jbrowse-plugin-graphgenomeviewer 7.3.2 → 7.4.0

package/dist/chunks/{chunk-B5SVBPXN.js → chunk-D5PRXUSS.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=chunk-D5PRXUSS.js.map

package/dist/chunks/{chunk-B5SVBPXN.js.map → chunk-D5PRXUSS.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-CPMHA4W5.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VACK24HF.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HMXCN6PG.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-AB35TJST.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-2VMKQKVO.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-DV5B5UU7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-T3H5ELLA.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BW2NMXRV.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ZANALBSX.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-CPMHA4W5.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VACK24HF.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HMXCN6PG.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-AB35TJST.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-2VMKQKVO.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-DV5B5UU7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-T3H5ELLA.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BW2NMXRV.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ZANALBSX.js"],
   "sourcesContent": ["// src/layout/rowSpacing.ts\nvar ROW_HEIGHT_PX = 20;\n\nexport {\n  ROW_HEIGHT_PX\n};\n", "import {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\n\n// src/util/geometry.ts\nfunction svgPath(points) {\n  const round = (v) => Math.round(v * 100) / 100;\n  return points.map((p, i) => `${i ? \"L\" : \"M\"}${round(p.x)},${round(p.y)}`).join(\"\");\n}\nfunction projectLine(x1, y1, x2, y2, distance) {\n  const d = Math.hypot(y2 - y1, x2 - x1);\n  if (d === 0) {\n    return [x2, y2];\n  }\n  const vx = (x2 - x1) / d;\n  const vy = (y2 - y1) / d;\n  return [x2 + distance * vx, y2 + distance * vy];\n}\nfunction curvePointAt(c, t) {\n  const u = 1 - t;\n  const a = u * u * u;\n  const b = 3 * u * u * t;\n  const d = 3 * u * t * t;\n  const e = t * t * t;\n  return {\n    x: a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1,\n    y: a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1\n  };\n}\nfunction curveMidpoint(curves) {\n  const mid = curves[Math.floor(curves.length / 2)];\n  return mid ? curvePointAt(mid, 0.5) : void 0;\n}\nfunction curveBounds(curves) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const c of curves) {\n    minX = Math.min(minX, c.x0, c.cx0, c.cx1, c.x1);\n    maxX = Math.max(maxX, c.x0, c.cx0, c.cx1, c.x1);\n    minY = Math.min(minY, c.y0, c.cy0, c.cy1, c.y1);\n    maxY = Math.max(maxY, c.y0, c.cy0, c.cy1, c.y1);\n  }\n  return { minX, minY, maxX, maxY };\n}\nfunction subCurve(c, t0, t1) {\n  const p0 = curvePointAt(c, t0);\n  const p1 = curvePointAt(c, t1);\n  const dt = (t1 - t0) / 3;\n  const d0 = curveTangentAt(c, t0);\n  const d1 = curveTangentAt(c, t1);\n  return {\n    x0: p0.x,\n    y0: p0.y,\n    cx0: p0.x + d0.x * dt,\n    cy0: p0.y + d0.y * dt,\n    cx1: p1.x - d1.x * dt,\n    cy1: p1.y - d1.y * dt,\n    x1: p1.x,\n    y1: p1.y\n  };\n}\nfunction curveTangentAt(c, t) {\n  const u = 1 - t;\n  const a = 3 * u * u;\n  const b = 6 * u * t;\n  const d = 3 * t * t;\n  return {\n    x: a * (c.cx0 - c.x0) + b * (c.cx1 - c.cx0) + d * (c.x1 - c.cx1),\n    y: a * (c.cy0 - c.y0) + b * (c.cy1 - c.cy0) + d * (c.y1 - c.cy1)\n  };\n}\nvar VISIBLE_SAMPLES = 32;\nfunction visibleStretches(curves, lengths, bounds, yToX) {\n  const stretches = [];\n  let start = 0;\n  curves.forEach((c, k) => {\n    const length = lengths[k];\n    const pad = length / VISIBLE_SAMPLES;\n    let last = curvePointAt(c, 0);\n    for (let i = 1; i <= VISIBLE_SAMPLES; i++) {\n      const next = curvePointAt(c, i / VISIBLE_SAMPLES);\n      if (Math.max(last.x, next.x) + pad >= bounds.minX && Math.min(last.x, next.x) - pad <= bounds.maxX && Math.max(last.y, next.y) + pad / yToX >= bounds.minY && Math.min(last.y, next.y) - pad / yToX <= bounds.maxY) {\n        const from = start + length * (i - 1) / VISIBLE_SAMPLES;\n        const to = start + length * i / VISIBLE_SAMPLES;\n        const prev = stretches.at(-1);\n        if (prev && prev[1] >= from) {\n          prev[1] = to;\n        } else {\n          stretches.push([from, to]);\n        }\n      }\n      last = next;\n    }\n    start += length;\n  });\n  return stretches;\n}\nfunction dashCurves(curves, dashWorld, yToX = 1, bounds) {\n  const lengths = curves.map(\n    (c) => Math.hypot(c.cx0 - c.x0, (c.cy0 - c.y0) * yToX) + Math.hypot(c.cx1 - c.cx0, (c.cy1 - c.cy0) * yToX) + Math.hypot(c.x1 - c.cx1, (c.y1 - c.cy1) * yToX)\n  );\n  const total = lengths.reduce((a, b) => a + b, 0);\n  const periods = Math.round(total / dashWorld);\n  const spans = Math.max(3, periods % 2 ? periods : periods + 1);\n  const stretches = bounds ? visibleStretches(curves, lengths, bounds, yToX) : void 0;\n  let seen = 0;\n  const out = [];\n  for (let i = 0; i < spans; i += 2) {\n    const from = i / spans * total;\n    const to = (i + 1) / spans * total;\n    if (stretches) {\n      while (seen < stretches.length && stretches[seen][1] < from) {\n        seen++;\n      }\n      if (seen === stretches.length) {\n        break;\n      }\n      if (stretches[seen][0] > to) {\n        continue;\n      }\n    }\n    const dash = [];\n    let start = 0;\n    curves.forEach((c, k) => {\n      const length = lengths[k];\n      const end = start + length;\n      if (length > 0 && end > from && start < to) {\n        dash.push(\n          subCurve(\n            c,\n            Math.max(0, (from - start) / length),\n            Math.min(1, (to - start) / length)\n          )\n        );\n      }\n      start = end;\n    });\n    if (dash.length) {\n      out.push(dash);\n    }\n  }\n  return out;\n}\nfunction translateCurves(curves, dx, dy) {\n  const out = new Array(curves.length);\n  for (let i = 0; i < curves.length; i++) {\n    const c = curves[i];\n    out[i] = {\n      x0: c.x0 + dx,\n      y0: c.y0 + dy,\n      cx0: c.cx0 + dx,\n      cy0: c.cy0 + dy,\n      cx1: c.cx1 + dx,\n      cy1: c.cy1 + dy,\n      x1: c.x1 + dx,\n      y1: c.y1 + dy\n    };\n  }\n  return out;\n}\nfunction attachment(segments, side) {\n  const last = segments.length - 1;\n  return side === \"end\" ? { at: segments[last], inward: segments[last - 1] } : { at: segments[0], inward: segments[1] };\n}\nvar TANGENT_SPAN_FACTOR = 0.5;\nvar MAX_TANGENT = 80;\nfunction ownStrand(id) {\n  return id.endsWith(\"-\") ? \"-\" : \"+\";\n}\nfunction strandSides(edge) {\n  const own = (id, strand) => (strand ?? ownStrand(id)) === ownStrand(id);\n  return {\n    from: own(edge.from, edge.fromStrand) ? \"end\" : \"start\",\n    to: own(edge.to, edge.toStrand) ? \"start\" : \"end\"\n  };\n}\nfunction spanOf(segments) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const s of segments) {\n    min = Math.min(min, s.x);\n    max = Math.max(max, s.x);\n  }\n  return { min, max };\n}\nfunction distanceToSpan(x, span) {\n  return Math.max(0, span.min - x, x - span.max);\n}\nfunction facingSide(segments, other, tieBreak) {\n  const startGap = distanceToSpan(segments[0].x, other);\n  const endGap = distanceToSpan(segments[segments.length - 1].x, other);\n  return startGap === endGap ? tieBreak : startGap < endGap ? \"start\" : \"end\";\n}\nfunction facingSides(fromSegments, toSegments) {\n  return {\n    from: facingSide(fromSegments, spanOf(toSegments), \"end\"),\n    to: facingSide(toSegments, spanOf(fromSegments), \"start\")\n  };\n}\nvar laidSides = /* @__PURE__ */ new WeakMap();\nfunction heldFacingSides(fromSegments, toSegments) {\n  let byTo = laidSides.get(fromSegments);\n  if (!byTo) {\n    byTo = /* @__PURE__ */ new WeakMap();\n    laidSides.set(fromSegments, byTo);\n  }\n  let sides = byTo.get(toSegments);\n  if (!sides) {\n    sides = facingSides(fromSegments, toSegments);\n    byTo.set(toSegments, sides);\n  }\n  return sides;\n}\nvar APEX_FRACTION = 0.75;\nvar BOW_CLEARANCE = 1.15;\nvar ALONG_FRACTION = 0.35;\nvar MAX_ROW_BOW_PX = 3 * ROW_HEIGHT_PX;\nfunction bowAround(p1x, p1y, p2x, p2y, toward, maxBow) {\n  const chord = Math.hypot(p2x - p1x, p2y - p1y);\n  const ux = chord === 0 ? 1 : (p2x - p1x) / chord;\n  const uy = chord === 0 ? 0 : (p2y - p1y) / chord;\n  let reach = 0;\n  let minAlong = Infinity;\n  let maxAlong = -Infinity;\n  for (const p of toward) {\n    const dx = p.x - p1x;\n    const dy = p.y - p1y;\n    const perp = dx * -uy + dy * ux;\n    if (Math.abs(perp) > Math.abs(reach)) {\n      reach = perp;\n    }\n    const along = dx * ux + dy * uy;\n    minAlong = Math.min(minAlong, along);\n    maxAlong = Math.max(maxAlong, along);\n  }\n  const span = toward.length ? maxAlong - minAlong : 0;\n  const uncapped = Math.max(\n    Math.abs(reach) * BOW_CLEARANCE / APEX_FRACTION,\n    span * ALONG_FRACTION\n  );\n  const size = maxBow === void 0 ? uncapped : Math.min(uncapped, maxBow);\n  return reach < 0 ? -size : size;\n}\nfunction yToXOf({ scaleX, scaleY }) {\n  return scaleY / scaleX;\n}\nvar PATH_RIBBON_SPACING_PX = 3;\nfunction drawnDirection(a, b, yToX) {\n  const dx = b.x - a.x;\n  const dy = (b.y - a.y) * yToX;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? void 0 : { x: dx / len, y: dy / len };\n}\nfunction pathRibbonOffsets(fromSegments, toSegments, count, axis) {\n  const yToX = yToXOf(axis);\n  const spacing = PATH_RIBBON_SPACING_PX / Math.max(axis.scaleX, 1e-6);\n  const dir = drawnDirection(\n    fromSegments[fromSegments.length - 1],\n    toSegments[0],\n    yToX\n  ) ?? drawnDirection(fromSegments[0], fromSegments.at(-1), yToX) ?? drawnDirection(toSegments[0], toSegments.at(-1), yToX) ?? { x: 1, y: 0 };\n  const offsets = [];\n  for (let i = 0; i < count; i++) {\n    const distance = (i - (count - 1) / 2) * spacing;\n    offsets.push({ x: -dir.y * distance, y: dir.x * distance / yToX });\n  }\n  return offsets;\n}\nfunction scaleYOf(points, yToX) {\n  return points.map((p) => ({ x: p.x, y: p.y * yToX }));\n}\nfunction unscaleYOf(curves, yToX) {\n  for (const c of curves) {\n    c.y0 /= yToX;\n    c.cy0 /= yToX;\n    c.cy1 /= yToX;\n    c.y1 /= yToX;\n  }\n  return curves;\n}\nfunction polylinePx(points, scaleX, scaleY) {\n  let total = 0;\n  for (let i = 1; i < points.length; i++) {\n    const a = points[i - 1];\n    const b = points[i];\n    total += Math.hypot((b.x - a.x) * scaleX, (b.y - a.y) * scaleY);\n  }\n  return total;\n}\nvar SELF_LOOP_MIN_PX = 12;\nvar SELF_LOOP_MAX_PX = 40;\nfunction selfLoopReach(segments, scale) {\n  const nodePx = polylinePx(segments, scale, scale);\n  const reachPx = Math.min(\n    SELF_LOOP_MAX_PX,\n    Math.max(SELF_LOOP_MIN_PX, nodePx / 2)\n  );\n  return reachPx / Math.max(scale, Number.EPSILON);\n}\nfunction selfLinkOf(edge) {\n  if (edge.from !== edge.to) {\n    return false;\n  }\n  return edge.fromStrand && edge.toStrand && edge.fromStrand !== edge.toStrand ? edge.fromStrand === \"+\" ? \"end\" : \"start\" : true;\n}\nfunction edgeJoinOf(edge, stranded = false) {\n  const self = selfLinkOf(edge);\n  if (!stranded) {\n    return self;\n  }\n  const sides = strandSides(edge);\n  return self === false ? sides : sides.from === sides.to ? sides.from : true;\n}\nfunction hairpinCurves(attach, reach) {\n  const { at, inward } = attach;\n  const dx = inward ? at.x - inward.x : 1;\n  const dy = inward ? at.y - inward.y : 0;\n  const len = Math.hypot(dx, dy) || 1;\n  const ux = dx / len;\n  const uy = dy / len;\n  const px = at.x;\n  const py = at.y;\n  const nearX = px + ux * reach / 3;\n  const nearY = py + uy * reach / 3;\n  const apexX = px + ux * reach;\n  const apexY = py + uy * reach;\n  const sideX = -uy * reach / 2;\n  const sideY = ux * reach / 2;\n  return [\n    {\n      x0: px,\n      y0: py,\n      cx0: nearX,\n      cy0: nearY,\n      cx1: apexX + sideX,\n      cy1: apexY + sideY,\n      x1: apexX,\n      y1: apexY\n    },\n    {\n      x0: apexX,\n      y0: apexY,\n      cx0: apexX - sideX,\n      cy0: apexY - sideY,\n      cx1: nearX,\n      cy1: nearY,\n      x1: px,\n      y1: py\n    }\n  ];\n}\nfunction computeEdgeCurves(fromSegments, toSegments, join, axis, bypassed = [], maxBowIn) {\n  const scale = axis.scaleX;\n  const yToX = yToXOf(axis);\n  const maxBow = maxBowIn ?? (axis.pixelRows ? MAX_ROW_BOW_PX : void 0);\n  if (join === false) {\n    join = heldFacingSides(fromSegments, toSegments);\n  }\n  if (yToX !== 1) {\n    return unscaleYOf(\n      computeEdgeCurves(\n        scaleYOf(fromSegments, yToX),\n        scaleYOf(toSegments, yToX),\n        join,\n        { scaleX: scale, scaleY: scale },\n        scaleYOf(bypassed, yToX),\n        // the cap is a y measure and the body works in x units, so it converts\n        // with everything else that crosses this boundary\n        maxBow === void 0 ? void 0 : maxBow * yToX\n      ),\n      yToX\n    );\n  }\n  if (typeof join === \"string\") {\n    return hairpinCurves(\n      attachment(fromSegments, join),\n      selfLoopReach(fromSegments, scale)\n    );\n  }\n  const loop = join === true;\n  const sides = join === true ? { from: \"end\", to: \"start\" } : join;\n  const fromAttach = attachment(fromSegments, sides.from);\n  const toAttach = attachment(toSegments, sides.to);\n  const fromEnd = fromAttach.at;\n  const toStart = toAttach.at;\n  const p1x = fromEnd.x;\n  const p1y = fromEnd.y;\n  const p2x = toStart.x;\n  const p2y = toStart.y;\n  if (loop) {\n    let segDirX = 1;\n    let segDirY = 0;\n    if (fromAttach.inward) {\n      const dx = fromEnd.x - fromAttach.inward.x;\n      const dy = fromEnd.y - fromAttach.inward.y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        segDirX = dx / len;\n        segDirY = dy / len;\n      }\n    }\n    const ext = selfLoopReach(fromSegments, scale);\n    const perpX = -segDirY;\n    const perpY = segDirX;\n    const midX = (fromEnd.x + toStart.x) / 2 + perpX * ext;\n    const midY = (fromEnd.y + toStart.y) / 2 + perpY * ext;\n    const cp1x = p1x + segDirX * ext;\n    const cp1y = p1y + segDirY * ext;\n    const cp2x = p2x - segDirX * ext;\n    const cp2y = p2y - segDirY * ext;\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cp1x,\n        cy0: cp1y,\n        cx1: cp1x + perpX * ext,\n        cy1: cp1y + perpY * ext,\n        x1: midX,\n        y1: midY\n      },\n      {\n        x0: midX,\n        y0: midY,\n        cx0: cp2x + perpX * ext,\n        cy0: cp2y + perpY * ext,\n        cx1: cp2x,\n        cy1: cp2y,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  } else {\n    const fromPrev = fromAttach.inward ?? {\n      x: fromEnd.x - (toStart.x - fromEnd.x),\n      y: fromEnd.y - (toStart.y - fromEnd.y)\n    };\n    const toNext = toAttach.inward ?? {\n      x: toStart.x - (fromEnd.x - toStart.x),\n      y: toStart.y - (fromEnd.y - toStart.y)\n    };\n    const dist = Math.hypot(p2x - p1x, p2y - p1y);\n    const tangentProj = (prev, at, towardX, towardY) => {\n      const dx = at.x - prev.x;\n      const dy = at.y - prev.y;\n      const len = Math.hypot(dx, dy);\n      const along = len === 0 ? 0 : (towardX * dx + towardY * dy) / len;\n      return Math.max(\n        0,\n        Math.min(dist * TANGENT_SPAN_FACTOR, MAX_TANGENT, along * 0.5)\n      );\n    };\n    const towardToX = toStart.x - fromEnd.x;\n    const towardToY = toStart.y - fromEnd.y;\n    const [cx1, cy1] = projectLine(\n      fromPrev.x,\n      fromPrev.y,\n      fromEnd.x,\n      fromEnd.y,\n      tangentProj(fromPrev, fromEnd, towardToX, towardToY)\n    );\n    const [cx2, cy2] = projectLine(\n      toNext.x,\n      toNext.y,\n      toStart.x,\n      toStart.y,\n      tangentProj(toNext, toStart, -towardToX, -towardToY)\n    );\n    const bulge = bypassed.length ? bowAround(p1x, p1y, p2x, p2y, bypassed, maxBow) : 0;\n    const chordLen = dist === 0 ? 1 : dist;\n    const ux = (p2x - p1x) / chordLen;\n    const uy = (p2y - p1y) / chordLen;\n    const bulgeX = -uy * bulge;\n    const bulgeY = ux * bulge;\n    const spreadX = ux * Math.abs(bulge);\n    const spreadY = uy * Math.abs(bulge);\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cx1 + bulgeX - spreadX,\n        cy0: cy1 + bulgeY - spreadY,\n        cx1: cx2 + bulgeX + spreadX,\n        cy1: cy2 + bulgeY + spreadY,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  }\n}\nfunction nearerEnd(segments, to) {\n  const start = segments[0];\n  const end = segments.at(-1);\n  return Math.hypot(start.x - to.x, start.y - to.y) < Math.hypot(end.x - to.x, end.y - to.y) ? \"start\" : \"end\";\n}\nfunction routedEdgeCurves(fromSegments, toSegments, route, sides) {\n  const fromAttach = attachment(\n    fromSegments,\n    sides?.from ?? nearerEnd(fromSegments, route[0])\n  );\n  const toAttach = attachment(\n    toSegments,\n    sides?.to ?? nearerEnd(toSegments, route.at(-1))\n  );\n  const points = [fromAttach.at, ...route, toAttach.at];\n  const tangent = (i) => {\n    const p = points[i];\n    const span = (q) => Math.hypot(q.x - p.x, q.y - p.y);\n    const along = (inward, next) => {\n      const len = inward ? span(inward) : 0;\n      const reach = span(next);\n      return len === 0 ? { x: next.x - p.x, y: next.y - p.y } : {\n        x: (p.x - inward.x) / len * reach,\n        y: (p.y - inward.y) / len * reach\n      };\n    };\n    if (i === 0) {\n      return along(fromAttach.inward, points[1]);\n    }\n    if (i === points.length - 1) {\n      const out = along(toAttach.inward, points[i - 1]);\n      return { x: -out.x, y: -out.y };\n    }\n    return {\n      x: (points[i + 1].x - points[i - 1].x) / 2,\n      y: (points[i + 1].y - points[i - 1].y) / 2\n    };\n  };\n  const curves = [];\n  for (let i = 0; i < points.length - 1; i++) {\n    const a = points[i];\n    const b = points[i + 1];\n    const ta = tangent(i);\n    const tb = tangent(i + 1);\n    curves.push({\n      x0: a.x,\n      y0: a.y,\n      cx0: a.x + ta.x / 3,\n      cy0: a.y + ta.y / 3,\n      cx1: b.x - tb.x / 3,\n      cy1: b.y - tb.y / 3,\n      x1: b.x,\n      y1: b.y\n    });\n  }\n  return curves;\n}\n\nexport {\n  svgPath,\n  projectLine,\n  curvePointAt,\n  curveMidpoint,\n  curveBounds,\n  dashCurves,\n  translateCurves,\n  ownStrand,\n  strandSides,\n  bowAround,\n  yToXOf,\n  PATH_RIBBON_SPACING_PX,\n  pathRibbonOffsets,\n  polylinePx,\n  selfLinkOf,\n  edgeJoinOf,\n  computeEdgeCurves,\n  routedEdgeCurves\n};\n", "// src/util/weakMemo.ts\nfunction weakMemo() {\n  const cache = /* @__PURE__ */ new WeakMap();\n  return (key, deps, compute) => {\n    const hit = cache.get(key);\n    if (hit?.deps.length === deps.length && hit.deps.every((d, i) => Object.is(d, deps[i]))) {\n      return hit.value;\n    }\n    const value = compute();\n    cache.set(key, { deps, value });\n    return value;\n  };\n}\n\nexport {\n  weakMemo\n};\n", "// src/overlayLabels.ts\nvar LABEL_PX = 11;\nvar LABEL_CHAR_PX = 6.2;\nvar LABEL_PAD = 4;\nfunction labelWidth(text) {\n  return text.length * LABEL_CHAR_PX + LABEL_PAD * 2;\n}\nfunction overlaps(a, b) {\n  return a.x0 < b.x1 && a.x1 > b.x0 && a.y0 < b.y1 && a.y1 > b.y0;\n}\nfunction offFrame(box, frame) {\n  return box.x1 <= 0 || box.x0 >= frame.width || box.y1 <= 0 || box.y0 >= frame.height;\n}\nfunction insideFrame(box, frame) {\n  return box.x0 >= 0 && box.x1 <= frame.width && box.y0 >= 0 && box.y1 <= frame.height;\n}\nfunction occupancy(frame, reserved = []) {\n  const placed = [...reserved];\n  return (box) => {\n    if (offFrame(box, frame) || placed.some((p) => overlaps(p, box))) {\n      return false;\n    }\n    placed.push(box);\n    return true;\n  };\n}\nfunction placeLabels(candidates, frame, take) {\n  const out = [];\n  const row = LABEL_PX + LABEL_PAD * 2;\n  const place = (c, text) => {\n    const w = labelWidth(text);\n    const direction = c.y > frame.height / 2 ? -1 : 1;\n    for (let tries = 0; tries <= (c.stack ?? 0); tries++) {\n      const y = c.y + direction * tries * row;\n      const box = {\n        x0: c.x - w / 2,\n        x1: c.x + w / 2,\n        y0: y - LABEL_PX - LABEL_PAD,\n        y1: y + LABEL_PAD\n      };\n      if (offFrame(box, frame)) {\n        return void 0;\n      }\n      if (insideFrame(box, frame) && (c.fits?.(box) ?? true) && take(box)) {\n        return { ...c, text, y, w };\n      }\n    }\n    return void 0;\n  };\n  for (const c of candidates) {\n    const placed = place(c, c.text) ?? (c.fallback === void 0 ? void 0 : place(c, c.fallback));\n    if (placed) {\n      out.push(placed);\n    }\n  }\n  return out;\n}\n\nexport {\n  LABEL_PX,\n  LABEL_CHAR_PX,\n  LABEL_PAD,\n  labelWidth,\n  overlaps,\n  occupancy,\n  placeLabels\n};\n", "import {\n  ownStrand,\n  strandSides\n} from \"./chunk-VACK24HF.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/mergeRuns.ts\nfunction flip(strand) {\n  return strand === \"+\" ? \"-\" : \"+\";\n}\nfunction mergeRuns(graph, alone = /* @__PURE__ */ new Set()) {\n  const sides = graph.edges.map(strandSides);\n  const at = /* @__PURE__ */ new Map();\n  const attach = (id, side, ei) => {\n    pushTo(at, `${id}|${side}`, ei);\n  };\n  graph.edges.forEach((edge, ei) => {\n    attach(edge.from, sides[ei].from, ei);\n    attach(edge.to, sides[ei].to, ei);\n  });\n  const joinAfter = (a) => {\n    const out = at.get(`${a}|end`);\n    if (out?.length !== 1) {\n      return void 0;\n    }\n    const ei = out[0];\n    const edge = graph.edges[ei];\n    return edge.from === a && edge.to !== a && !alone.has(a) && !alone.has(edge.to) && sides[ei].from === \"end\" && sides[ei].to === \"start\" && at.get(`${edge.to}|start`)?.length === 1 ? ei : void 0;\n  };\n  const joined = /* @__PURE__ */ new Set();\n  const runOf = /* @__PURE__ */ new Map();\n  const runs = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const into = at.get(`${node.id}|start`);\n    const pred = into?.length === 1 ? graph.edges[into[0]].from : void 0;\n    if (runOf.has(node.id) || pred !== void 0 && joinAfter(pred) === into[0]) {\n      continue;\n    }\n    const run = [node.id];\n    for (; ; ) {\n      const ei = joinAfter(run.at(-1));\n      const next = ei === void 0 ? void 0 : graph.edges[ei].to;\n      if (next === void 0 || runOf.has(next)) {\n        break;\n      }\n      joined.add(ei);\n      run.push(next);\n    }\n    for (const id of run) {\n      runOf.set(id, node.id);\n    }\n    if (run.length > 1) {\n      runs.set(node.id, run);\n    }\n  }\n  for (const node of graph.nodes) {\n    if (!runOf.has(node.id)) {\n      runOf.set(node.id, node.id);\n    }\n  }\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const nodes = [];\n  for (const node of graph.nodes) {\n    if (runOf.get(node.id) !== node.id) {\n      continue;\n    }\n    const run = runs.get(node.id);\n    if (!run) {\n      nodes.push(node);\n      continue;\n    }\n    const members = run.map((id) => byId.get(id));\n    const backbone = members.filter(isBackbone);\n    const first = backbone.length ? backbone.reduce((a, b) => a.stable.start <= b.stable.start ? a : b) : members[0];\n    nodes.push({\n      id: node.id,\n      name: node.name,\n      length: members.reduce((sum, n) => sum + n.length, 0),\n      depth: node.depth,\n      stable: first.stable\n    });\n  }\n  const seen = /* @__PURE__ */ new Set();\n  const edges = [];\n  graph.edges.forEach((edge, ei) => {\n    const from = runOf.get(edge.from);\n    const to = runOf.get(edge.to);\n    const side = sides[ei];\n    const key = `${from}|${side.from}>${to}|${side.to}`;\n    if (joined.has(ei) || seen.has(key)) {\n      return;\n    }\n    seen.add(key);\n    edges.push({\n      from,\n      to,\n      ...side.from === \"start\" ? { fromStrand: flip(ownStrand(from)) } : {},\n      ...side.to === \"end\" ? { toStrand: flip(ownStrand(to)) } : {}\n    });\n  });\n  return {\n    graph: { ...graph, nodes, edges, paths: void 0, pathVisits: void 0 },\n    runs\n  };\n}\nfunction splitRuns(positions, runs, weightOf) {\n  const out = { ...positions };\n  for (const [id, members] of runs) {\n    const line = positions[id];\n    if (!line?.length) {\n      continue;\n    }\n    delete out[id];\n    const arc = arcPrefix(line);\n    const total = arc.at(-1);\n    const weights = members.map((m) => Math.max(weightOf(m), 0));\n    const weightSum = weights.reduce((a, b) => a + b, 0);\n    let from = 0;\n    members.forEach((member, k) => {\n      const share = weightSum ? weights[k] / weightSum * total : total / members.length;\n      const to = k === members.length - 1 ? total : from + share;\n      out[member] = slice(line, arc, from, to);\n      from = to;\n    });\n  }\n  return out;\n}\nfunction polylineSlice(line, from, to) {\n  if (line.length === 0) {\n    return [];\n  }\n  const arc = arcPrefix(line);\n  const total = arc.at(-1);\n  return slice(line, arc, from * total, to * total);\n}\nfunction polylineMidpoint(line) {\n  const arc = arcPrefix(line);\n  return pointAt(line, arc, arc.at(-1) / 2);\n}\nfunction arcPrefix(line) {\n  const arc = [0];\n  for (let i = 1; i < line.length; i++) {\n    arc.push(\n      arc[i - 1] + Math.hypot(line[i].x - line[i - 1].x, line[i].y - line[i - 1].y)\n    );\n  }\n  return arc;\n}\nfunction firstReaching(arc, s) {\n  let lo = 0;\n  let hi = arc.length;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (arc[mid] < s) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\nfunction pointAt(line, arc, s) {\n  if (s <= 0) {\n    return { ...line[0] };\n  }\n  const i = firstReaching(arc, s);\n  if (i >= arc.length) {\n    return { ...line.at(-1) };\n  }\n  const span = arc[i] - arc[i - 1];\n  const t = span > 0 ? (s - arc[i - 1]) / span : 0;\n  const a = line[i - 1];\n  const b = line[i];\n  return { x: a.x + (b.x - a.x) * t, y: a.y + (b.y - a.y) * t };\n}\nfunction slice(line, arc, from, to) {\n  const points = [pointAt(line, arc, from)];\n  for (let i = firstReaching(arc, from); i < line.length && arc[i] < to; i++) {\n    if (arc[i] > from) {\n      points.push({ ...line[i] });\n    }\n  }\n  points.push(pointAt(line, arc, to));\n  return points;\n}\n\nexport {\n  mergeRuns,\n  splitRuns,\n  polylineSlice,\n  polylineMidpoint\n};\n", "import {\n  referenceVisitStarts\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  computeEdgeCurves,\n  edgeJoinOf,\n  routedEdgeCurves,\n  strandSides\n} from \"./chunk-VACK24HF.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  firstNodeAtOrAfter,\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/deletionEdges.ts\nvar MIN_DELETION_BP = 1;\nfunction bypassedPoints(nodePositions, bypassed) {\n  return bypassed.flatMap((id) => nodePositions[id] ?? []);\n}\nfunction edgeCurvesOf(nodePositions, edge, axis, bypassed, route, stranded) {\n  const from = nodePositions[edge.from];\n  const to = nodePositions[edge.to];\n  if (!from?.length || !to?.length) {\n    return void 0;\n  }\n  return route ? routedEdgeCurves(\n    from,\n    to,\n    route,\n    stranded ? strandSides(edge) : void 0\n  ) : computeEdgeCurves(\n    from,\n    to,\n    edgeJoinOf(edge, stranded),\n    axis,\n    bypassed ? bypassedPoints(nodePositions, bypassed) : []\n  );\n}\nfunction backboneBySequence(graph) {\n  const bySequence = groupBy(\n    graph.nodes.filter(isBackbone),\n    (node) => node.stable.refName\n  );\n  for (const list of bySequence.values()) {\n    list.sort((a, b) => a.stable.start - b.stable.start);\n  }\n  return bySequence;\n}\nfunction bypassedNodes(nodes, start, end) {\n  const bypassed = [];\n  if (nodes) {\n    for (let i = firstNodeAtOrAfter(nodes, start); i < nodes.length; i++) {\n      const node = nodes[i];\n      if (node.stable.start >= end) {\n        break;\n      }\n      if (node.stable.start + node.length <= end) {\n        bypassed.push(node.id);\n      }\n    }\n  }\n  return bypassed;\n}\nfunction skipsBetween(edge, from, to, forwards) {\n  const { fromStrand, toStrand } = edge;\n  if (fromStrand === void 0 || toStrand === void 0) {\n    return true;\n  }\n  const leavesRight = fromStrand === (from.stable.strand ?? \"+\");\n  const arrivesLeft = toStrand === (to.stable.strand ?? \"+\");\n  return forwards ? leavesRight && arrivesLeft : !leavesRight && !arrivesLeft;\n}\nfunction skippedSpan(edge, from, to, startsOf) {\n  let best;\n  for (const a of startsOf(from)) {\n    for (const b of startsOf(to)) {\n      const forwards = a <= b;\n      const span = forwards ? { start: a + from.length, end: b } : { start: b + to.length, end: a };\n      if (skipsBetween(edge, from, to, forwards) && (!best || Math.abs(span.end - span.start) < Math.abs(best.end - best.start))) {\n        best = span;\n      }\n    }\n  }\n  return best;\n}\nvar COPY_SWITCH_SHARE = 0.01;\nfunction repeatCopies(backbone, startsOf) {\n  const bySequence = /* @__PURE__ */ new Map();\n  for (const [refName, nodes] of backbone) {\n    const copies = nodes.flatMap((node) => {\n      const starts = startsOf(node);\n      return starts.slice(1).map((next, i) => ({\n        at: starts[i],\n        copy: next - starts[i]\n      }));\n    });\n    if (copies.length) {\n      bySequence.set(\n        refName,\n        copies.sort((a, b) => a.at - b.at)\n      );\n    }\n  }\n  return bySequence;\n}\nfunction switchesCopy(copies, start, bp) {\n  if (!copies) {\n    return false;\n  }\n  const i = partitionPoint(copies.length, (k) => copies[k].at < start);\n  const near = [copies[i - 1], copies[i]].filter((c) => c !== void 0).sort((a, b) => Math.abs(a.at - start) - Math.abs(b.at - start))[0];\n  return near !== void 0 && Math.abs(near.at - start) <= near.copy && Math.abs(bp - near.copy) <= near.copy * COPY_SWITCH_SHARE;\n}\nfunction deletionEdges(graph) {\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const backbone = backboneBySequence(graph);\n  const startsOf = referenceVisitStarts(graph);\n  const copies = repeatCopies(backbone, startsOf);\n  const found = [];\n  for (let edgeIndex = 0; edgeIndex < graph.edges.length; edgeIndex++) {\n    const edge = graph.edges[edgeIndex];\n    const from = byId.get(edge.from);\n    const to = byId.get(edge.to);\n    if (from !== void 0 && to !== void 0 && isBackbone(from) && isBackbone(to) && from.stable.refName === to.stable.refName) {\n      const span = skippedSpan(edge, from, to, startsOf);\n      const refName = from.stable.refName;\n      const bp = span ? span.end - span.start : 0;\n      if (span && bp >= MIN_DELETION_BP && !switchesCopy(copies.get(refName), span.start, bp)) {\n        const { start, end } = span;\n        found.push({\n          edgeIndex,\n          from: edge.from,\n          to: edge.to,\n          ...edge.fromStrand ? { fromStrand: edge.fromStrand } : {},\n          ...edge.toStrand ? { toStrand: edge.toStrand } : {},\n          refName,\n          start,\n          end,\n          bp,\n          bypassed: bypassedNodes(backbone.get(refName), start, end)\n        });\n      }\n    }\n  }\n  return found;\n}\nfunction closableDeletions(graph, deletions) {\n  const parent = /* @__PURE__ */ new Map();\n  const root = (id) => {\n    let r = id;\n    while (parent.has(r)) {\n      r = parent.get(r);\n    }\n    if (r !== id) {\n      parent.set(id, r);\n    }\n    return r;\n  };\n  const join = (a, b) => {\n    const [ra, rb] = [root(a), root(b)];\n    if (ra !== rb) {\n      parent.set(ra, rb);\n    }\n    return ra !== rb;\n  };\n  const candidates = new Set(deletions.map((d) => d.edgeIndex));\n  graph.edges.forEach((e, ei) => {\n    if (!candidates.has(ei)) {\n      join(e.from, e.to);\n    }\n  });\n  return new Set(\n    deletions.filter((d) => !join(d.from, d.to)).map((d) => d.edgeIndex)\n  );\n}\nvar drawings = /* @__PURE__ */ new WeakMap();\nfunction deletionDrawing(graph, deletions, show = true) {\n  let byShow = drawings.get(deletions);\n  if (!byShow) {\n    byShow = /* @__PURE__ */ new Map();\n    drawings.set(deletions, byShow);\n  }\n  let drawing = byShow.get(show);\n  if (!drawing) {\n    const hidden = show ? /* @__PURE__ */ new Set() : closableDeletions(graph, deletions);\n    drawing = {\n      shown: deletions.filter((d) => !hidden.has(d.edgeIndex)),\n      bypassed: new Map(deletions.map((d) => [d.edgeIndex, d.bypassed])),\n      hidden\n    };\n    byShow.set(show, drawing);\n  }\n  return drawing;\n}\n\nexport {\n  edgeCurvesOf,\n  deletionEdges,\n  closableDeletions,\n  deletionDrawing\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  labelWidth,\n  occupancy\n} from \"./chunk-AB35TJST.js\";\nimport {\n  polylineMidpoint\n} from \"./chunk-2VMKQKVO.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-DV5B5UU7.js\";\nimport {\n  curveBounds,\n  curveMidpoint,\n  polylinePx\n} from \"./chunk-VACK24HF.js\";\n\n// src/graphLabels.ts\nvar MIN_DELETION_LABEL_PX = 26;\nvar PX_PER_NODE_LABEL = 4e4;\nvar MIN_NODE_LABELS = 8;\nvar LEADER_GAP_PX = 8;\nvar LABEL_CHAR_PX = 5.7;\nvar LABEL_PAD_PX = 6;\nvar LABEL_HEIGHT_PX = 13;\nvar LABEL_GAP_PX = 3;\nvar MAX_LABEL_OVERHANG = 2;\nfunction labelHalfWidth(text) {\n  return (text.length * LABEL_CHAR_PX + LABEL_PAD_PX + LABEL_GAP_PX) / 2;\n}\nvar LABEL_HALF_HEIGHT = (LABEL_HEIGHT_PX + LABEL_GAP_PX) / 2;\nvar MIN_LABEL_HALF_WIDTH = labelHalfWidth(\"1 bp\");\nfunction boxAt(halfW, x, y) {\n  return {\n    x0: x - halfW,\n    x1: x + halfW,\n    y0: y - LABEL_HALF_HEIGHT,\n    y1: y + LABEL_HALF_HEIGHT\n  };\n}\nfunction rowLabelBox(text, screenY) {\n  return {\n    x0: 6,\n    x1: 6 + labelWidth(text) + LABEL_GAP_PX,\n    y0: screenY - 8 - LABEL_GAP_PX / 2,\n    y1: screenY + 8 + LABEL_GAP_PX / 2\n  };\n}\nfunction clamp(v, lo, hi) {\n  return hi < lo ? v : Math.min(Math.max(v, lo), hi);\n}\nfunction groupDigits(n) {\n  return String(n).replace(/\\B(?=(\\d{3})+$)/g, \",\");\n}\nfunction formatBp(bp) {\n  const [value, unit] = bp >= 999500 ? [bp / 1e6, \"Mb\"] : bp >= 1e3 ? [bp / 1e3, \"kb\"] : [];\n  if (value === void 0) {\n    return `${bp} bp`;\n  }\n  return `${+value.toFixed(value >= 100 ? 0 : 1)} ${unit}`;\n}\nfunction deletionText(bp) {\n  return `${formatBp(bp)} del`;\n}\nfunction arcOutward(curves, apex, scaleX, scaleY) {\n  const first = curves[0];\n  const last = curves[curves.length - 1];\n  const dx = (apex.x - (first.x0 + last.x1) / 2) * scaleX;\n  const dy = (apex.y - (first.y0 + last.y1) / 2) * scaleY;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? { x: 0, y: -1 } : { x: dx / len, y: dy / len };\n}\nfunction boxSupport(box, dir) {\n  return Math.abs(dir.x) * (box.x1 - box.x0) / 2 + Math.abs(dir.y) * (box.y1 - box.y0) / 2;\n}\nfunction boxRayCrossing(box, dir) {\n  const halfW = (box.x1 - box.x0) / 2;\n  const halfH = (box.y1 - box.y0) / 2;\n  return Math.min(\n    dir.x === 0 ? Infinity : halfW / Math.abs(dir.x),\n    dir.y === 0 ? Infinity : halfH / Math.abs(dir.y)\n  );\n}\nfunction runBounds(nodeIds, nodePositions) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const id of nodeIds) {\n    for (const p of nodePositions[id] ?? []) {\n      minX = Math.min(minX, p.x);\n      maxX = Math.max(maxX, p.x);\n      minY = Math.min(minY, p.y);\n      maxY = Math.max(maxY, p.y);\n    }\n  }\n  return minX === Infinity ? void 0 : { minX, minY, maxX, maxY };\n}\nvar nodeOrderCache = weakMemo();\nfunction labelOrder(nodePositions, nodeLengths) {\n  return nodeOrderCache(\n    nodePositions,\n    [nodeLengths],\n    () => Object.entries(nodePositions).filter(([id, segments]) => segments.length > 0 && nodeLengths.has(id)).sort(([a], [b]) => nodeLengths.get(b) - nodeLengths.get(a))\n  );\n}\nvar arcCache = weakMemo();\nfunction arcPlacements(nodePositions, deletions, axis, version, routes, stranded) {\n  const { scaleX, scaleY } = axis;\n  return arcCache(\n    nodePositions,\n    [deletions, routes, stranded, scaleX, scaleY, version],\n    () => {\n      const arcs = [];\n      for (const deletion of [...deletions].sort((a, b) => b.bp - a.bp)) {\n        const curves = edgeCurvesOf(\n          nodePositions,\n          deletion,\n          axis,\n          deletion.bypassed,\n          routes?.[deletion.edgeIndex],\n          stranded\n        );\n        const apex = curves ? curveMidpoint(curves) : void 0;\n        if (curves && apex) {\n          const { minX, minY, maxX, maxY } = curveBounds(curves);\n          arcs.push({\n            deletion,\n            curves,\n            apex,\n            // in screen px, so the two axes' units cannot be added by accident\n            extent: Math.max((maxX - minX) * scaleX, (maxY - minY) * scaleY)\n          });\n        }\n      }\n      return arcs;\n    }\n  );\n}\nfunction sizeLabelCandidates({\n  nodePositions,\n  nodeLengths,\n  deletions,\n  deletionRoutes,\n  stranded = false,\n  alleleDeletions,\n  axis,\n  translateX,\n  translateY,\n  width,\n  height,\n  version = 0\n}) {\n  const { scaleX, scaleY } = axis;\n  const deletionCandidates = [];\n  const nodeCandidates = [];\n  for (const { deletion, curves, apex, extent } of arcPlacements(\n    nodePositions,\n    deletions,\n    axis,\n    version,\n    deletionRoutes,\n    stranded\n  )) {\n    if (extent >= MIN_DELETION_LABEL_PX) {\n      const text = deletionText(deletion.bp);\n      const halfW = labelHalfWidth(text);\n      const box = boxAt(halfW, 0, 0);\n      const arcX = apex.x * scaleX + translateX;\n      const arcY = apex.y * scaleY + translateY;\n      if (arcX < 0 || arcX > width || arcY < 0 || arcY > height) {\n        continue;\n      }\n      const fits = extent >= halfW * 2 / MAX_LABEL_OVERHANG;\n      const bow = arcOutward(curves, apex, scaleX, scaleY);\n      const offset = boxSupport(box, bow) + LEADER_GAP_PX;\n      const x = fits ? arcX : clamp(arcX + bow.x * offset, halfW, width - halfW);\n      const y = fits ? arcY : clamp(\n        arcY + bow.y * offset,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      const away = Math.hypot(x - arcX, y - arcY);\n      let leader;\n      if (away > 0) {\n        const dir = { x: (x - arcX) / away, y: (y - arcY) / away };\n        const crossing = boxRayCrossing(box, dir);\n        leader = {\n          arcX,\n          arcY,\n          labelX: x - dir.x * crossing,\n          labelY: y - dir.y * crossing\n        };\n      }\n      deletionCandidates.push({\n        label: {\n          key: `del:${deletion.edgeIndex}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\",\n          leader\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  const labelledByDeletion = /* @__PURE__ */ new Set();\n  const alleleRuns = [...alleleDeletions ?? []].sort((a, b) => b.bp - a.bp);\n  for (const run of alleleRuns) {\n    const drawn = runBounds(run.nodeIds, nodePositions);\n    if (!drawn) {\n      continue;\n    }\n    const shownLeft = Math.max(drawn.minX * scaleX + translateX, 0);\n    const shownRight = Math.min(drawn.maxX * scaleX + translateX, width);\n    const shownTop = Math.max(drawn.minY * scaleY + translateY, 0);\n    const shownBottom = Math.min(drawn.maxY * scaleY + translateY, height);\n    if (shownRight < shownLeft || shownBottom < shownTop) {\n      continue;\n    }\n    const extent = Math.max(shownRight - shownLeft, shownBottom - shownTop);\n    const text = deletionText(run.bp);\n    const halfW = labelHalfWidth(text);\n    if (extent >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      for (const id of run.nodeIds) {\n        labelledByDeletion.add(id);\n      }\n      const x = clamp((shownLeft + shownRight) / 2, halfW, width - halfW);\n      const y = clamp(\n        (shownTop + shownBottom) / 2,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      deletionCandidates.push({\n        label: {\n          key: `alleledel:${run.nodeIds.join(\",\")}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\"\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  for (const [id, segments] of labelOrder(nodePositions, nodeLengths)) {\n    if (labelledByDeletion.has(id)) {\n      continue;\n    }\n    const { x, y } = polylineMidpoint(segments);\n    const screenY = y * scaleY + translateY;\n    if (screenY + LABEL_HALF_HEIGHT <= 0 || screenY - LABEL_HALF_HEIGHT >= height) {\n      continue;\n    }\n    const drawn = polylinePx(segments, scaleX, scaleY);\n    if (drawn < MIN_LABEL_HALF_WIDTH * 2 / MAX_LABEL_OVERHANG) {\n      continue;\n    }\n    const text = formatBp(nodeLengths.get(id));\n    const halfW = labelHalfWidth(text);\n    if (drawn >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      const screenX = x * scaleX + translateX;\n      nodeCandidates.push({\n        label: {\n          key: `node:${id}`,\n          text,\n          x: screenX,\n          y: screenY,\n          kind: \"node\"\n        },\n        box: boxAt(halfW, screenX, screenY)\n      });\n    }\n  }\n  return { deletions: deletionCandidates, nodes: nodeCandidates };\n}\nfunction nodeLabelBudget(width, height) {\n  return Math.max(\n    MIN_NODE_LABELS,\n    Math.floor(width * height / PX_PER_NODE_LABEL)\n  );\n}\nfunction placeSizeLabels(candidates, take, budget = Infinity) {\n  const labels = [];\n  for (const { label, box } of candidates) {\n    if (labels.length >= budget) {\n      break;\n    }\n    if (take(box)) {\n      labels.push(label);\n    }\n  }\n  return labels;\n}\nfunction graphLabels({\n  reserved,\n  take,\n  ...args\n}) {\n  take ??= occupancy(args, reserved);\n  const { deletions, nodes } = sizeLabelCandidates(args);\n  return [\n    ...placeSizeLabels(deletions, take),\n    ...placeSizeLabels(nodes, take, nodeLabelBudget(args.width, args.height))\n  ];\n}\n\nexport {\n  rowLabelBox,\n  groupDigits,\n  formatBp,\n  sizeLabelCandidates,\n  nodeLabelBudget,\n  placeSizeLabels,\n  graphLabels\n};\n", "import {\n  groupDigits\n} from \"./chunk-T3H5ELLA.js\";\nimport {\n  pathOrigin\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  isGenericSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathColors.ts\nfunction nameHue(name) {\n  let hash = 0;\n  for (let i = 0; i < name.length; i++) {\n    hash = name.charCodeAt(i) + ((hash << 5) - hash);\n  }\n  return Math.abs(hash % 360);\n}\nfunction pathHueAt(index, count) {\n  return index * 360 / count;\n}\nvar PATH_SATURATION = 0.7;\nvar PATH_LIGHTNESS = 0.5;\nvar MAX_PATH_COLORS = 16;\nfunction pathColorsLegible(pathCount) {\n  return pathCount > 0 && pathCount <= MAX_PATH_COLORS;\n}\nfunction pathCssColor(index, count) {\n  return `hsl(${pathHueAt(index, count)}, ${PATH_SATURATION * 100}%, ${PATH_LIGHTNESS * 100}%)`;\n}\nfunction pathGreyCssColor(index, count) {\n  const lightness = count > 1 ? 25 + 45 * index / (count - 1) : 45;\n  return `hsl(0, 0%, ${lightness}%)`;\n}\nfunction labelTiers(name) {\n  const parts = pathOrigin(name).name.split(\"#\");\n  const full = parts.join(\"#\");\n  if (parts.length >= 3 && isGenericSample(parts[0])) {\n    const contig = parts.slice(2).join(\"#\");\n    return [contig, contig, full];\n  }\n  return [parts[0], parts.slice(0, 2).join(\"#\"), full];\n}\nfunction offsetTiers(name, tiers) {\n  const { start } = pathOrigin(name);\n  return tiers.map((t) => `${t} @${groupDigits(start)}`);\n}\nfunction pathLegend(paths, colors) {\n  const firstOf = /* @__PURE__ */ new Map();\n  paths.forEach((path, i) => {\n    if (!firstOf.has(path.name)) {\n      firstOf.set(path.name, i);\n    }\n  });\n  const entries = [...firstOf].map(([name, i]) => ({ name, i }));\n  const named = entries.map((e) => labelTiers(e.name));\n  const candidates = [0, 1, 2].flatMap((t) => [\n    entries.map((_, k) => named[k][t]),\n    entries.map((e, k) => offsetTiers(e.name, named[k])[t])\n  ]);\n  const distinct = candidates.find(\n    (labels2) => new Set(labels2).size === entries.length\n  );\n  const labels = distinct ?? candidates.at(-1);\n  return entries.map(({ name, i }, k) => ({\n    name,\n    label: labels[k],\n    color: colors?.[i] ?? pathCssColor(i, paths.length)\n  }));\n}\nfunction walkLabelsOf(entries) {\n  const seen = /* @__PURE__ */ new Map();\n  return new Map(\n    [...entries].sort((a, b) => a.label.localeCompare(b.label)).map((e) => {\n      const n = (seen.get(e.label) ?? 0) + 1;\n      seen.set(e.label, n);\n      return [e.name, n > 1 ? `${e.label} (${n})` : e.label];\n    })\n  );\n}\n\nexport {\n  nameHue,\n  pathHueAt,\n  PATH_SATURATION,\n  PATH_LIGHTNESS,\n  MAX_PATH_COLORS,\n  pathColorsLegible,\n  pathCssColor,\n  pathGreyCssColor,\n  pathLegend,\n  walkLabelsOf\n};\n", "// src/nodeWidths.ts\nvar NODE_WIDTHS = [\n  {\n    value: \"depth\",\n    label: \"By depth\",\n    description: \"Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform.\"\n  },\n  {\n    value: \"uniform\",\n    label: \"Uniform\",\n    description: \"Every node the same thickness.\"\n  }\n];\nvar MIN_FACTOR = 0.3;\nvar MAX_FACTOR = 3;\nfunction meanDepth(graph) {\n  let weighted = 0;\n  let length = 0;\n  for (const node of graph.nodes) {\n    weighted += node.depth * node.length;\n    length += node.length;\n  }\n  return length > 0 ? weighted / length : 0;\n}\nfunction depthWidthFactor(node, mean) {\n  if (!(mean > 0) || !(node.depth > 0)) {\n    return 1;\n  }\n  return Math.min(\n    MAX_FACTOR,\n    Math.max(MIN_FACTOR, Math.sqrt(node.depth / mean))\n  );\n}\nfunction nodeWidthPx(node, contigThickness, nodeWidth, mean) {\n  return contigThickness * (nodeWidth === \"depth\" ? depthWidthFactor(node, mean) : 1);\n}\nfunction maxNodeWidthPx(contigThickness, nodeWidth) {\n  return contigThickness * (nodeWidth === \"depth\" ? MAX_FACTOR : 1);\n}\nvar MIN_WALK_LANE_PX = 4;\nfunction walkLaneWidthPx(width, lanes) {\n  return Math.max(width / lanes, MIN_WALK_LANE_PX);\n}\nfunction nodeInk(graph, nodeById, contigThickness, nodeWidth, lanes = 0) {\n  const mean = graph ? meanDepth(graph) : 0;\n  const reach = (width) => lanes > 0 ? walkLaneWidthPx(width, lanes) * lanes / 2 : width / 2;\n  return {\n    maxHalfWidthPx: reach(maxNodeWidthPx(contigThickness, nodeWidth)),\n    halfWidthPx: (id) => {\n      const node = nodeById?.get(id);\n      return reach(\n        node ? nodeWidthPx(node, contigThickness, nodeWidth, mean) : contigThickness\n      );\n    }\n  };\n}\n\nexport {\n  NODE_WIDTHS,\n  meanDepth,\n  nodeWidthPx,\n  maxNodeWidthPx,\n  walkLaneWidthPx,\n  nodeInk\n};\n"],
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"mid", "span", "t", "points", "MIN_DELETION_BP", "bypassedPoints", "nodePositions", "bypassed", "id", "edgeCurvesOf", "edge", "axis", "route", "stranded", "from", "to", "routedEdgeCurves", "strandSides", "computeEdgeCurves", "edgeJoinOf", "backboneBySequence", "graph", "bySequence", "groupBy", "isBackbone", "node", "list", "a", "b", "bypassedNodes", "nodes", "start", "end", "i", "firstNodeAtOrAfter", "skipsBetween", "forwards", "fromStrand", "toStrand", "leavesRight", "arrivesLeft", "skippedSpan", "startsOf", "best", "span", "COPY_SWITCH_SHARE", "repeatCopies", "backbone", "refName", "copies", "starts", "next", "switchesCopy", "bp", "partitionPoint", "k", "near", "c", "deletionEdges", "byId", "n", "referenceVisitStarts", "found", "edgeIndex", "closableDeletions", "deletions", "parent", "root", "r", "join", "ra", "rb", "candidates", "d", "e", "ei", "drawings", "deletionDrawing", "show", "byShow", "drawing", "hidden", "MIN_DELETION_LABEL_PX", "PX_PER_NODE_LABEL", "MIN_NODE_LABELS", "LEADER_GAP_PX", "LABEL_CHAR_PX", "LABEL_PAD_PX", "LABEL_HEIGHT_PX", "LABEL_GAP_PX", "MAX_LABEL_OVERHANG", "labelHalfWidth", "text", "LABEL_HALF_HEIGHT", "MIN_LABEL_HALF_WIDTH", "boxAt", "halfW", "x", "y", "rowLabelBox", "screenY", "labelWidth", "clamp", "v", "lo", "hi", "groupDigits", "n", "formatBp", "bp", "value", "unit", "deletionText", "arcOutward", "curves", "apex", "scaleX", "scaleY", "first", "last", "dx", "dy", "len", "boxSupport", "box", "dir", "boxRayCrossing", "halfH", "runBounds", "nodeIds", "nodePositions", "minX", "minY", "maxX", "maxY", "id", "p", "nodeOrderCache", "weakMemo", "labelOrder", "nodeLengths", "segments", "a", "b", "arcCache", "arcPlacements", "deletions", "axis", "version", "routes", "stranded", "arcs", "deletion", "edgeCurvesOf", "curveMidpoint", "curveBounds", "sizeLabelCandidates", "deletionRoutes", "alleleDeletions", "translateX", "translateY", "width", "height", "deletionCandidates", "nodeCandidates", "extent", "arcX", "arcY", "fits", "bow", "offset", "away", "leader", "crossing", "labelledByDeletion", "alleleRuns", "run", "drawn", "shownLeft", "shownRight", "shownTop", "shownBottom", "polylineMidpoint", "polylinePx", "screenX", "nodeLabelBudget", "placeSizeLabels", "candidates", "take", "budget", "labels", "label", "graphLabels", "reserved", "args", "occupancy", "nodes", "nameHue", "name", "hash", "i", "pathHueAt", "index", "count", "PATH_SATURATION", "PATH_LIGHTNESS", "MAX_PATH_COLORS", "pathColorsLegible", "pathCount", "pathCssColor", "pathGreyCssColor", "labelTiers", "parts", "pathOrigin", "full", "isGenericSample", "contig", "offsetTiers", "tiers", "start", "t", "groupDigits", "pathLegend", "paths", "colors", "firstOf", "path", "entries", "named", "e", "candidates", "_", "k", "labels", "labels2", "walkLabelsOf", "seen", "a", "b", "n", "NODE_WIDTHS", "MIN_FACTOR", "MAX_FACTOR", "meanDepth", "graph", "weighted", "length", "node", "depthWidthFactor", "mean", "nodeWidthPx", "contigThickness", "nodeWidth", "maxNodeWidthPx", "MIN_WALK_LANE_PX", "walkLaneWidthPx", "width", "lanes", "nodeInk", "nodeById", "reach", "id"]

package/dist/chunks/{chunk-PUFH6DMJ.js → chunk-JXOLZ5IZ.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-PUFH6DMJ.js.map
+import{h as B,k as M,n as F}from"./chunk-4XM5OBD5.js";import{b as O,h as _}from"./chunk-UW7INEQF.js";import{F as b,L as A}from"./chunk-D5PRXUSS.js";import{e as R}from"./chunk-YU7T5WOQ.js";import{D as P,E,H as m,d as v,o as T,q as I,r as L,s as w,t as N,w as x,y as D,z as G}from"./chunk-UGCNPRKC.js";import{b as t,c as i,d as k}from"./chunk-JMBDTNUR.js";var S=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function f({label:o,value:n,options:e,testId:s,size:c,sx:d,disabled:a,title:h,shown:g,onChange:Q}){let C=R();return i(w,{size:c,sx:d,disabled:a,title:h,children:[t(x,{id:C,shrink:!0,children:o}),t(P,{labelId:C,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:l=>g??e.find(z=>z.value===l)?.label??l,onChange:l=>{Q(l.target.value)},children:e.map(l=>t(G,{value:l.value,disabled:l.disabled,title:l.disabled?void 0:l.description,children:t(D,{primary:l.label,secondary:l.disabled?l.description:void 0})},l.value))})]})}var u=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function r({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function y({title:o,children:n}){let{classes:e}=u();return i("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:c}=u();return i("div",{className:c.section,children:[t(N,{control:t(E,{checked:n,onChange:d=>{e(d.target.checked)}}),label:o}),s]})}function p({children:o,...n}){let{classes:e}=u();return i("div",{className:e.section,children:[t(f,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function H(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function W({label:o,choices:n,stored:e,auto:s,testId:c,onChange:d,children:a}){return n.length>0?t(p,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:c,onChange:d,children:a}):null}var $=k(function(n){let{model:e,onClose:s,children:c}=n,{classes:d}=u();return i(v,{open:!0,onClose:s,title:"Graph settings",children:[i(L,{children:[i(y,{title:"Subgraph",children:[c,t(p,{label:"Node limit",value:String(e.maxGraphNodes),options:H(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(r,{children:"The most nodes a layout draws; past it the graph is declined. 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+//# sourceMappingURL=chunk-JXOLZ5IZ.js.map

package/dist/chunks/{chunk-PUFH6DMJ.js.map → chunk-JXOLZ5IZ.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../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 { useId } from 'react'\n\nimport {\n  FormControl,\n  InputLabel,\n  ListItemText,\n  MenuItem,\n  Select,\n} from '@mui/material'\n\nimport type { SxProps } from '@mui/material'\n\ninterface SelectOption<T extends string> {\n  value: T\n  label: string\n  // an option's tooltip, and the reason under a disabled one, whose tooltip\n  // cannot open\n  description?: string\n  disabled?: boolean\n}\n\n// One dropdown with its label tied to it, so a screen reader names the combobox\nexport default function LabelledSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  size,\n  sx,\n  disabled,\n  title,\n  shown,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly SelectOption<T>[]\n  testId?: string\n  size?: 'small' | 'medium'\n  sx?: SxProps\n  disabled?: boolean\n  title?: string\n  // what the closed select reads, when not the picked option's label\n  shown?: string\n  onChange: (value: T) => void\n}) {\n  const labelId = useId()\n  return (\n    <FormControl size={size} sx={sx} disabled={disabled} title={title}>\n      <InputLabel id={labelId} shrink>\n        {label}\n      </InputLabel>\n      <Select\n        labelId={labelId}\n        value={value}\n        label={label}\n        notched\n        displayEmpty\n        data-testid={testId}\n        renderValue={picked =>\n          shown ?? options.find(o => o.value === picked)?.label ?? picked\n        }\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(o => (\n          <MenuItem\n            key={o.value}\n            value={o.value}\n            disabled={o.disabled}\n            title={o.disabled ? undefined : o.description}\n          >\n            <ListItemText\n              primary={o.label}\n              secondary={o.disabled ? o.description : undefined}\n            />\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\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  FormControlLabel,\n  Switch,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from './LabelledSelect'\nimport { pickGeneTrack } from '../genes/geneFeatures'\nimport { pickRepeatTrack } from '../repeats/repeatFeatures'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  group: {\n    marginBottom: 16,\n  },\n  heading: {\n    marginBottom: 8,\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      component=\"div\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\nfunction Group({ title, children }: { title: string; children: ReactNode }) {\n  const { classes } = useStyles()\n  return (\n    <section className={classes.group}>\n      <Typography variant=\"subtitle1\" className={classes.heading}>\n        {title}\n      </Typography>\n      {children}\n    </section>\n  )\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, at the dialog's width, and its caption\nfunction SettingSelect<T extends string>({\n  children,\n  ...props\n}: Omit<Parameters<typeof LabelledSelect<T>>[0], 'size' | 'sx'> & {\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <LabelledSelect sx={{ minWidth: 200 }} {...props} />\n      {children}\n    </div>\n  )\n}\n\nconst NODE_LIMITS = [5000, 20_000, 50_000, 100_000]\n\n// the presets, with a limit a session states among them\nfunction nodeLimitOptions(current: number) {\n  return [...new Set([...NODE_LIMITS, current])]\n    .sort((a, b) => a - b)\n    .map(limit => ({ value: String(limit), label: limit.toLocaleString() }))\n}\n\ninterface NamedTrack {\n  trackId: string\n  name: string\n}\n\n// '' leaves the pick to the heuristic, so a session can go back to it\nfunction TrackPickSetting({\n  label,\n  choices,\n  stored,\n  auto,\n  testId,\n  onChange,\n  children,\n}: {\n  label: string\n  choices: NamedTrack[]\n  stored: string\n  auto: NamedTrack | undefined\n  testId: string\n  onChange: (trackId: string) => void\n  children: ReactNode\n}) {\n  return choices.length > 0 ? (\n    <SettingSelect\n      label={label}\n      value={choices.some(t => t.trackId === stored) ? stored : ''}\n      options={[\n        { value: '', label: `Automatic (${auto?.name ?? 'none'})` },\n        ...choices.map(({ trackId, name }) => ({\n          value: trackId,\n          label: name,\n        })),\n      ]}\n      testId={testId}\n      onChange={onChange}\n    >\n      {children}\n    </SettingSelect>\n  ) : null\n}\n\n// Toggles the menus already offer (halos, genes, color) stay out of here.\n// `children` is the host's own part of the subgraph group.\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <Group title=\"Subgraph\">\n          {children}\n          <SettingSelect\n            label=\"Node limit\"\n            value={String(model.maxGraphNodes)}\n            options={nodeLimitOptions(model.maxGraphNodes)}\n            testId=\"graph-node-limit-select\"\n            onChange={limit => {\n              model.setMaxGraphNodes(Number(limit))\n            }}\n          >\n            <Caption>\n              The most nodes a layout draws; past it the graph is declined. Walk\n              rows take no limit.\n            </Caption>\n          </SettingSelect>\n        </Group>\n\n        <Group title=\"Drawing\">\n          {model.anchorPaths.length > 1 ? (\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>The path the anchored layouts place x along</Caption>\n            </SettingSelect>\n          ) : null}\n\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              Depth as width. In a cut with walks, depth is how many haplotypes\n              carry the node.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSwitch\n            label=\"Draw paths\"\n            checked={model.drawPaths}\n            onChange={draw => {\n              model.setLayer('paths', draw)\n            }}\n          >\n            <Caption>\n              Color each node by the paths through it, one lane per path\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          <TrackPickSetting\n            label=\"Gene track\"\n            choices={model.geneTrackChoices}\n            stored={model.geneTrackId}\n            auto={pickGeneTrack(model.geneTrackChoices, '')}\n            testId=\"graph-gene-track-select\"\n            onChange={trackId => {\n              model.setGeneTrackId(trackId)\n            }}\n          >\n            <Caption>Where genes on the backbone come from</Caption>\n          </TrackPickSetting>\n\n          <TrackPickSetting\n            label=\"Repeat track\"\n            choices={model.repeatTrackChoices}\n            stored={model.repeatTrackId}\n            auto={pickRepeatTrack(model.repeatTrackChoices, '')}\n            testId=\"graph-repeat-track-select\"\n            onChange={trackId => {\n              model.setRepeatTrackId(trackId)\n            }}\n          >\n            <Caption>\n              The tandem repeat annotation walk rows measure and tile by\n            </Caption>\n          </TrackPickSetting>\n        </Group>\n\n        <Group title=\"Force-directed layout\">\n          {model.hasGraph && !model.usesLayoutEngine ? (\n            <div className={classes.section}>\n              <Caption warn>\n                No effect on the current layout until Layout is Force-directed\n              </Caption>\n            </div>\n          ) : null}\n\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            }}\n          >\n            <Caption>\n              Stress keeps the reference straight, so a zoom keeps the picture;\n              FMMM lets the whole graph settle.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Layout quality\"\n            value={String(model.layoutQuality)}\n            options={LAYOUT_QUALITIES.map(q => ({\n              value: String(q.value),\n              label: q.label,\n            }))}\n            testId=\"graph-layout-quality-select\"\n            onChange={quality => {\n              model.setLayoutQuality(Number(quality))\n            }}\n          >\n            <Caption>\n              The engine&apos;s iteration budget; higher is slower\n            </Caption>\n          </SettingSelect>\n\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            }}\n          >\n            <Caption>How far the layout opens a bubble</Caption>\n          </SettingSelect>\n\n          {model.layoutEngine === 'stress' ? null : (\n            <SettingSwitch\n              label=\"Linear layout\"\n              checked={model.linearLayout}\n              onChange={linear => {\n                model.setLinearLayout(linear)\n              }}\n            >\n              <Caption>Keeps a chain of nodes on one line where it can</Caption>\n            </SettingSwitch>\n          )}\n        </Group>\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-KPP5H27W.js

@@ -0,0 +1,2 @@
+import{a as m}from"./chunk-QASFRHPG.js";import{d as u,e as o,g as l,k as g}from"./chunk-OUHKJSKZ.js";import{h as i}from"./chunk-VIVPTP5Z.js";var B={steps:"walkStepBudget",bytes:"walkByteBudget"},b=class{constructor(t,e){this.file=t;this.adapter=e;this.reader=new l(t)}async haplotypeNames(t={}){let{haplotypes:e}=await this.reader.header(t);return e.length>0?e:void 0}budgets(){return{stepBudget:this.adapter.getConf("walkStepBudget"),byteBudget:this.adapter.getConf("walkByteBudget"),budgetNames:B}}async subgraph(t,e,{signal:n,haplotypes:d,walkRows:a,expand:r}){let s=this.budgets(),{graph:h,kept:c,fragments:f}=await this.reader.cut(t,e,{...s,stepBudget:a?1/0:s.stepBudget,signal:n,keep:o(d?.map(p=>i(this.adapter,p)),t),...r?.length?{expand:p=>r.includes(p)}:{}});return m(h.tables(c,f),e,a)}async referenceNodes(t,e,n){let d=[];await g(this.file,t,await this.reader.queryStart(e.start,{...n,refName:t,end:e.end}),e.end,{signal:n.signal,lineCallback:r=>{let s=r.split("	");s[3]==="ref"&&d.push(s)}});let a=new Set;return u(d).filter(r=>r.refName!==t||r.end<=e.start||r.start>=e.end||a.has(r.id)?!1:(a.add(r.id),!0))}};export{b as a};
+//# sourceMappingURL=chunk-KPP5H27W.js.map

package/dist/chunks/chunk-KPP5H27W.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/RgfaTabixAdapter/walkReader.ts"],
+  "sourcesContent": ["import { resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'\nimport { WalkReader, referenceNodes, walksKept } from '@jbrowse/graph-walks'\n\nimport { getLines } from '../tabixRange.ts'\nimport { walkCutFor } from './walkCut.ts'\n\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\n\n// The zoom-in notices name the config slots that set the budgets\nexport const BUDGET_SLOTS = {\n  steps: 'walkStepBudget',\n  bytes: 'walkByteBudget',\n}\n\n/**\n * A walk file and the answers both walk-indexed adapters give from it,\n * RgfaTabixAdapter and WalkTabixSyntenyAdapter, whose schemas declare the\n * budget slots. @jbrowse/graph-walks reads and cuts the file.\n */\nexport class WalkIndex {\n  readonly reader: WalkReader\n\n  constructor(\n    readonly file: TabixIndexedFile,\n    private adapter: BaseFeatureDataAdapter,\n  ) {\n    this.reader = new WalkReader(file)\n  }\n\n  /**\n   * The haplotypes the header names, `sample#haplotype` in byte order, or\n   * undefined when it names none\n   */\n  async haplotypeNames(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.reader.header(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\n  }\n\n  budgets() {\n    return {\n      stepBudget: this.adapter.getConf('walkStepBudget') as number,\n      byteBudget: this.adapter.getConf('walkByteBudget') as number,\n      budgetNames: BUDGET_SLOTS,\n    }\n  }\n\n  /**\n   * The graph display's cut of a window: the reference walk, the walks of\n   * `haplotypes` (every walk when unset), and the nodes and links they visit.\n   * Walk rows draw runs, so the step budget spares them.\n   */\n  async subgraph(\n    refName: string,\n    region: { start: number; end: number },\n    { signal, haplotypes, walkRows, expand }: SubgraphAdapterOptions,\n  ) {\n    const budgets = this.budgets()\n    const { graph, kept, fragments } = await this.reader.cut(refName, region, {\n      ...budgets,\n      stepBudget: walkRows ? Infinity : budgets.stepBudget,\n      signal,\n      keep: walksKept(\n        haplotypes?.map(lane => resolvePanSNPrefix(this.adapter, lane)),\n        refName,\n      ),\n      ...(expand?.length\n        ? { expand: (name: string) => expand.includes(name) }\n        : {}),\n    })\n    return walkCutFor(graph.tables(kept, fragments), region, walkRows)\n  }\n\n  /**\n   * The reference nodes overlapping a window, from the ref rows of its\n   * chunks. A row's tabix interval is its chunk's first base, and gfa-to-tabix\n   * files a node crossing in from a chunk before under that chunk, so the read\n   * starts at queryStart.\n   */\n  async referenceNodes(\n    refName: string,\n    region: { start: number; end: number },\n    opts: BaseOptions,\n  ) {\n    const refRows: string[][] = []\n    await getLines(\n      this.file,\n      refName,\n      await this.reader.queryStart(region.start, {\n        ...opts,\n        refName,\n        end: region.end,\n      }),\n      region.end,\n      {\n        signal: opts.signal,\n        lineCallback: line => {\n          const cols = line.split('\\t')\n          if (cols[3] === 'ref') {\n            refRows.push(cols)\n          }\n        },\n      },\n    )\n    const seen = new Set<number>()\n    return referenceNodes(refRows).filter(node => {\n      if (\n        node.refName !== refName ||\n        node.end <= region.start ||\n        node.start >= region.end ||\n        seen.has(node.id)\n      ) {\n        return false\n      }\n      seen.add(node.id)\n      return true\n    })\n  }\n}\n"],
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+}

package/dist/chunks/{chunk-Q55PHRHV.js → chunk-LTN6XZR5.js}

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+//# sourceMappingURL=chunk-LTN6XZR5.js.map

package/dist/chunks/{chunk-Q55PHRHV.js.map → chunk-LTN6XZR5.js.map}

@@ -1,6 +1,6 @@
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-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.6.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
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package/dist/chunks/{chunk-QQCTNB2Z.js → chunk-MLVBPMBU.js}

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