jbrowse-plugin-graphgenomeviewer 8.3.1 → 8.3.2

package/dist/chunks/chunk-EINURNZ6.js

@@ -0,0 +1,2 @@
+import{l as o}from"./chunk-Y7VFVMQI.js";function u(a,r,e){return e?{...a,walkRowRuns:o(a,r)}:a}export{u as a};
+//# sourceMappingURL=chunk-EINURNZ6.js.map

package/dist/chunks/chunk-EKIQ3ATV.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=chunk-EKIQ3ATV.js.map

package/dist/chunks/chunk-EKIQ3ATV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-YUIKEUKY.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GQZVR5DW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-URPU4XCM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-L4DBSRA2.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-YA3VYQH4.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ACGRXI3X.js"],
+  "sourcesContent": ["import {\n  slideAt\n} from \"./chunk-JJV2GT2Z.js\";\n\n// src/renderer/walkLanes.ts\nvar THREAD_PX = 2;\nvar THREAD_GAP_PX = 1.5;\nvar SLOT_GAP_PX = 4;\nvar LANE_SMOOTHING_PX = 12;\nvar THREAD_REACH_PX = 64;\nvar THREAD_TAPER_PX = 24;\nvar MAX_BAND_PX = 48;\nvar PASSES_KEY = \"a thread per pass through a node\";\nvar threadsPasses = (walks) => walks.length > 1 && walks.some((w) => w.mostPasses > 1);\nvar threadsWidth = (threads) => threads * THREAD_PX + Math.max(0, threads - 1) * THREAD_GAP_PX;\nvar sum = (values) => values.reduce((a, b) => a + b, 0);\nfunction slotLayout(spans, mostPasses, laneWidth) {\n  const widths = spans.map(\n    (m, i) => mostPasses[i] > 1 ? threadsWidth(m) : laneWidth * Math.min(1, m)\n  );\n  let seen = 0;\n  const gaps = spans.map((m) => {\n    const share = Math.min(1, m);\n    const gap = SLOT_GAP_PX * share * seen;\n    seen = Math.max(seen, share);\n    return gap;\n  });\n  return { widths, gaps, band: sum(widths) + sum(gaps) };\n}\nvar THREAD_PITCH_PX = THREAD_PX + THREAD_GAP_PX;\nfunction slotCentres(spans, mostPasses, held = spans) {\n  const { widths, gaps, band } = slotLayout(spans, mostPasses, THREAD_PX);\n  let at = -band / 2;\n  return widths.map((width, i) => {\n    at += gaps[i];\n    const slack = mostPasses[i] > 1 ? Math.max(0, width - threadsWidth(held[i])) : 0;\n    const centre = at + slack / 2 + THREAD_PX / 2;\n    at += width;\n    return centre;\n  });\n}\nvar bandWidthPx = (mostPasses) => slotLayout(mostPasses, mostPasses, THREAD_PX).band;\nvar bandScale = (mostPasses) => Math.min(1, MAX_BAND_PX / (bandWidthPx(mostPasses) || 1));\nvar passesKey = (walks) => bandScale(walks.map((w) => w.mostPasses)) < 1 ? `${PASSES_KEY}, thinned to fit` : PASSES_KEY;\nfunction laneSlideAt(start, end, along) {\n  const vector = ({ normal, offsetX: offsetX2 }) => ({\n    dx: normal.nx * offsetX2,\n    dy: normal.ny * offsetX2\n  });\n  const { dx, dy } = slideAt(vector(start), vector(end), along);\n  const offsetX = Math.hypot(dx, dy);\n  return offsetX > 0 ? { normal: { nx: dx / offsetX, ny: dy / offsetX }, offsetX } : { normal: { nx: 0, ny: 0 }, offsetX: 0 };\n}\nfunction pointIndex(run, p) {\n  const i = run.stepOf[p];\n  const k = p - run.starts[i];\n  return run.forward[i] ? k : run.starts[i + 1] - run.starts[i] - 1 - k;\n}\nvar gapOf = (a, b) => {\n  const dx = b.x - a.x;\n  const dy = b.y - a.y;\n  return Math.sqrt(dx * dx + dy * dy);\n};\nfunction arcOf(run) {\n  const s = new Float64Array(run.length);\n  for (let i = 1; i < run.length; i++) {\n    s[i] = s[i - 1] + gapOf(run[i - 1], run[i]);\n  }\n  return s;\n}\nfunction walkSteps(walkRoutes, nodePositions) {\n  const seen = /* @__PURE__ */ new Set();\n  return walkRoutes.map((routes) => {\n    const visits = /* @__PURE__ */ new Map();\n    return routes.map(\n      (route) => route.map((id) => {\n        const visit = visits.get(id) ?? 0;\n        visits.set(id, visit + 1);\n        const segments = nodePositions[id];\n        const owned = !!segments?.length && !seen.has(id);\n        if (owned) {\n          seen.add(id);\n        }\n        return { id, visit, owned, segments };\n      })\n    );\n  });\n}\nfunction laneRuns(steps, yToX, jump) {\n  const runs = [];\n  steps.forEach((pieces, walk) => {\n    let total = 0;\n    for (const piece of pieces) {\n      for (const { segments } of piece) {\n        total += segments?.length ?? 0;\n      }\n    }\n    const xs = new Float64Array(total);\n    const ys = new Float64Array(total);\n    let at = 0;\n    let from = 0;\n    let run = fresh();\n    function fresh() {\n      return {\n        walk,\n        ids: [],\n        visits: [],\n        forward: [],\n        owned: [],\n        starts: [0]\n      };\n    }\n    const breakRun = () => {\n      if (run.ids.length) {\n        const stepOf = new Int32Array(at - from);\n        for (let i = 0; i < run.ids.length; i++) {\n          stepOf.fill(i, run.starts[i], run.starts[i + 1]);\n        }\n        runs.push({\n          ...run,\n          xs: xs.subarray(from, at),\n          ys: ys.subarray(from, at),\n          stepOf\n        });\n      }\n      run = fresh();\n      from = at;\n    };\n    const gap = (x, y, p) => {\n      const dx = p.x - x;\n      const dy = p.y * yToX - y;\n      return Math.sqrt(dx * dx + dy * dy);\n    };\n    for (const piece of pieces) {\n      piece.forEach(({ id, visit, owned, segments }, k) => {\n        if (!segments?.length) {\n          breakRun();\n          return;\n        }\n        const first = segments[0];\n        const last = segments.at(-1);\n        let forward;\n        if (at > from) {\n          const x = xs[at - 1];\n          const y = ys[at - 1];\n          const toFirst = gap(x, y, first);\n          const toLast = gap(x, y, last);\n          forward = toFirst <= toLast;\n          if (Math.min(toFirst, toLast) > jump) {\n            breakRun();\n          }\n        } else {\n          const next = piece[k + 1]?.segments;\n          const toNext = (p) => next?.length ? Math.min(\n            gap(p.x, p.y * yToX, next[0]),\n            gap(p.x, p.y * yToX, next.at(-1))\n          ) : 0;\n          forward = toNext(last) <= toNext(first);\n        }\n        run.ids.push(id);\n        run.visits.push(visit);\n        run.forward.push(forward);\n        run.owned.push(owned);\n        for (let j = 0; j < segments.length; j++) {\n          const p = segments[forward ? j : segments.length - 1 - j];\n          xs[at] = p.x;\n          ys[at] = p.y * yToX;\n          at++;\n        }\n        run.starts.push(at - from);\n      });\n      breakRun();\n    }\n  });\n  return runs;\n}\nfunction ownedWindows(s, owned, margin) {\n  const windows = [];\n  for (let i = 0; i < owned.length; i++) {\n    if (!owned[i]) {\n      continue;\n    }\n    let j = i;\n    while (j + 1 < owned.length && owned[j + 1]) {\n      j++;\n    }\n    const last = windows.at(-1);\n    const floor = last ? last[1] : 0;\n    let lo = i;\n    while (lo > floor && s[i] - s[lo - 1] <= margin) {\n      lo--;\n    }\n    let hi = j;\n    while (hi + 1 < s.length && s[hi + 1] - s[j] <= margin) {\n      hi++;\n    }\n    if (last && lo <= last[1] + 1) {\n      last[1] = hi;\n    } else {\n      windows.push([lo, hi]);\n    }\n    i = j;\n  }\n  return windows;\n}\nfunction smoothedNormals(run, reach) {\n  const s = arcOf(run);\n  const end = s.at(-1);\n  const pointAt = (at, j) => {\n    const a = run[j];\n    const b = run[Math.min(j + 1, run.length - 1)];\n    const span = s[Math.min(j + 1, run.length - 1)] - s[j];\n    const f = span > 0 ? (at - s[j]) / span : 0;\n    return { x: a.x + (b.x - a.x) * f, y: a.y + (b.y - a.y) * f };\n  };\n  let lo = 0;\n  let hi = 0;\n  return run.map((_, i) => {\n    const back = Math.max(0, s[i] - reach / 2);\n    const ahead = Math.min(end, s[i] + reach / 2);\n    while (lo < run.length - 1 && s[lo + 1] <= back) {\n      lo++;\n    }\n    while (hi < run.length - 1 && s[hi + 1] <= ahead) {\n      hi++;\n    }\n    const a = pointAt(back, lo);\n    const b = pointAt(ahead, hi);\n    const len = gapOf(a, b);\n    return len > 0 ? { nx: -(b.y - a.y) / len, ny: (b.x - a.x) / len } : void 0;\n  });\n}\nfunction cutCurls(run, close, length) {\n  const s = arcOf(run);\n  const out = run.slice();\n  const picks = [];\n  s.forEach((at, k) => {\n    const last = picks.at(-1);\n    if (last === void 0 || at - s[last] >= close / 4) {\n      picks.push(k);\n    }\n  });\n  if (picks.at(-1) !== run.length - 1) {\n    picks.push(run.length - 1);\n  }\n  let a = 0;\n  while (a < picks.length) {\n    const i = picks[a];\n    let to = -1;\n    for (let b = a + 1; b < picks.length && s[picks[b]] - s[i] <= length; b++) {\n      const j2 = picks[b];\n      if (s[j2] - s[i] > Math.PI * close && gapOf(run[i], run[j2]) <= close) {\n        to = b;\n      }\n    }\n    if (to < 0) {\n      a++;\n      continue;\n    }\n    const j = picks[to];\n    const p = run[i];\n    const q = run[j];\n    for (let k = i + 1; k < j; k++) {\n      const f = (s[k] - s[i]) / (s[j] - s[i]);\n      out[k] = {\n        ...run[k],\n        x: p.x + (q.x - p.x) * f,\n        y: p.y + (q.y - p.y) * f\n      };\n    }\n    a = to;\n  }\n  return out;\n}\nfunction rounded(run, half) {\n  const n = run.length;\n  const s = arcOf(run);\n  const end = s[n - 1];\n  const sumW = new Float64Array(n + 1);\n  const sumX = new Float64Array(n + 1);\n  const sumY = new Float64Array(n + 1);\n  for (let i = 0; i < n; i++) {\n    const p = run[i];\n    const w = (s[Math.min(i + 1, n - 1)] - s[Math.max(i - 1, 0)]) / 2;\n    sumW[i + 1] = sumW[i] + w;\n    sumX[i + 1] = sumX[i] + w * p.x;\n    sumY[i + 1] = sumY[i] + w * p.y;\n  }\n  const out = new Array(n);\n  let lo = 0;\n  let hi = 0;\n  for (let i = 0; i < n; i++) {\n    const p = run[i];\n    const reach = Math.min(half, s[i], end - s[i]);\n    const from = s[i] - reach;\n    const to = s[i] + reach + 1e-9 * (1 + end);\n    while (lo < n && s[lo] < from) {\n      lo++;\n    }\n    while (hi < n && s[hi] < to) {\n      hi++;\n    }\n    const w = sumW[hi] - sumW[lo];\n    out[i] = w > 0 ? { x: (sumX[hi] - sumX[lo]) / w, y: (sumY[hi] - sumY[lo]) / w } : { x: p.x, y: p.y };\n  }\n  return out;\n}\nfunction tightPoints(line, radius) {\n  const n = line.length;\n  const s = arcOf(line);\n  const end = s[n - 1];\n  const tight = new Uint8Array(n);\n  const along = (j, at) => {\n    const a = line[j];\n    const b = line[j + 1];\n    if (!b) {\n      return a;\n    }\n    const span = s[j + 1] - s[j];\n    const f = span > 0 ? (at - s[j]) / span : 0;\n    return { x: a.x + (b.x - a.x) * f, y: a.y + (b.y - a.y) * f };\n  };\n  let lo = 0;\n  let hi = 0;\n  for (let i = 0; i < n; i++) {\n    if (s[i] < radius || end - s[i] < radius) {\n      continue;\n    }\n    while (lo + 1 < n && s[lo + 1] <= s[i] - radius) {\n      lo++;\n    }\n    while (hi + 1 < n && s[hi + 1] <= s[i] + radius) {\n      hi++;\n    }\n    const p = line[i];\n    const a = along(lo, s[i] - radius);\n    const b = along(hi, s[i] + radius);\n    const twice = Math.abs(\n      (b.x - a.x) * (p.y - a.y) - (b.y - a.y) * (p.x - a.x)\n    );\n    tight[i] = twice > 0 && gapOf(a, b) * gapOf(a, p) * gapOf(p, b) / (2 * twice) < radius ? 1 : 0;\n  }\n  return { tight, s };\n}\nfunction loosened(line, radius) {\n  const out = line.slice();\n  const { tight, s } = tightPoints(out, radius);\n  let windows = ownedWindows(\n    s,\n    Array.from(tight, (t) => t > 0),\n    3 * radius\n  );\n  for (let pass = 0; pass < 8 && windows.length; pass++) {\n    windows = windows.filter(([lo, hi]) => {\n      const part = out.slice(lo, hi + 1);\n      const local = tightPoints(part, radius);\n      if (!local.tight.includes(1)) {\n        return false;\n      }\n      const weight = windowMean(local.s, local.tight, radius);\n      const smoother = rounded(part, radius);\n      for (let k = 0; k < part.length; k++) {\n        const w = Math.min(1, 3 * weight[k]);\n        if (w > 0) {\n          const p = part[k];\n          const q = smoother[k];\n          out[lo + k] = { x: p.x + (q.x - p.x) * w, y: p.y + (q.y - p.y) * w };\n        }\n      }\n      return true;\n    });\n  }\n  return out;\n}\nfunction runSigns(s, own, canonical, forward, settle, half) {\n  const n = own.length;\n  const agreement = new Float64Array(n);\n  let hi = 0;\n  let lo = 0;\n  let sum2 = 0;\n  let decided = 0;\n  let pending = 0;\n  for (let i = 0; i < n; i++) {\n    while (hi < n && s[hi] - s[i] <= half) {\n      const theirs = canonical(hi);\n      const mine = own[hi];\n      agreement[hi] = theirs && mine ? theirs.nx * mine.nx + theirs.ny * mine.ny : 0;\n      sum2 += agreement[hi];\n      hi++;\n    }\n    while (s[i] - s[lo] > half) {\n      sum2 -= agreement[lo++];\n    }\n    if (Math.abs(sum2) > 1e-9) {\n      decided = sum2 < 0 ? -1 : 1;\n    }\n    if (!decided) {\n      continue;\n    }\n    for (; pending <= i; pending++) {\n      settle(pending, decided);\n    }\n  }\n  if (pending < n) {\n    let along = 0;\n    for (let k = 0; k < n; k++) {\n      along += forward(k) ? 1 : -1;\n    }\n    for (; pending < n; pending++) {\n      settle(pending, along < 0 ? -1 : 1);\n    }\n  }\n}\nfunction laneLines(runs, yToX, reach, band, smooth = true) {\n  const turn = Math.max(reach, 2 * band);\n  const curl = Math.PI * band;\n  const context = smooth ? curl + 3 * band + turn / 2 : turn / 2;\n  const frames = /* @__PURE__ */ new Map();\n  const firsts = /* @__PURE__ */ new Map();\n  const arcs = [];\n  const stepFrames = [];\n  const newFrame = (length) => ({\n    normals: new Array(length),\n    shifts: smooth ? new Array(length) : []\n  });\n  const place = (id, walk, visit, f) => {\n    let byWalk = frames.get(id);\n    if (!byWalk) {\n      byWalk = [];\n      frames.set(id, byWalk);\n    }\n    ;\n    (byWalk[walk] ??= [])[visit] = f;\n  };\n  runs.forEach((run, r) => {\n    const { walk, ids, visits, owned, starts, xs, ys, stepOf } = run;\n    const steps = ids.length;\n    const n = xs.length;\n    const own = new Array(steps);\n    for (let i = 0; i < steps; i++) {\n      if (owned[i]) {\n        own[i] = newFrame(starts[i + 1] - starts[i]);\n        firsts.set(ids[i], { run: r, step: i, frame: own[i] });\n        place(ids[i], walk, visits[i], own[i]);\n      }\n    }\n    const raw = new Float64Array(n);\n    for (let p = 1; p < n; p++) {\n      const dx = xs[p] - xs[p - 1];\n      const dy = ys[p] - ys[p - 1];\n      raw[p] = raw[p - 1] + Math.sqrt(dx * dx + dy * dy);\n    }\n    const end = raw[n - 1];\n    const firstRun = new Int32Array(steps).fill(-1);\n    const firstStep = new Int32Array(steps);\n    const firstFrame = new Array(steps);\n    for (let i = 0; i < steps; i++) {\n      const first = owned[i] ? void 0 : firsts.get(ids[i]);\n      if (first) {\n        firstRun[i] = first.run;\n        firstStep[i] = first.step;\n        firstFrame[i] = first.frame;\n      }\n    }\n    const plus = new Int32Array(steps);\n    const minus = new Int32Array(steps);\n    for (let i = 0; i + 1 < steps; i++) {\n      const same = firstRun[i] >= 0 && firstRun[i + 1] === firstRun[i];\n      const d = same ? firstStep[i + 1] - firstStep[i] : 0;\n      plus[i + 1] = plus[i] + (d === 1 ? 1 : 0);\n      minus[i + 1] = minus[i] + (d === -1 ? 1 : 0);\n    }\n    const shared = new Array(steps);\n    let reachFrom = 0;\n    let reachTo = 0;\n    for (let i = 0; i < steps; i++) {\n      if (!smooth) {\n        shared[i] = !owned[i];\n        continue;\n      }\n      const from = raw[starts[i]] - context;\n      const to = raw[starts[i + 1] - 1] + context;\n      while (raw[reachFrom] < from) {\n        reachFrom++;\n      }\n      while (reachTo + 1 < n && raw[reachTo + 1] <= to) {\n        reachTo++;\n      }\n      const lo = stepOf[Math.max(0, reachFrom - 1)];\n      const hi = stepOf[Math.min(n - 1, reachTo + 1)];\n      const span = hi - lo;\n      const forward = plus[hi] - plus[lo];\n      const backward = minus[hi] - minus[lo];\n      shared[i] = !owned[i] && from >= 0 && to <= end && span > 0 && (forward === span || backward === span);\n    }\n    for (let i = 0; i < steps; i++) {\n      if (owned[i]) {\n        continue;\n      }\n      const first = firstFrame[i];\n      own[i] = !smooth && shared[i] ? first : shared[i] ? { normals: first.normals, shifts: first.shifts } : newFrame(first.normals.length);\n      place(ids[i], walk, visits[i], own[i]);\n    }\n    stepFrames.push(own);\n    const apart = new Array(n);\n    for (let p = 0; p < n; p++) {\n      apart[p] = !shared[stepOf[p]];\n    }\n    for (const [from, to] of ownedWindows(raw, apart, context)) {\n      const points = [];\n      for (let p = from; p <= to; p++) {\n        points.push({ x: xs[p], y: ys[p] });\n      }\n      const line = smooth ? loosened(\n        rounded(cutCurls(points, band / 2, curl), band / 2),\n        band / 2\n      ) : points;\n      const normals = smoothedNormals(line, turn);\n      runSigns(\n        arcOf(line),\n        normals,\n        (k) => {\n          const i = stepOf[from + k];\n          return (owned[i] ? own[i] : firstFrame[i])?.normals[pointIndex(run, from + k)];\n        },\n        (k) => run.forward[stepOf[from + k]],\n        (k, sign) => {\n          const p = from + k;\n          const i = stepOf[p];\n          if (shared[i]) {\n            return;\n          }\n          const index = pointIndex(run, p);\n          const m = normals[k];\n          own[i].normals[index] = m && (sign > 0 ? m : { nx: -m.nx, ny: -m.ny });\n          if (smooth) {\n            own[i].shifts[index] = {\n              dx: line[k].x - points[k].x,\n              dy: (line[k].y - points[k].y) / yToX\n            };\n          }\n        },\n        turn\n      );\n    }\n    if (!smooth) {\n      arcs.push(raw);\n      return;\n    }\n    const s = new Float64Array(n);\n    let px = 0;\n    let py = 0;\n    for (let p = 0; p < n; p++) {\n      const shift = own[stepOf[p]].shifts[pointIndex(run, p)];\n      const x = xs[p] + (shift?.dx ?? 0);\n      const y = ys[p] + (shift?.dy ?? 0) * yToX;\n      s[p] = p ? s[p - 1] + Math.sqrt((x - px) ** 2 + (y - py) ** 2) : 0;\n      px = x;\n      py = y;\n    }\n    arcs.push(s);\n  });\n  return { frames, arcs, stepFrames };\n}\nfunction windowed(s, v, half, sign) {\n  const out = new Array(v.length);\n  const deque = [];\n  let head = 0;\n  let next = 0;\n  for (let i = 0; i < v.length; i++) {\n    while (next < v.length && s[next] - s[i] <= half) {\n      while (deque.length > head && sign * v[deque.at(-1)] <= sign * v[next]) {\n        deque.pop();\n      }\n      deque.push(next++);\n    }\n    while (s[i] - s[deque[head]] > half) {\n      head++;\n    }\n    out[i] = v[deque[head]];\n  }\n  return out;\n}\nfunction windowMean(s, v, half, counted = () => true) {\n  const n = v.length;\n  const sumW = new Float64Array(n + 1);\n  const sumWV = new Float64Array(n + 1);\n  for (let i = 0; i < n; i++) {\n    const w = !counted(v[i]) ? 0 : n > 1 ? (s[Math.min(i + 1, n - 1)] - s[Math.max(i - 1, 0)]) / 2 : 1;\n    sumW[i + 1] = sumW[i] + w;\n    sumWV[i + 1] = sumWV[i] + w * v[i];\n  }\n  const out = new Float64Array(n);\n  let lo = 0;\n  let hi = 0;\n  for (let i = 0; i < n; i++) {\n    while (s[i] - s[lo] > half) {\n      lo++;\n    }\n    while (hi < n && s[hi] - s[i] <= half) {\n      hi++;\n    }\n    const w = sumW[hi] - sumW[lo];\n    out[i] = w > 0 ? (sumWV[hi] - sumWV[lo]) / w : v[i];\n  }\n  return out;\n}\nvar ONE_THREAD = [0];\nfunction repeats(passes) {\n  for (const p of passes.values()) {\n    if (p > 1) {\n      return true;\n    }\n  }\n  return false;\n}\nfunction walkThreads(route, passes, nodePositions, yToX, reach) {\n  if (!repeats(passes)) {\n    return {\n      span: passes,\n      nodeThreads: /* @__PURE__ */ new Map(),\n      threadPasses: /* @__PURE__ */ new Map(),\n      threadAt: /* @__PURE__ */ new Map(),\n      linkThreads: /* @__PURE__ */ new Map()\n    };\n  }\n  const index = /* @__PURE__ */ new Map();\n  const ids = [];\n  const widths = [];\n  const visits = [];\n  const steps = [];\n  const stepVisits = [];\n  const stepWants = [];\n  const stepGlides = [];\n  for (const piece of route) {\n    const points = [];\n    const nodes = [];\n    for (const id of piece) {\n      let k = index.get(id);\n      if (k === void 0) {\n        k = ids.length;\n        index.set(id, k);\n        ids.push(id);\n        widths.push(0);\n        visits.push(0);\n      }\n      nodes.push(k);\n      const segments = nodePositions[id];\n      const mid = segments?.[Math.floor(segments.length / 2)];\n      points.push(\n        mid ? { x: mid.x, y: mid.y * yToX } : points.at(-1) ?? { x: 0, y: 0 }\n      );\n    }\n    const s = arcOf(points);\n    const p = piece.map((id) => passes.get(id) ?? 1);\n    const most = windowed(s, p, reach / 2, 1);\n    const copy = nodes.map((k) => ++visits[k]);\n    const n = piece.length;\n    const before = new Int32Array(n);\n    let last = -1;\n    for (let i = 0; i < n; i++) {\n      last = p[i] === most[i] ? i : last;\n      before[i] = last;\n    }\n    const after = new Int32Array(n);\n    last = -1;\n    for (let i = n - 1; i >= 0; i--) {\n      last = p[i] === most[i] ? i : last;\n      after[i] = last;\n    }\n    const wants = new Array(n);\n    const glides = new Array(n).fill(NaN);\n    for (let i = 0; i < n; i++) {\n      const b = before[i];\n      const a = after[i];\n      const nearest = b < 0 ? a : a < 0 ? b : s[i] - s[b] <= s[a] - s[i] ? b : a;\n      const want = (k) => Math.min(copy[k], most[i]) - 1;\n      wants[i] = want(nearest);\n      if (p[i] === 1 && b >= 0 && a >= 0 && want(a) !== want(b)) {\n        const f = (s[i] - s[b]) / (s[a] - s[b] || 1);\n        glides[i] = want(b) + (want(a) - want(b)) * f;\n      }\n      widths[nodes[i]] = Math.max(widths[nodes[i]], most[i]);\n    }\n    steps.push(nodes);\n    stepVisits.push(copy);\n    stepWants.push(wants);\n    stepGlides.push(glides);\n  }\n  const taken = [];\n  const threadOf = [];\n  const free = (k, want) => {\n    const width = widths[k];\n    const own = taken[k] ??= /* @__PURE__ */ new Set();\n    for (let d = 0; d < width; d++) {\n      for (const c of [want - d, want + d]) {\n        if (c >= 0 && c < width && !own.has(c)) {\n          return c;\n        }\n      }\n    }\n    return want;\n  };\n  const glideOf = [];\n  steps.forEach((nodes, piece) => {\n    nodes.forEach((k, i) => {\n      if (widths[k] > 1) {\n        const glide = stepGlides[piece][i];\n        const t = free(\n          k,\n          Number.isNaN(glide) ? stepWants[piece][i] : Math.round(glide)\n        );\n        taken[k].add(t);\n        (threadOf[k] ??= [])[stepVisits[piece][i]] = t;\n        if (!Number.isNaN(glide)) {\n          ;\n          (glideOf[k] ??= [])[t] = glide;\n        }\n      }\n    });\n  });\n  const span = /* @__PURE__ */ new Map();\n  const nodeThreads = /* @__PURE__ */ new Map();\n  const threadPasses = /* @__PURE__ */ new Map();\n  const threadAt = /* @__PURE__ */ new Map();\n  ids.forEach((id, k) => {\n    if (glideOf[k]) {\n      threadAt.set(id, glideOf[k]);\n    }\n    span.set(id, widths[k]);\n    nodeThreads.set(\n      id,\n      taken[k] ? [...taken[k]].sort((a, b) => a - b) : ONE_THREAD\n    );\n    const passOf = [];\n    threadOf[k]?.forEach((thread, visit) => {\n      passOf[thread] = visit - 1;\n    });\n    threadPasses.set(id, passOf);\n  });\n  const linkThreads = /* @__PURE__ */ new Map();\n  steps.forEach((nodes, piece) => {\n    const visit = stepVisits[piece];\n    for (let i = 1; i < nodes.length; i++) {\n      const from = nodes[i - 1];\n      const to = nodes[i];\n      const pair = [\n        threadOf[from]?.[visit[i - 1]] ?? 0,\n        threadOf[to]?.[visit[i]] ?? 0\n      ];\n      let ahead = linkThreads.get(ids[from]);\n      if (!ahead) {\n        ahead = /* @__PURE__ */ new Map();\n        linkThreads.set(ids[from], ahead);\n      }\n      const list = ahead.get(ids[to]);\n      if (!list) {\n        ahead.set(ids[to], [pair]);\n      } else if (!list.some(([a, b]) => a === pair[0] && b === pair[1])) {\n        list.push(pair);\n      }\n    }\n  });\n  return { span, nodeThreads, threadPasses, threadAt, linkThreads };\n}\nfunction bandSpans(runs, arcs, spans, { reach, taper }) {\n  const out = /* @__PURE__ */ new Map();\n  runs.forEach((run, r) => {\n    const s = arcs[r];\n    const along = run.ids.map((_, i) => {\n      const length = run.starts[i + 1] - run.starts[i];\n      const middle = Math.floor(length / 2);\n      return s[run.starts[i] + (run.forward[i] ? middle : length - 1 - middle)];\n    });\n    for (const [lo, hi] of ownedWindows(\n      along,\n      run.owned,\n      reach / 2 + taper / 2\n    )) {\n      const at = along.slice(lo, hi + 1);\n      const ids = run.ids.slice(lo, hi + 1);\n      const eased = spans.map((own) => {\n        const raw = ids.map((id) => own.get(id) ?? 0);\n        return raw.every((v) => v === raw[0]) ? { slot: raw, held: raw } : {\n          slot: windowMean(at, windowed(at, raw, reach / 2, 1), taper / 2),\n          held: windowMean(at, raw, taper / 2, (v) => v > 0)\n        };\n      });\n      ids.forEach((id, i) => {\n        if (run.owned[lo + i]) {\n          out.set(id, {\n            slot: eased.map((e) => e.slot[i]),\n            held: eased.map((e) => e.held[i])\n          });\n        }\n      });\n    }\n  });\n  return out;\n}\nfunction easeOffsets(runs, stepFrames, arcs, spans, passes, threads, half) {\n  const plain = slotCentres(passes, passes);\n  const byNode = /* @__PURE__ */ new Map();\n  const centresAt = (id) => {\n    let centres = byNode.get(id);\n    if (!centres) {\n      const own = spans.get(id);\n      centres = own ? slotCentres(own.slot, passes, own.held) : plain;\n      byNode.set(id, centres);\n    }\n    return centres;\n  };\n  runs.forEach((run, r) => {\n    const { walk, ids, visits, starts } = run;\n    const { threadPasses, threadAt } = threads[walk];\n    const raw = new Float64Array(run.xs.length);\n    ids.forEach((id, i) => {\n      const thread = Math.max(0, threadPasses.get(id)?.indexOf(visits[i]) ?? 0);\n      const place = threadAt.get(id)?.[thread] ?? thread;\n      raw.fill(\n        centresAt(id)[walk] + place * THREAD_PITCH_PX,\n        starts[i],\n        starts[i + 1]\n      );\n    });\n    const eased = windowMean(arcs[r], raw, half);\n    stepFrames[r].forEach((frame, i) => {\n      const from = starts[i];\n      const to = starts[i + 1];\n      let constant = true;\n      for (let p = from + 1; constant && p < to; p++) {\n        constant = Math.abs(eased[p] - eased[from]) < 1e-9;\n      }\n      if (constant) {\n        frame.offset = eased[from];\n        return;\n      }\n      const offsets = new Array(to - from);\n      for (let p = from; p < to; p++) {\n        offsets[pointIndex(run, p)] = eased[p];\n      }\n      frame.offsets = offsets;\n    });\n  });\n}\nfunction liftLanes(walks, nodePositions, yToX, worldPerScreenPx, steps = walkSteps(\n  walks.map((w) => w.route),\n  nodePositions\n)) {\n  const threaded = threadsPasses(walks);\n  const passes = walks.map((w) => w.mostPasses);\n  const reach = THREAD_REACH_PX * worldPerScreenPx;\n  const runs = laneRuns(steps, yToX, LANE_SMOOTHING_PX * worldPerScreenPx);\n  const band = bandWidthPx(passes) * (threaded ? bandScale(passes) : 1) * worldPerScreenPx;\n  const lines = laneLines(\n    runs,\n    yToX,\n    LANE_SMOOTHING_PX * worldPerScreenPx,\n    band,\n    threaded\n  );\n  const threads = threaded ? walks.map((w) => walkThreads(w.route, w.passes, nodePositions, yToX, reach)) : void 0;\n  const spans = threads ? bandSpans(\n    runs,\n    lines.arcs,\n    threads.map((t) => t.span),\n    { reach, taper: THREAD_TAPER_PX * worldPerScreenPx }\n  ) : void 0;\n  if (spans && threads) {\n    easeOffsets(\n      runs,\n      lines.stepFrames,\n      lines.arcs,\n      spans,\n      passes,\n      threads,\n      THREAD_TAPER_PX / 2 * worldPerScreenPx\n    );\n  }\n  const furthestShift = { dx: 0, dy: 0 };\n  const seenShifts = /* @__PURE__ */ new Set();\n  for (const byWalk of lines.frames.values()) {\n    for (const { shifts } of byWalk.flat()) {\n      if (seenShifts.has(shifts)) {\n        continue;\n      }\n      seenShifts.add(shifts);\n      for (const shift of shifts) {\n        furthestShift.dx = Math.max(furthestShift.dx, Math.abs(shift?.dx ?? 0));\n        furthestShift.dy = Math.max(furthestShift.dy, Math.abs(shift?.dy ?? 0));\n      }\n    }\n  }\n  return { lines, threads, spans, furthestShift };\n}\n\nexport {\n  THREAD_PX,\n  THREAD_GAP_PX,\n  SLOT_GAP_PX,\n  LANE_SMOOTHING_PX,\n  THREAD_REACH_PX,\n  THREAD_TAPER_PX,\n  MAX_BAND_PX,\n  PASSES_KEY,\n  threadsPasses,\n  THREAD_PITCH_PX,\n  slotCentres,\n  bandWidthPx,\n  bandScale,\n  passesKey,\n  laneSlideAt,\n  walkSteps,\n  laneRuns,\n  laneLines,\n  walkThreads,\n  bandSpans,\n  liftLanes\n};\n", "// src/renderer/colorBits.ts\nfunction packAbgr(r, g, b, a) {\n  return (a << 24 | b << 16 | g << 8 | r) >>> 0;\n}\nfunction abgrRed(c) {\n  return c & 255;\n}\nfunction abgrGreen(c) {\n  return c >>> 8 & 255;\n}\nfunction abgrBlue(c) {\n  return c >>> 16 & 255;\n}\nfunction abgrAlpha(c) {\n  return c >>> 24 & 255;\n}\nfunction abgrToCssRgba(c) {\n  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;\n}\nfunction normalizedRgbToCssRgba(c, alpha) {\n  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;\n}\nfunction fadeAbgr(c, alpha) {\n  return packAbgr(\n    abgrRed(c),\n    abgrGreen(c),\n    abgrBlue(c),\n    Math.round(abgrAlpha(c) * alpha)\n  );\n}\nfunction brightenAbgr(c, factor) {\n  const t = Math.max(0, 1 - 1 / factor);\n  const lift = (v) => Math.round(v + (255 - v) * t);\n  return packAbgr(\n    lift(abgrRed(c)),\n    lift(abgrGreen(c)),\n    lift(abgrBlue(c)),\n    abgrAlpha(c)\n  );\n}\n\nexport {\n  packAbgr,\n  abgrRed,\n  abgrGreen,\n  abgrBlue,\n  abgrAlpha,\n  abgrToCssRgba,\n  normalizedRgbToCssRgba,\n  fadeAbgr,\n  brightenAbgr\n};\n", "// src/referenceRampCss.ts\nvar REFERENCE_RAMP_MAX_HUE = 300;\nvar REFERENCE_RAMP_SATURATION = 0.7;\nvar REFERENCE_RAMP_LIGHTNESS = 0.5;\nfunction rampHueCss(hue) {\n  return `hsl(${hue}, ${REFERENCE_RAMP_SATURATION * 100}%, ${REFERENCE_RAMP_LIGHTNESS * 100}%)`;\n}\nfunction rampHueAt(frac) {\n  return Math.max(0, Math.min(1, frac)) * REFERENCE_RAMP_MAX_HUE;\n}\nfunction rampHue(bp, domain) {\n  return rampHueAt((bp - domain.start) / (domain.end - domain.start));\n}\nvar HUE_STOP_DEG = 30;\nfunction rampStops({ start, bp, reversed }, domain) {\n  const low = rampHue(start, domain);\n  const high = rampHue(start + bp, domain);\n  if (high - low < 1) {\n    return [(low + high) / 2];\n  }\n  const n = Math.ceil((high - low) / HUE_STOP_DEG);\n  return Array.from(\n    { length: n + 1 },\n    (_, i) => rampHue(start + bp * (reversed ? n - i : i) / n, domain)\n  );\n}\nvar RAMP_GRADIENT_STOPS = Array.from({ length: 7 }, (_, i) => ({\n  offset: i / 6,\n  color: rampHueCss(i / 6 * REFERENCE_RAMP_MAX_HUE)\n}));\nvar RAMP_GRADIENT_CSS = `linear-gradient(to right, ${RAMP_GRADIENT_STOPS.map(\n  (s) => `${s.color} ${s.offset * 100}%`\n).join(\", \")})`;\n\nexport {\n  REFERENCE_RAMP_MAX_HUE,\n  REFERENCE_RAMP_SATURATION,\n  REFERENCE_RAMP_LIGHTNESS,\n  rampHueCss,\n  rampHueAt,\n  rampHue,\n  rampStops,\n  RAMP_GRADIENT_STOPS,\n  RAMP_GRADIENT_CSS\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-ALGYCMMH.js\";\n\n// src/util/edgeCurves.ts\nvar cache = weakMemo();\nfunction baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {\n  return cache(\n    nodePositions,\n    [graph, axis.scaleX, axis.scaleY, deletions, routes, stranded, version],\n    () => {\n      const curves = /* @__PURE__ */ new Map();\n      for (let ei = 0; ei < graph.edges.length; ei++) {\n        const bypassed = deletions?.get(ei);\n        const edgeCurves = edgeCurvesOf(\n          nodePositions,\n          graph.edges[ei],\n          axis,\n          bypassed,\n          bypassed && routes?.[ei],\n          stranded\n        );\n        if (edgeCurves) {\n          curves.set(ei, edgeCurves);\n        }\n      }\n      return curves;\n    }\n  );\n}\n\nexport {\n  baseEdgeCurves\n};\n", "import {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/referenceSpan.ts\nvar MAX_BACKBONE_HOPS = 4;\nfunction buildNeighbors(graph) {\n  const neighbors = /* @__PURE__ */ new Map();\n  for (const edge of graph.edges) {\n    pushTo(neighbors, edge.from, edge.to);\n    pushTo(neighbors, edge.to, edge.from);\n  }\n  return neighbors;\n}\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const seen = /* @__PURE__ */ new Set([nodeId]);\n  let frontier = [nodeId];\n  let minEnd = Infinity;\n  let maxStart = -Infinity;\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next = [];\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  return minEnd === Infinity ? void 0 : {\n    start: Math.min(minEnd, maxStart),\n    end: Math.max(minEnd, maxStart)\n  };\n}\nfunction nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const node = nodeById.get(nodeId);\n  return node === void 0 ? void 0 : isBackbone(node) ? { start: node.stable.start, end: node.stable.start + node.length } : flankingSpan({ nodeId, nodeById, neighbors });\n}\nfunction referenceMidpoints(graph) {\n  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));\n  const neighbors = buildNeighbors(graph);\n  const midpoints = /* @__PURE__ */ new Map();\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}\nfunction referencePositions(graph) {\n  const positions = referenceMidpoints(graph);\n  const neighbors = buildNeighbors(graph);\n  let frontier = [...positions.keys()];\n  while (frontier.length > 0) {\n    const next = [];\n    for (const id of frontier) {\n      for (const neighborId of neighbors.get(id) ?? []) {\n        if (!positions.has(neighborId)) {\n          positions.set(neighborId, positions.get(id));\n          next.push(neighborId);\n        }\n      }\n    }\n    frontier = next;\n  }\n  return positions;\n}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints,\n  referencePositions\n};\n", "import {\n  THREAD_PITCH_PX,\n  THREAD_PX,\n  bandScale,\n  bandWidthPx,\n  liftLanes,\n  slotCentres,\n  threadsPasses,\n  walkSteps\n} from \"./chunk-YUIKEUKY.js\";\nimport {\n  abgrToCssRgba,\n  fadeAbgr,\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\nimport {\n  baseEdgeCurves\n} from \"./chunk-URPU4XCM.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-HI5GLE7C.js\";\nimport {\n  nodeWidthPx,\n  walkLaneWidthPx,\n  widthNorm\n} from \"./chunk-XWH4LB56.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-L4DBSRA2.js\";\nimport {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  dashSpans,\n  pathRibbonOffsets,\n  polylinePx,\n  slideCurves,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-JJV2GT2Z.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  busiestEdge,\n  edgeWidthFactor\n} from \"./chunk-DAEEMZ74.js\";\n\n// src/renderer/GeometryBuilder.ts\nvar EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);\nvar EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);\nvar EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);\nvar DELETION_THICKNESS_FACTOR = 2.2;\nvar LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255);\nvar FADED_ALPHA = 0.18;\nvar MOVED_ALPHA = 0.45;\nvar LIFT_BACKDROP_CSS = abgrToCssRgba(\n  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)\n);\nvar DELETION_DASH_PX = 11;\nvar MIN_PATH_STRIPE_PX = 1.2;\nvar MIN_SCALE_FOR_OFFSET = 1e-6;\nvar ARROW_LENGTH_BASE_PX = 7;\nvar ARROW_LENGTH_PER_EDGE_PX = 3;\nvar ARROW_HALF_WIDTH_BASE_PX = 3;\nvar ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;\nvar MIN_LINK_HEADS = 3;\nvar MIN_ARROW_FIT = 0.5;\nvar MIN_ARROW_SCALE = 0.45;\nvar ARROW_CURVE_STEPS = 12;\nvar ABUTTING_PX = 1e-6;\nvar walkX = new Float64Array(64);\nvar walkY = new Float64Array(64);\nvar walkPx = new Float64Array(64);\nfunction backFromEnd(curves, scale, yToX, untilPx) {\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}\nfunction walkPointAt(n, px) {\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}\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments\n}) {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;\n  const n = backFromEnd(\n    curves,\n    scale,\n    yToX,\n    nodeHalfWidth + MIN_LINK_HEADS * length\n  );\n  const lengthPx = walkPx[n - 1];\n  const abutting = lengthPx < ABUTTING_PX;\n  const inset = Math.min(nodeHalfWidth, lengthPx);\n  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, scale * yToX) / length) : 1;\n  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {\n    return void 0;\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: Math.hypot(dx, dy) > 0 ? Math.atan2(dy, dx) : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth: (ARROW_HALF_WIDTH_BASE_PX + ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) * fit,\n    color\n  };\n}\nvar FIRST_THREADS = [[0, 0]];\nvar ONE_PASS = [0];\nvar NO_SHIFT = { dx: 0, dy: 0 };\nfunction nearerStart(at, segments, yToX) {\n  const gap = (p) => Math.hypot(p.x - at.x, (p.y - at.y) * yToX);\n  return gap(segments[0]) < gap(segments.at(-1));\n}\nfunction leavesStart(edge, segments, first, stranded, yToX) {\n  return stranded ? strandSides(edge).from === \"start\" : nearerStart({ x: first.x0, y: first.y0 }, segments, yToX);\n}\nfunction intoDirection(last, toSegments) {\n  if (toSegments.length < 2) {\n    return void 0;\n  }\n  const first = toSegments[0];\n  const final = toSegments[toSegments.length - 1];\n  const atStart = Math.hypot(last.x1 - first.x, last.y1 - first.y) <= Math.hypot(last.x1 - final.x, last.y1 - final.y);\n  return atStart ? { from: first, to: toSegments[1] } : { from: final, to: toSegments[toSegments.length - 2] };\n}\nfunction normal(a, b) {\n  if (!a || !b) {\n    return void 0;\n  }\n  const dx = b.x - a.x;\n  const dy = b.y - a.y;\n  const len = Math.hypot(dx, dy);\n  return len > 0 ? { nx: -dy / len, ny: dx / len } : void 0;\n}\nvar MITRE_LIMIT = 0.1;\nvar LONGEST_NORMAL = 1 / Math.sqrt(MITRE_LIMIT);\nfunction pointNormalsOf(rawPoints, yToX = 1) {\n  const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));\n  return points.map((p, i) => {\n    const before = normal(points[i - 1], p);\n    const after = normal(p, points[i + 1]);\n    if (before && after) {\n      const nx = (before.nx + after.nx) / 2;\n      const ny = (before.ny + after.ny) / 2;\n      const dot = before.nx * nx + before.ny * ny;\n      return dot > MITRE_LIMIT ? { nx: nx / dot, ny: ny / dot } : { nx, ny };\n    }\n    return before ?? after ?? { nx: 0, ny: 0 };\n  });\n}\nfunction offsetPolyline(points, normals, distance, yToX = 1) {\n  const out = new Array(points.length);\n  for (let i = 0; i < points.length; i++) {\n    const d = typeof distance === \"number\" ? distance : distance[i];\n    out[i] = {\n      x: points[i].x + normals[i].nx * d,\n      y: points[i].y + normals[i].ny * d / yToX\n    };\n  }\n  return out;\n}\nfunction hslToRgb(h, s, l) {\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}\nfunction packHsl(h, s, l, a = 1) {\n  const [r, g, b] = hslToRgb(h, s, l);\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}\nvar DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37]\n];\nvar STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122]\n];\nvar NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220]\n];\nfunction sampleGradient(stops, t) {\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}\nfunction hashColor(str, alpha) {\n  return packHsl(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS, alpha);\n}\nvar REFERENCE_RAMP_ALT_RGB = [60, 65, 72];\nvar REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);\nvar REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(\", \")})`;\nfunction rampFraction(node, ramp) {\n  const mid = ramp.midpoints.get(node.id);\n  return isBackbone(node) && mid !== void 0 ? (mid - ramp.start) / ramp.span : void 0;\n}\nfunction computeReferenceRamp(graph, domain) {\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}\nfunction computeColorSchemeRange(graph, referenceRamp) {\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 !== void 0 && 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    referenceRamp\n  };\n}\nfunction getNodeColor(node, nodeIndex, colorScheme, range) {\n  switch (colorScheme) {\n    case \"random\":\n      return hashColor(node.id, 1);\n    case \"depth\":\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth) : 0.5\n      );\n    case \"node-length\":\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength ? (node.length - range.minLength) / (range.maxLength - range.minLength) : 0.5\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 === void 0 ? packAbgr(160, 160, 160, 255) : node.stable.rank === 0 ? packAbgr(52, 152, 219, 255) : sampleGradient(\n        STABLE_RANK_GRADIENT,\n        range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0\n      );\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state, so only the backbone takes a hue\n    case \"reference-position\": {\n      const ramp = range.referenceRamp;\n      if (ramp === void 0) {\n        return packAbgr(160, 160, 160, 255);\n      }\n      const t = rampFraction(node, ramp);\n      return t === void 0 ? REFERENCE_RAMP_ALT_COLOR : packHsl(\n        rampHueAt(t),\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS\n      );\n    }\n    case \"grey\":\n      return packAbgr(160, 160, 160, 255);\n    case \"rainbow\": {\n      const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;\n      return packHsl(hue, 0.75, 0.5);\n    }\n    default:\n      return packAbgr(52, 152, 219, 255);\n  }\n}\nfunction endTangent(c, yToX = 1, into) {\n  const candidates = [\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 ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x) : 0;\n}\nfunction isPolylineInBounds(segments, bounds) {\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 = Math.max(a.x, b.x) >= bounds.minX && Math.min(a.x, b.x) <= bounds.maxX && Math.max(a.y, b.y) >= bounds.minY && Math.min(a.y, b.y) <= bounds.maxY;\n  }\n  return hit;\n}\nfunction isBezierInBounds(curves, bounds, growX = 0, growY = 0) {\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 (cMaxX >= bounds.minX - growX && cMinX <= bounds.maxX + growX && cMaxY >= bounds.minY - growY && cMinY <= bounds.maxY + growY) {\n      return true;\n    }\n  }\n  return false;\n}\nvar paletteCache = /* @__PURE__ */ new WeakMap();\nfunction pathPaletteOf(graph) {\n  let palette = paletteCache.get(graph);\n  if (!palette) {\n    const pathColorByIndex = [];\n    const pathIndexByName = /* @__PURE__ */ new Map();\n    const paths = graph.paths ?? [];\n    for (let i = 0; i < paths.length; i++) {\n      pathColorByIndex.push(\n        packHsl(\n          pathHueAt(i, paths.length),\n          PATH_SATURATION,\n          PATH_LIGHTNESS,\n          0.85\n        )\n      );\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}\nvar slotsCache = /* @__PURE__ */ new WeakMap();\nvar NO_SLOTS = /* @__PURE__ */ new Map();\nfunction pathSlotsOf(graph) {\n  let slots = slotsCache.get(graph);\n  if (!slots) {\n    slots = /* @__PURE__ */ new Map();\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        pushTo(slots, nodeId, pathIdx);\n      }\n    }\n    slotsCache.set(graph, slots);\n  }\n  return slots;\n}\nvar lanesCache = weakMemo();\nvar stepsCache = weakMemo();\nvar linksCache = /* @__PURE__ */ new WeakMap();\nfunction linksOf(graph) {\n  let links = linksCache.get(graph);\n  if (!links) {\n    links = /* @__PURE__ */ new Map();\n    for (const { from, to } of graph.edges) {\n      let out = links.get(from);\n      if (!out) {\n        out = /* @__PURE__ */ new Set();\n        links.set(from, out);\n      }\n      out.add(to);\n    }\n    linksCache.set(graph, links);\n  }\n  return links;\n}\nfunction buildGeometry(options) {\n  const {\n    nodePositions,\n    graph,\n    nodeById,\n    colorScheme,\n    contigThickness,\n    connectorThickness,\n    drawPaths,\n    nodeWidth = \"uniform\",\n    edgeWidth = \"uniform\",\n    highlight,\n    axis,\n    linearLayout,\n    viewportBounds,\n    referenceRamp,\n    deletions,\n    deletionRoutes,\n    stranded,\n    hiddenEdges,\n    version = 0\n  } = options;\n  const widthScale = widthNorm(graph, nodeWidth);\n  const busiest = edgeWidth === \"walks\" ? busiestEdge(graph) : 0;\n  const scale = axis.scaleX;\n  const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n  const yToX = yToXOf(axis);\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n    deletionRoutes,\n    stranded\n  );\n  const nodeStrokes = [];\n  const nodeStrokeRuns = /* @__PURE__ */ new Map();\n  const arrows = [];\n  const arrowRuns = /* @__PURE__ */ new Map();\n  const edgeCurves = [];\n  const edgeCurveRuns = /* @__PURE__ */ new Map();\n  const colorRange = computeColorSchemeRange(graph, referenceRamp);\n  const nodeIndexMap = /* @__PURE__ */ new Map();\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  const pathCount = graph.paths?.length ?? 0;\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph);\n  const pathColorByName = (name) => pathColorByIndex[pathIndexByName.get(name) ?? -1] ?? EDGE_PATH_FALLBACK_COLOR;\n  const nodePathSlots = drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS;\n  const liftedWalks = highlight?.walks ?? [];\n  const threaded = threadsPasses(liftedWalks);\n  const lanePasses = liftedWalks.map((w) => w.mostPasses);\n  const thinned = threaded ? bandScale(lanePasses) : 1;\n  const fields = highlight && liftedWalks.length > 1 ? lanesCache(\n    highlight,\n    [nodePositions, version, axis.scaleX, axis.scaleY],\n    () => liftLanes(\n      liftedWalks,\n      nodePositions,\n      yToX,\n      worldPerScreenPx,\n      stepsCache(\n        highlight,\n        [nodePositions, version],\n        () => walkSteps(\n          liftedWalks.map((w) => w.route),\n          nodePositions\n        )\n      )\n    )\n  ) : void 0;\n  const lines = fields?.lines;\n  const threads = fields?.threads;\n  const spanField = fields?.spans;\n  const plainCentres = threaded ? slotCentres(lanePasses, lanePasses) : [];\n  const centresByNode = /* @__PURE__ */ new Map();\n  const centresOf = (nodeId) => {\n    let centres = centresByNode.get(nodeId);\n    if (!centres) {\n      const spans = spanField?.get(nodeId);\n      centres = spans ? slotCentres(spans.slot, lanePasses, spans.held) : plainCentres;\n      centresByNode.set(nodeId, centres);\n    }\n    return centres;\n  };\n  const laneOffset = (nodeId, laneWidth, lane, pass) => threaded ? (centresOf(nodeId)[lane] + pass * THREAD_PITCH_PX) * thinned : (lane - (liftedWalks.length - 1) / 2) * laneWidth;\n  const threadOffsetAt = (frame, at, fallback) => {\n    const eased = frame?.offsets?.[at] ?? frame?.offset;\n    return eased === void 0 ? fallback : eased * thinned;\n  };\n  const laneHalfWidth = (laneWidth) => threaded ? THREAD_PX / 2 * thinned : laneWidth / 2;\n  const plainNormals = /* @__PURE__ */ new Map();\n  const visitNormals = /* @__PURE__ */ new WeakMap();\n  const visitOf = (lane, nodeId, thread) => threads?.[lane]?.threadPasses.get(nodeId)?.[thread] ?? 0;\n  const plainNormalsOf = (nodeId, segments) => {\n    let normals = plainNormals.get(nodeId);\n    if (!normals) {\n      normals = pointNormalsOf(segments, yToX);\n      plainNormals.set(nodeId, normals);\n    }\n    return normals;\n  };\n  const laneNormalsOf = (nodeId, segments, frame) => {\n    if (!frame) {\n      return plainNormalsOf(nodeId, segments);\n    }\n    let normals = visitNormals.get(frame.normals);\n    if (!normals) {\n      normals = plainNormalsOf(nodeId, segments).map(\n        (n, i) => frame.normals[i] ?? n\n      );\n      visitNormals.set(frame.normals, normals);\n    }\n    return normals;\n  };\n  const laneWidths = /* @__PURE__ */ new Map();\n  const laneWidthOf = (id) => {\n    let width = laneWidths.get(id);\n    if (width === void 0) {\n      const node = nodeById.get(id);\n      width = walkLaneWidthPx(\n        node ? nodeWidthPx(node, contigThickness, nodeWidth, widthScale) : contigThickness,\n        liftedWalks.length\n      );\n      laneWidths.set(id, width);\n    }\n    return width;\n  };\n  const laneEndOf = (id, frames, segments, atStart, lane, thread) => {\n    const at = atStart ? 0 : segments.length - 1;\n    const frame = frames?.[lane]?.[visitOf(lane, id, thread)];\n    const eased = frame?.offsets?.[at] ?? frame?.offset;\n    return {\n      normal: frame?.normals[at] ?? plainNormalsOf(id, segments)[at] ?? { nx: 0, ny: 0 },\n      shift: frame?.shifts[at] ?? NO_SHIFT,\n      offset: eased === void 0 ? laneOffset(id, laneWidthOf(id), lane, thread) : eased * thinned\n    };\n  };\n  const lanesMayShow = (curves, fromId) => {\n    if (!viewportBounds) {\n      return true;\n    }\n    const offset = threaded ? bandWidthPx(lanePasses) * thinned : (liftedWalks.length - 1) / 2 * laneWidthOf(fromId);\n    const reach = LONGEST_NORMAL * offset * worldPerScreenPx;\n    return isBezierInBounds(\n      curves,\n      viewportBounds,\n      reach + (fields?.furthestShift.dx ?? 0),\n      reach / yToX + (fields?.furthestShift.dy ?? 0)\n    );\n  };\n  const threadPairs = (lane, from, to) => {\n    const own = threads?.[lane]?.linkThreads;\n    if (!own?.size) {\n      return FIRST_THREADS;\n    }\n    const ahead = own.get(from)?.get(to);\n    const back = linksOf(graph).get(to)?.has(from) ? void 0 : own.get(to)?.get(from);\n    if (!back) {\n      return ahead ?? FIRST_THREADS;\n    }\n    const turned = back.map(([a, b]) => [b, a]);\n    return ahead ? [...ahead, ...turned] : turned;\n  };\n  const threadColor = (lane, nodeId, thread) => liftedWalks[lane]?.passColors.get(nodeId)?.[threads?.[lane]?.threadPasses.get(nodeId)?.[thread] ?? 0];\n  const visitPoints = /* @__PURE__ */ new WeakMap();\n  const lanePointsOf = (segments, frame) => {\n    if (!frame || !threaded) {\n      return segments;\n    }\n    let points = visitPoints.get(frame.shifts);\n    if (!points) {\n      const { shifts } = frame;\n      points = segments.map((p, i) => {\n        const { dx, dy } = shifts[i] ?? NO_SHIFT;\n        return { ...p, x: p.x + dx, y: p.y + dy };\n      });\n      visitPoints.set(frame.shifts, points);\n    }\n    return points;\n  };\n  const showArrows = scale > (linearLayout ? 1 : MIN_ARROW_SCALE);\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 (!fromSegments?.length || !toSegments?.length || !baseCurves || hiddenEdges?.has(ei)) {\n      continue;\n    }\n    const numPaths = edge.pathIds?.length ?? 0;\n    const bypassed = deletions?.get(ei);\n    const isDeletion = bypassed !== void 0;\n    const onWalk = highlight?.edgeIndexes.has(ei) ?? false;\n    const ribbonThickness = connectorThickness / 2 * (isDeletion ? DELETION_THICKNESS_FACTOR : 1);\n    const walkFactor = edgeWidthFactor(numPaths, busiest, edgeWidth);\n    const edgeThickness = connectorThickness / 2 * (!isDeletion ? walkFactor : edgeWidth === \"walks\" && busiest > 0 ? Math.max(1, walkFactor) : DELETION_THICKNESS_FACTOR);\n    const ribbons = drawPaths && numPaths > 0;\n    const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR;\n    const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);\n    const toNode = nodeById.get(edge.to);\n    const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, widthScale) : contigThickness) / 2;\n    const inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);\n    const dashesOf = (curves) => dashSpans(curves, DELETION_DASH_PX / scale, yToX, viewportBounds);\n    const stroke = (curves, thickness, color) => {\n      if (!isDeletion) {\n        edgeCurves.push({ curves, thickness, color });\n        return;\n      }\n      for (const dash of dashesOf(curves)) {\n        edgeCurves.push({ curves: dash.curves, thickness, color });\n      }\n    };\n    const laneStroke = (curves, thickness, color, walk, pass, normal2, offsetX, endNormal, endOffsetX) => {\n      edgeCurves.push({\n        curves,\n        thickness,\n        color,\n        walk,\n        pass,\n        normal: normal2,\n        offsetX,\n        endNormal,\n        endOffsetX\n      });\n    };\n    const arrowOn = (curves) => {\n      const head = showArrows ? arrowheadFor({\n        curves,\n        edgeHalfWidth: isDeletion || ribbons ? connectorThickness / 2 : edgeThickness,\n        nodeHalfWidth: intoHalfWidth,\n        scale,\n        yToX,\n        color: edgeColor,\n        fromSegments,\n        toSegments\n      }) : void 0;\n      if (head) {\n        arrows.push(head);\n      }\n    };\n    const edgeCurveStart = edgeCurves.length;\n    const arrowStart = arrows.length;\n    const laneWalks = highlight?.walks.length && onWalk && !ribbons ? highlight.walks : void 0;\n    if (laneWalks && !lanesMayShow(baseCurves, edge.from)) {\n      continue;\n    }\n    if (laneWalks) {\n      const fromAtStart = leavesStart(\n        edge,\n        fromSegments,\n        baseCurves[0],\n        stranded,\n        yToX\n      );\n      const last = baseCurves.at(-1);\n      const toAtStart = nearerStart(\n        { x: last.x1, y: last.y1 },\n        toSegments,\n        yToX\n      );\n      const single = laneWalks.length === 1;\n      const thickness = laneHalfWidth(laneWidthOf(edge.from));\n      const fromFrames = lines?.frames.get(edge.from);\n      const toFrames = lines?.frames.get(edge.to);\n      for (let lane = 0; lane < laneWalks.length; lane++) {\n        const walk = laneWalks[lane];\n        if (!walk.edgeIndexes.has(ei)) {\n          continue;\n        }\n        for (const [pass, toPass] of threadPairs(lane, edge.from, edge.to)) {\n          const from = laneEndOf(\n            edge.from,\n            fromFrames,\n            fromSegments,\n            fromAtStart,\n            lane,\n            pass\n          );\n          const to = threaded ? laneEndOf(edge.to, toFrames, toSegments, toAtStart, lane, toPass) : from;\n          const offsetX = single ? 0 : from.offset * worldPerScreenPx;\n          const endOffsetX = threaded ? to.offset * worldPerScreenPx : offsetX;\n          const curves = threaded ? slideCurves(\n            baseCurves,\n            from.shift.dx + from.normal.nx * offsetX,\n            from.shift.dy + from.normal.ny * offsetX / yToX,\n            to.shift.dx + to.normal.nx * endOffsetX,\n            to.shift.dy + to.normal.ny * endOffsetX / yToX\n          ) : offsetX === 0 ? baseCurves : translateCurves(\n            baseCurves,\n            from.normal.nx * offsetX,\n            from.normal.ny * offsetX / yToX\n          );\n          if (inView(curves)) {\n            laneStroke(\n              curves,\n              thickness,\n              threadColor(lane, edge.from, pass) ?? threadColor(lane, edge.to, toPass) ?? plainEdgeColor,\n              lane,\n              pass,\n              from.normal,\n              offsetX,\n              to.normal,\n              endOffsetX\n            );\n          }\n        }\n      }\n      if (edgeCurves.length > edgeCurveStart) {\n        arrowOn(baseCurves);\n      }\n    } else if (!ribbons) {\n      if (inView(baseCurves)) {\n        stroke(baseCurves, edgeThickness, edgeColor);\n        arrowOn(baseCurves);\n      }\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      );\n      const arrowRibbon = Math.floor((numPaths - 1) / 2);\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const { x, y } = offsets[pathIdx];\n        const curves = x === 0 && y === 0 ? baseCurves : translateCurves(baseCurves, x, y);\n        if (!inView(curves)) {\n          continue;\n        }\n        const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);\n        stroke(\n          curves,\n          ribbonThickness,\n          highlight && (highlight.walks.length ? !highlight.names.has(edge.pathIds[pathIdx]) : !onWalk) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor\n        );\n        if (pathIdx === arrowRibbon) {\n          arrowOn(curves);\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  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId);\n    if (!node) {\n      continue;\n    }\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue;\n    }\n    const faded = highlight !== void 0 && !highlight.nodeIds.has(nodeId);\n    const own = faded ? LIFT_BACKDROP_COLOR : getNodeColor(\n      node,\n      nodeIndexMap.get(nodeId) ?? 0,\n      colorScheme,\n      colorRange\n    );\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : node.moved ? fadeAbgr(own, MOVED_ALPHA) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, widthScale);\n    const nodeThickness = width / 2;\n    const start = nodeStrokes.length;\n    const slots = nodePathSlots.get(nodeId);\n    const slotWidth = width / pathCount;\n    const drawable = segments.length >= 2;\n    const lanes = highlight?.walks.length && !faded && !slots?.length ? highlight.walks : void 0;\n    if (drawable && lanes) {\n      const laneWidth = walkLaneWidthPx(width, lanes.length);\n      const thickness = laneHalfWidth(laneWidth);\n      const frames = lines?.frames.get(nodeId);\n      for (let lane = 0; lane < lanes.length; lane++) {\n        const laneColor = lanes[lane].colors.get(nodeId);\n        if (laneColor === void 0) {\n          continue;\n        }\n        const onThreads = threads?.[lane]?.nodeThreads.get(nodeId) ?? ONE_PASS;\n        for (const pass of onThreads) {\n          const color2 = threadColor(lane, nodeId, pass) ?? laneColor;\n          if (lanes.length === 1) {\n            nodeStrokes.push({\n              points: segments,\n              thickness,\n              color: color2,\n              walk: lane,\n              pass\n            });\n            continue;\n          }\n          const frame = frames?.[lane]?.[visitOf(lane, nodeId, pass)];\n          const normals = laneNormalsOf(nodeId, segments, frame);\n          const points = lanePointsOf(segments, frame);\n          const plain = laneOffset(nodeId, laneWidth, lane, pass);\n          const offsets = frame?.offsets?.map(\n            (o) => o * thinned * worldPerScreenPx\n          );\n          const offsetX = offsets ? offsets[Math.floor(offsets.length / 2)] : threadOffsetAt(frame, 0, plain) * worldPerScreenPx;\n          nodeStrokes.push({\n            points: offsetPolyline(points, normals, offsets ?? offsetX, yToX),\n            thickness,\n            color: color2,\n            walk: lane,\n            pass,\n            normals,\n            offsetX,\n            ...offsets && { offsets }\n          });\n        }\n      }\n    } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {\n      const normals = pointNormalsOf(segments, yToX);\n      for (const slot of slots) {\n        const offset = (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  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns\n  };\n}\n\nexport {\n  LIFT_BACKDROP_COLOR,\n  FADED_ALPHA,\n  LIFT_BACKDROP_CSS,\n  hslToRgb,\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  rampFraction,\n  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  hslToRgb\n} from \"./chunk-YA3VYQH4.js\";\nimport {\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\n\n// src/walkEncoding.ts\nvar WALK_FIELDS = [\n  { value: \"progress\", label: \"Progress along the walk\" },\n  { value: \"walk\", label: \"One colour for the walk\" },\n  { value: \"reference\", label: \"Reference position\" }\n];\nvar 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: \"orange\", label: \"Peach to rust\", ends: [\"#ffc285\", \"#8f3a00\"] },\n  { value: \"rainbow\", label: \"Rainbow\" }\n];\nvar FAMILIES = [\"blue\", \"red\", \"purple\", \"green\"];\nvar isField = (v) => WALK_FIELDS.some((f) => f.value === v);\nvar isScheme = (v) => WALK_SCHEMES.some((s) => s.value === v);\nfunction resolveEncoding(layer, reference, picked, alone = true) {\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) ? askedScheme === \"rainbow\" && field !== \"reference\" ? family : askedScheme : family;\n  const round = Math.floor(picked / FAMILIES.length) % SHADES.length;\n  return field === \"walk\" && scheme === family && round > 0 ? { field, scheme, shade: SHADES[round] } : alone || field === \"walk\" ? { field, scheme } : { field, scheme, darkest: TOGETHER_DARKEST };\n}\nvar TOGETHER_DARKEST = 0.55;\nvar BASE_T = 0.5;\nvar SHADES = [BASE_T, 0.85, 0.2];\nvar STRETCH_GAP = 0.08;\nvar rampsOn = ({ field, scheme }) => field !== \"walk\" && scheme !== \"rainbow\";\nfunction splitFamilies(encodings) {\n  const counts = /* @__PURE__ */ new Map();\n  for (const e of encodings) {\n    if (rampsOn(e)) {\n      counts.set(e.scheme, (counts.get(e.scheme) ?? 0) + 1);\n    }\n  }\n  const seen = /* @__PURE__ */ new Map();\n  return encodings.map((e) => {\n    const k = rampsOn(e) ? counts.get(e.scheme) : 1;\n    if (k < 2) {\n      return e;\n    }\n    const j = seen.get(e.scheme) ?? 0;\n    seen.set(e.scheme, j + 1);\n    const half = STRETCH_GAP / 2;\n    return {\n      ...e,\n      stretch: [\n        j / k + (j > 0 ? half : 0),\n        (j + 1) / k - (j < k - 1 ? half : 0)\n      ]\n    };\n  });\n}\nvar along = ({ stretch }, t) => stretch ? stretch[0] + (stretch[1] - stretch[0]) * t : t;\nvar toLinear = (c) => c <= 0.04045 ? c / 12.92 : ((c + 0.055) / 1.055) ** 2.4;\nvar toGamma = (c) => c <= 31308e-7 ? c * 12.92 : 1.055 * c ** (1 / 2.4) - 0.055;\nfunction oklab(hex) {\n  const [r, g, b] = [1, 3, 5].map(\n    (i) => toLinear(Number.parseInt(hex.slice(i, i + 2), 16) / 255)\n  );\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}\nfunction oklabToRgb([L, a, b]) {\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}\nvar endsCache = /* @__PURE__ */ new Map();\nfunction oklabEnds(scheme) {\n  if (!endsCache.has(scheme)) {\n    const family = WALK_SCHEMES.find((s) => s.value === scheme);\n    endsCache.set(\n      scheme,\n      family && \"ends\" in family ? family.ends.map(oklab) : void 0\n    );\n  }\n  return endsCache.get(scheme);\n}\nfunction schemeRgb(scheme, t, darkest = 0) {\n  const x = Math.max(0, Math.min(1, t));\n  const ends = oklabEnds(scheme);\n  if (!ends) {\n    return hslToRgb(\n      rampHueAt(x),\n      REFERENCE_RAMP_SATURATION,\n      REFERENCE_RAMP_LIGHTNESS\n    ).map((c) => c * 255);\n  }\n  const [from, to] = ends;\n  const light = from[0];\n  const dark = to[0];\n  const reach = dark < darkest && light > darkest ? (light - darkest) / (light - dark) : 1;\n  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x * reach));\n}\nfunction schemeCss(scheme, t, darkest) {\n  const [r, g, b] = schemeRgb(scheme, t, darkest).map(Math.round);\n  return `rgb(${r}, ${g}, ${b})`;\n}\nfunction schemeColor(scheme, t, darkest) {\n  const [r, g, b] = schemeRgb(scheme, t, darkest).map(Math.round);\n  return packAbgr(r, g, b, 255);\n}\nfunction encodedColor(encoding, t) {\n  const { field, scheme, darkest, shade = BASE_T } = encoding;\n  return field === \"walk\" ? schemeColor(scheme, shade) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, along(encoding, t), darkest);\n}\nvar NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;\nfunction encodingStops(encoding) {\n  const { field, scheme, darkest, shade = BASE_T } = encoding;\n  const stop = (offset, t) => ({\n    offset,\n    color: schemeCss(scheme, t, darkest),\n    abgr: schemeColor(scheme, t, darkest)\n  });\n  return field === \"walk\" ? [stop(0, shade)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, along(encoding, i / 6)));\n}\nfunction encodingSwatchCss(encoding) {\n  const stops = encodingStops(encoding);\n  return stops.length === 1 ? stops[0].color : `linear-gradient(to right, ${stops.map((s) => `${s.color} ${s.offset * 100}%`).join(\", \")})`;\n}\n\nexport {\n  WALK_FIELDS,\n  WALK_SCHEMES,\n  resolveEncoding,\n  splitFamilies,\n  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\n};\n"],
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+  "names": ["THREAD_PX", "THREAD_GAP_PX", "SLOT_GAP_PX", "LANE_SMOOTHING_PX", "THREAD_REACH_PX", "THREAD_TAPER_PX", "MAX_BAND_PX", "PASSES_KEY", "threadsPasses", "walks", "w", "threadsWidth", "threads", "sum", "values", "a", "b", "slotLayout", "spans", "mostPasses", "laneWidth", "widths", "m", "i", "seen", "gaps", "share", "gap", "THREAD_PITCH_PX", "slotCentres", "held", "band", "at", "width", "slack", "centre", "bandWidthPx", "bandScale", "passesKey", "pointIndex", "run", "p", "i", "k", "gapOf", "a", "b", "dx", "dy", "arcOf", "s", "walkSteps", "walkRoutes", "nodePositions", "seen", "routes", "visits", "route", "id", "visit", "segments", "owned", "laneRuns", "steps", "yToX", "jump", "runs", "pieces", "walk", "total", "piece", "xs", "ys", "at", "from", "fresh", "breakRun", "stepOf", "gap", "x", "y", "first", "last", "forward", "toFirst", "toLast", "next", "toNext", "j", "ownedWindows", "margin", "windows", "floor", "lo", "hi", "smoothedNormals", "reach", "end", "pointAt", "span", "f", "_", "back", "ahead", "len", "cutCurls", "close", "length", "out", "picks", "to", "j2", "q", "rounded", "half", "n", "sumW", "sumX", "sumY", "w", "tightPoints", "line", "radius", "tight", "along", "twice", "loosened", "t", "pass", "part", "local", "weight", "windowMean", "smoother", "runSigns", "own", "canonical", "settle", "agreement", "sum2", "decided", "pending", "theirs", "mine", "laneLines", "band", "smooth", "turn", "curl", "context", "frames", "firsts", "arcs", "stepFrames", "newFrame", "place", "byWalk", "r", "ids", "starts", "raw", "firstRun", "firstStep", "firstFrame", "plus", "minus", "d", "shared", "reachFrom", "reachTo", "backward", "apart", "points", "normals", "sign", "index", "m", "px", "py", "shift", "windowed", "v", "deque", "head", "counted", "sumWV", "ONE_THREAD", "repeats", "passes", "walkThreads", "widths", "stepVisits", "stepWants", "stepGlides", "nodes", "mid", "most", "copy", "before", "after", "wants", "glides", "nearest", "want", "taken", "threadOf", "free", "width", "c", "glideOf", "glide", "nodeThreads", "threadPasses", "threadAt", "passOf", "thread", "linkThreads", "pair", "list", "bandSpans", "spans", "taper", "middle", "eased", "e", "easeOffsets", "threads", "plain", "slotCentres", "byNode", "centresAt", "centres", "THREAD_PITCH_PX", "frame", "constant", "offsets", "liftLanes", "walks", "worldPerScreenPx", "threaded", "threadsPasses", "THREAD_REACH_PX", "LANE_SMOOTHING_PX", "bandWidthPx", "bandScale", "lines", "THREAD_TAPER_PX", "furthestShift", "seenShifts", "shifts", "packAbgr", "r", "g", "b", "a", "abgrRed", "c", "abgrGreen", "abgrBlue", "abgrAlpha", "abgrToCssRgba", "normalizedRgbToCssRgba", "alpha", "fadeAbgr", "brightenAbgr", "factor", "t", "lift", "v", "REFERENCE_RAMP_MAX_HUE", "REFERENCE_RAMP_SATURATION", "REFERENCE_RAMP_LIGHTNESS", "rampHueCss", "hue", "rampHueAt", "frac", "rampHue", "bp", "domain", "HUE_STOP_DEG", "rampStops", "start", "reversed", "low", "high", "n", "_", "RAMP_GRADIENT_STOPS", "i", "RAMP_GRADIENT_CSS", "s", "cache", "weakMemo", "baseEdgeCurves", "nodePositions", "graph", "axis", "deletions", "version", "routes", "stranded", "curves", "ei", "bypassed", "edgeCurves", "edgeCurvesOf", "MAX_BACKBONE_HOPS", "buildNeighbors", "graph", "neighbors", "edge", "pushTo", "flankingSpan", "nodeId", "nodeById", "seen", "frontier", "minEnd", "maxStart", "hop", "next", "id", "adjacent", "neighborId", "neighbor", "isBackbone", "nodeReferenceSpan", "node", "referenceMidpoints", "midpoints", "span", "EDGE_DEFAULT_COLOR", "packAbgr", "EDGE_PATH_FALLBACK_COLOR", "EDGE_DELETION_COLOR", "DELETION_THICKNESS_FACTOR", "LIFT_BACKDROP_COLOR", "FADED_ALPHA", "MOVED_ALPHA", "LIFT_BACKDROP_CSS", "abgrToCssRgba", "fadeAbgr", "DELETION_DASH_PX", "MIN_PATH_STRIPE_PX", "MIN_SCALE_FOR_OFFSET", "ARROW_LENGTH_BASE_PX", "ARROW_LENGTH_PER_EDGE_PX", "ARROW_HALF_WIDTH_BASE_PX", "ARROW_HALF_WIDTH_PER_EDGE_PX", "MIN_LINK_HEADS", "MIN_ARROW_FIT", "MIN_ARROW_SCALE", "ARROW_CURVE_STEPS", "ABUTTING_PX", "walkX", "walkY", "walkPx", "backFromEnd", "curves", "scale", "yToX", "untilPx", "most", "last", "n", "px", "ci", "c", "k", "t", "a", "b", "d", "e", "x", "y", "walkPointAt", "i", "from", "to", "f", "arrowheadFor", "edgeHalfWidth", "nodeHalfWidth", "color", "fromSegments", "toSegments", "length", "lengthPx", "abutting", "inset", "fit", "polylinePx", "tip", "base", "dx", "dy", "endTangent", "intoDirection", "FIRST_THREADS", "ONE_PASS", "NO_SHIFT", "nearerStart", "at", "segments", "gap", "p", "leavesStart", "edge", "first", "stranded", "strandSides", "final", "normal", "len", "MITRE_LIMIT", "LONGEST_NORMAL", "pointNormalsOf", "rawPoints", "points", "before", "after", "nx", "ny", "dot", "offsetPolyline", "normals", "distance", "out", "hslToRgb", "h", "s", "l", "m", "r", "g", "packHsl", "DEPTH_GRADIENT", "STABLE_RANK_GRADIENT", "NODE_LENGTH_GRADIENT", "sampleGradient", "stops", "pos", "hashColor", "str", "alpha", "nameHue", "PATH_SATURATION", "PATH_LIGHTNESS", "REFERENCE_RAMP_ALT_RGB", "REFERENCE_RAMP_ALT_COLOR", "REFERENCE_RAMP_ALT_CSS", "rampFraction", "node", "ramp", "mid", "isBackbone", "computeReferenceRamp", "graph", "domain", "midpoints", "referenceMidpoints", "min", "max", "computeColorSchemeRange", "referenceRamp", "minDepth", "maxDepth", "minLength", "maxLength", "maxRank", "getNodeColor", "nodeIndex", "colorScheme", "range", "rampHueAt", "REFERENCE_RAMP_SATURATION", "REFERENCE_RAMP_LIGHTNESS", "hue", "into", "candidates", "isPolylineInBounds", "bounds", "hit", "isBezierInBounds", "growX", "growY", "cMinX", "cMaxX", "cMinY", "cMaxY", "paletteCache", "pathPaletteOf", "palette", "pathColorByIndex", "pathIndexByName", "paths", "pathHueAt", "slotsCache", "NO_SLOTS", "pathSlotsOf", "slots", "pathIdx", "path", "nodeId", "pushTo", "lanesCache", "weakMemo", "stepsCache", "linksCache", "linksOf", "links", "buildGeometry", "options", "nodePositions", "nodeById", "contigThickness", "connectorThickness", "drawPaths", "nodeWidth", "edgeWidth", "highlight", "axis", "linearLayout", "viewportBounds", "deletions", "deletionRoutes", "hiddenEdges", "version", "widthScale", "widthNorm", "busiest", "busiestEdge", "worldPerScreenPx", "yToXOf", "sharedCurves", "baseEdgeCurves", "nodeStrokes", "nodeStrokeRuns", "arrows", "arrowRuns", "edgeCurves", "edgeCurveRuns", "colorRange", "nodeIndexMap", "pathCount", "pathColorByName", "name", "nodePathSlots", "liftedWalks", "threaded", "threadsPasses", "lanePasses", "w", "thinned", "bandScale", "fields", "liftLanes", "walkSteps", "lines", "threads", "spanField", "plainCentres", "slotCentres", "centresByNode", "centresOf", "centres", "spans", "laneOffset", "laneWidth", "lane", "pass", "THREAD_PITCH_PX", "threadOffsetAt", "frame", "fallback", "eased", "laneHalfWidth", "THREAD_PX", "plainNormals", "visitNormals", "visitOf", "thread", "plainNormalsOf", "laneNormalsOf", "laneWidths", "laneWidthOf", "id", "width", "walkLaneWidthPx", "nodeWidthPx", "laneEndOf", "frames", "atStart", "lanesMayShow", "fromId", "offset", "bandWidthPx", "reach", "threadPairs", "own", "ahead", "back", "turned", "threadColor", "visitPoints", "lanePointsOf", "shifts", "showArrows", "ei", "baseCurves", "numPaths", "isDeletion", "onWalk", "ribbonThickness", "walkFactor", "edgeWidthFactor", "edgeThickness", "ribbons", "plainEdgeColor", "edgeColor", "toNode", "intoHalfWidth", "inView", "dashesOf", "dashSpans", "stroke", "thickness", "dash", "laneStroke", "walk", "normal2", "offsetX", "endNormal", "endOffsetX", "arrowOn", "head", "edgeCurveStart", "arrowStart", "laneWalks", "fromAtStart", "toAtStart", "single", "fromFrames", "toFrames", "toPass", "slideCurves", "translateCurves", "offsets", "pathRibbonOffsets", "arrowRibbon", "ribbonColor", "edgeCurveCount", "arrowCount", "faded", "nodeThickness", "start", "slotWidth", "drawable", "lanes", "laneColor", "onThreads", "color2", "plain", "o", "slot", "stripe", "count", "WALK_FIELDS", "WALK_SCHEMES", "FAMILIES", "isField", "v", "f", "isScheme", "s", "resolveEncoding", "layer", "reference", "picked", "alone", "askedField", "askedScheme", "field", "family", "scheme", "round", "SHADES", "TOGETHER_DARKEST", "BASE_T", "STRETCH_GAP", "rampsOn", "splitFamilies", "encodings", "counts", "seen", "k", "j", "half", "along", "stretch", "t", "toLinear", "c", "toGamma", "oklab", "hex", "r", "g", "b", "i", "l", "m", "oklabToRgb", "L", "a", "endsCache", "oklabEnds", "schemeRgb", "darkest", "x", "ends", "hslToRgb", "rampHueAt", "REFERENCE_RAMP_SATURATION", "REFERENCE_RAMP_LIGHTNESS", "from", "to", "light", "dark", "reach", "schemeCss", "schemeColor", "packAbgr", "encodedColor", "encoding", "shade", "NO_VALUE_COLOR", "REFERENCE_RAMP_ALT_COLOR", "encodingStops", "stop", "offset", "_"]
+}

package/dist/chunks/{chunk-WA7FCDLQ.js → chunk-HM7XSNBN.js}

@@ -1,2 +1,2 @@
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n&&$.test(n)?n.length:void 0}function m(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=n===""||n===null||n===void 0?NaN:Number(n);return Number.isFinite(r)?r:void 0})}function N(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=String(n??"").trim();return r===""||r==="."?void 0:r})}var w="<CNV:TR>";function K(e){let t=N(i(e,"ALT"));if(!t.includes(w))return;let n=m(d(e,"RN")),r=N(d(e,"RUS")),s=m(d(e,"RUL")),o=m(d(e,"RUC")),a=m(d(e,"RB")),c=0;return t.map((u,f)=>{let p=n[f]??(u===w?1:0),k=0,S=0;for(let F=0;F<p;F++,c++){let y=r[c],L=s[c]??(y&&$.test(y)?y.length:void 0),_=o[c],C=a[c]??(L&&_!==void 0?Math.round(L*_):void 0);C!==void 0&&(k+=C,S++)}return u===w&&p>0&&S===p?k:void 0})}function Y(e,t,n){let r=e?.includes("|");return(e??"").split(/[/|]/).flatMap((s,o)=>{let a=s===""?NaN:Number(s),c=a>0?t[a-1]:n;return!Number.isInteger(a)||c===void 0?[]:[{bp:c,...r?{haplotype:o+1}:{}}]})}function W(e,t,n){let r=i(e,"samples"),s={};for(let[o,a]of 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package/dist/chunks/{chunk-WA7FCDLQ.js.map → chunk-HM7XSNBN.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
   "sourcesContent": ["import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\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\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\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 = ownField(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 = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(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(ownField(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 = index === '' ? NaN : 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 = ownField(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}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\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", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\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}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\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  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. A\n// feature with none of those names is left out: its raw ID, RefSeq's\n// `id-NC_000913.3:1978503..1979270`, only restates where it is.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (ownField(f, 'gene_name') as string | undefined) ??\n      (ownField(f, 'name') as string | undefined) ??\n      (ownField(f, 'gene') as string | undefined) ??\n      (ownField(f, 'gene_id') as string | undefined)\n    const start = ownField(f, 'start') as number\n    const end = ownField(f, 'end') as number\n    if (\n      !name ||\n      !(end > start) ||\n      WHOLE_SEQUENCE_TYPES.has(ownField(f, 'type') as string)\n    ) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: ownField(f, 'refName') as string,\n      start,\n      end,\n      strand: (ownField(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? mergedIntervals(exons) : [{ start, end }],\n    })\n  }\n  return mergeOverlappingByName(genes)\n}\n", "const host = JBrowseExports[\"tss-react/mui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"tss-react/mui\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host"],
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package/dist/chunks/{chunk-IUBWMYUA.js → chunk-IQQOJGX3.js}

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