jbrowse-plugin-graphgenomeviewer 7.2.0 → 7.2.1

package/dist/chunks/chunk-2M4XYSLG.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GQZVR5DW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-WA5WNP6V.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VX656OAZ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-XSF4RQRP.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GM7M25NW.js"],
+  "sourcesContent": ["// 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-CGMSKIEO.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  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-WA5WNP6V.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-3GP3KT5L.js\";\nimport {\n  meanDepth,\n  nodeWidthPx\n} from \"./chunk-CRCD3ODN.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-VX656OAZ.js\";\nimport {\n  dashCurves,\n  pathRibbonOffsets,\n  polylinePx,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-UBQSRCWR.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_WALK_LANE_PX = 4;\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}\nfunction leavesStart(edge, segments, first, stranded, yToX) {\n  if (stranded) {\n    return strandSides(edge).from === \"start\";\n  }\n  const gap = (p) => Math.hypot(p.x - first.x0, (p.y - first.y0) * yToX);\n  return gap(segments[0]) < gap(segments.at(-1));\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}\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 > 0.1 ? { 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  return points.map((p, i) => ({\n    x: p.x + normals[i].nx * distance,\n    y: p.y + normals[i].ny * distance / yToX\n  }));\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 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 mid = ramp.midpoints.get(node.id);\n      if (!isBackbone(node) || mid === void 0) {\n        return REFERENCE_RAMP_ALT_COLOR;\n      }\n      return packHsl(\n        rampHueAt((mid - ramp.start) / ramp.span),\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) {\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 && cMinX <= bounds.maxX && cMaxY >= bounds.minY && cMinY <= bounds.maxY) {\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}\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 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 stroke = (curves, thickness, color) => {\n      if (isDeletion) {\n        for (const dash of dashCurves(curves, DELETION_DASH_PX / scale)) {\n          edgeCurves.push({ curves: dash, thickness, color });\n        }\n      } else {\n        edgeCurves.push({ curves, thickness, color });\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) {\n      const fromNode = nodeById.get(edge.from);\n      const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm) : contigThickness;\n      const laneWidth = Math.max(width / laneWalks.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(fromSegments, yToX);\n      const { nx, ny } = (leavesStart(\n        edge,\n        fromSegments,\n        baseCurves[0],\n        stranded,\n        yToX\n      ) ? normals[0] : normals.at(-1)) ?? {\n        nx: 0,\n        ny: 0\n      };\n      laneWalks.forEach((walk, lane) => {\n        if (!walk.edgeIndexes.has(ei)) {\n          return;\n        }\n        const offset = (lane - (laneWalks.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        const curves = offset === 0 ? baseCurves : translateCurves(baseCurves, nx * offset, ny * offset / yToX);\n        if (inView(curves)) {\n          stroke(\n            curves,\n            laneWidth / 2,\n            walk.colors.get(edge.from) ?? walk.colors.get(edge.to) ?? plainEdgeColor\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 = Math.max(width / lanes.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(segments, yToX);\n      lanes.forEach((walk, lane) => {\n        const laneColor = walk.colors.get(nodeId);\n        if (laneColor === void 0) {\n          return;\n        }\n        const offset = (lane - (lanes.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        nodeStrokes.push({\n          points: lanes.length === 1 ? segments : offsetPolyline(segments, normals, offset, yToX),\n          thickness: laneWidth / 2,\n          color: laneColor\n        });\n      });\n    } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {\n      const normals = pointNormalsOf(segments, yToX);\n      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  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  hslToRgb\n} from \"./chunk-XSF4RQRP.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  return { field, scheme };\n}\nvar BASE_T = 0.5;\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}\nfunction schemeRgb(scheme, t) {\n  const x = Math.max(0, Math.min(1, t));\n  const family = WALK_SCHEMES.find((s) => s.value === scheme);\n  if (!family || !(\"ends\" in family)) {\n    return hslToRgb(\n      rampHueAt(x),\n      REFERENCE_RAMP_SATURATION,\n      REFERENCE_RAMP_LIGHTNESS\n    ).map((c) => c * 255);\n  }\n  const from = oklab(family.ends[0]);\n  const to = oklab(family.ends[1]);\n  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x));\n}\nfunction schemeCss(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return `rgb(${r}, ${g}, ${b})`;\n}\nfunction schemeColor(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return packAbgr(r, g, b, 255);\n}\nfunction encodedColor({ field, scheme }, t) {\n  return field === \"walk\" ? schemeColor(scheme, BASE_T) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, t);\n}\nvar NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;\nfunction encodingStops({ field, scheme }) {\n  const stop = (offset, t) => ({\n    offset,\n    color: schemeCss(scheme, t),\n    abgr: schemeColor(scheme, t)\n  });\n  return field === \"walk\" ? [stop(0, BASE_T)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, 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  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\n};\n"],
+  "mappings": 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package/dist/chunks/{chunk-JLGPQO5L.js → chunk-2O3YVA2I.js}

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+  "sources": ["../../node_modules/.pnpm/@jbrowse+graph-fmmm-layout@1.0.2/node_modules/@jbrowse/graph-fmmm-layout/esm/loadFmmm.js", "../../node_modules/.pnpm/@jbrowse+graph-fmmm-layout@1.0.2/node_modules/@jbrowse/graph-fmmm-layout/esm/fmmmLayout.js", "../../node_modules/.pnpm/@jbrowse+graph-stress-layout@1.0.0/node_modules/@jbrowse/graph-stress-layout/esm/stressPlacement.js", "../../node_modules/.pnpm/@jbrowse+graph-stress-layout@1.0.0/node_modules/@jbrowse/graph-stress-layout/esm/stressEngine.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-JMABOQWL.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-34BOZKIE.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HKYXWZQS.js"],
   "sourcesContent": ["let cached;\nexport function loadFmmm() {\n    cached !== null && cached !== void 0 ? cached : (cached = import('./bandage-layout.js')\n        .then(mod => mod.default())\n        .catch((e) => {\n        cached = undefined;\n        throw e;\n    }));\n    return cached;\n}\n", "import { loadFmmm } from \"./loadFmmm.js\";\nexport async function fmmmLayout(request) {\n    const engine = await loadFmmm();\n    return engine.computeLayout(request.graph, request.options);\n}\n", "// A node whose id starts with this is a deletion's route rather than sequence,\n// placed as an arch over the backbone.\nexport const ROUTE_ID = '\\u0000deletion:';\n// Where the stress engine starts an anchored graph. The backbone lies straight\n// along x at drawn length (its seeds). Every other node belongs to a piece: a\n// connected set of unplaced nodes, anchored where its links meet chains already\n// placed. A piece whose anchors sit on one placed curve is drawn in that\n// curve's frame (arc length along it, depth out of it): two anchors give a\n// spine along a circular arc of the piece's drawn length, a lens when it fits\n// its gap and a teardrop when longer, pushed out (legs, then a dropped chord,\n// then a tilt) until it clears what is drawn; a spine shorter than its gap is\n// a straight bar under it, hung deeper the wider the gap so its links leave\n// the lane; one anchor gives a straight tip. Anchors on\n// different curves use the chord between them. What a spine leaves unplaced\n// becomes pieces anchored on it, so nesting recurses. Deletion routes arch\n// above the backbone. Components with no backbone stay NaN for the engine's\n// random start.\nconst MIN_DEPTH = 12;\nconst LANE_GAP = 15;\nconst CLEAR = LANE_GAP * 0.7;\nconst TIP_ANGLE = (25 * Math.PI) / 180;\n// how deep a deletion arch rises, or a short bar hangs, per unit of its gap\nconst BOW = 0.25;\nconst BOW_CAP = 150;\n// a teardrop beside another leans away from it rather than dropping\nconst TEARDROP_TILTS = [0, -0.35, 0.35, -0.7, 0.7, -1.05, 1.05, -1.4, 1.4];\nconst SIDES = [0, 1];\nfunction other(side) {\n    return side ? 0 : 1;\n}\nfunction unit(a, b) {\n    const dx = b.x - a.x;\n    const dy = b.y - a.y;\n    const m = Math.hypot(dx, dy) || 1;\n    return { x: dx / m, y: dy / m };\n}\nfunction lerp(a, b, f) {\n    return { x: a.x + (b.x - a.x) * f, y: a.y + (b.y - a.y) * f };\n}\nfunction centroidOf(pts) {\n    let x = 0;\n    let y = 0;\n    for (const p of pts) {\n        x += p.x;\n        y += p.y;\n    }\n    return { x: x / pts.length, y: y / pts.length };\n}\nfunction arcLengths(pts) {\n    const arc = new Float64Array(pts.length);\n    for (let i = 1; i < pts.length; i++) {\n        arc[i] =\n            arc[i - 1] +\n                Math.hypot(pts[i].x - pts[i - 1].x, pts[i].y - pts[i - 1].y);\n    }\n    return arc;\n}\nfunction polylineLength(pts) {\n    var _a;\n    return (_a = arcLengths(pts)[pts.length - 1]) !== null && _a !== void 0 ? _a : 0;\n}\n// arc angle theta in (0, 2pi) with L/c = theta / (2 sin(theta/2)); a piece's\n// candidates ask for a handful of ratios hundreds of times\nconst arcAngles = new Map();\nfunction arcAngle(ratio) {\n    const known = arcAngles.get(ratio);\n    if (known !== undefined) {\n        return known;\n    }\n    const angle = solveArcAngle(ratio);\n    if (arcAngles.size > 10000) {\n        arcAngles.clear();\n    }\n    arcAngles.set(ratio, angle);\n    return angle;\n}\nfunction solveArcAngle(ratio) {\n    let lo = 1e-6;\n    let hi = 2 * Math.PI - 1e-6;\n    for (let i = 0; i < 60; i++) {\n        const mid = (lo + hi) / 2;\n        if (mid / (2 * Math.sin(mid / 2)) < ratio) {\n            lo = mid;\n        }\n        else {\n            hi = mid;\n        }\n    }\n    return (lo + hi) / 2;\n}\n// arc length of the circular arc with chord c and sagitta s\nfunction archLength(c, s) {\n    if (c < 1e-9) {\n        return Math.PI * s;\n    }\n    const R = ((c * c) / 4 + s * s) / (2 * s);\n    const theta = 2 * Math.asin(Math.min(1, c / (2 * R)));\n    return R * (s > R ? 2 * Math.PI - theta : theta);\n}\n// from (0, drop) to (c, drop) in `length`: legs of h along v joined by a\n// circular arc\nfunction arcFlat(c, length, h, drop) {\n    const arc = length - 2 * h;\n    const theta = c < 1e-9 ? 2 * Math.PI : arcAngle(arc / c);\n    const R = arc / theta;\n    const cos = Math.cos(theta / 2);\n    const cu = c / 2;\n    const cv = drop + h - R * cos;\n    return {\n        at: t => {\n            if (t <= h) {\n                return { u: 0, v: drop + t };\n            }\n            if (t >= length - h) {\n                return { u: c, v: drop + length - t };\n            }\n            const a = (t - h) / R - theta / 2;\n            return { u: cu + R * Math.sin(a), v: cv + R * Math.cos(a) };\n        },\n        apex: drop + h + R * (1 - cos),\n        length,\n    };\n}\n// The flat curve rotated about its chord's midpoint, which moves its feet\n// off the anchors by (c/2) sin(angle): one up, one down. A shear that kept\n// the feet swung a deep loop across its neighbours and raised link crossings\n// by half on the KIV-2 eight-haplotype cut.\nfunction tilted(flat, c, angle) {\n    if (!angle) {\n        return flat;\n    }\n    const cos = Math.cos(angle);\n    const sin = Math.sin(angle);\n    return {\n        ...flat,\n        at: t => {\n            const { u, v } = flat.at(t);\n            const du = u - c / 2;\n            return { u: c / 2 + du * cos - v * sin, v: du * sin + v * cos };\n        },\n    };\n}\n// whether any of the flat curve lies behind its frame: a loop's top poking\n// up through the reference line, which read as a glitch on every walk panel\nfunction behindFrame(flat) {\n    for (let i = 0; i <= 32; i++) {\n        if (flat.at((flat.length * i) / 32).v < -1e-6) {\n            return true;\n        }\n    }\n    return false;\n}\nfunction lineFlat(u0, v0, du, dv, length) {\n    return {\n        at: t => ({ u: u0 + du * t, v: v0 + dv * t }),\n        apex: v0 + Math.max(0, dv) * length,\n        length,\n    };\n}\n// A placed curve: dense samples with cumulative arc length and outward normals.\nclass Curve {\n    constructor(pts, normals, straight = false) {\n        var _a;\n        this.pts = pts;\n        this.normals = normals;\n        this.straight = straight;\n        this.arc = arcLengths(pts);\n        this.total = (_a = this.arc[pts.length - 1]) !== null && _a !== void 0 ? _a : 0;\n    }\n    segment(t) {\n        const { arc } = this;\n        let lo = 1;\n        let hi = arc.length - 1;\n        while (lo < hi) {\n            const mid = (lo + hi) >> 1;\n            if (arc[mid] < t) {\n                lo = mid + 1;\n            }\n            else {\n                hi = mid;\n            }\n        }\n        return lo;\n    }\n    fraction(i, t) {\n        const span = this.arc[i] - this.arc[i - 1];\n        return span > 0 ? (t - this.arc[i - 1]) / span : 0;\n    }\n    pointAt(t) {\n        const { pts } = this;\n        const last = pts.length - 1;\n        if (last === 0) {\n            return { ...pts[0] };\n        }\n        if (t <= 0) {\n            const d = unit(pts[0], pts[1]);\n            return { x: pts[0].x + d.x * t, y: pts[0].y + d.y * t };\n        }\n        if (t >= this.total) {\n            const d = unit(pts[last - 1], pts[last]);\n            const r = t - this.total;\n            return { x: pts[last].x + d.x * r, y: pts[last].y + d.y * r };\n        }\n        const i = this.segment(t);\n        return lerp(pts[i - 1], pts[i], this.fraction(i, t));\n    }\n    normalAt(t) {\n        const { normals } = this;\n        if (normals.length === 1 || t <= 0) {\n            return normals[0];\n        }\n        if (t >= this.total) {\n            return normals[normals.length - 1];\n        }\n        const i = this.segment(t);\n        const { x, y } = lerp(normals[i - 1], normals[i], this.fraction(i, t));\n        const m = Math.hypot(x, y) || 1;\n        return { x: x / m, y: y / m };\n    }\n}\n// A polyline's outward normals: the perpendicular pointing away from its\n// centroid where the shape is fat enough to say, else the frame's own outward.\nfunction outwardNormals(pts, outRef) {\n    const centroid = centroidOf(pts);\n    return pts.map((p, i) => {\n        const t = unit(pts[Math.max(0, i - 1)], pts[Math.min(pts.length - 1, i + 1)]);\n        const n = { x: -t.y, y: t.x };\n        const rx = p.x - centroid.x;\n        const ry = p.y - centroid.y;\n        const rm = Math.hypot(rx, ry);\n        const dot = n.x * rx + n.y * ry;\n        const ref = outRef[i];\n        const sign = rm > 1e-9 && Math.abs(dot) > 0.3 * rm\n            ? Math.sign(dot)\n            : Math.sign(n.x * ref.x + n.y * ref.y) || 1;\n        return { x: n.x * sign, y: n.y * sign };\n    });\n}\n// the flat curve carried into the frame from arc length tA, outward by sign,\n// sampled every `step` at most\nfunction mapFlat(frame, tA, sign, flat, step) {\n    const ds = Math.min(step, Math.max(flat.length / 24, 0.5));\n    const pts = [];\n    const refs = [];\n    for (let t = 0; t <= flat.length + 1e-9; t += ds) {\n        const { u, v } = flat.at(Math.min(t, flat.length));\n        const q = frame.pointAt(tA + u);\n        const nr = frame.normalAt(tA + u);\n        const ox = nr.x * sign;\n        const oy = nr.y * sign;\n        pts.push({ x: q.x + ox * v, y: q.y + oy * v });\n        refs.push({ x: ox, y: oy });\n    }\n    return { pts, refs };\n}\nconst FINE_STEP = 5;\nconst COARSE_STEP = CLEAR / 2;\n// the flat curve whose image in a curved frame has the asked length, within\n// a tenth of a percent or six tries\nfunction fitted(frame, tA, sign, make, length, step) {\n    let flatLength = length;\n    let mapped = mapFlat(frame, tA, sign, make(flatLength), step);\n    if (frame.straight) {\n        return mapped;\n    }\n    for (let i = 0; i < 6; i++) {\n        const got = polylineLength(mapped.pts);\n        if (!(got > 0) || Math.abs(got / length - 1) < 1e-3) {\n            break;\n        }\n        flatLength *= length / got;\n        mapped = mapFlat(frame, tA, sign, make(flatLength), step);\n    }\n    return mapped;\n}\nfunction depths(from, n) {\n    return Array.from({ length: n }, (_, i) => from + (i * LANE_GAP) / 2);\n}\nfunction spanOf(anchors) {\n    if (anchors.length === 0) {\n        return Infinity;\n    }\n    let lo = Infinity;\n    let hi = -Infinity;\n    for (const a of anchors) {\n        lo = Math.min(lo, a.point.x);\n        hi = Math.max(hi, a.point.x);\n    }\n    return hi - lo;\n}\nfunction cellKey(gx, gy) {\n    return (gx * 73856093) ^ (gy * 19349663);\n}\nclass Placer {\n    constructor(c) {\n        this.c = c;\n        this.grid = new Map();\n        const { ids, first, count, per, seedX, seedY, backbone } = c;\n        const N = ids.length;\n        this.points = Array.from({ length: N }, () => undefined);\n        this.params = Array.from({ length: N }, () => undefined);\n        this.curves = Array.from({ length: N }, () => undefined);\n        this.links = c.links.map((sides, k) => sides.map(out => out.filter(([v]) => v !== k)));\n        this.route = ids.map(id => id.startsWith(ROUTE_ID));\n        let min = Infinity;\n        let max = -Infinity;\n        for (let k = 0; k < N; k++) {\n            const start = first[k];\n            if (!backbone[start] || Number.isNaN(seedX[start])) {\n                continue;\n            }\n            min = Math.min(min, seedX[start]);\n            max = Math.max(max, seedX[start] + per[k] * (count[k] - 1));\n        }\n        this.backbone = new Curve([\n            { x: min, y: 0 },\n            { x: max, y: 0 },\n        ], [\n            { x: 0, y: 1 },\n            { x: 0, y: 1 },\n        ], true);\n        this.backboneCentroid = { x: (min + max) / 2, y: 0 };\n        for (let k = 0; k < N; k++) {\n            const start = first[k];\n            if (!backbone[start] || Number.isNaN(seedX[start])) {\n                continue;\n            }\n            const pts = [];\n            const ts = [];\n            for (let i = 0; i < count[k]; i++) {\n                const x = seedX[start] + i * per[k];\n                pts.push({ x, y: seedY[start] });\n                ts.push(x - min);\n            }\n            this.points[k] = pts;\n            this.params[k] = ts;\n            this.curves[k] = this.backbone;\n            this.occupy(pts, this.backbone);\n        }\n    }\n    static hasBackbone(c) {\n        for (let k = 0; k < c.ids.length; k++) {\n            const start = c.first[k];\n            if (c.backbone[start] && !Number.isNaN(c.seedX[start])) {\n                return true;\n            }\n        }\n        return false;\n    }\n    run() {\n        const free = [];\n        for (let k = 0; k < this.points.length; k++) {\n            if (!this.points[k]) {\n                free.push(k);\n            }\n        }\n        // Narrow pieces first, short before long, except that pieces on the same\n        // feet go longest first so an inner loop nests inside the outer one rather\n        // than crossing it. A wide loop whose foot lies inside a narrower loop's\n        // disc still drives its leg through it; making the narrow loop yield and\n        // re-place after the wide one freed it but re-placed it as a hairpin on\n        // long legs, 243/411/13 to 229/459/21 link-node/link-link/node-node\n        // crossings on the KIV-2 eight-haplotype cut at twice the time, and\n        // leaning the re-placed loop by shear at 0.1-0.4 rad gave 310/480/25.\n        const pieces = this.componentsOf(free)\n            .map(members => ({ members, anchors: this.anchorsOf(members) }))\n            .filter(p => p.anchors.length)\n            .map(p => ({\n            members: p.members,\n            span: spanOf(p.anchors),\n            drawn: p.members.reduce((s, k) => s + this.drawn(k), 0),\n            feet: p.anchors\n                .map(a => `${a.point.x},${a.point.y}`)\n                .sort()\n                .join(' '),\n        }))\n            .sort((a, b) => a.span - b.span ||\n            (a.feet === b.feet ? b.drawn - a.drawn : a.drawn - b.drawn));\n        for (const p of pieces) {\n            this.placePiece(p.members, this.backboneCentroid);\n        }\n    }\n    write(X, Y) {\n        const { first } = this.c;\n        this.points.forEach((pts, k) => {\n            pts === null || pts === void 0 ? void 0 : pts.forEach((p, i) => {\n                X[first[k] + i] = p.x;\n                Y[first[k] + i] = p.y;\n            });\n        });\n    }\n    drawn(k) {\n        return this.c.per[k] * (this.c.count[k] - 1);\n    }\n    endIndex(k, side) {\n        return side ? this.c.count[k] - 1 : 0;\n    }\n    occupy(pts, curve) {\n        for (const p of pts) {\n            const key = cellKey(Math.floor(p.x / CLEAR), Math.floor(p.y / CLEAR));\n            const list = this.grid.get(key);\n            const occupant = { x: p.x, y: p.y, curve };\n            if (list) {\n                list.push(occupant);\n            }\n            else {\n                this.grid.set(key, [occupant]);\n            }\n        }\n    }\n    // placed points within CLEAR of the candidate, off the exempt curve and\n    // beyond a lane of the anchors, up to `limit`. Exempting two lanes let\n    // teardrops off adjacent anchors cross at the neck: 3 node crossings on the\n    // HPRC KIV-2 cut against 1, and 2 on MHC class II against 0.\n    violations(pts, exempt, anchorPts, limit) {\n        var _a;\n        let n = 0;\n        for (const p of pts) {\n            if (anchorPts.some(a => Math.hypot(p.x - a.x, p.y - a.y) < LANE_GAP)) {\n                continue;\n            }\n            const cx = Math.floor(p.x / CLEAR);\n            const cy = Math.floor(p.y / CLEAR);\n            for (let gx = cx - 1; gx <= cx + 1; gx++) {\n                for (let gy = cy - 1; gy <= cy + 1; gy++) {\n                    for (const q of (_a = this.grid.get(cellKey(gx, gy))) !== null && _a !== void 0 ? _a : []) {\n                        if (q.curve !== exempt &&\n                            Math.hypot(p.x - q.x, p.y - q.y) < CLEAR) {\n                            n++;\n                            if (n >= limit) {\n                                return n;\n                            }\n                        }\n                    }\n                }\n            }\n        }\n        return n;\n    }\n    // The first candidate that clears what is drawn, else the least crowded.\n    // Exempting only the feet of pieces at the same anchor, or adding\n    // candidates with legs splayed a lane or more out from the anchors, moved\n    // no count that mattered on the HPRC cuts.\n    choose(candidates, exempt, anchorPts) {\n        let best;\n        let bestV = Infinity;\n        for (const candidate of candidates) {\n            const v = this.violations(candidate(COARSE_STEP).pts, exempt, anchorPts, bestV);\n            if (v === 0) {\n                return candidate(FINE_STEP);\n            }\n            if (v < bestV) {\n                bestV = v;\n                best = candidate;\n            }\n        }\n        return best(FINE_STEP);\n    }\n    anchorsOf(members) {\n        const set = new Set(members);\n        const out = [];\n        for (const u of members) {\n            for (const uSide of SIDES) {\n                for (const [v, vSide] of this.links[u][uSide]) {\n                    const pts = this.points[v];\n                    if (set.has(v) || !pts) {\n                        continue;\n                    }\n                    const i = this.endIndex(v, vSide);\n                    out.push({\n                        u,\n                        uSide,\n                        v,\n                        vSide,\n                        point: pts[i],\n                        curve: this.curves[v],\n                        t: this.params[v][i],\n                    });\n                }\n            }\n        }\n        return out;\n    }\n    componentsOf(members) {\n        const set = new Set(members);\n        const seen = new Set();\n        const comps = [];\n        for (const s of members) {\n            if (seen.has(s)) {\n                continue;\n            }\n            const queue = [s];\n            seen.add(s);\n            for (const u of queue) {\n                for (const side of SIDES) {\n                    for (const [v] of this.links[u][side]) {\n                        if (set.has(v) && !seen.has(v)) {\n                            seen.add(v);\n                            queue.push(v);\n                        }\n                    }\n                }\n            }\n            comps.push(queue);\n        }\n        return comps;\n    }\n    // side-consistent BFS over (node, entered side) within the piece; without a\n    // target, the path to the farthest state\n    spinePath(members, from, fromSide, to, toExitSide) {\n        const set = new Set(members);\n        const key = (k, s) => k * 2 + s;\n        const reached = (k, s) => k === to && other(s) === toExitSide;\n        const prev = new Map([[key(from, fromSide), -1]]);\n        const queue = [[from, fromSide]];\n        let far = [from, fromSide];\n        for (const [k, s] of queue) {\n            far = [k, s];\n            if (to !== undefined && reached(k, s)) {\n                break;\n            }\n            for (const [v, t] of this.links[k][other(s)]) {\n                if (!set.has(v) || prev.has(key(v, t))) {\n                    continue;\n                }\n                prev.set(key(v, t), key(k, s));\n                queue.push([v, t]);\n            }\n        }\n        if (to !== undefined && !reached(far[0], far[1])) {\n            return undefined;\n        }\n        const path = [];\n        for (let cur = key(far[0], far[1]); cur !== -1; cur = prev.get(cur)) {\n            path.push({ k: cur >> 1, enter: (cur & 1) });\n        }\n        return path.reverse();\n    }\n    loosePath(members, from, to) {\n        const set = new Set(members);\n        const prev = new Map([[from, -1]]);\n        const side = new Map([[from, 0]]);\n        const queue = [from];\n        for (const k of queue) {\n            if (k === to) {\n                break;\n            }\n            for (const s of SIDES) {\n                for (const [v, t] of this.links[k][s]) {\n                    if (!set.has(v) || prev.has(v)) {\n                        continue;\n                    }\n                    prev.set(v, k);\n                    side.set(v, t);\n                    queue.push(v);\n                }\n            }\n        }\n        const path = [];\n        for (let cur = to; cur !== -1; cur = prev.get(cur)) {\n            path.push({ k: cur, enter: side.get(cur) });\n        }\n        return path.reverse();\n    }\n    spineLength(spine) {\n        const { link } = this.c;\n        return spine.reduce((s, { k }) => s + this.drawn(k) + link, link);\n    }\n    // the spine's chains along the curve from arc length t0, at their own\n    // spacing unless one is given\n    layAlong(spine, curve, t0, spacing) {\n        const { count, per, link } = this.c;\n        let t = t0;\n        const all = [];\n        for (const { k, enter } of spine) {\n            const step = spacing !== null && spacing !== void 0 ? spacing : per[k];\n            const pts = [];\n            const ts = [];\n            for (let i = 0; i < count[k]; i++) {\n                pts.push(curve.pointAt(t + i * step));\n                ts.push(t + i * step);\n            }\n            if (enter === 1) {\n                pts.reverse();\n                ts.reverse();\n            }\n            this.points[k] = pts;\n            this.params[k] = ts;\n            this.curves[k] = curve;\n            all.push(...pts);\n            t += step * (count[k] - 1) + link;\n        }\n        return all;\n    }\n    arcCandidates(frame, tA, sign, c, L) {\n        const hMax = (L - c) / 2 - 1e-6;\n        const tilts = L > 2 * c ? TEARDROP_TILTS : [0];\n        const candidates = [];\n        for (const drop of depths(0, 8)) {\n            for (const tilt of tilts) {\n                for (let i = 0; i <= 16; i++) {\n                    const h = (hMax * i) / 16;\n                    const flat = tilted(arcFlat(c, L, h, drop), c, tilt);\n                    if ((i < 16 && flat.apex < MIN_DEPTH) || behindFrame(flat)) {\n                        continue;\n                    }\n                    candidates.push(step => fitted(frame, tA, sign, length => tilted(arcFlat(c, length, Math.min(h, (length - c) / 2 - 1e-6), drop), c, tilt), L, step));\n                }\n            }\n        }\n        return candidates;\n    }\n    placePiece(members, parent) {\n        var _a;\n        const { count, link } = this.c;\n        const anchors = this.anchorsOf(members);\n        if (anchors.length === 0) {\n            return;\n        }\n        const route = members.every(k => this.route[k]);\n        const shared = anchors.every(a => a.curve === anchors[0].curve)\n            ? anchors[0].curve\n            : undefined;\n        let frame;\n        let tA;\n        let tB;\n        let sign;\n        if (shared) {\n            anchors.sort((a, b) => a.t - b.t);\n            frame = shared;\n            tA = anchors[0].t;\n            tB = anchors[anchors.length - 1].t;\n            sign = frame === this.backbone && route ? -1 : 1;\n        }\n        else {\n            // A piece between curves hangs on the chord, and its links stay long.\n            // Relaxing just these pieces over their links with the rest held\n            // stretched the junction nodes across the gap instead: on the KIV-2\n            // eight-haplotype cut, chain length error 0.3% to 57% and node\n            // crossings 22 to 48. Hanging the piece on the curve with most anchors\n            // more than doubled that cut's link crossings.\n            anchors.sort((a, b) => a.point.x - b.point.x || a.point.y - b.point.y);\n            const a = anchors[0].point;\n            const b = anchors[anchors.length - 1].point;\n            const chord = Math.hypot(b.x - a.x, b.y - a.y);\n            const u = chord > 1e-9 ? unit(a, b) : { x: 1, y: 0 };\n            const n = { x: -u.y, y: u.x };\n            const mid = lerp(a, b, 0.5);\n            sign = anchors.some(x => x.curve === this.backbone)\n                ? (route ? -1 : 1) * (Math.sign(n.y) || 1)\n                : (mid.x - parent.x) * n.x + (mid.y - parent.y) * n.y >= 0\n                    ? 1\n                    : -1;\n            frame = new Curve([a, b], [n, n], true);\n            tA = 0;\n            tB = chord;\n        }\n        const A = anchors[0];\n        const B = anchors[anchors.length - 1];\n        const c = tB - tA;\n        const single = anchors.length === 1 || (A.u === B.u && A.uSide === B.uSide && c < 1e-9);\n        const anchorPts = [A.point, B.point];\n        const pick = (candidates) => this.choose(candidates, shared, anchorPts);\n        let spine;\n        let mapped;\n        let start = link;\n        let spacing;\n        if (single) {\n            spine = this.spinePath(members, A.u, A.uSide);\n            const L = this.spineLength(spine);\n            const next = A.vSide\n                ? Math.max(0, count[A.v] - 2)\n                : Math.min(1, count[A.v] - 1);\n            const dirU = A.t >= this.params[A.v][next] ? 1 : -1;\n            const du = dirU * Math.cos(TIP_ANGLE);\n            const dv = Math.sin(TIP_ANGLE);\n            mapped = pick(depths(0, 12).map(drop => (step) => fitted(frame, tA, sign, length => lineFlat(0, drop, du, dv, length), L, step)));\n        }\n        else {\n            spine =\n                (_a = this.spinePath(members, A.u, A.uSide, B.u, B.uSide)) !== null && _a !== void 0 ? _a : this.loosePath(members, A.u, B.u);\n            const L = this.spineLength(spine);\n            if (route) {\n                const d0 = Math.max(MIN_DEPTH, Math.min(BOW * c, BOW_CAP));\n                mapped = pick(depths(d0, 12).map(d => (step) => mapFlat(frame, tA, sign, arcFlat(c, archLength(c, d), 0, 0), step)));\n                const total = polylineLength(mapped.pts);\n                spacing = Math.max(1e-3, (total - 2 * link) / (count[spine[0].k] - 1));\n            }\n            else if (L > c + 1e-6) {\n                mapped = pick(this.arcCandidates(frame, tA, sign, c, L));\n            }\n            else {\n                const bar = L - 2 * link;\n                const d0 = Math.max(MIN_DEPTH, Math.min(BOW * (c - bar), BOW_CAP));\n                mapped = pick(depths(d0, 12).map(d => (step) => fitted(frame, tA, sign, length => lineFlat(c / 2 - length / 2, d, 1, 0, length), bar, step)));\n                start = 0;\n            }\n        }\n        const curve = new Curve(mapped.pts, outwardNormals(mapped.pts, mapped.refs));\n        const placed = this.layAlong(spine, curve, start, spacing);\n        this.occupy(placed, curve);\n        const centroid = centroidOf(placed);\n        const rest = members.filter(k => !this.points[k]);\n        const subs = this.componentsOf(rest)\n            .map(m => ({ members: m, span: spanOf(this.anchorsOf(m)) }))\n            .sort((a, b) => a.span - b.span);\n        for (const sub of subs) {\n            this.placePiece(sub.members, centroid);\n        }\n    }\n}\n// Initial positions per point, NaN where the placement reached nothing.\nexport function stressPlacement(c) {\n    const X = new Float64Array(c.n).fill(NaN);\n    const Y = new Float64Array(c.n).fill(NaN);\n    if (Placer.hasBackbone(c)) {\n        const placer = new Placer(c);\n        placer.run();\n        placer.write(X, Y);\n    }\n    return { X, Y };\n}\n", "import { stressPlacement } from \"./stressPlacement.js\";\n// A layout taking the Bandage engine's request: each node is the chain of\n// points FMMM would build, and the result is a polyline per node.\n//\n// A component with a seeded backbone is drawn by stressPlacement: the\n// backbone straight along x, every other node hung off it. The rest is a\n// stress layout by stochastic gradient descent (Zheng, Pawar & Goodman 2019)\n// with target distances from random walks, after odgi's path-guided SGD:\n// every point starts a few walks of log-uniform length each iteration, and\n// how far a walk got is how far apart its ends should sit, so a repeat's loop\n// draws as a ring of its own circumference. Stress has no repulsion, so a\n// final pass pushes apart points that are close but not joined.\n//\n// Running the schedule on a placed component twists its loops, since a walk\n// from a loop's leg runs on along the backbone and pulls the leg to lie along\n// it: 32 node crossings on HPRC MHC class II against the placement's 4.\n// walks per point and iterations by the quality the request names\nconst QUALITY = [\n    { walks: 2, iterations: 15 },\n    { walks: 4, iterations: 30 },\n    { walks: 8, iterations: 60 },\n    { walks: 12, iterations: 90 },\n    { walks: 16, iterations: 120 },\n];\nconst UNTANGLE_PASSES = 20;\n// the untangle radius, in link lengths\nconst UNTANGLE_LINKS = 3;\nconst UNTANGLE_PUSH = 0.3;\nconst SMOOTH_PASSES = 2;\n// a 20-link cap balls a 3k-node graph up\nconst MAX_HOPS = 200;\n// the step size the schedule ends on, as a share of the smallest pair's\nconst EPS = 0.1;\n// the share of the schedule a seeded component skips\nconst WARM = 0.5;\nconst isBackbone = (node) => { var _a; return ((_a = node.stable) === null || _a === void 0 ? void 0 : _a.rank) === 0; };\nfunction flipped(strand, name) {\n    const own = name.at(-1);\n    return ((strand === '+' || strand === '-') &&\n        (own === '+' || own === '-') &&\n        strand !== own);\n}\nfunction xorshift(seed) {\n    let s = Math.imul(seed, 2654435761) >>> 0 || 1;\n    return () => {\n        s ^= s << 13;\n        s >>>= 0;\n        s ^= s >>> 17;\n        s ^= s << 5;\n        s >>>= 0;\n        return s / 4294967296;\n    };\n}\nexport function num(value, fallback) {\n    return typeof value === 'number' && Number.isFinite(value) ? value : fallback;\n}\n// A node's drawn length, in layout units, from its bp\nexport function drawnLength(options, bp) {\n    return Math.max((num(options.nodeLengthPerMegabase, 1000) * bp) / 1000000, num(options.minimumNodeLength, 1));\n}\nexport function chains(request) {\n    const { nodes, edges } = request.graph;\n    const o = request.options;\n    const segment = num(o.nodeSegmentLength, 1);\n    const link = num(o.edgeLength, 1);\n    const ids = nodes.map(n => n.id);\n    const first = new Int32Array(nodes.length);\n    const count = new Int32Array(nodes.length);\n    const per = new Float64Array(nodes.length);\n    let n = 0;\n    nodes.forEach((node, k) => {\n        const drawn = drawnLength(o, node.length);\n        const steps = Math.max(1, Math.ceil(drawn / segment));\n        first[k] = n;\n        count[k] = steps + 1;\n        per[k] = drawn / steps;\n        n += steps + 1;\n    });\n    const chainOf = new Int32Array(n);\n    const indexOf = new Int32Array(n);\n    const seedX = new Float64Array(n).fill(NaN);\n    const seedY = new Float64Array(n).fill(NaN);\n    const backbone = new Uint8Array(n);\n    const adjacent = Array.from({ length: n }, () => []);\n    nodes.forEach((node, k) => {\n        const seeded = typeof node.x === 'number' && typeof node.y === 'number';\n        const reference = isBackbone(node) ? 1 : 0;\n        for (let i = 0; i < count[k]; i++) {\n            const v = first[k] + i;\n            chainOf[v] = k;\n            indexOf[v] = i;\n            backbone[v] = reference;\n            if (seeded) {\n                seedX[v] = node.x + i * per[k];\n                seedY[v] = node.y;\n            }\n            if (i > 0) {\n                adjacent[v - 1].push([v, per[k]]);\n                adjacent[v].push([v - 1, per[k]]);\n            }\n        }\n    });\n    const index = new Map(ids.map((id, k) => [id, k]));\n    const links = nodes.map(() => [[], []]);\n    for (const edge of edges) {\n        const a = index.get(edge.from);\n        const b = index.get(edge.to);\n        if (a === undefined || b === undefined) {\n            continue;\n        }\n        // a self link on a chain of one step has nowhere to go, as in FMMM\n        if (a === b && count[a] <= 2) {\n            continue;\n        }\n        const fromSide = flipped(edge.fromStrand, edge.from) ? 0 : 1;\n        const toSide = flipped(edge.toStrand, edge.to) ? 1 : 0;\n        const u = first[a] + (fromSide ? count[a] - 1 : 0);\n        const v = first[b] + (toSide ? count[b] - 1 : 0);\n        adjacent[u].push([v, link]);\n        adjacent[v].push([u, link]);\n        links[a][fromSide].push([b, toSide]);\n        links[b][toSide].push([a, fromSide]);\n    }\n    const off = new Int32Array(n + 1);\n    for (let i = 0; i < n; i++) {\n        off[i + 1] = off[i] + adjacent[i].length;\n    }\n    const nb = new Int32Array(off[n]);\n    const wt = new Float64Array(off[n]);\n    for (let i = 0; i < n; i++) {\n        adjacent[i].forEach(([v, w], k) => {\n            nb[off[i] + k] = v;\n            wt[off[i] + k] = w;\n        });\n    }\n    return {\n        ids,\n        first,\n        count,\n        per,\n        links,\n        chainOf,\n        indexOf,\n        seedX,\n        seedY,\n        backbone,\n        off,\n        nb,\n        wt,\n        n,\n        link,\n    };\n}\n// each point's connected component, and the points of each component\nfunction components(c) {\n    const { n, off, nb } = c;\n    const comp = new Int32Array(n).fill(-1);\n    const members = [];\n    for (let s = 0; s < n; s++) {\n        if (comp[s] >= 0) {\n            continue;\n        }\n        const queue = [s];\n        comp[s] = members.length;\n        for (const u of queue) {\n            for (let e = off[u]; e < off[u + 1]; e++) {\n                const v = nb[e];\n                if (comp[v] < 0) {\n                    comp[v] = members.length;\n                    queue.push(v);\n                }\n            }\n        }\n        members.push(queue);\n    }\n    return { comp, members };\n}\nexport function stressLayout(request, opts = {}) {\n    var _a, _b, _c;\n    const c = chains(request);\n    const { n, off, nb, wt, seedX, seedY, first, count, per, link } = c;\n    const o = request.options;\n    const quality = QUALITY[Math.max(0, Math.min(4, num((_a = opts.quality) !== null && _a !== void 0 ? _a : o.quality, 2)))];\n    const gap = num((_b = opts.componentSeparation) !== null && _b !== void 0 ? _b : o.componentSeparation, 15);\n    const rand = xorshift(num((_c = opts.seed) !== null && _c !== void 0 ? _c : o.seed, 1));\n    const X = new Float64Array(n);\n    const Y = new Float64Array(n);\n    const nodePositions = {};\n    if (n === 0) {\n        return { nodePositions };\n    }\n    const { comp, members } = components(c);\n    let dmin = Infinity;\n    let total = 0;\n    for (let e = 0; e < nb.length; e++) {\n        dmin = Math.min(dmin, wt[e]);\n        total += wt[e];\n    }\n    total /= 2;\n    let anySeed = false;\n    for (let i = 0; i < n; i++) {\n        if (!Number.isNaN(seedX[i])) {\n            anySeed = true;\n            break;\n        }\n    }\n    const placed = anySeed ? stressPlacement(c) : undefined;\n    const side = Math.sqrt(n) * 20;\n    for (let i = 0; i < n; i++) {\n        if (placed && !Number.isNaN(placed.X[i])) {\n            X[i] = placed.X[i];\n            Y[i] = placed.Y[i];\n        }\n        else if (anySeed && !Number.isNaN(seedX[i])) {\n            X[i] = seedX[i] + rand() - 0.5;\n            Y[i] = seedY[i] + rand() - 0.5;\n        }\n        else {\n            X[i] = rand() * side;\n            Y[i] = rand() * side;\n        }\n    }\n    // the points the schedule moves: those of components the placement did not\n    // draw whole, in index order so the schedule runs as it would alone\n    const drawn = members.map(points => placed !== undefined && points.every(i => !Number.isNaN(placed.X[i])));\n    const loose = [];\n    let looseSeeded = true;\n    for (let i = 0; i < n; i++) {\n        if (!drawn[comp[i]]) {\n            loose.push(i);\n            looseSeeded && (looseSeeded = !Number.isNaN(seedX[i]));\n        }\n    }\n    const dmax = Math.max(total / 4, dmin * 10);\n    const etaMax = dmax * dmax;\n    const etaMin = EPS * dmin * dmin;\n    const { walks, iterations } = quality;\n    const lambda = Math.log(etaMax / etaMin) / Math.max(1, iterations - 1);\n    const logMin = Math.log(dmin);\n    const logMax = Math.log(dmax);\n    const move = (i, j, d, eta) => {\n        let mu = eta / (d * d);\n        if (mu > 1) {\n            mu = 1;\n        }\n        const dx = X[i] - X[j];\n        const dy = Y[i] - Y[j];\n        const mag = Math.sqrt(dx * dx + dy * dy) || 1e-9;\n        const r = (mu * (mag - d)) / (2 * mag);\n        const rx = r * dx;\n        const ry = r * dy;\n        X[i] = X[i] - rx;\n        Y[i] = Y[i] - ry;\n        X[j] = X[j] + rx;\n        Y[j] = Y[j] + ry;\n    };\n    // The end of a walk of up to `length` from point i, with how far it got in\n    // `walked`: a walk stops short at a free chain end.\n    let walked = 0;\n    const walk = (i, length) => {\n        let chain = c.chainOf[i];\n        let idx = c.indexOf[i];\n        let dir = rand() < 0.5 ? -1 : 1;\n        let remaining = length;\n        for (let hops = 0; hops < MAX_HOPS; hops++) {\n            const points = count[chain];\n            const step = per[chain];\n            const toEnd = (dir > 0 ? points - 1 - idx : idx) * step;\n            if (remaining <= toEnd) {\n                const steps = Math.round(remaining / step);\n                walked = length - remaining + steps * step;\n                return first[chain] + idx + dir * steps;\n            }\n            remaining -= toEnd;\n            const out = c.links[chain][dir > 0 ? 1 : 0];\n            if (out.length === 0) {\n                walked = length - remaining;\n                return first[chain] + (dir > 0 ? points - 1 : 0);\n            }\n            const [next, enterSide] = out[Math.floor(rand() * out.length)];\n            remaining -= link;\n            chain = next;\n            dir = enterSide === 0 ? 1 : -1;\n            idx = enterSide === 0 ? 0 : count[next] - 1;\n            if (remaining <= 0) {\n                walked = length - remaining;\n                return first[chain] + idx;\n            }\n        }\n        return -1;\n    };\n    const adjacentTerms = (i, eta) => {\n        for (let e = off[i]; e < off[i + 1]; e++) {\n            const j = nb[e];\n            if (j > i) {\n                move(i, j, wt[e], eta);\n            }\n        }\n    };\n    const order = Int32Array.from(loose);\n    const warm = looseSeeded ? Math.floor(WARM * iterations) : 0;\n    for (let t = loose.length ? warm : iterations; t < iterations; t++) {\n        const eta = etaMax * Math.exp(-lambda * t);\n        for (let k = order.length - 1; k > 0; k--) {\n            const r = Math.floor(rand() * (k + 1));\n            const tmp = order[k];\n            order[k] = order[r];\n            order[r] = tmp;\n        }\n        for (const i of order) {\n            adjacentTerms(i, eta);\n            for (let w = 0; w < walks; w++) {\n                const length = Math.exp(logMin + rand() * (logMax - logMin));\n                const j = walk(i, length);\n                if (j >= 0 && j !== i && walked > 0) {\n                    move(i, j, walked, eta);\n                }\n            }\n        }\n    }\n    // untangle: points closer than the radius and not joined push apart, then\n    // a sweep over the links pulls each back towards its length\n    const radius = UNTANGLE_LINKS * link;\n    const key = (x, y) => (Math.floor(x / radius) * 73856093) ^ (Math.floor(y / radius) * 19349663);\n    for (let u = 0; u < (loose.length ? UNTANGLE_PASSES : 0); u++) {\n        const grid = new Map();\n        for (const i of loose) {\n            const k = key(X[i], Y[i]);\n            const list = grid.get(k);\n            if (list) {\n                list.push(i);\n            }\n            else {\n                grid.set(k, [i]);\n            }\n        }\n        for (const i of loose) {\n            const cx = Math.floor(X[i] / radius);\n            const cy = Math.floor(Y[i] / radius);\n            for (let gx = cx - 1; gx <= cx + 1; gx++) {\n                for (let gy = cy - 1; gy <= cy + 1; gy++) {\n                    const list = grid.get((gx * 73856093) ^ (gy * 19349663));\n                    if (!list) {\n                        continue;\n                    }\n                    for (const j of list) {\n                        if (j <= i) {\n                            continue;\n                        }\n                        let joined = false;\n                        for (let e = off[i]; e < off[i + 1]; e++) {\n                            if (nb[e] === j) {\n                                joined = true;\n                                break;\n                            }\n                        }\n                        if (joined) {\n                            continue;\n                        }\n                        const dx = X[i] - X[j];\n                        const dy = Y[i] - Y[j];\n                        const mag = Math.sqrt(dx * dx + dy * dy);\n                        if (mag >= radius) {\n                            continue;\n                        }\n                        let rx;\n                        let ry;\n                        if (mag > 1e-6) {\n                            const r = (UNTANGLE_PUSH * (radius - mag)) / (2 * mag);\n                            rx = r * dx;\n                            ry = r * dy;\n                        }\n                        else {\n                            rx = UNTANGLE_PUSH * radius * (rand() - 0.5);\n                            ry = UNTANGLE_PUSH * radius * (rand() - 0.5);\n                        }\n                        X[i] = X[i] + rx;\n                        Y[i] = Y[i] + ry;\n                        X[j] = X[j] - rx;\n                        Y[j] = Y[j] - ry;\n                    }\n                }\n            }\n        }\n        for (const i of loose) {\n            adjacentTerms(i, Infinity);\n        }\n    }\n    // each chain's interior points smoothed, so a node reads as one curve, then\n    // spaced evenly along it at its drawn length\n    for (let k = 0; k < count.length; k++) {\n        const a = first[k];\n        const m = count[k];\n        if (m < 3) {\n            continue;\n        }\n        for (let s = 0; s < SMOOTH_PASSES; s++) {\n            const xs = X.slice(a, a + m);\n            const ys = Y.slice(a, a + m);\n            for (let i = 1; i + 1 < m; i++) {\n                X[a + i] = 0.5 * xs[i] + 0.25 * (xs[i - 1] + xs[i + 1]);\n                Y[a + i] = 0.5 * ys[i] + 0.25 * (ys[i - 1] + ys[i + 1]);\n            }\n        }\n        respace(X, Y, a, m, per[k]);\n    }\n    packComponents(comp, members, X, Y, anySeed, gap);\n    for (let k = 0; k < c.ids.length; k++) {\n        const points = [];\n        for (let i = 0; i < count[k]; i++) {\n            points.push({ x: X[first[k] + i], y: Y[first[k] + i] });\n        }\n        nodePositions[c.ids[k]] = points;\n    }\n    return { nodePositions };\n}\n// Points a to a+m-1 moved to equal spacing along their polyline. Smoothing\n// shortens a curve, so the interior first bulges out from the chord between\n// the ends until the length is back, and the points then take their full\n// spacing. The ends stay, since extending them along their tangents ran a\n// node past its anchors and through the links there.\nfunction respace(X, Y, a, m, per) {\n    bulge(X, Y, a, m, per * (m - 1));\n    const lengths = new Float64Array(m);\n    for (let i = 1; i < m; i++) {\n        lengths[i] =\n            lengths[i - 1] +\n                Math.hypot(X[a + i] - X[a + i - 1], Y[a + i] - Y[a + i - 1]);\n    }\n    if (!lengths[m - 1]) {\n        return;\n    }\n    const total = lengths[m - 1];\n    const xs = X.slice(a, a + m);\n    const ys = Y.slice(a, a + m);\n    let seg = 1;\n    for (let i = 1; i + 1 < m; i++) {\n        const s = (total * i) / (m - 1);\n        while (seg < m - 1 && lengths[seg] < s) {\n            seg++;\n        }\n        const span = lengths[seg] - lengths[seg - 1];\n        const t = span > 0 ? (s - lengths[seg - 1]) / span : 0;\n        X[a + i] = xs[seg - 1] + (xs[seg] - xs[seg - 1]) * t;\n        Y[a + i] = ys[seg - 1] + (ys[seg] - ys[seg - 1]) * t;\n    }\n}\n// Interior points a+1 to a+m-2 pushed out from the chord between the ends,\n// their offsets from it scaled by one factor, until the polyline is `target`\n// long. A chain lying along its chord has nothing to push and keeps its\n// length.\nfunction bulge(X, Y, a, m, target) {\n    const b = a + m - 1;\n    const cx = X[a];\n    const cy = Y[a];\n    const chord = Math.hypot(X[b] - cx, Y[b] - cy);\n    const ux = chord > 1e-9 ? (X[b] - cx) / chord : 1;\n    const uy = chord > 1e-9 ? (Y[b] - cy) / chord : 0;\n    const along = new Float64Array(m);\n    const off = new Float64Array(m);\n    let flat = true;\n    for (let i = 0; i < m; i++) {\n        const dx = X[a + i] - cx;\n        const dy = Y[a + i] - cy;\n        along[i] = dx * ux + dy * uy;\n        off[i] = dy * ux - dx * uy;\n        flat && (flat = Math.abs(off[i]) < 1e-6);\n    }\n    const lengthAt = (f) => {\n        let total = 0;\n        for (let i = 1; i < m; i++) {\n            total += Math.hypot(along[i] - along[i - 1], f * (off[i] - off[i - 1]));\n        }\n        return total;\n    };\n    if (flat || lengthAt(1) >= target) {\n        return;\n    }\n    let lo = 1;\n    let hi = 2;\n    while (lengthAt(hi) < target && hi < 1e6) {\n        lo = hi;\n        hi *= 2;\n    }\n    for (let it = 0; it < 40; it++) {\n        const mid = (lo + hi) / 2;\n        if (lengthAt(mid) < target) {\n            lo = mid;\n        }\n        else {\n            hi = mid;\n        }\n    }\n    const f = (lo + hi) / 2;\n    for (let i = 1; i + 1 < m; i++) {\n        X[a + i] = cx + along[i] * ux - f * off[i] * uy;\n        Y[a + i] = cy + along[i] * uy + f * off[i] * ux;\n    }\n}\n// Components stacked top to bottom, left aligned, `gap` apart. A component\n// with no seeds is turned so its long axis runs along x; a seeded one keeps\n// the frame its seeds stated.\nfunction packComponents(comp, members, X, Y, anySeed, gap) {\n    if (!anySeed) {\n        for (const points of members) {\n            rotateToPrincipalAxis(X, Y, points);\n        }\n    }\n    if (members.length < 2) {\n        return;\n    }\n    const minX = new Float64Array(members.length).fill(Infinity);\n    const minY = new Float64Array(members.length).fill(Infinity);\n    const maxY = new Float64Array(members.length).fill(-Infinity);\n    for (let i = 0; i < X.length; i++) {\n        const k = comp[i];\n        minX[k] = Math.min(minX[k], X[i]);\n        minY[k] = Math.min(minY[k], Y[i]);\n        maxY[k] = Math.max(maxY[k], Y[i]);\n    }\n    const shift = new Float64Array(members.length);\n    let y = 0;\n    for (let k = 0; k < members.length; k++) {\n        shift[k] = y - minY[k];\n        y += maxY[k] - minY[k] + gap;\n    }\n    for (let i = 0; i < X.length; i++) {\n        const k = comp[i];\n        X[i] = X[i] - minX[k];\n        Y[i] = Y[i] + shift[k];\n    }\n}\nfunction rotateToPrincipalAxis(X, Y, points) {\n    if (points.length < 3) {\n        return;\n    }\n    let cx = 0;\n    let cy = 0;\n    for (const i of points) {\n        cx += X[i];\n        cy += Y[i];\n    }\n    cx /= points.length;\n    cy /= points.length;\n    let sxx = 0;\n    let syy = 0;\n    let sxy = 0;\n    for (const i of points) {\n        const dx = X[i] - cx;\n        const dy = Y[i] - cy;\n        sxx += dx * dx;\n        syy += dy * dy;\n        sxy += dx * dy;\n    }\n    const angle = -0.5 * Math.atan2(2 * sxy, sxx - syy);\n    const cos = Math.cos(angle);\n    const sin = Math.sin(angle);\n    for (const i of points) {\n        const dx = X[i] - cx;\n        const dy = Y[i] - cy;\n        X[i] = cx + cos * dx - sin * dy;\n        Y[i] = cy + sin * dx + cos * dy;\n    }\n}\n", "// src/layoutEngines.ts\nimport { fmmmLayout } from \"@jbrowse/graph-fmmm-layout\";\nimport { stressLayout } from \"@jbrowse/graph-stress-layout\";\nvar LAYOUT_ENGINES = [\n  {\n    value: \"fmmm\",\n    label: \"Bandage (FMMM)\",\n    description: \"Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm.\"\n  },\n  {\n    value: \"stress\",\n    label: \"Stress\",\n    description: \"Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference.\"\n  }\n];\nvar LAYOUT_ENGINE_VALUES = LAYOUT_ENGINES.map((e) => e.value);\nfunction isLayoutEngineKind(value) {\n  return LAYOUT_ENGINE_VALUES.includes(value);\n}\nvar layoutEngine = async (request) => {\n  if (request.options.engine === \"stress\") {\n    const start2 = performance.now();\n    const result2 = stressLayout(request);\n    return { result: result2, duration: performance.now() - start2 };\n  }\n  const start = performance.now();\n  const result = await fmmmLayout(request);\n  return { result, duration: performance.now() - start };\n};\n\nexport {\n  LAYOUT_ENGINES,\n  LAYOUT_ENGINE_VALUES,\n  isLayoutEngineKind,\n  layoutEngine\n};\n", "// src/layout/drawnScale.ts\nvar MEAN_NODE_LENGTH = 40;\nvar MIN_TOTAL_GRAPH_LENGTH = 500;\nvar BANDAGE_MINIMUM_NODE_LENGTH = 5;\nfunction drawnNodeLength(opts, length) {\n  return Math.max(\n    opts.nodeLengthPerMegabase * length / 1e6,\n    opts.minimumNodeLength\n  );\n}\nfunction bandageAutoScale(graph, minNodeLength = BANDAGE_MINIMUM_NODE_LENGTH) {\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0);\n  const megabases = totalLength / 1e6;\n  const target = Math.max(\n    graph.nodes.length * MEAN_NODE_LENGTH,\n    MIN_TOTAL_GRAPH_LENGTH\n  );\n  return {\n    nodeLengthPerMegabase: megabases > 0 ? target / megabases : 1e4,\n    minimumNodeLength: Math.max(BANDAGE_MINIMUM_NODE_LENGTH, minNodeLength),\n    edgeLength: 5,\n    nodeSegmentLength: 20\n  };\n}\nvar PROPORTIONAL_LENGTH = { power: 1, effect: 1 };\nfunction isProportional(law) {\n  return law.power === 1 && law.effect === 1;\n}\nfunction drawnLengthFor(graph, law) {\n  const count = graph.nodes.length;\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0);\n  const meanBp = count > 0 ? totalLength / count : 0;\n  const meanDrawn = count > 0 ? Math.max(count * MEAN_NODE_LENGTH, MIN_TOTAL_GRAPH_LENGTH) / count : MEAN_NODE_LENGTH;\n  return (bp) => {\n    if (meanBp <= 0) {\n      return meanDrawn;\n    }\n    const relative = (bp / meanBp) ** law.power;\n    return Math.max(\n      meanDrawn * ((relative - 1) * law.effect + 1),\n      BANDAGE_MINIMUM_NODE_LENGTH\n    );\n  };\n}\nvar LAYOUT_LENGTH_PRECISION = 1e3;\nvar PROPORTIONAL_SPREAD = {\n  law: PROPORTIONAL_LENGTH,\n  minNodeLength: 0\n};\nfunction layoutScaling(graph, spread = PROPORTIONAL_SPREAD) {\n  const { law, minNodeLength } = spread;\n  const opts = bandageAutoScale(graph, minNodeLength);\n  if (isProportional(law)) {\n    return { nodes: graph.nodes, opts };\n  }\n  const drawn = drawnLengthFor(graph, law);\n  return {\n    nodes: graph.nodes.map((node) => ({\n      ...node,\n      length: Math.round(drawn(node.length) * LAYOUT_LENGTH_PRECISION)\n    })),\n    opts: {\n      ...opts,\n      nodeLengthPerMegabase: 1e6 / LAYOUT_LENGTH_PRECISION,\n      // Bandage's own floor only. A law and a raised floor are alternatives\n      // rather than a stack: the law has already lifted the small end, and a\n      // floor on top of it would flatten exactly what it just spread.\n      minimumNodeLength: BANDAGE_MINIMUM_NODE_LENGTH\n    }\n  };\n}\nfunction drawnLengthOf(graph, spread = PROPORTIONAL_SPREAD) {\n  if (isProportional(spread.law)) {\n    const opts = bandageAutoScale(graph, spread.minNodeLength);\n    return (bp) => drawnNodeLength(opts, bp);\n  }\n  return drawnLengthFor(graph, spread.law);\n}\n\nexport {\n  MEAN_NODE_LENGTH,\n  drawnNodeLength,\n  bandageAutoScale,\n  PROPORTIONAL_LENGTH,\n  drawnLengthFor,\n  layoutScaling,\n  drawnLengthOf\n};\n", "import {\n  MEAN_NODE_LENGTH,\n  PROPORTIONAL_LENGTH\n} from \"./chunk-34BOZKIE.js\";\n\n// src/bubbleSpreads.ts\nvar BUBBLE_SPREADS = [\n  {\n    value: \"auto\",\n    label: \"Proportional\",\n    description: \"Bandage's own scale: a node draws proportional to its length, so a 1 bp allele is a speck.\",\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 0\n  },\n  {\n    value: \"open\",\n    label: \"Open bubbles\",\n    description: \"Give every allele a drawn length, so a bubble reads as two arms rather than a knot.\",\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 2.5\n  },\n  {\n    value: \"wide\",\n    label: \"Wide bubbles\",\n    description: \"As open, spread further. Best on a window of a dozen bubbles.\",\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 10\n  },\n  {\n    value: \"compress\",\n    label: \"Compress lengths\",\n    description: \"Pull the longest and shortest nodes towards the graph\\u2019s mean, so a cut spanning kb and bp fits one pane.\",\n    law: { power: 0.5, effect: 0.5 },\n    minNodeFactor: 0\n  }\n];\nvar BUBBLE_SPREAD_VALUES = BUBBLE_SPREADS.map((s) => s.value);\nfunction spreadFor(spread) {\n  const entry = BUBBLE_SPREADS.find((s) => s.value === spread);\n  return {\n    law: entry?.law ?? PROPORTIONAL_LENGTH,\n    minNodeLength: (entry?.minNodeFactor ?? 0) * MEAN_NODE_LENGTH\n  };\n}\n\nexport {\n  BUBBLE_SPREADS,\n  BUBBLE_SPREAD_VALUES,\n  spreadFor\n};\n"],
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