jbrowse-plugin-graphgenomeviewer 6.4.0 → 6.5.0

package/dist/chunks/{GraphGenomeView-ULQ6U5MK.js → GraphGenomeView-ZB4ED45M.js}

@@ -1,4 +1,4 @@
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 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
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package/dist/chunks/{LinearGraphDisplay-KM5SOSQQ.js → LinearGraphDisplay-TQX7ZJZF.js}

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+{
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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sourcesContent": ["// src/layoutQualities.ts\nvar LAYOUT_QUALITIES = [\n  { value: 0, label: \"Fastest\" },\n  { value: 1, label: \"Fast\" },\n  { value: 2, label: \"Default\" },\n  { value: 3, label: \"Fine\" },\n  { value: 4, label: \"Best\" }\n];\n\nexport {\n  LAYOUT_QUALITIES\n};\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { COLOR_SCHEMES } from '@jbrowse/bandage-core/colorSchemes'\nimport { LAYOUT_ENGINES } from '@jbrowse/bandage-core/layoutEngines'\nimport { LAYOUT_QUALITIES } from '@jbrowse/bandage-core/layoutQualities'\nimport { NODE_WIDTHS } from '@jbrowse/bandage-core/nodeWidths'\nimport { MAX_PATH_COLORS } from '@jbrowse/bandage-core/pathColors'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  InputLabel,\n  MenuItem,\n  Radio,\n  RadioGroup,\n  Select,\n  Switch,\n  Tooltip,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\nimport type { SxProps } from '@mui/material'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\n  },\n})\n\nfunction Caption({\n  warn = false,\n  children,\n}: {\n  warn?: boolean\n  children: ReactNode\n}) {\n  return (\n    <Typography\n      variant=\"caption\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\n// Layout quality and bubble spread are the engine's inputs, and an anchored\n// layout places a node from its coordinates without reaching it. Left enabled\n// so the force layout can be set up before switching to it.\nconst EngineOnly = observer(function EngineOnly({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  return model.hasGraph && !model.usesLayoutEngine ? (\n    <Caption warn>\n      No effect on this layout: only the force-directed layout is drawn by the\n      engine that reads this.\n    </Caption>\n  ) : null\n})\n\nfunction SettingSwitch({\n  label,\n  checked,\n  onChange,\n  children,\n}: {\n  label: string\n  checked: boolean\n  onChange: (checked: boolean) => void\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControlLabel\n        control={\n          <Switch\n            checked={checked}\n            onChange={e => {\n              onChange(e.target.checked)\n            }}\n          />\n        }\n        label={label}\n      />\n      {children}\n    </div>\n  )\n}\n\n// One dropdown setting; an option's description is its tooltip\nfunction SettingSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  sx,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly { value: T; label: string; description?: string }[]\n  testId?: string\n  sx?: SxProps\n  onChange: (value: T) => void\n}) {\n  const { classes } = useStyles()\n  return (\n    <FormControl className={classes.formControl} sx={sx}>\n      <InputLabel>{label}</InputLabel>\n      <Select\n        value={value}\n        label={label}\n        data-testid={testId}\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(({ value, label, description }) => (\n          <MenuItem key={value} value={value}>\n            {description ? (\n              <Tooltip title={description} placement=\"right\">\n                <span>{label}</span>\n              </Tooltip>\n            ) : (\n              label\n            )}\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n\nconst trackOptions = (tracks: { trackId: string; name: string }[]) =>\n  tracks.map(({ trackId, name }) => ({ value: trackId, label: name }))\n\n// `children` is the host's own section, between node width and colour\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  open: boolean\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, open, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open={open} onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Engine\"\n            value={model.layoutEngine}\n            options={LAYOUT_ENGINES}\n            testId=\"graph-layout-engine-select\"\n            onChange={engine => {\n              model.setLayoutEngine(engine)\n              void model.recomputeLayout()\n            }}\n          />\n          <Caption>\n            Which engine draws the force-directed layout. Stress reads distances\n            along the graph as distances on the page, so the reference draws\n            straight; it is experimental, and slower than FMMM on large cuts.\n          </Caption>\n          <EngineOnly model={model} />\n        </div>\n\n        <div className={classes.section}>\n          <FormControl fullWidth>\n            <FormLabel component=\"legend\">Layout quality</FormLabel>\n            <RadioGroup\n              value={model.layoutQuality}\n              onChange={e => {\n                model.setLayoutQuality(parseInt(e.target.value))\n                void model.recomputeLayout()\n              }}\n            >\n              {LAYOUT_QUALITIES.map(q => (\n                <FormControlLabel\n                  key={q.value}\n                  value={q.value}\n                  control={<Radio />}\n                  label={q.label}\n                />\n              ))}\n            </RadioGroup>\n            <Caption>\n              The engine&apos;s iteration budget; for FMMM the same scale\n              Bandage exposes. Higher is slower: on a thousand-node cut the top\n              setting is seconds rather than tenths.\n            </Caption>\n            <EngineOnly model={model} />\n          </FormControl>\n        </div>\n\n        <SettingSwitch\n          label=\"Draw paths\"\n          checked={model.drawPaths}\n          onChange={draw => {\n            model.setDrawPaths(draw)\n          }}\n        >\n          <Caption>\n            Color each node and connector by the paths through it, one lane per\n            path in legend order, so a path that skips a node leaves its lane\n            empty\n          </Caption>\n          {model.drawPaths && !model.effectiveDrawPaths ? (\n            <Caption warn>\n              {model.pathCount > MAX_PATH_COLORS\n                ? `Off: ${model.pathCount.toLocaleString()} paths is past the ${MAX_PATH_COLORS} this can tell apart`\n                : 'Off: this graph states no paths'}\n            </Caption>\n          ) : null}\n        </SettingSwitch>\n\n        <SettingSwitch\n          label=\"Mark bubbles\"\n          checked={model.showBubbles}\n          onChange={show => {\n            model.setShowBubbles(show)\n          }}\n        >\n          <Caption>\n            A halo along the nodes of each bubble, labelled by what it is, with\n            the label opening the bubble on its own\n          </Caption>\n        </SettingSwitch>\n\n        <SettingSwitch\n          label=\"Genes on the backbone\"\n          checked={model.showGenes}\n          onChange={show => {\n            model.setShowGenes(show)\n          }}\n        >\n          <Caption>\n            Exons along the reference nodes that carry them and each gene's name\n            at its midpoint, from the assembly's annotation track\n          </Caption>\n          {model.geneTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Gene track\"\n              value={model.geneTrack?.trackId ?? ''}\n              options={trackOptions(model.geneTrackChoices)}\n              testId=\"graph-gene-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setGeneTrackId(trackId)\n                void model.reloadGenes()\n              }}\n            />\n          ) : null}\n          {model.repeatTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Repeat track\"\n              value={model.repeatTrack?.trackId ?? ''}\n              options={trackOptions(model.repeatTrackChoices)}\n              testId=\"graph-repeat-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setRepeatTrackId(trackId)\n                void model.reloadRepeats()\n              }}\n            />\n          ) : null}\n        </SettingSwitch>\n\n        {model.anchorPaths.length > 1 ? (\n          <div className={classes.section}>\n            <SettingSelect\n              label=\"Reference path\"\n              value={model.activeReferencePath ?? ''}\n              options={model.anchorPaths.map(({ name }) => ({\n                value: name,\n                label: name,\n              }))}\n              testId=\"graph-reference-path-select\"\n              onChange={name => {\n                model.setReferencePath(name)\n                void model.recomputeLayout()\n              }}\n            />\n            <Caption>\n              Which path the anchored layouts draw x against. A GFA with no rGFA\n              tags states its coordinates only in its paths, and marks none of\n              them as the reference.\n            </Caption>\n          </div>\n        ) : null}\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Bubble spread\"\n            value={model.bubbleSpread}\n            options={BUBBLE_SPREADS}\n            testId=\"graph-bubble-spread-select\"\n            onChange={spread => {\n              model.setBubbleSpread(spread)\n              void model.recomputeLayout()\n            }}\n          />\n          <Caption>\n            How far the force layout opens a bubble. A pangenome allele is a few\n            bp, so at Bandage&apos;s own scale both arms land inside one node\n            thickness and the graph draws as a rope.\n          </Caption>\n          <EngineOnly model={model} />\n        </div>\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Node width\"\n            value={model.nodeWidth}\n            options={NODE_WIDTHS}\n            testId=\"graph-node-width-select\"\n            onChange={width => {\n              model.setNodeWidth(width)\n            }}\n          />\n          <Caption>\n            Bandage&apos;s depth as width. In a cut with walks, depth is how\n            many haplotypes carry the node.\n          </Caption>\n        </div>\n\n        {children}\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Color scheme\"\n            value={model.chosenColorScheme}\n            options={COLOR_SCHEMES}\n            onChange={scheme => {\n              model.setColorScheme(scheme)\n            }}\n          />\n          {model.colorSchemeLock ? (\n            <Caption warn>No effect now. {model.colorSchemeLock.why}</Caption>\n          ) : null}\n        </div>\n      </DialogContent>\n\n      <DialogActions>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GraphSettingsDialog\n"],
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+}

package/dist/chunks/chunk-OTI5X5W7.js

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+  "sourcesContent": ["module.exports = JBrowseExports[\"tss-react/mui\"];", "// src/layout/deletionRoutes.ts\nvar ROUTE_ID = \"\\0deletion:\";\nvar ROUTE_FRACTION = 0.5;\nfunction withDeletionRoutes(graph, deletions, dropped = /* @__PURE__ */ new Set()) {\n  const routes = new Map(\n    deletions.map((d) => [d.edgeIndex, `${ROUTE_ID}${d.edgeIndex}`])\n  );\n  const edges = [];\n  graph.edges.forEach((edge, ei) => {\n    const id = routes.get(ei);\n    if (dropped.has(ei)) {\n      return;\n    }\n    if (id === void 0) {\n      edges.push(edge);\n    } else {\n      const { fromStrand, toStrand } = edge;\n      edges.push(\n        { from: edge.from, to: id, ...fromStrand ? { fromStrand } : {} },\n        { from: id, to: edge.to, ...toStrand ? { toStrand } : {} }\n      );\n    }\n  });\n  return {\n    graph: {\n      ...graph,\n      nodes: [\n        ...graph.nodes,\n        ...[...routes.values()].map((id) => ({\n          id,\n          name: id,\n          length: 0,\n          depth: 0\n        }))\n      ],\n      edges\n    },\n    routes,\n    ids: new Set(routes.values())\n  };\n}\nfunction routeNodes(graph, deletions, routes, drawnOf, opts) {\n  const lengths = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  return deletions.map((d) => {\n    const skipped = d.bypassed.reduce(\n      (sum, id2) => sum + (lengths.get(id2) ?? 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2 * Math.PI - theta : theta);\n}\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}\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}\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}\nvar Curve = class {\n  constructor(pts, normals, straight = false) {\n    this.pts = pts;\n    this.normals = normals;\n    this.straight = straight;\n    this.arc = arcLengths(pts);\n    this.total = this.arc[pts.length - 1] ?? 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      } 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};\nfunction outwardNormals(pts, outRef) {\n  const centroid = centroidOf(pts);\n  return pts.map((p, i) => {\n    const t = unit(\n      pts[Math.max(0, i - 1)],\n      pts[Math.min(pts.length - 1, i + 1)]\n    );\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 ? Math.sign(dot) : Math.sign(n.x * ref.x + n.y * ref.y) || 1;\n    return { x: n.x * sign, y: n.y * sign };\n  });\n}\nfunction mapFlat(frame, tA, sign, flat) {\n  const ds = Math.min(5, 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}\nfunction fitted(frame, tA, sign, make, length) {\n  let flatLength = length;\n  let mapped = mapFlat(frame, tA, sign, make(flatLength));\n  if (frame.straight) {\n    return mapped;\n  }\n  for (let i = 0; i < 2; i++) {\n    const got = polylineLength(mapped.pts);\n    if (!(got > 0)) {\n      break;\n    }\n    flatLength *= length / got;\n    mapped = mapFlat(frame, tA, sign, make(flatLength));\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}\nvar Placer = class {\n  constructor(c) {\n    this.c = c;\n    this.grid = /* @__PURE__ */ new Map();\n    const { ids, first, count, per, seedX, seedY, backbone } = c;\n    const N = ids.length;\n    this.points = Array.from({ length: N }, () => void 0);\n    this.params = Array.from({ length: N }, () => void 0);\n    this.curves = Array.from({ length: N }, () => void 0);\n    this.links = c.links.map(\n      (sides, k) => sides.map((out) => out.filter(([v]) => v !== k))\n    );\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      [\n        { x: min, y: 0 },\n        { x: max, y: 0 }\n      ],\n      [\n        { x: 0, y: 1 },\n        { x: 0, y: 1 }\n      ],\n      true\n    );\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    const pieces = this.componentsOf(free).map((members) => ({ members, anchors: this.anchorsOf(members) })).filter((p) => p.anchors.length).map((p) => ({\n      members: p.members,\n      span: spanOf(p.anchors),\n      drawn: p.members.reduce((s, k) => s + this.drawn(k), 0)\n    })).sort((a, b) => a.span - b.span || 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?.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      } else {\n        this.grid.set(key, [occupant]);\n      }\n    }\n  }\n  // placed points within CLEAR of the candidate, off the exempt curve and away\n  // from the anchors, up to `limit`\n  violations(pts, exempt, anchorPts, limit) {\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) < 2 * 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 this.grid.get(cellKey(gx, gy)) ?? []) {\n            if (q.curve !== exempt && 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  choose(candidates, exempt, anchorPts) {\n    let best;\n    let bestV = Infinity;\n    for (const candidate of candidates) {\n      const m = candidate();\n      const v = this.violations(m.pts, exempt, anchorPts, bestV);\n      if (v === 0) {\n        return m;\n      }\n      if (v < bestV) {\n        bestV = v;\n        best = m;\n      }\n    }\n    return best;\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 = /* @__PURE__ */ 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 = /* @__PURE__ */ 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 !== void 0 && 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 !== void 0 && !reached(far[0], far[1])) {\n      return void 0;\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 = /* @__PURE__ */ new Map([[from, -1]]);\n    const side = /* @__PURE__ */ 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 ?? 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          if (i < 16 && arcFlat(c, L, h, drop).apex < MIN_DEPTH) {\n            continue;\n          }\n          candidates.push(\n            () => fitted(\n              frame,\n              tA,\n              sign,\n              (length) => tilted(\n                arcFlat(\n                  c,\n                  length,\n                  Math.min(h, (length - c) / 2 - 1e-6),\n                  drop\n                ),\n                c,\n                tilt\n              ),\n              L\n            )\n          );\n        }\n      }\n    }\n    return candidates;\n  }\n  placePiece(members, parent) {\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) ? anchors[0].curve : void 0;\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    } else {\n      anchors.sort((a2, b2) => a2.point.x - b2.point.x || a2.point.y - b2.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) ? (route ? -1 : 1) * (Math.sign(n.y) || 1) : (mid.x - parent.x) * n.x + (mid.y - parent.y) * n.y >= 0 ? 1 : -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 ? Math.max(0, count[A.v] - 2) : 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(\n        depths(0, 12).map(\n          (drop) => () => fitted(\n            frame,\n            tA,\n            sign,\n            (length) => lineFlat(0, drop, du, dv, length),\n            L\n          )\n        )\n      );\n    } else {\n      spine = this.spinePath(members, A.u, A.uSide, B.u, B.uSide) ?? 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(ROUTE_BOW * c, ROUTE_CAP));\n        mapped = pick(\n          depths(d0, 12).map(\n            (d) => () => mapFlat(frame, tA, sign, arcFlat(c, archLength(c, d), 0, 0))\n          )\n        );\n        const total = polylineLength(mapped.pts);\n        spacing = Math.max(1e-3, (total - 2 * link) / (count[spine[0].k] - 1));\n      } else if (L > c + 1e-6) {\n        mapped = pick(this.arcCandidates(frame, tA, sign, c, L));\n      } else {\n        const bar = L - 2 * link;\n        mapped = pick(\n          depths(MIN_DEPTH, 12).map(\n            (d) => () => fitted(\n              frame,\n              tA,\n              sign,\n              (length) => lineFlat(c / 2 - length / 2, d, 1, 0, length),\n              bar\n            )\n          )\n        );\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).map((m) => ({ members: m, span: spanOf(this.anchorsOf(m)) })).sort((a, b) => a.span - b.span);\n    for (const sub of subs) {\n      this.placePiece(sub.members, centroid);\n    }\n  }\n};\nfunction 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\nexport {\n  stressPlacement\n};\n", "import {\n  stressPlacement\n} from \"./chunk-LYJ4US66.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/stressEngine.ts\nvar 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];\nvar UNTANGLE_PASSES = 20;\nvar UNTANGLE_LINKS = 3;\nvar UNTANGLE_PUSH = 0.3;\nvar SMOOTH_PASSES = 2;\nvar MAX_HOPS = 200;\nvar EPS = 0.1;\nvar WARM = 0.5;\nfunction flipped(strand, name) {\n  const own = name.at(-1);\n  return (strand === \"+\" || strand === \"-\") && (own === \"+\" || own === \"-\") && 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}\nfunction num(value, fallback) {\n  return typeof value === \"number\" && Number.isFinite(value) ? value : fallback;\n}\nfunction chains(request) {\n  const { nodes, edges } = request.graph;\n  const o = request.options;\n  const perMegabase = num(o.nodeLengthPerMegabase, 1e3);\n  const minimum = num(o.minimumNodeLength, 1);\n  const segment = num(o.nodeSegmentLength, 1);\n  const link = num(o.edgeLength, 1);\n  const ids = nodes.map((n2) => n2.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 = Math.max(perMegabase * node.length / 1e6, minimum);\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 === void 0 || b === void 0) {\n      continue;\n    }\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}\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}\nfunction stressLayout(request, opts = {}) {\n  const c = chains(request);\n  const { n, off, nb, wt, seedX, seedY, backbone, first, count, per, link } = c;\n  const o = request.options;\n  const quality = QUALITY[Math.max(0, Math.min(4, num(opts.quality ?? o.quality, 2)))];\n  const gap = num(opts.componentSeparation ?? o.componentSeparation, 15);\n  const rand = xorshift(num(opts.seed ?? 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) : void 0;\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    } else if (anySeed && !Number.isNaN(seedX[i])) {\n      X[i] = seedX[i] + rand() - 0.5;\n      Y[i] = seedY[i] + rand() - 0.5;\n    } else {\n      X[i] = rand() * side;\n      Y[i] = rand() * side;\n    }\n  }\n  const refIdx = members.map(\n    (points) => Int32Array.from(\n      points.filter((i) => backbone[i] && !Number.isNaN(seedX[i])).sort((a, b) => seedX[a] - seedX[b])\n    )\n  );\n  const refX = refIdx.map((idx) => Float64Array.from(idx, (i) => seedX[i]));\n  let span = 0;\n  for (const xs of refX) {\n    if (xs.length) {\n      span = Math.max(span, xs[xs.length - 1] - xs[0]);\n    }\n  }\n  const dmax = Math.max(span, 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  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 referenceTerm = (i, eta) => {\n    const idx = refIdx[comp[i]];\n    if (!backbone[i] || idx.length < 2 || Number.isNaN(seedX[i])) {\n      return;\n    }\n    const xs = refX[comp[i]];\n    const target = seedX[i] + Math.exp(logMin + rand() * (logMax - logMin)) * (rand() < 0.5 ? -1 : 1);\n    let lo = 0;\n    let hi = xs.length;\n    while (lo < hi) {\n      const mid = lo + hi >> 1;\n      if (xs[mid] < target) {\n        lo = mid + 1;\n      } else {\n        hi = mid;\n      }\n    }\n    const j = idx[Math.min(lo, idx.length - 1)];\n    const d = seedX[j] - seedX[i];\n    if (j === i || d === 0) {\n      return;\n    }\n    let mu = eta / (d * d);\n    if (mu > 1) {\n      mu = 1;\n    }\n    const r = mu * (X[j] - X[i] - d) / 2;\n    X[i] = X[i] + r;\n    X[j] = X[j] - r;\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 = new Int32Array(n);\n  for (let i = 0; i < n; i++) {\n    order[i] = i;\n  }\n  const warm = anySeed ? Math.floor(WARM * iterations) : 0;\n  for (let t = warm; t < iterations; t++) {\n    const eta = etaMax * Math.exp(-lambda * t);\n    for (let k = n - 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 (let q = 0; q < n; q++) {\n      const i = order[q];\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      referenceTerm(i, eta);\n    }\n  }\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 < UNTANGLE_PASSES; u++) {\n    const grid = /* @__PURE__ */ new Map();\n    for (let i = 0; i < n; i++) {\n      const k = key(X[i], Y[i]);\n      const list = grid.get(k);\n      if (list) {\n        list.push(i);\n      } else {\n        grid.set(k, [i]);\n      }\n    }\n    for (let i = 0; i < n; i++) {\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            } 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 (let i = 0; i < n; i++) {\n      adjacentTerms(i, Infinity);\n      referenceTerm(i, etaMin * 4);\n    }\n  }\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}\nfunction respace(X, Y, a, m, per) {\n  const arc = new Float64Array(m);\n  for (let i = 1; i < m; i++) {\n    arc[i] = arc[i - 1] + Math.hypot(X[a + i] - X[a + i - 1], Y[a + i] - Y[a + i - 1]);\n  }\n  if (!arc[m - 1]) {\n    return;\n  }\n  const loss = per * (m - 1) - arc[m - 1];\n  if (loss > 0) {\n    extend(X, Y, a, a + 1, loss / 2);\n    extend(X, Y, a + m - 1, a + m - 2, loss / 2);\n    for (let i = 1; i < m; i++) {\n      arc[i] = arc[i - 1] + Math.hypot(X[a + i] - X[a + i - 1], Y[a + i] - Y[a + i - 1]);\n    }\n  }\n  const total = arc[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 && arc[seg] < s) {\n      seg++;\n    }\n    const span = arc[seg] - arc[seg - 1];\n    const t = span > 0 ? (s - arc[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}\nfunction extend(X, Y, end, next, by) {\n  const dx = X[end] - X[next];\n  const dy = Y[end] - Y[next];\n  const mag = Math.hypot(dx, dy);\n  if (mag > 0) {\n    X[end] = X[end] + dx / mag * by;\n    Y[end] = Y[end] + dy / mag * by;\n  }\n}\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\nexport {\n  chains,\n  stressLayout\n};\n", "// src/loadBandage.ts\nvar cached;\nfunction loadBandage() {\n  cached ??= import(\"./bandage-layout-3AR6BCUD.js\").then((mod) => mod.default()).catch((e) => {\n    cached = void 0;\n    throw e;\n  });\n  return cached;\n}\n\nexport {\n  loadBandage\n};\n", "import {\n  stressLayout\n} from \"./chunk-UNOE2NDN.js\";\nimport {\n  loadBandage\n} from \"./chunk-7XHHVYG7.js\";\n\n// src/layoutEngines.ts\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 (experimental)\",\n    description: \"Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.\"\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 bandage = await loadBandage();\n  const start = performance.now();\n  const result = bandage.computeLayout(request.graph, request.options);\n  return { result, duration: performance.now() - start };\n};\n\nexport {\n  LAYOUT_ENGINES,\n  LAYOUT_ENGINE_VALUES,\n  isLayoutEngineKind,\n  layoutEngine\n};\n", "// src/colorSchemes.ts\nvar COLOR_SCHEMES = [\n  // Mirrors `layoutModes`' 'auto': a value the model resolves rather than a\n  // colour of its own. It exists because 'uniform' was the default, so a\n  // launched graph opened flat grey and both tutorials spent a step saying \"now\n  // pick a colour\" \u2014 one figure literally drives that click. A graph with\n  // reference coordinates resolves to 'reference-position', which is the one\n  // ramp a linear track beside it can be painted with too; a graph with none\n  // keeps 'uniform', because there the ramp would be a hue nothing earned.\n  //\n  // Resolve through `effectiveColorScheme`; the dropdown reads the raw prop, so\n  // \"Auto\" stays selectable and visible as what it is.\n  { value: \"auto\", label: \"Auto\" },\n  { value: \"uniform\", label: \"Uniform\" },\n  { value: \"random\", label: \"Random\" },\n  { value: \"rainbow\", label: \"Rainbow\" },\n  { value: \"depth\", label: \"Depth\" },\n  { value: \"node-length\", label: \"Node length\" },\n  { value: \"stable-rank\", label: \"Stable rank\" },\n  { value: \"reference-position\", label: \"Reference position\" },\n  { value: \"grey\", label: \"Grey\" }\n];\nvar COLOR_SCHEME_VALUES = COLOR_SCHEMES.map((s) => s.value);\nfunction resolveColorScheme(scheme, graph) {\n  return scheme !== \"auto\" ? scheme : graph?.anchoredBy ? \"reference-position\" : \"uniform\";\n}\n\nexport {\n  COLOR_SCHEMES,\n  COLOR_SCHEME_VALUES,\n  resolveColorScheme\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  isProportional,\n  drawnLengthFor,\n  PROPORTIONAL_SPREAD,\n  layoutScaling,\n  drawnLengthOf\n};\n", "import {\n  MEAN_NODE_LENGTH,\n  PROPORTIONAL_LENGTH\n} from \"./chunk-6JEWNXCQ.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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