npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 7.4.3 → 7.4.4 - Mend

jbrowse-plugin-graphgenomeviewer 7.4.3 → 7.4.4

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package/dist/chunks/chunk-VZQ6VOUP.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-3BDQQTXY.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GQZVR5DW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-P2GJBFNA.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VX656OAZ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GDZQFELP.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-UEWIGD52.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}\nvar gapOf = (a, b) => Math.hypot(b.x - a.x, b.y - a.y);\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 laneRuns(routes, nodePositions, yToX, jump) {\n  const seen = /* @__PURE__ */ new Set();\n  const owns = routes.map(\n    (route) => route.map((id) => {\n      if (seen.has(id)) {\n        return false;\n      }\n      seen.add(id);\n      return !!nodePositions[id]?.length;\n    })\n  );\n  const gap = (a, b) => Math.hypot(b.x - a.x, b.y * yToX - a.y);\n  const runs = [];\n  const owned = [];\n  let run = [];\n  let mine = [];\n  const breakRun = () => {\n    if (run.length) {\n      runs.push(run);\n      owned.push(mine);\n    }\n    run = [];\n    mine = [];\n  };\n  routes.forEach((route, r) => {\n    if (!owns[r].includes(true)) {\n      return;\n    }\n    route.forEach((id, step) => {\n      const segments = nodePositions[id];\n      if (!segments?.length) {\n        breakRun();\n        return;\n      }\n      const first = segments[0];\n      const last = segments.at(-1);\n      const prev = run.at(-1);\n      const next = nodePositions[route[step + 1] ?? \"\"];\n      const toNext = (p) => {\n        const at = { x: p.x, y: p.y * yToX };\n        return next?.length ? Math.min(gap(at, next[0]), gap(at, next.at(-1))) : 0;\n      };\n      const forward = prev ? gap(prev, first) <= gap(prev, last) : toNext(last) <= toNext(first);\n      if (prev && gap(prev, forward ? first : last) > jump) {\n        breakRun();\n      }\n      const middle = Math.floor(segments.length / 2);\n      for (let k = 0; k < segments.length; k++) {\n        const index = forward ? k : segments.length - 1 - k;\n        const p = segments[index];\n        run.push({\n          x: p.x,\n          y: p.y * yToX,\n          id,\n          index,\n          middle: index === middle,\n          forward\n        });\n        mine.push(owns[r][step]);\n      }\n    });\n    breakRun();\n  });\n  return { runs, owned };\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 fieldSetter(field, nodePositions) {\n  return ({ id, index }, value) => {\n    let own = field.get(id);\n    if (!own) {\n      own = new Array(nodePositions[id].length);\n      field.set(id, own);\n    }\n    own[index] = value;\n  };\n}\nfunction laneLines(lanes, nodePositions, yToX, reach, band, smooth = true) {\n  const turn = Math.max(reach, 2 * band);\n  const curl = Math.PI * band;\n  const margin = smooth ? curl + band / 2 + turn / 2 : turn / 2;\n  const normals = /* @__PURE__ */ new Map();\n  const shifts = /* @__PURE__ */ new Map();\n  const setNormal = fieldSetter(normals, nodePositions);\n  const setShift = fieldSetter(shifts, nodePositions);\n  lanes.runs.forEach((run, r) => {\n    const owned = lanes.owned[r];\n    const pieces = ownedWindows(arcOf(run), owned, margin).map(([lo, hi]) => {\n      const points = run.slice(lo, hi + 1);\n      const line = smooth ? rounded(cutCurls(points, band / 2, curl), band / 2) : points;\n      return { lo, points, line, normals: smoothedNormals(line, turn) };\n    });\n    let agree = 0;\n    let along = 0;\n    for (const piece of pieces) {\n      piece.points.forEach((p, i) => {\n        const theirs = normals.get(p.id)?.[p.index];\n        const mine = piece.normals[i];\n        if (theirs && mine) {\n          agree += theirs.nx * mine.nx + theirs.ny * mine.ny;\n        }\n        along += p.forward ? 1 : -1;\n      });\n    }\n    const sign = (agree === 0 ? along : agree) < 0 ? -1 : 1;\n    for (const { lo, points, line, normals: own } of pieces) {\n      points.forEach((p, i) => {\n        if (!owned[lo + i]) {\n          return;\n        }\n        const n = own[i];\n        if (n) {\n          setNormal(p, sign > 0 ? n : { nx: -n.nx, ny: -n.ny });\n        }\n        if (smooth) {\n          setShift(p, {\n            dx: line[i].x - p.x,\n            dy: (line[i].y - p.y) / yToX\n          });\n        }\n      });\n    }\n  });\n  return { normals, shifts };\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 weight = s.map(\n    (_, i) => !counted(v[i]) ? 0 : n > 1 ? (s[Math.min(i + 1, n - 1)] - s[Math.max(i - 1, 0)]) / 2 : 1\n  );\n  const sumW = [0];\n  const sumWV = [0];\n  for (let i = 0; i < n; i++) {\n    sumW.push(sumW[i] + weight[i]);\n    sumWV.push(sumWV[i] + weight[i] * v[i]);\n  }\n  let lo = 0;\n  let hi = 0;\n  return v.map((value, 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    return w > 0 ? (sumWV[hi] - sumWV[lo]) / w : value;\n  });\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 { span: passes, nodeThreads: /* @__PURE__ */ new Map(), linkThreads: /* @__PURE__ */ new Map() };\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  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    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      wants[i] = Math.min(copy[nearest], most[i]) - 1;\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  }\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  steps.forEach((nodes, piece) => {\n    nodes.forEach((k, i) => {\n      if (widths[k] > 1) {\n        const t = free(k, stepWants[piece][i]);\n        taken[k].add(t);\n        (threadOf[k] ??= [])[stepVisits[piece][i]] = t;\n      }\n    });\n  });\n  const span = /* @__PURE__ */ new Map();\n  const nodeThreads = /* @__PURE__ */ new Map();\n  ids.forEach((id, k) => {\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  });\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, linkThreads };\n}\nfunction bandSpans(lanes, spans, { reach, taper }) {\n  const out = /* @__PURE__ */ new Map();\n  lanes.runs.forEach((run, r) => {\n    const s = arcOf(run);\n    const mids = run.flatMap((p, i) => p.middle ? [i] : []);\n    const along = mids.map((i) => s[i]);\n    const owned = mids.map((i) => lanes.owned[r][i]);\n    for (const [lo, hi] of ownedWindows(along, owned, reach / 2 + taper / 2)) {\n      const at = along.slice(lo, hi + 1);\n      const ids = mids.slice(lo, hi + 1).map((i) => run[i].id);\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 (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 liftLanes(walks, nodePositions, yToX, worldPerScreenPx) {\n  const threaded = threadsPasses(walks);\n  const passes = walks.map((w) => w.mostPasses);\n  const reach = THREAD_REACH_PX * worldPerScreenPx;\n  const runs = laneRuns(\n    walks.flatMap((w) => w.route),\n    nodePositions,\n    yToX,\n    LANE_SMOOTHING_PX * worldPerScreenPx\n  );\n  const lines = laneLines(\n    runs,\n    nodePositions,\n    yToX,\n    LANE_SMOOTHING_PX * worldPerScreenPx,\n    bandWidthPx(passes) * (threaded ? bandScale(passes) : 1) * worldPerScreenPx,\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    threads.map((t) => t.span),\n    { reach, taper: THREAD_TAPER_PX * worldPerScreenPx }\n  ) : void 0;\n  const furthestShift = { dx: 0, dy: 0 };\n  for (const own of lines.shifts.values()) {\n    for (const shift of own) {\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  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  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-3GORESBG.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}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints\n};\n", "import {\n  THREAD_PITCH_PX,\n  THREAD_PX,\n  bandScale,\n  bandWidthPx,\n  laneSlideAt,\n  liftLanes,\n  slotCentres,\n  threadsPasses\n} from \"./chunk-3BDQQTXY.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-P2GJBFNA.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-VQ353UDK.js\";\nimport {\n  meanDepth,\n  nodeWidthPx,\n  walkLaneWidthPx\n} from \"./chunk-ZANALBSX.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-VX656OAZ.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\";\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 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    out[i] = {\n      x: points[i].x + normals[i].nx * distance,\n      y: points[i].y + normals[i].ny * distance / 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 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    highlight,\n    axis,\n    linearLayout,\n    viewportBounds,\n    referenceRamp,\n    deletions,\n    deletionRoutes,\n    stranded,\n    hiddenEdges,\n    version = 0\n  } = options;\n  const depthNorm = nodeWidth === \"depth\" ? meanDepth(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(liftedWalks, nodePositions, yToX, worldPerScreenPx)\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 laneHalfWidth = (laneWidth) => threaded ? THREAD_PX / 2 * thinned : laneWidth / 2;\n  const laneNormals = /* @__PURE__ */ new Map();\n  const laneNormalsOf = (nodeId, segments) => {\n    let normals = laneNormals.get(nodeId);\n    if (!normals) {\n      const smoothed = lines?.normals.get(nodeId);\n      normals = smoothed ? pointNormalsOf(segments, yToX).map((n, i) => smoothed[i] ?? n) : pointNormalsOf(segments, yToX);\n      laneNormals.set(nodeId, 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, depthNorm) : contigThickness,\n        liftedWalks.length\n      );\n      laneWidths.set(id, width);\n    }\n    return width;\n  };\n  const laneShiftOf = (nodeId, index) => lines?.shifts.get(nodeId)?.[index] ?? NO_SHIFT;\n  const laneEndOf = (id, segments, atStart) => {\n    const at = atStart ? 0 : segments.length - 1;\n    return {\n      id,\n      laneWidth: laneWidthOf(id),\n      normal: laneNormalsOf(id, segments)[at] ?? { nx: 0, ny: 0 },\n      shift: laneShiftOf(id, at)\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 lanePointsOf = (nodeId, segments) => lines?.shifts.has(nodeId) ? segments.map((p, i) => {\n    const { dx, dy } = laneShiftOf(nodeId, i);\n    return { ...p, x: p.x + dx, y: p.y + dy };\n  }) : segments;\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 edgeThickness = connectorThickness / 2 * (isDeletion ? DELETION_THICKNESS_FACTOR : 1);\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, depthNorm) : 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      if (!isDeletion) {\n        edgeCurves.push({\n          curves,\n          thickness,\n          color,\n          walk,\n          pass,\n          normal: normal2,\n          offsetX,\n          endNormal,\n          endOffsetX\n        });\n        return;\n      }\n      const start = { normal: normal2, offsetX };\n      const end = { normal: endNormal, offsetX: endOffsetX };\n      for (const dash of dashesOf(curves)) {\n        const a = dash.startAlong === 0 ? start : laneSlideAt(start, end, dash.startAlong);\n        const b = dash.endAlong === 1 ? end : laneSlideAt(start, end, dash.endAlong);\n        edgeCurves.push({\n          curves: dash.curves,\n          thickness,\n          color,\n          walk,\n          pass,\n          normal: a.normal,\n          offsetX: a.offsetX,\n          endNormal: b.normal,\n          endOffsetX: b.offsetX\n        });\n      }\n    };\n    const arrowOn = (curves) => {\n      const head = showArrows ? arrowheadFor({\n        curves,\n        edgeHalfWidth: connectorThickness / 2,\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 from = laneEndOf(\n        edge.from,\n        fromSegments,\n        leavesStart(edge, fromSegments, baseCurves[0], stranded, yToX)\n      );\n      const last = baseCurves.at(-1);\n      const to = threaded ? laneEndOf(\n        edge.to,\n        toSegments,\n        nearerStart({ x: last.x1, y: last.y1 }, toSegments, yToX)\n      ) : from;\n      const single = laneWalks.length === 1;\n      const thickness = laneHalfWidth(from.laneWidth);\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 offsetX = single ? 0 : laneOffset(from.id, from.laneWidth, lane, pass) * worldPerScreenPx;\n          const endOffsetX = threaded ? laneOffset(to.id, to.laneWidth, lane, toPass) * 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              walk.colors.get(edge.from) ?? walk.colors.get(edge.to) ?? 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          edgeThickness,\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) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);\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 normals = lanes.length > 1 ? laneNormalsOf(nodeId, segments) : [];\n      const points = lanes.length > 1 ? lanePointsOf(nodeId, segments) : segments;\n      const thickness = laneHalfWidth(laneWidth);\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          if (lanes.length === 1) {\n            nodeStrokes.push({\n              points: segments,\n              thickness,\n              color: laneColor,\n              walk: lane,\n              pass\n            });\n            continue;\n          }\n          const offsetX = laneOffset(nodeId, laneWidth, lane, pass) * worldPerScreenPx;\n          nodeStrokes.push({\n            points: offsetPolyline(points, normals, offsetX, yToX),\n            thickness,\n            color: laneColor,\n            walk: lane,\n            pass,\n            normals,\n            offsetX\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-GDZQFELP.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: \"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\" ? 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+}

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