n    return 0;\n}\n// compare 2 reads which are completely within a single node\nfunction compareInternalReads(idxA, idxB) {\n    const a = reads[idxA];\n    const b = reads[idxB];\n    // compare by first base within first node\n    const aFirst = a.firstNodeOffset ?? 0;\n    const bFirst = b.firstNodeOffset ?? 0;\n    if (aFirst < bFirst)\n        return -1;\n    else if (aFirst > bFirst)\n        return 1;\n    // compare by last base within last node\n    const aLast = a.finalNodeCoverLength ?? 0;\n    const bLast = b.finalNodeCoverLength ?? 0;\n    if (aLast < bLast)\n        return -1;\n    else if (aLast > bLast)\n        return 1;\n    return 0;\n}\n// determine biggest y-coordinate for each order-value\nfunction calculateBottomY() {\n    const bottomY = [];\n    for (let i = 0; i <= maxOrder; i += 1) {\n        bottomY.push(0);\n    }\n    nodes.forEach(node => {\n        if (node.y !== undefined) {\n            bottomY[node.order] = Math.max(bottomY[node.order], node.y + node.contentHeight + 20);\n        }\n    });\n    tracks.forEach(track => {\n        track.path.forEach(element => {\n            bottomY[element.order] = Math.max(bottomY[element.order], (element.y ?? 0) + track.width);\n        });\n    });\n    return bottomY;\n}\n// generate path-info for each read\n// containing order, node and orientation, but no concrete coordinates\n// TODO: Duplicates a lot of the same work as generateLaneAssignment() does for non-read tracks.\nfunction generateBasicPathsForReads() {\n    reads.forEach(read => {\n        // add info for start of track\n        let currentNodeIndex = Math.abs(read.indexSequence[0]);\n        let currentNodeIsForward = isForwardIndex(read.indexSequence[0]);\n        let currentNode = nodes[currentNodeIndex];\n        let previousNode;\n        let previousNodeIsForward;\n        read.path = [];\n        read.path.push({\n            order: currentNode.order,\n            isForward: currentNodeIsForward,\n            node: currentNodeIndex,\n        });\n        for (let i = 1; i < read.sequence.length; i += 1) {\n            previousNode = currentNode;\n            previousNodeIsForward = currentNodeIsForward;\n            currentNodeIndex = Math.abs(read.indexSequence[i]);\n            currentNodeIsForward = isForwardIndex(read.indexSequence[i]);\n            currentNode = nodes[currentNodeIndex];\n            if (currentNode.order > previousNode.order) {\n                if (!previousNodeIsForward) {\n                    // backward to forward at previous node\n                    read.path.push({\n                        order: previousNode.order,\n                        isForward: true,\n                        node: null,\n                    });\n                }\n                for (let j = previousNode.order + 1; j < currentNode.order; j += 1) {\n                    // forward without nodes\n                    read.path.push({ order: j, isForward: true, node: null });\n                }\n                if (!currentNodeIsForward) {\n                    // forward to backward at current node\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: true,\n                        node: null,\n                    });\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                }\n                else {\n                    // current Node forward\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                }\n            }\n            else if (currentNode.order < previousNode.order) {\n                if (previousNodeIsForward) {\n                    // turnaround from fw to bw at previous node\n                    read.path.push({\n                        order: previousNode.order,\n                        isForward: false,\n                        node: null,\n                    });\n                }\n                for (let j = previousNode.order - 1; j > currentNode.order; j -= 1) {\n                    // bachward without nodes\n                    read.path.push({ order: j, isForward: false, node: null });\n                }\n                if (currentNodeIsForward) {\n                    // backward to forward at current node\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: false,\n                        node: null,\n                    });\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                }\n                else {\n                    // backward at current node\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                }\n            }\n            else {\n                if (currentNodeIsForward !== previousNodeIsForward) {\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                }\n                else {\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: !currentNodeIsForward,\n                        node: null,\n                    });\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                }\n            }\n        }\n    });\n}\n// reverse reads which are reversed\nfunction reverseReversedReads() {\n    reads.forEach(read => {\n        let pos = 0;\n        while (pos < read.sequence.length && read.sequence[pos].startsWith('-')) {\n            pos += 1;\n        }\n        if (pos === read.sequence.length) {\n            // completely reversed read\n            read.is_reverse = true;\n            read.sequence = read.sequence.reverse(); // invert sequence\n            for (let i = 0; i < read.sequence.length; i += 1) {\n                read.sequence[i] = forward(read.sequence[i]); // visit nodes forward\n                // TODO: Do we really want to visit all the nodes forward here? Are we\n                // sure we aren't in mixed orientation?\n            }\n            const sequenceNew = read.sequenceNew ?? [];\n            sequenceNew.reverse(); // invert sequence\n            read.sequenceNew = sequenceNew;\n            for (const entry of sequenceNew) {\n                entry.nodeName = forward(entry.nodeName); // visit nodes forward\n                reverseMismatches(entry.mismatches, nodeByName(entry.nodeName).sequenceLength);\n            }\n            // adjust firstNodeOffset and finalNodeCoverLength\n            const temp = read.firstNodeOffset ?? 0;\n            const firstLen = nodeByName(read.sequence[0]).sequenceLength;\n            read.firstNodeOffset = firstLen - (read.finalNodeCoverLength ?? 0);\n            const lastLen = nodeByName(read.sequence[read.sequence.length - 1]).sequenceLength;\n            read.finalNodeCoverLength = lastLen - temp;\n        }\n    });\n}\n// Flip a node's mismatches onto the opposite strand: positions are measured\n// from the other end of the node, and sequences are complemented.\n// sequenceLength (not node.width, which is only equal to it in 'normal'\n// node-width mode) is the right pivot because mismatch positions are base\n// offsets. Exported for testing.\nexport function reverseMismatches(mismatches, sequenceLength) {\n    mismatches.forEach(mm => {\n        if (mm.type === 'insertion') {\n            mm.pos = sequenceLength - mm.pos;\n        }\n        else if (mm.type === 'deletion') {\n            mm.pos = sequenceLength - mm.pos - (mm.length ?? 0);\n        }\n        else if (mm.type === 'substitution') {\n            mm.pos = sequenceLength - mm.pos - (mm.seq?.length ?? 0);\n        }\n        if (mm.seq !== undefined) {\n            // NOTE: reverse-complement followed by reverse is a plain complement.\n            // Preserved verbatim from the original code rather than \"fixed\" here.\n            mm.seq = getReverseComplement(mm.seq).split('').reverse().join('');\n        }\n    });\n}\nconst COMPLEMENT = { A: 'T', T: 'A', C: 'G', G: 'C' };\nfunction getReverseComplement(s) {\n    let result = '';\n    for (let i = s.length - 1; i >= 0; i -= 1) {\n        result += COMPLEMENT[s.charAt(i)] ?? 'N';\n    }\n    return result;\n}\n// for each track: generate sequence of node indices from seq. of node names\nfunction generateTrackIndexSequences(tracksOrReads) {\n    tracksOrReads.forEach(track => {\n        track.indexSequence = [];\n        track.sequence.forEach(rawNodeName => {\n            let nodeName = rawNodeName;\n            // if node was switched, reverse it here\n            // Q? Is flipping the index enough? It looks like yes. Or should we also flip the node name in 'sequence'?\n            const fwdIdx = nodeMap.get(forward(nodeName));\n            const switched = nodes[fwdIdx]?.switched ?? false;\n            if (switched) {\n                nodeName = flip(nodeName);\n            }\n            // Get the index to visit the node. If the node is switched, this means\n            // visiting it reverse. Otherwise, this means visiting it forward.\n            const nodeIndex = nodeMap.get(forward(nodeName));\n            if (nodeIndex === 0) {\n                // If a node index is ever 0, we can't visit it in reverse, so we don't allow that to happen.\n                throw new Error('Node ' + forward(nodeName) + ' has prohibited index 0');\n            }\n            if (isReverse(nodeName) !== switched) {\n                // If we visit the node in reverse XOR the node is switched, go through\n                // it right to left as displayed.\n                track.indexSequence.push(-nodeIndex);\n            }\n            else {\n                // If either the node isn't switched and we go through it forward, or\n                // the node is switched *and* we go through it backward, go through it\n                // left to right as displayed.\n                track.indexSequence.push(nodeIndex);\n            }\n        });\n    });\n}\n// Tracks enter and leave a node this far outside it horizontally. Note that\n// getImageDimensions() below only adds it on the right: the pannable area\n// understates the left edge of the drawing by this much.\nconst NODE_HORIZONTAL_SLACK = 20;\n// get the minimum and maximum coordinates used in the image to calculate image dimensions\nfunction getImageDimensions() {\n    // Sentinels, deliberately crossed: if nothing below runs, minZoom() and\n    // alignSVG() detect the empty content rather than computing a negative scale.\n    const bounds = { minX: 99, maxX: -99, minY: 99, maxY: -99 };\n    nodes.forEach(node => {\n        if (!node)\n            return;\n        if (node.x !== undefined) {\n            bounds.minX = Math.min(bounds.minX, node.x);\n            bounds.maxX = Math.max(bounds.maxX, node.x + NODE_HORIZONTAL_SLACK + node.pixelWidth);\n        }\n        if (node.y !== undefined) {\n            bounds.minY = Math.min(bounds.minY, node.y - 10);\n            bounds.maxY = Math.max(bounds.maxY, node.y + node.contentHeight + 10);\n        }\n    });\n    tracks.forEach(track => {\n        track.path.forEach(segment => {\n            const y = segment.y ?? 0;\n            bounds.maxY = Math.max(bounds.maxY, y + track.width);\n            bounds.minY = Math.min(bounds.minY, y);\n        });\n    });\n    imageBounds = bounds;\n}\n// Resolve a (possibly reverse-oriented) node name to its layout node. Every\n// caller runs after generateNodeMap, so a miss is a programming error.\nfunction nodeByName(nodeName) {\n    const index = nodeMap.get(forward(nodeName));\n    const node = index === undefined ? undefined : nodes[index];\n    if (node === undefined) {\n        throw new Error(`Unknown node ${nodeName}`);\n    }\n    return node;\n}\n// map node names to node indices\nfunction generateNodeMap() {\n    nodeMap = new Map();\n    nodes.forEach((node, index) => {\n        if (node) {\n            nodeMap.set(node.name, index);\n        }\n    });\n    return nodeMap;\n}\n// adds a successor-array to each node containing the indices of the nodes coming directly after the current node\nfunction generateNodeSuccessors() {\n    const successorSets = nodes.map(() => new Set());\n    const predecessorSets = nodes.map(() => new Set());\n    const addEdges = (track) => {\n        for (let i = 0; i < track.indexSequence.length - 1; i += 1) {\n            const current = Math.abs(track.indexSequence[i]);\n            const follower = Math.abs(track.indexSequence[i + 1]);\n            successorSets[current].add(follower);\n            predecessorSets[follower].add(current);\n        }\n    };\n    tracks.forEach(addEdges);\n    if (config.showReads && reads.length > 0) {\n        reads.forEach(addEdges);\n    }\n    nodes.forEach((node, i) => {\n        if (node) {\n            node.successors = Array.from(successorSets[i]);\n            node.predecessors = Array.from(predecessorSets[i]);\n        }\n    });\n}\nfunction generateNodeOrderOfSingleTrack(sequence) {\n    let forwardOrder = 0;\n    let backwardOrder = 0;\n    let minOrder = 0;\n    sequence.forEach(nodeIndex => {\n        const idx = Math.abs(nodeIndex);\n        if (nodeIndex < 0) {\n            if (nodeOrders[idx] === undefined)\n                nodeOrders[idx] = backwardOrder;\n            const order = nodeOrders[idx];\n            if (order < minOrder)\n                minOrder = order;\n            forwardOrder = order;\n            backwardOrder = order - 1;\n        }\n        else {\n            if (nodeOrders[idx] === undefined)\n                nodeOrders[idx] = forwardOrder;\n            const order = nodeOrders[idx];\n            forwardOrder = order + 1;\n            backwardOrder = order;\n        }\n    });\n    if (minOrder < 0) {\n        increaseOrderForAllNodes(-minOrder);\n    }\n}\n// calculate the order-value of nodes contained in sequence which are to the left of the first node which already has an order-value\nfunction generateNodeOrderTrackBeginning(sequence) {\n    let anchorIndex = 0;\n    let minOrder = 0;\n    while (anchorIndex < sequence.length &&\n        nodeOrders[Math.abs(sequence[anchorIndex])] === undefined) {\n        anchorIndex += 1; // anchor = first node in common with existing graph\n    }\n    if (anchorIndex >= sequence.length) {\n        return null;\n    }\n    const anchorSeqVal = sequence[anchorIndex];\n    let currentOrder;\n    let increment;\n    if (anchorSeqVal >= 0) {\n        // regular node\n        currentOrder = nodeOrders[anchorSeqVal] - 1;\n        increment = -1;\n    }\n    else {\n        // reverse node\n        currentOrder = nodeOrders[-anchorSeqVal] + 1;\n        increment = 1;\n    }\n    for (let j = anchorIndex - 1; j >= 0; j -= 1) {\n        // assign order to nodes which are left of anchor node\n        const idx = Math.abs(sequence[j]);\n        if (nodeOrders[idx] === undefined) {\n            nodeOrders[idx] = currentOrder;\n            minOrder = Math.min(minOrder, currentOrder);\n            currentOrder += increment;\n        }\n    }\n    if (minOrder < 0) {\n        increaseOrderForAllNodes(-minOrder);\n    }\n    return anchorIndex;\n}\n// Sentinel order for nodes no track or read reaches.\nexport const UNREACHABLE_ORDER = -1;\n// Replace every unassigned entry with UNREACHABLE_ORDER, producing a dense\n// array. Holes matter here: `new Array(n)` is all holes and forEach/map skip\n// them, so an in-place forEach would leave the sentinel unset.\nexport function fillUnassignedOrders(orders) {\n    const filled = [];\n    for (const order of orders) {\n        filled.push(order ?? UNREACHABLE_ORDER);\n    }\n    return filled;\n}\n// generate global sequence of nodes from left to right, starting with first track and adding other tracks sequentially\nfunction generateNodeOrder() {\n    let modifiedSequence;\n    let currentOrder;\n    let rightIndex;\n    let leftIndex;\n    let minOrder = 0;\n    const tracksAndReads = config.showReads && reads.length > 0 ? tracks.concat(reads) : tracks;\n    const reachability = {\n        stamp: new Int32Array(nodes.length),\n        generation: 0,\n    };\n    // fill() makes the array dense: `new Array(n)` alone is all holes, which\n    // forEach skips, so neither the sentinel pass nor the copy-back below ran.\n    nodeOrders = new Array(nodes.length).fill(undefined);\n    nodes.forEach(node => {\n        if (node) {\n            node.order = undefined;\n        }\n    });\n    generateNodeOrderOfSingleTrack(tracks[0].indexSequence);\n    for (let i = 1; i < tracksAndReads.length; i += 1) {\n        if (DEBUG)\n            console.log(`generating order for track ${i + 1}`);\n        rightIndex = generateNodeOrderTrackBeginning(tracksAndReads[i].indexSequence);\n        if (rightIndex === null) {\n            if (tracksAndReads[i].type === 'haplotype') {\n                generateNodeOrderOfSingleTrack(tracksAndReads[i].indexSequence);\n            }\n            else {\n                tracksAndReads.splice(i, 1);\n                reads.splice(i - tracks.length, 1);\n                i -= 1;\n            }\n            continue;\n        }\n        modifiedSequence = uninvert(tracksAndReads[i].indexSequence);\n        while (rightIndex < modifiedSequence.length) {\n            // move right until the end of the sequence\n            leftIndex = rightIndex;\n            rightIndex += 1;\n            while (rightIndex < modifiedSequence.length &&\n                nodeOrders[modifiedSequence[rightIndex]] === undefined) {\n                rightIndex += 1;\n            }\n            if (rightIndex < modifiedSequence.length) {\n                // middle segment between two anchors\n                currentOrder = nodeOrders[modifiedSequence[leftIndex]] + 1;\n                for (let j = leftIndex + 1; j < rightIndex; j += 1) {\n                    nodeOrders[modifiedSequence[j]] = currentOrder;\n                    currentOrder += 1;\n                }\n                if (nodeOrders[modifiedSequence[rightIndex]] >\n                    nodeOrders[modifiedSequence[leftIndex]]) {\n                    if (nodeOrders[modifiedSequence[rightIndex]] < currentOrder) {\n                        increaseOrderForSuccessors(modifiedSequence[rightIndex], modifiedSequence[rightIndex - 1], currentOrder);\n                    }\n                }\n                else {\n                    if (tracksAndReads[i].indexSequence[rightIndex] >= 0 &&\n                        !isSuccessor(modifiedSequence[rightIndex], modifiedSequence[leftIndex], reachability)) {\n                        // no real reversal\n                        increaseOrderForSuccessors(modifiedSequence[rightIndex], modifiedSequence[rightIndex - 1], currentOrder);\n                    }\n                    else {\n                        // real reversal\n                        if (tracksAndReads[i].indexSequence[leftIndex] < 0 ||\n                            (nodes[modifiedSequence[leftIndex + 1]].degree < 2 &&\n                                nodeOrders[modifiedSequence[rightIndex]] <\n                                    nodeOrders[modifiedSequence[leftIndex]])) {\n                            currentOrder = nodeOrders[modifiedSequence[leftIndex]] - 1;\n                            for (let j = leftIndex + 1; j < rightIndex; j += 1) {\n                                nodeOrders[modifiedSequence[j]] = currentOrder;\n                                minOrder = Math.min(minOrder, currentOrder);\n                                currentOrder -= 1;\n                            }\n                        }\n                    }\n                }\n            }\n            else {\n                // right segment to the right of last anchor\n                if (tracksAndReads[i].indexSequence[leftIndex] >= 0) {\n                    // elongate towards the right\n                    currentOrder = nodeOrders[modifiedSequence[leftIndex]] + 1;\n                    for (let j = leftIndex + 1; j < modifiedSequence.length; j += 1) {\n                        const idx = modifiedSequence[j];\n                        if (nodeOrders[idx] === undefined) {\n                            nodeOrders[idx] = currentOrder;\n                            currentOrder += 1;\n                        }\n                    }\n                }\n                else {\n                    // elongate towards the left\n                    currentOrder = nodeOrders[modifiedSequence[leftIndex]] - 1;\n                    for (let j = leftIndex + 1; j < modifiedSequence.length; j += 1) {\n                        const idx = modifiedSequence[j];\n                        if (nodeOrders[idx] === undefined) {\n                            nodeOrders[idx] = currentOrder;\n                            minOrder = Math.min(minOrder, currentOrder);\n                            currentOrder -= 1;\n                        }\n                    }\n                }\n            }\n        }\n    }\n    if (minOrder < 0)\n        increaseOrderForAllNodes(-minOrder);\n    // Nodes unreachable from any track get UNREACHABLE_ORDER so every node ends\n    // up with a defined order; downstream code uses `order >= 0` to skip them.\n    const finalOrders = fillUnassignedOrders(nodeOrders);\n    nodeOrders = finalOrders;\n    finalOrders.forEach((order, i) => {\n        const node = nodes[i];\n        if (node !== undefined) {\n            node.order = order;\n        }\n    });\n}\nfunction isSuccessor(first, second, scratch) {\n    scratch.generation += 1;\n    const { stamp, generation } = scratch;\n    const stack = [first];\n    stamp[first] = generation;\n    while (stack.length > 0) {\n        const current = stack.pop();\n        if (current === second)\n            return true;\n        for (const childIndex of nodes[current].successors) {\n            if (stamp[childIndex] !== generation) {\n                stamp[childIndex] = generation;\n                stack.push(childIndex);\n            }\n        }\n    }\n    return false;\n}\n// get order number of the rightmost node\nfunction getMaxOrder() {\n    let max = -1;\n    nodeOrders.forEach(order => {\n        if (order !== undefined && order > max)\n            max = order;\n    });\n    return max;\n}\n// generates sequence keeping the order but switching all reversed (negative) nodes to forward nodes\nfunction uninvert(sequence) {\n    return sequence.map(v => Math.abs(v));\n}\n// increases the order-value of all nodes by amount\nfunction increaseOrderForAllNodes(amount) {\n    nodeOrders.forEach((order, i) => {\n        if (order !== undefined)\n            nodeOrders[i] = order + amount;\n    });\n}\n// increases the order-value for currentNode and (if necessary) successor nodes recursively\nfunction increaseOrderForSuccessors(startingNode, tabuNode, newOrder) {\n    const increasedOrders = new Map();\n    // Walked with a head pointer rather than shift(), which is O(length) per pop.\n    const queue = [[startingNode, newOrder]];\n    let head = 0;\n    while (head < queue.length) {\n        const [currentNode, currentOrder] = queue[head];\n        head += 1;\n        const currentNodeOrder = nodeOrders[currentNode];\n        if (currentNodeOrder !== undefined && currentNodeOrder < currentOrder) {\n            if (!increasedOrders.has(currentNode) ||\n                increasedOrders.get(currentNode) < currentOrder) {\n                increasedOrders.set(currentNode, currentOrder);\n                nodes[currentNode].successors.forEach(successor => {\n                    if (nodeOrders[successor] > currentNodeOrder &&\n                        successor !== tabuNode) {\n                        // only increase order of successors to the right of currentNode\n                        queue.push([successor, currentOrder + 1]);\n                    }\n                });\n                if (currentNode !== startingNode) {\n                    nodes[currentNode].predecessors.forEach(predecessor => {\n                        if (nodeOrders[predecessor] > currentNodeOrder &&\n                            predecessor !== tabuNode) {\n                            // only increase order of predecessors to the right of currentNode\n                            queue.push([predecessor, currentOrder + 1]);\n                        }\n                    });\n                }\n            }\n        }\n    }\n    increasedOrders.forEach((value, key) => {\n        nodeOrders[key] = value;\n    });\n}\n// calculates the node degree: the number of tracks passing through the node / the node height\nfunction generateNodeDegree() {\n    nodes.forEach(node => {\n        node.tracks = [];\n    });\n    tracks.forEach(track => {\n        track.indexSequence.forEach(nodeIndex => {\n            nodes[Math.abs(nodeIndex)].tracks.push(track.id);\n        });\n    });\n    nodes.forEach(node => {\n        if (node.tracks !== undefined)\n            node.degree = node.tracks.length;\n    });\n}\n// Optimize the orientations for nodes in the global `nodes` for displaying the\n// paths in the global `tracks` and the read paths, if applicable, in the\n// global `reads`\nfunction switchNodeOrientation() {\n    const pivotPath = tracks[0];\n    let countPaths = tracks.slice(1, tracks.length);\n    if (config.showReads && reads.length > 0) {\n        countPaths = countPaths.concat(reads);\n    }\n    switchNodeOrientationForPaths(countPaths, pivotPath);\n    if (config.showReads && reads.length > 0) {\n        // Any changes should be committed back\n        for (let i = 0; i < reads.length; i++) {\n            if (reads[i] !== countPaths[i + tracks.length - 1]) {\n                throw new Error('Read inequality');\n            }\n        }\n    }\n}\n// If more of the given paths pass through a specific node in reverse direction than in\n// regular direction, switch its orientation. Processes all paths' nodes in\n// place, so if you want e.g. a first track with nodes fixed in that\n// orientation, pass it as pivotPath.\n// References and modifies the global nodes variable.\nfunction switchNodeOrientationForPaths(paths, pivotPath) {\n    const toSwitch = new Map();\n    const pivotNames = pivotPath ? new Set(pivotPath.sequence) : null;\n    for (const path of paths) {\n        const sequence = path.sequence;\n        for (let j = 0; j < sequence.length; j += 1) {\n            const nodeName = forward(sequence[j]);\n            const currentNode = nodeByName(nodeName);\n            if (pivotNames && !pivotNames.has(nodeName)) {\n                // do not change orientation for nodes which are part of the pivot path\n                const prevOrder = j > 0 ? nodeByName(sequence[j - 1]).order : undefined;\n                const nextOrder = j < sequence.length - 1\n                    ? nodeByName(sequence[j + 1]).order\n                    : undefined;\n                if ((prevOrder === undefined || prevOrder < currentNode.order) &&\n                    (nextOrder === undefined || currentNode.order < nextOrder)) {\n                    // Node is visited in increasing order along the path. Reverse\n                    // visits count towards switching, forward visits against it.\n                    addToSwitchScore(toSwitch, nodeName, isReverse(sequence[j]) ? 1 : -1);\n                }\n                if ((prevOrder === undefined || prevOrder > currentNode.order) &&\n                    (nextOrder === undefined || currentNode.order > nextOrder)) {\n                    // Node is visited in *decreasing* order along the path, so is already\n                    // backward: the votes are the other way round.\n                    addToSwitchScore(toSwitch, nodeName, isReverse(sequence[j]) ? -1 : 1);\n                }\n            }\n        }\n    }\n    for (const path of paths) {\n        path.sequence.forEach((node, nodeIndex) => {\n            const score = toSwitch.get(forward(node));\n            if (score !== undefined && score > 0) {\n                // This node is backward more so flip it around\n                path.sequence[nodeIndex] = flip(node);\n                path.indexSequence[nodeIndex] = -path.indexSequence[nodeIndex];\n            }\n        });\n    }\n    // invert the sequence within the nodes and mark them as \"switched\"\n    toSwitch.forEach((value, key) => {\n        if (value > 0) {\n            const node = nodeByName(key);\n            node.seq = getReverseComplement(node.seq);\n            node.switched = true;\n        }\n    });\n}\nfunction addToSwitchScore(scores, nodeName, delta) {\n    scores.set(nodeName, (scores.get(nodeName) ?? 0) + delta);\n}\n// calculates the concrete values for the nodes' x-coordinates\nfunction generateNodeXCoords() {\n    let currentX = 0;\n    let nextX = 20;\n    let currentOrder = -1;\n    const sortedNodes = nodes.slice();\n    sortedNodes.sort(compareNodesByOrder);\n    const extra = calculateExtraSpace();\n    sortedNodes.forEach(node => {\n        if (node.order >= 0) {\n            if (node.order > currentOrder) {\n                currentOrder = node.order;\n                currentX = nextX + 10 * extra[node.order];\n            }\n            node.x = currentX;\n            nextX = Math.max(nextX, currentX + 40 + node.pixelWidth);\n        }\n    });\n}\n// calculates additional horizontal space needed between two nodes\n// two neighboring nodes have to be moved further apart if there is a lot going on in between them\n// -> edges turning to vertical orientation should not overlap\nfunction calculateExtraSpace() {\n    const leftSideEdges = [];\n    const rightSideEdges = [];\n    const fallAngleAdjustment = [];\n    const extra = [];\n    for (let i = 0; i <= maxOrder; i += 1) {\n        leftSideEdges.push(0);\n        rightSideEdges.push(0);\n        fallAngleAdjustment.push(0);\n    }\n    tracks.forEach(track => {\n        for (let i = 1; i < track.path.length; i += 1) {\n            const seg = track.path[i];\n            const prevSeg = track.path[i - 1];\n            // Track is going to the same node, account for space taken up by edges looping around\n            if (seg.order === prevSeg.order) {\n                // repeat or translocation\n                if (seg.isForward) {\n                    leftSideEdges[seg.order] = leftSideEdges[seg.order] + 1;\n                }\n                else {\n                    rightSideEdges[seg.order] = rightSideEdges[seg.order] + 1;\n                }\n            }\n            else {\n                // Track is going to a different node; account for space needed to limit rise/fall angle\n                const yDifference = Math.abs((seg.y ?? 0) - (prevSeg.y ?? 0));\n                //TODO: Extra space should also be accounted when there are too many tracks curving at the nodes\n                fallAngleAdjustment[seg.order] = Math.max(yDifference / 17.5, fallAngleAdjustment[seg.order]);\n            }\n        }\n    });\n    extra.push(Math.max(0, leftSideEdges[0] - 1));\n    for (let i = 1; i <= maxOrder; i += 1) {\n        // Extra space uses space needed for edges(tracks looping), or space needed to limit rise/fall angle, whichever is larger\n        extra.push(Math.max(Math.max(0, leftSideEdges[i] - 1) +\n            Math.max(0, rightSideEdges[i - 1] - 1), fallAngleAdjustment[i]));\n    }\n    return extra;\n}\n// create and fill assignment-variable, which contains info about tracks and lanes for each order-value\nfunction generateLaneAssignment() {\n    let segmentNumber;\n    let currentNodeIndex;\n    let currentNodeIsForward;\n    let currentNode;\n    let previousNode;\n    let previousNodeIsForward;\n    // For each horizontal order slot, for each track number, holds the\n    // SegmentAssignment object for the visit of that track to that order slot.\n    // When an order slot is visited multiple times, holds whatever\n    // SegmentAssignment was created most recently.\n    const prevSegmentPerOrderPerTrack = [];\n    // Index into assignments[order] by node, so addToAssignment can find an\n    // existing entry without scanning the whole order slot.\n    const assignmentByOrderAndNode = [];\n    // create empty variables\n    for (let i = 0; i <= maxOrder; i += 1) {\n        assignments[i] = [];\n        assignmentByOrderAndNode[i] = new Map();\n        prevSegmentPerOrderPerTrack[i] = [];\n        for (let j = 0; j < tracks.length; j += 1) {\n            prevSegmentPerOrderPerTrack[i][j] = null;\n        }\n    }\n    tracks.forEach((track, trackNo) => {\n        // Trace along each track and create Segment objects in the track's path\n        // field, and SegmentAssignment objects in NodeAssignment objects in all\n        // the order slots that are visited by the track. Set up all the\n        // cross-reverencing indexes and work out when we need segments to let\n        // tracks pass nodes and turn around, but leave all the assigned lane\n        // values empty for now.\n        // add info for start of track\n        currentNodeIndex = Math.abs(track.indexSequence[0]);\n        currentNodeIsForward = isForwardIndex(track.indexSequence[0]);\n        currentNode = nodes[currentNodeIndex];\n        track.path = [];\n        track.path.push({\n            order: currentNode.order,\n            lane: null,\n            isForward: currentNodeIsForward,\n            node: currentNodeIndex,\n        });\n        addToAssignment(currentNode.order, currentNodeIndex, trackNo, 0, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n        segmentNumber = 1;\n        for (let i = 1; i < track.sequence.length; i += 1) {\n            previousNode = currentNode;\n            previousNodeIsForward = currentNodeIsForward;\n            currentNodeIndex = Math.abs(track.indexSequence[i]);\n            currentNodeIsForward = isForwardIndex(track.indexSequence[i]);\n            currentNode = nodes[currentNodeIndex];\n            if (currentNode.order > previousNode.order) {\n                if (!previousNodeIsForward) {\n                    // backward to forward at previous node\n                    track.path.push({\n                        order: previousNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: null,\n                    });\n                    addToAssignment(previousNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                for (let j = previousNode.order + 1; j < currentNode.order; j += 1) {\n                    // forward without nodes\n                    track.path.push({\n                        order: j,\n                        lane: null,\n                        isForward: true,\n                        node: null,\n                    });\n                    addToAssignment(j, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                if (!currentNodeIsForward) {\n                    // forward to backward at current node\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: null,\n                    });\n                    addToAssignment(currentNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                else {\n                    // current Node forward\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n            }\n            else if (currentNode.order < previousNode.order) {\n                if (previousNodeIsForward) {\n                    // turnaround from fw to bw at previous node\n                    track.path.push({\n                        order: previousNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: null,\n                    });\n                    addToAssignment(previousNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                for (let j = previousNode.order - 1; j > currentNode.order; j -= 1) {\n                    // bachward without nodes\n                    track.path.push({\n                        order: j,\n                        lane: null,\n                        isForward: false,\n                        node: null,\n                    });\n                    addToAssignment(j, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                if (currentNodeIsForward) {\n                    // backward to forward at current node\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: null,\n                    });\n                    addToAssignment(currentNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                else {\n                    // backward at current node\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n            }\n            else {\n                if (currentNodeIsForward !== previousNodeIsForward) {\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                else {\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: !currentNodeIsForward,\n                        node: null,\n                    });\n                    addToAssignment(currentNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n            }\n        }\n    });\n    // Now sweep left to right across order slots and assign vertical lanes to all the segments.\n    for (let i = 0; i <= maxOrder; i += 1) {\n        generateSingleLaneAssignment(assignments[i], i); // this is where the lanes get assigned\n    }\n}\nfunction addToAssignment(order, nodeIndex, trackNo, segmentID, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode) {\n    const segment = {\n        trackID: trackNo,\n        segmentID,\n        compareToFromSame: prevSegmentPerOrderPerTrack[order][trackNo] ?? null,\n    };\n    // A null node means the track is passing through / turning around here rather\n    // than visiting a node, so such segments never share a NodeAssignment.\n    const existing = nodeIndex === null\n        ? undefined\n        : assignmentByOrderAndNode[order].get(nodeIndex);\n    if (existing === undefined) {\n        const assignment = {\n            type: 'single',\n            node: nodeIndex,\n            tracks: [segment],\n        };\n        assignments[order].push(assignment);\n        if (nodeIndex !== null) {\n            assignmentByOrderAndNode[order].set(nodeIndex, assignment);\n        }\n    }\n    else {\n        // add to existing node in assignment\n        existing.type = 'multiple';\n        existing.tracks.push(segment);\n    }\n    prevSegmentPerOrderPerTrack[order][trackNo] = segment;\n}\n// looks at assignment and sets idealY and idealLane by looking at where the tracks come from\nfunction getIdealLanesAndCoords(assignment, order) {\n    let index;\n    assignment.forEach(node => {\n        node.idealLane = 0;\n        node.tracks.forEach(track => {\n            if (track.segmentID === 0) {\n                track.idealLane = track.trackID;\n                track.idealY = null;\n            }\n            else {\n                if (tracks[track.trackID].path[track.segmentID - 1].order ===\n                    order - 1) {\n                    track.idealLane =\n                        tracks[track.trackID].path[track.segmentID - 1].lane ?? undefined;\n                    track.idealY = tracks[track.trackID].path[track.segmentID - 1].y;\n                }\n                else if (track.segmentID < tracks[track.trackID].path.length - 1 &&\n                    tracks[track.trackID].path[track.segmentID + 1].order === order - 1) {\n                    track.idealLane =\n                        tracks[track.trackID].path[track.segmentID + 1].lane ?? undefined;\n                    track.idealY = tracks[track.trackID].path[track.segmentID + 1].y;\n                }\n                else {\n                    index = track.segmentID - 1;\n                    while (index >= 0 &&\n                        tracks[track.trackID].path[index].order !== order - 1) {\n                        index -= 1;\n                    }\n                    if (index < 0) {\n                        track.idealLane = track.trackID;\n                        track.idealY = null;\n                    }\n                    else {\n                        track.idealLane =\n                            tracks[track.trackID].path[index].lane ?? undefined;\n                        track.idealY = tracks[track.trackID].path[index].y;\n                    }\n                }\n            }\n            node.idealLane += track.idealLane;\n        });\n        node.idealLane /= node.tracks.length;\n    });\n}\n// assigns the optimal lanes for a single horizontal position (=order)\n// first an ideal lane is calculated for each track (which is ~ the lane of its predecessor)\n// then the nodes are sorted by their average ideal lane\n// and the whole construct is then moved up or down if necessary\nfunction generateSingleLaneAssignment(assignment, order) {\n    let currentLane = 0;\n    const potentialAdjustmentValues = new Set();\n    let currentY = 20;\n    let prevNameIsNull = false;\n    let prevTrack = -1;\n    getIdealLanesAndCoords(assignment, order);\n    assignment.sort(compareByIdealLane);\n    assignment.forEach(node => {\n        if (node.node !== null) {\n            nodes[node.node].topLane = currentLane;\n            if (prevNameIsNull)\n                currentY -= 10;\n            nodes[node.node].y = currentY;\n            nodes[node.node].contentHeight = 0;\n            prevNameIsNull = false;\n        }\n        else {\n            if (prevNameIsNull)\n                currentY -= 25;\n            else if (currentY > 20)\n                currentY -= 10;\n            prevNameIsNull = true;\n        }\n        node.tracks.sort(compareByIdealLane);\n        node.tracks.forEach(track => {\n            track.lane = currentLane;\n            if (track.trackID === prevTrack && node.node === null && prevNameIsNull) {\n                currentY += 10;\n            }\n            tracks[track.trackID].path[track.segmentID].lane = currentLane;\n            tracks[track.trackID].path[track.segmentID].y = currentY;\n            if (track.idealY != null) {\n                potentialAdjustmentValues.add(track.idealY - currentY);\n            }\n            currentLane += 1;\n            currentY += tracks[track.trackID].width;\n            if (node.node !== null) {\n                nodes[node.node].contentHeight += tracks[track.trackID].width;\n            }\n            prevTrack = track.trackID;\n        });\n        currentY += 25;\n    });\n    adjustVertically(assignment, potentialAdjustmentValues);\n}\n// moves all tracks at a single horizontal location (=order) up/down to minimize lane changes\nfunction adjustVertically(assignment, potentialAdjustmentValues) {\n    let verticalAdjustment = 0;\n    let minAdjustmentCost = Number.MAX_SAFE_INTEGER;\n    potentialAdjustmentValues.forEach(moveBy => {\n        if (getVerticalAdjustmentCost(assignment, moveBy) < minAdjustmentCost) {\n            minAdjustmentCost = getVerticalAdjustmentCost(assignment, moveBy);\n            verticalAdjustment = moveBy;\n        }\n    });\n    assignment.forEach(node => {\n        if (node.node !== null) {\n            nodes[node.node].y += verticalAdjustment;\n        }\n        node.tracks.forEach(track => {\n            const seg = tracks[track.trackID].path[track.segmentID];\n            seg.y = seg.y + verticalAdjustment;\n        });\n    });\n}\n// Budge down all nodes and out-of-node tracks below this node by this amount\nfunction adjustVertically3(node, adjustBy) {\n    if (node.order < 0 || assignments[node.order] === undefined)\n        return;\n    assignments[node.order].forEach(assignmentNode => {\n        if (assignmentNode.node !== null) {\n            const aNode = nodes[assignmentNode.node];\n            if (aNode !== node && aNode.y > node.y) {\n                aNode.y += adjustBy;\n                assignmentNode.tracks.forEach(track => {\n                    const seg = tracks[track.trackID].path[track.segmentID];\n                    seg.y = seg.y + adjustBy;\n                });\n            }\n        }\n        else {\n            // track-segment not within a node\n            assignmentNode.tracks.forEach(track => {\n                const seg = tracks[track.trackID].path[track.segmentID];\n                if (seg.y >= node.y) {\n                    seg.y = seg.y + adjustBy;\n                }\n            });\n        }\n    });\n    if (nodesPerOrder[node.order].length > 0) {\n        nodesPerOrder[node.order].forEach(nodeIndex => {\n            if (nodes[nodeIndex] !== node && nodes[nodeIndex].y > node.y) {\n                nodes[nodeIndex].y += adjustBy;\n            }\n        });\n    }\n}\n// calculates cost of vertical adjustment as vertical distance * width of track\nfunction getVerticalAdjustmentCost(assignment, moveBy) {\n    let result = 0;\n    assignment.forEach(node => {\n        node.tracks.forEach(track => {\n            if (track.idealY != null && tracks[track.trackID].type !== 'read') {\n                result +=\n                    Math.abs(track.idealY -\n                        moveBy -\n                        tracks[track.trackID].path[track.segmentID].y) * tracks[track.trackID].width;\n            }\n        });\n    });\n    return result;\n}\nfunction compareByIdealLane(a, b) {\n    if (a.idealLane !== undefined) {\n        if (b.idealLane !== undefined) {\n            if (a.idealLane < b.idealLane)\n                return -1;\n            else if (a.idealLane > b.idealLane)\n                return 1;\n            return 0;\n        }\n        return -1;\n    }\n    if (b.idealLane !== undefined) {\n        return 1;\n    }\n    return 0;\n}\nfunction compareNodesByOrder(a, b) {\n    if (!a) {\n        if (!b)\n            return 0;\n        return -1;\n    }\n    if (!b)\n        return 1;\n    if (a.order !== undefined) {\n        if (b.order !== undefined) {\n            if (a.order < b.order)\n                return -1;\n            else if (a.order > b.order)\n                return 1;\n            if (a.y !== undefined && b.y !== undefined) {\n                if (a.y < b.y)\n                    return -1;\n                else if (a.y > b.y)\n                    return 1;\n            }\n            return 0;\n        }\n        return -1;\n    }\n    if (b.order !== undefined)\n        return 1;\n    return 0;\n}\nfunction addTrackFeatures() {\n    let nodeStart;\n    let nodeEnd;\n    let feature = {};\n    bed.forEach(line => {\n        let i = 0;\n        while (i < tracks.length && tracks[i].name !== line.track)\n            i += 1;\n        if (i < tracks.length) {\n            nodeStart = 0;\n            tracks[i].path.forEach(node => {\n                if (node.node !== null) {\n                    feature = {};\n                    nodeEnd = nodeStart + nodes[node.node].sequenceLength - 1;\n                    if (nodeStart >= line.start && nodeStart <= line.end) {\n                        feature.start = 0;\n                    }\n                    if (nodeStart < line.start && nodeEnd >= line.start) {\n                        feature.start = line.start - nodeStart;\n                    }\n                    if (nodeEnd <= line.end && nodeEnd >= line.start) {\n                        feature.end = nodeEnd - nodeStart;\n                        if (nodeEnd < line.end)\n                            feature.continue = true;\n                    }\n                    if (nodeEnd > line.end && nodeStart <= line.end) {\n                        feature.end = line.end - nodeStart;\n                    }\n                    if (feature.start !== undefined) {\n                        feature.type = line.type;\n                        feature.name = line.name;\n                        if (node.features === undefined)\n                            node.features = [];\n                        node.features.push(feature);\n                    }\n                    nodeStart = nodeEnd + 1;\n                }\n            });\n        }\n    });\n}\nfunction calculateTrackWidth() {\n    // flag: if vg returns freq of 0 for all tracks, we will increase width manually\n    let allAreFour = true;\n    const NARROW_WIDTH = 4;\n    const WIDE_WIDTH = config.trackWidth;\n    tracks.forEach(track => {\n        if (track.freq !== undefined) {\n            // custom track width\n            track.width = Math.round((Math.log(track.freq) + 1) * NARROW_WIDTH);\n        }\n        else {\n            // default track width\n            track.width = WIDE_WIDTH;\n            if (track.type !== undefined && track.type === 'read') {\n                track.width = NARROW_WIDTH;\n            }\n        }\n        if (track.width !== NARROW_WIDTH) {\n            allAreFour = false;\n        }\n    });\n    if (allAreFour) {\n        tracks.forEach(track => {\n            if (track.freq !== undefined) {\n                track.width = WIDE_WIDTH;\n            }\n        });\n    }\n}\nfunction getReadXStart(read) {\n    const seg = read.path[0];\n    const node = nodes[seg.node];\n    const offset = read.firstNodeOffset ?? 0;\n    // read starts in forward direction, or backward from the node's far end\n    return clampedXCoordinateOfBaseWithinNode(node, seg.isForward ? offset : node.sequenceLength - offset);\n}\nfunction getReadXEnd(read) {\n    const seg = read.path[read.path.length - 1];\n    const node = nodes[seg.node];\n    const cover = read.finalNodeCoverLength ?? 0;\n    // read ends in forward direction, or backward from the node's far end\n    return clampedXCoordinateOfBaseWithinNode(node, seg.isForward ? cover : node.sequenceLength - cover);\n}\n// returns the x coordinate (in pixels) of (the left side) of the given base\n// position within the given node, or null if the position is past its end\nexport function getXCoordinateOfBaseWithinNode(node, base) {\n    if (base > node.sequenceLength)\n        return null; // equality is allowed\n    return clampedXCoordinateOfBaseWithinNode(node, base);\n}\n// Same, but a base outside the node maps to the nearest node edge. Callers that\n// have to produce a coordinate no matter what use this: falling back to 0 would\n// put the shape at the far left of the whole image instead.\nexport function clampedXCoordinateOfBaseWithinNode(node, base) {\n    const [nodeLeftX, nodeRightX] = nodePixelCoordinatesInX(node);\n    if (node.sequenceLength === 0) {\n        return nodeLeftX;\n    }\n    const clamped = Math.min(Math.max(base, 0), node.sequenceLength);\n    return nodeLeftX + (clamped / node.sequenceLength) * (nodeRightX - nodeLeftX);\n}\n// transforms the info in the tracks' path attribute into actual coordinates\n// and saves them in shapes.rectangles and shapes.curves\nfunction generateSVGShapesFromPath() {\n    let xStart;\n    let xEnd;\n    let yStart;\n    let yEnd;\n    let trackColor;\n    let trackAlpha;\n    let highlight;\n    let dummy;\n    let reversalFlag;\n    for (let i = 0; i <= maxOrder; i += 1) {\n        extraLeft.push(0);\n        extraRight.push(0);\n    }\n    // generate x coords where each order starts and ends\n    const orderStartX = [];\n    const orderEndX = [];\n    nodes.forEach(node => {\n        if (node.x !== undefined) {\n            orderStartX[node.order] = node.x;\n            if (orderEndX[node.order] === undefined) {\n                orderEndX[node.order] = node.x + node.pixelWidth;\n            }\n            else {\n                orderEndX[node.order] = Math.max(orderEndX[node.order], node.x + node.pixelWidth);\n            }\n        }\n    });\n    // Helps generation of verticalRectangles, correct increments of extraRight and extraLeft\n    tracks.sort(compareTrackByInitialOrdering);\n    tracks.forEach(track => {\n        highlight = 'plain';\n        // Both are pure functions of (track, highlight); alpha doesn't even look at\n        // highlight. Recomputing them per path segment was pure overhead.\n        trackColor = generateTrackColor(track, highlight);\n        trackAlpha = generateTrackAlpha(track);\n        let colorHighlight = highlight;\n        const colorForCurrentHighlight = () => {\n            if (colorHighlight !== highlight) {\n                colorHighlight = highlight;\n                trackColor = generateTrackColor(track, highlight);\n            }\n            return trackColor;\n        };\n        // start of path\n        yStart = track.path[0].y;\n        if (track.type !== 'read') {\n            if (track.sequence[0].startsWith('-')) {\n                // The track starts with an inversed node\n                xStart = orderEndX[track.path[0].order] + 20;\n            }\n            else {\n                // The track starts with a forward node\n                xStart = orderStartX[track.path[0].order] - 20;\n            }\n        }\n        else {\n            xStart = getReadXStart(track);\n        }\n        // middle of path\n        for (let i = 0; i < track.path.length; i += 1) {\n            if (track.path[i].y === yStart) {\n                if (track.path[i].features !== undefined) {\n                    reversalFlag =\n                        i > 0 && track.path[i - 1].order === track.path[i].order;\n                    dummy = createFeatureRectangle(track.path[i], orderStartX[track.path[i].order], orderEndX[track.path[i].order], highlight, track, xStart, yStart, trackColor, reversalFlag);\n                    highlight = dummy.highlight;\n                    xStart = dummy.xStart;\n                }\n            }\n            else {\n                if (track.path[i - 1].isForward) {\n                    xEnd = orderEndX[track.path[i - 1].order];\n                }\n                else {\n                    xEnd = orderStartX[track.path[i - 1].order];\n                }\n                if (xEnd !== xStart) {\n                    trackColor = colorForCurrentHighlight();\n                    shapes.rectangles.push({\n                        xStart: Math.min(xStart, xEnd),\n                        yStart,\n                        xEnd: Math.max(xStart, xEnd),\n                        yEnd: yStart + track.width - 1,\n                        color: trackColor,\n                        alpha: trackAlpha,\n                        // TODO: This is not actually the index of the track!\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n                if (track.path[i].order - 1 === track.path[i - 1].order) {\n                    // regular forward connection\n                    xStart = xEnd;\n                    xEnd = orderStartX[track.path[i].order];\n                    yEnd = track.path[i].y;\n                    trackColor = colorForCurrentHighlight();\n                    shapes.curves.push({\n                        xStart,\n                        yStart,\n                        xEnd: xEnd + 1,\n                        yEnd,\n                        width: track.width,\n                        color: trackColor,\n                        alpha: trackAlpha,\n                        laneChange: Math.abs(track.path[i].lane - track.path[i - 1].lane),\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                        nodeStart: track.path[i - 1]?.node,\n                        nodeEnd: track.path[i]?.node,\n                    });\n                    xStart = xEnd;\n                    yStart = yEnd;\n                }\n                else if (track.path[i].order + 1 === track.path[i - 1].order) {\n                    // regular backward connection\n                    xStart = xEnd;\n                    xEnd = orderEndX[track.path[i].order];\n                    yEnd = track.path[i].y;\n                    trackColor = colorForCurrentHighlight();\n                    shapes.curves.push({\n                        xStart: xStart + 1,\n                        yStart,\n                        xEnd,\n                        yEnd,\n                        width: track.width,\n                        color: trackColor,\n                        alpha: trackAlpha,\n                        laneChange: Math.abs(track.path[i].lane - track.path[i - 1].lane),\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                        nodeStart: track.path[i - 1]?.node,\n                        nodeEnd: track.path[i]?.node,\n                    });\n                    xStart = xEnd;\n                    yStart = yEnd;\n                }\n                else {\n                    // change of direction\n                    if (track.path[i - 1].isForward) {\n                        yEnd = track.path[i].y;\n                        generateTurnaround(1, xEnd, yStart, yEnd, track.width, trackColor, track.id, track.path[i].order, track.type, track.name);\n                        xStart = orderEndX[track.path[i].order];\n                        yStart = track.path[i].y;\n                    }\n                    else {\n                        yEnd = track.path[i].y;\n                        generateTurnaround(-1, xEnd, yStart, yEnd, track.width, trackColor, track.id, track.path[i].order, track.type, track.name);\n                        xStart = orderStartX[track.path[i].order];\n                        yStart = track.path[i].y;\n                    }\n                }\n                if (track.path[i].features !== undefined) {\n                    reversalFlag = track.path[i - 1].order === track.path[i].order;\n                    dummy = createFeatureRectangle(track.path[i], orderStartX[track.path[i].order], orderEndX[track.path[i].order], highlight, track, xStart, yStart, trackColor, reversalFlag);\n                    highlight = dummy.highlight;\n                    xStart = dummy.xStart;\n                }\n            }\n        }\n        // ending edges\n        if (track.type !== 'read') {\n            if (!track.path[track.path.length - 1].isForward) {\n                // The track ends with an inversed node\n                xEnd = orderStartX[track.path[track.path.length - 1].order] - 20;\n            }\n            else {\n                // The track ends with a forward node\n                xEnd = orderEndX[track.path[track.path.length - 1].order] + 20;\n            }\n        }\n        else {\n            xEnd = getReadXEnd(track);\n        }\n        shapes.rectangles.push({\n            xStart: Math.min(xStart, xEnd),\n            yStart,\n            xEnd: Math.max(xStart, xEnd),\n            yEnd: yStart + track.width - 1,\n            color: trackColor,\n            alpha: trackAlpha,\n            id: track.id,\n            name: track.name,\n            type: track.type,\n        });\n    });\n}\n// Sankey-mode synthesis: one synthetic \"read\" per (srcSigned \u2192 dstSigned) edge,\n// fed through the normal placeReads/generateSVGShapesFromPath pipeline so the\n// band gets the same lane assignment, loop topology, bezier shape, AND color\n// scheme as a real read \u2014 colors come from generateTrackColor's natural\n// `id % palette.length` rotation, no custom palette needed.\n//\n// Synthetic-track ids live above this base so they don't collide with real\n// track ids and so click/hover handlers can show count info instead of the\n// per-read info dialog.\nconst COARSENED_ID_BASE = 1_000_000_000;\nexport const isCoarsenedId = (id) => id >= COARSENED_ID_BASE;\n// Build one synthetic read per (srcSigned \u2192 dstSigned) edge in `source`\n// (real reads, or the alt haplotype tracks). The synthetic reads replace the\n// real ones BEFORE placeReads runs, so:\n//   \u2022 placeReads sees N_edges reads instead of N_reads (huge node-height win),\n//   \u2022 each band gets a lane and an \"right-down-left-up-right\" loop topology\n//     for free (placeReads handles reversals and out-of-order jumps),\n//   \u2022 generateSVGShapesFromPath emits exactly one TrackCurve per band using\n//     the same bezier as a real read \u2014 no special draw path needed.\n//\n// The synthetic track's `sequence` is just the two signed node names. After\n// generateTrackIndexSequences runs, indexSequence is set and the rest of the\n// layout follows.\nfunction buildCoarsenedSyntheticBands(source, unit) {\n    coarsenedEdgeMeta = new Map();\n    const edges = new Map();\n    // When ignoring strand, (+A\u2192+B) and (-B\u2192-A) refer to the same underlying\n    // graph connection \u2014 collapse both into one canonical key. We pick the\n    // lexicographically smaller of the two orientations so a stable canonical\n    // form is chosen; whichever orientation is seen first determines the\n    // visual band direction.\n    const ignoreStrand = config.ignoreStrand;\n    for (const item of source) {\n        const seq = item.indexSequence;\n        if (!seq || seq.length < 2)\n            continue;\n        for (let i = 0; i < seq.length - 1; i += 1) {\n            const sSigned = seq[i];\n            const dSigned = seq[i + 1];\n            const sIdx = Math.abs(sSigned);\n            const dIdx = Math.abs(dSigned);\n            const srcNode = nodes[sIdx];\n            const dstNode = nodes[dIdx];\n            if (!srcNode || !dstNode)\n                continue;\n            let key;\n            if (ignoreStrand) {\n                const a = `${sSigned}>${dSigned}`;\n                const b = `${-dSigned}>${-sSigned}`;\n                key = a < b ? a : b;\n            }\n            else {\n                key = `${sSigned}>${dSigned}`;\n            }\n            const existing = edges.get(key);\n            if (existing === undefined) {\n                edges.set(key, {\n                    sSigned,\n                    dSigned,\n                    sName: sSigned < 0 ? `-${srcNode.name}` : srcNode.name,\n                    dName: dSigned < 0 ? `-${dstNode.name}` : dstNode.name,\n                    count: 1,\n                    sourceTrackID: item.sourceTrackID,\n                });\n            }\n            else {\n                existing.count += 1;\n            }\n        }\n    }\n    // Square-root scaling on count gives heavy edges visible weight without\n    // letting one massive edge dwarf everything else. Min stays near READ_WIDTH\n    // so single-read edges still look like a normal read; max is generous so\n    // hot edges read as obvious \"highways.\"\n    let maxEdgeCount = 0;\n    for (const e of edges.values()) {\n        if (e.count > maxEdgeCount)\n            maxEdgeCount = e.count;\n    }\n    const BAND_MIN_WIDTH = READ_WIDTH;\n    const BAND_MAX_WIDTH = 60;\n    const widthForCount = (c) => {\n        if (maxEdgeCount <= 1)\n            return BAND_MIN_WIDTH;\n        return (BAND_MIN_WIDTH +\n            (BAND_MAX_WIDTH - BAND_MIN_WIDTH) * Math.sqrt(c / maxEdgeCount));\n    };\n    const synthetic = [];\n    let i = 0;\n    for (const edge of edges.values()) {\n        const id = COARSENED_ID_BASE + i;\n        const label = `${edge.count.toLocaleString()} ${unit}${edge.count === 1 ? '' : 's'}: Node ${edge.sName} \u2192 Node ${edge.dName}`;\n        coarsenedEdgeMeta.set(id, { count: edge.count, label });\n        // Place each synthetic band so it touches *only* its endpoint nodes' edges:\n        //   \u2022 firstNodeOffset = src.sequenceLength \u2192 curve exits at src's right\n        //     pixel edge, no rectangle drawn inside src.\n        //   \u2022 finalNodeCoverLength = 0 \u2192 curve enters at dst's left pixel edge,\n        //     no rectangle drawn inside dst.\n        // The crucial side effect is in placeReadSet's conflict check: at any\n        // node B with an incoming edge (A\u2192B) and an outgoing edge (B\u2192C), the\n        // incoming's finalNodeCoverLength=0 and the outgoing's firstNodeOffset=\n        // B.length leave them with no horizontal overlap, so they share a single\n        // lane. Node heights collapse from ~(N_in + N_out) lanes down to\n        // ~max(N_in, N_out) lanes.\n        //\n        // Note: reverseReversedReads will swap firstNodeOffset/finalNodeCoverLength\n        // for fully-reverse synthetics. The math works out: pre-flip values of\n        // (srcLen, 0) become post-flip (newSrcLen, 0), which is the same pattern\n        // \u2014 bands stay edge-only regardless of orientation.\n        const srcLen = nodes[Math.abs(edge.sSigned)]?.sequenceLength ?? 0; // node may be absent for a dangling edge\n        synthetic.push({\n            id,\n            sourceTrackID: edge.sourceTrackID,\n            type: 'read',\n            // Human-readable so the name surfaces sensibly in any UI that uses it\n            // (right-click \u2192 add to group, etc.) \u2014 and so trackTooltipText fallback\n            // shows something meaningful.\n            name: label,\n            sequence: [edge.sName, edge.dName],\n            indexSequence: [],\n            path: [],\n            // Pre-set width so placeReads / placeReadSet allocate the right vertical\n            // space and assignReadsToNodes (patched to honor pre-set widths) leaves\n            // it alone.\n            width: widthForCount(edge.count),\n            firstNodeOffset: srcLen,\n            finalNodeCoverLength: 0,\n            sequenceNew: [\n                { nodeName: edge.sName, mismatches: [] },\n                { nodeName: edge.dName, mismatches: [] },\n            ],\n            mapping_quality: 0,\n            is_secondary: false,\n            sample_name: null,\n            read_group: null,\n            score: edge.count,\n        });\n        i += 1;\n    }\n    // Single-line debug summary so the user can verify node sizing.\n    let tallestName = '?';\n    let tallestH = 0;\n    for (const n of nodes) {\n        if (!n)\n            continue;\n        const h = n.contentHeight;\n        if (h > tallestH) {\n            tallestH = h;\n            tallestName = n.name;\n        }\n    }\n    if (DEBUG) {\n        console.log(`[coarsened] ${unit}s_in=${source.length} edges_out=${synthetic.length} ` +\n            `tallestNodeBeforePlace=${tallestName}(${tallestH.toFixed(1)})`);\n    }\n    return synthetic;\n}\nfunction createFeatureRectangle(node, nodeXStart, nodeXEnd, highlight, track, rectXStart, yStart, trackColor, reversalFlag) {\n    let currentHighlight = highlight;\n    let c;\n    let co;\n    let featureXStart;\n    let featureXEnd;\n    nodeXStart -= 8;\n    nodeXEnd += 8;\n    const nodeWidth = nodes[node.node].sequenceLength;\n    node.features.sort((a, b) => a.start - b.start);\n    node.features.forEach(feature => {\n        if (currentHighlight !== feature.type) {\n            // finish incoming rectangle\n            c = generateTrackColor(track, currentHighlight);\n            if (node.isForward) {\n                featureXStart =\n                    nodeXStart +\n                        Math.round((feature.start * (nodeXEnd - nodeXStart + 1)) / nodeWidth);\n                // overwrite narrow post-inversion rectangle if highlight starts near beginning of node\n                if (reversalFlag && featureXStart < nodeXStart + 8) {\n                    featureXEnd =\n                        nodeXStart +\n                            Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                            1;\n                    co = generateTrackColor(track, feature.type);\n                    shapes.featureRectangles.push({\n                        xStart: featureXStart,\n                        yStart,\n                        xEnd: featureXEnd,\n                        yEnd: yStart + track.width - 1,\n                        color: co,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n                if (featureXStart > rectXStart + 1) {\n                    shapes.featureRectangles.push({\n                        xStart: rectXStart,\n                        yStart,\n                        xEnd: featureXStart - 1,\n                        yEnd: yStart + track.width - 1,\n                        color: c,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n            }\n            else {\n                featureXStart =\n                    nodeXEnd -\n                        Math.round((feature.start * (nodeXEnd - nodeXStart + 1)) / nodeWidth);\n                // overwrite narrow post-inversion rectangle if highlight starts near beginning of node\n                if (reversalFlag && featureXStart > nodeXEnd - 8) {\n                    featureXEnd =\n                        nodeXEnd -\n                            Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                            1;\n                    co = generateTrackColor(track, feature.type);\n                    shapes.featureRectangles.push({\n                        xStart: featureXEnd,\n                        yStart,\n                        xEnd: featureXStart,\n                        yEnd: yStart + track.width - 1,\n                        color: co,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n                if (rectXStart > featureXStart + 1) {\n                    shapes.featureRectangles.push({\n                        xStart: featureXStart + 1,\n                        yStart,\n                        xEnd: rectXStart,\n                        yEnd: yStart + track.width - 1,\n                        color: c,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n            }\n            rectXStart = featureXStart;\n            currentHighlight = feature.type;\n        }\n        if (feature.end < nodeWidth - 1 || feature.continue === undefined) {\n            // finish internal rectangle\n            c = generateTrackColor(track, currentHighlight);\n            if (node.isForward) {\n                featureXEnd =\n                    nodeXStart +\n                        Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                        1;\n                shapes.featureRectangles.push({\n                    xStart: rectXStart,\n                    yStart,\n                    xEnd: featureXEnd,\n                    yEnd: yStart + track.width - 1,\n                    color: c,\n                    id: track.id,\n                    name: track.name,\n                    type: track.type,\n                });\n            }\n            else {\n                featureXEnd =\n                    nodeXEnd -\n                        Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                        1;\n                shapes.featureRectangles.push({\n                    xStart: featureXEnd,\n                    yStart,\n                    xEnd: rectXStart,\n                    yEnd: yStart + track.width - 1,\n                    color: c,\n                    id: track.id,\n                    name: track.name,\n                    type: track.type,\n                });\n            }\n            rectXStart = featureXEnd + 1;\n            currentHighlight = 'plain';\n        }\n    });\n    return { xStart: rectXStart, highlight: currentHighlight };\n}\nconst MIN_BEND_WIDTH = 7;\n// Emit the vertical rectangles + rounded corners for a track turning around at\n// one end of an order slot. The two directions are mirror images of each other:\n// a forward-to-reverse turn bulges out to the right of the node and consumes an\n// `extraRight` slot, a reverse-to-forward turn bulges out to the left and\n// consumes an `extraLeft` slot. `dir` is +1 for right, -1 for left.\nfunction generateTurnaround(dir, x, yStart, yEnd, trackWidth, trackColor, trackID, order, type, trackName) {\n    const extra = dir === 1 ? extraRight : extraLeft;\n    const offset = 10 * extra[order];\n    // The turn's apex, and the outward direction from it.\n    const apex = x + dir * (offset + 5);\n    const radius = MIN_BEND_WIDTH;\n    const stem = Math.min(MIN_BEND_WIDTH, trackWidth);\n    const yTop = Math.min(yStart, yEnd);\n    const yBottom = Math.max(yStart, yEnd);\n    // The incoming/outgoing stubs run from the node's edge out to the apex. The\n    // one-pixel asymmetry between the two directions is carried over verbatim\n    // from the original pair of functions.\n    const stubNear = dir === 1 ? x : apex - 1;\n    const stubFar = dir === 1 ? apex : x;\n    const horizontal = (segTop) => {\n        shapes.verticalRectangles.push({\n            xStart: stubNear,\n            yStart: segTop,\n            xEnd: stubFar,\n            yEnd: segTop + trackWidth - 1,\n            color: trackColor,\n            id: trackID,\n            name: trackName,\n            type,\n        });\n    };\n    // elongate the incoming and outgoing rectangles a bit past the node\n    horizontal(yStart);\n    shapes.verticalRectangles.push({\n        xStart: dir === 1 ? apex + radius : apex - radius - stem,\n        yStart: yTop + trackWidth + radius - 1,\n        xEnd: dir === 1 ? apex + radius + stem - 1 : apex - radius - 1,\n        yEnd: yBottom - radius + 1,\n        color: trackColor,\n        id: trackID,\n        name: trackName,\n        type,\n    });\n    horizontal(yEnd);\n    const inner = apex + dir * radius;\n    const outer = apex + dir * (radius + stem);\n    // bottom 90 degree bend\n    let d = `M ${apex} ${yBottom}`;\n    d += ` Q ${inner} ${yBottom} ${inner} ${yBottom - radius}`;\n    d += ` H ${outer}`;\n    d += ` Q ${outer} ${yBottom + trackWidth} ${apex} ${yBottom + trackWidth}`;\n    d += ' Z ';\n    shapes.corners.push({ path: d, color: trackColor, id: trackID, type });\n    // top 90 degree bend\n    d = `M ${apex} ${yTop}`;\n    d += ` Q ${outer} ${yTop} ${outer} ${yTop + trackWidth + radius}`;\n    d += ` H ${inner}`;\n    d += ` Q ${inner} ${yTop + trackWidth} ${apex} ${yTop + trackWidth}`;\n    d += ' Z ';\n    shapes.corners.push({ path: d, color: trackColor, id: trackID, type });\n    extra[order] += 1;\n}\nexport function nodePixelCoordinatesInX(node) {\n    // Add and subtract 4 to account for stroke width - TODO: figure out what the 4 means\n    const nodeLeftX = node.x - 4;\n    const nodeRightX = node.x + node.pixelWidth + 4;\n    return [nodeLeftX, nodeRightX];\n}\n// calculate node widths depending on sequence lengths and chosen calculation method\nfunction generateNodeWidth() {\n    // Promote the input's optional sequenceLength; Node declares it required, so\n    // widen to InputNode to make the still-possibly-undefined read explicit.\n    nodes.forEach((node) => {\n        if (node.sequenceLength === undefined) {\n            node.sequenceLength = node.seq.length;\n        }\n    });\n    switch (config.nodeWidthOption) {\n        case 'compressed':\n            nodes.forEach(node => {\n                node.width = 1 + Math.log(node.sequenceLength) / Math.log(2);\n                node.pixelWidth = Math.round((node.width - 1) * 8.401);\n            });\n            break;\n        case 'small':\n            nodes.forEach(node => {\n                node.width = node.sequenceLength / 100;\n                node.pixelWidth = Math.round((node.width - 1) * 8.401);\n            });\n            break;\n        case 'fixed':\n            // when there's no reads in the node, it should be a little wider\n            nodes.forEach(node => {\n                node.width = 10;\n                node.pixelWidth = Math.round(node.width * 8.401);\n            });\n            break;\n        case 'normal': {\n            // The sequence is drawn in a monospace font, so one character's width,\n            // which the caller measures, sizes every node.\n            const charWidth = config.charWidth;\n            nodes.forEach(node => {\n                node.width = node.sequenceLength;\n                const len = node.seq?.length ?? 1;\n                node.pixelWidth = Math.round(charWidth * len);\n            });\n            break;\n        }\n        default:\n            throw new Error(`${config.nodeWidthOption} not implemented`);\n    }\n}\n// remove redundant nodes\n// two nodes A and B can be merged if all tracks leaving A go directly into B\n// and all tracks entering B come directly from A\n// (plus no inversions involved)\nfunction mergeNodes() {\n    let nodeName;\n    let nodeName2;\n    // One set per node index, including the hole at 0 (Array.from materializes\n    // holes, unlike forEach/map).\n    const predSets = Array.from(nodes, () => new Set());\n    const succSets = Array.from(nodes, () => new Set());\n    let tracksAndReads;\n    if (config.showReads && reads.length > 0)\n        tracksAndReads = tracks.concat(reads);\n    else\n        tracksAndReads = tracks;\n    tracksAndReads.forEach(track => {\n        for (let i = 0; i < track.sequence.length; i += 1) {\n            if (!isReverse(track.sequence[i])) {\n                // forward Node\n                if (i > 0) {\n                    nodeName = track.sequence[i - 1];\n                    predSets[nodeMap.get(track.sequence[i])].add(nodeName);\n                    if (isReverse(nodeName)) {\n                        // add 2 predecessors, to make sure there is no node merging in this case\n                        predSets[nodeMap.get(track.sequence[i])].add(forward(nodeName));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    predSets[nodeMap.get(track.sequence[i])].add('None');\n                }\n                if (i < track.sequence.length - 1) {\n                    nodeName = track.sequence[i + 1];\n                    succSets[nodeMap.get(track.sequence[i])].add(nodeName);\n                    if (isReverse(nodeName)) {\n                        // add 2 successors, to make sure there is no node merging in this case\n                        succSets[nodeMap.get(track.sequence[i])].add(forward(nodeName));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    succSets[nodeMap.get(track.sequence[i])].add('None');\n                }\n            }\n            else {\n                // reverse Node\n                nodeName = forward(track.sequence[i]);\n                if (i > 0) {\n                    nodeName2 = track.sequence[i - 1];\n                    if (isReverse(nodeName2)) {\n                        succSets[nodeMap.get(nodeName)].add(forward(nodeName2));\n                    }\n                    else {\n                        // add 2 successors, to make sure there is no node merging in this case\n                        succSets[nodeMap.get(nodeName)].add(nodeName2);\n                        succSets[nodeMap.get(nodeName)].add(reverse(nodeName2));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    succSets[nodeMap.get(nodeName)].add('None');\n                }\n                if (i < track.sequence.length - 1) {\n                    nodeName2 = track.sequence[i + 1];\n                    if (isReverse(nodeName2)) {\n                        predSets[nodeMap.get(nodeName)].add(forward(nodeName2));\n                    }\n                    else {\n                        predSets[nodeMap.get(nodeName)].add(nodeName2);\n                        predSets[nodeMap.get(nodeName)].add(reverse(nodeName2));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    predSets[nodeMap.get(nodeName)].add('None');\n                }\n            }\n        }\n    });\n    // convert sets to arrays\n    const pred = predSets.map(s => Array.from(s));\n    const succ = succSets.map(s => Array.from(s));\n    // update reads which pass through merging nodes\n    if (config.showReads && reads.length > 0) {\n        // sort nodes by order, then by y-coordinate\n        const sortedNodes = nodes.slice();\n        sortedNodes.sort(compareNodesByOrder);\n        // iterate over all nodes and calculate their position within the new merged node\n        // Both maps carry an entry for each orientation of every node name (\"7\"\n        // and \"-7\"), because the read update below looks up whichever orientation\n        // the read happens to visit.\n        const mergeOffset = new Map();\n        // maps to leftmost node of a node's \"merging cascade\"\n        const mergeOrigin = new Map();\n        const offsetOf = (nodeName) => {\n            const offset = mergeOffset.get(nodeName);\n            if (offset === undefined) {\n                throw new Error(`No merge offset recorded for node ${nodeName}`);\n            }\n            return offset;\n        };\n        const originOf = (nodeName) => {\n            const origin = mergeOrigin.get(nodeName);\n            if (origin === undefined) {\n                throw new Error(`No merge origin recorded for node ${nodeName}`);\n            }\n            return origin;\n        };\n        sortedNodes.forEach(node => {\n            const predecessor = mergeableWithPred(nodeMap.get(node.name), pred, succ);\n            if (predecessor) {\n                // Nodes are visited in order, so the predecessor of a merge cascade is\n                // always recorded before the node that follows it.\n                const offset = offsetOf(predecessor) + nodeByName(predecessor).sequenceLength;\n                mergeOffset.set(node.name, offset);\n                mergeOffset.set(reverse(node.name), offset);\n                mergeOrigin.set(node.name, originOf(predecessor));\n                mergeOrigin.set(reverse(node.name), originOf(predecessor));\n            }\n            else {\n                mergeOffset.set(node.name, 0);\n                mergeOffset.set(reverse(node.name), 0);\n                mergeOrigin.set(node.name, node.name);\n                mergeOrigin.set(reverse(node.name), node.name);\n            }\n        });\n        reads.forEach(read => {\n            const sequenceNew = read.sequenceNew ?? [];\n            read.firstNodeOffset =\n                (read.firstNodeOffset ?? 0) + offsetOf(read.sequence[0]);\n            read.finalNodeCoverLength =\n                (read.finalNodeCoverLength ?? 0) +\n                    offsetOf(read.sequence[read.sequence.length - 1]);\n            for (let i = read.sequence.length - 1; i >= 0; i -= 1) {\n                const nodeName = forward(read.sequence[i]);\n                const predecessor = mergeableWithPred(nodeMap.get(nodeName), pred, succ);\n                if (predecessor &&\n                    mergeableWithSucc(nodeMap.get(predecessor), pred, succ)) {\n                    if (i > 0) {\n                        read.sequence.splice(i, 1);\n                        // adjust position of mismatches\n                        const predLength = nodeByName(predecessor).sequenceLength;\n                        sequenceNew[i].mismatches.forEach(mismatch => {\n                            mismatch.pos += predLength;\n                        });\n                        // append mismatches to previous entry's mismatches\n                        sequenceNew[i - 1].mismatches = sequenceNew[i - 1].mismatches.concat(sequenceNew[i].mismatches);\n                        sequenceNew.splice(i, 1);\n                    }\n                    else {\n                        read.sequence[0] = originOf(read.sequence[0]);\n                        const firstEntry = sequenceNew[0];\n                        const firstOffset = offsetOf(firstEntry.nodeName);\n                        firstEntry.mismatches.forEach(mismatch => {\n                            mismatch.pos += firstOffset;\n                        });\n                        firstEntry.nodeName = originOf(firstEntry.nodeName);\n                    }\n                }\n            }\n        });\n    }\n    // update node sequences + sequence lengths\n    for (let i = 0; i < nodes.length; i += 1) {\n        if (mergeableWithSucc(i, pred, succ) && !mergeableWithPred(i, pred, succ)) {\n            let donor = i;\n            while (mergeableWithSucc(donor, pred, succ)) {\n                donor = nodeMap.get(forward(succ[donor][0]));\n                nodes[i].sequenceLength += nodes[donor].sequenceLength;\n                nodes[i].seq += nodes[donor].seq;\n            }\n        }\n    }\n    // actually merge the nodes by removing the corresponding nodes from track data\n    tracks.forEach(track => {\n        for (let i = track.sequence.length - 1; i >= 0; i -= 1) {\n            nodeName = forward(track.sequence[i]);\n            const nodeIndex = nodeMap.get(nodeName);\n            if (mergeableWithPred(nodeIndex, pred, succ)) {\n                track.sequence.splice(i, 1);\n            }\n        }\n    });\n    // remove the nodes from node-array\n    for (let i = nodes.length - 1; i >= 0; i -= 1) {\n        if (mergeableWithPred(i, pred, succ)) {\n            nodes.splice(i, 1);\n        }\n    }\n}\nfunction mergeableWithPred(index, pred, succ) {\n    if (pred[index].length !== 1)\n        return false;\n    if (pred[index][0] === 'None')\n        return false;\n    const predecessor = forward(pred[index][0]);\n    const predecessorIndex = nodeMap.get(predecessor);\n    if (succ[predecessorIndex].length !== 1)\n        return false;\n    if (succ[predecessorIndex][0] === 'None')\n        return false;\n    return predecessor;\n}\nfunction mergeableWithSucc(index, pred, succ) {\n    if (succ[index].length !== 1)\n        return false;\n    if (succ[index][0] === 'None')\n        return false;\n    const successor = forward(succ[index][0]);\n    const successorIndex = nodeMap.get(successor);\n    if (pred[successorIndex].length !== 1)\n        return false;\n    if (pred[successorIndex][0] === 'None')\n        return false;\n    return true;\n}\nfunction filterReads(readList) {\n    const focusNames = config.focusReadNames\n        ? new Set(config.focusReadNames)\n        : null;\n    return readList.filter(read => read.is_secondary !== true &&\n        (read.mapping_quality ?? 0) >= config.mappingQualityCutoff &&\n        (focusNames === null ||\n            (read.name !== undefined && focusNames.has(read.name))));\n}\n", "function groupBy(items, key) {\n    const groups = new Map();\n    for (const item of items) {\n        const k = key(item);\n        const group = groups.get(k);\n        if (group === undefined) {\n            groups.set(k, [item]);\n        }\n        else {\n            group.push(item);\n        }\n    }\n    return groups;\n}\nfunction compareCurvesByXYStartValue(a, b) {\n    if (a.xStart < b.xStart)\n        return 1;\n    else if (a.xStart > b.xStart)\n        return -1;\n    else if (a.yStart > b.yStart)\n        return 1;\n    else if (a.yStart < b.yStart)\n        return -1;\n    return 0;\n}\n// The curves of one track type in draw order, each with its `path` set. Curves\n// between the same pair of nodes form a group whose control points fan out, so\n// a bundle of tracks changing lanes together stays parallel rather than\n// crossing at one x.\nexport function curvePaths(curves, type) {\n    const groupedCurves = groupBy(curves.filter(curve => curve.type === type), curve => `${curve.nodeStart},${curve.nodeEnd}`);\n    groupedCurves.forEach(curveGroup => {\n        // Control point adjustment range: 30% to 70% of the original x values\n        let adjustValue = 0.3;\n        let adjustIncrement = 0.4 / curveGroup.length;\n        // Ignore Beziar Curve skewing when a group is not too big\n        if (curveGroup.length <= 5) {\n            adjustValue = 0.5;\n            adjustIncrement = 0;\n        }\n        curveGroup.sort(compareCurvesByXYStartValue);\n        curveGroup.forEach(curve => {\n            let xAdjusted;\n            // NextAdjusted is used to try to draw a parallel curve on the way back\n            let xNextAdjusted;\n            if (curve.yStart < curve.yEnd) {\n                xAdjusted =\n                    curve.xStart + (curve.xEnd - curve.xStart) * (1 - adjustValue);\n                adjustValue += adjustIncrement;\n                xNextAdjusted =\n                    curve.xStart + (curve.xEnd - curve.xStart) * (1 - adjustValue);\n            }\n            else {\n                xAdjusted = curve.xStart + (curve.xEnd - curve.xStart) * adjustValue;\n                adjustValue += adjustIncrement;\n                xNextAdjusted = curve.xStart + (curve.xEnd - curve.xStart) * adjustValue;\n            }\n            let d = `M ${curve.xStart} ${curve.yStart}`;\n            d += ` C ${xAdjusted} ${curve.yStart} ${xAdjusted} ${curve.yEnd} ${curve.xEnd} ${curve.yEnd}`;\n            d += ` V ${curve.yEnd + curve.width}`;\n            d += ` C ${xNextAdjusted} ${curve.yEnd + curve.width} ${xNextAdjusted} ${curve.yStart + curve.width} ${curve.xStart} ${curve.yStart + curve.width}`;\n            d += ' Z';\n            curve.path = d;\n        });\n    });\n    // One flat list ordered by group, then by the within-group sort\n    const groupKeys = Array.from(groupedCurves.keys());\n    groupKeys.sort(function (a, b) {\n        const aParts = a.split(',').map(Number);\n        const bParts = b.split(',').map(Number);\n        const a0 = aParts[0] ?? 0;\n        const a1 = aParts[1] ?? 0;\n        const b0 = bParts[0] ?? 0;\n        const b1 = bParts[1] ?? 0;\n        if (a0 < b0) {\n            return -1;\n        }\n        else if (a0 > b0) {\n            return 1;\n        }\n        else {\n            if (a1 < b1) {\n                return -1;\n            }\n            else if (a1 > b1) {\n                return 1;\n            }\n            else {\n                return 0;\n            }\n        }\n    });\n    const flattenedGroups = [];\n    for (const key of groupKeys) {\n        const group = groupedCurves.get(key);\n        if (group !== undefined) {\n            flattenedGroups.push(...group);\n        }\n    }\n    return flattenedGroups;\n}\n// A node's outline: a rounded box 9 units outside the node's x extent and its\n// content height, the tracks through it inside.\nexport function nodeOutlinePath(node) {\n    // top left arc\n    let d = `M ${node.x - 9} ${node.y} Q ${node.x - 9} ${node.y - 9} ${node.x} ${node.y - 9}`;\n    let x = node.x;\n    let y = node.y - 9;\n    // top straight\n    if (node.width > 1) {\n        x += node.pixelWidth;\n        d += ` L ${x} ${y}`;\n    }\n    // top right arc\n    d += ` Q ${x + 9} ${y} ${x + 9} ${y + 9}`;\n    x += 9;\n    y += 9;\n    // right straight\n    if (node.contentHeight > 0) {\n        y += node.contentHeight - 0;\n        d += ` L ${x} ${y}`;\n    }\n    // bottom right arc\n    d += ` Q ${x} ${y + 9} ${x - 9} ${y + 9}`;\n    x -= 9;\n    y += 9;\n    // bottom straight\n    if (node.width > 1) {\n        x -= node.pixelWidth;\n        d += ` L ${x} ${y}`;\n    }\n    // bottom left arc\n    d += ` Q ${x - 9} ${y} ${x - 9} ${y - 9}`;\n    x -= 9;\n    y -= 9;\n    // left straight\n    if (node.contentHeight > 0) {\n        y -= node.contentHeight - 0;\n        d += ` L ${x} ${y}`;\n    }\n    return d;\n}\n", "import { layoutTubeMap } from '@gmod/tubemap-core'\n\nimport { isBackbone } from '../anchoredNodes'\nimport { pathOrigin } from '../pathAnchoring'\nimport { pathCssColor, pathGreyCssColor } from '../pathColors'\nimport {\n  canonicalStrand,\n  readColor,\n  stepName,\n  tubeMapReads,\n} from '../tubeMap/reads'\n\nimport type { Coarsened } from '../tubeMap/coarsen'\nimport type { Graph, LayoutResult, NodeSegment } from '../types'\nimport type {\n  InputNode,\n  InputTrack,\n  LayoutNode,\n  TubeMapLayout,\n} from '@gmod/tubemap-core'\n\n// The sequenceTubeMap drawing of a graph's paths: every P or W line a tube,\n// every node a box the tubes pass through, laid out by @gmod/tubemap-core. The\n// canvas draws none of it; TubeMapOverlay draws the shapes, and nodePositions\n// is each box's centreline, for the hit test, the fit and the labels.\n//\n// Two x axes. `own` is the tube map's: columns in node order, a node as wide as\n// log2 of its length, which is the compact picture sequenceTubeMap draws.\n// `reference` pins each column to the reference bp its backbone node covers,\n// so the tubes line up with the linear view's other tracks; the overlay makes\n// room for the curves between columns when it draws (tubeMapWarp.ts).\n\n// A column of the tube map: the nodes at one `order`, the tube x they were\n// drawn over, and under the reference axis the reference bp they stand for.\nexport interface TubeMapColumn {\n  order: number\n  x0: number\n  x1: number\n  bp0: number\n  bp1: number\n}\n\nexport interface TubeMapDrawing {\n  layout: TubeMapLayout\n  // each path's tube colour, in the order the graph states its paths\n  pathColors: string[]\n  // tube y minus this is the drawing's y, so the drawing starts at 0\n  yOffset: number\n  // set on the reference axis, sorted by order\n  columns?: TubeMapColumn[]\n  // set when the cut was folded before layout (coarsen.ts): the drawing's node\n  // ids are the coarse graph's, not the cut's\n  coarse?: Coarsened\n}\n\n// Strand of every visit a path makes to a segment, in walk order, so the k-th\n// time a path reaches a segment reads the k-th entry. Visits name a path\n// without the range suffix `odgi extract` appends (pathOrigin).\nexport function visitStrands(graph: Graph) {\n  const strands = new Map<string, ('+' | '-')[]>()\n  for (const [segment, visits] of graph.pathVisits ?? []) {\n    for (const visit of visits) {\n      const key = `${visit.path}\\t${segment}`\n      const list = strands.get(key)\n      if (list) {\n        list.push(visit.strand)\n      } else {\n        strands.set(key, [visit.strand])\n      }\n    }\n  }\n  return strands\n}\n\n// A tube map track per path, the reference first: the layout straightens\n// track 0 and orders every other node around it. A step reads its node in\n// reverse where the path walks the segment against the strand the node is\n// drawn in.\nexport function tubeMapTracks(graph: Graph): InputTrack[] {\n  const nodeById = new Map(graph.nodes.map(n => [n.id, n]))\n  const strands = visitStrands(graph)\n  const paths = (graph.paths ?? []).map((path, index) => ({ path, index }))\n  const reference = paths.findIndex(\n    p => pathOrigin(p.path.name).name === graph.referencePath,\n  )\n  if (reference > 0) {\n    paths.unshift(...paths.splice(reference, 1))\n  }\n  return paths.flatMap(({ path, index }) => {\n    const visitName = pathOrigin(path.name).name\n    const seen = new Map<string, number>()\n    const sequence = path.nodeIds.flatMap(id => {\n      const node = nodeById.get(id)\n      if (!node) {\n        return []\n      }\n      const k = seen.get(node.name) ?? 0\n      seen.set(node.name, k + 1)\n      const strand =\n        strands.get(`${visitName}\\t${node.name}`)?.[k] ?? canonicalStrand(node)\n      return [stepName(node, strand)]\n    })\n    return sequence.length > 0\n      ? [\n          {\n            id: index,\n            name: path.name,\n            sequence,\n            sourceTrackID: 0,\n            type: 'haplotype' as const,\n          },\n        ]\n      : []\n  })\n}\n\nfunction tubeMapNodes(graph: Graph): InputNode[] {\n  return graph.nodes.map(n => ({\n    name: n.id,\n    seq: '',\n    sequenceLength: Math.max(1, n.length),\n  }))\n}\n\nexport function hasTubeMapPaths(graph: Graph) {\n  return (graph.paths?.length ?? 0) > 0\n}\n\n// Tubes narrow as paths are added, so ninety haplotypes stack about as tall as\n// forty at full width rather than filling a screen and a half each.\nconst STACK_PX = 600\nconst MIN_TUBE_PX = 3\nconst MAX_TUBE_PX = 15\n\nexport function tubeWidth(trackCount: number) {\n  return Math.max(\n    MIN_TUBE_PX,\n    Math.min(MAX_TUBE_PX, Math.floor(STACK_PX / Math.max(1, trackCount))),\n  )\n}\n\nfunction runTubeMap(graph: Graph) {\n  const paths = graph.paths ?? []\n  const tracks = tubeMapTracks(graph)\n  const reads = graph.reads\n    ? tubeMapReads(graph, graph.reads, paths.length)\n    : []\n  const tubeColor = reads.length > 0 ? pathGreyCssColor : pathCssColor\n  const pathColors = paths.map((_, i) => tubeColor(i, paths.length))\n  const layout = layoutTubeMap(tubeMapNodes(graph), tracks, reads, {\n    nodeWidthOption: 'compressed',\n    trackWidth: tubeWidth(tracks.length),\n    trackColor: track =>\n      track.type === 'read' ? readColor(track) : pathColors[track.id]!,\n  })\n  return layout ? { layout, pathColors } : undefined\n}\n\n// Drawn nodes only: an unreached one has no x.\nfunction drawnNodes(layout: TubeMapLayout) {\n  const nodes: LayoutNode[] = []\n  layout.nodes.forEach(node => {\n    if (node.order >= 0) {\n      nodes.push(node)\n    }\n  })\n  return nodes\n}\n\nfunction centreline(node: LayoutNode, yOffset: number, x0: number, x1: number) {\n  const y = node.y + node.contentHeight / 2 - yOffset\n  return [\n    { x: x0, y },\n    { x: x1, y },\n  ]\n}\n\nfunction extentOf(layout: TubeMapLayout, yOffset: number) {\n  return {\n    minY: layout.bounds.minY - yOffset,\n    maxY: layout.bounds.maxY - yOffset,\n  }\n}\n\nexport function tubeMapLayout(graph: Graph): LayoutResult | undefined {\n  const run = hasTubeMapPaths(graph) ? runTubeMap(graph) : undefined\n  if (!run) {\n    return undefined\n  }\n  const { layout, pathColors } = run\n  const yOffset = layout.bounds.minY\n  const nodePositions: Record<string, NodeSegment[]> = {}\n  for (const node of drawnNodes(layout)) {\n    nodePositions[node.name] = centreline(\n      node,\n      yOffset,\n      node.x,\n      node.x + node.pixelWidth,\n    )\n  }\n  const { minY, maxY } = extentOf(layout, yOffset)\n  return {\n    nodePositions,\n    tubeMap: { layout, yOffset, pathColors },\n    extent: {\n      minX: layout.bounds.minX,\n      maxX: layout.bounds.maxX,\n      minY,\n      maxY,\n    },\n  }\n}\n\n// Each column's reference bp: the span of its backbone nodes, whose merged\n// length the layout summed, or a point where the previous column ended for a\n// column of inserted sequence alone. Clamped to run left to right, so an\n// inversion the reference walks backwards cannot fold the axis over.\nfunction tubeMapColumns(graph: Graph, layout: TubeMapLayout): TubeMapColumn[] {\n  const nodeById = new Map(graph.nodes.map(n => [n.id, n]))\n  const byOrder = new Map<number, LayoutNode[]>()\n  for (const node of drawnNodes(layout)) {\n    const list = byOrder.get(node.order)\n    if (list) {\n      list.push(node)\n    } else {\n      byOrder.set(node.order, [node])\n    }\n  }\n  const columns: TubeMapColumn[] = []\n  let end = -Infinity\n  for (const order of [...byOrder.keys()].sort((a, b) => a - b)) {\n    const nodes = byOrder.get(order)!\n    let bp0 = Infinity\n    let bp1 = -Infinity\n    for (const node of nodes) {\n      const graphNode = nodeById.get(node.name)\n      if (graphNode && isBackbone(graphNode)) {\n        bp0 = Math.min(bp0, graphNode.stable.start)\n        bp1 = Math.max(bp1, graphNode.stable.start + node.sequenceLength)\n      }\n    }\n    if (bp0 === Infinity) {\n      bp0 = bp1 = end\n    }\n    if (bp0 < end) {\n      bp0 = end\n      bp1 = Math.max(end, bp1)\n    }\n    end = Math.max(end, bp1)\n    columns.push({\n      order,\n      x0: Math.min(...nodes.map(n => n.x)),\n      x1: Math.max(...nodes.map(n => n.x + n.pixelWidth)),\n      bp0,\n      bp1,\n    })\n  }\n  // columns before the first backbone node take its start\n  const first = columns.find(c => c.bp0 !== -Infinity)\n  for (const column of columns) {\n    if (column.bp0 === -Infinity) {\n      column.bp0 = column.bp1 = first?.bp0 ?? 0\n    }\n  }\n  return columns\n}\n\nfunction pathsReachBackbone(graph: Graph) {\n  return graph.nodes.some(isBackbone) && hasTubeMapPaths(graph)\n}\n\nexport function tubeMapReferenceLayout(graph: Graph): LayoutResult | undefined {\n  const run = pathsReachBackbone(graph) ? runTubeMap(graph) : undefined\n  if (!run) {\n    return undefined\n  }\n  const { layout, pathColors } = run\n  const columns = tubeMapColumns(graph, layout)\n  const byOrder = new Map(columns.map(c => [c.order, c]))\n  const yOffset = layout.bounds.minY\n  const nodePositions: Record<string, NodeSegment[]> = {}\n  for (const node of drawnNodes(layout)) {\n    const column = byOrder.get(node.order)!\n    nodePositions[node.name] = centreline(node, yOffset, column.bp0, column.bp1)\n  }\n  return {\n    nodePositions,\n    tubeMap: { layout, yOffset, columns, pathColors },\n    referenceAxis: true,\n    pixelRows: true,\n    extent: extentOf(layout, yOffset),\n  }\n}\n", "import { panSNSample } from '../pansn'\nimport { pathOrigin } from '../pathAnchoring'\n\nimport type { Graph, GraphPath } from '../types'\n\n// Each haplotype walk on its own bp axis, so what a walk carries through the\n// window is its bar length. Reference-anchored rows cannot state that: a\n// haplotype's private copies of a repeat consume no reference and collapse to\n// a mark, which is why the KIV-2 array reads as a knot in every node layout\n// and as a ladder here.\n//\n// A base-level graph does not revisit reference nodes through a repeat array,\n// so a copy count is not a visit count; it is the sequence a walk spends\n// between the reference nodes flanking the window, divided by the unit. Runs\n// distinguish sequence the reference walk also carries from sequence it does\n// not, so an expansion is the off-reference stretch of a row.\n\nexport interface WalkRun {\n  // bp offset from the start of this walk's slice\n  start: number\n  bp: number\n  onReference: boolean\n  // lowest reference bp an on-reference run covers; the run covers `bp` of\n  // reference contiguously. In a tandem array that is the reference copy the\n  // graph threads this copy through, which need not be the one it most\n  // resembles.\n  referenceStart?: number\n  // the walk crosses that reference from its end back to its start\n  reversed?: true\n}\n\nexport interface WalkRow {\n  name: string\n  label: string\n  sample: string\n  haplotype?: number\n  bp: number\n  offReferenceBp: number\n  // false when the walk does not reach both flanking reference nodes, in which\n  // case the whole walk is measured and the bar says so\n  complete: boolean\n  runs: WalkRun[]\n}\n\nexport interface WalkRows {\n  // reference bp the rows' bars start at, so a row's x is origin + run.start\n  origin: number\n  // repeat unit in bp when a repeat annotation supplied one; the bars tile by it\n  unit?: number\n  reference: WalkRow\n  // every other walk, longest first\n  rows: WalkRow[]\n}\n\nfunction sampleOf(path: GraphPath) {\n  return path.sample ?? panSNSample(path.name)\n}\n\nfunction labelOf(path: GraphPath) {\n  return path.haplotype !== undefined && path.sample !== undefined\n    ? `${path.sample}#${path.haplotype}`\n    : sampleOf(path)\n}\n\n// Each walk is cut at the nearest reference nodes IT visits on either side of\n// the region, so a walk that skips one flanking node at a SNP is still measured\n// between flanks rather than whole.\nfunction sliceBetween(\n  nodeIds: string[],\n  span: Map<string, { start: number; end: number }>,\n  region: { start: number; end: number } | undefined,\n  flanked = true,\n) {\n  // A cut that stops at the window carries no flanking reference for anyone,\n  // so every walk is whole and the slice is the walk.\n  if (!region || !flanked) {\n    return { ids: nodeIds, complete: true }\n  }\n  let i0 = -1\n  let i1 = -1\n  let bestEnd = -Infinity\n  let bestStart = Infinity\n  nodeIds.forEach((id, i) => {\n    const s = span.get(id)\n    if (s) {\n      if (s.end <= region.start && s.end > bestEnd) {\n        bestEnd = s.end\n        i0 = i\n      }\n      if (s.start >= region.end && s.start < bestStart) {\n        bestStart = s.start\n        i1 = i\n      }\n    }\n  })\n  if (i0 < 0 || i1 < 0) {\n    return { ids: nodeIds, complete: false }\n  }\n  const ids = nodeIds.slice(Math.min(i0, i1) + 1, Math.max(i0, i1))\n  return { ids: i0 < i1 ? ids : ids.reverse(), complete: true }\n}\n\nexport function walkRows(\n  graph: Graph,\n  region?: { start: number; end: number },\n  unit?: number,\n): WalkRows | undefined {\n  const paths = graph.paths ?? []\n  // `referencePath` is the anchor name, which pathOrigin has already stripped\n  // of the range suffix odgi leaves on a P record's name\n  const reference =\n    paths.find(p => pathOrigin(p.name).name === graph.referencePath) ?? paths[0]\n  if (!reference || paths.length < 2) {\n    return undefined\n  }\n  const lengthOf = new Map(graph.nodes.map(n => [n.id, n.length]))\n  const referenceStart =\n    graph.anchorPaths?.find(p => p.name === pathOrigin(reference.name).name)\n      ?.start ?? 0\n\n  const cut = region && region.end > region.start ? region : undefined\n  const span = new Map<string, { start: number; end: number }>()\n  let pos = referenceStart\n  for (const id of reference.nodeIds) {\n    const len = lengthOf.get(id) ?? 0\n    if (!span.has(id)) {\n      span.set(id, { start: pos, end: pos + len })\n    }\n    pos += len\n  }\n\n  // Whether the reference reaches past the region on both sides, i.e. whether\n  // a flanking node exists for any walk to be cut at.\n  const flanked =\n    cut === undefined ||\n    ([...span.values()].some(s => s.end <= cut.start) &&\n      [...span.values()].some(s => s.start >= cut.end))\n\n  const rowOf = (path: GraphPath): WalkRow => {\n    const { ids, complete } = sliceBetween(path.nodeIds, span, cut, flanked)\n    const runs: WalkRun[] = []\n    let bp = 0\n    let offReferenceBp = 0\n    // which way the last run steps through the reference, 0 while it holds\n    // one node\n    let step = 0\n    for (const id of ids) {\n      const len = lengthOf.get(id) ?? 0\n      const s = span.get(id)\n      const last = runs.at(-1)\n      const at = last?.referenceStart\n      const forward =\n        s && at !== undefined && step >= 0 && at + last!.bp === s.start\n      const backward = s && at !== undefined && step <= 0 && s.end === at\n      if (!s && last && !last.onReference) {\n        last.bp += len\n      } else if (forward || backward) {\n        last!.bp += len\n        if (!forward) {\n          last!.referenceStart = s.start\n          last!.reversed = true\n        }\n        step = forward ? 1 : -1\n      } else {\n        runs.push({\n          start: bp,\n          bp: len,\n          onReference: s !== undefined,\n          referenceStart: s?.start,\n        })\n        step = 0\n      }\n      bp += len\n      if (!s) {\n        offReferenceBp += len\n      }\n    }\n    return {\n      name: path.name,\n      label: labelOf(path),\n      sample: sampleOf(path),\n      haplotype: path.haplotype,\n      bp,\n      offReferenceBp,\n      complete,\n      runs,\n    }\n  }\n\n  // A cut can hand one walk back in pieces, and a piece reached only through\n  // context meets no reference node, so nothing places it against the window.\n  // It is dropped when another piece of the same walk does meet the reference.\n  const meetsReference = (p: GraphPath) => p.nodeIds.some(id => span.has(id))\n  const placedWalks = new Set(\n    paths.filter(p => p !== reference && meetsReference(p)).map(p => p.name),\n  )\n  const origin = cut ? cut.start : referenceStart\n  return {\n    origin,\n    unit,\n    reference: rowOf(reference),\n    rows: paths\n      .filter(\n        p => p !== reference && (meetsReference(p) || !placedWalks.has(p.name)),\n      )\n      .map(rowOf)\n      .sort(\n        (a, b) =>\n          Number(b.complete) - Number(a.complete) ||\n          b.bp - a.bp ||\n          a.label.localeCompare(b.label),\n      ),\n  }\n}\n", "import { ROW_HEIGHT_PX } from './rowSpacing'\nimport { walkRows } from './walkRows'\nimport { backboneNodes, backbonePositions } from '../anchoredNodes'\n\nimport type { WalkRows } from './walkRows'\nimport type { Graph, LayoutResult, RowLabel } from '../types'\n\n// The reference walk as the backbone on row 0, at its bp, and a row per other\n// walk below it. The rows themselves are not nodes: a node the renderer draws\n// once cannot sit on nine rows, so WalkRowsOverlay draws each walk's bar from\n// `walkRows`, and this layout only reserves the rows and states how far the\n// bars reach so the fit and the pane height include them.\n// The fit leaves this much past the longest bar for its readout and the legend.\nconst READOUT_ROOM = 1.3\n\n// How far the bars reach, so the fit and the pane height include them. The\n// model reads it again for the bars it actually draws, which a repeat pick or\n// a sample filter can narrow after this layout ran.\nexport function walkRowsExtent(walks: WalkRows) {\n  let longest = walks.reference.bp\n  for (const row of walks.rows) {\n    longest = Math.max(longest, row.bp)\n  }\n  return {\n    maxX: walks.origin + longest * READOUT_ROOM,\n    maxY: walks.rows.length * ROW_HEIGHT_PX,\n  }\n}\n\nexport function walkRowLayout(\n  graph: Graph,\n  region?: { start: number; end: number },\n): LayoutResult | undefined {\n  const backbone = backboneNodes(graph)\n  const walks = walkRows(graph, region)\n  if (backbone.length === 0 || !walks) {\n    return undefined\n  }\n  const nodePositions = backbonePositions(backbone)\n  const rowLabels: RowLabel[] = [\n    { label: walks.reference.label, y: 0 },\n    ...walks.rows.map((row, i) => ({\n      label: row.label,\n      y: (i + 1) * ROW_HEIGHT_PX,\n    })),\n  ]\n  return {\n    nodePositions,\n    rowLabels,\n    referenceAxis: true,\n    pixelRows: true,\n    extent: walkRowsExtent(walks),\n  }\n}\n", "import { isBackbone, isOffReference } from './anchoredNodes'\nimport { anchoredLayout } from './layout/anchoredLayout'\nimport { orderedLayout } from './layout/orderedLayout'\nimport { sampleRowLayout } from './layout/sampleRowLayout'\nimport {\n  hasTubeMapPaths,\n  tubeMapLayout,\n  tubeMapReferenceLayout,\n} from './layout/tubeMapLayout'\nimport { walkRowLayout } from './layout/walkRowLayout'\n\nimport type { Graph, LayoutResult } from './types'\n\n// The force layout's menu label. jbrowse-components' check-menu-labels scans\n// this src/ for string literals, so a documented **Layout \u2192 \u2026** path is held\n// to what the dropdown renders.\nexport const FORCE_LAYOUT_LABEL = 'Force-directed layout'\n\n// One table drives the persisted enum, the toolbar dropdown, and the dispatch in\n// the model, so adding a layout is one entry rather than several edits that can\n// disagree.\n//\n// `run` returning undefined means \"this mode can't draw this graph\" and hands\n// off to the remote Bandage FMMM engine. 'auto' uses it when a GFA has no\n// rank-0 backbone \u2014 neither declared in rGFA tags nor derivable from P/W lines\n// (pathAnchoring.ts) \u2014 and 'force' is simply the mode that always takes it.\nexport interface LayoutMode {\n  value: string\n  label: string\n  description: string\n  // `region` is the interval the cut was made for, absent for a whole-file\n  // import. The reference-anchored modes scale their rows and their allele\n  // floor against it rather than against the backbone they were handed, which\n  // a long-range allele's far anchor stretches well past the window\n  // (referenceSpan). `keepRows` is the sample rows on screen, which only the\n  // sample-row layout reads (LayoutResult.sampleRows).\n  run: (\n    graph: Graph,\n    region?: { start: number; end: number },\n    keepRows?: readonly string[],\n  ) => LayoutResult | undefined\n  // whether this mode can draw this graph at all; the dropdown greys out the\n  // rest rather than hiding them, so the reason a mode is unavailable stays\n  // visible instead of the menu silently changing shape between graphs\n  available: (graph: Graph) => boolean\n  // whether a cut for this mode carries a window-width margin each side, to\n  // pan over before the next cut. A mode that draws a picture of the window\n  // \u2014 force, ordered, and walk rows, whose bars are lengths through it \u2014 is\n  // cut to the window alone.\n  cutMargins: boolean\n  // whether this mode measures each haplotype's walk whole, so a GBZ cut\n  // follows every snarl that leaves the window rather than breaking a walk\n  // where it leaves the window's snarls: at a duplication array the lighter\n  // cut hands one walk back in pieces\n  wholeWalks: boolean\n  // whether `run` draws this graph itself, as opposed to handing off to the\n  // engine. Not the same question as `available` and not derivable from it:\n  // 'force' is available for every graph and draws none of them itself. The two\n  // coincide for the anchored modes, which is stated by sharing the predicate\n  // rather than by restating it.\n  drawsLocally: (graph: Graph) => boolean\n}\n\nconst hasBackbone = (graph: Graph) => graph.nodes.some(isBackbone)\nconst hasWalks = (graph: Graph) =>\n  hasBackbone(graph) && (graph.paths?.length ?? 0) > 1\nconst hasTubeMapBackbone = (graph: Graph) =>\n  hasBackbone(graph) && hasTubeMapPaths(graph)\nconst hasAlleles = (graph: Graph) =>\n  hasBackbone(graph) && graph.nodes.some(isOffReference)\n\n// `satisfies` rather than a `: LayoutMode[]` annotation: the annotation widened\n// every `value` to string, which collapsed LayoutModeValue to string and left the\n// persisted enum unable to state which values it accepts.\nexport const LAYOUT_MODES = [\n  {\n    value: 'auto',\n    label: 'Anchored',\n    description:\n      'x is reference bp, one row per stable rank. Needs rGFA tags or a reference path.',\n    run: anchoredLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasBackbone,\n    drawsLocally: hasBackbone,\n  },\n  {\n    value: 'samplerows',\n    label: 'Sample rows',\n    description:\n      'x is reference bp, one row per contributing assembly. Needs rGFA tags or a reference path.',\n    run: sampleRowLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasAlleles,\n    drawsLocally: hasAlleles,\n  },\n  {\n    value: 'walkrows',\n    label: 'Walk rows',\n    description:\n      \"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.\",\n    run: walkRowLayout,\n    cutMargins: false,\n    wholeWalks: true,\n    available: hasWalks,\n    drawsLocally: hasWalks,\n  },\n  {\n    value: 'ordered',\n    label: 'Ordered',\n    description:\n      'x is reference order, not bp: every node gets room, bubbles read as lenses. Needs rGFA tags or a reference path.',\n    run: orderedLayout,\n    cutMargins: false,\n    wholeWalks: false,\n    available: hasBackbone,\n    drawsLocally: hasBackbone,\n  },\n  {\n    value: 'tubemap',\n    label: 'Tube map',\n    description:\n      'sequenceTubeMap: every path a coloured tube through boxed nodes, columns in node order and node widths log-scaled. Needs P or W lines.',\n    run: tubeMapLayout,\n    cutMargins: false,\n    wholeWalks: false,\n    available: hasTubeMapPaths,\n    drawsLocally: hasTubeMapPaths,\n  },\n  {\n    value: 'tubemapref',\n    label: 'Tube map on reference',\n    description:\n      'The tube map with each column at the reference bp it covers, so the tubes line up with the tracks around them. Needs P or W lines and a reference path.',\n    run: tubeMapReferenceLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasTubeMapBackbone,\n    drawsLocally: hasTubeMapBackbone,\n  },\n  {\n    value: 'force',\n    label: FORCE_LAYOUT_LABEL,\n    description: 'OGDF FMMM, via the external Bandage engine.',\n    run: () => undefined,\n    cutMargins: false,\n    wholeWalks: false,\n    available: () => true,\n    drawsLocally: () => false,\n  },\n] as const satisfies readonly LayoutMode[]\n\nexport type LayoutModeValue = (typeof LAYOUT_MODES)[number]['value']\n\nexport const LAYOUT_MODE_VALUES = LAYOUT_MODES.map(m => m.value)\n\n// Whether the drawing a mode produces for a graph comes from the FMMM engine.\n// The settings that only the engine reads \u2014 layout quality, bubble spread \u2014\n// are shown against this, so a control that cannot do anything to the drawing\n// on screen says so instead of appearing to work.\nexport function modeUsesLayoutEngine(value: string, graph: Graph) {\n  return !layoutModeByValue(value).drawsLocally(graph)\n}\n\nexport function layoutModeByValue(value: string) {\n  // An unknown value can only come from a snapshot written by a build that had\n  // a mode this one doesn't. It falls back to 'auto' rather than to the model's\n  // own default of 'force', because 'auto' declines any graph it cannot draw and\n  // hands off to force anyway, so this is the fallback that covers both.\n  return LAYOUT_MODES.find(m => m.value === value) ?? LAYOUT_MODES[0]\n}\n", "import { SATURATED_PATH_COUNT } from './bubbleLine'\n\nimport type { MinigraphBubble } from './bubbleLine'\n\n// What kind of variation a bubble is, read off the numbers `gfatools bubble`\n// states: the reference interval it replaces, its shortest and longest route,\n// how many routes, and whether one of them inverts. The reference route is one\n// of the routes and its length is the interval, so the shortest and longest\n// against the interval say whether the alternatives add sequence, remove it,\n// or swap it. Whether it is a repeat is not in those numbers: a\n// presence/absence insertion carried by many haplotypes has the same shape as\n// an expanding array, so that comes from the session's repeat annotation.\nexport type BubbleKind =\n  | 'snp'\n  | 'substitution'\n  | 'insertion'\n  | 'deletion'\n  | 'inversion'\n  | 'repeat'\n  | 'superbubble'\n  | 'complex'\n\nexport interface BubbleClass {\n  kind: BubbleKind\n  label: string\n}\n\n// An annotated tandem repeat array over the cut (repeats/repeatFeatures).\n// Its refName is not compared: the arrays are read over the same window as\n// the bubbles, which spell the reference their own way (PanSN).\nexport interface RepeatSpan {\n  start: number\n  end: number\n  name?: string\n}\n\n// How far past its reference length an array's alleles may run and still be\n// copies of it: KIV-2's 40 kb array carries 175 kb alleles\nconst REPEAT_GROWTH = 10\n\n// The array covering at least half the bubble's reference interval, or the\n// point of an insertion, and long enough to account for its alleles: a\n// microsatellite at an insertion point does not make the insertion a repeat.\nfunction coveringRepeat(b: MinigraphBubble, repeats: readonly RepeatSpan[]) {\n  const span = b.end - b.start\n  const growth = b.longestAlleleLength - b.shortestAlleleLength\n  return repeats.find(\n    r =>\n      growth <= REPEAT_GROWTH * (r.end - r.start) &&\n      (span === 0\n        ? r.start <= b.start && b.start <= r.end\n        : Math.min(b.end, r.end) - Math.max(b.start, r.start) >= span / 2),\n  )\n}\n\nconst SUPERBUBBLE_SEGMENTS = 40\n\nexport function formatBp(bp: number) {\n  if (bp >= 10_000) {\n    return `${(bp / 1000).toFixed(0)} kb`\n  }\n  if (bp >= 1000) {\n    return `${(bp / 1000).toFixed(1)} kb`\n  }\n  return `${bp} bp`\n}\n\nfunction formatBpRange(shortest: number, longest: number) {\n  const low = formatBp(shortest)\n  const high = formatBp(longest)\n  const unit = high.slice(high.indexOf(' '))\n  return low.endsWith(unit)\n    ? `${low.slice(0, -unit.length)}\u2013${high}`\n    : `${low}\u2013${high}`\n}\n\nfunction routes(count: number) {\n  if (count >= SATURATED_PATH_COUNT) {\n    return '\u22652.1B routes'\n  }\n  if (count >= 100_000) {\n    return `${(count / 1000).toFixed(0)}k routes`\n  }\n  return `${count} routes`\n}\n\nexport function classifyBubble(\n  b: MinigraphBubble,\n  repeats: readonly RepeatSpan[] = [],\n): BubbleClass {\n  const c = classifyShape(b, repeats)\n  return b.partial ? { ...c, label: `${c.label}, partial` } : c\n}\n\nfunction classifyShape(\n  b: MinigraphBubble,\n  repeats: readonly RepeatSpan[],\n): BubbleClass {\n  const refSpan = b.end - b.start\n  const {\n    shortestAlleleLength: shortest,\n    longestAlleleLength: longest,\n    pathCount,\n    segmentCount,\n    inversion,\n  } = b\n  const range = formatBpRange(shortest, longest)\n  if (segmentCount >= SUPERBUBBLE_SEGMENTS) {\n    return {\n      kind: 'superbubble',\n      label: `${range} superbubble, ${segmentCount} segments, ${routes(pathCount)}${inversion ? ', inv' : ''}`,\n    }\n  }\n  if (inversion) {\n    return { kind: 'inversion', label: `${formatBp(longest)} inv` }\n  }\n  // routes of one length are substitutions inside an array, not copies\n  const repeat = longest !== shortest ? coveringRepeat(b, repeats) : undefined\n  if (repeat) {\n    const name = repeat.name ? ` (${repeat.name})` : ''\n    return {\n      kind: 'repeat',\n      label: `${range} repeat array${name}, ${routes(pathCount)}`,\n    }\n  }\n  const alleles = pathCount > 2 ? `, ${pathCount} alleles` : ''\n  if (shortest === longest && shortest === refSpan) {\n    return refSpan <= 1\n      ? { kind: 'snp', label: 'SNP' }\n      : { kind: 'substitution', label: `${formatBp(refSpan)} sub` }\n  }\n  if (refSpan === 0 || shortest === refSpan) {\n    return {\n      kind: 'insertion',\n      label: `\u2264${formatBp(longest - refSpan)} ins${alleles}`,\n    }\n  }\n  if (longest === refSpan) {\n    return {\n      kind: 'deletion',\n      label: `${formatBp(refSpan - shortest)} del${alleles}`,\n    }\n  }\n  return {\n    kind: 'complex',\n    label: `${formatBp(refSpan)} ref \u2192 ${range}, ${pathCount} alleles`,\n  }\n}\n\n// One hue per kind, the deletion arc's near-black and the reference blue kept\n// clear of, so a glyph is not mistaken for either.\nexport const BUBBLE_KIND_COLORS: Record<BubbleKind, string> = {\n  snp: '#5b6b7a',\n  substitution: '#5b6b7a',\n  insertion: '#2f8fd6',\n  deletion: '#c94040',\n  inversion: '#e07b00',\n  repeat: '#8e3fbf',\n  superbubble: '#8e3fbf',\n  complex: '#8e3fbf',\n}\n\n// The kind as a short name, for a place that has no room for the label\nexport const BUBBLE_KIND_NAMES: Record<BubbleKind, string> = {\n  snp: 'SNP',\n  substitution: 'substitution',\n  insertion: 'insertion',\n  deletion: 'deletion',\n  inversion: 'inversion',\n  repeat: 'repeat array',\n  superbubble: 'superbubble',\n  complex: 'site',\n}\n\nexport function bubbleSegmentIds(b: MinigraphBubble) {\n  return b.segments.split(',').filter(Boolean)\n}\n", "// Minimal GFA (Graphical Fragment Assembly) text parser shared by the graph\n// pangenome plugins (GraphGenomeView, TubeMapView). Handles GFA1/GFA2 segment,\n// link, edge, path and walk records plus header tags.\n\n// Only the first two colons delimit a tag; everything after them is the value.\n// A Z value may contain colons of its own, and rGFA stable names routinely do\n// (`SN:Z:chr1:1-1000` from a sliced reference), where splitting on every colon\n// silently truncates the name to `chr1` and mis-anchors the whole layout.\nfunction parseTag(tag: string, tags: Record<string, string | number>) {\n  const nameEnd = tag.indexOf(':')\n  const typeEnd = tag.indexOf(':', nameEnd + 1)\n  if (nameEnd !== -1 && typeEnd !== -1) {\n    const name = tag.slice(0, nameEnd)\n    const type = tag.slice(nameEnd + 1, typeEnd)\n    const val = tag.slice(typeEnd + 1)\n    if (type === 'i' || type === 'f') {\n      tags[name] = +val\n    } else if (type === 'Z') {\n      tags[name] = val\n    }\n  }\n}\n\nfunction parseTags(fields: string[]) {\n  const tags: Record<string, string | number> = {}\n  for (const field of fields) {\n    parseTag(field, tags)\n  }\n  return tags\n}\n\nexport interface GFANode {\n  id: string\n  length: number\n  sequence: string\n  tags: Record<string, string | number>\n}\n\n// rGFA (minigraph) anchors every segment to a reference coordinate: SN is the\n// stable sequence name, SO the offset on it, and SR the stable rank, where 0 is\n// the reference backbone and higher ranks are the sequence that diverges from\n// it. Plain GFA (pggb, odgi, Minigraph-Cactus) carries none of these, which is\n// why coordinates there exist only inside the P/W lines.\nexport interface StableCoordinate {\n  refName: string\n  start: number\n  rank: number\n  // How the anchoring path reads this segment. Only path-derived coordinates\n  // set it: an rGFA segment is by construction forward on the sequence SN\n  // names, so there is nothing there for it to say.\n  strand?: '+' | '-'\n}\n\nexport function stableCoordinate(node: GFANode): StableCoordinate | undefined {\n  const { SN, SO, SR } = node.tags\n  return typeof SN === 'string' &&\n    typeof SO === 'number' &&\n    typeof SR === 'number'\n    ? { refName: SN, start: SO, rank: SR }\n    : undefined\n}\n\nexport interface GFALink {\n  source: string\n  target: string\n  strand1?: string\n  strand2?: string\n  cigar: string\n  tags: Record<string, string | number>\n}\n\nexport interface GFAPath {\n  name: string\n  path: string\n  rest: string[]\n}\n\nexport interface GFAWalkSegment {\n  id: string\n  strand: string\n}\n\nexport interface GFAWalk {\n  sample: string\n  haplotype: number\n  contig: string\n  start: number\n  end: number\n  segments: GFAWalkSegment[]\n  tags: Record<string, string | number>\n}\n\nconst GT = 62 // '>'\nconst LT = 60 // '<'\n\n// A W record's body is `>s1<s2>s3\u2026`, and on a Minigraph-Cactus graph one record\n// is the whole walk of one haplotype across a chromosome \u2014 hundreds of\n// thousands of steps in a single field.\n//\n// So the ids are cut out by index rather than accumulated a character at a\n// time. `current += ch` builds and discards one string per character of every\n// id, and it dominated the parse: a file whose single W record walks 200k steps\n// went from ~55 ms to ~24 ms by slicing instead. `pnpm bench` keeps the number.\nfunction parseWalkBody(body: string) {\n  const segments: GFAWalkSegment[] = []\n  let strand = '+'\n  let start = 0\n  // An empty run \u2014 a leading delimiter, or two in a row \u2014 names no segment.\n  function push(end: number) {\n    if (end > start) {\n      segments.push({ id: body.slice(start, end), strand })\n    }\n  }\n  for (let i = 0; i < body.length; i++) {\n    const ch = body.charCodeAt(i)\n    if (ch === GT || ch === LT) {\n      push(i)\n      strand = ch === GT ? '+' : '-'\n      start = i + 1\n    }\n  }\n  push(body.length)\n  return segments\n}\n\nexport interface GFAGraph {\n  nodes: GFANode[]\n  links: GFALink[]\n  paths: GFAPath[]\n  walks: GFAWalk[]\n  header: Record<string, string | number>[]\n  id: string\n}\n\nexport function parseGFA(file: string) {\n  const graph: GFAGraph = {\n    nodes: [],\n    links: [],\n    paths: [],\n    walks: [],\n    header: [],\n    id: '',\n  }\n\n  // \\r is stripped rather than split on, so a CRLF file does not leave it on\n  // whichever field happens to be last: a trailing Z tag would carry it into a\n  // stable name and a trailing cigar into the CIGAR string.\n  //\n  // Stripped per line inside the loop rather than with a .map() over the split,\n  // which would hold a second copy of every line in the file at once.\n  for (const rawLine of file.split('\\n')) {\n    const line = rawLine.endsWith('\\r') ? rawLine.slice(0, -1) : rawLine\n    if (line.startsWith('H')) {\n      const [, ...rest] = line.split('\\t')\n      graph.header.push(parseTags(rest))\n    } else if (line.startsWith('S')) {\n      const [, name, ...rest] = line.split('\\t')\n      let len: number\n      let seq: string\n      let tagfields: string[]\n      let gfa1 = false\n      // A truncated record has no field to read; `*` is what the spec writes for\n      // a segment whose sequence is absent, so treating a missing one the same\n      // way yields a 0 bp segment instead of throwing partway through the file.\n      const first = rest[0] ?? '*'\n      // GFA2 puts an integer length in this field, GFA1 the sequence. Testing\n      // the digits rather than the coerced number keeps a GFA2 `S sid 0 *` from\n      // being read as a GFA1 sequence of \"0\".\n      if (/^\\d+$/.test(first)) {\n        len = +first\n        seq = rest[1] ?? '*'\n        tagfields = rest.slice(2)\n      } else {\n        gfa1 = true\n        seq = first\n        // `*` is GFA1's \"no sequence here\"; its length is whatever LN says\n        // below, and 0 if the file states none. Counting the placeholder's own\n        // character instead reports every such segment as 1 bp.\n        len = seq === '*' ? 0 : seq.length\n        tagfields = rest.slice(1)\n      }\n      const tags = parseTags(tagfields)\n      if (gfa1 && 'LN' in tags) {\n        len = +tags.LN\n      }\n      graph.nodes.push({ id: name!, length: len, sequence: seq, tags })\n    } else if (line.startsWith('E')) {\n      // From here down, a record cut off before the fields that make it a\n      // link, walk or path states nothing drawable and is dropped; the file\n      // around it still reads. A link missing only its overlap is kept.\n      const [, , source, target, , , , , cigar, ...rest] = line.split('\\t')\n      if (source && target) {\n        graph.links.push({\n          source: source.slice(0, -1),\n          target: target.slice(0, -1),\n          strand1: source.at(-1),\n          strand2: target.at(-1),\n          cigar: cigar ?? '*',\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('L')) {\n      const [, source, strand1, target, strand2, cigar, ...rest] =\n        line.split('\\t')\n      if (source && target && strand2) {\n        graph.links.push({\n          source,\n          target,\n          strand1,\n          strand2,\n          cigar: cigar ?? '*',\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('W')) {\n      const [, sample, hap, contig, start, end, body, ...rest] =\n        line.split('\\t')\n      if (sample && hap && contig && start && end && body) {\n        graph.walks.push({\n          sample,\n          haplotype: +hap,\n          contig,\n          start: start === '*' ? -1 : +start,\n          end: end === '*' ? -1 : +end,\n          segments: parseWalkBody(body),\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('P')) {\n      const [, name, path, ...rest] = line.split('\\t')\n      if (name && path) {\n        graph.paths.push({ name, path, rest })\n      }\n    }\n  }\n  return graph\n}\n", "import { stableCoordinate } from '../gfa-core/index'\nimport { pathOrigin, surveyPaths } from '../pathAnchoring'\n\nimport type { GFAGraph, GFANode } from '../gfa-core/index'\nimport type { PathSteps } from '../pathAnchoring'\nimport type { Graph, GraphEdge, GraphNode, GraphPath } from '../types'\n\n// Single pass over every reference a GFA makes to a segment, collecting the two\n// things the drawn graph needs from them.\n//\n// `canonical` is the one orientation each segment is drawn in, which is what\n// Bandage calls single-node mode. A segment is the same sequence read either\n// way (`L 1 + 2 +` is the same edge as `L 2 - 1 -`), so `1+` and `1-` are one\n// node, not two: drawing both doubles every segment, and since the L lines only\n// wire one of the pair, the other copy has no edges at all and scatters loose\n// across the layout. Links carry the topology, so their orientation wins; a\n// segment only paths mention takes the orientation they walk it in.\n//\n// `traversals` is how many paths cross each segment. Assembly GFAs carry read\n// depth in a dp/RC/FC/KC tag, but a pangenome GFA (odgi, vg) carries none \u2014\n// there the meaningful depth is how many samples go through the segment, i.e.\n// core versus accessory sequence.\nfunction surveySegments(gfaGraph: GFAGraph) {\n  const canonical = new Map<string, '+' | '-'>()\n  const traversals = new Map<string, number>()\n  function claim(id: string, strand: '+' | '-') {\n    if (!canonical.has(id)) {\n      canonical.set(id, strand)\n    }\n  }\n  function traverse(id: string, strand: '+' | '-') {\n    claim(id, strand)\n    traversals.set(id, (traversals.get(id) ?? 0) + 1)\n  }\n  for (const link of gfaGraph.links) {\n    claim(link.source, link.strand1 === '-' ? '-' : '+')\n    claim(link.target, link.strand2 === '-' ? '-' : '+')\n  }\n  for (const gfaPath of gfaGraph.paths) {\n    for (const segment of gfaPath.path.split(',')) {\n      traverse(segment.slice(0, -1), segment.endsWith('-') ? '-' : '+')\n    }\n  }\n  for (const walk of gfaGraph.walks) {\n    for (const seg of walk.segments) {\n      traverse(seg.id, seg.strand === '-' ? '-' : '+')\n    }\n  }\n  return { canonical, traversals }\n}\n\n// P and W state the same thing in different shapes: a P body is a comma-joined\n// `<id><strand>` list whose start offset lives in the record's *name*, a W\n// record arrives already split into steps and states its start as a field.\n// Normalized here so the coordinate walk sees one kind of path.\nfunction anchorablePaths(gfaGraph: GFAGraph): PathSteps[] {\n  return [\n    ...gfaGraph.paths.map(p => ({\n      ...pathOrigin(p.name),\n      steps: p.path.split(',').map(segment => ({\n        id: segment.slice(0, -1),\n        strand: segment.endsWith('-') ? ('-' as const) : ('+' as const),\n      })),\n    })),\n    ...gfaGraph.walks.map(w => ({\n      name: `${w.sample}#${w.haplotype}#${w.contig}`,\n      // `*` parses to -1, meaning the record declines to say; 0 is then the\n      // only offset that can be assumed, and it makes the walk self-relative\n      // rather than wrong\n      start: w.start === -1 ? 0 : w.start,\n      steps: w.segments.map(s => ({\n        id: s.id,\n        strand: s.strand === '-' ? ('-' as const) : ('+' as const),\n      })),\n    })),\n  ]\n}\n\n// Carriage stated as a tag rather than derived from a walk. `RgfaTabixAdapter`\n// synthesizes its S-lines from a segs.bed whose sixth column is a list of GFA\n// tags, and `scripts/pggb_gfa_to_bed.py` in jbrowse-components puts every\n// haplotype that visits a segment there as `SM:Z:K12.1,Sakai.1`. That is the\n// only way carriage reaches an INDEXED graph: the cut has no P or W lines to\n// walk, so `pathAnchoring` has no visits to derive it from.\n//\n// It does not compete with that walk. `pathAnchoring.anchorNode` rebuilds\n// `samples` from the visits whenever there are any, so a graph loaded as a file\n// keeps the authoritative path-derived set and this is what a tabix cut falls\n// back to.\nfunction carriedSamples(gfaNode: GFANode) {\n  const sm = gfaNode.tags.SM\n  if (typeof sm !== 'string') {\n    return undefined\n  }\n  const samples = sm\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\nconst positive = (v: unknown) =>\n  typeof v === 'number' && v > 0 ? v : undefined\n\n// The depth a segment states, or undefined. DP is a depth in either case it is\n// written. RC, FC and KC are read, fragment and k-mer counts, so depth is the\n// count over the length: taken raw, a 100 kb node at 5x outweighed a 1 kb node\n// at 50x tenfold in every width drawn from it.\nfunction statedDepth({ tags, length }: GFANode) {\n  const count = positive(tags.RC) ?? positive(tags.FC) ?? positive(tags.KC)\n  return (\n    positive(tags.dp) ??\n    positive(tags.DP) ??\n    (count !== undefined && length > 0 ? count / length : undefined)\n  )\n}\n\nfunction makeNode(\n  gfaNode: GFANode,\n  strand: '+' | '-',\n  depth: number,\n): GraphNode {\n  return {\n    id: `${gfaNode.id}${strand}`,\n    name: gfaNode.id,\n    length: gfaNode.length,\n    depth,\n    stable: stableCoordinate(gfaNode),\n    samples: carriedSamples(gfaNode),\n  }\n}\n\nexport function convertGFAToGraph(gfaGraph: GFAGraph, name = 'Imported GFA') {\n  const nodes: GraphNode[] = []\n  const edges: GraphEdge[] = []\n\n  const { canonical, traversals } = surveySegments(gfaGraph)\n  // segments no link, path, or walk mentions are drawn forward-strand\n  const nodeId = (segmentId: string) =>\n    `${segmentId}${canonical.get(segmentId) ?? '+'}`\n\n  for (const gfaNode of gfaGraph.nodes) {\n    const depth =\n      statedDepth(gfaNode) ?? Math.max(traversals.get(gfaNode.id) ?? 1, 1)\n    nodes.push(makeNode(gfaNode, canonical.get(gfaNode.id) ?? '+', depth))\n  }\n\n  for (const link of gfaGraph.links) {\n    edges.push({\n      from: nodeId(link.source),\n      to: nodeId(link.target),\n      fromStrand: link.strand1 === '-' ? '-' : '+',\n      toStrand: link.strand2 === '-' ? '-' : '+',\n    })\n  }\n\n  const paths: GraphPath[] = []\n  const edgeToPathsMap = new Map<string, Set<string>>()\n\n  // A path that walks the graph on the reverse strand visits an edge's nodes in\n  // the opposite order to the L line that declared it, so the key is unordered.\n  const edgeKey = (a: string, b: string) => [a, b].sort().join('--')\n\n  function recordPathEdges(nodeIds: string[], name: string) {\n    for (let i = 0; i < nodeIds.length - 1; i++) {\n      const key = edgeKey(nodeIds[i]!, nodeIds[i + 1]!)\n      if (!edgeToPathsMap.has(key)) {\n        edgeToPathsMap.set(key, new Set())\n      }\n      edgeToPathsMap.get(key)!.add(name)\n    }\n  }\n\n  for (const gfaPath of gfaGraph.paths) {\n    // path segments arrive as `<id><strand>`; the node they land on is the\n    // segment's canonical orientation, whichever way this path reads it\n    const nodeIds = gfaPath.path\n      .split(',')\n      .map(segment => nodeId(segment.slice(0, -1)))\n    paths.push({ name: gfaPath.name, nodeIds } satisfies GraphPath)\n    recordPathEdges(nodeIds, gfaPath.name)\n  }\n\n  for (const walk of gfaGraph.walks) {\n    const nodeIds = walk.segments.map(seg => nodeId(seg.id))\n    // The full PanSN name, contig included, which is also what `anchorablePaths`\n    // above calls the same record. Dropping the contig made a path's name an\n    // ASSEMBLY's name, and one assembly walks one W record per contig: two walks\n    // of `HG00438#1` then shared an identity, so `edgeToPathsMap` merged them,\n    // `pathColors` (keyed by name) kept only the last colour written while the\n    // node stripes kept the first, and the key drew one haplotype twice in two\n    // colours. That is the ordinary Minigraph-Cactus shape, not a corner case.\n    //\n    // The legend narrows it back: `labelTiers` tries sample, then sample and\n    // haplotype, then the whole name, so a graph with one contig per haplotype\n    // is labelled exactly as before and only a colliding one widens.\n    const name = `${walk.sample}#${walk.haplotype}#${walk.contig}`\n    paths.push({\n      name,\n      nodeIds,\n      sample: walk.sample,\n      haplotype: walk.haplotype,\n      contig: walk.contig,\n    } satisfies GraphPath)\n    recordPathEdges(nodeIds, name)\n  }\n\n  for (const edge of edges) {\n    const pathIds = edgeToPathsMap.get(edgeKey(edge.from, edge.to))\n    if (pathIds && pathIds.size > 0) {\n      edge.pathIds = [...pathIds]\n    }\n  }\n\n  // Only walked when the file has paths to walk, so an rGFA \u2014 which has none at\n  // all \u2014 pays nothing for it. `lengthOf` reads the segment table rather than\n  // the nodes just built, because a path may name a segment no S line declared.\n  const lengths = new Map(gfaGraph.nodes.map(n => [n.id, n.length]))\n  const anchoring =\n    gfaGraph.paths.length > 0 || gfaGraph.walks.length > 0\n      ? surveyPaths(anchorablePaths(gfaGraph), id => lengths.get(id) ?? 0)\n      : undefined\n\n  return {\n    name,\n    nodes,\n    edges,\n    paths: paths.length > 0 ? paths : undefined,\n    anchorPaths: anchoring?.anchorPaths,\n    pathVisits: anchoring?.pathVisits,\n    // rGFA's own tags win wherever they are present; pathAnchoring only ever\n    // fills in for a graph that carries none.\n    anchoredBy: nodes.some(n => n.stable) ? 'tags' : undefined,\n  } satisfies Graph\n}\n", "import { isBackbone } from '../anchoredNodes'\n\nimport type { Graph, NodeSegment } from '../types'\n\ntype Positions = Record<string, NodeSegment[]>\n\n// Turn a finished force layout so the reference runs left to right: the\n// rotation that best maps backbone midpoints onto their reference coordinate\n// (a one-dimensional orthogonal Procrustes fit, weighted by segment length),\n// then a reflection so the off-reference mass sits below the axis. A rigid\n// transform, so the drawing FMMM made is unchanged; only its frame moves.\n//\n// About the length-weighted centroid, and translated back, so a drawing that is\n// already oriented comes back where it was rather than recentred on the origin.\nexport function orientToReference(graph: Graph, positions: Positions) {\n  const backbone = graph.nodes.filter(\n    node => isBackbone(node) && (positions[node.id]?.length ?? 0) > 0,\n  )\n  if (backbone.length < 2) {\n    return positions\n  }\n  const points = backbone.map(node => {\n    const segments = positions[node.id]!\n    const mid = segments[Math.floor(segments.length / 2)]!\n    return {\n      x: mid.x,\n      y: mid.y,\n      r: node.stable!.start + node.length / 2,\n      w: node.length,\n    }\n  })\n  const weight = points.reduce((sum, p) => sum + p.w, 0)\n  const cx = points.reduce((sum, p) => sum + p.x * p.w, 0) / weight\n  const cy = points.reduce((sum, p) => sum + p.y * p.w, 0) / weight\n  const cr = points.reduce((sum, p) => sum + p.r * p.w, 0) / weight\n  // cross-covariance of (x, y) against (r, 0); only the first row is non-zero\n  let sxr = 0\n  let syr = 0\n  for (const p of points) {\n    sxr += p.w * (p.x - cx) * (p.r - cr)\n    syr += p.w * (p.y - cy) * (p.r - cr)\n  }\n  // the rotation taking the direction (sxr, syr) onto +x\n  const angle = -Math.atan2(syr, sxr)\n  const c = Math.cos(angle)\n  const s = Math.sin(angle)\n\n  const out: Positions = {}\n  for (const [id, segments] of Object.entries(positions)) {\n    out[id] = segments.map(p => {\n      const x = p.x - cx\n      const y = p.y - cy\n      return { x: cx + c * x - s * y, y: cy + s * x + c * y }\n    })\n  }\n\n  let below = 0\n  let above = 0\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      continue\n    }\n    for (const p of out[node.id] ?? []) {\n      if (p.y > cy) {\n        below++\n      } else {\n        above++\n      }\n    }\n  }\n  if (above > below) {\n    for (const segments of Object.values(out)) {\n      for (const p of segments) {\n        p.y = 2 * cy - p.y\n      }\n    }\n  }\n  return out\n}\n", "import { isBackbone } from '../anchoredNodes'\nimport { buildNeighbors } from '../referenceSpan'\nimport { drawnNodeLength } from './drawnScale'\n\nimport type { LayoutScaling } from './drawnScale'\nimport type { Graph, GraphNode } from '../types'\n\n// A node as the engine takes it: an optional `x`/`y` is where FMMM starts the\n// node's chain (`addToOgdfGraph`, graphlayout.cpp).\nexport type LayoutNode = GraphNode & { x?: number; y?: number }\n\nexport interface Seed {\n  x: number\n  y: number\n}\n\n// y per BFS step off the backbone. FMMM keeps only the coarse shape of these\n// (OGDF applies the initial placement at its coarsest multilevel graph), so\n// the gap needs to say \"below the line\", not to place a lane.\nconst LANE_GAP = 30\n\n// Initial positions for a reference-anchored graph: the backbone end to end\n// along x at drawn length, each off-reference node at the midpoint of the node\n// a BFS from the backbone reached it from, a lane lower per step. Two alleles\n// off one anchor share a seed; FMMM separates them. Nodes no backbone reaches\n// spread along x below everything rather than piling on one point.\n//\n// Lengths come from `scaling.nodes`, not the graph's bp: under a compressing\n// spread a node's `length` crosses the RPC as drawn units times 1000 with a\n// matching `nodeLengthPerMegabase`, and a seed from bp would misplace every\n// chain against the one the engine builds.\nexport function referenceSeeds(\n  graph: Graph,\n  scaling: LayoutScaling,\n): Map<string, Seed> {\n  const { opts } = scaling\n  const drawn = new Map(\n    scaling.nodes.map(node => [node.id, drawnNodeLength(opts, node.length)]),\n  )\n  const drawnOf = (id: string) => drawn.get(id) ?? opts.minimumNodeLength\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort((a, b) => a.stable.start - b.stable.start)\n\n  const seeds = new Map<string, Seed>()\n  let x = 0\n  for (const node of backbone) {\n    seeds.set(node.id, { x, y: 0 })\n    x += drawnOf(node.id) + opts.edgeLength\n  }\n\n  const adjacent = buildNeighbors(graph)\n\n  const depth = new Map(backbone.map(node => [node.id, 0]))\n  // for-of over an array that grows as it goes: the iterator reads the live\n  // length, so nodes pushed here are visited\n  const queue = backbone.map(node => node.id)\n  for (const id of queue) {\n    const at = seeds.get(id)!\n    const next = depth.get(id)! + 1\n    for (const neighbour of adjacent.get(id) ?? []) {\n      if (depth.has(neighbour)) {\n        continue\n      }\n      depth.set(neighbour, next)\n      seeds.set(neighbour, { x: at.x + drawnOf(id) / 2, y: LANE_GAP * next })\n      queue.push(neighbour)\n    }\n  }\n\n  let unreached = 0\n  for (const node of graph.nodes) {\n    if (!seeds.has(node.id)) {\n      seeds.set(node.id, {\n        x: (unreached++ * x) / graph.nodes.length,\n        y: LANE_GAP * 3,\n      })\n    }\n  }\n  return seeds\n}\n\nexport function seededNodes(\n  graph: Graph,\n  scaling: LayoutScaling,\n): LayoutNode[] {\n  const seeds = referenceSeeds(graph, scaling)\n  return scaling.nodes.map(node => ({ ...node, ...seeds.get(node.id) }))\n}\n", "import { isBackbone } from './anchoredNodes'\nimport { spreadFor } from './bubbleSpreads'\nimport { convertGFAToGraph } from './gfa/gfaConverter'\nimport { parseGFA } from './gfa-core/index'\nimport { drawnNodeLength, layoutScaling } from './layout/drawnScale'\nimport { mergeRuns, splitRuns } from './layout/mergeRuns'\nimport { orientToReference } from './layout/orientToReference'\nimport { seededNodes } from './layout/referenceSeeds'\nimport { anchorGraph } from './pathAnchoring'\n\nimport type { BubbleSpread } from './bubbleSpreads'\nimport type { LayoutScaling } from './layout/drawnScale'\nimport type { LayoutNode } from './layout/referenceSeeds'\nimport type { Graph, LayoutResult, NodeSegment } from './types'\n\n// The graph a view draws, from GFA text to layouts, with no host in it: the\n// GraphGenomeView model and a standalone page both drive this.\n\nexport interface Bounds {\n  minX: number\n  minY: number\n  maxX: number\n  maxY: number\n}\n\n// A general GFA states its coordinates only in its P/W lines, so the walk that\n// recovers them happens before anything reads `stable`; otherwise the anchored\n// layouts see an unanchored graph and hand off to force. `maxNodes` is checked\n// here because it is upstream of everything that scales with the node count.\nexport function loadGraph(\n  text: string,\n  name: string,\n  opts: { referencePath?: string; maxNodes?: number } = {},\n) {\n  const graph = anchorGraph(\n    convertGFAToGraph(parseGFA(text), name),\n    opts.referencePath,\n  )\n  if (graph.nodes.length === 0) {\n    throw new Error(`No graph segments in ${name}`)\n  }\n  if (opts.maxNodes !== undefined && graph.nodes.length > opts.maxNodes) {\n    throw new Error(\n      `Graph too large to draw: ${graph.nodes.length.toLocaleString()} nodes (limit ${opts.maxNodes.toLocaleString()}). Zoom in to a smaller region, or raise maxGraphNodes on this view.`,\n    )\n  }\n  return graph\n}\n\n// What the Bandage engine is handed. A node may carry an `x`/`y` seed, which\n// the engine reads as where its chain starts (referenceSeeds.ts).\nexport interface EngineRequest {\n  graph: { nodes: LayoutNode[]; edges: Graph['edges'] }\n  options: Record<string, unknown>\n}\n\nexport type LayoutEngine = (\n  request: EngineRequest,\n) => Promise<{ result: LayoutResult; duration: number }>\n\nexport interface EngineSettings {\n  quality: number\n  linearLayout: boolean\n  bubbleSpread: BubbleSpread\n}\n\n// `scaling.nodes` rather than the graph's own: under a compressing drawn-length\n// law a node's `length` crosses this boundary as a drawn length, which is all\n// the engine ever reads it as. An anchored graph also carries a seed per node,\n// the backbone along x, and asks the engine not to rotate components: FMMM\n// then keeps the reference's coarse shape instead of curling it into a C\n// (ADR-042).\nexport function engineRequest(\n  graph: Graph,\n  scaling: LayoutScaling,\n  settings: EngineSettings,\n): EngineRequest {\n  const anchored = graph.nodes.some(isBackbone)\n  return {\n    graph: {\n      nodes: anchored ? seededNodes(graph, scaling) : scaling.nodes,\n      edges: graph.edges,\n    },\n    options: {\n      quality: settings.quality,\n      linearLayout: settings.linearLayout,\n      ...scaling.opts,\n      ...(anchored ? { rotateComponents: false } : {}),\n    },\n  }\n}\n\n// What a force layout of this graph is a function of, as a cache key: the\n// settings `engineRequest` reads, whether it seeds, and the reference path the\n// seeds follow.\nexport function engineKey(graph: Graph, settings: EngineSettings) {\n  const anchored = graph.nodes.some(isBackbone)\n  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${anchored}|${graph.referencePath ?? ''}`\n}\n\n// The engine lays out the runs, not the nodes: a base-level cut is thousands\n// of nodes in unbranching chains, and one chain per run is the same drawing at\n// a third of the time. Members take their share of the run's polyline by drawn\n// length, so the picture is per node again before anything else sees it, and\n// it is turned so the reference reads left to right.\nexport async function forceLayout(\n  graph: Graph,\n  settings: EngineSettings,\n  engine: LayoutEngine,\n) {\n  const spread = spreadFor(settings.bubbleSpread)\n  const merged = mergeRuns(graph)\n  const { result, duration } = await engine(\n    engineRequest(merged.graph, layoutScaling(merged.graph, spread), settings),\n  )\n  const scaling = layoutScaling(graph, spread)\n  const drawn = new Map(\n    scaling.nodes.map(n => [n.id, drawnNodeLength(scaling.opts, n.length)]),\n  )\n  const positions = splitRuns(\n    result.nodePositions,\n    merged.runs,\n    id => drawn.get(id) ?? 0,\n  )\n  return {\n    result: {\n      ...result,\n      nodePositions: graph.nodes.some(isBackbone)\n        ? orientToReference(graph, positions)\n        : positions,\n    },\n    duration,\n  }\n}\n\nexport function layoutExtent(\n  nodePositions: Record<string, NodeSegment[]>,\n): Bounds {\n  let minX = Infinity\n  let minY = Infinity\n  let maxX = -Infinity\n  let maxY = -Infinity\n  for (const segments of Object.values(nodePositions)) {\n    for (const seg of segments) {\n      minX = Math.min(minX, seg.x)\n      minY = Math.min(minY, seg.y)\n      maxX = Math.max(maxX, seg.x)\n      maxY = Math.max(maxY, seg.y)\n    }\n  }\n  return { minX, minY, maxX, maxY }\n}\n\n// Gap between the drawing and the edge of the pane, on all four sides.\nexport const FIT_PADDING = 40\n\n// The floor keeps a scale positive and finite, and has to clear the smallest\n// scale a real layout asks for: fitting a chromosome-scale rGFA (250 Mbp) into\n// ~720 px needs ~3e-6.\nconst MIN_ZOOM = 1e-6\nconst MAX_ZOOM = 100\n\nexport function clampZoom(zoom: number) {\n  return Math.max(MIN_ZOOM, Math.min(MAX_ZOOM, zoom))\n}\n\n// Centre the leftover, but only when there IS leftover. A row layout fits on x\n// alone, so its drawing is routinely taller than the pane, and centring an\n// overflow would push the top row, the reference backbone, off the top.\nexport function fittedTranslateY(\n  bounds: { minY: number; h: number },\n  usableHeight: number,\n  yScale: number,\n  padTop = FIT_PADDING,\n) {\n  const leftoverY = usableHeight - bounds.h * yScale\n  return padTop - bounds.minY * yScale + Math.max(0, leftoverY) / 2\n}\n\n// The transform that fits `bounds` in the pane, or undefined when there is\n// nothing to fit or nothing to fit into. Each axis constrains the scale only\n// when it has extent, since an anchored window holding only backbone puts every\n// node on row 0. A row layout (`pixelRows`) fits on x alone and keeps y in\n// screen px; an isotropic one fits on whichever axis binds. Below `minScale`\n// the drawing overflows x instead, its left end at the padding. `padLeft`\n// widens the left gap past the row labels pinned to that edge, `padTop` the\n// top one for the gene rows over a tube map.\nexport function fitTransform(\n  bounds: { minX: number; minY: number; w: number; h: number },\n  paneWidth: number,\n  paneHeight: number,\n  pixelRows: boolean,\n  {\n    minScale = 0,\n    padLeft = FIT_PADDING,\n    padTop = FIT_PADDING,\n    padRight = FIT_PADDING,\n    padBottom = FIT_PADDING,\n  } = {},\n) {\n  const usableWidth = paneWidth - padLeft - padRight\n  const usableHeight = paneHeight - padTop - padBottom\n  if (\n    usableWidth <= 0 ||\n    usableHeight <= 0 ||\n    !(bounds.w > 0 || (!pixelRows && bounds.h > 0))\n  ) {\n    return undefined\n  }\n  const fitX = bounds.w > 0 ? usableWidth / bounds.w : Infinity\n  const fitY = bounds.h > 0 ? usableHeight / bounds.h : Infinity\n  const scale = clampZoom(\n    Math.max(minScale, pixelRows ? fitX : Math.min(fitX, fitY)),\n  )\n  const leftoverX = usableWidth - bounds.w * scale\n  return {\n    scale,\n    translateX: padLeft - bounds.minX * scale + Math.max(0, leftoverX) / 2,\n    translateY: fittedTranslateY(\n      bounds,\n      usableHeight,\n      pixelRows ? 1 : scale,\n      padTop,\n    ),\n  }\n}\n\n// Extent of the drawing in layout units, which the fit and the pane height\n// read. On a reference-bp layout x is the cut window rather than how far the\n// drawing reaches: an allele anchored far outside it is a fact about the\n// graph, not a reason to draw the window at 6% of the frame. `extent` stands\n// in for the layout's own when an overlay's rows reach further (walk rows).\nexport function drawingBounds(\n  layout: LayoutResult,\n  opts: {\n    region?: { start: number; end: number }\n    extent?: LayoutResult['extent']\n  } = {},\n) {\n  let { minX, minY, maxX, maxY } = layoutExtent(layout.nodePositions)\n  const { region } = opts\n  if (layout.referenceAxis && region && region.end > region.start) {\n    minX = region.start\n    maxX = region.end\n  }\n  const extent = opts.extent ?? layout.extent\n  if (extent) {\n    minX = Math.min(minX, extent.minX ?? minX)\n    minY = Math.min(minY, extent.minY ?? minY)\n    maxX = Math.max(maxX, extent.maxX ?? maxX)\n    maxY = Math.max(maxY, extent.maxY ?? maxY)\n  }\n  return { minX, minY, w: maxX - minX, h: maxY - minY }\n}\n", "import { abgrToCssRgba } from '@jbrowse/core/util/colorBits'\n\nimport { isBackbone } from './anchoredNodes'\nimport {\n  FADED_ALPHA,\n  LIFT_BACKDROP_COLOR,\n  computeColorSchemeRange,\n  getNodeColor,\n} from './renderer/GeometryBuilder'\nimport { fadeAbgr } from './renderer/colorBits'\n\nimport type { ResolvedColorScheme } from './colorSchemes'\nimport type { ReferenceRamp } from './renderer/GeometryBuilder'\nimport type { Graph, NodeSegment } from './types'\n\n// A force or ordered drawing inside a linear view has no bp axis, so a strip\n// along the top of the track draws each reference segment at its bp there, in\n// the colour its node has in the graph below, faded where the graph fades it\n// off a lifted walk. Under the reference-position ramp that is the hue a\n// reader matches between the two; the lit node gets a\n// leader from its span on the strip to where the graph drew it, as the\n// variant matrix ties a column to its variant.\n\nexport const REFERENCE_STRIP_PX = 10\n// the strip, and the gap under it the fit leaves the drawing\nexport const REFERENCE_STRIP_ZONE_PX = REFERENCE_STRIP_PX + 8\n// a triangle at a strip end: reference the graph draws runs past that edge\nconst OVERHANG_PX = 5\n\nexport interface StripBlock {\n  node: string\n  bp0: number\n  bp1: number\n  color: string\n}\n\nexport function referenceStripBlocks(\n  graph: Graph,\n  {\n    colorScheme,\n    referenceRamp,\n    walkNodes,\n    walkColors,\n  }: {\n    colorScheme: ResolvedColorScheme\n    referenceRamp?: ReferenceRamp\n    // the nodes lifted walks visit, and the reference walk's lane colours\n    // when it is one of them: the strip then takes those, else grey\n    walkNodes?: ReadonlySet<string>\n    walkColors?: ReadonlyMap<string, number>\n  },\n) {\n  const range = { ...computeColorSchemeRange(graph), referenceRamp }\n  const out: StripBlock[] = []\n  graph.nodes.forEach((node, index) => {\n    if (isBackbone(node)) {\n      const own = walkNodes\n        ? (walkColors?.get(node.id) ?? LIFT_BACKDROP_COLOR)\n        : getNodeColor(node, index, colorScheme, range)\n      out.push({\n        node: node.id,\n        bp0: node.stable.start,\n        bp1: node.stable.start + node.length,\n        color: abgrToCssRgba(\n          walkNodes && !walkNodes.has(node.id)\n            ? fadeAbgr(own, FADED_ALPHA)\n            : own,\n        ),\n      })\n    }\n  })\n  return out.sort((a, b) => a.bp0 - b.bp0)\n}\n\n// bp to screen x, as the linear view places it; a reversed block's is negative\nexport interface BpFrame {\n  scale: number\n  translateX: number\n}\n\nfunction span(frame: BpFrame, bp0: number, bp1: number): [number, number] {\n  const a = bp0 * frame.scale + frame.translateX\n  const b = bp1 * frame.scale + frame.translateX\n  return a < b ? [a, b] : [b, a]\n}\n\n// A SNP's block is a sliver, so the pointer gets a few px either side of one\nconst HIT_SLOP_PX = 2\n\n// How much backbone the graph draws past each edge of the window, in bp\nexport function stripOverhang(\n  blocks: readonly StripBlock[],\n  frame: BpFrame,\n  width: number,\n) {\n  const a = -frame.translateX / frame.scale\n  const b = (width - frame.translateX) / frame.scale\n  const lo = Math.min(a, b)\n  const hi = Math.max(a, b)\n  let below = 0\n  let above = 0\n  for (const block of blocks) {\n    below += Math.max(0, Math.min(block.bp1, lo) - block.bp0)\n    above += Math.max(0, block.bp1 - Math.max(block.bp0, hi))\n  }\n  // a reversed window puts low bp on the right\n  return frame.scale >= 0\n    ? { left: Math.round(below), right: Math.round(above) }\n    : { left: Math.round(above), right: Math.round(below) }\n}\n\nexport function stripBlockAt(\n  blocks: readonly StripBlock[],\n  frame: BpFrame,\n  sx: number,\n  sy: number,\n) {\n  if (sy < 0 || sy > REFERENCE_STRIP_PX + HIT_SLOP_PX) {\n    return undefined\n  }\n  let hit: string | undefined\n  let best = HIT_SLOP_PX\n  for (const b of blocks) {\n    const [x0, x1] = span(frame, b.bp0, b.bp1)\n    const dist = Math.max(0, x0 - sx, sx - x1)\n    if (dist <= best) {\n      best = dist\n      hit = b.node\n    }\n  }\n  return hit\n}\n\n// Where the graph drew a node, in screen px: the middle of its polyline\nexport function nodeAnchor(\n  segments: readonly NodeSegment[] | undefined,\n  toScreen: (p: NodeSegment) => { x: number; y: number },\n) {\n  const p = segments?.[Math.floor(segments.length / 2)]\n  return p ? toScreen(p) : undefined\n}\n\nexport interface StripLit {\n  start: number\n  end: number\n  anchor?: { x: number; y: number }\n}\n\n// A triangle with its tip on the strip's edge, pointing off it; `inward` is\n// +1 from the left edge and -1 from the right\nfunction drawOverhang(\n  ctx: CanvasRenderingContext2D,\n  tipX: number,\n  inward: number,\n) {\n  const mid = REFERENCE_STRIP_PX / 2\n  const baseX = tipX + inward * (OVERHANG_PX + 1)\n  ctx.moveTo(tipX + inward, mid)\n  ctx.lineTo(baseX, mid - OVERHANG_PX / 1.4)\n  ctx.lineTo(baseX, mid + OVERHANG_PX / 1.4)\n  ctx.closePath()\n}\n\nexport function drawReferenceStrip(\n  ctx: CanvasRenderingContext2D,\n  blocks: readonly StripBlock[],\n  frame: BpFrame,\n  {\n    width,\n    lit,\n    darkMode,\n  }: {\n    width: number\n    lit?: StripLit\n    darkMode?: boolean\n  },\n) {\n  const ink = darkMode ? '#ffffff' : '#18181c'\n  ctx.fillStyle = darkMode ? '#1f1f1f' : '#ffffff'\n  ctx.fillRect(0, 0, width, REFERENCE_STRIP_ZONE_PX)\n  for (const b of blocks) {\n    const [x0, x1] = span(frame, b.bp0, b.bp1)\n    if (x1 >= 0 && x0 <= width) {\n      ctx.fillStyle = b.color\n      ctx.fillRect(x0, 0, Math.max(x1 - x0, 1), REFERENCE_STRIP_PX)\n    }\n  }\n  const overhang = stripOverhang(blocks, frame, width)\n  if (overhang.left > 0 || overhang.right > 0) {\n    ctx.beginPath()\n    if (overhang.left > 0) {\n      drawOverhang(ctx, 0, 1)\n    }\n    if (overhang.right > 0) {\n      drawOverhang(ctx, width, -1)\n    }\n    ctx.fillStyle = ink\n    ctx.fill()\n    ctx.strokeStyle = darkMode ? '#1f1f1f' : '#ffffff'\n    ctx.lineWidth = 1\n    ctx.stroke()\n  }\n  if (lit) {\n    const [x0, x1] = span(frame, lit.start, lit.end)\n    const w = Math.max(x1 - x0, 3)\n    const left = (x0 + x1) / 2 - w / 2\n    ctx.strokeStyle = ink\n    ctx.lineWidth = 1.5\n    ctx.strokeRect(left, 0.75, w, REFERENCE_STRIP_PX - 1.5)\n    if (lit.anchor) {\n      ctx.beginPath()\n      ctx.moveTo(left + w / 2, REFERENCE_STRIP_PX)\n      ctx.lineTo(lit.anchor.x, lit.anchor.y)\n      ctx.lineWidth = 1\n      ctx.stroke()\n    }\n  }\n}\n", "import { isBackbone } from '../anchoredNodes'\nimport { formatBp } from '../graphLabels'\n\nimport type { TubeMapFrame } from './draw'\nimport type { Graph } from '../types'\nimport type { TubeMapLayout } from '@gmod/tubemap-core'\n\n// The reference's boxes carry bp, so a reference coordinate maps into tube x\n// through the box that holds it. On the own axis a box is log-scaled, so bp\n// per tube px varies box to box; on the reference axis frame.ts warps the\n// result back onto the linear view's bp.\n\nexport interface Box {\n  bp0: number\n  bp1: number\n  x0: number\n  x1: number\n}\n\n// keyed by the graph's refName, `GRCh38#0#chr6`\nexport function referenceBoxes(graph: Graph, layout: TubeMapLayout) {\n  const nodeById = new Map(graph.nodes.map(n => [n.id, n]))\n  const byRefName = new Map<string, Box[]>()\n  // sparse: an unreached node has no entry\n  layout.nodes.forEach(node => {\n    const graphNode = nodeById.get(node.name)\n    if (node.order >= 0 && graphNode && isBackbone(graphNode)) {\n      const { refName, start } = graphNode.stable\n      const boxes =\n        byRefName.get(refName) ?? byRefName.set(refName, []).get(refName)!\n      boxes.push({\n        bp0: start,\n        bp1: start + node.sequenceLength,\n        x0: node.x,\n        x1: node.x + node.pixelWidth,\n      })\n    }\n  })\n  for (const boxes of byRefName.values()) {\n    boxes.sort((a, b) => a.bp0 - b.bp0)\n  }\n  return byRefName\n}\n\nexport type ReferenceBoxes = ReturnType<typeof referenceBoxes>\n\n// A bp the cut has no box for (a gap in the backbone) takes the next box's\n// left edge. A bp on a boundary between boxes belongs to the box after it, or\n// to the one before for the end of a span, so a span stays off the curves\n// between.\nexport function tubeX(boxes: readonly Box[], bp: number, isEnd = false) {\n  let lo = 0\n  let hi = boxes.length - 1\n  while (lo < hi) {\n    const mid = (lo + hi) >> 1\n    const bp1 = boxes[mid]!.bp1\n    if (isEnd ? bp1 < bp : bp1 <= bp) {\n      lo = mid + 1\n    } else {\n      hi = mid\n    }\n  }\n  const box = boxes[lo]!\n  if (bp <= box.bp0) {\n    return box.x0\n  }\n  const span = box.bp1 - box.bp0\n  return span > 0\n    ? box.x0 + ((Math.min(bp, box.bp1) - box.bp0) / span) * (box.x1 - box.x0)\n    : box.x0\n}\n\nexport function tubeSpan(boxes: readonly Box[], start: number, end: number) {\n  const a = tubeX(boxes, start)\n  const b = tubeX(boxes, end, true)\n  return { x0: Math.min(a, b), x1: Math.max(a, b) }\n}\n\n// The refName most of the cut's reference lies on, for the ruler\nexport function rulerBoxes(byRefName: ReferenceBoxes) {\n  let best: Box[] | undefined\n  for (const boxes of byRefName.values()) {\n    if (!best || boxes.length > best.length) {\n      best = boxes\n    }\n  }\n  return best\n}\n\nconst TICK_PX = 5\nconst LABEL_GAP_PX = 10\nconst TARGET_TICK_PX = 110\n// narrower than this a box draws as one tick rather than a bracket\nconst MIN_BRACKET_PX = 3\n\nexport function rulerInk(darkMode?: boolean) {\n  return darkMode ? '#b0b0b8' : '#55555c'\n}\n\ninterface Label {\n  text: string\n  at: number\n  width: number\n}\n\nfunction niceStep(raw: number) {\n  const pow = 10 ** Math.floor(Math.log10(raw))\n  const m = raw / pow\n  return (m <= 1 ? 1 : m <= 2 ? 2 : m <= 5 ? 5 : 10) * pow\n}\n\n// In order, dropping any that would overlap one already placed\nfunction placeLabels(candidates: readonly Label[]) {\n  const placed: Label[] = []\n  for (const a of candidates) {\n    if (\n      placed.every(\n        b => Math.abs(a.at - b.at) >= (a.width + b.width) / 2 + LABEL_GAP_PX,\n      )\n    ) {\n      placed.push(a)\n    }\n  }\n  return placed.map(({ text, at }) => ({ text, at }))\n}\n\nexport interface RulerMarks {\n  // each box's span; the gaps between them stay blank, since the lane changes\n  // drawn there cover no reference\n  spans: { x0: number; x1: number }[]\n  ticks: number[]\n  labels: { text: string; at: number }[]\n}\n\n// On the reference axis the boxes sit on their bp, so one scale runs across\n// the ruler and its ticks fall on round positions.\nfunction scaleMarks(\n  boxes: readonly Box[],\n  x: (tx: number) => number,\n  width: number,\n  measure: (text: string) => number,\n): RulerMarks | undefined {\n  const first = boxes[0]\n  const last = boxes.at(-1)\n  if (!first || !last) {\n    return undefined\n  }\n  const from = x(first.x0)\n  const to = x(last.x1)\n  const bpSpan = last.bp1 - first.bp0\n  if (to <= from || bpSpan <= 0) {\n    return undefined\n  }\n  const step = niceStep((bpSpan / (to - from)) * TARGET_TICK_PX)\n  const ticks: number[] = []\n  const positions: Label[] = []\n  for (\n    let bp = Math.ceil(first.bp0 / step) * step;\n    bp <= last.bp1;\n    bp += step\n  ) {\n    const sx = Math.round(x(tubeX(boxes, bp))) + 0.5\n    if (sx >= 0 && sx <= width) {\n      ticks.push(sx)\n      const text = bp.toLocaleString('en-US')\n      positions.push({ text, at: sx, width: measure(text) })\n    }\n  }\n  return {\n    spans: [{ x0: from, x1: to }],\n    ticks,\n    labels: placeLabels(positions),\n  }\n}\n\n// On the own axis every box is as wide as the log of its length (tubemap-core's\n// compressed widths: 2 bp is 8 px, 100 bp 56, 1 kb 84, 22 kb 121), so no box is\n// to scale and no one scale runs across them. The ruler treats every box alike:\n// a bracket under it, a tick at each end, its length where that fits inside it,\n// and positions at box boundaries. Labels are placed in that order after the\n// two ends of what is on screen.\nfunction boxMarks(\n  boxes: readonly Box[],\n  x: (tx: number) => number,\n  width: number,\n  measure: (text: string) => number,\n): RulerMarks | undefined {\n  const shown = boxes\n    .map(box => ({ box, s0: x(box.x0), s1: x(box.x1) }))\n    .filter(({ s0, s1 }) => s1 >= 0 && s0 <= width)\n  const first = shown[0]\n  const last = shown.at(-1)\n  if (!first || !last) {\n    return undefined\n  }\n  const label = (text: string, at: number) => ({\n    text,\n    at,\n    width: measure(text),\n  })\n  const position = (bp: number, at: number) =>\n    label(bp.toLocaleString('en-US'), at)\n  const spans: RulerMarks['spans'] = []\n  const ticks: number[] = []\n  const lengths: Label[] = []\n  const boundaries: Label[] = []\n  for (const { box, s0, s1 } of shown) {\n    spans.push({ x0: s0, x1: s1 })\n    ticks.push(Math.round(s0) + 0.5)\n    if (s1 - s0 >= MIN_BRACKET_PX) {\n      ticks.push(Math.round(s1) + 0.5)\n    }\n    const length = label(formatBp(box.bp1 - box.bp0), (s0 + s1) / 2)\n    if (length.width <= s1 - s0) {\n      lengths.push(length)\n    }\n    if (box !== first.box) {\n      boundaries.push(position(box.bp0, s0))\n    }\n  }\n  const ends = [\n    position(first.box.bp0, first.s0),\n    position(last.box.bp1, last.s1),\n  ]\n  return {\n    spans,\n    ticks,\n    labels: placeLabels([...ends, ...lengths, ...boundaries]),\n  }\n}\n\nexport function rulerMarks(\n  boxes: readonly Box[],\n  x: (tx: number) => number,\n  width: number,\n  measure: (text: string) => number,\n  referenceAxis = false,\n) {\n  return (referenceAxis ? scaleMarks : boxMarks)(boxes, x, width, measure)\n}\n\n// Reference bp along the tubes: round positions on the reference axis, a\n// bracket per box on the own axis\nexport function drawTubeMapRuler(\n  ctx: CanvasRenderingContext2D,\n  boxes: readonly Box[],\n  frame: TubeMapFrame,\n  top: number,\n  referenceAxis = false,\n) {\n  const { x, width, darkMode } = frame\n  ctx.font = '10px sans-serif'\n  const marks = rulerMarks(\n    boxes,\n    x,\n    width,\n    text => ctx.measureText(text).width,\n    referenceAxis,\n  )\n  if (!marks) {\n    return\n  }\n  const ink = rulerInk(darkMode)\n  const y = top + 0.5\n  ctx.strokeStyle = ink\n  ctx.fillStyle = ink\n  ctx.lineWidth = 1\n  ctx.textAlign = 'center'\n  ctx.textBaseline = 'top'\n  ctx.beginPath()\n  for (const { x0, x1 } of marks.spans) {\n    ctx.moveTo(Math.max(0, x0), y)\n    ctx.lineTo(Math.min(width, x1), y)\n  }\n  for (const sx of marks.ticks) {\n    ctx.moveTo(sx, top)\n    ctx.lineTo(sx, top + TICK_PX)\n  }\n  ctx.stroke()\n  for (const { text, at } of marks.labels) {\n    ctx.fillText(text, at, top + TICK_PX + 2)\n  }\n}\n", "import { isBackbone } from '../anchoredNodes'\n\nimport type { Graph } from '../types'\nimport type { TubeMapLayout } from '@gmod/tubemap-core'\n\n// On its own axis a tube map keeps none of the linear view's bp: a box is as\n// wide as log2 of its length, and the lane changes between boxes take px that\n// cover no reference at all. A band from each reference box up to the bp it\n// covers on the linear view's ruler ties the two back together, the way the\n// LD display ties its matrix columns to their variants.\n\nexport interface ReferenceNode {\n  node: string\n  bp0: number\n  bp1: number\n  x0: number\n  x1: number\n}\n\n// A reference node's band, in screen px: its bp span along the top of the\n// zone, its box's span along the bottom\nexport interface Connector {\n  node: string\n  top0: number\n  top1: number\n  bottom0: number\n  bottom1: number\n}\n\nexport function referenceNodes(graph: Graph, layout: TubeMapLayout) {\n  const nodeById = new Map(graph.nodes.map(n => [n.id, n]))\n  const out: ReferenceNode[] = []\n  // sparse: an unreached node has no entry\n  layout.nodes.forEach(node => {\n    const graphNode = nodeById.get(node.name)\n    if (node.order >= 0 && graphNode && isBackbone(graphNode)) {\n      out.push({\n        node: node.name,\n        bp0: graphNode.stable.start,\n        bp1: graphNode.stable.start + node.sequenceLength,\n        x0: node.x,\n        x1: node.x + node.pixelWidth,\n      })\n    }\n  })\n  return out\n}\n\n// The bands whose box is on screen. A band's top may still run off the side,\n// which is the linear view saying that box is outside its window.\nexport function tubeMapConnectors(\n  nodes: readonly ReferenceNode[],\n  bpToScreen: (bp: number) => number,\n  tubeToScreen: (tx: number) => number,\n  width: number,\n): Connector[] {\n  const out: Connector[] = []\n  for (const n of nodes) {\n    const bottom0 = tubeToScreen(n.x0)\n    const bottom1 = tubeToScreen(n.x1)\n    if (bottom1 >= 0 && bottom0 <= width) {\n      out.push({\n        node: n.node,\n        top0: bpToScreen(n.bp0),\n        top1: bpToScreen(n.bp1),\n        bottom0,\n        bottom1,\n      })\n    }\n  }\n  return out\n}\n\n// A SNP's band is a sliver, so the pointer gets a few px either side of one\nconst HIT_SLOP_PX = 3\n\nexport function connectorAt(\n  connectors: readonly Connector[],\n  zoneBottom: number,\n  sx: number,\n  sy: number,\n) {\n  if (zoneBottom <= 0 || sy < 0 || sy > zoneBottom) {\n    return undefined\n  }\n  const t = sy / zoneBottom\n  let hit: string | undefined\n  let best = HIT_SLOP_PX\n  for (const c of connectors) {\n    const a = c.top0 + (c.bottom0 - c.top0) * t\n    const b = c.top1 + (c.bottom1 - c.top1) * t\n    const dist = Math.max(0, Math.min(a, b) - sx, sx - Math.max(a, b))\n    if (dist < best) {\n      best = dist\n      hit = c.node\n    }\n  }\n  return hit\n}\n\nfunction band(ctx: CanvasRenderingContext2D, c: Connector, bottom: number) {\n  ctx.moveTo(c.top0, 0)\n  ctx.lineTo(c.top1, 0)\n  ctx.lineTo(c.bottom1, bottom)\n  ctx.lineTo(c.bottom0, bottom)\n  ctx.closePath()\n}\n\nfunction sides(ctx: CanvasRenderingContext2D, c: Connector, bottom: number) {\n  ctx.moveTo(c.top0, 0)\n  ctx.lineTo(c.bottom0, bottom)\n  ctx.moveTo(c.top1, 0)\n  ctx.lineTo(c.bottom1, bottom)\n}\n\n// One fill and one stroke for every band, so where hundreds of them converge\n// on the ruler the ink composites once rather than going black. The lit band\n// takes the tube map's own highlight.\nexport function drawTubeMapConnectors(\n  ctx: CanvasRenderingContext2D,\n  connectors: readonly Connector[],\n  bottom: number,\n  {\n    highlightNode,\n    darkMode,\n  }: { highlightNode?: string | null; darkMode?: boolean },\n) {\n  if (bottom <= 0 || connectors.length === 0) {\n    return\n  }\n  const ink = darkMode ? '255,255,255' : '0,0,0'\n  ctx.beginPath()\n  for (const c of connectors) {\n    band(ctx, c, bottom)\n  }\n  ctx.fillStyle = `rgba(${ink},0.07)`\n  ctx.fill()\n  ctx.beginPath()\n  for (const c of connectors) {\n    sides(ctx, c, bottom)\n  }\n  ctx.strokeStyle = `rgba(${ink},0.35)`\n  ctx.lineWidth = 0.5\n  ctx.stroke()\n  const lit = connectors.find(c => c.node === highlightNode)\n  if (lit) {\n    ctx.beginPath()\n    band(ctx, lit, bottom)\n    ctx.fillStyle = 'rgba(255,192,203,0.5)'\n    ctx.fill()\n    ctx.beginPath()\n    sides(ctx, lit, bottom)\n    ctx.strokeStyle = '#ff0000'\n    ctx.lineWidth = 1\n    ctx.stroke()\n  }\n}\n", "import { isBackbone } from '../anchoredNodes'\n\nimport type { Deviation } from './coarsen'\nimport type { TubeMapFrame } from './draw'\nimport type { Graph } from '../types'\nimport type { LayoutNode, TubeMapLayout } from '@gmod/tubemap-core'\n\n// A folded variant on the tube of the walk that carries it, in tube\n// coordinates. Placed by bp through the box that holds it, since tubemap-core\n// may merge the coarsened nodes again and a box can stand for several.\nexport interface DeviationMark {\n  x0: number\n  x1: number\n  y: number\n  height: number\n}\n\ninterface Box {\n  bp0: number\n  bp1: number\n  index: number\n  node: LayoutNode\n}\n\nfunction boxesOf(graph: Graph, layout: TubeMapLayout) {\n  const nodeById = new Map(graph.nodes.map(n => [n.id, n]))\n  const boxes: Box[] = []\n  layout.nodes.forEach((node, index) => {\n    const g = nodeById.get(node.name)\n    if (node.order >= 0 && g && isBackbone(g)) {\n      const bp0 = g.stable.start\n      boxes.push({ bp0, bp1: bp0 + node.sequenceLength, index, node })\n    }\n  })\n  return boxes.sort((a, b) => a.bp0 - b.bp0)\n}\n\n// The box holding `bp` that this walk passes through; an insertion on a\n// boundary between two boxes sits on whichever the walk visits\nfunction boxAt(\n  boxes: readonly Box[],\n  bp: number,\n  visited: Map<number, number>,\n) {\n  let lo = 0\n  let hi = boxes.length - 1\n  while (lo < hi) {\n    const mid = (lo + hi + 1) >> 1\n    if (boxes[mid]!.bp0 <= bp) {\n      lo = mid\n    } else {\n      hi = mid - 1\n    }\n  }\n  return [boxes[lo], boxes[lo - 1]].find(\n    box => box && visited.has(box.index) && box.bp0 <= bp && bp <= box.bp1,\n  )\n}\n\nexport function deviationMarks(\n  graph: Graph,\n  layout: TubeMapLayout,\n  deviations: Map<string, Deviation[]>,\n) {\n  const boxes = boxesOf(graph, layout)\n  const marks: DeviationMark[] = []\n  for (const track of layout.tracks) {\n    const devs = track.name ? deviations.get(track.name) : undefined\n    if (devs?.length) {\n      // a walk that loops through a box twice marks its first pass\n      const visited = new Map<number, number>()\n      for (const segment of track.path) {\n        if (\n          segment.node !== null &&\n          segment.y !== undefined &&\n          !visited.has(segment.node)\n        ) {\n          visited.set(segment.node, segment.y)\n        }\n      }\n      for (const d of devs) {\n        const box = boxAt(boxes, d.start, visited)\n        if (box) {\n          const { node, bp0, bp1 } = box\n          const at = (bp: number) =>\n            node.x + ((Math.min(bp, bp1) - bp0) / (bp1 - bp0)) * node.pixelWidth\n          marks.push({\n            x0: at(d.start),\n            x1: at(d.end),\n            y: visited.get(box.index)!,\n            height: track.width,\n          })\n        }\n      }\n    }\n  }\n  return marks\n}\n\n// Dark on light and light on dark, since the tubes themselves carry every hue\nexport function deviationInk(darkMode?: boolean) {\n  return darkMode ? 'rgba(255,255,255,0.9)' : 'rgba(0,0,0,0.8)'\n}\n\n// A tick at least a px wide across the tube\nexport function drawDeviationMarks(\n  ctx: CanvasRenderingContext2D,\n  marks: readonly DeviationMark[],\n  { x, y, width, darkMode }: TubeMapFrame,\n) {\n  if (marks.length === 0) {\n    return\n  }\n  ctx.fillStyle = deviationInk(darkMode)\n  ctx.beginPath()\n  for (const m of marks) {\n    const left = x(m.x0)\n    const right = Math.max(x(m.x1), left + 1)\n    if (right >= 0 && left <= width) {\n      const top = y(m.y)\n      ctx.rect(left, top, right - left, y(m.y + m.height) - top)\n    }\n  }\n  ctx.fill()\n}\n", "import { forward, getXCoordinateOfBaseWithinNode } from '@gmod/tubemap-core'\n\nimport type { Track, TubeMapLayout } from '@gmod/tubemap-core'\n\n// Where a read differs from the nodes it runs through, in tube coordinates:\n// the marks sequenceTubeMap's drawMismatches puts on a read's tube. Each mark\n// spans the bases it covers and sits on the tube of the read that carries it\n// (`y` is the tube's top, `height` its width), so a painter only maps them\n// through the frame. `nodeY` is the top of the node, which a hover draws a\n// leader up to.\ninterface MarkBase {\n  readId: number\n  y: number\n  height: number\n  nodeY: number\n}\n\nexport type TubeMapMismatch =\n  | (MarkBase & {\n      kind: 'insertion'\n      x: number\n      seq?: string\n      // at the read's first or last base, where an aligner clips rather than\n      // inserts; sequenceTubeMap hides these unless soft clips are shown\n      softClip: boolean\n    })\n  | (MarkBase & { kind: 'deletion'; x0: number; x1: number })\n  | (MarkBase & { kind: 'substitution'; x0: number; x1: number; seq: string })\n\nfunction readMismatches(read: Track, layout: TubeMapLayout) {\n  const marks: TubeMapMismatch[] = []\n  const entries = read.sequenceNew ?? []\n  entries.forEach((entry, i) => {\n    const nodeIndex = layout.nodeMap.get(forward(entry.nodeName))\n    const node = nodeIndex === undefined ? undefined : layout.nodes[nodeIndex]\n    // Node merging can drop a visit, so the segment for entry i is at or after\n    // path[i], and the walk stops at the path's end.\n    let pathIndex = i\n    while (\n      pathIndex < read.path.length &&\n      read.path[pathIndex]!.node !== nodeIndex\n    ) {\n      pathIndex += 1\n    }\n    const y = read.path[pathIndex]?.y\n    if (node && y !== undefined) {\n      const base = { readId: read.id, y, height: read.width, nodeY: node.y }\n      // A base past a merged node's end has no x.\n      const at = (pos: number) => getXCoordinateOfBaseWithinNode(node, pos)\n      for (const mm of entry.mismatches) {\n        const x0 = at(mm.pos)\n        if (x0 !== null) {\n          if (mm.type === 'insertion') {\n            const softClip =\n              (i === 0 && mm.pos === read.firstNodeOffset) ||\n              (i === entries.length - 1 && mm.pos === read.finalNodeCoverLength)\n            marks.push({\n              ...base,\n              kind: 'insertion',\n              x: x0,\n              seq: mm.seq,\n              softClip,\n            })\n          } else if (mm.type === 'deletion' && mm.length !== undefined) {\n            const x1 = at(mm.pos + mm.length)\n            if (x1 !== null) {\n              marks.push({ ...base, kind: 'deletion', x0, x1 })\n            }\n          } else if (mm.type === 'substitution' && mm.seq !== undefined) {\n            const x1 = at(mm.pos + mm.seq.length)\n            if (x1 !== null) {\n              marks.push({ ...base, kind: 'substitution', x0, x1, seq: mm.seq })\n            }\n          }\n        }\n      }\n    }\n  })\n  return marks\n}\n\nexport function tubeMapMismatches(layout: TubeMapLayout) {\n  return layout.reads.flatMap(read => readMismatches(read, layout))\n}\n", "import { curvePaths, nodeOutlinePath } from '@gmod/tubemap-core'\n\nimport { tubeMapMismatches } from './mismatches'\n\nimport type { TubeMapTransform } from './frame'\nimport type { TubeMapMismatch } from './mismatches'\nimport type { TrackType, TubeMapLayout } from '@gmod/tubemap-core'\n\n// Paints a tube map layout on a 2D canvas, in the order sequenceTubeMap's d3\n// drawing stacks it: haplotype tubes, their lane changes and turnarounds, then\n// reads the same way, then the node boxes over all of them. Everything goes\n// through `x` and `y`, tube coordinates to screen px, so the one painter serves\n// the tube map's own axis (an affine map) and the reference axis (warp.ts).\n//\n// The package states curves, corners and node outlines as SVG path data. They\n// are parsed once per layout into commands whose points can be mapped, since\n// a Path2D built from the string could only be transformed affinely.\n\ntype Command =\n  | { op: 'M' | 'L'; x: number; y: number }\n  | { op: 'Q'; x1: number; y1: number; x: number; y: number }\n  | {\n      op: 'C'\n      x1: number\n      y1: number\n      x2: number\n      y2: number\n      x: number\n      y: number\n    }\n  | { op: 'H'; x: number }\n  | { op: 'V'; y: number }\n  | { op: 'Z' }\n\n// The absolute M/L/H/V/Q/C/Z subset tubemap-core writes\nexport function parsePath(d: string): Command[] {\n  const tokens = d.trim().split(/[\\s,]+/)\n  const commands: Command[] = []\n  let i = 0\n  const num = () => Number(tokens[i++])\n  while (i < tokens.length) {\n    const op = tokens[i++]\n    if (op === 'M' || op === 'L') {\n      commands.push({ op, x: num(), y: num() })\n    } else if (op === 'H') {\n      commands.push({ op, x: num() })\n    } else if (op === 'V') {\n      commands.push({ op, y: num() })\n    } else if (op === 'Q') {\n      commands.push({ op, x1: num(), y1: num(), x: num(), y: num() })\n    } else if (op === 'C') {\n      commands.push({\n        op,\n        x1: num(),\n        y1: num(),\n        x2: num(),\n        y2: num(),\n        x: num(),\n        y: num(),\n      })\n    } else if (op === 'Z') {\n      commands.push({ op })\n    }\n  }\n  return commands\n}\n\ninterface Filled {\n  color: string\n  alpha: number\n  // tube x extent, for culling\n  x0: number\n  x1: number\n}\n\ninterface Rect extends Filled {\n  y0: number\n  y1: number\n}\n\ninterface Shape extends Filled {\n  commands: Command[]\n}\n\ninterface Layer {\n  rects: Rect[]\n  shapes: Shape[]\n}\n\nexport interface TubeMapPicture {\n  bounds: TubeMapLayout['bounds']\n  layers: Layer[]\n  nodes: { name: string; commands: Command[]; x0: number; x1: number }[]\n  mismatches: TubeMapMismatch[]\n}\n\nfunction extentOf(commands: Command[]) {\n  let x0 = Infinity\n  let x1 = -Infinity\n  for (const c of commands) {\n    if ('x' in c) {\n      x0 = Math.min(x0, c.x)\n      x1 = Math.max(x1, c.x)\n    }\n    if ('x1' in c) {\n      x0 = Math.min(x0, c.x1)\n      x1 = Math.max(x1, c.x1)\n    }\n  }\n  return { x0, x1 }\n}\n\nfunction shapeOf(d: string, color: string, alpha: number): Shape {\n  const commands = parsePath(d)\n  return { commands, color, alpha, ...extentOf(commands) }\n}\n\nfunction layerOf(layout: TubeMapLayout, type: TrackType): Layer {\n  const { shapes } = layout\n  const rects = [...shapes.rectangles, ...shapes.verticalRectangles]\n    .filter(r => r.type === type)\n    .map(r => ({\n      color: r.color,\n      alpha: r.alpha ?? 1,\n      x0: r.xStart,\n      x1: r.xEnd + 1,\n      y0: r.yStart,\n      y1: r.yEnd + 1,\n    }))\n  const curves = curvePaths(shapes.curves, type).map(c =>\n    shapeOf(c.path!, c.color, c.alpha ?? 1),\n  )\n  const corners = shapes.corners\n    .filter(c => c.type === type)\n    .map(c => shapeOf(c.path, c.color, 1))\n  return { rects, shapes: [...curves, ...corners] }\n}\n\n// Everything a frame needs that does not depend on the transform\nexport function tubeMapPicture(layout: TubeMapLayout): TubeMapPicture {\n  const nodes: TubeMapPicture['nodes'] = []\n  layout.nodes.forEach(node => {\n    if (node.order >= 0) {\n      const commands = parsePath(nodeOutlinePath(node))\n      nodes.push({ name: node.name, commands, ...extentOf(commands) })\n    }\n  })\n  return {\n    bounds: layout.bounds,\n    layers: [layerOf(layout, 'haplotype'), layerOf(layout, 'read')],\n    nodes,\n    mismatches: tubeMapMismatches(layout).filter(\n      m => m.kind !== 'insertion' || !m.softClip,\n    ),\n  }\n}\n\nfunction trace(\n  ctx: CanvasRenderingContext2D,\n  commands: Command[],\n  x: (tx: number) => number,\n  y: (ty: number) => number,\n) {\n  let cx = 0\n  let cy = 0\n  for (const c of commands) {\n    switch (c.op) {\n      case 'M':\n        cx = c.x\n        cy = c.y\n        ctx.moveTo(x(cx), y(cy))\n        break\n      case 'L':\n        cx = c.x\n        cy = c.y\n        ctx.lineTo(x(cx), y(cy))\n        break\n      case 'H':\n        cx = c.x\n        ctx.lineTo(x(cx), y(cy))\n        break\n      case 'V':\n        cy = c.y\n        ctx.lineTo(x(cx), y(cy))\n        break\n      case 'Q':\n        cx = c.x\n        cy = c.y\n        ctx.quadraticCurveTo(x(c.x1), y(c.y1), x(cx), y(cy))\n        break\n      case 'C':\n        cx = c.x\n        cy = c.y\n        ctx.bezierCurveTo(x(c.x1), y(c.y1), x(c.x2), y(c.y2), x(cx), y(cy))\n        break\n      case 'Z':\n        ctx.closePath()\n        break\n    }\n  }\n}\n\nexport interface TubeMapFrame extends TubeMapTransform {\n  width: number\n  highlightNode?: string | null\n  darkMode?: boolean\n}\n\n// One fill per colour per layer: a layer's shapes do not overlap in a way the\n// order within it would decide, and a fill per shape costs a draw call each.\nfunction fillByColor<T extends Filled>(\n  ctx: CanvasRenderingContext2D,\n  items: T[],\n  visible: (item: T) => boolean,\n  addTo: (item: T) => void,\n) {\n  const byColor = new Map<string, T[]>()\n  for (const item of items) {\n    if (visible(item)) {\n      const key = `${item.color}|${item.alpha}`\n      const list = byColor.get(key)\n      if (list) {\n        list.push(item)\n      } else {\n        byColor.set(key, [item])\n      }\n    }\n  }\n  for (const list of byColor.values()) {\n    ctx.fillStyle = list[0]!.color\n    ctx.globalAlpha = list[0]!.alpha\n    ctx.beginPath()\n    for (const item of list) {\n      addTo(item)\n    }\n    ctx.fill()\n  }\n  ctx.globalAlpha = 1\n}\n\n// Zoomed out, a box is a few px of outline and a cut's boxes ink over the\n// tubes between them, so an outline fades as its box narrows\nconst FULL_OUTLINE_PX = 12\nconst MIN_OUTLINE_ALPHA = 0.15\n\nfunction outlineAlpha(screenWidth: number) {\n  return Math.max(MIN_OUTLINE_ALPHA, Math.min(1, screenWidth / FULL_OUTLINE_PX))\n}\n\nexport function drawTubeMap(\n  ctx: CanvasRenderingContext2D,\n  picture: TubeMapPicture,\n  frame: TubeMapFrame,\n) {\n  const { x, y, width } = frame\n  const visible = (item: { x0: number; x1: number }) =>\n    x(item.x1) >= 0 && x(item.x0) <= width\n  for (const layer of picture.layers) {\n    fillByColor(ctx, layer.rects, visible, r => {\n      const left = x(r.x0)\n      const top = y(r.y0)\n      ctx.rect(left, top, x(r.x1) - left, y(r.y1) - top)\n    })\n    fillByColor(ctx, layer.shapes, visible, s => {\n      trace(ctx, s.commands, x, y)\n    })\n  }\n  const stroke = frame.darkMode ? '#d0d0d0' : '#000000'\n  const fill = frame.darkMode ? 'rgba(40,40,40,0.4)' : 'rgba(255,255,255,0.4)'\n  ctx.lineWidth = 2 * Math.max(0.25, Math.min(1, frame.yScale))\n  for (const node of picture.nodes) {\n    if (visible(node)) {\n      const lit = node.name === frame.highlightNode\n      ctx.beginPath()\n      trace(ctx, node.commands, x, y)\n      ctx.fillStyle = lit ? 'rgba(255,192,203,0.5)' : fill\n      ctx.strokeStyle = lit ? '#ff0000' : stroke\n      ctx.fill()\n      ctx.globalAlpha = lit ? 1 : outlineAlpha(x(node.x1) - x(node.x0))\n      ctx.stroke()\n      ctx.globalAlpha = 1\n    }\n  }\n  drawMismatches(ctx, picture.mismatches, frame)\n}\n\n// sequenceTubeMap's marks, which it draws at 12px and hides once zoomed out\n// below half size\nconst MISMATCH_FONT_PX = 12\nconst MIN_MISMATCH_FONT_PX = 6\n\nexport function mismatchesLegible(yScale: number) {\n  return MISMATCH_FONT_PX * yScale >= MIN_MISMATCH_FONT_PX\n}\n\nexport function mismatchOnScreen(\n  m: TubeMapMismatch,\n  { x, width }: Pick<TubeMapFrame, 'x' | 'width'>,\n) {\n  const [x0, x1] = m.kind === 'insertion' ? [m.x, m.x] : [m.x0, m.x1]\n  return x(x1) >= 0 && x(x0) <= width\n}\n\nfunction drawMismatches(\n  ctx: CanvasRenderingContext2D,\n  marks: readonly TubeMapMismatch[],\n  frame: TubeMapFrame,\n) {\n  const { x, y, yScale, darkMode } = frame\n  if (!mismatchesLegible(yScale) || marks.length === 0) {\n    return\n  }\n  const fontPx = MISMATCH_FONT_PX * yScale\n  ctx.fillStyle = 'grey'\n  ctx.beginPath()\n  for (const m of marks) {\n    if (m.kind === 'deletion' && mismatchOnScreen(m, frame)) {\n      const left = x(m.x0)\n      const top = y(m.y)\n      ctx.rect(left, top, x(m.x1) - left, y(m.y + m.height) - top)\n    }\n  }\n  ctx.fill()\n  ctx.font = `${fontPx}px monospace`\n  ctx.textBaseline = 'alphabetic'\n  ctx.fillStyle = darkMode ? '#ffffff' : '#000000'\n  for (const m of marks) {\n    if (!mismatchOnScreen(m, frame)) {\n      continue\n    }\n    if (m.kind === 'substitution') {\n      ctx.fillText(m.seq, x(m.x0) + 1, y(m.y + m.height))\n    } else if (m.kind === 'insertion') {\n      ctx.fillText('*', x(m.x) - 3, y(m.y + m.height))\n    }\n  }\n}\n", "import { tubeSpan } from './axis'\n\nimport type { ReferenceBoxes } from './axis'\nimport type { TubeMapFrame } from './draw'\nimport type { GeneModel } from '../genes/genePins'\n\n// A gene over the tube map, in tube x, mapped through the reference's boxes\n// (axis.ts)\nexport interface TubeMapGene {\n  gene: GeneModel\n  x0: number\n  x1: number\n  exons: { x0: number; x1: number }[]\n}\n\n// A gene takes the boxes of the refName it equals, as in genePins\nexport function tubeMapGenes(\n  byRefName: ReferenceBoxes,\n  genes: readonly GeneModel[],\n): TubeMapGene[] {\n  const out: TubeMapGene[] = []\n  for (const gene of genes) {\n    const boxes = byRefName.get(gene.refName)\n    const first = boxes?.[0]\n    const last = boxes?.at(-1)\n    if (!boxes || !first || !last) {\n      continue\n    }\n    const start = Math.max(gene.start, first.bp0)\n    const end = Math.min(gene.end, last.bp1)\n    if (end <= start) {\n      continue\n    }\n    out.push({\n      gene,\n      ...tubeSpan(boxes, start, end),\n      exons: gene.exons\n        .filter(e => e.end > start && e.start < end)\n        .map(e =>\n          tubeSpan(boxes, Math.max(e.start, start), Math.min(e.end, end)),\n        ),\n    })\n  }\n  return out\n}\n\nexport const GENE_ROW_PX = 22\nconst MAX_GENE_ROWS = 4\nconst EXON_PX = 8\nconst NAME_FONT = '11px sans-serif'\nconst NAME_GAP_PX = 8\n\n// The rows the genes need at least: as many as overlap at one point, which\n// holds at every zoom. A name wider than its gene can want more, and shares\n// the top row.\nexport function tubeMapGeneRows(genes: readonly TubeMapGene[]) {\n  const edges = genes\n    .flatMap(g => [\n      { x: g.x0, step: 1 },\n      { x: g.x1, step: -1 },\n    ])\n    .sort((a, b) => a.x - b.x || a.step - b.step)\n  let depth = 0\n  let most = 0\n  for (const { step } of edges) {\n    depth += step\n    most = Math.max(most, depth)\n  }\n  return Math.min(MAX_GENE_ROWS, most)\n}\n\n// Rows of genes above the tubes, bottom row nearest them, packed so neither\n// glyphs nor names overlap. Packed per frame, since the reference axis warps x\n// by zoom. The rows go up to `top`; past that, genes share the top row.\nexport function drawTubeMapGenes(\n  ctx: CanvasRenderingContext2D,\n  genes: readonly TubeMapGene[],\n  frame: TubeMapFrame,\n  bottom: number,\n  top = 0,\n) {\n  const { x, width, darkMode } = frame\n  const rows = Math.max(1, Math.floor((bottom - top) / GENE_ROW_PX))\n  const rowEnds: number[] = []\n  const ink = darkMode ? '#e0e0e6' : '#1c1c22'\n  ctx.font = NAME_FONT\n  ctx.textAlign = 'center'\n  ctx.textBaseline = 'alphabetic'\n  ctx.fillStyle = ink\n  ctx.strokeStyle = ink\n  ctx.lineWidth = 1\n  const placed = genes\n    .map(g => ({ g, s0: x(g.x0), s1: x(g.x1) }))\n    .filter(({ s0, s1 }) => s1 >= 0 && s0 <= width)\n    .sort((a, b) => a.s0 - b.s0)\n  for (const { g, s0, s1 } of placed) {\n    const arrow = g.gene.strand > 0 ? ' \u2192' : g.gene.strand < 0 ? '\u2190 ' : ''\n    const label =\n      g.gene.strand < 0 ? `${arrow}${g.gene.name}` : `${g.gene.name}${arrow}`\n    const mid = (Math.max(s0, 0) + Math.min(s1, width)) / 2\n    const half = ctx.measureText(label).width / 2\n    const left = Math.min(s0, mid - half)\n    const right = Math.max(s1, mid + half)\n    let row = rowEnds.findIndex(end => end + NAME_GAP_PX <= left)\n    if (row === -1) {\n      row = Math.min(rowEnds.length, rows - 1)\n    }\n    rowEnds[row] = Math.max(rowEnds[row] ?? -Infinity, right)\n    const glyphY = bottom - row * GENE_ROW_PX - EXON_PX / 2\n    ctx.beginPath()\n    ctx.moveTo(s0, glyphY + 0.5)\n    ctx.lineTo(s1, glyphY + 0.5)\n    ctx.stroke()\n    for (const e of g.exons) {\n      const e0 = x(e.x0)\n      ctx.fillRect(e0, glyphY - EXON_PX / 2, Math.max(1, x(e.x1) - e0), EXON_PX)\n    }\n    ctx.fillText(label, mid, glyphY - EXON_PX / 2 - 2)\n  }\n}\n", "import { clampZoom } from './pipeline'\n\nimport type { Bounds } from './pipeline'\nimport type { AxisScale } from './util/geometry'\n\n// The pan and zoom arithmetic a pane runs, in layout units, with no host in it.\n\nexport interface PaneTransform {\n  scale: number\n  translateX: number\n  translateY: number\n}\n\n// The zoom as a pair of axis scales. `pixelRows` rides along rather than being\n// derived downstream: the deletion bow is capped in a row layout and not in\n// the isotropic one, and `scaleY !== scaleX` coincides at one zoom level.\nexport function axisScaleOf(scale: number, pixelRows: boolean): AxisScale {\n  return { scaleX: scale, scaleY: pixelRows ? 1 : scale, pixelRows }\n}\n\n// What a pane of `width` x `height` css px shows, in layout units.\nexport function viewportOf(\n  t: { translateX: number; translateY: number },\n  axis: AxisScale,\n  width: number,\n  height: number,\n): Bounds {\n  return {\n    minX: -t.translateX / axis.scaleX,\n    minY: -t.translateY / axis.scaleY,\n    maxX: (width - t.translateX) / axis.scaleX,\n    maxY: (height - t.translateY) / axis.scaleY,\n  }\n}\n\n// The window a geometry build covers: the pane plus `panes` whole panes on\n// every side, so an ordinary pan never blanks its margins for the debounce and\n// never rebuilds at all.\nexport function padded(v: Bounds, panes: number): Bounds {\n  const w = (v.maxX - v.minX) * panes\n  const h = (v.maxY - v.minY) * panes\n  return {\n    minX: v.minX - w,\n    minY: v.minY - h,\n    maxX: v.maxX + w,\n    maxY: v.maxY + h,\n  }\n}\n\nexport function contains(outer: Bounds, inner: Bounds) {\n  return (\n    inner.minX >= outer.minX &&\n    inner.maxX <= outer.maxX &&\n    inner.minY >= outer.minY &&\n    inner.maxY <= outer.maxY\n  )\n}\n\n// Zoom by `factor` about a screen point. y only follows when it is on the same\n// scale: a row layout's y is screen px, so moving it by the ratio would slide\n// the rows off under the cursor while their pitch stayed put.\nexport function zoomAbout(\n  t: PaneTransform,\n  factor: number,\n  centerX: number,\n  centerY: number,\n  pixelRows: boolean,\n): PaneTransform {\n  const scale = clampZoom(t.scale * factor)\n  const ratio = scale / t.scale\n  return {\n    scale,\n    translateX: centerX - (centerX - t.translateX) * ratio,\n    translateY: pixelRows\n      ? t.translateY\n      : centerY - (centerY - t.translateY) * ratio,\n  }\n}\n\n// Where a screen point falls in layout units.\nexport function screenToLayout(\n  x: number,\n  y: number,\n  t: { translateX: number; translateY: number },\n  axis: AxisScale,\n) {\n  return {\n    x: (x - t.translateX) / axis.scaleX,\n    y: (y - t.translateY) / axis.scaleY,\n  }\n}\n", "import type { SubgraphRegion } from '../GetSubgraph'\n\n// The members of a LinearGenomeView a hosted pane reads and drives.\n// Structural, because this plugin takes no runtime dependency on the LGV\n// plugin (see hoverSync/index.tsx).\nexport interface HostBlock {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  offsetPx: number\n  reversed?: boolean\n  displayedRegionIndex?: number\n}\n\nexport interface LinearHost {\n  id: string\n  initialized: boolean\n  bpPerPx: number\n  offsetPx: number\n  width: number\n  displayedRegions: readonly { start: number; end: number }[]\n  dynamicBlocks: { contentBlocks: readonly HostBlock[] }\n  coarseDynamicBlocks: readonly HostBlock[]\n  horizontalScroll: (distance: number) => number\n  zoomTo: (bpPerPx: number, offset?: number) => number\n  // whether the view's body is mounted, which an off-screen view's is not\n  effectiveBodyMounted?: boolean\n  hasVisibleContent?: boolean\n}\n\nexport function isLinearHost(view: unknown): view is LinearHost {\n  if (typeof view !== 'object' || view === null) {\n    return false\n  }\n  const v = view as Record<string, unknown>\n  return (\n    typeof v.horizontalScroll === 'function' &&\n    typeof v.zoomTo === 'function' &&\n    'coarseDynamicBlocks' in v &&\n    'dynamicBlocks' in v\n  )\n}\n\nfunction widest(blocks: readonly HostBlock[]) {\n  return blocks.reduce<HostBlock | undefined>(\n    (best, b) => (best && best.end - best.start >= b.end - b.start ? best : b),\n    undefined,\n  )\n}\n\nexport interface HostWindow {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  bpPerPx: number\n  // the view's width in bp, which the margin is sized by: a block at a contig\n  // end is clipped, the zoom is not\n  span: number\n  regionStart: number\n  regionEnd: number\n}\n\n// x is reference bp on an anchored layout, so the graph shows what the linear\n// view shows when one bp is as many px in both and the cut's refName sits at\n// the same screen x. Undefined when the linear view shows no block of that\n// refName, which is a re-cut's job rather than the frame's. A reversed block\n// runs bp right to left, which only the tube map's connectors can draw.\nexport function hostFrame(view: LinearHost, region: SubgraphRegion) {\n  const block = widest(\n    view.dynamicBlocks.contentBlocks.filter(\n      b =>\n        b.refName === region.refName && b.assemblyName === region.assemblyName,\n    ),\n  )\n  const { bpPerPx } = view\n  if (!block || !(bpPerPx > 0)) {\n    return undefined\n  }\n  const left = block.offsetPx - view.offsetPx\n  return block.reversed\n    ? { scale: -1 / bpPerPx, translateX: left + block.end / bpPerPx }\n    : { scale: 1 / bpPerPx, translateX: left - block.start / bpPerPx }\n}\n\n// Read off the LIVE blocks even when the coarse ones woke the caller: those\n// name where the window was half a second ago (SyntenyFollow/CLAUDE.md).\nexport function hostWindow(view: LinearHost): HostWindow | undefined {\n  const block = widest(view.dynamicBlocks.contentBlocks)\n  const displayed =\n    block?.displayedRegionIndex === undefined\n      ? undefined\n      : view.displayedRegions[block.displayedRegionIndex]\n  return block && view.bpPerPx > 0\n    ? {\n        refName: block.refName,\n        assemblyName: block.assemblyName,\n        start: block.start,\n        end: block.end,\n        bpPerPx: view.bpPerPx,\n        span: view.bpPerPx * view.width,\n        regionStart: displayed?.start ?? block.start,\n        regionEnd: displayed?.end ?? block.end,\n      }\n    : undefined\n}\n\n// The window plus one window-width each side, clamped to the displayed\n// region, with the margins narrowed until the whole cut fits under `capBp`.\nexport function hostCut(\n  window: HostWindow,\n  capBp: number,\n  margins = true,\n): SubgraphRegion {\n  const visible = window.end - window.start\n  const margin = margins\n    ? Math.max(0, Math.min(window.span, (capBp - visible) / 2))\n    : 0\n  let start = Math.max(window.regionStart, Math.floor(window.start - margin))\n  let end = Math.min(window.regionEnd, Math.ceil(window.end + margin))\n  // Rounding outward can put a cut a base or two past the cap, which the load\n  // refuses whole; trim it back rather than lose the cut.\n  const over = end - start - capBp\n  if (over > 0) {\n    start += Math.floor(over / 2)\n    end -= Math.ceil(over / 2)\n  }\n  return {\n    refName: window.refName,\n    assemblyName: window.assemblyName,\n    start,\n    end,\n  }\n}\n\n// With margins, a cut holds while the window is inside it; without, only the\n// window itself does, since the drawing is the window.\nexport function cutHolds(\n  cut: SubgraphRegion | undefined,\n  window: HostWindow,\n  margins = true,\n) {\n  if (\n    cut?.refName !== window.refName ||\n    cut.assemblyName !== window.assemblyName\n  ) {\n    return false\n  }\n  // to the base, since a cut trimmed to its cap can end a base inside the window\n  if (margins) {\n    return cut.start <= window.start + 1 && window.end <= cut.end + 1\n  }\n  const exact = hostCut(window, Infinity, false)\n  return (\n    Math.abs(cut.start - exact.start) < 1 && Math.abs(cut.end - exact.end) < 1\n  )\n}\n", "import type { RepeatCall } from './repeatFeatures'\n\n// Which genotyped allele belongs to which haplotype walk. A VCF states a\n// sample's alleles in genotype order, which is the genotyper's own order and\n// carries no correspondence to the assembly's haplotype numbering \u2014 TRGTdb's\n// ABCA7 record, for one, lists them shortest first. So the walks and the\n// alleles are paired by length instead: the pairing whose total difference is\n// smallest, which for lengths on a line is the non-crossing one.\n//\n// A walk that does not reach both flanking reference nodes is measured whole\n// rather than across the array, and an allele no read spanned is a copy of the\n// one that was called. Neither states a length for this array, so they pair\n// last and take no verdict \u2014 pairing them first let a walk that stops inside\n// the array take the allele that fit one spanning it, and the spanning walk\n// then read as a disagreement.\n\nexport interface WalkCall extends RepeatCall {\n  // undefined where the walk and the allele are not both measurements\n  agrees?: boolean\n}\n\n// Every walk/call pair over the 94 HPRC samples TRGT genotyped at the ABCA7\n// VNTR is either within 8% of its allele or more than 14% from it, so any\n// threshold across that gap separates them the same way.\nexport const CALL_TOLERANCE = 0.1\n\nfunction agrees(walkBp: number, callBp: number) {\n  return Math.abs(callBp - walkBp) <= CALL_TOLERANCE * Math.max(walkBp, callBp)\n}\n\n// Pair two ascending lists of lengths, leaving out the surplus of whichever is\n// longer. `out[i]` is the index in `calls` that `walks[i]` took.\nfunction nearest(walks: number[], calls: number[]) {\n  const W = walks.length\n  const C = calls.length\n  const cost = Array.from({ length: W + 1 }, () => new Array(C + 1).fill(0))\n  const paired = Array.from({ length: W + 1 }, () =>\n    new Array<boolean>(C + 1).fill(false),\n  )\n  for (let i = W - 1; i >= 0; i--) {\n    for (let j = C - 1; j >= 0; j--) {\n      const together = Math.abs(walks[i]! - calls[j]!) + cost[i + 1]![j + 1]!\n      const dropWalk = W - i > C - j ? cost[i + 1]![j]! : Infinity\n      const dropCall = C - j > W - i ? cost[i]![j + 1]! : Infinity\n      cost[i]![j] = Math.min(together, dropWalk, dropCall)\n      paired[i]![j] = cost[i]![j] === together\n    }\n  }\n  const out = new Array<number | undefined>(W).fill(undefined)\n  for (let i = 0, j = 0; i < W && j < C;) {\n    if (paired[i]![j]) {\n      out[i++] = j++\n    } else if (W - i > C - j) {\n      i++\n    } else {\n      j++\n    }\n  }\n  return out\n}\n\nfunction byLength<T>(items: T[], bp: (item: T) => number) {\n  return items\n    .map((item, i) => ({ item, i }))\n    .sort((a, b) => bp(a.item) - bp(b.item))\n}\n\nconst backed = (call: RepeatCall) => call.spanningReads !== 0\n\nfunction scored(row: { bp: number; complete: boolean }, call: RepeatCall) {\n  return {\n    ...call,\n    agrees: row.complete && backed(call) ? agrees(row.bp, call.bp) : undefined,\n  }\n}\n\n// A phased genotype names its walk's haplotype outright. The rest go by\n// length: the walks that span the array against the alleles reads spanned,\n// then everything else against what those two left. That decides the\n// ambiguous cases on merit: which walk carries the one allele a lone spanning\n// read supports, and which allele a walk that stops inside the array is drawn\n// against.\nfunction pairSample<\n  R extends { bp: number; complete: boolean; haplotype?: number },\n>(rows: R[], calls: RepeatCall[]) {\n  const out = new Map<number, WalkCall>()\n  const taken = new Set<RepeatCall>()\n  rows.forEach((row, i) => {\n    const call = calls.find(\n      c => c.haplotype !== undefined && c.haplotype === row.haplotype,\n    )\n    if (call) {\n      taken.add(call)\n      out.set(i, scored(row, call))\n    }\n  })\n  const unphased = calls.filter(call => call.haplotype === undefined)\n  const ranked = byLength(rows, r => r.bp)\n  const stages = [\n    [ranked.filter(r => r.item.complete), unphased.filter(backed)],\n    [ranked, unphased],\n  ] as const\n  for (const [pool, group] of stages) {\n    const free = pool.filter(r => !out.has(r.i))\n    const open = byLength(\n      group.filter(call => !taken.has(call)),\n      call => call.bp,\n    )\n    nearest(\n      free.map(r => r.item.bp),\n      open.map(c => c.item.bp),\n    ).forEach((pick, k) => {\n      if (pick !== undefined) {\n        const row = free[k]!\n        const call = open[pick]!.item\n        taken.add(call)\n        out.set(row.i, scored(row.item, call))\n      }\n    })\n  }\n  return out\n}\n\nexport function withCalls<\n  R extends {\n    sample: string\n    bp: number\n    complete: boolean\n    haplotype?: number\n  },\n>(rows: R[], calls: Record<string, RepeatCall[]> | undefined) {\n  if (!calls) {\n    return rows as (R & { call?: WalkCall })[]\n  }\n  const paired = new Map<R, WalkCall>()\n  const bySample = new Map<string, R[]>()\n  for (const row of rows) {\n    bySample.set(row.sample, [...(bySample.get(row.sample) ?? []), row])\n  }\n  for (const [sample, group] of bySample) {\n    const called = calls[sample]\n    if (called) {\n      for (const [i, call] of pairSample(group, called)) {\n        paired.set(group[i]!, call)\n      }\n    }\n  }\n  return rows.map(row => ({ ...row, call: paired.get(row) }))\n}\n", "import { bubbleSegmentIds, classifyBubble, formatBp } from './classifyBubble'\nimport { isBackbone } from '../anchoredNodes'\nimport { svgPath } from '../util/geometry'\n\nimport type { BubbleRoute, MinigraphBubble } from './bubbleLine'\nimport type { BubbleKind, RepeatSpan } from './classifyBubble'\nimport type { Graph, NodeSegment } from '../types'\n\n// A bubble drawn over the graph itself: a wide translucent stroke along the\n// nodes inside it, in layout coordinates, so the same halo follows the nodes\n// through the force layout's loops as through the ordered layout's lenses. The\n// two backbone nodes a bubble hangs between are not inside it, and are left\n// out so neighbouring halos do not touch.\nexport interface BubbleHalo {\n  bubble: MinigraphBubble\n  kind: BubbleKind\n  label: string\n  // an SVG path in layout units; a drawing transform puts it on screen\n  path: string\n  // where the name goes, in layout units: over the middle of its nodes, at the\n  // height of the highest\n  labelAt: NodeSegment\n  members: number\n  // the ids of those nodes, so a lifted walk can say which bubbles it enters\n  nodeIds: string[]\n  // the bubble is the whole drawing, as a popped bubble's own row is: its\n  // label still names it, but a halo around everything marks nothing\n  whole: boolean\n  // each route the walks take through the bubble, the reference's own\n  // included, named for the haplotypes that take it; a route with no steps, a\n  // deletion, has nowhere to carry a chip\n  routes: RouteLabel[]\n}\n\nexport interface RouteLabel {\n  route: BubbleRoute\n  at: NodeSegment\n  text: string\n}\n\nconst WHOLE_FRACTION = 0.9\nconst NAMED_WALKS = 2\n// a SNP's routes are a dot each; chips are for loops a reader can see\nconst MIN_CHIPPED_BP = 1000\n\nexport function bubbleHalos(\n  graph: Graph,\n  bubbles: MinigraphBubble[],\n  positions: Record<string, NodeSegment[]>,\n  walkLabel: (name: string) => string = name => name,\n  repeats: readonly RepeatSpan[] = [],\n): BubbleHalo[] {\n  const byName = new Map(graph.nodes.map(n => [n.name, n]))\n  const halos: BubbleHalo[] = []\n  for (const bubble of bubbles) {\n    const parts: string[] = []\n    let minX = Infinity\n    let maxX = -Infinity\n    let minY = Infinity\n    const nodeIds: string[] = []\n    const ends: NodeSegment[] = []\n    for (const name of bubbleSegmentIds(bubble)) {\n      const node = byName.get(name)\n      const line = node && positions[node.id]\n      if (!node || !line?.length) {\n        continue\n      }\n      if (\n        isBackbone(node) &&\n        (node.stable.start < bubble.start || node.stable.start >= bubble.end)\n      ) {\n        ends.push(line[Math.floor(line.length / 2)]!)\n        continue\n      }\n      nodeIds.push(node.id)\n      // a one-point line still needs a segment to stroke as a dot\n      parts.push(svgPath(line.length === 1 ? [line[0]!, line[0]!] : line))\n      for (const p of line) {\n        minX = Math.min(minX, p.x)\n        maxX = Math.max(maxX, p.x)\n        minY = Math.min(minY, p.y)\n      }\n    }\n    if (nodeIds.length === 0) {\n      continue\n    }\n    const labelAt = { x: (minX + maxX) / 2, y: minY }\n    const anchor = ends.length\n      ? {\n          x: ends.reduce((s, p) => s + p.x, 0) / ends.length,\n          y: ends.reduce((s, p) => s + p.y, 0) / ends.length,\n        }\n      : labelAt\n    // A chip goes on the stretch that is the route's own: among the nodes the\n    // fewest other routes share, the point farthest from the bubble's ends.\n    // Routes through a repeat array share most of their copies, and the far\n    // point of a shared copy would put every chip on one loop.\n    const sharing = new Map<string, number>()\n    for (const route of bubble.routes ?? []) {\n      for (const id of new Set(route.steps)) {\n        sharing.set(id, (sharing.get(id) ?? 0) + 1)\n      }\n    }\n    const routes: RouteLabel[] = []\n    for (const route of bubble.routes ?? []) {\n      if (bubble.longestAlleleLength < MIN_CHIPPED_BP) {\n        break\n      }\n      if (route.steps.length === 0) {\n        continue\n      }\n      const rarest = Math.min(...route.steps.map(id => sharing.get(id)!))\n      let at: NodeSegment | undefined\n      let far = -1\n      for (const id of route.steps) {\n        if (sharing.get(id) !== rarest) {\n          continue\n        }\n        for (const p of positions[id] ?? []) {\n          const d = Math.hypot(p.x - anchor.x, p.y - anchor.y)\n          if (d > far) {\n            far = d\n            at = p\n          }\n        }\n      }\n      if (at) {\n        routes.push({ route, at, text: routeText(route, walkLabel) })\n      }\n    }\n    halos.push({\n      bubble,\n      ...classifyBubble(bubble, repeats),\n      path: parts.join(''),\n      labelAt,\n      members: nodeIds.length,\n      nodeIds,\n      whole: nodeIds.length >= WHOLE_FRACTION * graph.nodes.length,\n      routes,\n    })\n  }\n  return halos\n}\n\nfunction routeText(route: BubbleRoute, walkLabel: (name: string) => string) {\n  const names = [...new Set(route.walks.map(walkLabel))].sort()\n  const shown = names.slice(0, NAMED_WALKS).join(', ')\n  const more =\n    names.length > NAMED_WALKS ? ` +${names.length - NAMED_WALKS}` : ''\n  return `${shown}${more} \u00B7 ${formatBp(route.bp)}`\n}\n", "import { SATURATED_PATH_COUNT } from './bubbleLine'\nimport { isBackbone } from '../anchoredNodes'\nimport { referenceOrder } from '../layout/orderedLayout'\n\nimport type { BubbleRoute, MinigraphBubble } from './bubbleLine'\nimport type { Graph, GraphNode } from '../types'\n\n// Bubbles from the graph alone, off the reference order the ordered layout is\n// also drawn from (referenceOrder): a backbone node no link reaches across is a\n// bubble boundary, and whatever sorts between two consecutive boundaries is a\n// bubble. Needs a reference, not an index, so it works on a GBZ cut, a pggb\n// file and the inside of a popped superbubble alike.\n//\n// Read off the order itself, not off the layers the drawing puts it in. A\n// layer is where a node is drawn, and one nothing leads into is drawn in the\n// first layer wherever it sorts. That is every node a walk enters the cut at,\n// the ordinary shape of a GBZ cut whose context stops short of a haplotype's\n// walk: its link into the backbone then crossed every layer between, and the\n// bubbles on either side of those boundaries fused into one.\n//\n// Route statistics come from the walks when the graph has paths (exact, and\n// immune to a repeat array whose copies the order cannot direct), and from a\n// DP over the ordered DAG otherwise. A reversed stretch comes out as one\n// bubble whose interior runs against the reference, not as an inversion flag.\n\ninterface Routes {\n  min: number\n  max: number\n  n: number\n}\n\nexport function bubblesFromGraph(graph: Graph): MinigraphBubble[] {\n  if (!graph.nodes.some(isBackbone)) {\n    return []\n  }\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const order = referenceOrder(graph)\n  const indexOf = new Map(order.map((id, i) => [id, i]))\n  // how many links reach across each place in the order, as a running sum of\n  // where each one starts and stops\n  const reach = new Int32Array(order.length + 1)\n  // successors as a set: a repeat's back edge is the same DAG edge as its\n  // forward one, and counting it twice doubles every route through the copy\n  const succ = new Map<string, Set<string>>()\n  const linked = new Set<string>()\n  for (const e of graph.edges) {\n    const a = indexOf.get(e.from)\n    const b = indexOf.get(e.to)\n    if (a === undefined || b === undefined || a === b) {\n      continue\n    }\n    linked.add(`${e.from}>${e.to}`).add(`${e.to}>${e.from}`)\n    const [lo, hi] = a < b ? [a, b] : [b, a]\n    reach[lo + 1]!++\n    reach[hi]!--\n    const [from, to] = a < b ? [e.from, e.to] : [e.to, e.from]\n    ;(succ.get(from) ?? succ.set(from, new Set()).get(from)!).add(to)\n  }\n  for (let i = 1; i < reach.length; i++) {\n    reach[i]! += reach[i - 1]!\n  }\n  // Boundaries are nodes: every backbone node no link reaches across, plus the\n  // window's first and last backbone node whatever reaches across them, since a\n  // repeat array whose copies reach the last backbone node would otherwise\n  // never close.\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort((a, b) => a.stable.start - b.stable.start)\n  const ends = new Set([backbone[0]!.id, backbone.at(-1)!.id])\n  const boundaries = backbone\n    .map(node => [node, indexOf.get(node.id)!] as const)\n    .filter(([node, i]) => ends.has(node.id) || reach[i] === 0)\n    .sort(([a, ia], [b, ib]) => ia - ib || a.stable.start - b.stable.start)\n  const walkIndex = graph.paths?.map(p => {\n    const at = new Map<string, number>()\n    p.nodeIds.forEach((id, i) => {\n      if (!at.has(id)) {\n        at.set(id, i)\n      }\n    })\n    return at\n  })\n\n  const bubbles: MinigraphBubble[] = []\n  for (let i = 0; i + 1 < boundaries.length; i++) {\n    const [start, i0] = boundaries[i]!\n    const [end, i1] = boundaries[i + 1]!\n    const interior = order.slice(i0 + 1, i1)\n    if (interior.length === 0) {\n      continue\n    }\n\n    const best = new Map<string, Routes>([[start.id, { min: 0, max: 0, n: 1 }]])\n    for (const id of [start.id, ...interior]) {\n      const cur = best.get(id)\n      if (!cur) {\n        continue\n      }\n      for (const t of succ.get(id) ?? []) {\n        const ti = indexOf.get(t)!\n        if (ti > i1) {\n          continue\n        }\n        const add = t === end.id ? 0 : byId.get(t)!.length\n        const prev = best.get(t)\n        best.set(t, {\n          min: Math.min(prev?.min ?? Infinity, cur.min + add),\n          max: Math.max(prev?.max ?? -Infinity, cur.max + add),\n          n: Math.min(SATURATED_PATH_COUNT, cur.n + (prev?.n ?? 0)),\n        })\n      }\n    }\n    const walked =\n      walkIndex && walkRoutes(graph, byId, walkIndex, start.id, end.id)\n    const crossed = walked?.n ? walked : undefined\n    const routes = crossed ?? best.get(end.id) ?? { min: 0, max: 0, n: 0 }\n    // A walk that enters the bubble and never reaches its other end left the\n    // cut: a GBZ cut of a repeat array at 1 kb of context splits each\n    // haplotype's walk into pieces, and the routes seen are then a floor.\n    const walksLeave = walked !== undefined && walked.left > 0\n\n    const refStart = start.stable.start + start.length\n    const refEnd = end.stable.start\n    // The reference route exists in the cut only if every backbone pair inside\n    // is linked; a flank the hop reached from an allele is not.\n    const chain = [\n      start.id,\n      ...interior.filter(id => isBackbone(byId.get(id)!)),\n      end.id,\n    ]\n    const chainBroken = chain.some(\n      (id, k) => k > 0 && !linked.has(`${chain[k - 1]}>${id}`),\n    )\n    const partial = chainBroken || walksLeave\n    const fallback = chainBroken && !crossed\n    bubbles.push({\n      refName: start.stable.refName,\n      start: refStart,\n      end: refEnd,\n      segmentCount: interior.length + 2,\n      pathCount: routes.n,\n      // a real inversion test needs each walk's direction relative to the\n      // reference; the first visit's strand is just whichever path anchored the\n      // node\n      inversion: false,\n      shortestAlleleLength: fallback ? refEnd - refStart : routes.min,\n      longestAlleleLength: fallback ? refEnd - refStart : routes.max,\n      segments: [start, ...interior.map(id => byId.get(id)!), end]\n        .map(n => n.name)\n        .join(','),\n      shortestAllele: undefined,\n      longestAllele: undefined,\n      partial,\n      routes: crossed?.routes,\n    })\n  }\n  return bubbles\n}\n\n// For every walk that passes both boundary nodes, the bp between them and the\n// step sequence, so routes are distinct sequences and lengths are the true\n// haplotype lengths. `left` counts the walks that pass one boundary and end\n// before the other.\n//\n// `byId` is the caller's: this runs once per bubble, and a map of every node\n// built here made the whole pass quadratic, seven seconds at 15k nodes.\nfunction walkRoutes(\n  graph: Graph,\n  byId: Map<string, GraphNode>,\n  walkIndex: Map<string, number>[],\n  startId: string,\n  endId: string,\n): (Routes & { left: number; routes: BubbleRoute[] }) | undefined {\n  const seen = new Map<string, BubbleRoute>()\n  let min = Infinity\n  let max = -Infinity\n  let left = 0\n  graph.paths!.forEach((p, k) => {\n    const i0 = walkIndex[k]!.get(startId)\n    const i1 = walkIndex[k]!.get(endId)\n    if (i0 === undefined || i1 === undefined) {\n      if (i0 !== undefined || i1 !== undefined) {\n        left++\n      }\n      return\n    }\n    // Start to end, whichever way the walk crosses: a contig on the reverse\n    // strand takes the same route, and read end-first it keyed as a second one.\n    const steps = p.nodeIds.slice(Math.min(i0, i1) + 1, Math.max(i0, i1))\n    if (i1 < i0) {\n      steps.reverse()\n    }\n    let bp = 0\n    for (const id of steps) {\n      bp += byId.get(id)?.length ?? 0\n    }\n    const key = steps.join(',')\n    const route = seen.get(key) ?? { steps, bp, walks: [] }\n    route.walks.push(p.name)\n    seen.set(key, route)\n    min = Math.min(min, bp)\n    max = Math.max(max, bp)\n  })\n  return seen.size || left\n    ? { min, max, n: seen.size, left, routes: [...seen.values()] }\n    : undefined\n}\n", "import type { Graph } from '../types'\n\n// The graph inside one bubble: the segments the bubble row names, with the\n// links among them. The row's list includes the two backbone segments the\n// bubble hangs between, so the cut keeps its anchors and every layout that\n// needs a backbone still has one. A walk keeps the steps it takes inside the\n// bubble, so the bubbles derived inside it still read their routes and\n// lengths off the haplotypes, and carriage still sets node width.\nexport function bubbleSubgraph(graph: Graph, segmentIds: string[]): Graph {\n  const keep = new Set(segmentIds)\n  const nodes = graph.nodes.filter(n => keep.has(n.name))\n  const ids = new Set(nodes.map(n => n.id))\n  const paths = graph.paths\n    ?.map(p => ({ ...p, nodeIds: p.nodeIds.filter(id => ids.has(id)) }))\n    .filter(p => p.nodeIds.length > 0)\n  return {\n    name: graph.name,\n    nodes,\n    edges: graph.edges.filter(e => ids.has(e.from) && ids.has(e.to)),\n    ...(paths?.length ? { paths } : {}),\n    anchorPaths: graph.anchorPaths,\n    pathVisits: graph.pathVisits,\n    anchoredBy: graph.anchoredBy,\n    referencePath: graph.referencePath,\n  }\n}\n", "import { firstNodeAtOrAfter, isBackbone } from '../anchoredNodes'\nimport { polylineSlice } from '../layout/mergeRuns'\nimport { svgPath } from '../util/geometry'\n\nimport type { AnchoredNode } from '../anchoredNodes'\nimport type { Graph, NodeSegment } from '../types'\n\n// A gene as the pins need it: its name, its span on the reference, and the\n// exons of all its transcripts merged into one set of intervals.\nexport interface GeneModel {\n  name: string\n  refName: string\n  start: number\n  end: number\n  strand: number\n  exons: { start: number; end: number }[]\n}\n\n// A gene drawn onto the graph: its exons as stretches of the backbone nodes\n// that carry them, in layout units, and one point on the backbone to pin its\n// name to. Only the backbone has coordinates, so an allele shows no exon even\n// where a haplotype's own annotation would put one.\nexport interface GenePin {\n  gene: GeneModel\n  // an SVG path of the exon stretches, in layout units\n  exons: string\n  // where the name goes: the backbone point at the gene's midpoint, or the\n  // nearest backbone point inside the gene where the midpoint is not in the cut\n  at: NodeSegment\n  // how much of the gene's span the cut's backbone covers, so a label can say\n  // when a gene runs off the cut\n  covered: number\n}\n\n// The backbone of one refName in offset order, for finding the nodes a gene\n// lies over without reading the rest. `reach` is the longest node: a node over\n// a gene's start begins no further before it than that.\ninterface RefNameBackbone {\n  nodes: AnchoredNode[]\n  reach: number\n}\n\n// A gene lands on the backbone refName it equals. An assembly's `chr6` lands\n// on none, so a host renames its genes onto the graph's `GRCh38#0#chr6` with\n// featuresOnBackbone once it knows the backbone lies on that assembly.\nexport function genePins(\n  graph: Graph,\n  genes: GeneModel[],\n  positions: Record<string, NodeSegment[]>,\n): GenePin[] {\n  // Per refName and sorted once, so a gene reads the few nodes it lies over.\n  // Every gene used to read every backbone node on each frame of a node drag:\n  // 199 ms for 100 genes over 15k nodes, now 12.\n  const byRefName = new Map<string, RefNameBackbone>()\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName } = node.stable\n      if (positions[node.id]?.length) {\n        const entry =\n          byRefName.get(refName) ??\n          byRefName.set(refName, { nodes: [], reach: 0 }).get(refName)!\n        entry.nodes.push(node)\n        entry.reach = Math.max(entry.reach, node.length)\n      }\n    }\n  }\n  for (const { nodes } of byRefName.values()) {\n    nodes.sort((a, b) => a.stable.start - b.stable.start)\n  }\n  const pins: GenePin[] = []\n  for (const gene of genes) {\n    const backbone = byRefName.get(gene.refName)\n    if (!backbone) {\n      continue\n    }\n    const parts: string[] = []\n    let at: NodeSegment | undefined\n    let atDistance = Infinity\n    let covered = 0\n    const mid = (gene.start + gene.end) / 2\n    const { nodes, reach } = backbone\n    for (\n      let i = firstNodeAtOrAfter(nodes, gene.start - reach);\n      i < nodes.length && nodes[i]!.stable.start < gene.end;\n      i++\n    ) {\n      const node = nodes[i]!\n      const nodeStart = node.stable.start\n      const nodeEnd = nodeStart + node.length\n      if (nodeEnd <= gene.start) {\n        continue\n      }\n      const line = positions[node.id]!\n      covered += Math.min(nodeEnd, gene.end) - Math.max(nodeStart, gene.start)\n      for (const exon of gene.exons) {\n        const a = Math.max(exon.start, nodeStart)\n        const b = Math.min(exon.end, nodeEnd)\n        if (b <= a) {\n          continue\n        }\n        const stretch = polylineSlice(\n          line,\n          (a - nodeStart) / node.length,\n          (b - nodeStart) / node.length,\n        )\n        if (stretch.length === 1) {\n          stretch.push({ ...stretch[0]! })\n        }\n        parts.push(svgPath(stretch))\n      }\n      const pinBp = Math.min(Math.max(mid, nodeStart), nodeEnd)\n      const distance = Math.abs(pinBp - mid)\n      if (distance < atDistance) {\n        atDistance = distance\n        const [p] = polylineSlice(\n          line,\n          (pinBp - nodeStart) / node.length,\n          (pinBp - nodeStart) / node.length,\n        )\n        at = p\n      }\n    }\n    if (at) {\n      pins.push({\n        gene,\n        exons: parts.join(''),\n        at,\n        covered: covered / (gene.end - gene.start),\n      })\n    }\n  }\n  return pins\n}\n", "import { isBackbone } from '../anchoredNodes'\nimport { pathOrigin } from '../pathAnchoring'\n\nimport type { Graph, GraphPath, PathOrigin, PathVisit } from '../types'\n\n// A cut reaches past its window by the track's context, which is what lets\n// walk rows see where a walk ends. A tube map is a picture of the window, so\n// it draws each walk only from its first reference node overlapping the\n// window to its last, and the nodes and links those stretches use.\n//\n// A graph with no reference node in the window, or none at all, is returned\n// as it is: there is nothing to trim it to.\nexport function trimToWindow(\n  graph: Graph,\n  window: { start: number; end: number },\n): Graph {\n  const inWindow = new Set(\n    graph.nodes\n      .filter(\n        n =>\n          isBackbone(n) &&\n          n.stable.start < window.end &&\n          n.stable.start + n.length > window.start,\n      )\n      .map(n => n.id),\n  )\n  const paths = graph.paths ?? []\n  if (inWindow.size === 0 || paths.length === 0) {\n    return graph\n  }\n  const lengthOf = new Map(graph.nodes.map(n => [n.id, n.length]))\n\n  // each walk's kept stretch, as indexes into its steps; none when it never\n  // meets the window's reference\n  const spans = paths.map(path => {\n    let first = -1\n    let last = -1\n    path.nodeIds.forEach((id, i) => {\n      if (inWindow.has(id)) {\n        if (first < 0) {\n          first = i\n        }\n        last = i\n      }\n    })\n    return first < 0 ? undefined : { first, last }\n  })\n  if (\n    spans.every(\n      (span, i) =>\n        span?.first === 0 && span.last === paths[i]!.nodeIds.length - 1,\n    )\n  ) {\n    return graph\n  }\n\n  const kept = new Set<string>()\n  const trimmed: GraphPath[] = []\n  const droppedBp = new Map<string, number>()\n  paths.forEach((path, i) => {\n    const span = spans[i]\n    if (span) {\n      const nodeIds = path.nodeIds.slice(span.first, span.last + 1)\n      for (const id of nodeIds) {\n        kept.add(id)\n      }\n      trimmed.push({ ...path, nodeIds })\n      droppedBp.set(\n        path.name,\n        path.nodeIds\n          .slice(0, span.first)\n          .reduce((sum, id) => sum + (lengthOf.get(id) ?? 0), 0),\n      )\n    }\n  })\n\n  return {\n    ...graph,\n    nodes: graph.nodes.filter(n => kept.has(n.id)),\n    edges: graph.edges.filter(e => kept.has(e.from) && kept.has(e.to)),\n    paths: trimmed,\n    pathVisits:\n      graph.pathVisits &&\n      trimVisits(\n        graph.pathVisits,\n        paths,\n        spans,\n        new Map(graph.nodes.map(n => [n.id, n.name])),\n      ),\n    anchorPaths:\n      graph.anchorPaths && shiftOrigins(graph.anchorPaths, paths, droppedBp),\n  }\n}\n\n// Visits are keyed by segment name and listed in walk order, and a walk in\n// several pieces lists its pieces in the order the paths are, so replaying\n// every path's steps consumes the visits one for one; a visit is kept when its\n// step lies in the kept stretch.\nfunction trimVisits(\n  visits: Map<string, PathVisit[]>,\n  paths: GraphPath[],\n  spans: ({ first: number; last: number } | undefined)[],\n  nameOf: Map<string, string>,\n) {\n  const cursor = new Map<string, number>()\n  const out = new Map<string, PathVisit[]>()\n  paths.forEach((path, p) => {\n    const origin = pathOrigin(path.name).name\n    const span = spans[p]\n    path.nodeIds.forEach((id, i) => {\n      const segment = nameOf.get(id) ?? id\n      const list = visits.get(segment)\n      if (!list) {\n        return\n      }\n      const key = `${origin}\\t${segment}`\n      let at = cursor.get(key) ?? 0\n      while (at < list.length && list[at]!.path !== origin) {\n        at++\n      }\n      const visit = list[at]\n      cursor.set(key, at + 1)\n      if (visit && span && i >= span.first && i <= span.last) {\n        const keptVisits = out.get(segment)\n        if (keptVisits) {\n          keptVisits.push(visit)\n        } else {\n          out.set(segment, [visit])\n        }\n      }\n    })\n  })\n  return out\n}\n\n// A walk whose front was trimmed starts that much further along its sequence\nfunction shiftOrigins(\n  origins: PathOrigin[],\n  paths: GraphPath[],\n  droppedBp: Map<string, number>,\n) {\n  const pieces = new Map<string, number>()\n  for (const path of paths) {\n    const origin = pathOrigin(path.name).name\n    pieces.set(origin, (pieces.get(origin) ?? 0) + 1)\n  }\n  return origins.map(o => {\n    const path = paths.find(p => pathOrigin(p.name).name === o.name)\n    const dropped = path ? droppedBp.get(path.name) : undefined\n    return dropped && pieces.get(o.name) === 1\n      ? { ...o, start: o.start + dropped }\n      : o\n  })\n}\n", "import { isBackbone } from '../anchoredNodes'\nimport { visitStrands } from '../layout/tubeMapLayout'\nimport { pathOrigin } from '../pathAnchoring'\nimport { canonicalStrand } from './reads'\n\nimport type { AnchoredNode } from '../anchoredNodes'\nimport type {\n  Graph,\n  GraphEdge,\n  GraphNode,\n  GraphPath,\n  PathVisit,\n} from '../types'\n\n// A tube map of a human window is mostly SNP bubbles: MICB's 22 kb cut draws\n// 475 columns for 238 bubbles, one of them 50 bp or more. This folds every\n// variant under `sigma` into the reference, as svSTM does (van den Brandt et\n// al., EuroVis 2025), so the reference between two structural variants is one\n// node and each walk keeps what it carries there as deviations at their bp.\n//\n// Cut from each walk's own runs over the reference, not from the bubbles:\n// derived bubbles are chain level, so a kept superbubble keeps every SNP inside\n// it raw, and a one-node inversion never forms one.\n\ntype Strand = '+' | '-'\n\n// A variant a walk carries inside a merged node: it leaves the reference at\n// `start`, rejoins it at `end`, and carries `bp` of its own in between\nexport interface Deviation {\n  start: number\n  end: number\n  bp: number\n  inverted?: true\n}\n\nexport type CutCause =\n  | 'variant'\n  | 'backward'\n  | 'inversion'\n  | 'walk-end'\n  | 'overlap'\n  | 'reference-gap'\n\nexport interface Coarsened {\n  graph: Graph\n  // coarse node id to the original node ids it stands for\n  members: Map<string, string[]>\n  // original node id to the coarse node that draws it\n  coarseOf: Map<string, string>\n  // by path name, the variants folded into the merged nodes it visits\n  deviations: Map<string, Deviation[]>\n  cuts: Map<number, CutCause>\n}\n\ninterface Step {\n  node: GraphNode\n  strand: Strand\n}\n\n// A stretch of reference a walk reads contiguously, in reference order\n// whichever way it reads it\ninterface Run {\n  start: number\n  end: number\n  inverted: boolean\n}\n\ninterface Gap {\n  a: number\n  b: number\n  detour: Step[]\n  bp: number\n}\n\n// A walk as runs over the reference and the detours between them. A detour\n// before the first run or after the last has no reference on that side.\ninterface Walk {\n  path: GraphPath\n  runs: Run[]\n  // gaps[i] lies between runs[i - 1] and runs[i]; gaps[runs.length] trails\n  gaps: Gap[]\n}\n\nfunction readWalk(\n  path: GraphPath,\n  nodeById: Map<string, GraphNode>,\n  strands: Map<string, Strand[]>,\n): Walk {\n  const visitName = pathOrigin(path.name).name\n  const seen = new Map<string, number>()\n  const runs: Run[] = []\n  const open = (): Gap => ({ a: -Infinity, b: Infinity, detour: [], bp: 0 })\n  const gaps: Gap[] = [open()]\n  for (const id of path.nodeIds) {\n    const node = nodeById.get(id)\n    if (!node) {\n      continue\n    }\n    const k = seen.get(node.name) ?? 0\n    seen.set(node.name, k + 1)\n    const strand =\n      strands.get(`${visitName}\\t${node.name}`)?.[k] ?? canonicalStrand(node)\n    const gap = gaps.at(-1)!\n    const last = runs.at(-1)\n    if (isBackbone(node)) {\n      const start = node.stable.start\n      const end = start + node.length\n      const inverted = strand !== (node.stable.strand ?? '+')\n      const joins = last !== undefined && gap.detour.length === 0\n      if (joins && !last.inverted && !inverted && last.end === start) {\n        last.end = end\n      } else if (joins && last.inverted && inverted && last.start === end) {\n        last.start = start\n      } else {\n        runs.push({ start, end, inverted })\n        gaps.push(open())\n      }\n    } else {\n      gap.detour.push({ node, strand })\n      gap.bp += node.length\n    }\n  }\n  runs.forEach((run, i) => {\n    gaps[i]!.b = run.start\n    gaps[i + 1]!.a = run.end\n  })\n  return { path, runs, gaps }\n}\n\nfunction isSmall(gap: Gap, sigma: number) {\n  return (\n    Number.isFinite(gap.a) &&\n    Number.isFinite(gap.b) &&\n    gap.b >= gap.a &&\n    Math.max(gap.b - gap.a, gap.bp) < sigma\n  )\n}\n\nfunction strictlyInside(cuts: readonly number[], a: number, b: number) {\n  let lo = 0\n  let hi = cuts.length\n  while (lo < hi) {\n    const mid = (lo + hi) >> 1\n    if (cuts[mid]! <= a) {\n      lo = mid + 1\n    } else {\n      hi = mid\n    }\n  }\n  return lo < cuts.length && cuts[lo]! < b\n}\n\n// Both sides of a hole in the reference, which a walk that seems to step over\n// it has not stepped over any reference\nfunction referenceGaps(backbone: readonly AnchoredNode[]) {\n  const cuts = new Map<number, CutCause>()\n  for (let i = 1; i < backbone.length; i++) {\n    const prev = backbone[i - 1]!\n    const node = backbone[i]!\n    const end = prev.stable.start + prev.length\n    if (end !== node.stable.start) {\n      cuts.set(end, 'reference-gap')\n      cuts.set(node.stable.start, 'reference-gap')\n    }\n  }\n  return cuts\n}\n\n// Where the reference is cut. A small variant that straddles another walk's cut\n// would skip a whole merged node, so it is cut too, until nothing changes.\nfunction findCuts(\n  walks: readonly Walk[],\n  sigma: number,\n  cuts: Map<number, CutCause>,\n) {\n  const cut = (bp: number, cause: CutCause) => {\n    if (Number.isFinite(bp) && !cuts.has(bp)) {\n      cuts.set(bp, cause)\n    }\n  }\n  for (const { runs, gaps } of walks) {\n    const first = runs[0]\n    const last = runs.at(-1)\n    if (first && last) {\n      cut(first.start, 'walk-end')\n      cut(last.end, 'walk-end')\n    }\n    for (const run of runs) {\n      if (run.inverted && run.end - run.start >= sigma) {\n        cut(run.start, 'inversion')\n        cut(run.end, 'inversion')\n      }\n    }\n    for (const gap of gaps) {\n      if (gap.b < gap.a) {\n        cut(gap.a, 'backward')\n        cut(gap.b, 'backward')\n      } else if (!isSmall(gap, sigma)) {\n        cut(gap.a, 'variant')\n        cut(gap.b, 'variant')\n      }\n    }\n  }\n  for (let changed = true; changed;) {\n    changed = false\n    const sorted = [...cuts.keys()].sort((x, y) => x - y)\n    const spans = walks.flatMap(({ runs, gaps }) => [\n      ...gaps.filter(g => isSmall(g, sigma)).map(g => [g.a, g.b] as const),\n      ...runs\n        .filter(r => r.inverted && r.end - r.start < sigma)\n        .map(r => [r.start, r.end] as const),\n    ])\n    for (const [a, b] of spans) {\n      if (strictlyInside(sorted, a, b)) {\n        changed ||= !cuts.has(a) || !cuts.has(b)\n        cut(a, 'overlap')\n        cut(b, 'overlap')\n      }\n    }\n  }\n  return cuts\n}\n\ninterface Merged {\n  node: GraphNode\n  members: AnchoredNode[]\n}\n\nfunction mergeReference(\n  backbone: readonly AnchoredNode[],\n  cuts: Map<number, CutCause>,\n) {\n  const merged: Merged[] = []\n  let group: AnchoredNode[] = []\n  const close = () => {\n    const first = group[0]\n    const last = group.at(-1)\n    if (first && last) {\n      const bp0 = first.stable.start\n      const bp1 = last.stable.start + last.length\n      const name = `${bp0}-${bp1}`\n      merged.push({\n        node: {\n          id: `${name}+`,\n          name,\n          length: bp1 - bp0,\n          depth: 0,\n          stable: {\n            refName: first.stable.refName,\n            start: bp0,\n            rank: 0,\n            strand: '+',\n          },\n        },\n        members: group,\n      })\n    }\n    group = []\n  }\n  for (const node of backbone) {\n    if (cuts.has(node.stable.start)) {\n      close()\n    }\n    group.push(node)\n  }\n  close()\n  return merged\n}\n\nexport function coarsenTubeMap(\n  graph: Graph,\n  sigma: number,\n): Coarsened | undefined {\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort((a, b) => a.stable.start - b.stable.start)\n  const paths = graph.paths ?? []\n  if (backbone.length === 0 || paths.length === 0) {\n    return undefined\n  }\n  const nodeById = new Map(graph.nodes.map(n => [n.id, n]))\n  const strands = visitStrands(graph)\n  const walks = paths.map(p => readWalk(p, nodeById, strands))\n  const cuts = findCuts(walks, sigma, referenceGaps(backbone))\n  const sortedCuts = [...cuts.keys()].sort((x, y) => x - y)\n  const merged = mergeReference(backbone, cuts)\n  const starts = merged.map(m => m.node.stable!.start)\n  const mergedAt = (bp: number) => {\n    let lo = 0\n    let hi = starts.length - 1\n    while (lo < hi) {\n      const mid = (lo + hi + 1) >> 1\n      if (starts[mid]! <= bp) {\n        lo = mid\n      } else {\n        hi = mid - 1\n      }\n    }\n    return lo\n  }\n\n  const members = new Map<string, string[]>()\n  const coarseOf = new Map<string, string>()\n  for (const m of merged) {\n    members.set(\n      m.node.id,\n      m.members.map(n => n.id),\n    )\n    for (const n of m.members) {\n      coarseOf.set(n.id, m.node.id)\n    }\n  }\n\n  // One node per distinct detour a structural gap takes, shared by the walks\n  // that take the same one\n  const routes = new Map<string, GraphNode>()\n  const routeFor = (gap: Gap) => {\n    const key = `${gap.a}\\t${gap.b}\\t${gap.detour.map(s => s.node.id + s.strand).join(',')}`\n    let node = routes.get(key)\n    if (!node) {\n      const name = `r${routes.size}`\n      node = {\n        id: `${name}+`,\n        name,\n        length: gap.bp,\n        depth: 0,\n        stable: {\n          refName: backbone[0]!.stable.refName,\n          start: Number.isFinite(gap.a) ? gap.a : gap.b,\n          rank: 1,\n          strand: '+',\n        },\n      }\n      routes.set(key, node)\n      members.set(\n        node.id,\n        gap.detour.map(s => s.node.id),\n      )\n      for (const s of gap.detour) {\n        if (!coarseOf.has(s.node.id)) {\n          coarseOf.set(s.node.id, node.id)\n        }\n      }\n    }\n    return node\n  }\n\n  const deviations = new Map<string, Deviation[]>()\n  const coarsePaths: GraphPath[] = []\n  const pathVisits = new Map<string, PathVisit[]>()\n  const edges = new Map<string, GraphEdge>()\n  const depth = new Map<string, number>()\n\n  for (const { path, runs, gaps } of walks) {\n    const steps: { node: GraphNode; strand: Strand }[] = []\n    const devs: Deviation[] = []\n    // a structural gap ends the stretch a merged node may be continued over\n    let continuing = false\n    const append = (node: GraphNode, strand: Strand) => {\n      const last = steps.at(-1)\n      if (!(continuing && last?.node === node && last.strand === strand)) {\n        steps.push({ node, strand })\n      }\n      continuing = true\n    }\n    const structural = (gap: Gap) => {\n      continuing = false\n      if (gap.detour.length > 0) {\n        append(routeFor(gap), '+')\n        continuing = false\n      }\n    }\n    const fold = (gap: Gap) => {\n      if (gap.bp > 0 || gap.b > gap.a) {\n        devs.push({ start: gap.a, end: gap.b, bp: gap.bp })\n      }\n      const home = merged[mergedAt(gap.b > gap.a ? gap.a : gap.a - 1)]!\n      for (const s of gap.detour) {\n        if (!coarseOf.has(s.node.id)) {\n          coarseOf.set(s.node.id, home.node.id)\n          members.get(home.node.id)!.push(s.node.id)\n        }\n      }\n    }\n    runs.forEach((run, i) => {\n      const gap = gaps[i]!\n      if (isSmall(gap, sigma) && !strictlyInside(sortedCuts, gap.a, gap.b)) {\n        fold(gap)\n      } else {\n        structural(gap)\n      }\n      const i0 = mergedAt(run.start)\n      const i1 = mergedAt(run.end - 1)\n      const small = run.end - run.start < sigma\n      if (run.inverted && !small) {\n        continuing = false\n        for (let j = i1; j >= i0; j--) {\n          append(merged[j]!.node, '-')\n        }\n        continuing = false\n      } else {\n        if (run.inverted) {\n          devs.push({\n            start: run.start,\n            end: run.end,\n            bp: run.end - run.start,\n            inverted: true,\n          })\n        }\n        for (let j = i0; j <= i1; j++) {\n          append(merged[j]!.node, '+')\n        }\n      }\n    })\n    structural(gaps.at(-1)!)\n\n    const visitName = pathOrigin(path.name).name\n    let pos = 0\n    steps.forEach(({ node, strand }, i) => {\n      depth.set(node.id, (depth.get(node.id) ?? 0) + 1)\n      const visits = pathVisits.get(node.name) ?? []\n      visits.push({\n        path: visitName,\n        sample: path.sample ?? visitName,\n        start: pos,\n        strand,\n      })\n      pathVisits.set(node.name, visits)\n      pos += node.length\n      const next = steps[i + 1]\n      if (next) {\n        const key = `${node.id}${strand}\\t${next.node.id}${next.strand}`\n        const edge = edges.get(key)\n        if (edge) {\n          edge.pathIds!.push(path.name)\n        } else {\n          edges.set(key, {\n            from: node.id,\n            to: next.node.id,\n            fromStrand: strand,\n            toStrand: next.strand,\n            pathIds: [path.name],\n          })\n        }\n      }\n    })\n    coarsePaths.push({ ...path, nodeIds: steps.map(s => s.node.id) })\n    deviations.set(path.name, devs)\n  }\n\n  const nodes = [...merged.map(m => m.node), ...routes.values()]\n    .filter(n => depth.has(n.id))\n    .map(n => ({ ...n, depth: depth.get(n.id)! }))\n  return {\n    graph: {\n      ...graph,\n      nodes,\n      edges: [...edges.values()],\n      paths: coarsePaths,\n      pathVisits,\n      reads: undefined,\n    },\n    members,\n    coarseOf,\n    deviations,\n    cuts,\n  }\n}\n", "import type { TubeMapColumn } from '../layout/tubeMapLayout'\n\n// Tube x to screen x under the reference axis. A column covers the screen span\n// of the reference bp its backbone node covers, which puts the tubes under the\n// linear view's other tracks. But the tube map changes lanes BETWEEN columns,\n// and adjacent reference nodes abut in bp, so the curves would have no width\n// at all. At each boundary the gap the tube map drew (its curves, and any\n// columns of inserted sequence, which cover no reference) gets its tube px\n// back, up to MAX_GAP_PX, where there is room: first from reference no\n// column covers, then from up to half of each neighbouring column. Zoomed in that is a\n// few px off a wide node; zoomed out the columns are thin, the gap gets what\n// they can spare and the curves steepen.\n//\n// Piecewise linear, so a curve's bezier, which lies inside one gap, maps\n// exactly by mapping its control points.\n\nexport interface Knot {\n  tx: number\n  sx: number\n}\n\n// The most screen a boundary claims. The tube map spaces its columns to keep\n// the lane changes shallow, which with many haplotypes is hundreds of px a\n// gap; on the reference axis the curves steepen instead.\nconst MAX_GAP_PX = 24\n\nconst isReal = (c: TubeMapColumn) => c.bp1 > c.bp0\n\nexport function referenceKnots(\n  columns: readonly TubeMapColumn[],\n  bpToScreen: (bp: number) => number,\n): Knot[] {\n  const real = columns.filter(isReal)\n  if (real.length === 0) {\n    const first = columns[0]\n    return first ? [{ tx: first.x0, sx: bpToScreen(first.bp0) }] : []\n  }\n  const screen = real.map(c => ({\n    c,\n    s0: bpToScreen(c.bp0),\n    s1: bpToScreen(c.bp1),\n    trimLeft: 0,\n    trimRight: 0,\n  }))\n  for (let i = 0; i + 1 < screen.length; i++) {\n    const left = screen[i]!\n    const right = screen[i + 1]!\n    const demand = Math.min(right.c.x0 - left.c.x1, MAX_GAP_PX)\n    const short = demand - (right.s0 - left.s1)\n    if (short > 0) {\n      const capLeft = (left.s1 - left.s0) / 2\n      const capRight = (right.s1 - right.s0) / 2\n      let fromLeft = Math.min(short / 2, capLeft)\n      const fromRight = Math.min(short - fromLeft, capRight)\n      fromLeft = Math.min(short - fromRight, capLeft)\n      left.trimRight = fromLeft\n      right.trimLeft = fromRight\n    }\n  }\n  const knots: Knot[] = []\n  for (const { c, s0, s1, trimLeft, trimRight } of screen) {\n    knots.push(\n      { tx: c.x0, sx: s0 + trimLeft },\n      { tx: c.x1, sx: s1 - trimRight },\n    )\n  }\n  return knots\n}\n\n// Beyond the first and last knot the drawing continues at one screen px per\n// tube px, which is where the track stubs past the end nodes go.\nexport function warpX(knots: readonly Knot[], tx: number) {\n  const n = knots.length\n  if (n === 0) {\n    return tx\n  }\n  const first = knots[0]!\n  const last = knots[n - 1]!\n  if (tx <= first.tx) {\n    return first.sx + (tx - first.tx)\n  }\n  if (tx >= last.tx) {\n    return last.sx + (tx - last.tx)\n  }\n  let lo = 0\n  let hi = n - 1\n  while (hi - lo > 1) {\n    const mid = (lo + hi) >> 1\n    if (knots[mid]!.tx <= tx) {\n      lo = mid\n    } else {\n      hi = mid\n    }\n  }\n  const a = knots[lo]!\n  const b = knots[hi]!\n  const span = b.tx - a.tx\n  return span > 0 ? a.sx + ((tx - a.tx) / span) * (b.sx - a.sx) : a.sx\n}\n", "import { referenceKnots, warpX } from './warp'\n\nimport type { TubeMapDrawing } from '../layout/tubeMapLayout'\n\nexport interface TubeMapView {\n  scaleX: number\n  translateX: number\n  scaleY: number\n  translateY: number\n  // the pane's height less its fit padding\n  usableHeight: number\n}\n\n// Tube coordinates to screen px\nexport interface TubeMapTransform {\n  x: (tx: number) => number\n  y: (ty: number) => number\n  // screen px per tube px in y, which thins the node outlines of a squeezed\n  // stack along with its tubes\n  yScale: number\n}\n\nconst MIN_TUBE_Y_SCALE = 0.05\n\n// How far a node's box reaches past its tubes (tubemap-core's nodeOutlinePath)\nconst NODE_BOX_PAD = 9\n\n// On the reference axis y is px and a linear view has no vertical pan, so a\n// stack of tubes taller than the track squeezes to fit it; dragging the track\n// taller gives the tubes back their width.\nfunction squeeze(drawing: TubeMapDrawing, usableHeight: number) {\n  const { minY, maxY } = drawing.layout.bounds\n  const h = maxY - minY\n  return drawing.columns && h > 0\n    ? Math.max(MIN_TUBE_Y_SCALE, Math.min(1, usableHeight / h))\n    : 1\n}\n\n// The tube map's own axis is the layout's x; the reference axis warps each\n// column onto the bp it covers (warp.ts).\nexport function tubeMapFrame(\n  drawing: TubeMapDrawing,\n  view: TubeMapView,\n): TubeMapTransform {\n  const { scaleX, translateX, translateY } = view\n  const yScale = view.scaleY * squeeze(drawing, view.usableHeight)\n  const y = (ty: number) => (ty - drawing.yOffset) * yScale + translateY\n  const { columns } = drawing\n  if (columns) {\n    const knots = referenceKnots(columns, bp => bp * scaleX + translateX)\n    return { x: tx => warpX(knots, tx), y, yScale }\n  }\n  return { x: tx => tx * scaleX + translateX, y, yScale }\n}\n\n// The node whose box is under a screen point. The canvas's hit test measures\n// from a centreline and a stroke width, and a tube map box is as tall as the\n// tubes through it.\nexport function tubeMapNodeAt(\n  drawing: TubeMapDrawing,\n  { x, y }: TubeMapTransform,\n  sx: number,\n  sy: number,\n): string | null {\n  let hit: string | null = null\n  drawing.layout.nodes.forEach(node => {\n    if (\n      node.order >= 0 &&\n      x(node.x - NODE_BOX_PAD) <= sx &&\n      sx <= x(node.x + node.pixelWidth + NODE_BOX_PAD) &&\n      y(node.y - NODE_BOX_PAD) <= sy &&\n      sy <= y(node.y + node.contentHeight + NODE_BOX_PAD)\n    ) {\n      hit = node.name\n    }\n  })\n  return hit\n}\n", "import { panSNContig } from './pansn'\nimport { pathOrigin } from './pathAnchoring'\nimport { encodedColor, resolveEncoding } from './walkEncoding'\n\nimport type { ReferenceRamp } from './renderer/GeometryBuilder'\nimport type { Graph } from './types'\nimport type { WalkEncoding, WalkLayer } from './walkEncoding'\n\n// One walk lifted out of the drawing: the nodes it visits and the links it\n// takes, how far along the walk each node is, and what it carries through the\n// window against the reference walk.\nexport interface WalkHighlight {\n  name: string\n  // whether this is the graph's reference walk, which keeps the node colours\n  reference: boolean\n  nodeIds: Set<string>\n  edgeIndexes: Set<number>\n  // each node's first visit, as the fraction of the walk's bp before its\n  // midpoint: 0 at the walk's start, 1 at its end\n  progress: Map<string, number>\n  steps: number\n  bp: number\n  referenceBp?: number\n  // where the walk's stretch of the cut sits on its own contig, from its W or\n  // P record: its start where it begins and its end where it ends\n  range?: { contig: string; start: number; end: number }\n}\n\nexport interface LiftedWalk extends WalkHighlight {\n  encoding: WalkEncoding\n  // the lane colour at each node the walk visits\n  colors: Map<string, number>\n  // the nodes it crosses the other way from the reference walk, and their\n  // bp; empty for the reference\n  reversed: Set<string>\n  reversedBp: number\n}\n\n// The walks lifted together, reference first and the rest in the order they\n// were picked, each in its lane of the nodes it visits. A node or link on any\n// of them keeps its ink.\nexport interface WalkLift {\n  walks: LiftedWalk[]\n  // the reference interval a lane coloured by reference position spans\n  referenceDomain?: { start: number; end: number }\n  nodeIds: Set<string>\n  edgeIndexes: Set<number>\n  names: Set<string>\n}\n\nfunction referenceOf(graph: Graph) {\n  // `referencePath` is the anchor name, which pathOrigin has stripped of the\n  // range suffix odgi leaves on a P record's name\n  return graph.referencePath\n    ? graph.paths?.find(p => pathOrigin(p.name).name === graph.referencePath)\n    : undefined\n}\n\nexport function walkHighlight(\n  graph: Graph,\n  name: string,\n): WalkHighlight | undefined {\n  const path = graph.paths?.find(p => p.name === name)\n  if (!path) {\n    return undefined\n  }\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const edgeAt = new Map<string, number>()\n  graph.edges.forEach((e, i) => {\n    edgeAt.set(`${e.from}>${e.to}`, i)\n  })\n  const edgeIndexes = new Set<number>()\n  for (let i = 1; i < path.nodeIds.length; i++) {\n    const a = path.nodeIds[i - 1]!\n    const b = path.nodeIds[i]!\n    const index = edgeAt.get(`${a}>${b}`) ?? edgeAt.get(`${b}>${a}`)\n    if (index !== undefined) {\n      edgeIndexes.add(index)\n    }\n  }\n  const lengthOf = (id: string) => byId.get(id)?.length ?? 0\n  const bp = path.nodeIds.reduce((sum, id) => sum + lengthOf(id), 0)\n  const progress = new Map<string, number>()\n  let before = 0\n  for (const id of path.nodeIds) {\n    const length = lengthOf(id)\n    if (!progress.has(id)) {\n      progress.set(id, bp > 0 ? (before + length / 2) / bp : 0)\n    }\n    before += length\n  }\n  const reference = referenceOf(graph)\n  const originName = pathOrigin(name).name\n  const origin =\n    graph.anchorPaths?.find(a => a.name === originName && a.length === bp) ??\n    graph.anchorPaths?.find(a => a.name === originName)\n  return {\n    name,\n    reference: reference === path,\n    range: origin\n      ? {\n          contig: path.contig ?? panSNContig(origin.name),\n          start: origin.start,\n          end: origin.start + origin.length,\n        }\n      : undefined,\n    nodeIds: new Set(path.nodeIds),\n    edgeIndexes,\n    progress,\n    steps: path.nodeIds.length,\n    bp,\n    referenceBp:\n      reference && reference !== path\n        ? reference.nodeIds.reduce((sum, id) => sum + lengthOf(id), 0)\n        : undefined,\n  }\n}\n\n// Each node's value for the walk's field, through its scheme\nfunction laneColors(\n  graph: Graph,\n  walk: WalkHighlight,\n  encoding: WalkEncoding,\n  ramp: ReferenceRamp | undefined,\n) {\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const colors = new Map<string, number>()\n  for (const [id, progress] of walk.progress) {\n    const node = byId.get(id)\n    const mid = ramp?.midpoints.get(id)\n    const t =\n      encoding.field === 'progress'\n        ? progress\n        : ramp && mid !== undefined && !(node?.stable && node.stable.rank > 0)\n          ? (mid - ramp.start) / ramp.span\n          : undefined\n    colors.set(id, encodedColor(encoding, t))\n  }\n  return colors\n}\n\n// The nodes a walk reads on the other strand from the reference walk\nfunction reversedNodes(graph: Graph, walk: WalkHighlight) {\n  const reference = referenceOf(graph)\n  const reversed = new Set<string>()\n  let bp = 0\n  if (!reference || walk.reference) {\n    return { reversed, bp }\n  }\n  const walkPath = pathOrigin(walk.name).name\n  const referencePath = pathOrigin(reference.name).name\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  for (const id of walk.progress.keys()) {\n    const node = byId.get(id)\n    const visits = node ? graph.pathVisits?.get(node.name) : undefined\n    const own = visits?.find(v => v.path === walkPath)?.strand\n    const theirs = visits?.find(v => v.path === referencePath)?.strand\n    if (own && theirs && own !== theirs) {\n      reversed.add(id)\n      bp += node!.length\n    }\n  }\n  return { reversed, bp }\n}\n\nexport function walkLift(\n  graph: Graph,\n  layers: readonly WalkLayer[],\n  ramp?: ReferenceRamp,\n): WalkLift | undefined {\n  const seen = new Set<string>()\n  const lifted = layers\n    .filter(layer => !seen.has(layer.walk) && seen.add(layer.walk))\n    .flatMap(layer => {\n      const walk = walkHighlight(graph, layer.walk)\n      return walk ? [{ walk, layer }] : []\n    })\n    .sort((a, b) => Number(b.walk.reference) - Number(a.walk.reference))\n  if (lifted.length === 0) {\n    return undefined\n  }\n  let picked = 0\n  const walks = lifted.map(({ walk, layer }) => {\n    const encoding = resolveEncoding(\n      layer,\n      walk.reference,\n      walk.reference ? 0 : picked++,\n      lifted.length === 1,\n    )\n    const { reversed, bp } = reversedNodes(graph, walk)\n    return {\n      ...walk,\n      encoding,\n      colors: laneColors(graph, walk, encoding, ramp),\n      reversed,\n      reversedBp: bp,\n    }\n  })\n  return {\n    walks,\n    referenceDomain: ramp\n      ? { start: ramp.start, end: ramp.start + ramp.span }\n      : undefined,\n    nodeIds: new Set(walks.flatMap(w => [...w.nodeIds])),\n    edgeIndexes: new Set(walks.flatMap(w => [...w.edgeIndexes])),\n    names: new Set(walks.map(w => w.name)),\n  }\n}\n", "import {\n  backboneNodes,\n  backboneSpan,\n} from '@jbrowse/bandage-core/anchoredNodes'\nimport { BUBBLE_SPREAD_VALUES } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { bubbleHalos } from '@jbrowse/bandage-core/bubbles/bubbleHalos'\nimport { sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { bubblesFromGraph } from '@jbrowse/bandage-core/bubbles/bubblesFromGraph'\nimport {\n  BUBBLE_KIND_NAMES,\n  bubbleSegmentIds,\n  classifyBubble,\n} from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { bubbleSubgraph } from '@jbrowse/bandage-core/bubbles/popBubble'\nimport {\n  COLOR_SCHEMES,\n  COLOR_SCHEME_VALUES,\n  resolveColorScheme,\n} from '@jbrowse/bandage-core/colorSchemes'\nimport { deletionEdges } from '@jbrowse/bandage-core/deletionEdges'\nimport { genePins } from '@jbrowse/bandage-core/genes/genePins'\nimport { rowLabelBox } from '@jbrowse/bandage-core/graphLabels'\nimport {\n  LEGEND_INSET_PX,\n  layoutLabels,\n} from '@jbrowse/bandage-core/labelLayout'\nimport { ROW_HEIGHT_PX } from '@jbrowse/bandage-core/layout/rowSpacing'\nimport { trimToWindow } from '@jbrowse/bandage-core/layout/trimToWindow'\nimport { walkRowsExtent } from '@jbrowse/bandage-core/layout/walkRowLayout'\nimport { walkRows } from '@jbrowse/bandage-core/layout/walkRows'\nimport {\n  LAYOUT_MODES,\n  LAYOUT_MODE_VALUES,\n  layoutModeByValue,\n  modeUsesLayoutEngine,\n} from '@jbrowse/bandage-core/layoutModes'\nimport { NODE_WIDTH_VALUES, nodeInk } from '@jbrowse/bandage-core/nodeWidths'\nimport {\n  anchorFromPaths,\n  chooseReferencePath,\n} from '@jbrowse/bandage-core/pathAnchoring'\nimport { pathColorsLegible, pathLegend } from '@jbrowse/bandage-core/pathColors'\nimport {\n  FIT_PADDING,\n  clampZoom,\n  drawingBounds,\n  engineKey,\n  fitTransform,\n  fittedTranslateY,\n  forceLayout,\n  loadGraph,\n} from '@jbrowse/bandage-core/pipeline'\nimport {\n  assemblyWalk,\n  backboneAssembly,\n  featuresOnBackbone,\n  graphBackbone,\n} from '@jbrowse/bandage-core/reference'\nimport {\n  buildNeighbors,\n  nodeReferenceSpan,\n} from '@jbrowse/bandage-core/referenceSpan'\nimport {\n  REFERENCE_STRIP_ZONE_PX,\n  nodeAnchor,\n  referenceStripBlocks,\n  stripBlockAt,\n  stripOverhang,\n} from '@jbrowse/bandage-core/referenceStrip'\nimport {\n  buildGeometry,\n  computeReferenceRamp,\n} from '@jbrowse/bandage-core/renderer/GeometryBuilder'\nimport { referenceBoxes, rulerBoxes } from '@jbrowse/bandage-core/tubeMap/axis'\nimport { coarsenTubeMap } from '@jbrowse/bandage-core/tubeMap/coarsen'\nimport {\n  connectorAt,\n  referenceNodes,\n  tubeMapConnectors,\n} from '@jbrowse/bandage-core/tubeMap/connectors'\nimport { deviationMarks } from '@jbrowse/bandage-core/tubeMap/deviations'\nimport {\n  mismatchOnScreen,\n  mismatchesLegible,\n  tubeMapPicture,\n} from '@jbrowse/bandage-core/tubeMap/draw'\nimport {\n  tubeMapFrame,\n  tubeMapNodeAt,\n} from '@jbrowse/bandage-core/tubeMap/frame'\nimport {\n  GENE_ROW_PX,\n  tubeMapGeneRows,\n  tubeMapGenes,\n} from '@jbrowse/bandage-core/tubeMap/genes'\nimport {\n  axisScaleOf,\n  contains,\n  padded,\n  viewportOf,\n  zoomAbout,\n} from '@jbrowse/bandage-core/viewport'\nimport { WALK_FIELDS, WALK_SCHEMES } from '@jbrowse/bandage-core/walkEncoding'\nimport { walkLift } from '@jbrowse/bandage-core/walkHighlight'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { pushLaunchViewMenuItem } from '@jbrowse/core/ui'\nimport {\n  getContainingTrack,\n  getContainingView,\n  getRpcSessionId,\n  getSession,\n  isSessionModelWithWidgets,\n  statusMessageText,\n} from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { addDisposer, flow, isAlive, types } from '@jbrowse/mobx-state-tree'\nimport { RenderLifecycleMixin } from '@jbrowse/render-core/RenderLifecycleMixin'\nimport { getDpr } from '@jbrowse/render-core/canvas2dUtils'\nimport { autorun, reaction, untracked } from 'mobx'\n\nimport {\n  GENE_ADAPTER_TYPES,\n  geneModelsFrom,\n  pickGeneTrack,\n} from './genes/geneFeatures'\nimport { hostFrame, isLinearHost } from './host'\nimport { lenientMaybeEnum, lenientOptionalEnum } from './lenientEnum'\nimport { namesReads } from '../GetGraphReads'\nimport {\n  REPEAT_ADAPTER_TYPES,\n  pickRepeatTrack,\n  repeatArraysFrom,\n} from './repeats/repeatFeatures'\nimport { withCalls } from './repeats/walkCalls'\nimport {\n  hoverInRegion,\n  nodeForLgvHover,\n  readLgvHover,\n} from '../hoverSync/lgvHover'\nimport {\n  contributingAssemblies,\n  locLabel,\n  nodeOwnLocation,\n  resolveContributors,\n  resolveLocationAssembly,\n} from '../launchFromGraph/contributors'\nimport { graphLaunchMenuItems } from '../launchFromGraph/graphMenuItems'\nimport {\n  highlightInLinearView,\n  launchSyntenyView,\n  paddedLocation,\n  showInLinearView,\n  withReferenceRegion,\n} from '../launchFromGraph/launchFromGraph'\nimport { launchTracks } from '../launchFromGraph/launchTracks'\nimport { linearViewTarget, withRows } from '../launchFromGraph/linearViewTarget'\nimport { launchableSyntenyTracks } from '../launchFromGraph/syntenyTracks'\n\nimport type { LinearHost } from './host'\nimport type { SubgraphCutOptions, SubgraphRegion } from '../GetSubgraph'\nimport type { RepeatArray } from './repeats/repeatFeatures'\nimport type { GafReads } from '../gaf/gafFile'\nimport type { GraphLocation } from '../launchFromGraph/contributors'\nimport type { BubbleSpread } from '@jbrowse/bandage-core/bubbleSpreads'\nimport type { MinigraphBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport type {\n  ColorScheme,\n  ResolvedColorScheme,\n} from '@jbrowse/bandage-core/colorSchemes'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { LayoutModeValue } from '@jbrowse/bandage-core/layoutModes'\nimport type { NodeWidth } from '@jbrowse/bandage-core/nodeWidths'\nimport type { Bounds, EngineRequest } from '@jbrowse/bandage-core/pipeline'\nimport type { AssemblyNames } from '@jbrowse/bandage-core/reference'\nimport type {\n  RenderBatch,\n  Renderer,\n} from '@jbrowse/bandage-core/renderer/types'\nimport type {\n  Graph,\n  GraphNode,\n  LayoutResult,\n} from '@jbrowse/bandage-core/types'\nimport type { AxisScale } from '@jbrowse/bandage-core/util/geometry'\nimport type { NodeInk } from '@jbrowse/bandage-core/util/hitDetection'\nimport type {\n  WalkEncoding,\n  WalkLayer,\n} from '@jbrowse/bandage-core/walkEncoding'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport type { MenuItem } from '@jbrowse/core/ui'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation } from '@jbrowse/core/util/types'\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n// Ceiling on the pane, and what it falls back to before there is a layout to\n// size against. A roughly square drawing (FMMM) hits this and keeps the\n// scrollable pane it has always had.\nconst MAX_CANVAS_HEIGHT = 600\n// Floor, so a window holding only backbone \u2014 one row, no height at all \u2014 still\n// leaves room to hover a node and read its tooltip.\nconst MIN_CANVAS_HEIGHT = 160\n// The facet grid: panels this far apart, each with a title row over a drawing\n// padded this much, at most this many across. A drawing this much wider than\n// it is tall stacks its panels in one column.\nexport const FACET_GAP_PX = 8\nexport const FACET_TITLE_PX = 34\nexport const FACET_PAD_PX = 12\nconst FACET_MAX_COLUMNS = 3\nconst FACET_WIDE = 2.5\nconst MIN_FACET_PANEL_PX = 60\n// The thinnest a fit draws a tube map's tubes\nconst MIN_FIT_TUBE_PX = 5\n\nconst TUBE_MAP_MODES = new Set<string>(['tubemap', 'tubemapref'])\n\n// The sizes a tube map folds variants under. MICB's 22 kb cut draws 475\n// columns whole, 34 under 3 bp and one under 50, where only its structural\n// variants would stand: human windows are mostly SNPs.\nconst TUBE_MAP_FOLDS = [\n  { bp: 0, label: 'None' },\n  { bp: 3, label: 'Under 3 bp' },\n  { bp: 10, label: 'Under 10 bp' },\n  { bp: 50, label: 'Under 50 bp, leaving structural variants' },\n  { bp: 1000, label: 'Under 1 kb' },\n]\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\n// The rGFA index prefix an adapter config names, from either spelling the\n// config schema accepts: the `uri` shorthand or an explicit segments location.\nfunction bubblePrefix(adapterConfig: Record<string, unknown>) {\n  if (typeof adapterConfig.uri === 'string') {\n    return adapterConfig.uri\n  }\n  const segments = adapterConfig.segmentsLocation as\n    { uri?: string } | undefined\n  const uri = segments?.uri\n  return typeof uri === 'string' && uri.endsWith(SEGMENTS_SUFFIX)\n    ? uri.slice(0, -SEGMENTS_SUFFIX.length)\n    : undefined\n}\nconst HOVER_BRIGHTEN = 1.4\nconst SELECT_BRIGHTEN = 1.6\nconst VIEWPORT_DEBOUNCE_MS = 150\nconst VIEWPORT_PANES_BUILT = 1\n\n// What the canvas draws under the tube map, whose ink is all TubeMapOverlay's\nconst EMPTY_BATCH: RenderBatch = {\n  nodeStrokes: [],\n  nodeStrokeRuns: new Map(),\n  arrows: [],\n  arrowRuns: new Map(),\n  edgeCurves: [],\n  edgeCurveRuns: new Map(),\n}\n\n// MobX tracks every observable read while a computed or autorun runs, so\n// passing values here registers them as dependencies without otherwise using\n// them.\nfunction dependOn(..._values: unknown[]) {}\n\n// Hard size cap for the single-mode graph view. Past it the view declines with a\n// \"zoom in\" message rather than switching to a degraded rendering mode \u2014 one mode\n// only, since the large-region case is a linear synteny view, not a graph.\n// (The `adr-027` citation this used to carry was stale: that number was reused\n// for wheel-input semantics after the large-mode ADR was removed in 9d8102f0b5.)\n//\n// This bounds the *fetch*, and it is the only cap that can be applied before one\n// happens. It is a poor proxy for cost, because cost tracks node count, so the\n// number is chosen against the density of the graphs it can actually guard: a\n// region is fetched through `getSubgraph`, and the rGFA cut is what this number\n// was chosen against (the GBZ cut is base-level and has its own `nodeLimit`,\n// which trips long before 5 Mb). Both measured rGFAs are sparse, and at 5 Mb\n// both land at or under the ~2k nodes that redraw in under 10 ms (see agent-docs/GRAPH_SCALE_AND_LOD.md):\n//\n//   HPRC MC GRCh38   ~7,000 bp/segment   whole 4.9 Mb MHC   1,173 nodes\n//   ecoli minigraph   3,078 bp/segment   whole 4.6 Mb genome 2,415 nodes\n//\n// Fetch cost does not scale with the window either: against the hosted HPRC\n// index a 4.9 Mb links query and a 100 kb one both cost ~1.3 s, being dominated\n// by HTTP setup. FMMM is the slowest consumer at this size and stays tolerable,\n// ~0.1-3 s for ~1k nodes depending on layout quality (bandage-layout-js), and it\n// runs off the main thread.\n//\n// A dense graph is what this cannot protect against, because bp per node varies\n// by orders of magnitude between graph types \u2014 a base-level pggb graph runs ~17\n// bp/node, where 5 Mb would be hundreds of thousands. Such a graph has no region\n// query to reach this check with today, and the node budget below is the cap that\n// catches it if one ever does.\nexport const MAX_GRAPH_REGION_BP = 5_000_000\n\n// The cap in a message, in the unit that reads: `5 Mb`, not `5000 kb`.\nexport function formatSpanBp(bp: number) {\n  return bp >= 1_000_000\n    ? `${+(bp / 1_000_000).toFixed(1)} Mb`\n    : `${Math.round(bp / 1000)} kb`\n}\n\n// What the view will actually draw, checked once the graph is parsed and so\n// applying to a whole-file import as much as to a subgraph fetch. Measured on\n// bubble-chain graphs: ~1-2k nodes redraws in under 10 ms, 10k takes ~43 ms of\n// geometry and ~125k canvas draw calls per frame (single-digit fps while\n// panning), and 100k needs 632 ms and 75 MB of vertex buffers. So this is set\n// where the tab stops being usable rather than where it stops being smooth, and\n// it is a view prop rather than a constant so a session can raise it \u2014 the same\n// escape hatch strangepg gives with `-T N`.\nexport const DEFAULT_MAX_GRAPH_NODES = 20_000\n\ntype ViewportOwner = 'fit' | 'user' | 'host'\n\ninterface BuiltViewport {\n  scale: number\n  bounds: Bounds\n  viewportDirty: number\n}\n\nfunction geometryPainted(model: {\n  viewportRebuildPending: boolean\n  viewportDirty: number\n  builtViewport?: BuiltViewport\n  paintedViewport?: BuiltViewport\n}) {\n  return (\n    model.builtViewport !== undefined &&\n    model.paintedViewport === model.builtViewport &&\n    model.builtViewport.viewportDirty === model.viewportDirty &&\n    !model.viewportRebuildPending\n  )\n}\n\n// What the pane shows, in layout units.\nfunction paneViewportOf(model: {\n  translateX: number\n  translateY: number\n  paneWidth: number\n  axisScale: AxisScale\n  canvasHeight: number\n}): Bounds {\n  return viewportOf(model, model.axisScale, model.paneWidth, model.canvasHeight)\n}\n\n// Force layouts already computed for a graph, keyed by the view props the\n// engine reads. Every layout mode is local and costs a millisecond except this\n// one, which is seconds: measured on the committed engine, a 1,201-node bubble\n// chain is 0.6 s proportional, 4.3 s at 'Wide bubbles' and 3.4 s at the highest\n// quality.\n//\n// Worth keeping because a session revisits the same layout. The two drawings\n// answer different questions and the README's own figure is one subgraph in\n// both, so Anchored <-> Force is a round trip a reader makes repeatedly \u2014 and\n// every control in the settings dialog calls `recomputeLayout` on change\n// whether or not the current mode reads what it changed, which made picking a\n// reference path in force mode a multi-second re-run of an identical layout.\n// Both are hits.\n//\n// Entries are the live position objects rather than copies, which a node drag\n// mutates in place (see moveNode), so a layout comes back arranged the way it\n// was left rather than snapping back.\n//\n// Weak on the graph so nothing has to invalidate it: a graph is rebuilt by\n// every load and dropped by `clearGraph`, and its layouts go with it.\nconst forceLayouts = new WeakMap<Graph, Map<string, LayoutResult>>()\n\n// Enough to hold the settings a comparison moves between; past that the oldest\n// goes, since a big graph's positions are megabytes.\nconst FORCE_LAYOUT_CACHE_SIZE = 4\n\nfunction forceLayoutsOf(graph: Graph) {\n  let cache = forceLayouts.get(graph)\n  if (!cache) {\n    cache = new Map()\n    forceLayouts.set(graph, cache)\n  }\n  return cache\n}\n\n// Re-anchoring builds a new Graph, and the force layout of it is the same\n// drawing: `anchorFromPaths` rewrites each node's `stable` and `samples` and\n// touches neither the ids, the lengths, the depths nor the edges, which are all\n// the engine reads. So the layouts follow the graph they were computed for\n// rather than being thrown away with it.\nfunction inheritForceLayouts(from: Graph, to: Graph) {\n  const cache = forceLayouts.get(from)\n  if (cache && from !== to) {\n    forceLayouts.set(to, cache)\n  }\n}\n\nfunction remember(\n  cache: Map<string, LayoutResult>,\n  key: string,\n  result: LayoutResult,\n) {\n  if (cache.size >= FORCE_LAYOUT_CACHE_SIZE) {\n    cache.delete(cache.keys().next().value!)\n  }\n  cache.set(key, result)\n}\n\nexport function GraphPaneMixin() {\n  return types\n    .compose(\n      'GraphPane',\n      RenderLifecycleMixin(),\n      types.model({\n        // FMMM's iteration budget, 0-4, the same scale Bandage's own settings\n        // dialog exposes: 3+1 iterations at 0, 15+10 at 1, 30+20 at 2, 60+40 at\n        // 3, 120+60 at 4 (BandageNG layout/graphlayoutworker.cpp).\n        //\n        // 2 because that is what the engine we vendor ships as its default\n        // (`graphLayoutQuality = IntSetting(2, 0, 4)`, program/settings.cpp).\n        // This was 1 for no recorded reason, i.e. one step BELOW upstream, and a\n        // first sight of any graph is the default: review kept asking whether\n        // the drawing could be iterated more (\"are you sure you can't iterate it\n        // more times for better layout?\") of figures that were simply on a lower\n        // setting than the tool they come from. Cost at the sizes this view\n        // draws is milliseconds, and the header states the layout time so the\n        // difference is visible rather than asserted.\n        layoutQuality: types.optional(types.number, 2),\n        linearLayout: types.optional(types.boolean, false),\n        // unset takes the host's default: force in a view of its own, the\n        // display config's in a track\n        layoutMode: lenientMaybeEnum(LAYOUT_MODE_VALUES),\n        colorScheme: lenientMaybeEnum(COLOR_SCHEME_VALUES),\n        // How far the force layout opens a bubble, which on a variation graph is\n        // the difference between a legible drawing and a rope. See\n        // BUBBLE_SPREADS; no effect on the reference-anchored layouts, which\n        // place a node from its coordinates rather than from a force sim.\n        bubbleSpread: lenientOptionalEnum(BUBBLE_SPREAD_VALUES, 'auto'),\n        // Node thickness by depth, Bandage's own device; see NODE_WIDTHS.\n        nodeWidth: lenientOptionalEnum(NODE_WIDTH_VALUES, 'depth'),\n        // Whether the node layouts draw each bubble as a halo along its nodes\n        // with a label that opens it. Off by default: on a base-level cut\n        // every SNP's halo is a blob.\n        showBubbles: types.optional(types.boolean, false),\n        showDeletionEdges: types.optional(types.boolean, false),\n        // The session's genes drawn onto the backbone: exons along the nodes\n        // that carry them, names pinned at their midpoints. See genes/.\n        showGenes: types.optional(types.boolean, true),\n        // Whether a drawing in its own coordinates inside a linear view gets\n        // the strip of reference segments at their bp. See referenceStrip.ts.\n        showReferenceStrip: types.optional(types.boolean, true),\n        // Variants under this many bp fold into the reference before a tube map\n        // is laid out, each kept as a tick on its walk's tube (coarsen.ts); 0\n        // draws every one\n        tubeMapFold: types.optional(types.number, 0),\n        // Which track the genes come from; empty picks the assembly's\n        // annotation track (pickGeneTrack).\n        geneTrackId: types.optional(types.string, ''),\n        // Which track the walk rows read tandem repeat arrays from; empty\n        // picks a track whose name says repeats (pickRepeatTrack).\n        repeatTrackId: types.optional(types.string, ''),\n        // The array the walk rows measure between and tile by, as\n        // RepeatArray.key; empty measures the whole window untiled.\n        repeatKey: types.optional(types.string, ''),\n        // Samples whose walks the walk rows show, by the name before the\n        // haplotype number; undefined shows every walk the cut holds.\n        walkRowSamples: types.maybe(types.frozen<string[]>()),\n        // Walks lifted out of the drawing, each a layer with a lane of its own\n        // and the rest fading, coloured by the encoding it states or by the\n        // default one. See walkEncoding.ts. Empty lifts none.\n        walkLayers: types.optional(types.frozen<WalkLayer[]>(), []),\n        // Facets, as a grammar of graphics splits a plot: 'walk' draws the\n        // pane once per lifted walk, side by side on the same layout, each\n        // panel with that walk alone. See facetPanels.\n        facet: lenientOptionalEnum<'none' | 'walk'>(['none', 'walk'], 'none'),\n        // Which of a general GFA's paths the anchored layouts put on x. A path\n        // GFA's names are arbitrary and none of them is marked as the\n        // reference, so this is a choice; empty means \"infer\", which is the\n        // assembly a subgraph was cut against, and the first path in the file\n        // for a whole-file import. No effect on an rGFA, whose segments carry\n        // their own coordinates. See pathAnchoring.ts.\n        referencePath: types.optional(types.string, ''),\n        // Whether the toolbar spells out `fetch 12371ms \u00B7 layout 4ms \u00B7 geom 9ms`.\n        // Off by default because it was in the toolbar of every published graph\n        // figure, where a machine's fetch time is noise a reader has to skip\n        // past. The numbers themselves are always on the element as `data-*`\n        // attributes, which is what browser tests assert against, so hiding the\n        // text costs no coverage.\n        showPerf: types.optional(types.boolean, false),\n        contigThickness: types.optional(types.number, 6),\n        connectorThickness: types.optional(types.number, 2),\n        darkMode: types.optional(types.boolean, false),\n        scale: types.optional(types.number, 1),\n        translateX: types.optional(types.number, 0),\n        translateY: types.optional(types.number, 0),\n        drawPaths: types.optional(types.boolean, false),\n        // Ceiling on the drawing pane, in css px, for a session or a figure that\n        // wants a shorter one than the drawing asks for. Unset means the built-in\n        // MAX_CANVAS_HEIGHT, which is what every existing session gets.\n        //\n        // Why this is a knob rather than a smaller default: the pane is as tall\n        // as the drawing's own aspect ratio (see canvasHeight), which is right \u2014\n        // a graph that is twice as tall as it is wide should not be squeezed\n        // into a strip. But one very long node in a cut of short ones makes that\n        // aspect ratio all arc: the HPRC CHM13 figure draws a 142 kb allele\n        // among sub-kb backbone segments, pins the 600 px ceiling and spends\n        // most of it on the loop, with the chain squashed along the bottom edge.\n        // Lowering the ceiling there scales the whole drawing down, which is\n        // exactly the trade that figure wants and the wrong default for a graph\n        // whose height is carrying information.\n        paneHeight: types.maybe(types.number),\n        // Raise to draw a bigger graph than the default budget allows; see\n        // DEFAULT_MAX_GRAPH_NODES for what the numbers cost.\n        maxGraphNodes: types.optional(types.number, DEFAULT_MAX_GRAPH_NODES),\n        // The reference span the reference-position ramp runs over, for a graph\n        // with no region of its own to span it\n        colorDomain: types.maybe(\n          types.frozen<{ start: number; end: number }>(),\n        ),\n        // the linear view a graph of its own is paired with for the hover sync\n        connectedViewId: types.maybe(types.string),\n      }),\n    )\n    .volatile(() => ({\n      graph: undefined as Graph | undefined,\n      // the reference window the graph on screen was cut for, set with it\n      graphRegion: undefined as SubgraphRegion | undefined,\n      // The walk the track's graph lies on for the region's assembly, which\n      // the track's config declares; x starts along it unless the user chose\n      // another. Undefined for an rGFA, whose backbone is fixed, and for a\n      // graph with no region.\n      loadedReferencePath: undefined as string | undefined,\n      layoutResult: undefined as LayoutResult | undefined,\n      // what the legends in the pane's top-right corner measure, so no label\n      // is placed under them\n      legendSize: { width: 0, height: 0 },\n      // The bubble index rows over the cut window, when the source track has\n      // one beside its segments. Undefined for a graph with no index, whose\n      // bubbles are `derivedBubbles` instead.\n      indexBubbles: undefined as MinigraphBubble[] | undefined,\n      // the genes over the cut window, read once per cut from the gene track\n      geneFeatures: undefined as GeneModel[] | undefined,\n      // the tandem repeat arrays over the cut window, from the repeat track\n      repeatArrays: undefined as RepeatArray[] | undefined,\n      // The graphs the open bubble was popped out of, outermost first, each\n      // with what closing back to it restores without a refetch. A stack so a\n      // popped superbubble can be mapped and popped again.\n      popStack: [] as {\n        graph: Graph\n        layoutMode: LayoutModeValue\n        label: string\n        indexBubbles: MinigraphBubble[] | undefined\n      }[],\n\n      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n      error: undefined as unknown,\n      isLoading: false,\n      loadCanceled: false,\n      statusMessage: '',\n      hoveredNode: null as string | null,\n      // the bubble whose label the pointer is on\n      hoveredBubble: null as MinigraphBubble | null,\n      // whether the pointer is over this pane, whose own hit test then says\n      // what it is on\n      pointerInPane: false,\n      hoveredEdge: null as number | null,\n      selectedNode: null as string | null,\n      viewportDirty: 0,\n      // Bumped when the layout's positions are mutated IN PLACE, which only a\n      // node drag does. Separate from `viewportDirty` because that one also\n      // fires on pan and zoom, and the things keyed off this \u2014 the two hit\n      // indexes and the label placement's per-layout caches \u2014 do not depend on\n      // the transform at all. Rebuilding a 12k-edge hit index because the user\n      // panned cost ~14 ms of the first mousemove after every gesture.\n      positionsVersion: 0,\n      // Bumped per upload, so the hover autorun re-states its highlights\n      // against the batch the renderer now holds.\n      geometryVersion: 0,\n      // The zoom and the window the current batch was built for; a pan that\n      // stays inside it needs no rebuild.\n      builtViewport: undefined as BuiltViewport | undefined,\n      // The builtViewport whose batch is on the canvas\n      paintedViewport: undefined as BuiltViewport | undefined,\n      draggingNode: null as string | null,\n      // Dragging the background rather than a node. Lives here beside\n      // draggingNode instead of in a component ref+state pair, so the two\n      // mutually exclusive drag modes are one piece of state read from one place.\n      isPanning: false,\n      // Who places the view. 'fit' refits it to every new layout, 'user' leaves\n      // it where a gesture or a restored session put it, and 'host' takes x\n      // from the linear view the pane sits in. Not derived from\n      // `isDefaultViewport`, which zoomToFit itself invalidates on its first\n      // run \u2014 that made the fit fire once against not-yet-measured dimensions\n      // and then never re-fit.\n      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n      viewportOwner: 'fit' as ViewportOwner,\n      viewportDirtyTimer: undefined as\n        ReturnType<typeof setTimeout> | undefined,\n      // 0 is never a live rAF handle, so it doubles as \"nothing pending\"\n      positionsDirtyFrame: 0,\n      // Performance instrumentation, surfaced in GraphStats for browser tests\n      // to assert against budgets. `fetchMs` is the GetSubgraph RPC round-trip,\n      // `layoutMs` is the Bandage FMMM compute time reported by the\n      // GraphComputeLayout RPC, `geometryMs` is the main-thread buildGeometry\n      // pass and `geometryStrokeCount` the node strokes it produced.\n      lastFetchMs: undefined as number | undefined,\n      // how many of the cut's reads the tube map was handed, of how many\n      readsShown: undefined as { shown: number; total: number } | undefined,\n      lastLayoutMs: undefined as number | undefined,\n      lastGeometryMs: undefined as number | undefined,\n      lastGeometryStrokeCount: undefined as number | undefined,\n      viewportRebuildPending: false,\n    }))\n    .views(self => ({\n      get defaultLayoutMode(): LayoutModeValue {\n        return 'force'\n      },\n      get defaultColorScheme(): ColorScheme {\n        return 'auto'\n      },\n      // a source declared but not yet loaded\n      get hasPendingSource() {\n        return false\n      },\n      get canRetryLoad() {\n        return false\n      },\n      // the track the graph is cut from: the one the pane is a display of\n      get sourceTrack(): AnyConfigurationModel | undefined {\n        try {\n          return getContainingTrack(self).configuration\n        } catch {\n          return undefined\n        }\n      },\n    }))\n    .views(self => ({\n      get chosenLayoutMode() {\n        return self.layoutMode ?? self.defaultLayoutMode\n      },\n      get chosenColorScheme() {\n        return self.colorScheme ?? self.defaultColorScheme\n      },\n    }))\n    .views(self => ({\n      get paneWidth() {\n        return getContainingView(self).width\n      },\n      // The graph the drawing's node ids address: a folded tube map's coarse\n      // graph, the cut otherwise. Hover, details and labels read it, so a\n      // merged node reports its own span and length.\n      get drawnGraph() {\n        return self.layoutResult?.tubeMap?.coarse?.graph ?? self.graph\n      },\n    }))\n    .views(self => ({\n      get nodeById() {\n        if (self.drawnGraph) {\n          const m = new Map<string, GraphNode>()\n          for (const n of self.drawnGraph.nodes) {\n            m.set(n.id, n)\n          }\n          return m\n        }\n        return undefined\n      },\n      // bp per node id, which is all the label overlay needs of a GraphNode.\n      // Held here rather than rebuilt in the component: that render runs on\n      // every pan, and the map is a fact about the graph (measured 6.9 ms an\n      // allocation on a 30k-node cut).\n      get nodeLengths() {\n        const m = new Map<string, number>()\n        for (const n of self.drawnGraph?.nodes ?? []) {\n          m.set(n.id, n.length)\n        }\n        return m\n      },\n      get nodeCount() {\n        return self.graph?.nodes.length ?? 0\n      },\n      get edgeCount() {\n        return self.graph?.edges.length ?? 0\n      },\n      get pathCount() {\n        return self.graph?.paths?.length ?? 0\n      },\n      get hasGraph() {\n        return self.graph !== undefined\n      },\n      get geometryPainted() {\n        return geometryPainted(self)\n      },\n      // The app-wide readiness contract (AppReadyMarker, @jbrowse/capture)\n      // reads this: a declared source still fetching, or a graph whose\n      // settled geometry is not on the canvas yet.\n      get showLoading() {\n        return (\n          self.error === undefined &&\n          (self.isLoading ||\n            self.hasPendingSource ||\n            (self.graph !== undefined && !geometryPainted(self)))\n        )\n      },\n      // Only before anything is drawn: past that point a reload is superseded\n      // by the next setting change, and stopping one midway would leave a new\n      // graph under the previous graph's layout.\n      get canCancelLoad() {\n        return self.isLoading && !self.layoutResult\n      },\n      // Whether the drawing on screen is the FMMM engine's. False before there\n      // is a graph, since nothing is drawn by anything yet.\n      //\n      // Read by the settings that only the engine looks at: the layout quality\n      // and the bubble spread do nothing at all to an anchored drawing, which\n      // places a node from its coordinates, and the guide says so in prose\n      // precisely because the dialog did not. A control that silently does\n      // nothing is worse than one that says it cannot \u2014 the same rule the\n      // `drawPaths` switch already follows.\n      get usesLayoutEngine() {\n        return self.graph\n          ? modeUsesLayoutEngine(self.chosenLayoutMode, self.graph)\n          : false\n      },\n      // A rank-0 backbone to draw x against, whether the segments declared it\n      // (rGFA) or a path walk derived it. Only a GFA with neither tags nor\n      // paths has no backbone at all, and there force is the one honest layout.\n      get canAnchorLayout() {\n        return self.graph?.nodes.some(n => n.stable?.rank === 0) ?? false\n      },\n      // The paths this graph could be anchored on, for the picker. Empty for an\n      // rGFA, which has no P/W records and needs none.\n      get anchorPaths() {\n        return self.graph?.anchorPaths ?? []\n      },\n      // Which haplotype each ribbon colour belongs to, in the order the file\n      // states the paths \u2014 the same list and the same order the geometry keys\n      // its colours off, so the key cannot name a colour that is not drawn.\n      // Empty unless the ribbons are actually on: a colour key beside a drawing\n      // with no colours in it is a legend for nothing.\n      // The tube map colours its tubes whether or not paths are drawn on the\n      // nodes, so under it the key follows the tubes, and names the colours\n      // the tubes were drawn in.\n      get pathLegend() {\n        const paths = self.graph?.paths\n        const tubeMap = self.layoutResult?.tubeMap\n        const colouring = self.drawPaths || tubeMap\n        return colouring && paths && pathColorsLegible(paths.length)\n          ? pathLegend(paths, tubeMap?.pathColors)\n          : []\n      },\n      // Every walk the graph carries, named for a picker, whatever the count.\n      get walkChoices() {\n        const paths = self.graph?.paths\n        return paths?.length ? pathLegend(paths) : []\n      },\n      // Whether the drawing is actually painted per path, which is not the same\n      // question as whether the user asked for it: past MAX_PATH_COLORS the\n      // colours say nothing and cost a stroke per path per edge. A bare getter\n      // returning a resolved value, the same shape and for the same reason as\n      // `effectiveColorScheme` \u2014 every consumer of a path colour reads this\n      // one, so the geometry, the hit index and the key cannot disagree about\n      // whether there are any. The switch in the settings dialog reads the raw\n      // `drawPaths`, so the user's choice stays visible as the choice it is.\n      get effectiveDrawPaths() {\n        return (\n          self.drawPaths && pathColorsLegible(self.graph?.paths?.length ?? 0)\n        )\n      },\n      // The path x is currently drawn on, which is not necessarily the one\n      // `referencePath` asked for: an unmatched name falls back rather than\n      // leaving the graph unanchored, and the picker has to show what happened.\n      get activeReferencePath() {\n        return self.graph?.referencePath\n      },\n      // Undefined for a graph with neither, where the ramp spans the drawn\n      // extent (computeReferenceRamp)\n      get rampDomain() {\n        return self.colorDomain ?? self.graphRegion\n      },\n      // The lifted walks the graph on screen carries, or undefined when none\n      // is named or it carries none of those that were. A walk coloured by\n      // reference position reads the ramp whatever the node colour scheme.\n      get walkLift() {\n        const { graph } = self\n        return graph && self.walkLayers.length > 0\n          ? walkLift(\n              graph,\n              self.walkLayers,\n              computeReferenceRamp(graph, this.rampDomain),\n            )\n          : undefined\n      },\n      // One panel per lifted walk while the pane is faceted by walk, each a\n      // lift of that walk alone. The panels share one scale, light to dark\n      // along each walk, as a faceted plot shares its axes, so they compare\n      // at a glance; a colour a layer states still wins.\n      get facetPanels() {\n        const { graph } = self\n        const lift = this.walkLift\n        if (self.facet !== 'walk' || !graph || !lift || lift.walks.length < 2) {\n          return undefined\n        }\n        const ramp = computeReferenceRamp(graph, this.rampDomain)\n        return lift.walks.flatMap(w => {\n          const layer = self.walkLayers.find(l => l.walk === w.name)\n          const panel = walkLift(\n            graph,\n            [\n              {\n                walk: w.name,\n                color: { field: 'progress', scheme: 'red', ...layer?.color },\n              },\n            ],\n            ramp,\n          )\n          return panel ? [panel] : []\n        })\n      },\n      // The scheme the renderer actually paints with, which is the raw prop\n      // unless it is 'auto'. A bare getter returns a resolved value (root\n      // CLAUDE.md): every consumer of a colour reads this one, and the two\n      // dropdowns read `colorScheme` so \"Auto\" stays visible as the choice it\n      // is.\n      //\n      // 'auto' asks the GRAPH, not the layout. A hue along the reference is\n      // meaningful whenever the segments have reference coordinates \u2014\n      // `anchoredBy` is exactly that question \u2014 and a force-directed drawing of\n      // an rGFA is the case that proves it: the layout has no reference axis and\n      // the ramp still says where on the reference each node came from, which is\n      // the only quantity a linear track beside it can be painted with too.\n      get effectiveColorScheme(): ResolvedColorScheme {\n        return resolveColorScheme(self.chosenColorScheme, self.graph)\n      },\n      get nodePositions() {\n        return self.layoutResult?.nodePositions\n      },\n      // a length label would sit on the lanes of lifted walks\n      get labelsNodeSizes() {\n        return !self.layoutResult?.tubeMap && !this.walkLift\n      },\n      // Empty rather than undefined: every consumer maps over it, and a layout\n      // with no row structure (FMMM) is a normal state, not a missing one.\n      get rowLabels() {\n        return self.layoutResult?.rowLabels ?? []\n      },\n      // Deletions the layout found inside an allele, empty for the same reason\n      // rowLabels is: a layout drawn at sequence scale states none, because\n      // there a node's drawn extent already IS its length. `deletions` beside\n      // this one is the bare-edge kind, which every layout has.\n      get alleleDeletions() {\n        return self.layoutResult?.alleleDeletions ?? []\n      },\n      // Whether the current layout states y in screen px rather than in the same\n      // units as x (LayoutResult.pixelRows). Everything that has to put the two\n      // axes in one expression reads this through scaleX/scaleY.\n      get pixelRows() {\n        return self.layoutResult?.pixelRows ?? false\n      },\n      get zoomPercent() {\n        return `${(self.scale * 100).toFixed(1)}%`\n      },\n      // True while the persisted transform is still the schema default, i.e.\n      // neither a restored session nor the user has positioned this view yet,\n      // so an incoming layout is free to zoom-to-fit.\n      get isDefaultViewport() {\n        return (\n          self.scale === 1 && self.translateX === 0 && self.translateY === 0\n        )\n      },\n    }))\n    .views(self => ({\n      get poppedFrom() {\n        return self.popStack.at(-1)\n      },\n      // The bubbles the graph itself states, for a graph with no index: a GBZ\n      // cut, a pggb file, the inside of a popped bubble.\n      get derivedBubbles() {\n        return self.graph ? bubblesFromGraph(self.graph) : []\n      },\n    }))\n    .views(self => ({\n      // The bubbles halos draw and pops open. Index rows win where both exist:\n      // gfatools measured every allele, the layered order only bounds them.\n      get bubbles() {\n        return self.indexBubbles?.length\n          ? self.indexBubbles\n          : self.derivedBubbles\n      },\n    }))\n    .views(self => ({\n      get sourceAdapter() {\n        const track = self.sourceTrack\n        return track\n          ? (readConfObject(track, 'adapter') as Record<string, unknown>)\n          : undefined\n      },\n      get sourceTrackId() {\n        const track = self.sourceTrack\n        return track ? (readConfObject(track, 'trackId') as string) : undefined\n      },\n      get assemblyTrackChoices() {\n        const region = self.graphRegion\n        if (!region) {\n          return []\n        }\n        return getSession(self)\n          .tracks.filter(t =>\n            (readConfObject(t, 'assemblyNames') as string[]).includes(\n              region.assemblyName,\n            ),\n          )\n          .map(t => ({\n            trackId: t.trackId as string,\n            name: readConfObject(t, 'name') as string,\n            adapterType: (readConfObject(t, 'adapter') as { type: string })\n              .type,\n          }))\n      },\n    }))\n    .views(self => ({\n      get geneTrackChoices() {\n        return self.assemblyTrackChoices.filter(t =>\n          GENE_ADAPTER_TYPES.has(t.adapterType),\n        )\n      },\n      // The session's feature tracks a repeat annotation could be, for the\n      // picker; which one is read is pickRepeatTrack's choice.\n      get repeatTrackChoices() {\n        return self.assemblyTrackChoices.filter(t =>\n          REPEAT_ADAPTER_TYPES.has(t.adapterType),\n        )\n      },\n      // The arrays over the window that state a unit, for the Repeat picker.\n      get repeatChoices() {\n        return self.repeatArrays ?? []\n      },\n    }))\n    .views(self => ({\n      get repeatTrack() {\n        return pickRepeatTrack(self.repeatTrackChoices, self.repeatTrackId)\n      },\n      get selectedRepeat() {\n        return self.repeatChoices.find(r => r.key === self.repeatKey)\n      },\n      get backbone() {\n        return self.graph ? graphBackbone(self.graph) : undefined\n      },\n      // An assembly by each name a backbone may spell it with: the session's\n      // name and aliases, and the PanSN prefix the source track maps each of\n      // those to.\n      assemblySpellings(assemblyName: string): AssemblyNames {\n        const { assemblyManager } = getSession(self)\n        const assembly = assemblyManager.has(assemblyName)\n          ? assemblyManager.get(assemblyName)\n          : undefined\n        const panSN = (self.sourceAdapter?.assemblyNameToPanSN ?? {}) as Record<\n          string,\n          string\n        >\n        const names = [\n          assemblyName,\n          ...(assembly ? [assembly.name, ...assembly.aliases] : []),\n        ]\n        return {\n          name: assemblyName,\n          aliases: [...names, ...names.flatMap(n => panSN[n] ?? [])],\n        }\n      },\n      // Whether x lies along the reference the track's graph came with, not a\n      // walk \"Draw x along\" picked. An rGFA's backbone is fixed.\n      get drawsLoadedReference() {\n        const graph = self.graph\n        return (\n          graph?.anchoredBy === 'tags' ||\n          (graph?.referencePath !== undefined &&\n            graph.referencePath === self.loadedReferencePath)\n        )\n      },\n    }))\n    .views(self => ({\n      // the assembly the genes were read for\n      get geneAssembly() {\n        const region = self.graphRegion\n        return region ? self.assemblySpellings(region.assemblyName) : undefined\n      },\n    }))\n    .views(self => ({\n      // The genes on the drawn backbone under its own refNames. The track's\n      // config puts its reference on the cut's assembly, whatever the walk's\n      // name. After \"Draw x along\" another walk, the backbone takes the genes\n      // only where its PanSN prefix names their assembly.\n      get backboneGenes() {\n        const { backbone, geneAssembly, geneFeatures } = self\n        const binds =\n          self.drawsLoadedReference ||\n          (geneAssembly !== undefined &&\n            backboneAssembly(backbone, [geneAssembly]) !== undefined)\n        return backbone && geneFeatures && binds\n          ? featuresOnBackbone(geneFeatures, backbone)\n          : undefined\n      },\n    }))\n    .views(self => ({\n      get nodeNeighbors() {\n        return self.drawnGraph ? buildNeighbors(self.drawnGraph) : undefined\n      },\n      get nodeInk(): NodeInk {\n        return nodeInk(\n          self.drawnGraph,\n          self.nodeById,\n          self.contigThickness,\n          self.nodeWidth,\n        )\n      },\n      // Links that skip reference sequence, i.e. the deletions this graph\n      // holds. Computed once per graph rather than per geometry rebuild: it is\n      // a pass over the edges and the drawing rebuilds on every pan.\n      // Walk rows state what each walk skips as its own bar length, so the arcs\n      // over the backbone would only say it again, across the bars.\n      get deletions() {\n        return self.graph &&\n          self.chosenLayoutMode !== 'walkrows' &&\n          !self.layoutResult?.tubeMap\n          ? deletionEdges(self.graph)\n          : []\n      },\n      // One bar per haplotype walk on its own bp axis, for the walk-rows\n      // overlay. Empty under every other layout.\n      get walkRowBars() {\n        if (self.chosenLayoutMode !== 'walkrows' || !self.graph) {\n          return undefined\n        }\n        const repeat = self.selectedRepeat\n        const bars = repeat\n          ? walkRows(self.graph, repeat, repeat.unit)\n          : walkRows(self.graph, self.graphRegion)\n        if (!bars) {\n          return undefined\n        }\n        const samples = self.walkRowSamples\n        const rows = samples\n          ? bars.rows\n              .filter(r => samples.includes(r.sample))\n              .sort(\n                (a, b) =>\n                  samples.indexOf(a.sample) - samples.indexOf(b.sample) ||\n                  a.label.localeCompare(b.label),\n              )\n          : bars.rows\n        const [reference, ...paired] = withCalls(\n          [bars.reference, ...rows],\n          repeat?.calls,\n        )\n        return { ...bars, reference: reference!, rows: paired }\n      },\n      // The labels drawn beside the rows. Walk rows label from the bars\n      // themselves, which follow the selected repeat and sample filter that\n      // the layout, run once per cut, cannot.\n      get drawnRowLabels() {\n        const bars = this.walkRowBars\n        return bars\n          ? [bars.reference, ...bars.rows].map((row, i) => ({\n              label: row.label,\n              y: i * ROW_HEIGHT_PX,\n            }))\n          : self.rowLabels\n      },\n      // The row labels are pinned to the pane's left edge, so the fit starts\n      // the drawing past the widest one.\n      get fitPadLeft() {\n        return Math.max(\n          FIT_PADDING,\n          ...this.drawnRowLabels.map(r => rowLabelBox(r.label, 0).x1 + 6),\n        )\n      },\n      // Exons and names on the backbone, in layout units. Reads\n      // positionsVersion so a dragged node takes its exons with it.\n      get genePins() {\n        dependOn(self.positionsVersion)\n        const positions = self.layoutResult?.nodePositions\n        return self.showGenes &&\n          self.chosenLayoutMode !== 'walkrows' &&\n          !self.layoutResult?.tubeMap &&\n          self.graph &&\n          self.backboneGenes &&\n          positions\n          ? genePins(self.graph, self.backboneGenes, positions)\n          : []\n      },\n      // The bubbles as halos along their nodes.\n      // Reads positionsVersion so a dragged node takes its halo with it.\n      get bubbleHalos() {\n        dependOn(self.positionsVersion)\n        const positions = self.layoutResult?.nodePositions\n        if (\n          !self.showBubbles ||\n          self.chosenLayoutMode === 'walkrows' ||\n          self.layoutResult?.tubeMap ||\n          !self.graph ||\n          !positions\n        ) {\n          return []\n        }\n        const labels = new Map(self.walkChoices.map(c => [c.name, c.label]))\n        return bubbleHalos(\n          self.graph,\n          self.bubbles,\n          positions,\n          name => labels.get(name) ?? name,\n          self.repeatArrays,\n        )\n      },\n      // Every node's midpoint on the reference plus the interval the hue ramps\n      // over \u2014 what `reference-position` paints from, and undefined under every\n      // other scheme so the walk is never run for a colouring that ignores it.\n      //\n      // Here for the same reason `deletions` is, only more so: deriving it is a\n      // bounded neighbour walk PER NODE (referenceMidpoints), it depends on\n      // nothing the transform touches, and it was being redone inside every\n      // geometry rebuild \u2014 1.6 ms at 1.5k nodes, 45 ms at 30k, on a pass that\n      // reruns on each debounced pan and each drag frame. `reference-position`\n      // is also what `auto` resolves to on any anchored graph, so this was the\n      // default path rather than an opt-in one.\n      get referenceRamp() {\n        return self.effectiveColorScheme === 'reference-position' &&\n          self.graph &&\n          !self.layoutResult?.tubeMap\n          ? computeReferenceRamp(self.graph, self.rampDomain)\n          : undefined\n      },\n      // The assemblies this view is showing, which is the interface every\n      // assembly-aware piece of the app looks for \u2014 `viewTitle` first among\n      // them, which falls back through it and otherwise names the view\n      // \"Untitled view\". Every published HPRC figure showed that.\n      // `launchSubgraphView` only avoids it by writing `displayName`, so a\n      // declaratively-instantiated view (a session snapshot, a figure spec) got\n      // the fallback.\n      //\n      // A whole-file import has none: its stable names are a GFA's business and\n      // need not name anything the session has loaded. Empty rather than\n      // undefined, matching what an LGV with no displayed regions reports.\n      get assemblyNames() {\n        const region = self.graphRegion\n        return region ? [region.assemblyName] : []\n      },\n      // Screen px per layout unit, per axis. `scale` is the x zoom and the whole\n      // of what a user's wheel moves; y is a second question the layout answers\n      // for itself.\n      //\n      // On a row layout the pitch is already in screen px (rowSpacing.ts), so\n      // scaleY is 1 and stays 1: rows are a track's row height, unchanged by\n      // zoom, and the backbone under them zooms the way the ruler above it does.\n      // On an isotropic layout (FMMM) x and y are one simulation space and one\n      // number scales both, exactly as before.\n      //\n      // Everything that mixes the two axes takes their ratio as `yToX`\n      // (scaleY / scaleX) \u2014 see computeEdgeCurves.\n      get scaleX() {\n        return axisScaleOf(self.scale, self.pixelRows).scaleX\n      },\n      get scaleY() {\n        return axisScaleOf(self.scale, self.pixelRows).scaleY\n      },\n      // The pair, for everything that draws or hit-tests. Handed over as one\n      // value on purpose: every consumer needs both, and passing them separately\n      // let a caller supply the x scale and default y, which compiles and draws\n      // a wrong picture. See AxisScale.\n      get axisScale() {\n        return axisScaleOf(self.scale, self.pixelRows)\n      },\n      // Extent of the drawing in layout units, shared by the pane height and\n      // zoomToFit. On a reference-bp layout x is the cut window rather than\n      // how far the drawing reaches: an allele anchored far outside it is a\n      // fact about the graph, not a reason to draw the window at 6% of the\n      // frame. A popped bubble fits to what it drew. Walk rows reach as far as\n      // the bars on screen, which a repeat pick or a sample filter narrows\n      // after the layout ran.\n      get layoutBounds() {\n        const layout = self.layoutResult\n        const bars = this.walkRowBars\n        return layout\n          ? drawingBounds(layout, {\n              region: self.popStack.length === 0 ? self.graphRegion : undefined,\n              extent: bars && layout.extent ? walkRowsExtent(bars) : undefined,\n            })\n          : undefined\n      },\n    }))\n    .views(self => ({\n      get geneTrack() {\n        return pickGeneTrack(self.geneTrackChoices, self.geneTrackId)\n      },\n      // Which of `graph.edges` are deletions, and what each one bypasses, keyed\n      // the way the geometry and the hit index address an edge. One map per\n      // graph rather than per rebuild, since both of those take it on every\n      // pan.\n      get deletionEdgeIndexes() {\n        return new Map(self.deletions.map(d => [d.edgeIndex, d.bypassed]))\n      },\n      get hiddenEdgeIndexes() {\n        return new Set(\n          self.showDeletionEdges ? [] : self.deletions.map(d => d.edgeIndex),\n        )\n      },\n      // The interval the reference-position ramp runs over, for the key beside\n      // the drawing, and undefined when no key should be drawn. Two tutorials\n      // carry \"red to magenta is left to right of the cut window\" as a sentence\n      // in prose because nothing on screen said it.\n      //\n      // Read off the ramp the drawing is actually painted with rather than\n      // re-derived from the domain, so the key cannot come to describe a\n      // different interval from the hues beside it \u2014 and so a graph that states\n      // no domain, whose interval has to be measured, does not pay for a second\n      // neighbour walk to say what the first one already worked out.\n      get referenceRampDomain() {\n        const ramp = self.referenceRamp\n        return ramp\n          ? { start: ramp.start, end: ramp.start + ramp.span }\n          : undefined\n      },\n      // A node's reference interval, an allele's between its flanks\n      nodeSpan(nodeId: string) {\n        const { nodeById, nodeNeighbors: neighbors } = self\n        return nodeById && neighbors\n          ? nodeReferenceSpan({ nodeId, nodeById, neighbors })\n          : undefined\n      },\n    }))\n    .views(self => ({\n      // The reference interval under the pointer: the hovered node's, or the\n      // hovered bubble's\n      get hoveredSpan() {\n        const nodeId = self.hoveredNode\n        const bubble = self.hoveredBubble\n        return nodeId !== null\n          ? self.nodeSpan(nodeId)\n          : bubble\n            ? { start: bubble.start, end: bubble.end }\n            : undefined\n      },\n    }))\n    .views(self => ({\n      // The hovered span, for a connected linear view to highlight. Only a\n      // graph cut from a track has one: a whole-file import has no region, and\n      // its stable names need not name anything in a loaded assembly.\n      get hoverHighlight() {\n        const region = self.graphRegion\n        const span = self.hoveredSpan\n        return region && span\n          ? {\n              refName: region.refName,\n              assemblyName: region.assemblyName,\n              ...span,\n            }\n          : undefined\n      },\n    }))\n    .views(self => ({\n      // Every assembly this graph names a segment from, with the locus each one\n      // contributes here. rGFA's SN tag is what makes this knowable: the graph\n      // states its own contributors, so the view can offer a way out to each of\n      // them without consulting an alignment.\n      //\n      // Gaps larger than the backbone span split a contributor's segments into\n      // separate loci and the widest wins, so a sample that also contributes\n      // sequence from a distant duplication is launched at the locus on screen\n      // rather than at the union of the two.\n      get contributingAssemblies() {\n        const graph = self.graph\n        const backbone = graph ? backboneNodes(graph) : []\n        return graph\n          ? contributingAssemblies(graph, {\n              maxGap: backbone.length > 0 ? backboneSpan(backbone) : Infinity,\n            })\n          : []\n      },\n    }))\n    .views(self => ({\n      // A node's PanSN sample as an assembly this session can open, or\n      // undefined. The graph's spelling and the assembly's need not agree:\n      // HPRC writes `CHM13` where the assembly is UCSC's `hs1`. The track the\n      // graph was cut from states that pairing in its `assemblyNameToPanSN`,\n      // so its map is read first, then `assemblyManager`'s names and aliases.\n      //\n      // `has` before `get`, deliberately: `get` reports an unknown name to\n      // `Core-handleUnrecognizedAssembly`, which asks every installed plugin to\n      // go supply it, and this is a probe run for hundreds of haplotypes per\n      // graph.\n      get assemblyResolver() {\n        const { assemblyManager } = getSession(self)\n        const panSN = self.sourceAdapter?.assemblyNameToPanSN as\n          Record<string, string> | undefined\n        const byPrefix = new Map(\n          Object.entries(panSN ?? {}).map(([asm, prefix]) => [prefix, asm]),\n        )\n        const loaded = (name: string | undefined) =>\n          name !== undefined && assemblyManager.has(name)\n            ? (assemblyManager.get(name)?.name ?? name)\n            : undefined\n        return (sample: string) =>\n          loaded(byPrefix.get(sample)) ?? loaded(sample)\n      },\n    }))\n    .views(self => ({\n      // The contributors a view can actually be opened on: those naming an\n      // assembly this session has loaded. Every strain of an E. coli pangenome\n      // demo is its own assembly, so all of them resolve; an HPRC graph names\n      // hundreds of haplotypes that no session loads, so only the reference\n      // does.\n      get launchableAssemblies() {\n        return resolveContributors(\n          withReferenceRegion(self.contributingAssemblies, self.graphRegion),\n          self.assemblyResolver,\n        )\n      },\n      // Whether there is a linear view this graph may draw a highlight into \u2014\n      // the paired one, or the session's only one on the reference assembly.\n      // Read by the node menu, which offers the item only when it would land\n      // somewhere.\n      get canHighlightInLinearView() {\n        const region = self.graphRegion\n        return (\n          region !== undefined &&\n          linearViewTarget({\n            views: [...getSession(self).views],\n            connectedViewId: self.connectedViewId,\n            assemblyName: region.assemblyName,\n          }) !== undefined\n        )\n      },\n      // Where one node can be opened: on its own assembly, and on the reference\n      // the graph was cut against. Both are padded to a readable window \u2014 a\n      // base-level allele is a few bp, and a linear view framed on exactly that\n      // shows no context at all.\n      nodeLaunchTargets(nodeId: string) {\n        const node = self.nodeById?.get(nodeId)\n        const own = node ? nodeOwnLocation(node) : undefined\n        const ownAssembly = own\n          ? resolveLocationAssembly(self.assemblyResolver, own)\n          : undefined\n        const region = self.graphRegion\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        const span =\n          region && nodeById && neighbors\n            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })\n            : undefined\n        const onReference =\n          region && span\n            ? {\n                sample: region.assemblyName,\n                haplotype: undefined,\n                refName: region.refName,\n                ...span,\n              }\n            : undefined\n        return {\n          own:\n            own && ownAssembly\n              ? { location: paddedLocation(own), assembly: ownAssembly }\n              : undefined,\n          reference:\n            region && onReference\n              ? {\n                  location: paddedLocation(onReference),\n                  assembly: region.assemblyName,\n                }\n              : undefined,\n          // Unpadded: a mark is of the node, the same span its hover band\n          // draws. The padding above is room to read a view opened on it.\n          highlight:\n            region && onReference\n              ? { location: onReference, assembly: region.assemblyName }\n              : undefined,\n        }\n      },\n    }))\n    .views(self => ({\n      // The linear view this pane draws inside, when a display hosts it: x is\n      // that view's window and the cut is re-made when the window leaves it.\n      // A pane that is a view of its own has none.\n      get host(): LinearHost | undefined {\n        let view: unknown\n        try {\n          view = getContainingView(self)\n        } catch {\n          return undefined\n        }\n        return isLinearHost(view) ? view : undefined\n      },\n    }))\n    .views(self => ({\n      // Whether the drawing's x is reference bp a host can place. Walk rows\n      // put the backbone at its bp too, but their bars are lengths, so the\n      // mode's `cutMargins` is what says the drawing is a picture.\n      get xIsReferenceBp() {\n        return (\n          self.layoutResult?.referenceAxis === true &&\n          layoutModeByValue(self.chosenLayoutMode).cutMargins\n        )\n      },\n    }))\n    .views(self => ({\n      // Whether the host places x. Only a layout whose x is reference bp can\n      // take the window's transform; force, ordered and walk rows draw in\n      // their own coordinates inside the track, and a popped bubble is a\n      // picture of its own.\n      get hostPlacesX() {\n        const { host, graphRegion: region } = self\n        return (\n          host !== undefined &&\n          host.initialized &&\n          region !== undefined &&\n          self.xIsReferenceBp &&\n          self.popStack.length === 0 &&\n          !host.dynamicBlocks.contentBlocks.some(\n            b => b.refName === region.refName && b.reversed,\n          )\n        )\n      },\n    }))\n    .views(self => ({\n      get hostFrame() {\n        const { host, graphRegion } = self\n        return self.hostPlacesX && host && graphRegion\n          ? hostFrame(host, graphRegion)\n          : undefined\n      },\n      get tubeMapPicture() {\n        const drawing = self.layoutResult?.tubeMap\n        return drawing ? tubeMapPicture(drawing.layout) : undefined\n      },\n      get tubeMapReference() {\n        const drawing = self.layoutResult?.tubeMap\n        return drawing && self.drawnGraph\n          ? referenceBoxes(self.drawnGraph, drawing.layout)\n          : undefined\n      },\n      // the folded variants, as ticks on the tubes of the walks carrying them\n      get tubeMapDeviations() {\n        const coarse = self.layoutResult?.tubeMap?.coarse\n        const layout = self.layoutResult?.tubeMap?.layout\n        return coarse && layout\n          ? deviationMarks(coarse.graph, layout, coarse.deviations)\n          : []\n      },\n      // the reference boxes a linear view's connectors tie to its bp, which\n      // the reference axis already puts under that bp\n      get tubeMapReferenceNodes() {\n        const layout = self.layoutResult\n        return layout?.tubeMap && !layout.referenceAxis && self.drawnGraph\n          ? referenceNodes(self.drawnGraph, layout.tubeMap.layout)\n          : undefined\n      },\n    }))\n    .views(self => ({\n      // A linear view has the genes in a track of their own, at their bp\n      get tubeMapGenes() {\n        const reference = self.tubeMapReference\n        return self.showGenes && !self.host && reference && self.backboneGenes\n          ? tubeMapGenes(reference, self.backboneGenes)\n          : []\n      },\n      // A drawing of nodes in its own coordinates inside a linear view, whose\n      // reference segments the strip can put back at their bp. A tube map has\n      // its own bands, and walk rows' bars are lengths, not nodes.\n      get referenceStripApplies() {\n        const { host, layoutResult } = self\n        return (\n          !!host?.initialized &&\n          !!layoutResult &&\n          !layoutResult.tubeMap &&\n          !self.hostPlacesX &&\n          self.chosenLayoutMode !== 'walkrows'\n        )\n      },\n    }))\n    .views(self => ({\n      get referenceStripBlocks() {\n        const { graph } = self\n        return self.showReferenceStrip && self.referenceStripApplies && graph\n          ? referenceStripBlocks(graph, {\n              colorScheme: self.effectiveColorScheme,\n              referenceRamp: self.referenceRamp,\n              walkNodes: self.walkLift?.nodeIds,\n              walkColors: self.walkLift?.walks.find(w => w.reference)?.colors,\n            })\n          : []\n      },\n      // Read off the live blocks, so the strip follows every frame of a pan\n      // in the linear view\n      get referenceStripFrame() {\n        const { host, graphRegion } = self\n        return host?.initialized && graphRegion\n          ? hostFrame(host, graphRegion)\n          : undefined\n      },\n    }))\n    .views(self => ({\n      get referenceStripShown() {\n        return (\n          self.referenceStripBlocks.length > 0 &&\n          self.referenceStripFrame !== undefined\n        )\n      },\n      // Whether the graph draws reference past the window's edges. A boolean\n      // rather than the bp, which moves on every frame of a pan and would\n      // resize the legend with it.\n      get referenceStripOverhangs() {\n        const frame = self.referenceStripFrame\n        if (!frame || self.referenceStripBlocks.length === 0) {\n          return false\n        }\n        const { left, right } = stripOverhang(\n          self.referenceStripBlocks,\n          frame,\n          self.paneWidth,\n        )\n        return left > 0 || right > 0\n      },\n    }))\n    .views(self => ({\n      // The lit span on the strip, and where the graph drew what it is of:\n      // the hovered node, the hovered bubble's name, or the selected node\n      get referenceStripLit() {\n        if (!self.referenceStripShown) {\n          return undefined\n        }\n        const toScreen = (p: { x: number; y: number }) => ({\n          x: p.x * self.scaleX + self.translateX,\n          y: p.y * self.scaleY + self.translateY,\n        })\n        const bubble = self.hoveredNode === null ? self.hoveredBubble : null\n        if (bubble) {\n          const halo = self.bubbleHalos.find(h => sameBubble(h.bubble, bubble))\n          return {\n            start: bubble.start,\n            end: bubble.end,\n            anchor: halo ? toScreen(halo.labelAt) : undefined,\n          }\n        }\n        const nodeId = self.hoveredNode ?? self.selectedNode\n        const span = nodeId === null ? undefined : self.nodeSpan(nodeId)\n        return span && nodeId !== null\n          ? {\n              ...span,\n              anchor: nodeAnchor(self.nodePositions?.[nodeId], toScreen),\n            }\n          : undefined\n      },\n      referenceStripNodeAt(sx: number, sy: number) {\n        const frame = self.referenceStripFrame\n        return self.referenceStripShown && frame\n          ? stripBlockAt(self.referenceStripBlocks, frame, sx, sy)\n          : undefined\n      },\n      // the strip, and the gap the fit leaves under it\n      get referenceStripZonePx() {\n        return self.referenceStripShown ? REFERENCE_STRIP_ZONE_PX : 0\n      },\n    }))\n    .views(self => ({\n      // `paneHeight` replaces the built-in ceiling rather than adding a second\n      // clamp under it, and the floor still wins: a pane shorter than\n      // MIN_CANVAS_HEIGHT leaves no room to hover a node and read its tooltip,\n      // which is the reason that floor exists.\n      get paneCeiling() {\n        return Math.max(MIN_CANVAS_HEIGHT, self.paneHeight ?? MAX_CANVAS_HEIGHT)\n      },\n      // Room over a tube map for the rows its genes need, one inside the\n      // padding and one more for each further gene that overlaps it, and\n      // room for the reference strip\n      get fitPadTop() {\n        const rows = tubeMapGeneRows(self.tubeMapGenes)\n        return (\n          FIT_PADDING +\n          Math.max(0, rows - 1) * GENE_ROW_PX +\n          self.referenceStripZonePx\n        )\n      },\n      // A tube map on its own axis reads by panning along it, as in\n      // sequenceTubeMap. Rather than shrink a long cut to a strip, the fit\n      // stops where its tubes are MIN_FIT_TUBE_PX wide, or at whatever fits\n      // the tallest pane, with the cut's left end on screen.\n      get minFitScale() {\n        const bounds = self.layoutBounds\n        const layout = self.layoutResult\n        const tubePx = layout?.tubeMap?.layout.tracks[0]?.width\n        return bounds && bounds.h > 0 && tubePx && !layout.referenceAxis\n          ? Math.min(\n              MIN_FIT_TUBE_PX / tubePx,\n              (this.paneCeiling - this.fitPadTop - FIT_PADDING) / bounds.h,\n            )\n          : 0\n      },\n      // The pane is as tall as the drawing, rather than a fixed box the drawing\n      // floats in. A row layout's rows are px, so its height is a sum; an\n      // isotropic layout has no height of its own and takes its aspect ratio\n      // at the width's fit. Neither reads `scale`, so the fit reads this\n      // without feeding back into it.\n      // Lifted walks' legend rows carry their scales, which makes the legend\n      // wide, so the fit leaves it that width rather than draw under it\n      get fitPadRight() {\n        return self.walkLift\n          ? Math.max(FIT_PADDING, self.legendSize.width + 2 * LEGEND_INSET_PX)\n          : FIT_PADDING\n      },\n      // How the facet panels tile the pane: columns, and each panel's drawing\n      // size, as tall as its drawing needs at the panel's width but no taller\n      // than the pane's ceiling leaves room for\n      get facetGrid() {\n        const panels = self.facetPanels\n        const bounds = self.layoutBounds\n        if (!panels || !bounds || !(bounds.w > 0)) {\n          return undefined\n        }\n        const columns =\n          bounds.w > FACET_WIDE * bounds.h\n            ? 1\n            : Math.min(panels.length, FACET_MAX_COLUMNS)\n        const rows = Math.ceil(panels.length / columns)\n        const width = Math.floor(\n          (self.paneWidth - (columns - 1) * FACET_GAP_PX) / columns,\n        )\n        const drawn = self.pixelRows\n          ? bounds.h\n          : (bounds.h * (width - 2 * FACET_PAD_PX)) / bounds.w\n        const room =\n          (this.paneCeiling -\n            rows * FACET_TITLE_PX -\n            (rows - 1) * FACET_GAP_PX) /\n          rows\n        const height = Math.floor(\n          Math.max(\n            MIN_FACET_PANEL_PX,\n            Math.min(drawn + 2 * FACET_PAD_PX, room),\n          ),\n        )\n        return {\n          columns,\n          width,\n          height,\n          total: rows * (height + FACET_TITLE_PX) + (rows - 1) * FACET_GAP_PX,\n        }\n      },\n      get canvasHeight() {\n        const bounds = self.layoutBounds\n        const usableWidth = self.paneWidth - FIT_PADDING - this.fitPadRight\n        const ceiling = this.paneCeiling\n        if (!bounds) {\n          return ceiling\n        }\n        const grid = this.facetGrid\n        if (grid) {\n          return Math.max(MIN_CANVAS_HEIGHT, grid.total)\n        }\n        // never shorter than the legend, which a flat drawing would clip\n        const floor = Math.max(\n          MIN_CANVAS_HEIGHT,\n          self.legendSize.height +\n            2 * LEGEND_INSET_PX +\n            self.referenceStripZonePx,\n        )\n        if (self.pixelRows) {\n          return Math.min(\n            ceiling,\n            Math.max(floor, bounds.h + this.fitPadTop + FIT_PADDING),\n          )\n        }\n        return bounds.w > 0 && usableWidth > 0\n          ? Math.min(\n              ceiling,\n              Math.max(\n                floor,\n                bounds.h * Math.max(usableWidth / bounds.w, this.minFitScale) +\n                  this.fitPadTop +\n                  FIT_PADDING,\n              ),\n            )\n          : ceiling\n      },\n      // Where the fit puts the drawing, or undefined until there is a layout\n      // and a measured canvas to fit it into\n      get fittedTransform() {\n        const bounds = self.layoutBounds\n        return bounds\n          ? fitTransform(\n              bounds,\n              self.paneWidth,\n              this.canvasHeight,\n              self.pixelRows,\n              {\n                minScale: this.minFitScale,\n                padLeft: self.fitPadLeft,\n                padTop: this.fitPadTop,\n                padRight: this.fitPadRight,\n              },\n            )\n          : undefined\n      },\n    }))\n    .views(self => ({\n      get overlayLabels() {\n        return layoutLabels(self)\n      },\n      get tubeMapFrame() {\n        const drawing = self.layoutResult?.tubeMap\n        return drawing\n          ? tubeMapFrame(drawing, {\n              scaleX: self.scaleX,\n              translateX: self.translateX,\n              scaleY: self.scaleY,\n              translateY: self.translateY,\n              usableHeight: self.canvasHeight - self.fitPadTop - FIT_PADDING,\n            })\n          : undefined\n      },\n    }))\n    .views(self => ({\n      // the reference ruler under the tubes, unless the linear view's ruler\n      // is already the axis\n      get tubeMapRulerBoxes() {\n        const reference = self.tubeMapReference\n        return reference && !self.hostPlacesX\n          ? rulerBoxes(reference)\n          : undefined\n      },\n      // The connectors run from the top of the pane down to the tubes' top\n      get connectorZoneBottom() {\n        const picture = self.tubeMapPicture\n        const frame = self.tubeMapFrame\n        return picture && frame ? frame.y(picture.bounds.minY) - 2 : 0\n      },\n      // Read off the live blocks, so the bands' tops follow every frame of a\n      // pan in the linear view and their bottoms every pan of the tubes\n      get tubeMapConnectors() {\n        const nodes = self.tubeMapReferenceNodes\n        const frame = self.tubeMapFrame\n        const { host, graphRegion } = self\n        const bp =\n          nodes && frame && host?.initialized && graphRegion\n            ? hostFrame(host, graphRegion)\n            : undefined\n        return nodes && frame && bp\n          ? tubeMapConnectors(\n              nodes,\n              b => b * bp.scale + bp.translateX,\n              frame.x,\n              self.paneWidth,\n            )\n          : []\n      },\n    }))\n    .views(self => ({\n      // What the tube map's legend has to explain: that on the own axis a\n      // box is as wide as the log of its length, the fold its walks' ticks\n      // stand for, the reads' strands, and the marks on the reads in view\n      get tubeMapKeys() {\n        const layout = self.layoutResult\n        const reads = layout?.tubeMap?.layout.reads ?? []\n        const picture = self.tubeMapPicture\n        const frame = self.tubeMapFrame\n        const shown =\n          picture && frame && mismatchesLegible(frame.yScale)\n            ? picture.mismatches.filter(m =>\n                mismatchOnScreen(m, { x: frame.x, width: self.paneWidth }),\n              )\n            : []\n        return {\n          logWidths: layout?.tubeMap !== undefined && !layout.referenceAxis,\n          foldBp:\n            self.tubeMapDeviations.length > 0 ? self.tubeMapFold : undefined,\n          forwardReads: reads.some(r => !r.is_reverse),\n          reverseReads: reads.some(r => r.is_reverse),\n          mismatches: new Set(shown.map(m => m.kind)),\n        }\n      },\n      tubeMapNodeAt(sx: number, sy: number) {\n        const drawing = self.layoutResult?.tubeMap\n        const frame = self.tubeMapFrame\n        return (\n          (drawing && frame ? tubeMapNodeAt(drawing, frame, sx, sy) : null) ??\n          connectorAt(\n            self.tubeMapConnectors,\n            self.connectorZoneBottom,\n            sx,\n            sy,\n          ) ??\n          null\n        )\n      },\n    }))\n    .actions(self => ({\n      setError(error: unknown) {\n        self.error = error\n        self.isLoading = false\n        self.statusMessage = ''\n      },\n      finishLoading() {\n        self.isLoading = false\n        self.statusMessage = ''\n      },\n      setStatusMessage(message: string) {\n        self.statusMessage = message\n      },\n      setFetchMs(ms: number) {\n        self.lastFetchMs = ms\n      },\n      setLayoutMs(ms: number) {\n        self.lastLayoutMs = ms\n      },\n      setGeometryMetrics(\n        ms: number,\n        strokeCount: number,\n        built: { scale: number; bounds: Bounds },\n      ) {\n        self.lastGeometryMs = ms\n        self.lastGeometryStrokeCount = strokeCount\n        self.builtViewport = { ...built, viewportDirty: self.viewportDirty }\n        self.geometryVersion++\n      },\n      markPainted() {\n        self.paintedViewport = self.builtViewport\n      },\n      setLayoutQuality(quality: number) {\n        self.layoutQuality = quality\n      },\n      setLinearLayout(linear: boolean) {\n        self.linearLayout = linear\n      },\n      setLayoutMode(mode: LayoutModeValue) {\n        self.layoutMode = mode\n      },\n      // Re-anchor in place rather than re-parsing: the coordinate walk is\n      // already recorded on the graph, and only which path counts as rank 0\n      // changes. The caller recomputes the layout, the same way it does after\n      // setLayoutMode. An rGFA is left alone \u2014 its coordinates are not derived.\n      setReferencePath(name: string) {\n        self.referencePath = name\n        const graph = self.graph\n        if (graph?.anchoredBy === 'paths') {\n          const reanchored = anchorFromPaths(graph, name)\n          inheritForceLayouts(graph, reanchored)\n          self.graph = reanchored\n        }\n      },\n      setDrawPaths(draw: boolean) {\n        self.drawPaths = draw\n      },\n      setShowPerf(show: boolean) {\n        self.showPerf = show\n      },\n      setColorScheme(scheme: ColorScheme) {\n        self.colorScheme = scheme\n      },\n      setBubbleSpread(spread: BubbleSpread) {\n        self.bubbleSpread = spread\n      },\n      setNodeWidth(width: NodeWidth) {\n        self.nodeWidth = width\n      },\n      setShowBubbles(show: boolean) {\n        self.showBubbles = show\n      },\n      setShowDeletionEdges(show: boolean) {\n        self.showDeletionEdges = show\n      },\n      setShowGenes(show: boolean) {\n        self.showGenes = show\n      },\n      setShowReferenceStrip(show: boolean) {\n        self.showReferenceStrip = show\n      },\n      setTubeMapFold(bp: number) {\n        self.tubeMapFold = bp\n      },\n      setGeneTrackId(trackId: string) {\n        self.geneTrackId = trackId\n      },\n      setRepeatTrackId(trackId: string) {\n        self.repeatTrackId = trackId\n      },\n      setRepeatKey(key: string) {\n        self.repeatKey = key\n      },\n      setWalkLayers(layers: WalkLayer[]) {\n        self.walkLayers = layers\n      },\n      // Lift the walks named, in that order, keeping the colour any of them\n      // already had\n      liftWalks(names: string[]) {\n        const had = new Map(self.walkLayers.map(l => [l.walk, l]))\n        self.walkLayers = names.map(walk => had.get(walk) ?? { walk })\n      },\n      setFacet(facet: 'none' | 'walk') {\n        self.facet = facet\n      },\n      toggleWalk(walk: string) {\n        const layers = self.walkLayers\n        self.walkLayers = layers.some(l => l.walk === walk)\n          ? layers.filter(l => l.walk !== walk)\n          : [...layers, { walk }]\n      },\n      setWalkColor(walk: string, color: Partial<WalkEncoding>) {\n        self.walkLayers = self.walkLayers.map(l =>\n          l.walk === walk ? { ...l, color: { ...l.color, ...color } } : l,\n        )\n      },\n\n      // Undefined restores the built-in ceiling. Nothing recomputes: the pane\n      // reads canvasHeight and the drawing is placed by zoomToFit, which the\n      // caller runs if it wants the drawing refitted into the new pane.\n      setPaneHeight(px: number | undefined) {\n        self.paneHeight = px\n      },\n      setWalkRowSamples(samples: string[] | undefined) {\n        self.walkRowSamples = samples\n      },\n      // Pair with a linear view for the hover sync, without ever repointing an\n      // existing pairing: a graph launched *from* an LGV is already paired with\n      // it, and stealing that would break the sync the user came in on. So a\n      // launch out of the graph only claims the slot when it is empty.\n      //\n      // A slot naming a view that has been closed is empty too. Held, the view\n      // the graph opened next never got its hover, since a highlight is drawn\n      // only in the paired view.\n      pairWithLinearView(viewId: string) {\n        const paired = self.connectedViewId\n        const stillOpen =\n          paired !== undefined &&\n          withRows([...getSession(self).views]).some(\n            view => (view as { id?: unknown }).id === paired,\n          )\n        if (!stillOpen) {\n          self.connectedViewId = viewId\n        }\n      },\n      setHoveredNode(nodeId: string | null) {\n        self.hoveredNode = nodeId\n      },\n      setHoveredBubble(bubble: MinigraphBubble | null) {\n        self.hoveredBubble = bubble\n      },\n      setPointerInPane(inside: boolean) {\n        self.pointerInPane = inside\n      },\n      setLegendSize(size: { width: number; height: number }) {\n        self.legendSize = size\n      },\n      setHoveredEdge(edgeIdx: number | null) {\n        self.hoveredEdge = edgeIdx\n      },\n      setSelectedNode(nodeId: string | null) {\n        self.selectedNode = nodeId\n      },\n      setDraggingNode(nodeId: string | null) {\n        self.draggingNode = nodeId\n      },\n      setPanning(panning: boolean) {\n        self.isPanning = panning\n      },\n      stopDragging() {\n        self.draggingNode = null\n        self.isPanning = false\n      },\n      // Everything that names a part of the current graph. Reset when the graph\n      // is replaced, and by clearGraph.\n      clearInteractionState() {\n        self.hoveredNode = null\n        self.hoveredBubble = null\n        self.hoveredEdge = null\n        self.selectedNode = null\n        self.draggingNode = null\n        self.isPanning = false\n      },\n      showNodeDetails(nodeId: string) {\n        const node = self.nodeById?.get(nodeId)\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        if (node && nodeById && neighbors) {\n          const session = getSession(self)\n          const region = self.graphRegion\n          // refName/start/end are what makes the widget show a location rather\n          // than a bare id, and they are the same span the linear view\n          // highlights on hover.\n          const span = region\n            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })\n            : undefined\n          if (isSessionModelWithWidgets(session)) {\n            session.showWidget(\n              session.addWidget('BaseFeatureWidget', 'baseFeature', {\n                featureData: {\n                  id: node.id,\n                  name: node.name,\n                  length: node.length,\n                  depth: node.depth,\n                  rank: node.stable?.rank,\n                  stableName: node.stable?.refName,\n                  // The assembly that contributed this segment, split off the\n                  // stable name. On an HPRC graph this is the only thing that\n                  // says which of 400-odd haplotypes an allele came from.\n                  contributingAssembly: nodeOwnLocation(node)?.sample,\n                  // and the haplotype, where the graph's names state one:\n                  // the assembly to load to open this node on its own\n                  // coordinates\n                  contributingHaplotype: nodeOwnLocation(node)?.haplotype,\n                  // Every assembly that traverses it, which is a different\n                  // question and one only a path GFA can answer. Absent on an\n                  // rGFA rather than approximated, so the two are never\n                  // confused: there `contributingAssembly` is first-seen, not\n                  // carriage.\n                  carriedBy: node.samples?.join(', '),\n                  ...(region && span\n                    ? {\n                        refName: region.refName,\n                        assemblyName: region.assemblyName,\n                        start: span.start,\n                        end: span.end,\n                      }\n                    : {}),\n                },\n              }),\n            )\n          }\n        }\n      },\n\n      // A gesture on a hosted graph moves the linear view, and the frame\n      // clock brings x back here; y stays the pane's own.\n      setTransform(s: number, tx: number, ty: number) {\n        const { host } = self\n        if (self.viewportOwner === 'host' && host) {\n          host.horizontalScroll(self.translateX - tx)\n        } else {\n          self.viewportOwner = 'user'\n          self.scale = clampZoom(s)\n          self.translateX = tx\n        }\n        self.translateY = ty\n      },\n      zoom(factor: number, centerX: number, centerY: number) {\n        const { host } = self\n        if (self.viewportOwner === 'host' && host) {\n          host.zoomTo(host.bpPerPx / factor, centerX)\n          return\n        }\n        self.viewportOwner = 'user'\n        const t = zoomAbout(self, factor, centerX, centerY, self.pixelRows)\n        self.scale = t.scale\n        self.translateX = t.translateX\n        self.translateY = t.translateY\n      },\n      setViewportDirty() {\n        self.viewportRebuildPending = false\n        self.viewportDirty++\n      },\n      // The positions themselves moved, as opposed to the window onto them.\n      setPositionsDirty() {\n        self.positionsVersion++\n      },\n      zoomToFit() {\n        // A host owns x, so a fit while hosted places the rows only.\n        if (self.viewportOwner === 'host') {\n          const bounds = self.layoutBounds\n          const usableHeight = self.canvasHeight - FIT_PADDING * 2\n          if (bounds && usableHeight > 0) {\n            self.translateY = fittedTranslateY(\n              bounds,\n              usableHeight,\n              self.scaleY,\n            )\n          }\n          return\n        }\n        // Nothing to fit into before the canvas is measured. The fit autorun\n        // runs again once width lands, so skipping beats persisting a negative\n        // scale into the session snapshot.\n        const fit = self.fittedTransform\n        if (fit) {\n          self.scale = fit.scale\n          self.translateX = fit.translateX\n          self.translateY = fit.translateY\n        }\n      },\n      clearPerfMetrics() {\n        self.lastFetchMs = undefined\n        self.lastLayoutMs = undefined\n        self.lastGeometryMs = undefined\n        self.lastGeometryStrokeCount = undefined\n        self.builtViewport = undefined\n      },\n    }))\n    .actions(self => ({\n      // The frame clock. Unclamped, since clampZoom's floor is there to keep a\n      // scale finite and 1 / bpPerPx already is; clamped, a whole-chromosome\n      // window would stop lining up.\n      hostTransform(scale: number, translateX: number) {\n        const engaging = self.viewportOwner !== 'host'\n        if (engaging) {\n          self.viewportOwner = 'host'\n        }\n        self.scale = scale\n        self.translateX = translateX\n        if (engaging) {\n          self.zoomToFit()\n        }\n      },\n      // A drawing still on the reference stays where the host left it; one\n      // whose x no longer means bp is refit.\n      releaseHost() {\n        if (self.viewportOwner === 'host') {\n          if (self.xIsReferenceBp) {\n            self.viewportOwner = 'user'\n          } else {\n            self.viewportOwner = 'fit'\n            self.zoomToFit()\n          }\n        }\n      },\n    }))\n    .actions(self => {\n      // Pan/zoom can wait: the geometry on screen is still correct while the\n      // gesture runs (the viewport bounds carry 20% overscan), so rebuilding is\n      // deferred until the user settles.\n      function scheduleViewportDirty() {\n        clearTimeout(self.viewportDirtyTimer)\n        self.viewportRebuildPending = true\n        self.viewportDirtyTimer = setTimeout(() => {\n          if (isAlive(self)) {\n            self.setViewportDirty()\n          }\n        }, VIEWPORT_DEBOUNCE_MS)\n      }\n\n      // A node drag cannot wait \u2014 the node only moves on screen when its\n      // geometry is rebuilt \u2014 but a bump costs a full geometry rebuild plus\n      // invalidation of both hit-detection indexes, and mousemove fires in\n      // bursts well above the frame rate. Coalescing to the next frame keeps the\n      // drag live while bounding that work to once per frame instead of once\n      // per event.\n      function requestPositionsDirtyFrame() {\n        cancelAnimationFrame(self.positionsDirtyFrame)\n        self.positionsDirtyFrame = requestAnimationFrame(() => {\n          if (isAlive(self)) {\n            self.setPositionsDirty()\n          }\n        })\n      }\n\n      return {\n        // Moves the position objects IN PLACE, which is the one thing\n        // jbrowse-components' upload invariant says not to do (\"per-region\n        // upload values must be freshly constructed, never mutated \u2014 backends\n        // diff by reference identity\"), so it is worth saying why this is not\n        // that case and what it costs instead.\n        //\n        // Nothing here diffs by identity: the geometry is rebuilt wholesale and\n        // handed over as one batch, so `nodePositions` identity is not a\n        // protocol between the model and the backend the way a per-region map\n        // is. What identity DOES drive is the fit: the zoom-to-fit autorun and\n        // `layoutBounds` \u2014 and so `canvasHeight` \u2014 key off `layoutResult`, and\n        // they mean \"a new LAYOUT arrived\", not \"a node moved\". Publishing a\n        // fresh positions record per frame of a drag would refit the drawing\n        // and resize the pane under the cursor, sixty times a second.\n        //\n        // So the change is announced by `positionsVersion` instead, and every\n        // cache that would otherwise trust identity takes it as a key. The cost\n        // of that trade is that the version is a thing to remember: a caller\n        // that mutates here and does not bump it gets stale curves, stale hit\n        // boxes and stale labels, silently. Everything downstream of it is\n        // reached from this one action.\n        moveNode(nodeId: string, dx: number, dy: number) {\n          const positions = self.layoutResult?.nodePositions\n          if (positions?.[nodeId]) {\n            for (const seg of positions[nodeId]) {\n              seg.x += dx\n              seg.y += dy\n            }\n            requestPositionsDirtyFrame()\n          }\n        },\n        scheduleViewportDirty,\n      }\n    })\n    .actions(self => {\n      let loadController: AbortController | undefined\n\n      function callEngine(request: EngineRequest) {\n        const { rpcManager } = getSession(self)\n        return rpcManager.call(getRpcSessionId(self), 'GraphComputeLayout', {\n          ...request,\n          signal: loadController?.signal,\n          // A StatusCallback takes an RpcStatus, not a string \u2014 it may be a\n          // bare label, a phase, or a phase that threw. `statusMessageText` is\n          // core's reader for the human-facing line.\n          statusCallback: status => {\n            self.setStatusMessage(statusMessageText(status) ?? '')\n          },\n        }) as Promise<{ result: LayoutResult; duration: number }>\n      }\n\n      // The engine's inputs, and only those: the graph, plus what `callLayout`\n      // puts in `options`. The reference path is there because the seeds are a\n      // function of it; the colour scheme and the anchored modes' own settings\n      // are absent because none of them reaches the engine.\n      function forceLayoutKey(graph: Graph) {\n        return engineKey(graph, {\n          quality: self.layoutQuality,\n          linearLayout: self.linearLayout,\n          bubbleSpread: self.bubbleSpread,\n        })\n      }\n\n      // Single dispatch point for every layout mode. A mode that returns a\n      // result computed it locally; one that returns undefined can't draw this\n      // graph and hands off to the remote FMMM engine, which is also how\n      // 'force' is expressed. See LAYOUT_MODES.\n      function* computeLayout(graph: Graph) {\n        const start = performance.now()\n        const tubeMap = TUBE_MAP_MODES.has(self.chosenLayoutMode)\n        // a tube map draws the window; the cut's context is for walk rows\n        const region = self.graphRegion\n        const drawn = tubeMap && region ? trimToWindow(graph, region) : graph\n        // reads are placed by the cut's segment names, which a fold renames\n        const coarse =\n          tubeMap && self.tubeMapFold > 0 && !drawn.reads\n            ? coarsenTubeMap(drawn, self.tubeMapFold)\n            : undefined\n        const local = layoutModeByValue(self.chosenLayoutMode).run(\n          coarse?.graph ?? drawn,\n          self.graphRegion,\n          self.host ? self.layoutResult?.sampleRows : undefined,\n        )\n        if (local) {\n          const result =\n            coarse && local.tubeMap\n              ? { ...local, tubeMap: { ...local.tubeMap, coarse } }\n              : local\n          return { result, duration: performance.now() - start }\n        }\n        const cache = forceLayoutsOf(graph)\n        const key = forceLayoutKey(graph)\n        const hit = cache.get(key)\n        if (hit) {\n          return { result: hit, duration: performance.now() - start }\n        }\n        const oriented = (yield forceLayout(\n          graph,\n          {\n            quality: self.layoutQuality,\n            linearLayout: self.linearLayout,\n            bubbleSpread: self.bubbleSpread,\n          },\n          callEngine,\n        )) as { result: LayoutResult; duration: number }\n        // Under the key read BEFORE the call: the settings that produced this\n        // drawing are not necessarily the ones on screen now, and filing it\n        // under the current ones would serve it up as a layout it is not.\n        remember(cache, key, oriented.result)\n        return oriented\n      }\n\n      // Which layout request is the live one. A layout is async and nothing in\n      // the UI waits for it, so several are routinely in flight: every control\n      // in the settings dialog fires `recomputeLayout` on change, and a force\n      // layout takes seconds where an anchored one is instant.\n      //\n      // The graph identity below is not enough to order them, because the\n      // competing requests are usually layouts of the SAME graph. Left to\n      // resolve order the last one to FINISH won rather than the last one\n      // asked for, so switching away from a slow force layout \u2014 to an anchored\n      // mode, a cheaper bubble spread, a lower quality \u2014 drew the abandoned\n      // one over the top of the chosen one seconds later, with the dropdown\n      // still naming the choice that was discarded.\n      let liveRequest = 0\n\n      // Applied under a guard because a layout is async and the user can load a\n      // different graph, or ask for a different layout of it, while one is in\n      // flight; the stale result must not land.\n      function* layoutInto(graph: Graph) {\n        const request = ++liveRequest\n        const isLive = () => self.graph === graph && request === liveRequest\n        const signal = loadController?.signal\n        let computed\n        try {\n          computed = yield* computeLayout(graph)\n        } catch (e) {\n          // A discarded layout's failure is not the user's problem: the drawing\n          // they asked for is on screen or on its way, and raising a banner\n          // over it reports a graph as broken because a setting they moved on\n          // from could not be drawn. An aborted one was discarded by the load\n          // that replaced it, even when the graph is still the same object.\n          if (!isLive() || signal?.aborted) {\n            return false\n          }\n          throw e\n        }\n        const live = isLive()\n        if (live) {\n          self.layoutResult = computed.result\n          self.setLayoutMs(computed.duration)\n        }\n        return live\n      }\n\n      // The walk a path graph's track puts on the region's assembly: the one\n      // that names it, else the one chooseReferencePath infers\n      function loadedReference(graph: Graph, region: SubgraphRegion) {\n        const paths = graph.anchorPaths\n        return graph.anchoredBy === 'paths' && paths\n          ? (\n              assemblyWalk(\n                graph,\n                self.assemblySpellings(region.assemblyName),\n              ) ?? chooseReferencePath(paths, region.assemblyName)\n            )?.name\n          : undefined\n      }\n\n      // `keepSelection` for a re-cut of the same source: node ids survive one\n      // where edge indexes do not, so the selection is found again by id.\n      // `readsOf` fetches the reads over the parsed graph before its one\n      // layout, since the tube map lays them out with the paths.\n      function* parseAndLayout(\n        text: string,\n        name: string,\n        region: SubgraphRegion | undefined,\n        keepSelection = false,\n        readsOf?: (graph: Graph) => Promise<GafReads>,\n      ) {\n        const signal = loadController?.signal\n        self.setStatusMessage('Parsing GFA')\n        const parsed = loadGraph(text, name, {\n          referencePath: self.referencePath || region?.assemblyName,\n          maxNodes: self.maxGraphNodes,\n        })\n        const loaded = region ? loadedReference(parsed, region) : undefined\n        const graph =\n          !self.referencePath &&\n          loaded !== undefined &&\n          loaded !== parsed.referencePath\n            ? anchorFromPaths(parsed, loaded)\n            : parsed\n        if (readsOf) {\n          self.setStatusMessage('Reading alignments')\n          try {\n            const { records, total } = (yield readsOf(graph)) as GafReads\n            graph.reads = records\n            self.readsShown = { shown: records.length, total }\n          } catch (e) {\n            if (signal?.aborted) {\n              return\n            }\n            console.warn('[GraphGenomeView] no reads for this graph', e)\n            self.readsShown = undefined\n          }\n          if (signal?.aborted) {\n            return\n          }\n        } else {\n          self.readsShown = undefined\n        }\n        const selected = keepSelection ? self.selectedNode : null\n        self.graph = graph\n        self.graphRegion = region\n        self.loadedReferencePath = loaded\n        self.indexBubbles = undefined\n        self.geneFeatures = undefined\n        self.repeatArrays = undefined\n        self.popStack = []\n        // hoveredEdge is an index into graph.edges and hoveredNode/selectedNode\n        // are ids, so all three address the graph being replaced here. Carrying\n        // them over points the tooltip and the highlight at whatever now happens\n        // to sit at that index.\n        self.clearInteractionState()\n        if (selected !== null && self.nodeById?.has(selected)) {\n          self.selectedNode = selected\n        }\n        self.setStatusMessage('Computing layout')\n        yield* layoutInto(graph)\n      }\n\n      // Which load is the live one, for the reason liveRequest orders layouts:\n      // every change in the settings dialog re-cuts, a remote cut takes seconds,\n      // and the last one to finish is not the last one asked for.\n      let liveLoad = 0\n\n      function beginLoad() {\n        const load = ++liveLoad\n        loadController?.abort()\n        loadController = new AbortController()\n        self.loadCanceled = false\n        return {\n          isLive: () => load === liveLoad,\n          signal: loadController.signal,\n        }\n      }\n\n      // The bubble index that the hosted HPRC build keeps beside its segments,\n      // `<prefix>.bubbles.bed.gz`, read through the bubble adapter over the same\n      // window. A graph whose source has no such file, the ordinary case for a\n      // graph of one's own, keeps its derived bubbles, so a failure here is not\n      // the graph's problem. A coarse cut reads none: its nodes are the\n      // bubbles, and the index over its window can run to a chromosome's rows.\n      function* loadBubbles(\n        adapterConfig: Record<string, unknown>,\n        region: SubgraphRegion,\n        isLive: () => boolean,\n      ) {\n        // The track config arrives as written, so the prefix is either the\n        // `uri` shorthand or the segments location it expands to.\n        const prefix = bubblePrefix(adapterConfig)\n        if (adapterConfig.type !== 'RgfaTabixAdapter' || prefix === undefined) {\n          return\n        }\n        try {\n          const features = (yield getSession(self).rpcManager.call(\n            getRpcSessionId(self),\n            'CoreGetFeatures',\n            {\n              adapterConfig: {\n                type: 'MinigraphBubbleAdapter',\n                uri: `${prefix}.bubbles.bed.gz`,\n                baseUri: adapterConfig.baseUri,\n                assemblyNameToPanSN: adapterConfig.assemblyNameToPanSN,\n              },\n              regions: [region],\n            },\n          )) as Feature[]\n          if (isLive()) {\n            self.indexBubbles = features.map(f => ({\n              refName: region.refName,\n              start: f.get('start'),\n              end: f.get('end'),\n              segmentCount: f.get('segmentCount') as number,\n              pathCount: (f.get('pathCount') as number | undefined) ?? 0,\n              inversion: f.get('inversion') as boolean,\n              shortestAlleleLength: f.get('shortestAlleleLength') as number,\n              longestAlleleLength: f.get('longestAlleleLength') as number,\n              segments: f.get('segments') as string,\n              shortestAllele: undefined,\n              longestAllele: undefined,\n            }))\n          }\n        } catch (e) {\n          console.warn('[GraphGenomeView] no bubble index for this graph', e)\n        }\n      }\n\n      // A session track's features over the cut. Undefined when the session\n      // has no such track or the read fails: an annotation is never the\n      // graph's problem.\n      function* trackFeatures(\n        trackId: string | undefined,\n        region: SubgraphRegion,\n        what: string,\n      ) {\n        const session = getSession(self)\n        const config = trackId\n          ? session.tracks.find(t => t.trackId === trackId)\n          : undefined\n        if (!config) {\n          return undefined\n        }\n        try {\n          return (yield session.rpcManager.call(\n            getRpcSessionId(self),\n            'CoreGetFeatures',\n            {\n              adapterConfig: readConfObject(config, 'adapter'),\n              regions: [region],\n            },\n          )) as Feature[]\n        } catch (e) {\n          console.warn(`[GraphGenomeView] no ${what} for this graph`, e)\n          return undefined\n        }\n      }\n\n      // The genes over the cut, from the session's annotation track for the\n      // assembly, so the backbone can carry its exons and names.\n      function* loadGenes(region: SubgraphRegion, isLive: () => boolean) {\n        const features = yield* trackFeatures(\n          self.geneTrack?.trackId,\n          region,\n          'genes',\n        )\n        if (features && isLive()) {\n          self.geneFeatures = geneModelsFrom(features)\n        }\n      }\n\n      // The tandem repeat arrays over the cut, from the session's repeat\n      // track, for the walk rows to measure between and tile by.\n      function* loadRepeats(region: SubgraphRegion, isLive: () => boolean) {\n        const features = yield* trackFeatures(\n          self.repeatTrack?.trackId,\n          region,\n          'repeats',\n        )\n        if (features && isLive()) {\n          self.repeatArrays = repeatArraysFrom(features)\n        }\n      }\n\n      // Raises `isLoading` before any fetch, so a view waiting on a remote file\n      // shows its loading state instead of the import form. Text already in\n      // hand is parsed without yielding first. `region` is the window a\n      // declared file was stated beside, which the parse anchors on.\n      function* loadWholeGFA(\n        name: string,\n        source: string | ((signal: AbortSignal) => Promise<string>),\n        region?: SubgraphRegion,\n      ) {\n        const { isLive, signal } = beginLoad()\n        self.isLoading = true\n        self.error = undefined\n        try {\n          const text =\n            typeof source === 'string'\n              ? source\n              : ((yield source(signal)) as string)\n          if (isLive()) {\n            yield* parseAndLayout(text, name, region)\n          }\n        } catch (e) {\n          if (isLive()) {\n            console.error('[GraphGenomeView.loadWholeGFA]', e)\n            self.error = e\n          }\n        } finally {\n          if (isLive()) {\n            self.finishLoading()\n          }\n        }\n        return isLive()\n      }\n\n      function abortLoad() {\n        loadController?.abort()\n        loadController = undefined\n        liveLoad++\n        liveRequest++\n      }\n\n      return {\n        // Back to the import form: drop the graph and everything derived from\n        // it. Any load in flight ends here too, or it would land its graph\n        // afterwards.\n        clearGraph() {\n          abortLoad()\n          self.graph = undefined\n          self.graphRegion = undefined\n          self.loadedReferencePath = undefined\n          self.layoutResult = undefined\n          self.indexBubbles = undefined\n          self.geneFeatures = undefined\n          self.repeatArrays = undefined\n          self.popStack = []\n          self.error = undefined\n          self.isLoading = false\n          self.loadCanceled = false\n          self.statusMessage = ''\n          self.clearInteractionState()\n          self.clearPerfMetrics()\n        },\n        // The user's stop, leaving whatever is drawn under it\n        stopLoad() {\n          abortLoad()\n          self.isLoading = false\n          self.statusMessage = ''\n          self.loadCanceled = true\n        },\n        beforeDestroy() {\n          abortLoad()\n        },\n        loadGFA: flow(function* (text: string, name = 'Imported GFA') {\n          yield* loadWholeGFA(name, text)\n        }),\n        loadGFAFromLocation: flow(function* (\n          location: FileLocation,\n          region?: SubgraphRegion,\n        ) {\n          self.setStatusMessage('Fetching GFA')\n          const live = yield* loadWholeGFA(\n            'uri' in location\n              ? (location.uri.split('/').pop() ?? 'GFA')\n              : 'GFA',\n            signal =>\n              openLocation(location).readFile({ encoding: 'utf8', signal }),\n            region,\n          )\n          if (region && live && self.graph) {\n            yield* loadRepeats(region, () => self.graphRegion === region)\n          }\n        }),\n        // One cut of a region, laid out with the annotations over it. Whether\n        // the region may be cut is the caller's call; overlapping cuts are\n        // ordered by liveLoad, so the latest one lands.\n        cutSubgraph: flow(function* (\n          adapterConfig: Record<string, unknown>,\n          region: SubgraphRegion,\n          opts: SubgraphCutOptions = {},\n        ) {\n          const { isLive, signal } = beginLoad()\n          self.isLoading = true\n          self.error = undefined\n          self.setStatusMessage('Fetching subgraph')\n          try {\n            const fetchStart = performance.now()\n            const gfaText = (yield getSession(self).rpcManager.call(\n              getRpcSessionId(self),\n              'GetSubgraph',\n              { adapterConfig, region, opts, signal },\n            )) as string\n            if (!isLive()) {\n              return\n            }\n            self.setFetchMs(performance.now() - fetchStart)\n            if (!gfaText) {\n              throw new Error(\n                'Adapter returned no GFA \u2014 region may be outside indexed data or the adapter does not implement getSubgraph',\n              )\n            }\n            yield* parseAndLayout(\n              gfaText,\n              locLabel(region),\n              region,\n              true,\n              namesReads(adapterConfig)\n                ? graph =>\n                    getSession(self).rpcManager.call(\n                      getRpcSessionId(self),\n                      'GetGraphReads',\n                      {\n                        adapterConfig,\n                        nodeNames: graph.nodes.map(n => n.name),\n                        signal,\n                      },\n                    )\n                : undefined,\n            )\n            if (!isLive()) {\n              return\n            }\n            // Independent remote reads, each landing as it arrives. A coarse\n            // cut reads no bubble index: its nodes are the bubbles, and the\n            // index over its window can run to a chromosome's rows.\n            self.setStatusMessage('Reading annotations')\n            yield Promise.all([\n              opts.tier === 'coarse'\n                ? undefined\n                : flow(loadBubbles)(adapterConfig, region, isLive),\n              flow(loadGenes)(region, isLive),\n              flow(loadRepeats)(region, isLive),\n            ])\n          } catch (e) {\n            if (isLive()) {\n              console.error('[GraphGenomeView.cutSubgraph]', e)\n              self.error = e\n            }\n          } finally {\n            if (isLive()) {\n              self.finishLoading()\n            }\n          }\n        }),\n        // Re-read one annotation track alone, for a track change. The graph,\n        // its layout and any open bubble stay as they are. Live only while the\n        // track it read is still the one chosen, so a slow read cannot land\n        // over the pick that followed it.\n        reloadRepeats: flow(function* () {\n          const region = self.graphRegion\n          const trackId = self.repeatTrack?.trackId\n          if (region) {\n            yield* loadRepeats(\n              region,\n              () =>\n                self.graphRegion === region &&\n                self.repeatTrack?.trackId === trackId,\n            )\n          }\n        }),\n        reloadGenes: flow(function* () {\n          const region = self.graphRegion\n          const trackId = self.geneTrack?.trackId\n          if (region) {\n            yield* loadGenes(\n              region,\n              () =>\n                self.graphRegion === region &&\n                self.geneTrack?.trackId === trackId,\n            )\n          }\n        }),\n        // Open one bubble: the graph becomes the segments the bubble row names,\n        // drawn in the layout the reader is in. The graph it came from stays\n        // behind it, one click away, and the popped graph gets its own derived\n        // bubbles, so a superbubble opens progressively.\n        popBubble: flow(function* (bubble: MinigraphBubble) {\n          const graph = self.graph\n          if (!graph) {\n            return\n          }\n          const sub = bubbleSubgraph(graph, bubbleSegmentIds(bubble))\n          if (sub.nodes.length === 0) {\n            getSession(self).notify(\n              'None of the segments of this bubble are in the cut; widen the graph context to open it',\n              'info',\n            )\n            return\n          }\n          const { isLive } = beginLoad()\n          self.popStack = [\n            ...self.popStack,\n            {\n              graph,\n              layoutMode: self.chosenLayoutMode,\n              label: graph.name,\n              indexBubbles: self.indexBubbles,\n            },\n          ]\n          self.indexBubbles = undefined\n          const label = `${BUBBLE_KIND_NAMES[classifyBubble(bubble, self.repeatArrays).kind]} at ${bubble.refName}:${bubble.start.toLocaleString()}`\n          self.graph = { ...sub, name: label }\n          self.clearInteractionState()\n          self.viewportOwner = 'fit'\n          self.isLoading = true\n          try {\n            if (yield* layoutInto(self.graph)) {\n              self.finishLoading()\n            }\n          } catch (e) {\n            if (isLive()) {\n              self.error = e\n              self.finishLoading()\n            }\n          }\n        }),\n        unpopBubble: flow(function* () {\n          const from = self.poppedFrom\n          if (!from) {\n            return\n          }\n          self.popStack = self.popStack.slice(0, -1)\n          self.graph = from.graph\n          self.layoutMode = from.layoutMode\n          self.indexBubbles = from.indexBubbles\n          self.clearInteractionState()\n          self.viewportOwner = 'fit'\n          self.isLoading = true\n          try {\n            if (yield* layoutInto(from.graph)) {\n              self.finishLoading()\n            }\n          } catch (e) {\n            self.error = e\n            self.finishLoading()\n          }\n        }),\n        recomputeLayout: flow(function* () {\n          const graph = self.graph\n          if (!graph) {\n            return\n          }\n          self.isLoading = true\n          self.setStatusMessage('Computing layout')\n\n          try {\n            // A superseded request leaves the spinner to the request that\n            // replaced it: clearing it here reports \"done\" while the layout the\n            // user actually asked for is still being computed, which is the\n            // common case when a cheap choice follows an expensive one.\n            if (yield* layoutInto(graph)) {\n              self.finishLoading()\n            }\n          } catch (e) {\n            console.error('[GraphGenomeView.recomputeLayout]', e)\n            self.error = e\n            self.finishLoading()\n          }\n        }),\n      }\n    })\n    .actions(self => ({\n      startRenderingBackend(backend: Renderer) {\n        if (!self.autorunsInstalled) {\n          // Autorun: keep the view fitted to the graph until the user moves it.\n          // Reading fittedTransform tracks everything the fit depends on, so\n          // it re-fits as the layout arrives, the canvas is measured and the\n          // genes over a tube map claim their rows. A manual pan/zoom (or a\n          // restored-session transform) makes the viewport the user's, and a\n          // host makes it the linear view's.\n          addDisposer(\n            self,\n            autorun(() => {\n              if (\n                self.fittedTransform &&\n                untracked(() => self.viewportOwner === 'fit')\n              ) {\n                self.zoomToFit()\n              }\n            }),\n          )\n\n          // Autorun: mirror a connected linear view's hover onto the graph. An\n          // LGV writes `{hoverPosition, hoverFeature}` to session.hovered on\n          // every mousemove; neither field names the source view, so the guard\n          // is that the position lies in the region this graph was cut from.\n          // A pointer over the pane itself is the host's too, at a bp its x\n          // only means on a reference-axis layout, so there the pane's own hit\n          // test is the hover.\n          //\n          // Only `hovered` is tracked \u2014 the graph reads are untracked, so a\n          // geometry rebuild can't re-fire this and clobber a hover the canvas\n          // itself set. Assigning an unchanged id doesn't notify, so a hover\n          // that travels within one segment costs nothing downstream.\n          addDisposer(\n            self,\n            autorun(() => {\n              const hover = readLgvHover(getSession(self).hovered)\n              untracked(() => {\n                const region = self.graphRegion\n                const graph = self.graph\n                if (region && graph && !self.pointerInPane) {\n                  self.setHoveredNode(\n                    hover && hoverInRegion(hover, region)\n                      ? nodeForLgvHover({ hover, nodes: graph.nodes })\n                      : null,\n                  )\n                }\n              })\n            }),\n          )\n\n          // Reaction: drop a hover the pointer cannot still be over.\n          //\n          // A hover is set by a mousemove on the canvas, and here the drawing\n          // moves under a STATIONARY cursor on three axes \u2014 the wheel zoom, the\n          // toolbar's zoom and fit buttons, and a pan \u2014 none of which fire a\n          // pointer event. Left alone the tooltip goes on naming the node that\n          // used to be under the cursor, `hoverHighlight` goes on publishing its\n          // span, and the paired linear view paints a band over the wrong\n          // sequence until the mouse happens to move.\n          //\n          // This is jbrowse-components' `installClearHoverOnViewportChange`\n          // (BaseLinearDisplay), whose three axes are bpPerPx / offsetPx /\n          // scrollTop; a graph view's are its own transform. Its rule is worth\n          // restating rather than just citing: a sticky canvas gets no\n          // mousemove and no mouseleave for any of them. Not imported because\n          // it lives in the LGV plugin and reads a containing LGV, and this\n          // plugin deliberately takes no runtime dependency on that plugin\n          // (see hoverSync/index.tsx).\n          //\n          // A `reaction`, not an autorun, for the reason stated there: the\n          // effect touches hover state, and an autorun would re-enter itself.\n          // Selection is untouched \u2014 a click is a choice, and the content\n          // moving does not unmake it.\n          addDisposer(\n            self,\n            reaction(\n              () => `${self.scale}-${self.translateX}-${self.translateY}`,\n              () => {\n                self.setHoveredNode(null)\n                self.setHoveredBubble(null)\n                self.setHoveredEdge(null)\n              },\n              { name: 'GraphClearHoverOnViewportChange' },\n            ),\n          )\n\n          // Autorun: a zoom, or a pan that leaves the window the last build\n          // covered, schedules a debounced rebuild. A pan inside it costs a\n          // repaint and nothing else. Skips the first run.\n          let firstViewport = true\n          addDisposer(\n            self,\n            autorun(() => {\n              const { scale } = self\n              const viewport = paneViewportOf(self)\n              if (firstViewport) {\n                firstViewport = false\n                return\n              }\n              const built = untracked(() => self.builtViewport)\n              if (built?.scale === scale && contains(built.bounds, viewport)) {\n                return\n              }\n              self.scheduleViewportDirty()\n            }),\n          )\n\n          // Autorun: hover/select are draw-time colour overrides, stated whole\n          // on every change, so there is nothing to restore and nothing to go\n          // stale when a rebuild renumbers the batch. Tracks `geometryVersion`\n          // because an upload drops the renderer's edge highlight.\n          addDisposer(\n            self,\n            autorun(() => {\n              const b = self.currentRenderingBackend as Renderer | undefined\n              const hoveredNode = self.hoveredNode\n              const hoveredEdge = self.hoveredEdge\n              const selectedNode = self.selectedNode\n              dependOn(self.geometryVersion)\n              if (b) {\n                const nodes = new Map<string, number>()\n                if (selectedNode !== null) {\n                  nodes.set(selectedNode, SELECT_BRIGHTEN)\n                }\n                if (hoveredNode !== null && hoveredNode !== selectedNode) {\n                  nodes.set(hoveredNode, HOVER_BRIGHTEN)\n                }\n                b.setNodeHighlights(nodes)\n                b.setEdgeHighlight(hoveredEdge, HOVER_BRIGHTEN)\n                self.renderNow()\n              }\n            }),\n          )\n        }\n\n        // The second argument is a SETUP THUNK, not the callbacks themselves:\n        // anything it closes over lives exactly as long as the callbacks that\n        // read it, which is what lets a per-backend memo work.\n        self.attachRenderingBackend<Renderer>(backend, () => ({\n          // Autorun: rebuild geometry when graph data or display options\n          // change. scale/translate are untracked so they don't trigger a full\n          // rebuild \u2014 only the debounced viewportDirty flag does.\n          upload: (b: Renderer) => {\n            b.resize(self.paneWidth, self.canvasHeight)\n            const nodeById = self.nodeById\n            if (self.layoutResult?.tubeMap) {\n              dependOn(self.viewportDirty)\n              b.uploadGeometry(EMPTY_BATCH)\n              self.setGeometryMetrics(0, 0, {\n                scale: untracked(() => self.scale),\n                bounds: untracked(() => paneViewportOf(self)),\n              })\n              return true\n            }\n            if (self.nodePositions && self.graph && nodeById) {\n              // The window moved (debounced pan/zoom), or the positions did (a\n              // node drag, coalesced to a frame). Both change the drawing;\n              // everything below reads them untracked or not at all.\n              dependOn(self.viewportDirty, self.positionsVersion)\n              const geometryStart = performance.now()\n              const viewportBounds = untracked(() =>\n                padded(paneViewportOf(self), VIEWPORT_PANES_BUILT),\n              )\n              const batch = buildGeometry({\n                nodePositions: self.nodePositions,\n                graph: self.graph,\n                nodeById,\n                colorScheme: self.effectiveColorScheme,\n                contigThickness: self.contigThickness,\n                connectorThickness: self.connectorThickness,\n                drawPaths: self.effectiveDrawPaths,\n                nodeWidth: self.nodeWidth,\n                highlight: self.walkLift,\n                // Untracked, so a zoom does not eagerly rebuild geometry \u2014 the\n                // debounced viewportDirty bump drives the scale-dependent\n                // rebuild (flatness, arrow visibility, viewport culling), same\n                // as pan.\n                axis: untracked(() => self.axisScale),\n                linearLayout: self.linearLayout,\n                viewportBounds,\n                // Where each node sits on the reference and what interval the\n                // hue spans. Held against the graph rather than derived here,\n                // the same way `deletions` is and for the same reason \u2014 see\n                // the `referenceRamp` view.\n                referenceRamp: self.referenceRamp,\n                deletions: self.deletionEdgeIndexes,\n                hiddenEdges: self.hiddenEdgeIndexes,\n                // Read tracked above; passed here so the shared edge-curve\n                // cache can tell a drag from a pan.\n                version: self.positionsVersion,\n              })\n              b.uploadGeometry(batch)\n              self.setGeometryMetrics(\n                performance.now() - geometryStart,\n                batch.nodeStrokes.length,\n                { scale: untracked(() => self.scale), bounds: viewportBounds },\n              )\n              return true\n            }\n            // Nothing reached the backend, so the autorun may skip the redraw\n            // it would otherwise force. Safe despite the resize above: with no\n            // positions there is nothing to draw, which is the same case\n            // `render` below returns false for.\n            return false\n          },\n          // Autorun: re-render on pan/zoom/darkMode without rebuilding geometry\n          render: (b: Renderer) => {\n            if (!self.nodePositions) {\n              return false\n            }\n            // getDpr(), never a bare `devicePixelRatio`: it is capped at\n            // MAX_DPR so this canvas costs what every other canvas in the app\n            // costs on a 3x display (the square of the ratio, i.e. 9x the\n            // pixels of 1x against the 4x everything else pays), and it is the\n            // same read `syncCanvasSize` sizes the backing store with \u2014 two\n            // call sites reading the global separately can disagree, and then\n            // the geometry lands at a different scale from the canvas under it.\n            const dpr = getDpr()\n            b.updateTransform({\n              scaleX: self.scaleX * dpr,\n              scaleY: self.scaleY * dpr,\n              translateX: self.translateX * dpr,\n              translateY: self.translateY * dpr,\n              // Handed over rather than read again by the backend: the\n              // thicknesses in the vertex buffer are css px and are expanded\n              // after this transform, so they need the same ratio the fields\n              // above were already multiplied by. See TransformUniform.dpr.\n              dpr,\n            })\n            b.render(self.darkMode ? [0.12, 0.12, 0.12, 1] : [1, 1, 1, 1])\n            self.markPainted()\n            return true\n          },\n        }))\n      },\n    }))\n    .actions(self => ({\n      // A layout picked from a menu: the mode, then the drawing it makes.\n      switchLayout(mode: LayoutModeValue) {\n        self.setLayoutMode(mode)\n        return self.recomputeLayout()\n      },\n      cancelLoad() {\n        if (self.canCancelLoad) {\n          self.stopLoad()\n          self.graph = undefined\n        }\n      },\n      // loads the source again, for a host that has one\n      retryLoad() {},\n      afterAttach() {\n        // A restored session that already carries a non-default transform is\n        // the user's own view \u2014 mark it so the fit autorun leaves it alone.\n        if (!self.isDefaultViewport) {\n          self.viewportOwner = 'user'\n        }\n      },\n    }))\n    .actions(self => ({\n      // Move the linear view already on screen, or open one if there is none,\n      // and pair with whichever it was. A view being created gets the session's\n      // annotation for the assembly it opens on (see launchTracks), led by the\n      // graph's own segments track when the launch is on the reference \u2014 the one\n      // assembly that track is configured for.\n      //\n      // Only a view on the reference is paired with. A node's hover band is on\n      // that assembly, so paired with a view on another the band fails that\n      // view's assembly check and the reference view's id check, and is drawn\n      // nowhere.\n      showInLinearView(target: { location: GraphLocation; assembly: string }) {\n        const session = getSession(self)\n        const onReference = target.assembly === self.graphRegion?.assemblyName\n        const viewId = showInLinearView({\n          session,\n          location: target.location,\n          assembly: target.assembly,\n          connectedViewId: self.connectedViewId,\n          tracks: launchTracks({\n            session,\n            assemblyName: target.assembly,\n            first: onReference ? self.sourceTrackId : undefined,\n          }),\n        })\n        if (onReference) {\n          self.pairWithLinearView(viewId)\n        }\n      },\n      // Mark the node's reference interval in the linear view beside the graph.\n      // Not an action that opens anything: with no view to mark, the menu does\n      // not offer it (see nodeLaunchMenuItems).\n      highlightInLinearView(target: {\n        location: GraphLocation\n        assembly: string\n      }) {\n        highlightInLinearView({\n          session: getSession(self),\n          location: target.location,\n          assembly: target.assembly,\n          connectedViewId: self.connectedViewId,\n        })\n      },\n      showSyntenyView(trackId: string) {\n        launchSyntenyView({\n          session: getSession(self),\n          contributors: self.launchableAssemblies,\n          trackId,\n          graphTrackId: self.sourceTrackId,\n        })\n      },\n    }))\n    .views(self => ({\n      // Synteny datasets that could fill the panels of a multi-genome launch.\n      // Below two openable contributors there is nothing to compare, so the scan\n      // is skipped rather than run and discarded.\n      get syntenyLaunchTracks() {\n        const samples = self.launchableAssemblies.map(c => c.sample)\n        return samples.length >= 2\n          ? launchableSyntenyTracks(getSession(self), samples)\n          : []\n      },\n    }))\n    .views(self => ({\n      // The graph's way out, in the same shared \"Launch view\" submenu every\n      // other view contributes to. Until this existed the triangle had two edges:\n      // a linear view could open a graph or a synteny view of a locus, and the\n      // graph could open nothing at all.\n      graphMenuItems(): MenuItem[] {\n        const walks = self.walkChoices\n        return [\n          {\n            label: 'Layout',\n            subMenu: LAYOUT_MODES.map(mode => ({\n              type: 'radio' as const,\n              label: mode.label,\n              checked: self.chosenLayoutMode === mode.value,\n              disabled: self.graph ? !mode.available(self.graph) : false,\n              onClick: () => {\n                void self.switchLayout(mode.value)\n              },\n            })),\n          },\n          {\n            label: 'Color',\n            subMenu: COLOR_SCHEMES.map(scheme => ({\n              type: 'radio' as const,\n              label: scheme.label,\n              checked: self.chosenColorScheme === scheme.value,\n              onClick: () => {\n                self.setColorScheme(scheme.value)\n              },\n            })),\n          },\n          ...(walks.length > 0\n            ? [\n                {\n                  label: 'Walk',\n                  subMenu: [\n                    {\n                      label: 'None',\n                      onClick: () => {\n                        self.setWalkLayers([])\n                      },\n                    },\n                    ...(self.walkLayers.length > 1\n                      ? [\n                          {\n                            type: 'checkbox' as const,\n                            label: 'Side by side',\n                            checked: self.facet === 'walk',\n                            onClick: () => {\n                              self.setFacet(\n                                self.facet === 'walk' ? 'none' : 'walk',\n                              )\n                            },\n                          },\n                        ]\n                      : []),\n                    ...walks.map(walk => ({\n                      type: 'checkbox' as const,\n                      label: walk.label,\n                      checked: self.walkLayers.some(l => l.walk === walk.name),\n                      onClick: () => {\n                        self.toggleWalk(walk.name)\n                      },\n                    })),\n                    ...(self.walkLift?.walks ?? []).map(lifted => ({\n                      label: `Colour ${walks.find(w => w.name === lifted.name)?.label ?? lifted.name}`,\n                      subMenu: [\n                        { type: 'subHeader' as const, label: 'Colour by' },\n                        ...WALK_FIELDS.map(field => ({\n                          type: 'radio' as const,\n                          label: field.label,\n                          checked: lifted.encoding.field === field.value,\n                          onClick: () => {\n                            self.setWalkColor(lifted.name, {\n                              field: field.value,\n                            })\n                          },\n                        })),\n                        { type: 'subHeader' as const, label: 'Palette' },\n                        // the rainbow is the reference-position ramp\n                        ...WALK_SCHEMES.filter(\n                          scheme =>\n                            scheme.value !== 'rainbow' ||\n                            lifted.encoding.field === 'reference',\n                        ).map(scheme => ({\n                          type: 'radio' as const,\n                          label: scheme.label,\n                          checked: lifted.encoding.scheme === scheme.value,\n                          onClick: () => {\n                            self.setWalkColor(lifted.name, {\n                              scheme: scheme.value,\n                            })\n                          },\n                        })),\n                      ],\n                    })),\n                  ],\n                },\n              ]\n            : []),\n          ...(TUBE_MAP_MODES.has(self.chosenLayoutMode)\n            ? [\n                {\n                  label: 'Fold variants',\n                  subMenu: TUBE_MAP_FOLDS.map(({ bp, label }) => ({\n                    type: 'radio' as const,\n                    label,\n                    checked: self.tubeMapFold === bp,\n                    disabled: bp > 0 && self.graph?.reads !== undefined,\n                    onClick: () => {\n                      self.setTubeMapFold(bp)\n                      void self.recomputeLayout()\n                    },\n                  })),\n                },\n              ]\n            : []),\n          ...(self.chosenLayoutMode === 'walkrows' &&\n          self.repeatChoices.length > 0\n            ? [\n                {\n                  label: 'Repeat',\n                  subMenu: [\n                    {\n                      type: 'radio' as const,\n                      label: 'Whole window',\n                      checked: self.repeatKey === '',\n                      onClick: () => {\n                        self.setRepeatKey('')\n                      },\n                    },\n                    ...self.repeatChoices.map(({ key, name, unit }) => ({\n                      type: 'radio' as const,\n                      label: `${name} \u00B7 ${unit.toLocaleString()} bp unit`,\n                      checked: self.repeatKey === key,\n                      onClick: () => {\n                        self.setRepeatKey(key)\n                      },\n                    })),\n                  ],\n                },\n              ]\n            : []),\n          ...(self.hostPlacesX\n            ? []\n            : [\n                {\n                  label: 'Zoom in',\n                  onClick: () => {\n                    self.zoom(1.5, self.paneWidth / 2, self.canvasHeight / 2)\n                  },\n                },\n                {\n                  label: 'Zoom out',\n                  onClick: () => {\n                    self.zoom(\n                      1 / 1.5,\n                      self.paneWidth / 2,\n                      self.canvasHeight / 2,\n                    )\n                  },\n                },\n                {\n                  label: 'Zoom to fit',\n                  onClick: () => {\n                    self.zoomToFit()\n                  },\n                },\n              ]),\n          {\n            type: 'checkbox',\n            label: 'Mark bubbles',\n            checked: self.showBubbles,\n            onClick: () => {\n              self.setShowBubbles(!self.showBubbles)\n            },\n          },\n          {\n            type: 'checkbox',\n            label: 'Show deletion edges',\n            checked: self.showDeletionEdges,\n            onClick: () => {\n              self.setShowDeletionEdges(!self.showDeletionEdges)\n            },\n          },\n          {\n            type: 'checkbox',\n            label: 'Genes on the backbone',\n            checked: self.showGenes,\n            onClick: () => {\n              self.setShowGenes(!self.showGenes)\n            },\n          },\n          ...(self.referenceStripApplies\n            ? [\n                {\n                  type: 'checkbox' as const,\n                  label: 'Reference strip at bp',\n                  checked: self.showReferenceStrip,\n                  onClick: () => {\n                    self.setShowReferenceStrip(!self.showReferenceStrip)\n                  },\n                },\n              ]\n            : []),\n        ]\n      },\n      launchMenuItems(): MenuItem[] {\n        const items: MenuItem[] = []\n        for (const item of graphLaunchMenuItems({\n          contributors: self.launchableAssemblies,\n          syntenyTracks: self.syntenyLaunchTracks,\n          onShowLinear: target => {\n            self.showInLinearView(target)\n          },\n          onShowSynteny: trackId => {\n            self.showSyntenyView(trackId)\n          },\n        })) {\n          pushLaunchViewMenuItem(items, item)\n        }\n        return items\n      },\n    }))\n}\n\nexport type GraphPaneModel = Instance<ReturnType<typeof GraphPaneMixin>>\n", "import type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { Feature } from '@jbrowse/core/util'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// Which of the session's tracks to read genes from: the named one, else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first gene-bearing track at all.\nexport function pickGeneTrack<\n  T extends { trackId: string; name?: string; adapterType: string },\n>(tracks: T[], named: string) {\n  if (named) {\n    return tracks.find(t => t.trackId === named)\n  }\n  const candidates = tracks.filter(t => GENE_ADAPTER_TYPES.has(t.adapterType))\n  return (\n    candidates.find(t =>\n      GENE_TRACK_HINT.test(`${t.trackId} ${t.name ?? ''}`),\n    ) ?? candidates[0]\n  )\n}\n\ntype FeatureLike = Feature | Record<string, unknown>\n\nfunction field(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = field(f, 'type')\n  if (type === 'exon') {\n    into.push({\n      start: field(f, 'start') as number,\n      end: field(f, 'end') as number,\n    })\n  }\n  const children = field(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\nfunction merged(intervals: { start: number; end: number }[]) {\n  const sorted = [...intervals].sort((a, b) => a.start - b.start)\n  const out: { start: number; end: number }[] = []\n  for (const iv of sorted) {\n    const last = out.at(-1)\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end)\n    } else {\n      out.push({ ...iv })\n    }\n  }\n  return out\n}\n\n// Genes from a track's features: every top-level feature, named by the first\n// of gene_name, name and id it carries, with the exons found anywhere under it\n// merged. A feature with no exons is one exon, its whole span.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (field(f, 'gene_name') as string | undefined) ??\n      (field(f, 'name') as string | undefined) ??\n      (field(f, 'id') as string | undefined)\n    const start = field(f, 'start') as number\n    const end = field(f, 'end') as number\n    if (!name || !(end > start)) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: field(f, 'refName') as string,\n      start,\n      end,\n      strand: (field(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? merged(exons) : [{ start, end }],\n    })\n  }\n  return genes\n}\n", "import { types } from '@jbrowse/mobx-state-tree'\n\n// Persisted choices that read a value outside `values` as unset. A plain\n// `types.enumeration` throws on one, so a session saved by a build that had an\n// option this one dropped failed to load at all; here it opens on the default.\nfunction knownOrUnset<T extends string>(values: readonly T[]) {\n  return (value: string | undefined) =>\n    values.includes(value as T) ? (value as T) : undefined\n}\n\nexport function lenientMaybeEnum<T extends string>(values: T[]) {\n  return types.snapshotProcessor(types.maybe(types.enumeration(values)), {\n    preProcessor: knownOrUnset(values),\n  })\n}\n\nexport function lenientOptionalEnum<T extends string>(\n  values: T[],\n  fallback: T,\n) {\n  return types.snapshotProcessor(\n    types.optional(types.enumeration(values), fallback),\n    { preProcessor: knownOrUnset(values) },\n  )\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nconst REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<\n  T extends { trackId: string; name?: string; adapterType: string },\n>(tracks: T[], named: string) {\n  if (named) {\n    return tracks.find(t => t.trackId === named)\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t =>\n    REPEAT_TRACK_HINT.test(`${t.trackId} ${t.name ?? ''}`),\n  )\n}\n\ntype FeatureLike = Feature | Record<string, unknown>\n\nfunction own(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = own(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = own(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = own(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(own(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = own(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString()}-${end.toLocaleString()}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "import { isBackbone } from '@jbrowse/bandage-core/anchoredNodes'\n\nimport type { GraphNode } from '@jbrowse/bandage-core/types'\n\n// What a LinearGenomeView writes to `session.hovered` on every mousemove (see\n// LinearGenomeViewContainer): the bp under the cursor, plus the feature under it\n// if the topmost track had one. Nothing names the source VIEW, so a graph view\n// filters by whether the position falls in the region it was cut from \u2014 but the\n// position does name the source ASSEMBLY, and that turns out to be the half\n// that matters.\nexport interface LgvHover {\n  refName: string\n  // The 0-based base under the pointer, the convention `stable.start` and the\n  // cut region are in. Not the LGV's own `coord`, which is 1-based for display.\n  coord: number\n  // The assembly the hovered view is showing. `hoverPosition` is a\n  // `PxToBpResult`, i.e. the displayed region the pointer landed in spread flat,\n  // so this is that region's own `assemblyName`.\n  //\n  // Read because refName alone does not identify a locus in a session holding\n  // several assemblies, which is every session these graphs are launched in. A\n  // PanSN name reduces to a bare contig \u2014 the E. coli pangenome loads five\n  // strains each with one refName `chr`, and HPRC's hg38 and a GenArk haplotype\n  // both call it `chr6` \u2014 so a synteny stack's rows all answer to the same\n  // name at unrelated coordinates. Without this the hover on ANY row lit up a\n  // node in the graph, and the node then published its own reference interval\n  // back into every linear view.\n  //\n  // Optional because the channel is typed `unknown` and read structurally: a\n  // hover that states no assembly is taken at its word rather than dropped.\n  assemblyName?: string\n  featureName?: string\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\ninterface FeatureLike {\n  get: (key: string) => unknown\n}\n\nfunction isFeatureLike(value: unknown): value is FeatureLike {\n  return isRecord(value) && typeof value.get === 'function'\n}\n\n// A display hovers either a Feature, read with `get`, or a plain hit item with\n// a `name` of its own, which is what the canvas feature display hands over.\n// Reading only the first left the exact segment match dead on that display.\nfunction hoveredName(feature: unknown) {\n  const name = isFeatureLike(feature)\n    ? feature.get('name')\n    : isRecord(feature)\n      ? feature.name\n      : undefined\n  return typeof name === 'string' ? name : undefined\n}\n\n// `hovered` is typed `unknown` on the session by design \u2014 it is a shared channel\n// every view writes its own shape to \u2014 so this reads the LGV's shape out of it\n// structurally rather than asserting a type onto it.\nexport function readLgvHover(hovered: unknown): LgvHover | undefined {\n  let result: LgvHover | undefined\n  if (isRecord(hovered) && isRecord(hovered.hoverPosition)) {\n    const { refName, coord, coord0, assemblyName } = hovered.hoverPosition\n    if (typeof refName === 'string' && typeof coord === 'number') {\n      result = {\n        refName,\n        // `coord` is 1-based; a host that states the 0-based `coord0` is\n        // taken at its word. Read as 0-based, the last base of every node lit\n        // the next one, and a 1 bp node could not be reached at all.\n        coord: typeof coord0 === 'number' ? coord0 : coord - 1,\n        assemblyName:\n          typeof assemblyName === 'string' ? assemblyName : undefined,\n        featureName: hoveredName(hovered.hoverFeature),\n      }\n    }\n  }\n  return result\n}\n\n// Whether a hover is one this graph can answer: the same assembly, the same\n// stable sequence, and inside the window the cut was made for.\n//\n// The assembly is checked FIRST and is the whole reason this is not just a\n// coordinate test. See LgvHover.assemblyName: a graph cut from K12 and a\n// synteny row on Sakai both call their sequence `chr`, so on refName and\n// coordinate alone every row of the stack matched and the graph highlighted a\n// K12 node at Sakai's offset. A hover that names no assembly still passes,\n// which is what a hand-written channel writer and the older LGVs get.\nexport function hoverInRegion(\n  hover: LgvHover,\n  region: { refName: string; assemblyName: string; start: number; end: number },\n) {\n  return (\n    (hover.assemblyName === undefined ||\n      hover.assemblyName === region.assemblyName) &&\n    hover.refName === region.refName &&\n    hover.coord >= region.start &&\n    hover.coord < region.end\n  )\n}\n\n// The graph node a linear-view hover points at.\n//\n// The feature under the cursor is the exact answer when the graph's own segments\n// track is what's hovered: an RgfaTabixAdapter feature's name is the segment id,\n// which is `GraphNode.name` (`GraphNode.id` carries a strand suffix, so the\n// match has to be on name). Any other track \u2014 genes, bubbles \u2014 supplies only a\n// coordinate, which still identifies the backbone segment covering it: the\n// backbone tiles the reference exactly once, whether rGFA's rank 0 declared it\n// or a reference path's own steps did.\nexport function nodeForLgvHover({\n  hover,\n  nodes,\n}: {\n  hover: LgvHover\n  nodes: GraphNode[]\n}) {\n  let byName: string | undefined\n  let byCoord: string | undefined\n  for (const node of nodes) {\n    if (node.name === hover.featureName) {\n      byName = node.id\n    } else if (\n      byCoord === undefined &&\n      isBackbone(node) &&\n      hover.coord >= node.stable.start &&\n      hover.coord < node.stable.start + node.length\n    ) {\n      byCoord = node.id\n    }\n  }\n  // An exact segment match wins over the coordinate it happens to sit at.\n  return byName ?? byCoord ?? null\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\n\nimport { locLabel, locString } from './contributors'\nimport { linearViewTarget } from './linearViewTarget'\n\nimport type { Contributor, GraphLocation } from './contributors'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\nexport interface TrackScanSession {\n  tracks: AnyConfigurationModel[]\n  assemblies: AnyConfigurationModel[]\n}\n\nexport interface GraphLaunchSession extends TrackScanSession {\n  addView: (type: string, snapshot?: Record<string, unknown>) => { id: string }\n  // The session's own loader for a view whose state model is registered\n  // lazily (JBrowse 4's LinearSyntenyView); absent on an older core, where\n  // addView is enough\n  launchView?: (\n    type: string,\n    snapshot?: Record<string, unknown>,\n  ) => Promise<{ id: string }>\n  assemblyNames: string[]\n  views: unknown[]\n  // optional, as a hand-built session in a test has none\n  notifyError?: (message: string, error?: unknown) => void\n}\n\n// A launch is a promise nothing waits on. Let go, a refusal moved nothing and\n// said nothing; this is where it is told to the user instead.\nfunction reportFailure(\n  session: GraphLaunchSession,\n  what: string,\n  launch: Promise<unknown>,\n) {\n  launch.catch((error: unknown) => {\n    console.error(`[GraphGenomeView] ${what}`, error)\n    session.notifyError?.(`${what}: ${error}`, error)\n  })\n}\n\n// A node is often shorter than a line of text \u2014 a base-level allele can be a\n// handful of bp \u2014 and a linear view opened on exactly that span shows the span\n// and no context at all. Padding to a minimum window puts the node in the middle\n// of something readable.\nconst MIN_LAUNCH_SPAN_BP = 1000\n\nexport function paddedLocation(\n  loc: GraphLocation,\n  minSpan = MIN_LAUNCH_SPAN_BP,\n): GraphLocation {\n  const pad = Math.max(0, Math.ceil((minSpan - (loc.end - loc.start)) / 2))\n  return { ...loc, start: Math.max(0, loc.start - pad), end: loc.end + pad }\n}\n\n// Restate the rank-0 contributor in the terms of the region the graph was cut\n// from. Two separate corrections, both required:\n//\n//   - the *assembly*. A backbone segment's SN is the graph's own spelling of the\n//     reference, which need not be the name of any loaded assembly: the HPRC\n//     graph says `GRCh38#0#chr6` in a session whose assembly is `hg38`. Taking\n//     the PanSN sample there resolves to nothing and the graph offers no way out\n//     at all. The cut region is authoritative \u2014 the adapter resolved that\n//     assembly to that stable sequence to cut the subgraph in the first place.\n//     The backbone's `haplotype` (`GRCh38#0`) goes with it, since\n//     resolveLocationAssembly tries that before the sample.\n//   - the *locus*. The cut region is what the user framed in the linear view, and\n//     it is the span every other panel of a synteny launch is compared against;\n//     the union of backbone segments differs from it whenever the window ends\n//     inside a bubble.\n//\n// A subgraph is cut on one reference, so there is at most one rank-0\n// contributor. Must run before contributors are resolved against the session's\n// assemblies, or the reference is filtered out by the name this replaces.\nexport function withReferenceRegion(\n  contributors: Contributor[],\n  region:\n    | { refName: string; assemblyName: string; start: number; end: number }\n    | undefined,\n): Contributor[] {\n  return region\n    ? contributors.map(c =>\n        c.rank === 0\n          ? {\n              ...c,\n              sample: region.assemblyName,\n              haplotype: undefined,\n              refName: region.refName,\n              start: region.start,\n              end: region.end,\n            }\n          : c,\n      )\n    : contributors\n}\n\n// Show a location in a linear view: move the one already on screen if there is\n// one to move, open a pane only if there isn't.\n//\n// This is the difference between \"flip to the linear view\" and \"accumulate\n// panes\". The pangenome sessions this ships in are a linear view above a graph,\n// and there the answer to \"where is this node?\" should be that the linear view\n// scrolls to it \u2014 see linearViewTarget for which view counts as the one to move.\n//\n// `tracks` is only applied to a view being created; a view already open keeps\n// whatever the user has turned on. Returns the id of the view that ended up\n// showing the location, so the graph can pair with it for the hover sync.\nexport function showInLinearView({\n  session,\n  location,\n  assembly,\n  connectedViewId,\n  tracks = [],\n}: {\n  session: GraphLaunchSession\n  location: GraphLocation\n  assembly: string\n  connectedViewId?: string\n  tracks?: string[]\n}) {\n  const existing = linearViewTarget({\n    views: session.views,\n    connectedViewId,\n    assemblyName: assembly,\n  })\n  let viewId: string\n  if (existing) {\n    reportFailure(\n      session,\n      `Could not show ${assembly} ${locLabel(location)}`,\n      Promise.resolve(existing.navToLocString(locString(location), assembly)),\n    )\n    viewId = existing.id\n  } else {\n    viewId = session.addView('LinearGenomeView', {\n      displayName: `${assembly} \u2014 ${locLabel(location)}`,\n      init: { assembly, loc: locString(location), tracks },\n    }).id\n  }\n  return viewId\n}\n\n// Mark where a node sits on the reference, in the linear view already on\n// screen, instead of scrolling that view to it. Review: \"need to be able to\n// just highlight lineargenomeview coords\".\n//\n// The other half of the pair above, and the half that survives being let go of:\n// hover sync draws a band for as long as the pointer is over the node, where a\n// highlight is written into the view's own list and stays until it is removed.\n// It also keeps the reader's frame \u2014 the interesting comparison at a pangenome\n// locus is usually the whole window, not the 200 bp the node occupies.\n//\n// Nothing to mark when no linear view on that assembly is ours to move (see\n// linearViewTarget); the caller offers the item only when there is.\nexport function highlightInLinearView({\n  session,\n  location,\n  assembly,\n  connectedViewId,\n}: {\n  session: GraphLaunchSession\n  location: GraphLocation\n  assembly: string\n  connectedViewId?: string\n}) {\n  const target = linearViewTarget({\n    views: session.views,\n    connectedViewId,\n    assemblyName: assembly,\n  })\n  target?.addToHighlights?.({\n    refName: location.refName,\n    start: location.start,\n    end: location.end,\n    assemblyName: assembly,\n  })\n  return target !== undefined\n}\n\n// Which assemblies a track config says it covers, for deciding whether a panel\n// can draw it at all. A trackId naming nothing in the session reads as covering\n// nothing, so a stale id drops the lane rather than adding one the panel would\n// fail to load.\nfunction assemblyNamesOfTrack(\n  session: GraphLaunchSession,\n  trackId: string | undefined,\n) {\n  if (trackId === undefined) {\n    return []\n  }\n  const track = session.tracks.find(\n    t => readConfObject(t, 'trackId') === trackId,\n  )\n  const names: unknown = track ? readConfObject(track, 'assemblyNames') : []\n  return Array.isArray(names) ? names.filter(n => typeof n === 'string') : []\n}\n\n// One panel per contributing assembly, each framed on the locus that assembly\n// contributes here, with the graph's own reference panel on top.\n//\n// The panel loci come from the graph rather than from the synteny track: rGFA\n// states where each contributor's sequence sits on its own coordinates, so the\n// launch needs no mate discovery, no PAF lookup and no dialog. That is the whole\n// point of launching from the graph instead of from a linear view.\n//\n// Panels carry THE GRAPH'S OWN TRACK and nothing else, which is a narrower rule\n// than the single-view launch's (see launchTracks, which scans the session for\n// the assembly's annotation). Tried that here: a gene track per panel takes\n// about 160px of a row that is otherwise a ruler, so on five strains the\n// annotation is most of the viewport and the ribbons \u2014 the thing the launch\n// exists to draw \u2014 are squeezed into the gaps, and `collapseEmptyRows` is here\n// to prevent exactly that.\n//\n// The graph's own track does not have that shape. It goes only in the panels\n// whose assembly its config declares, which is where the graph HAS coordinates:\n// the HPRC segments track names two, so both its panels get one lane, while the\n// E. coli one names K12 alone and a five-strain launch adds a single lane rather\n// than five. And it is the lane that makes the band readable, since the ribbons\n// otherwise connect two bare rulers and the reader has nothing to match across\n// them.\nexport function launchSyntenyView({\n  session,\n  contributors,\n  trackId,\n  graphTrackId,\n}: {\n  session: GraphLaunchSession\n  contributors: Contributor[]\n  trackId?: string\n  graphTrackId?: string\n}) {\n  const graphTrackAssemblies = assemblyNamesOfTrack(session, graphTrackId)\n  // The panels the chosen track aligns, in the order given. A pairwise track is\n  // offered beside an all-vs-all, two assemblies being a synteny view, and over\n  // every contributor it sat on each level and could draw on one at most. A\n  // track that states no assemblies keeps them all.\n  const aligned = assemblyNamesOfTrack(session, trackId)\n  const covered = contributors.filter(c => aligned.includes(c.sample))\n  const panels = covered.length >= 2 ? covered : contributors\n  const snapshot = {\n    init: {\n      views: panels.map(c => ({\n        assembly: c.sample,\n        loc: locString(c),\n        ...(graphTrackId !== undefined &&\n        graphTrackAssemblies.includes(c.sample)\n          ? { tracks: [graphTrackId] }\n          : {}),\n      })),\n      // One entry per LEVEL, not one for the track. `init.tracks` is 2D \u2014 the\n      // gap between views[i] and views[i+1] \u2014 and a flat `[trackId]` is read as\n      // the level-0 shorthand, so on a five-strain launch only the top band got\n      // the alignment and the four below it opened as bare rulers. The same\n      // all-vs-all track fills every level: it carries all the pairs.\n      tracks: trackId ? panels.slice(1).map(() => [trackId]) : [],\n      collapseEmptyRows: true,\n    },\n  }\n  // launchView where the session has it: a synteny view's state model is\n  // loaded on demand and addView throws until it is\n  if (session.launchView) {\n    reportFailure(\n      session,\n      'Could not open the synteny view',\n      session.launchView('LinearSyntenyView', snapshot),\n    )\n  } else {\n    session.addView('LinearSyntenyView', snapshot)\n  }\n}\n", "export interface NavigableLinearView {\n  id: string\n  assemblyNames: string[]\n  navToLocString: (locString: string, assemblyName?: string) => unknown\n  // The other way of answering \"where is this node\": mark it rather than scroll\n  // to it. Optional, and not part of isLinearView's test \u2014 navigating is what\n  // makes a view a target here, and a view that cannot be marked can still be\n  // moved.\n  addToHighlights?: (highlight: {\n    refName: string\n    start: number\n    end: number\n    assemblyName: string\n  }) => unknown\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\n// Reads `session.views` structurally, the same way graphViewHighlights does: the\n// members needed here are declared by LinearGenomeView, not by the\n// AbstractViewModel the session array is typed as.\nfunction isLinearView(view: unknown): view is NavigableLinearView {\n  return (\n    isRecord(view) &&\n    view.type === 'LinearGenomeView' &&\n    typeof view.id === 'string' &&\n    typeof view.navToLocString === 'function' &&\n    Array.isArray(view.assemblyNames)\n  )\n}\n\n// The view a graph was launched from is not always in `session.views`: a row of\n// a LinearSyntenyView, LinearComparativeView or BreakpointSplitView sits in\n// that view's own `views[]`, so the candidates are the session's views plus one\n// level of rows.\nexport function withRows(views: unknown[]) {\n  return views.flatMap(view =>\n    isRecord(view) && Array.isArray(view.views)\n      ? [view, ...view.views]\n      : [view],\n  )\n}\n\n// The linear view a \"show me this\" from the graph should move, rather than\n// opening a pane beside it. Three cases, in order:\n//\n//   - the view this graph is paired with (`connectedViewId`), which is either\n//     the view the graph was launched from or the one it later opened itself.\n//     Explicit, so it wins.\n//   - failing that, the only linear view in the session showing this assembly.\n//     The pangenome sessions this view ships in are a linear view above a graph\n//     with no pairing recorded, and there \"the linear view\" is unambiguous \u2014 the\n//     same reasoning hoverSync's isConnected already applies to highlights.\n//   - two or more candidates and no pairing: nothing. Guessing which of the\n//     user's views to scroll is worse than opening one that is ours to move.\n//\n// Assembly-gated throughout: a linear view on a different assembly cannot show\n// this location at all.\nexport function linearViewTarget({\n  views,\n  connectedViewId,\n  assemblyName,\n}: {\n  views: unknown[]\n  connectedViewId: string | undefined\n  assemblyName: string\n}) {\n  const candidates = withRows(views)\n    .filter(view => isLinearView(view))\n    .filter(view => view.assemblyNames.includes(assemblyName))\n  const connected = candidates.find(view => view.id === connectedViewId)\n  return connected ?? (candidates.length === 1 ? candidates[0] : undefined)\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\n\nimport type { TrackScanSession } from './launchFromGraph'\n\nconst ANNOTATION_TRACK_TYPE = 'FeatureTrack'\n\n// What to turn on in a linear view the graph opens on `assemblyName`.\n//\n// A launch used to carry the graph's own track and nothing else, and that track\n// is configured for the reference alone \u2014 so `Launch view` \u2192 `CFT073 chr:\u2026`\n// landed on `No tracks active`, which answers \"where is this strain's sequence?\"\n// with an empty pane. What the session does hold for a contributing assembly is\n// that assembly's own annotation, and on a pangenome config that is one track\n// per strain (`CFT073_genes`), which is exactly what makes the landing readable.\n//\n// Annotation tracks only, not everything configured for the assembly. A launch\n// is a jump to a locus, and an alignments or coverage track turned on behind the\n// user's back fetches data nobody asked for; a FeatureTrack at a 50 kb window is\n// a tabix range query.\n//\n// `first` is the graph's own track when the launch is on the reference, so the\n// segments the graph drew sit at the top of the view rather than wherever config\n// order puts them.\nexport function launchTracks({\n  session,\n  assemblyName,\n  first,\n}: {\n  session: TrackScanSession\n  assemblyName: string\n  first?: string\n}) {\n  const found: string[] = []\n  for (const track of session.tracks) {\n    const type: unknown = readConfObject(track, 'type')\n    const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      type === ANNOTATION_TRACK_TYPE &&\n      Array.isArray(assemblyNames) &&\n      assemblyNames.includes(assemblyName) &&\n      typeof trackId === 'string' &&\n      trackId !== first\n    ) {\n      found.push(trackId)\n    }\n  }\n  return first ? [first, ...found] : found\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\nimport { getTrackName } from '@jbrowse/core/util/tracks'\nimport { getEnv, isStateTreeNode } from '@jbrowse/mobx-state-tree'\n\nimport type { TrackScanSession } from './launchFromGraph'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\nexport interface LaunchableSyntenyTrack {\n  trackId: string\n  name: string\n  // how many of the requested assemblies this track covers, so a whole-set\n  // all-vs-all sorts above a pairwise alignment covering two of them\n  coverage: number\n}\n\nconst SYNTENY_TRACK_TYPE = 'SyntenyTrack'\nconst SYNTENY_ADAPTER_CATEGORY = 'Synteny adapters'\n\n// A SyntenyTrack, or any track reading a synteny adapter (a GraphTrack over a\n// gbz-base database). Core's isSyntenyTrack makes the same test on newer hosts.\nfunction isSyntenyTrack(track: AnyConfigurationModel) {\n  if (readConfObject(track, 'type') === SYNTENY_TRACK_TYPE) {\n    return true\n  }\n  const adapterType: unknown = track.adapter?.type\n  if (typeof adapterType !== 'string' || !isStateTreeNode(track)) {\n    return false\n  }\n  const { pluginManager } = getEnv<{ pluginManager?: PluginManager }>(track)\n  return (\n    !!pluginManager?.hasAdapterType(adapterType) &&\n    pluginManager.getAdapterType(adapterType).adapterMetadata?.category ===\n      SYNTENY_ADAPTER_CATEGORY\n  )\n}\n\n// Synteny datasets in the session that align at least two of `assemblyNames`.\n//\n// Two is the floor because that is the floor for a synteny view; more is better,\n// and an all-vs-all covering every contributing assembly is what makes the\n// multi-panel launch worth offering at all.\nexport function launchableSyntenyTracks(\n  session: TrackScanSession,\n  assemblyNames: string[],\n) {\n  const wanted = new Set(assemblyNames)\n  const found: LaunchableSyntenyTrack[] = []\n  for (const track of session.tracks) {\n    const trackAssemblies: unknown = readConfObject(track, 'assemblyNames')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      isSyntenyTrack(track) &&\n      typeof trackId === 'string' &&\n      Array.isArray(trackAssemblies)\n    ) {\n      const coverage = trackAssemblies.filter(name => wanted.has(name)).length\n      if (coverage >= 2) {\n        found.push({ trackId, name: getTrackName(track, session), coverage })\n      }\n    }\n  }\n  return found.sort((a, b) => b.coverage - a.coverage)\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6\"\n}), 'Settings');"],
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+}