jbrowse-plugin-graphgenomeviewer 7.1.0 → 7.1.2

package/dist/chunks/{chunk-DZ4OUKQV.js → chunk-FITPB5X6.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{chunk-DZ4OUKQV.js.map → chunk-FITPB5X6.js.map}

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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.6/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.6/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ZY2AFL4Y.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.6/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ES2N6V56.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.6/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-A4PFFC4Q.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.6/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VQC7KELB.js"],
   "sourcesContent": ["// src/renderer/colorBits.ts\nfunction packAbgr(r, g, b, a) {\n  return (a << 24 | b << 16 | g << 8 | r) >>> 0;\n}\nfunction abgrRed(c) {\n  return c & 255;\n}\nfunction abgrGreen(c) {\n  return c >>> 8 & 255;\n}\nfunction abgrBlue(c) {\n  return c >>> 16 & 255;\n}\nfunction abgrAlpha(c) {\n  return c >>> 24 & 255;\n}\nfunction abgrToCssRgba(c) {\n  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;\n}\nfunction normalizedRgbToCssRgba(c, alpha) {\n  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;\n}\nfunction fadeAbgr(c, alpha) {\n  return packAbgr(\n    abgrRed(c),\n    abgrGreen(c),\n    abgrBlue(c),\n    Math.round(abgrAlpha(c) * alpha)\n  );\n}\nfunction brightenAbgr(c, factor) {\n  const t = Math.max(0, 1 - 1 / factor);\n  const lift = (v) => Math.round(v + (255 - v) * t);\n  return packAbgr(\n    lift(abgrRed(c)),\n    lift(abgrGreen(c)),\n    lift(abgrBlue(c)),\n    abgrAlpha(c)\n  );\n}\n\nexport {\n  packAbgr,\n  abgrRed,\n  abgrGreen,\n  abgrBlue,\n  abgrAlpha,\n  abgrToCssRgba,\n  normalizedRgbToCssRgba,\n  fadeAbgr,\n  brightenAbgr\n};\n", "import {\n  edgeCurvesOf\n} from \"./chunk-24WITXQY.js\";\n\n// src/util/edgeCurves.ts\nvar cache = /* @__PURE__ */ new WeakMap();\nfunction baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {\n  const { scaleX, scaleY } = axis;\n  const cached = cache.get(nodePositions);\n  if (cached?.graph === graph && cached.scaleX === scaleX && cached.scaleY === scaleY && cached.deletions === deletions && cached.routes === routes && cached.stranded === stranded && cached.version === version) {\n    return cached.curves;\n  }\n  const curves = /* @__PURE__ */ new Map();\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const bypassed = deletions?.get(ei);\n    const edgeCurves = edgeCurvesOf(\n      nodePositions,\n      graph.edges[ei],\n      axis,\n      bypassed,\n      bypassed && routes?.[ei],\n      stranded\n    );\n    if (edgeCurves) {\n      curves.set(ei, edgeCurves);\n    }\n  }\n  cache.set(nodePositions, {\n    graph,\n    scaleX,\n    scaleY,\n    deletions,\n    routes,\n    stranded,\n    version,\n    curves\n  });\n  return curves;\n}\n\nexport {\n  baseEdgeCurves\n};\n", "import {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/referenceSpan.ts\nvar MAX_BACKBONE_HOPS = 4;\nfunction buildNeighbors(graph) {\n  const neighbors = /* @__PURE__ */ new Map();\n  function add(from, to) {\n    const list = neighbors.get(from);\n    if (list) {\n      list.push(to);\n    } else {\n      neighbors.set(from, [to]);\n    }\n  }\n  for (const edge of graph.edges) {\n    add(edge.from, edge.to);\n    add(edge.to, edge.from);\n  }\n  return neighbors;\n}\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const seen = /* @__PURE__ */ new Set([nodeId]);\n  let frontier = [nodeId];\n  let minEnd = Infinity;\n  let maxStart = -Infinity;\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next = [];\n    for (const id of frontier) {\n      const adjacent = neighbors.get(id);\n      if (adjacent) {\n        for (const neighborId of adjacent) {\n          if (!seen.has(neighborId)) {\n            seen.add(neighborId);\n            const neighbor = nodeById.get(neighborId);\n            if (neighbor && isBackbone(neighbor)) {\n              minEnd = Math.min(minEnd, neighbor.stable.start + neighbor.length);\n              maxStart = Math.max(maxStart, neighbor.stable.start);\n            } else {\n              next.push(neighborId);\n            }\n          }\n        }\n      }\n    }\n    frontier = next;\n  }\n  return minEnd === Infinity ? void 0 : {\n    start: Math.min(minEnd, maxStart),\n    end: Math.max(minEnd, maxStart)\n  };\n}\nfunction nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const node = nodeById.get(nodeId);\n  return node === void 0 ? void 0 : isBackbone(node) ? { start: node.stable.start, end: node.stable.start + node.length } : flankingSpan({ nodeId, nodeById, neighbors });\n}\nfunction referenceMidpoints(graph) {\n  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));\n  const neighbors = buildNeighbors(graph);\n  const midpoints = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const span = nodeReferenceSpan({ nodeId: node.id, nodeById, neighbors });\n    if (span) {\n      midpoints.set(node.id, (span.start + span.end) / 2);\n    }\n  }\n  return midpoints;\n}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints\n};\n", "import {\n  abgrToCssRgba,\n  fadeAbgr,\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  baseEdgeCurves\n} from \"./chunk-ZY2AFL4Y.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-3XSM4OZU.js\";\nimport {\n  meanDepth,\n  nodeWidthPx\n} from \"./chunk-JBCZIBFC.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-ES2N6V56.js\";\nimport {\n  dashCurves,\n  pathRibbonOffsets,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-7SRWJLSC.js\";\n\n// src/renderer/GeometryBuilder.ts\nvar EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);\nvar EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);\nvar EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);\nvar DELETION_THICKNESS_FACTOR = 2.2;\nvar LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255);\nvar FADED_ALPHA = 0.18;\nvar LIFT_BACKDROP_CSS = abgrToCssRgba(\n  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)\n);\nvar DELETION_DASH_PX = 11;\nvar MIN_PATH_STRIPE_PX = 1.2;\nvar MIN_WALK_LANE_PX = 4;\nvar MIN_SCALE_FOR_OFFSET = 1e-6;\nvar ARROW_LENGTH_BASE_PX = 7;\nvar ARROW_LENGTH_PER_EDGE_PX = 3;\nvar ARROW_HALF_WIDTH_BASE_PX = 3;\nvar ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;\nvar MIN_LINK_HEADS = 3;\nvar MIN_ARROW_FIT = 0.5;\nvar MIN_ARROW_SCALE = 0.45;\nvar ARROW_CURVE_STEPS = 12;\nvar ABUTTING_PX = 1e-6;\nvar walkX = new Float64Array(64);\nvar walkY = new Float64Array(64);\nvar walkPx = new Float64Array(64);\nfunction backFromEnd(curves, scale, yToX, untilPx) {\n  const most = curves.length * ARROW_CURVE_STEPS + 1;\n  if (walkX.length < most) {\n    walkX = new Float64Array(most);\n    walkY = new Float64Array(most);\n    walkPx = new Float64Array(most);\n  }\n  const last = curves[curves.length - 1];\n  walkX[0] = last.x1;\n  walkY[0] = last.y1;\n  walkPx[0] = 0;\n  let n = 1;\n  let px = 0;\n  for (let ci = curves.length - 1; ci >= 0 && px < untilPx; ci--) {\n    const c = curves[ci];\n    for (let k = 1; k <= ARROW_CURVE_STEPS && px < untilPx; k++) {\n      const t = 1 - (k / ARROW_CURVE_STEPS) ** 2;\n      const u = 1 - t;\n      const a = u * u * u;\n      const b = 3 * u * u * t;\n      const d = 3 * u * t * t;\n      const e = t * t * t;\n      const x = a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1;\n      const y = a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1;\n      px += Math.hypot(x - walkX[n - 1], (y - walkY[n - 1]) * yToX) * scale;\n      walkX[n] = x;\n      walkY[n] = y;\n      walkPx[n] = px;\n      n++;\n    }\n  }\n  return n;\n}\nfunction walkPointAt(n, px) {\n  let i = 1;\n  while (i < n - 1 && walkPx[i] < px) {\n    i++;\n  }\n  const from = walkPx[i - 1];\n  const to = walkPx[i];\n  const f = to > from ? Math.min(1, Math.max(0, (px - from) / (to - from))) : 0;\n  return {\n    x: walkX[i - 1] + (walkX[i] - walkX[i - 1]) * f,\n    y: walkY[i - 1] + (walkY[i] - walkY[i - 1]) * f\n  };\n}\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments\n}) {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;\n  const n = backFromEnd(\n    curves,\n    scale,\n    yToX,\n    nodeHalfWidth + MIN_LINK_HEADS * length\n  );\n  const lengthPx = walkPx[n - 1];\n  const abutting = lengthPx < ABUTTING_PX;\n  const inset = Math.min(nodeHalfWidth, lengthPx);\n  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, yToX) / length) : 1;\n  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {\n    return void 0;\n  }\n  const tip = walkPointAt(n, inset);\n  const base = walkPointAt(n, inset + length * fit);\n  const dx = tip.x - base.x;\n  const dy = (tip.y - base.y) * yToX;\n  const last = curves[curves.length - 1];\n  return {\n    x: tip.x,\n    y: tip.y,\n    angle: Math.hypot(dx, dy) > 0 ? Math.atan2(dy, dx) : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth: (ARROW_HALF_WIDTH_BASE_PX + ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) * fit,\n    color\n  };\n}\nfunction polylinePx(segments, scale, yToX) {\n  let length = 0;\n  for (let i = 1; i < segments.length; i++) {\n    length += Math.hypot(\n      segments[i].x - segments[i - 1].x,\n      (segments[i].y - segments[i - 1].y) * yToX\n    );\n  }\n  return length * scale;\n}\nfunction leavesStart(edge, segments, first, stranded, yToX) {\n  if (stranded) {\n    return strandSides(edge).from === \"start\";\n  }\n  const gap = (p) => Math.hypot(p.x - first.x0, (p.y - first.y0) * yToX);\n  return gap(segments[0]) < gap(segments.at(-1));\n}\nfunction intoDirection(last, toSegments) {\n  if (toSegments.length < 2) {\n    return void 0;\n  }\n  const first = toSegments[0];\n  const final = toSegments[toSegments.length - 1];\n  const atStart = Math.hypot(last.x1 - first.x, last.y1 - first.y) <= Math.hypot(last.x1 - final.x, last.y1 - final.y);\n  return atStart ? { from: first, to: toSegments[1] } : { from: final, to: toSegments[toSegments.length - 2] };\n}\nfunction pointNormalsOf(rawPoints, yToX = 1) {\n  const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));\n  const pointNormals = [];\n  for (let i = 0; i < points.length; i++) {\n    let nx = 0;\n    let ny = 0;\n    if (i === 0) {\n      const dx = points[1].x - points[0].x;\n      const dy = points[1].y - points[0].y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        nx = -dy / len;\n        ny = dx / len;\n      }\n    } else if (i === points.length - 1) {\n      const dx = points[i].x - points[i - 1].x;\n      const dy = points[i].y - points[i - 1].y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        nx = -dy / len;\n        ny = dx / len;\n      }\n    } else {\n      const dx1 = points[i].x - points[i - 1].x;\n      const dy1 = points[i].y - points[i - 1].y;\n      const len1 = Math.hypot(dx1, dy1);\n      const dx2 = points[i + 1].x - points[i].x;\n      const dy2 = points[i + 1].y - points[i].y;\n      const len2 = Math.hypot(dx2, dy2);\n      if (len1 > 0 && len2 > 0) {\n        const nx1 = -dy1 / len1;\n        const ny1 = dx1 / len1;\n        const nx2 = -dy2 / len2;\n        const ny2 = dx2 / len2;\n        nx = (nx1 + nx2) / 2;\n        ny = (ny1 + ny2) / 2;\n        const dot = nx1 * nx + ny1 * ny;\n        if (dot > 0.1) {\n          nx /= dot;\n          ny /= dot;\n        }\n      } else if (len1 > 0) {\n        nx = -dy1 / len1;\n        ny = dx1 / len1;\n      } else if (len2 > 0) {\n        nx = -dy2 / len2;\n        ny = dx2 / len2;\n      }\n    }\n    pointNormals.push({ nx, ny });\n  }\n  return pointNormals;\n}\nfunction offsetPolyline(points, normals, distance, yToX = 1) {\n  return points.map((p, i) => ({\n    x: p.x + normals[i].nx * distance,\n    y: p.y + normals[i].ny * distance / yToX\n  }));\n}\nfunction packNorm(r, g, b, a) {\n  return packAbgr(\n    Math.round(r * 255),\n    Math.round(g * 255),\n    Math.round(b * 255),\n    Math.round(a * 255)\n  );\n}\nfunction hslToRgb(h, s, l) {\n  const c = (1 - Math.abs(2 * l - 1)) * s;\n  const x = c * (1 - Math.abs(h / 60 % 2 - 1));\n  const m = l - c / 2;\n  let r = 0;\n  let g = 0;\n  let b = 0;\n  if (h < 60) {\n    r = c;\n    g = x;\n  } else if (h < 120) {\n    r = x;\n    g = c;\n  } else if (h < 180) {\n    g = c;\n    b = x;\n  } else if (h < 240) {\n    g = x;\n    b = c;\n  } else if (h < 300) {\n    r = x;\n    b = c;\n  } else {\n    r = c;\n    b = x;\n  }\n  return [r + m, g + m, b + m];\n}\nvar DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37]\n];\nvar STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122]\n];\nvar NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220]\n];\nfunction sampleGradient(stops, t) {\n  const pos = Math.max(0, Math.min(1, t)) * (stops.length - 1);\n  const i = Math.min(stops.length - 2, Math.floor(pos));\n  const f = pos - i;\n  const a = stops[i];\n  const b = stops[i + 1];\n  return packAbgr(\n    Math.round(a[0] + (b[0] - a[0]) * f),\n    Math.round(a[1] + (b[1] - a[1]) * f),\n    Math.round(a[2] + (b[2] - a[2]) * f),\n    255\n  );\n}\nfunction hashColor(str, alpha) {\n  const [r, g, b] = hslToRgb(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS);\n  return packNorm(r, g, b, alpha);\n}\nvar REFERENCE_RAMP_MAX_HUE = 300;\nvar REFERENCE_RAMP_SATURATION = 0.7;\nvar REFERENCE_RAMP_LIGHTNESS = 0.5;\nvar REFERENCE_RAMP_ALT_RGB = [60, 65, 72];\nvar REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);\nvar REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(\", \")})`;\nfunction computeReferenceRamp(graph, domain) {\n  const midpoints = referenceMidpoints(graph);\n  if (domain && domain.end > domain.start) {\n    return {\n      start: domain.start,\n      span: domain.end - domain.start,\n      midpoints\n    };\n  }\n  let min = Infinity;\n  let max = -Infinity;\n  for (const mid of midpoints.values()) {\n    min = Math.min(min, mid);\n    max = Math.max(max, mid);\n  }\n  return {\n    start: min === Infinity ? 0 : min,\n    span: max > min ? max - min : 1,\n    midpoints\n  };\n}\nfunction computeColorSchemeRange(graph) {\n  let minDepth = Infinity;\n  let maxDepth = -Infinity;\n  let minLength = Infinity;\n  let maxLength = -Infinity;\n  let maxRank = 0;\n  for (const n of graph.nodes) {\n    if (n.stable !== void 0 && n.stable.rank > maxRank) {\n      maxRank = n.stable.rank;\n    }\n    if (n.depth < minDepth) {\n      minDepth = n.depth;\n    }\n    if (n.depth > maxDepth) {\n      maxDepth = n.depth;\n    }\n    if (n.length < minLength) {\n      minLength = n.length;\n    }\n    if (n.length > maxLength) {\n      maxLength = n.length;\n    }\n  }\n  return {\n    minDepth,\n    maxDepth,\n    minLength,\n    maxLength,\n    maxRank,\n    nodeCount: graph.nodes.length\n  };\n}\nfunction getNodeColor(node, nodeIndex, colorScheme, range) {\n  switch (colorScheme) {\n    case \"random\":\n      return hashColor(node.id, 1);\n    case \"depth\":\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth) : 0.5\n      );\n    case \"node-length\":\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength ? (node.length - range.minLength) / (range.maxLength - range.minLength) : 0.5\n      );\n    // rGFA states the backbone rather than leaving it to be inferred: rank 0 is\n    // the reference, higher ranks are the sequence that diverges from it. A\n    // graph with no SR tags draws every node as unranked.\n    case \"stable-rank\":\n      return node.stable === void 0 ? packAbgr(160, 160, 160, 255) : node.stable.rank === 0 ? packAbgr(52, 152, 219, 255) : sampleGradient(\n        STABLE_RANK_GRADIENT,\n        range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0\n      );\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state. A node with no reference position at\n    // all \u2014 nothing anchored, or an allele whose flanks fell outside the cut \u2014\n    // is grey rather than a hue it has not earned.\n    case \"reference-position\": {\n      const ramp = range.referenceRamp;\n      const mid = ramp?.midpoints.get(node.id);\n      if (ramp === void 0 || mid === void 0) {\n        return packAbgr(160, 160, 160, 255);\n      }\n      if (node.stable !== void 0 && node.stable.rank > 0) {\n        return REFERENCE_RAMP_ALT_COLOR;\n      }\n      const frac = Math.max(0, Math.min(1, (mid - ramp.start) / ramp.span));\n      const [r, g, b] = hslToRgb(\n        frac * REFERENCE_RAMP_MAX_HUE,\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS\n      );\n      return packNorm(r, g, b, 1);\n    }\n    case \"grey\":\n      return packAbgr(160, 160, 160, 255);\n    case \"rainbow\": {\n      const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;\n      const [r, g, b] = hslToRgb(hue, 0.75, 0.5);\n      return packNorm(r, g, b, 1);\n    }\n    default:\n      return packAbgr(52, 152, 219, 255);\n  }\n}\nfunction endTangent(c, yToX = 1, into) {\n  const candidates = [\n    [c.cx1, c.cy1],\n    [c.cx0, c.cy0],\n    [c.x0, c.y0]\n  ];\n  for (const [x, y] of candidates) {\n    const dx = c.x1 - x;\n    const dy = (c.y1 - y) * yToX;\n    if (Math.hypot(dx, dy) > 0) {\n      return Math.atan2(dy, dx);\n    }\n  }\n  return into ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x) : 0;\n}\nfunction isPolylineInBounds(segments, bounds) {\n  let hit = false;\n  for (let i = 0; i < segments.length - 1 && !hit; i++) {\n    const a = segments[i];\n    const b = segments[i + 1];\n    hit = Math.max(a.x, b.x) >= bounds.minX && Math.min(a.x, b.x) <= bounds.maxX && Math.max(a.y, b.y) >= bounds.minY && Math.min(a.y, b.y) <= bounds.maxY;\n  }\n  return hit;\n}\nfunction isBezierInBounds(curves, bounds) {\n  for (const c of curves) {\n    const cMinX = Math.min(c.x0, c.cx0, c.cx1, c.x1);\n    const cMaxX = Math.max(c.x0, c.cx0, c.cx1, c.x1);\n    const cMinY = Math.min(c.y0, c.cy0, c.cy1, c.y1);\n    const cMaxY = Math.max(c.y0, c.cy0, c.cy1, c.y1);\n    if (cMaxX >= bounds.minX && cMinX <= bounds.maxX && cMaxY >= bounds.minY && cMinY <= bounds.maxY) {\n      return true;\n    }\n  }\n  return false;\n}\nvar paletteCache = /* @__PURE__ */ new WeakMap();\nfunction pathPaletteOf(graph) {\n  let palette = paletteCache.get(graph);\n  if (!palette) {\n    const pathColorByIndex = [];\n    const pathIndexByName = /* @__PURE__ */ new Map();\n    const paths = graph.paths ?? [];\n    for (let i = 0; i < paths.length; i++) {\n      const [r, g, b] = hslToRgb(\n        pathHueAt(i, paths.length),\n        PATH_SATURATION,\n        PATH_LIGHTNESS\n      );\n      pathColorByIndex.push(packNorm(r, g, b, 0.85));\n      if (!pathIndexByName.has(paths[i].name)) {\n        pathIndexByName.set(paths[i].name, i);\n      }\n    }\n    palette = { pathColorByIndex, pathIndexByName };\n    paletteCache.set(graph, palette);\n  }\n  return palette;\n}\nvar slotsCache = /* @__PURE__ */ new WeakMap();\nvar NO_SLOTS = /* @__PURE__ */ new Map();\nfunction pathSlotsOf(graph) {\n  let slots = slotsCache.get(graph);\n  if (!slots) {\n    slots = /* @__PURE__ */ new Map();\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        const visits = slots.get(nodeId);\n        if (visits) {\n          visits.push(pathIdx);\n        } else {\n          slots.set(nodeId, [pathIdx]);\n        }\n      }\n    }\n    slotsCache.set(graph, slots);\n  }\n  return slots;\n}\nfunction buildGeometry(options) {\n  const {\n    nodePositions,\n    graph,\n    nodeById,\n    colorScheme,\n    contigThickness,\n    connectorThickness,\n    drawPaths,\n    nodeWidth = \"uniform\",\n    highlight,\n    axis,\n    linearLayout,\n    viewportBounds,\n    referenceRamp,\n    deletions,\n    deletionRoutes,\n    stranded,\n    hiddenEdges,\n    version = 0\n  } = options;\n  const depthNorm = nodeWidth === \"depth\" ? meanDepth(graph) : 0;\n  const scale = axis.scaleX;\n  const yToX = yToXOf(axis);\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n    deletionRoutes,\n    stranded\n  );\n  const nodeStrokes = [];\n  const nodeStrokeRuns = /* @__PURE__ */ new Map();\n  const arrows = [];\n  const arrowRuns = /* @__PURE__ */ new Map();\n  const edgeCurves = [];\n  const edgeCurveRuns = /* @__PURE__ */ new Map();\n  const colorRange = { ...computeColorSchemeRange(graph), referenceRamp };\n  const nodeIndexMap = /* @__PURE__ */ new Map();\n  if (colorScheme === \"rainbow\") {\n    for (let i = 0; i < graph.nodes.length; i++) {\n      nodeIndexMap.set(graph.nodes[i].id, i);\n    }\n  }\n  const pathCount = graph.paths?.length ?? 0;\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph);\n  const pathColorByName = (name) => pathColorByIndex[pathIndexByName.get(name) ?? -1] ?? EDGE_PATH_FALLBACK_COLOR;\n  const nodePathSlots = drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS;\n  const showArrows = scale > (linearLayout ? 1 : MIN_ARROW_SCALE);\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei];\n    const fromSegments = nodePositions[edge.from];\n    const toSegments = nodePositions[edge.to];\n    const baseCurves = sharedCurves.get(ei);\n    if (!fromSegments?.length || !toSegments?.length || !baseCurves || hiddenEdges?.has(ei)) {\n      continue;\n    }\n    const numPaths = edge.pathIds?.length ?? 0;\n    const bypassed = deletions?.get(ei);\n    const isDeletion = bypassed !== void 0;\n    const onWalk = highlight?.edgeIndexes.has(ei) ?? false;\n    const edgeThickness = connectorThickness / 2 * (isDeletion ? DELETION_THICKNESS_FACTOR : 1);\n    const ribbons = drawPaths && numPaths > 0;\n    const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR;\n    const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);\n    const toNode = nodeById.get(edge.to);\n    const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, depthNorm) : contigThickness) / 2;\n    const inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);\n    const stroke = (curves, thickness, color) => {\n      if (isDeletion) {\n        for (const dash of dashCurves(curves, DELETION_DASH_PX / scale)) {\n          edgeCurves.push({ curves: dash, thickness, color });\n        }\n      } else {\n        edgeCurves.push({ curves, thickness, color });\n      }\n    };\n    const arrowOn = (curves) => {\n      const head = showArrows ? arrowheadFor({\n        curves,\n        edgeHalfWidth: connectorThickness / 2,\n        nodeHalfWidth: intoHalfWidth,\n        scale,\n        yToX,\n        color: edgeColor,\n        fromSegments,\n        toSegments\n      }) : void 0;\n      if (head) {\n        arrows.push(head);\n      }\n    };\n    const edgeCurveStart = edgeCurves.length;\n    const arrowStart = arrows.length;\n    const laneWalks = highlight?.walks.length && onWalk && !ribbons ? highlight.walks : void 0;\n    if (laneWalks) {\n      const fromNode = nodeById.get(edge.from);\n      const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm) : contigThickness;\n      const laneWidth = Math.max(width / laneWalks.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(fromSegments, yToX);\n      const { nx, ny } = (leavesStart(\n        edge,\n        fromSegments,\n        baseCurves[0],\n        stranded,\n        yToX\n      ) ? normals[0] : normals.at(-1)) ?? {\n        nx: 0,\n        ny: 0\n      };\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      laneWalks.forEach((walk, lane) => {\n        if (!walk.edgeIndexes.has(ei)) {\n          return;\n        }\n        const offset = (lane - (laneWalks.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        const curves = offset === 0 ? baseCurves : translateCurves(baseCurves, nx * offset, ny * offset / yToX);\n        if (inView(curves)) {\n          stroke(\n            curves,\n            laneWidth / 2,\n            walk.colors.get(edge.from) ?? walk.colors.get(edge.to) ?? plainEdgeColor\n          );\n        }\n      });\n      if (edgeCurves.length > edgeCurveStart) {\n        arrowOn(baseCurves);\n      }\n    } else if (!ribbons) {\n      if (inView(baseCurves)) {\n        stroke(baseCurves, edgeThickness, edgeColor);\n        arrowOn(baseCurves);\n      }\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      );\n      const arrowRibbon = Math.floor((numPaths - 1) / 2);\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const { x, y } = offsets[pathIdx];\n        const curves = x === 0 && y === 0 ? baseCurves : translateCurves(baseCurves, x, y);\n        if (!inView(curves)) {\n          continue;\n        }\n        const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);\n        stroke(\n          curves,\n          edgeThickness,\n          highlight && (highlight.walks.length ? !highlight.names.has(edge.pathIds[pathIdx]) : !onWalk) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor\n        );\n        if (pathIdx === arrowRibbon) {\n          arrowOn(curves);\n        }\n      }\n    }\n    const edgeCurveCount = edgeCurves.length - edgeCurveStart;\n    if (edgeCurveCount > 0) {\n      edgeCurveRuns.set(ei, { start: edgeCurveStart, count: edgeCurveCount });\n    }\n    const arrowCount = arrows.length - arrowStart;\n    if (arrowCount > 0) {\n      arrowRuns.set(ei, { start: arrowStart, count: arrowCount });\n    }\n  }\n  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId);\n    if (!node) {\n      continue;\n    }\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue;\n    }\n    const faded = highlight !== void 0 && !highlight.nodeIds.has(nodeId);\n    const own = faded ? LIFT_BACKDROP_COLOR : getNodeColor(\n      node,\n      nodeIndexMap.get(nodeId) ?? 0,\n      colorScheme,\n      colorRange\n    );\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);\n    const nodeThickness = width / 2;\n    const start = nodeStrokes.length;\n    const slots = nodePathSlots.get(nodeId);\n    const slotWidth = width / pathCount;\n    const drawable = segments.length >= 2;\n    const lanes = highlight?.walks.length && !faded && !slots?.length ? highlight.walks : void 0;\n    if (drawable && lanes) {\n      const laneWidth = Math.max(width / lanes.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(segments, yToX);\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      lanes.forEach((walk, lane) => {\n        const laneColor = walk.colors.get(nodeId);\n        if (laneColor === void 0) {\n          return;\n        }\n        const offset = (lane - (lanes.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        nodeStrokes.push({\n          points: lanes.length === 1 ? segments : offsetPolyline(segments, normals, offset, yToX),\n          thickness: laneWidth / 2,\n          color: laneColor\n        });\n      });\n    } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {\n      const normals = pointNormalsOf(segments, yToX);\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      for (const slot of slots) {\n        const offset = (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx;\n        const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR;\n        nodeStrokes.push({\n          points: offsetPolyline(segments, normals, offset, yToX),\n          thickness: slotWidth / 2,\n          // a node off the lifted walk fades whichever way it is painted\n          color: faded ? fadeAbgr(stripe, FADED_ALPHA) : stripe\n        });\n      }\n    } else if (drawable) {\n      nodeStrokes.push({ points: segments, thickness: nodeThickness, color });\n    }\n    const count = nodeStrokes.length - start;\n    if (count > 0) {\n      nodeStrokeRuns.set(nodeId, { start, count });\n    }\n  }\n  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns\n  };\n}\n\nexport {\n  LIFT_BACKDROP_COLOR,\n  FADED_ALPHA,\n  LIFT_BACKDROP_CSS,\n  hslToRgb,\n  REFERENCE_RAMP_MAX_HUE,\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_MAX_HUE,\n  hslToRgb\n} from \"./chunk-A4PFFC4Q.js\";\nimport {\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\n\n// src/walkEncoding.ts\nvar WALK_FIELDS = [\n  { value: \"progress\", label: \"Progress along the walk\" },\n  { value: \"walk\", label: \"One colour for the walk\" },\n  { value: \"reference\", label: \"Reference position\" }\n];\nvar WALK_SCHEMES = [\n  { value: \"grey\", label: \"Grey to black\", ends: [\"#a3a3a3\", \"#151515\"] },\n  { value: \"blue\", label: \"Cyan to navy\", ends: [\"#6ee0f0\", \"#0b2c7a\"] },\n  { value: \"red\", label: \"Yellow to red\", ends: [\"#ffd24a\", \"#b3121b\"] },\n  { value: \"purple\", label: \"Pink to plum\", ends: [\"#f5a3d8\", \"#5e1a6e\"] },\n  { value: \"green\", label: \"Lime to forest\", ends: [\"#b6e36c\", \"#0b5d3b\"] },\n  { value: \"rainbow\", label: \"Rainbow\" }\n];\nvar FAMILIES = [\"blue\", \"red\", \"purple\", \"green\"];\nvar isField = (v) => WALK_FIELDS.some((f) => f.value === v);\nvar isScheme = (v) => WALK_SCHEMES.some((s) => s.value === v);\nfunction resolveEncoding(layer, reference, picked, alone = true) {\n  const { field: askedField, scheme: askedScheme } = layer.color ?? {};\n  const field = isField(askedField) ? askedField : alone ? \"progress\" : \"walk\";\n  const family = reference ? \"grey\" : FAMILIES[picked % FAMILIES.length];\n  const scheme = isScheme(askedScheme) ? askedScheme === \"rainbow\" && field !== \"reference\" ? family : askedScheme : family;\n  return { field, scheme };\n}\nvar BASE_T = 0.5;\nvar toLinear = (c) => c <= 0.04045 ? c / 12.92 : ((c + 0.055) / 1.055) ** 2.4;\nvar toGamma = (c) => c <= 31308e-7 ? c * 12.92 : 1.055 * c ** (1 / 2.4) - 0.055;\nfunction oklab(hex) {\n  const [r, g, b] = [1, 3, 5].map(\n    (i) => toLinear(Number.parseInt(hex.slice(i, i + 2), 16) / 255)\n  );\n  const l = Math.cbrt(0.4122214708 * r + 0.5363325363 * g + 0.0514459929 * b);\n  const m = Math.cbrt(0.2119034982 * r + 0.6806995451 * g + 0.1073969566 * b);\n  const s = Math.cbrt(0.0883024619 * r + 0.2817188376 * g + 0.6299787005 * b);\n  return [\n    0.2104542553 * l + 0.793617785 * m - 0.0040720468 * s,\n    1.9779984951 * l - 2.428592205 * m + 0.4505937099 * s,\n    0.0259040371 * l + 0.7827717662 * m - 0.808675766 * s\n  ];\n}\nfunction oklabToRgb([L, a, b]) {\n  const l = (L + 0.3963377774 * a + 0.2158037573 * b) ** 3;\n  const m = (L - 0.1055613458 * a - 0.0638541728 * b) ** 3;\n  const s = (L - 0.0894841775 * a - 1.291485548 * b) ** 3;\n  return [\n    4.0767416621 * l - 3.3077115913 * m + 0.2309699292 * s,\n    -1.2684380046 * l + 2.6097574011 * m - 0.3413193965 * s,\n    -0.0041960863 * l - 0.7034186147 * m + 1.707614701 * s\n  ].map((c) => toGamma(Math.max(0, Math.min(1, c))) * 255);\n}\nfunction schemeRgb(scheme, t) {\n  const x = Math.max(0, Math.min(1, t));\n  const family = WALK_SCHEMES.find((s) => s.value === scheme);\n  if (!family || !(\"ends\" in family)) {\n    return hslToRgb(x * REFERENCE_RAMP_MAX_HUE, 0.7, 0.5).map((c) => c * 255);\n  }\n  const from = oklab(family.ends[0]);\n  const to = oklab(family.ends[1]);\n  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x));\n}\nfunction schemeCss(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return `rgb(${r}, ${g}, ${b})`;\n}\nfunction schemeColor(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return packAbgr(r, g, b, 255);\n}\nfunction encodedColor({ field, scheme }, t) {\n  return field === \"walk\" ? schemeColor(scheme, BASE_T) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, t);\n}\nvar NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;\nfunction encodingStops({ field, scheme }) {\n  return field === \"walk\" ? [{ offset: 0, color: schemeCss(scheme, BASE_T) }] : Array.from({ length: 7 }, (_, i) => ({\n    offset: i / 6,\n    color: schemeCss(scheme, i / 6)\n  }));\n}\nfunction encodingSwatchCss(encoding) {\n  const stops = encodingStops(encoding);\n  return stops.length === 1 ? stops[0].color : `linear-gradient(to right, ${stops.map((s) => `${s.color} ${s.offset * 100}%`).join(\", \")})`;\n}\n\nexport {\n  WALK_FIELDS,\n  WALK_SCHEMES,\n  resolveEncoding,\n  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\n};\n"],
   "mappings": 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package/dist/chunks/chunk-FVK2THE4.js

@@ -0,0 +1,2 @@
+import{a as pe,c as me,d as de}from"./chunk-ZMOMFU2B.js";var J=1,be=2,$=4;function We(s,a,c){return c?{...s,walkRowRuns:ke(s,a)}:s}function Re(s){let a=pe(s),c=me(s);return{name:s,sample:a,haplotype:c===void 0?void 0:+c.slice(a.length+1),contig:de(s)}}var K=class{constructor(){this.start=[];this.bp=[];this.referenceStart=[];this.flags=[];this.offsets=[0]}get length(){return this.bp.length}push(a,c,d,R){this.start.push(a),this.bp.push(c),this.flags.push(d),this.referenceStart.push(R)}endRow(){this.offsets.push(this.bp.length)}};function ke({nodes:s,walks:a},c){let d=s.lengths.length,R=e=>e<d?s.lengths[e]:0,S=[];for(let e=0;e<a.names.length;e++)a.offsets[e+1]>a.offsets[e]&&S.push({...Re(a.names[e]),start:a.starts[e],from:a.offsets[e],to:a.offsets[e+1]});let A=S.filter(e=>e.name===S[0]?.name).sort((e,n)=>e.start-n.start),D=A[0],Q=S.filter(e=>e.name!==D?.name);if(!D||Q.length===0)return;let H=new Map;for(let e of Q){let n=H.get(e.name);n?n.push(e):H.set(e.name,[e])}let m=new Float64Array(s.names.length).fill(Number.NaN),F=new Float64Array(s.names.length),X=!1,Y=!1,b=c&&c.end>c.start?c:void 0;for(let e of A){let n=e.start;for(let w=e.from;w<e.to;w++){let g=a.steps[w],o=R(g);Number.isNaN(m[g])&&(m[g]=n,F[g]=n+o,b&&(X||=n+o<=b.start,Y||=n>=b.end)),n+=o}}let he=b===void 0||X&&Y,u=new K,h=new Int32Array(0),k=new Float64Array(0),Z=e=>{let n=e[0],w=[...e].sort((t,r)=>t.start-r.start),g=w.length-1;for(let t of w)g+=t.to-t.from;g>h.length&&(h=new Int32Array(g*2),k=new Float64Array(g*2));let o=0,oe=!1,W;for(let t of w){W!==void 0&&t.start<W&&(oe=!0),W!==void 0&&t.start>W&&(h[o]=-(t.start-W),k[o++]=W);let r=t.start;for(let l=t.from;l<t.to;l++){let f=a.steps[l];h[o]=f,k[o++]=r,r+=f<d?s.lengths[f]:0}W=r}let we=(t,r)=>{let l=t>=0?t:r,f=-1;for(let _=1;f<0&&_<o;_++)for(let j of[l-_,l+_]){let ue=j>=0&&j<o?h[j]:-1;f<0&&ue>=0&&!Number.isNaN(m[ue])&&(f=j)}if(f<0)return;let i=f>l==m[h[f]]>m[h[l]],p=i===(l===t),I=p?o-1:0,y=h[I],B=y>=0&&!Number.isNaN(m[y]);return{stop:{contigEnds:B,shortBp:B?Math.max(0,b.start-F[y],m[y]-b.end):0},lo:p?l+1:0,hi:p?o:l,backward:!i,axisStart:i?p?V(l):k[0]:p?V(o-1):k[l]}},V=t=>{let r=h[t];return k[t]+(r<0?-r:R(r))},O=0,T=o,G=!1,le=!0,P=-1,fe=-1,q,z;if(b&&he){let t=-1,r=-1,l=-1/0,f=1/0;for(let i=0;i<o;i++){let p=h[i];p>=0&&!Number.isNaN(m[p])&&(F[p]<=b.start&&F[p]>l&&(l=F[p],t=i),m[p]>=b.end&&m[p]<f&&(f=m[p],r=i))}if(t<0||r<0){le=!1;let i=t>=0||r>=0?we(t,r):void 0;i&&({lo:O,hi:T,backward:G,axisStart:q,stop:z}=i)}else O=Math.min(t,r)+1,T=Math.max(t,r),G=t>r,P=t,fe=r}let Ne=oe||o===0?void 0:q!==void 0?{contig:n.contig,start:q,reversed:G}:P<0?{contig:n.contig,start:k[0],reversed:!1}:P<fe?{contig:n.contig,start:V(P),reversed:!1}:{contig:n.contig,start:k[P],reversed:!0},v=0,ie=0,ce=0,M=0,N=-1,x=0,U=Number.NaN;for(let t=O;t<T;t++){let r=h[G?T-1-(t-O):t];if(r<0){u.push(v,-r,$,Number.NaN),N=u.length-1,x=$,U=Number.NaN,v+=-r,ce+=-r,M=0;continue}let l=R(r),f=m[r],i=!Number.isNaN(f),p=U,I=N>=0&&!Number.isNaN(p),y=i&&I&&M>=0&&p+(u.bp[N]??0)===f,B=i&&I&&M<=0&&F[r]===p;!i&&N>=0&&!(x&J)&&!(x&$)?u.bp[N]+=l:y||B?(u.bp[N]+=l,y||(U=f,u.referenceStart[N]=f,x|=be,u.flags[N]=x),M=y?1:-1):(x=i?J:0,U=i?f:Number.NaN,u.push(v,l,x,U),N=u.length-1,M=0),v+=l,i||(ie+=l)}return u.endRow(),{name:n.name,label:n.haplotype===void 0?n.sample:`${n.sample}#${n.haplotype}`,sample:n.sample,haplotype:n.haplotype,bp:v,offReferenceBp:ie,gapBp:ce,complete:le,...z?{stop:z}:{},axis:Ne}},ge=Z(A),L=[...H.values()].map(e=>({meta:Z(e),row:u.offsets.length-2}));L.sort((e,n)=>Number(n.meta.complete)-Number(e.meta.complete)||n.meta.bp-e.meta.bp||e.meta.label.localeCompare(n.meta.label));let ee=[0,...L.map(e=>e.row)],C=u.length,te=new Uint32Array(ee.length+1),ne=new Float64Array(C),re=new Float64Array(C),se=new Float64Array(C),ae=new Uint8Array(C),E=0;return ee.forEach((e,n)=>{let w=u.offsets[e],g=u.offsets[e+1];for(let o=w;o<g;o++,E++)ne[E]=u.start[o],re[E]=u.bp[o],se[E]=u.referenceStart[o],ae[E]=u.flags[o];te[n+1]=E}),{origin:b?b.start:D.start,rows:[ge,...L.map(e=>e.meta)],offsets:te,start:ne,bp:re,referenceStart:se,flags:ae}}function ye(s,a){let c=s.flags[a],d={start:s.start[a],bp:s.bp[a],onReference:(c&J)!==0};return c&$?d.gap=!0:d.referenceStart=Number.isNaN(s.referenceStart[a])?void 0:s.referenceStart[a],c&be&&(d.reversed=!0),d}function xe(s,a){let c=s.rows.map((d,R)=>{let S=[];for(let A=s.offsets[R];A<s.offsets[R+1];A++)S.push(ye(s,A));return{...d,runs:S}});return{origin:s.origin,unit:a,reference:c[0],rows:c.slice(1)}}export{We as a,Re as b,ke as c,xe as d};
+//# sourceMappingURL=chunk-FVK2THE4.js.map

package/dist/chunks/chunk-FVK2THE4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/RgfaTabixAdapter/walkRowRuns.ts"],
+  "sourcesContent": ["import {\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from '@jbrowse/bandage-core/pansn'\n\nimport type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'\nimport type {\n  WalkAxis,\n  WalkRow,\n  WalkRows,\n  WalkRun,\n  WalkStop,\n} from '@jbrowse/bandage-core/layout/walkRows'\n\nconst RUN_ON_REFERENCE = 1\nconst RUN_REVERSED = 2\nconst RUN_GAP = 4\n\ntype WalkRowMeta = Omit<WalkRow, 'runs'>\n\n/**\n * A cut for walk rows: the tables, and the rows' runs over the window, which\n * the main thread draws without a Graph of the walks' steps\n */\nexport type WalkCut = GraphTables & { walkRowRuns?: WalkRowRuns }\n\nexport function walkCutFor(\n  tables: GraphTables,\n  region: { start: number; end: number },\n  walkRows: boolean | undefined,\n): WalkCut {\n  return walkRows\n    ? { ...tables, walkRowRuns: walkRowRuns(tables, region) }\n    : tables\n}\n\n/**\n * bandage-core's `walkRows` over a cut's tables, each row's runs as typed\n * arrays that cross from the worker beside the tables. Row 0 is the\n * reference.\n */\nexport interface WalkRowRuns {\n  origin: number\n  rows: WalkRowMeta[]\n  offsets: Uint32Array\n  start: Float64Array\n  bp: Float64Array\n  referenceStart: Float64Array\n  flags: Uint8Array\n}\n\n/**\n * A walk's PanSN fields: `HG002#1#chr1`, or a pggb P-line's `chm13#chr1`,\n * which has no haplotype\n */\nexport function walkPath(name: string) {\n  const sample = panSNSample(name)\n  const haplotype = panSNHaplotype(name)\n  return {\n    name,\n    sample,\n    haplotype:\n      haplotype === undefined ? undefined : +haplotype.slice(sample.length + 1),\n    contig: panSNContig(name),\n  }\n}\n\ntype Path = ReturnType<typeof walkPath> & {\n  start: number\n  from: number\n  to: number\n}\n\nclass RunWriter {\n  start: number[] = []\n  bp: number[] = []\n  referenceStart: number[] = []\n  flags: number[] = []\n  offsets = [0]\n\n  get length() {\n    return this.bp.length\n  }\n\n  push(start: number, bp: number, flags: number, referenceStart: number) {\n    this.start.push(start)\n    this.bp.push(bp)\n    this.flags.push(flags)\n    this.referenceStart.push(referenceStart)\n  }\n\n  endRow() {\n    this.offsets.push(this.bp.length)\n  }\n}\n\n/**\n * `walkRows(graphFromTables(tables), region)` for a cut whose first walk is\n * the reference, which every walk-file and GBZ cut is, in as many pieces as\n * the cut breaks it into; a step is a node index. A gap between two pieces of\n * one haplotype is a step of `-bp`. Two differences: a walk reaching only one of the region's flanks measures from\n * that flank, where walkRows takes the whole walk the cut holds, so its length\n * is a lower bound that no longer grows with the cut's context; and a row\n * keeps its walk's name whole, where graphFromTables reads a two-part name\n * (`chm13#chr1`) as a haplotype `chr1` with no contig.\n */\nexport function walkRowRuns(\n  { nodes: n, walks: w }: GraphTables,\n  region?: { start: number; end: number },\n): WalkRowRuns | undefined {\n  const declared = n.lengths.length\n  const lengthOf = (node: number) => (node < declared ? n.lengths[node]! : 0)\n  const paths: Path[] = []\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1]! > w.offsets[p]!) {\n      paths.push({\n        ...walkPath(w.names[p]!),\n        start: w.starts[p]!,\n        from: w.offsets[p]!,\n        to: w.offsets[p + 1]!,\n      })\n    }\n  }\n  const referencePieces = paths\n    .filter(p => p.name === paths[0]?.name)\n    .sort((a, b) => a.start - b.start)\n  const first = referencePieces[0]\n  const others = paths.filter(p => p.name !== first?.name)\n  if (!first || others.length === 0) {\n    return undefined\n  }\n  const walks = new Map<string, Path[]>()\n  for (const path of others) {\n    const list = walks.get(path.name)\n    if (list) {\n      list.push(path)\n    } else {\n      walks.set(path.name, [path])\n    }\n  }\n\n  const spanStart = new Float64Array(n.names.length).fill(Number.NaN)\n  const spanEnd = new Float64Array(n.names.length)\n  let flankedBefore = false\n  let flankedAfter = false\n  const cut = region && region.end > region.start ? region : undefined\n  for (const piece of referencePieces) {\n    let pos = piece.start\n    for (let s = piece.from; s < piece.to; s++) {\n      const node = w.steps[s]!\n      const len = lengthOf(node)\n      if (Number.isNaN(spanStart[node]!)) {\n        spanStart[node] = pos\n        spanEnd[node] = pos + len\n        if (cut) {\n          flankedBefore ||= pos + len <= cut.start\n          flankedAfter ||= pos >= cut.end\n        }\n      }\n      pos += len\n    }\n  }\n  const flanked = cut === undefined || (flankedBefore && flankedAfter)\n\n  const out = new RunWriter()\n  let steps = new Int32Array(0)\n  let stepStart = new Float64Array(0)\n  const rowOf = (pieces: Path[]): WalkRowMeta => {\n    const path = pieces[0]!\n    const ordered = [...pieces].sort((a, b) => a.start - b.start)\n    // the walk's steps, each piece's gap from the last as a step of -bp\n    let count = ordered.length - 1\n    for (const piece of ordered) {\n      count += piece.to - piece.from\n    }\n    if (count > steps.length) {\n      steps = new Int32Array(count * 2)\n      stepStart = new Float64Array(count * 2)\n    }\n    let length = 0\n    let overlaps = false\n    let end: number | undefined\n    for (const piece of ordered) {\n      if (end !== undefined && piece.start < end) {\n        overlaps = true\n      }\n      if (end !== undefined && piece.start > end) {\n        steps[length] = -(piece.start - end)\n        stepStart[length++] = end\n      }\n      let pos = piece.start\n      for (let s = piece.from; s < piece.to; s++) {\n        const node = w.steps[s]!\n        steps[length] = node\n        stepStart[length++] = pos\n        pos += node < declared ? n.lengths[node]! : 0\n      }\n      end = pos\n    }\n    // A walk with one flank, whose contig ends inside the window: the steps\n    // past that flank, read in the reference's direction. Which side is\n    // inside follows the walk's direction along the reference at the\n    // flank, from the nearest other step on it.\n    const partialSide = (i0: number, i1: number) => {\n      const flank = i0 >= 0 ? i0 : i1\n      let near = -1\n      for (let d = 1; near < 0 && d < length; d++) {\n        for (const j of [flank - d, flank + d]) {\n          const id = j >= 0 && j < length ? steps[j]! : -1\n          if (near < 0 && id >= 0 && !Number.isNaN(spanStart[id]!)) {\n            near = j\n          }\n        }\n      }\n      if (near < 0) {\n        return undefined\n      }\n      const forward =\n        near > flank === spanStart[steps[near]!]! > spanStart[steps[flank]!]!\n      const after = forward === (flank === i0)\n      const end = after ? length - 1 : 0\n      const endId = steps[end]!\n      const contigEnds = endId >= 0 && !Number.isNaN(spanStart[endId]!)\n      const stop: WalkStop = {\n        contigEnds,\n        shortBp: contigEnds\n          ? Math.max(\n              0,\n              cut!.start - spanEnd[endId]!,\n              spanStart[endId]! - cut!.end,\n            )\n          : 0,\n      }\n      return {\n        stop,\n        lo: after ? flank + 1 : 0,\n        hi: after ? length : flank,\n        backward: !forward,\n        axisStart: forward\n          ? after\n            ? stepEnd(flank)\n            : stepStart[0]!\n          : after\n            ? stepEnd(length - 1)\n            : stepStart[flank]!,\n      }\n    }\n    const stepEnd = (i: number) => {\n      const id = steps[i]!\n      return stepStart[i]! + (id < 0 ? -id : lengthOf(id))\n    }\n\n    let lo = 0\n    let hi = length\n    let backward = false\n    let complete = true\n    let from = -1\n    let to = -1\n    let axisStart: number | undefined\n    let stop: WalkStop | undefined\n    if (cut && flanked) {\n      let i0 = -1\n      let i1 = -1\n      let bestEnd = -Infinity\n      let bestStart = Infinity\n      for (let i = 0; i < length; i++) {\n        const id = steps[i]!\n        if (id >= 0 && !Number.isNaN(spanStart[id]!)) {\n          if (spanEnd[id]! <= cut.start && spanEnd[id]! > bestEnd) {\n            bestEnd = spanEnd[id]!\n            i0 = i\n          }\n          if (spanStart[id]! >= cut.end && spanStart[id]! < bestStart) {\n            bestStart = spanStart[id]!\n            i1 = i\n          }\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        complete = false\n        const inside = i0 >= 0 || i1 >= 0 ? partialSide(i0, i1) : undefined\n        if (inside) {\n          ;({ lo, hi, backward, axisStart, stop } = inside)\n        }\n      } else {\n        lo = Math.min(i0, i1) + 1\n        hi = Math.max(i0, i1)\n        backward = i0 > i1\n        from = i0\n        to = i1\n      }\n    }\n    const axis: WalkAxis | undefined =\n      overlaps || length === 0\n        ? undefined\n        : axisStart !== undefined\n          ? { contig: path.contig, start: axisStart, reversed: backward }\n          : from < 0\n            ? { contig: path.contig, start: stepStart[0]!, reversed: false }\n            : from < to\n              ? { contig: path.contig, start: stepEnd(from), reversed: false }\n              : { contig: path.contig, start: stepStart[from]!, reversed: true }\n\n    let bp = 0\n    let offReferenceBp = 0\n    let gapBp = 0\n    let step = 0\n    let lastAt = -1\n    let lastFlags = 0\n    let lastRef = Number.NaN\n    for (let k = lo; k < hi; k++) {\n      const id = steps[backward ? hi - 1 - (k - lo) : k]!\n      if (id < 0) {\n        out.push(bp, -id, RUN_GAP, Number.NaN)\n        lastAt = out.length - 1\n        lastFlags = RUN_GAP\n        lastRef = Number.NaN\n        bp += -id\n        gapBp += -id\n        step = 0\n        continue\n      }\n      const len = lengthOf(id)\n      const sStart = spanStart[id]!\n      const onRef = !Number.isNaN(sStart)\n      const at = lastRef\n      const hasAt = lastAt >= 0 && !Number.isNaN(at)\n      const forward =\n        onRef && hasAt && step >= 0 && at + (out.bp[lastAt] ?? 0) === sStart\n      const back = onRef && hasAt && step <= 0 && spanEnd[id] === at\n      if (\n        !onRef &&\n        lastAt >= 0 &&\n        !(lastFlags & RUN_ON_REFERENCE) &&\n        !(lastFlags & RUN_GAP)\n      ) {\n        out.bp[lastAt]! += len\n      } else if (forward || back) {\n        out.bp[lastAt]! += len\n        if (!forward) {\n          lastRef = sStart\n          out.referenceStart[lastAt] = sStart\n          lastFlags |= RUN_REVERSED\n          out.flags[lastAt] = lastFlags\n        }\n        step = forward ? 1 : -1\n      } else {\n        lastFlags = onRef ? RUN_ON_REFERENCE : 0\n        lastRef = onRef ? sStart : Number.NaN\n        out.push(bp, len, lastFlags, lastRef)\n        lastAt = out.length - 1\n        step = 0\n      }\n      bp += len\n      if (!onRef) {\n        offReferenceBp += len\n      }\n    }\n    out.endRow()\n    return {\n      name: path.name,\n      label:\n        path.haplotype === undefined\n          ? path.sample\n          : `${path.sample}#${path.haplotype}`,\n      sample: path.sample,\n      haplotype: path.haplotype,\n      bp,\n      offReferenceBp,\n      gapBp,\n      complete,\n      ...(stop ? { stop } : {}),\n      axis,\n    }\n  }\n\n  const reference = rowOf(referencePieces)\n  const rowList = [...walks.values()].map(pieces => ({\n    meta: rowOf(pieces),\n    row: out.offsets.length - 2,\n  }))\n  rowList.sort(\n    (a, b) =>\n      Number(b.meta.complete) - Number(a.meta.complete) ||\n      b.meta.bp - a.meta.bp ||\n      a.meta.label.localeCompare(b.meta.label),\n  )\n  // rows in drawn order: the reference, then the sorted walks\n  const order = [0, ...rowList.map(r => r.row)]\n  const total = out.length\n  const offsets = new Uint32Array(order.length + 1)\n  const start = new Float64Array(total)\n  const bpOut = new Float64Array(total)\n  const referenceStart = new Float64Array(total)\n  const flags = new Uint8Array(total)\n  let at = 0\n  order.forEach((row, i) => {\n    const a = out.offsets[row]!\n    const b = out.offsets[row + 1]!\n    for (let k = a; k < b; k++, at++) {\n      start[at] = out.start[k]!\n      bpOut[at] = out.bp[k]!\n      referenceStart[at] = out.referenceStart[k]!\n      flags[at] = out.flags[k]!\n    }\n    offsets[i + 1] = at\n  })\n  return {\n    origin: cut ? cut.start : first.start,\n    rows: [reference, ...rowList.map(r => r.meta)],\n    offsets,\n    start,\n    bp: bpOut,\n    referenceStart,\n    flags,\n  }\n}\n\nfunction runAt(t: WalkRowRuns, k: number): WalkRun {\n  const f = t.flags[k]!\n  const run: WalkRun = {\n    start: t.start[k]!,\n    bp: t.bp[k]!,\n    onReference: (f & RUN_ON_REFERENCE) !== 0,\n  }\n  if (f & RUN_GAP) {\n    run.gap = true\n  } else {\n    run.referenceStart = Number.isNaN(t.referenceStart[k]!)\n      ? undefined\n      : t.referenceStart[k]\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true\n  }\n  return run\n}\n\n/** The rows as bandage-core's `WalkRows`, a run object per run */\nexport function walkRowsOf(t: WalkRowRuns, unit?: number): WalkRows {\n  const rows = t.rows.map((meta, i) => {\n    const runs: WalkRun[] = []\n    for (let k = t.offsets[i]!; k < t.offsets[i + 1]!; k++) {\n      runs.push(runAt(t, k))\n    }\n    return { ...meta, runs }\n  })\n  return { origin: t.origin, unit, reference: rows[0]!, rows: rows.slice(1) }\n}\n"],
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+  "names": ["RUN_ON_REFERENCE", "RUN_REVERSED", "RUN_GAP", "walkCutFor", "tables", "region", "walkRows", "walkRowRuns", "walkPath", "name", "sample", "panSNSample", "haplotype", "panSNHaplotype", "panSNContig", "RunWriter", "start", "bp", "flags", "referenceStart", "n", "w", "declared", "lengthOf", "node", "paths", "p", "referencePieces", "a", "b", "first", "others", "walks", "path", "list", "spanStart", "spanEnd", "flankedBefore", "flankedAfter", "cut", "piece", "pos", "s", "len", "flanked", "out", "steps", "stepStart", "rowOf", "pieces", "ordered", "count", "length", "overlaps", "end", "partialSide", "i0", "i1", "flank", "near", "d", "id", "forward", "after", "endId", "contigEnds", "stepEnd", "i", "lo", "hi", "backward", "complete", "from", "to", "axisStart", "stop", "bestEnd", "bestStart", "inside", "axis", "offReferenceBp", "gapBp", "step", "lastAt", "lastFlags", "lastRef", "k", "sStart", "onRef", "at", "hasAt", "back", "reference", "rowList", "order", "r", "total", "offsets", "bpOut", "row", "runAt", "t", "f", "run", "walkRowsOf", "unit", "rows", "meta", "runs"]
+}

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package/dist/chunks/chunk-MND7GAOG.js.map

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+{
+  "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 './walkRowRuns.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 }: 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    })\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, opts),\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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+  "names": ["BUDGET_SLOTS", "WalkIndex", "file", "adapter", "WalkReader", "opts", "haplotypes", "refName", "region", "signal", "walkRows", "budgets", "graph", "kept", "fragments", "walksKept", "lane", "resolvePanSNPrefix", "walkCutFor", "refRows", "getLines", "line", "cols", "seen", "referenceNodes", "node"]
+}

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