jbrowse-plugin-graphgenomeviewer 7.4.4 → 7.6.0

package/dist/chunks/{WalkTabixSyntenyAdapter-3WRVNDLB.js.map → WalkTabixSyntenyAdapter-JFNFX3JP.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
-  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type { WalkFragment, WalkNode } from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  return (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return { same, opposite }\n  }\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport { anchorAligner, chainFeature, lanePairAligner } from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { WalkFragment } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n    this,\n  )\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.file,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolve(region, { signal: opts.signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes.\n  // Named lanes come back in full where format 5 abridged them: an abridged\n  // walk is two reference steps, which drew 15 of the HPRC MHC launch's 32\n  // lanes empty.\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    const keep = walksKept(prefixes, refName)\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep,\n          expand: keep,\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneAssemblyName(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
-  "mappings": 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+  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type { WalkFragment, WalkNode } from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  return (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return { same, opposite }\n  }\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport { anchorAligner, chainFeature, lanePairAligner } from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { WalkFragment } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n    this,\n  )\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.file,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolveForCut(region, {\n      signal: opts.signal,\n    })\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes.\n  // Named lanes come back in full where format 5 abridged them: an abridged\n  // walk is two reference steps, which drew 15 of the HPRC MHC launch's 32\n  // lanes empty.\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    const keep = walksKept(prefixes, refName)\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep,\n          expand: keep,\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneAssemblyName(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
+  "mappings": 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 }

package/dist/chunks/{chunk-KIYRMZWP.js → chunk-2CPD5NX2.js}

@@ -1,4 +1,4 @@
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+import{a as I,b as L,f as S,h as w}from"./chunk-G4OPM6G7.js";import{p as T}from"./chunk-ZFJGNGIB.js";var O=62,Z=60,G=9,k=48,z=57,_=/^(?:LN:i|SN:Z|SO:i|SR:i):/,q=/^[PEOUFG]\t/,C=e=>e.endsWith("\r")?e.slice(0,-1):e;function P(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var R=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(e){return this.byName.has(e)}add(e){let s=this.names.length;this.byName.set(e,s),this.names.push(e);let t=+e;return Number.isSafeInteger(t)&&String(t)===e&&this.byNumber.set(t,s),s}of(e){return this.byName.get(e)??this.add(e)}ofNumber(e){return this.byNumber.get(e)}};function U(e){let[,s,t="*",...r]=e.split("	");if(!s||/^\d+$/.test(t))return;let i=t==="*"?0:t.length,n,f,o;for(let c of r){if(!_.test(c))return;let a=c.slice(5),p=c.slice(0,2);p==="LN"?i=+a:p==="SN"?n=a:p==="SO"?f=+a:o=+a}return{name:s,length:i,stable:n!==void 0&&f!==void 0&&o!==void 0?{refName:n,start:f,rank:o}:void 0}}function $(e,s,t,r){let i=0,n=-1,f=0,o=!0,d=a=>{if(n>=0&&a>n){let p=o&&a-n<16&&(a-n===1||e.charCodeAt(n)!==k)?t.ofNumber(f):void 0;r.nodes.push(p??t.of(e.slice(n,a))),r.reversed.push(i)}},c=s;for(;c<e.length;c++){let a=e.charCodeAt(c);if(a===O||a===Z)d(c),i=a===Z?1:0,n=c+1,f=0,o=!0;else{if(a===G)break;o&&a>=k&&a<=z?f=f*10+a-k:o=!1}}return d(c),c}function x(e){let s=[],t=0;for(;s.length<6;){let d=e.indexOf("	",t);if(d===-1)return;s.push(e.slice(t,d)),t=d+1}let[,r,i,n,f,o]=s;return r&&i&&n&&f&&o&&t<e.length?{sample:r,haplotype:i,contig:n,start:f,end:o,body:t}:void 0}function K(e){let s=e.split(`
 `),t=new R,r=[],i=[],n=[],f=[],o=[],d=new Map;for(let u of s){if(q.test(u))return;if(u.startsWith("S	")){let l=U(C(u));if(!l||t.has(l.name))return;t.add(l.name),r.push(l.length);let h=-1;l.stable&&(h=d.get(l.stable.refName)??o.length,h===o.length&&(o.push(l.stable.refName),d.set(l.stable.refName,h))),i.push(h),n.push(l.stable?.start??0),f.push(l.stable?.rank??0)}}let c=[],a=[],p=[],v=[],E=[],W=[],y=[0],g=P(),A=new w,N=new w;for(let u of s)if(u.startsWith("L	")){let[,l,h,b,m]=C(u).split("	");l&&b&&m&&(c.push(t.of(l)),a.push(t.of(b)),p.push((h==="-"?1:0)|(m==="-"?2:0)))}else if(u.startsWith("W	")){let l=C(u),h=x(l);if(h){v.push(`${h.sample}#${h.haplotype}#${h.contig}`),E.push(h.start==="*"?0:+h.start),W.push(h.end==="*"?-1:+h.end);let b=$(l,h.body,t,g),m=F(l,b);if(m===void 0||(m.before&&A.push(m.before),m.after&&N.push(m.after),g.nodes.length===y.at(-1)))return;y.push(g.nodes.length)}}if(![A.kinds.length,N.kinds.length].some(u=>u>0&&u<v.length))return{nodes:{names:t.names,lengths:Int32Array.from(r),refs:Int32Array.from(i),starts:Float64Array.from(n),ranks:Int32Array.from(f),refNames:o},links:{from:Int32Array.from(c),to:Int32Array.from(a),strands:Uint8Array.from(p)},walks:{names:v,starts:Float64Array.from(E),ends:Float64Array.from(W),offsets:Int32Array.from(y),steps:g.nodes.data.slice(0,g.nodes.length),reversed:g.reversed.data.slice(0,g.reversed.length),...B(v.length,A,N)}}}function F(e,s){let t={};for(let r of s<e.length?e.slice(s+1).split("	"):[]){let i=r.slice(5);if(r.startsWith(`${I}:Z:`)){if(t.before=S(i),!t.before)return}else if(r.startsWith(`${L}:Z:`)&&(t.after=S(i),!t.after))return}return t}function B(e,s,t){return{...s.kinds.length===e&&e>0?{before:s.table()}:{},...t.kinds.length===e&&e>0?{after:t.table()}:{}}}var D=/([><])([^><]+)/g;function M(e){if(!e.startsWith(">")&&!e.startsWith("<"))return;let s=[];for(let[,t,r]of e.matchAll(D))s.push({name:r,strand:t===">"?"+":"-"});return s}function Q(e){let s=e.trimEnd(),t=s.split("	");if(t.length<12||s.startsWith("#"))return;let r=M(t[5]);if(!r)return;let i,n=!1;for(let f=12;f<t.length;f++){let o=t[f];o.startsWith("cs:Z:")?i=o.slice(5):o==="tp:A:S"&&(n=!0)}return{name:t[0],queryLength:+t[1],queryStart:+t[2],queryEnd:+t[3],strand:t[4]==="-"?"-":"+",path:r,pathLength:+t[6],pathStart:+t[7],pathEnd:+t[8],matches:+t[9],blockLength:+t[10],mappingQuality:+t[11],secondary:n,...i===void 0?{}:{cs:i}}}function Y(e){let s=[];for(let t of e.split(`
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-//# sourceMappingURL=chunk-KIYRMZWP.js.map
+//# sourceMappingURL=chunk-2CPD5NX2.js.map

package/dist/chunks/{chunk-KIYRMZWP.js.map → chunk-2CPD5NX2.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.14.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VSSIYQYF.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.14.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
   "sourcesContent": ["import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  Column\n} from \"./chunk-ZPZ7GNBT.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? this.add(name);\n  }\n  ofNumber(n) {\n    return this.byNumber.get(n);\n  }\n};\nfunction readSegment(line) {\n  const [, name, sequence = \"*\", ...tags] = line.split(\"\t\");\n  if (!name || /^\\d+$/.test(sequence)) {\n    return void 0;\n  }\n  let length = sequence === \"*\" ? 0 : sequence.length;\n  let refName;\n  let start;\n  let rank;\n  for (const tag of tags) {\n    if (!TABLE_TAG.test(tag)) {\n      return void 0;\n    }\n    const value = tag.slice(5);\n    const key = tag.slice(0, 2);\n    if (key === \"LN\") {\n      length = +value;\n    } else if (key === \"SN\") {\n      refName = value;\n    } else if (key === \"SO\") {\n      start = +value;\n    } else {\n      rank = +value;\n    }\n  }\n  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;\n  return { name, length, stable };\n}\nfunction readWalkBody(line, from, segments, steps) {\n  let reversed = 0;\n  let start = -1;\n  let value = 0;\n  let decimal = true;\n  const finish = (end) => {\n    if (start >= 0 && end > start) {\n      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? segments.ofNumber(value) : void 0;\n      steps.nodes.push(node ?? segments.of(line.slice(start, end)));\n      steps.reversed.push(reversed);\n    }\n  };\n  let i = from;\n  for (; i < line.length; i++) {\n    const ch = line.charCodeAt(i);\n    if (ch === GT || ch === LT) {\n      finish(i);\n      reversed = ch === LT ? 1 : 0;\n      start = i + 1;\n      value = 0;\n      decimal = true;\n    } else if (ch === TAB) {\n      break;\n    } else if (decimal && ch >= ZERO && ch <= NINE) {\n      value = value * 10 + ch - ZERO;\n    } else {\n      decimal = false;\n    }\n  }\n  finish(i);\n  return i;\n}\nfunction walkFields(line) {\n  const fields = [];\n  let at = 0;\n  while (fields.length < 6) {\n    const tab = line.indexOf(\"\t\", at);\n    if (tab === -1) {\n      return void 0;\n    }\n    fields.push(line.slice(at, tab));\n    at = tab + 1;\n  }\n  const [, sample, haplotype, contig, start, end] = fields;\n  return sample && haplotype && contig && start && end && at < line.length ? { sample, haplotype, contig, start, end, body: at } : void 0;\n}\nfunction gfaTables(text) {\n  const lines = text.split(\"\\n\");\n  const segments = new SegmentIndex();\n  const lengths = [];\n  const refs = [];\n  const starts = [];\n  const ranks = [];\n  const refNames = [];\n  const refIndex = /* @__PURE__ */ new Map();\n  for (const raw of lines) {\n    if (UNTABLED_RECORD.test(raw)) {\n      return void 0;\n    }\n    if (raw.startsWith(\"S\t\")) {\n      const s = readSegment(trimCR(raw));\n      if (!s || segments.has(s.name)) {\n        return void 0;\n      }\n      segments.add(s.name);\n      lengths.push(s.length);\n      let ref = -1;\n      if (s.stable) {\n        ref = refIndex.get(s.stable.refName) ?? refNames.length;\n        if (ref === refNames.length) {\n          refNames.push(s.stable.refName);\n          refIndex.set(s.stable.refName, ref);\n        }\n      }\n      refs.push(ref);\n      starts.push(s.stable?.start ?? 0);\n      ranks.push(s.stable?.rank ?? 0);\n    }\n  }\n  const from = [];\n  const to = [];\n  const strands = [];\n  const names = [];\n  const walkStarts = [];\n  const walkEnds = [];\n  const offsets = [0];\n  const steps = stepColumns();\n  const before = new StopColumns();\n  const after = new StopColumns();\n  for (const raw of lines) {\n    if (raw.startsWith(\"L\t\")) {\n      const [, source, strand1, target, strand2] = trimCR(raw).split(\"\t\");\n      if (source && target && strand2) {\n        from.push(segments.of(source));\n        to.push(segments.of(target));\n        strands.push((strand1 === \"-\" ? 1 : 0) | (strand2 === \"-\" ? 2 : 0));\n      }\n    } else if (raw.startsWith(\"W\t\")) {\n      const line = trimCR(raw);\n      const w = walkFields(line);\n      if (w) {\n        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);\n        walkStarts.push(w.start === \"*\" ? 0 : +w.start);\n        walkEnds.push(w.end === \"*\" ? -1 : +w.end);\n        const end = readWalkBody(line, w.body, segments, steps);\n        const tags = walkTags(line, end);\n        if (tags === void 0) {\n          return void 0;\n        }\n        if (tags.before) {\n          before.push(tags.before);\n        }\n        if (tags.after) {\n          after.push(tags.after);\n        }\n        if (steps.nodes.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.nodes.length);\n      }\n    }\n  }\n  if ([before.kinds.length, after.kinds.length].some(\n    (n) => n > 0 && n < names.length\n  )) {\n    return void 0;\n  }\n  return {\n    nodes: {\n      names: segments.names,\n      lengths: Int32Array.from(lengths),\n      refs: Int32Array.from(refs),\n      starts: Float64Array.from(starts),\n      ranks: Int32Array.from(ranks),\n      refNames\n    },\n    links: {\n      from: Int32Array.from(from),\n      to: Int32Array.from(to),\n      strands: Uint8Array.from(strands)\n    },\n    walks: {\n      names,\n      starts: Float64Array.from(walkStarts),\n      ends: Float64Array.from(walkEnds),\n      offsets: Int32Array.from(offsets),\n      steps: steps.nodes.data.slice(0, steps.nodes.length),\n      reversed: steps.reversed.data.slice(0, steps.reversed.length),\n      ...stopColumns(names.length, before, after)\n    }\n  };\n}\nfunction walkTags(line, from) {\n  const out = {};\n  for (const tag of from < line.length ? line.slice(from + 1).split(\"\t\") : []) {\n    const value = tag.slice(5);\n    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {\n      out.before = parseStopTag(value);\n      if (!out.before) {\n        return void 0;\n      }\n    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {\n      out.after = parseStopTag(value);\n      if (!out.after) {\n        return void 0;\n      }\n    }\n  }\n  return out;\n}\nfunction stopColumns(walks, before, after) {\n  return {\n    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},\n    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}\n  };\n}\n\nexport {\n  gfaTables\n};\n", "// src/gaf/parseGaf.ts\nvar STEP = /([><])([^><]+)/g;\nfunction parseGafPath(column) {\n  if (!column.startsWith(\">\") && !column.startsWith(\"<\")) {\n    return void 0;\n  }\n  const steps = [];\n  for (const [, arrow, name] of column.matchAll(STEP)) {\n    steps.push({ name, strand: arrow === \">\" ? \"+\" : \"-\" });\n  }\n  return steps;\n}\nfunction parseGafLine(text) {\n  const line = text.trimEnd();\n  const columns = line.split(\"\t\");\n  if (columns.length < 12 || line.startsWith(\"#\")) {\n    return void 0;\n  }\n  const path = parseGafPath(columns[5]);\n  if (!path) {\n    return void 0;\n  }\n  let cs;\n  let secondary = false;\n  for (let i = 12; i < columns.length; i++) {\n    const tag = columns[i];\n    if (tag.startsWith(\"cs:Z:\")) {\n      cs = tag.slice(5);\n    } else if (tag === \"tp:A:S\") {\n      secondary = true;\n    }\n  }\n  return {\n    name: columns[0],\n    queryLength: +columns[1],\n    queryStart: +columns[2],\n    queryEnd: +columns[3],\n    strand: columns[4] === \"-\" ? 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Walk rows take no limit."})})]}),r(k,{title:"Drawing",children:[e.anchorPaths.length>1?t(c,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(l,{children:"The path the anchored layouts place x along"})}):null,t(c,{label:"Node width",value:e.nodeWidth,options:W,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(l,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),t(c,{label:"Link width",value:e.linkWidth,options:S,testId:"graph-link-width-select",onChange:a=>{e.setLinkWidth(a)},children:t(l,{children:"Walks as width, so a common route reads heavy and a private one thin."})}),r(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(l,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(l,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(H,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:F(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(l,{children:"Where genes on the backbone come from"})}),t(H,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(l,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),r(k,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:p.section,children:t(l,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(c,{label:"Engine",value:e.layoutEngine,options:_,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(l,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(c,{label:"Layout quality",value:String(e.layoutQuality),options:f.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(l,{children:"The engine's iteration budget; higher is slower"})}),t(c,{label:"Bubble spread",value:e.bubbleSpread,options:A,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(l,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(l,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(L,{children:t(I,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),fe=q;export{y as a,fe as b};
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package/dist/chunks/{chunk-6VNU7SD4.js.map → chunk-5LFPNQWH.js.map}

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 {
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-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/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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-  "names": ["LAYOUT_QUALITIES", "LabelledSelect", "label", "value", "options", "testId", "size", "sx", "disabled", "title", "shown", "onChange", "labelId", "useId", "jsxs", "FormControl", "jsx", "InputLabel", "Select", "picked", "o", "e", "MenuItem", "ListItemText", "useStyles", "makeStyles", "Caption", "warn", "children", "jsx", "Typography", "Group", "title", "classes", "jsxs", "SettingSwitch", "label", "checked", "onChange", "FormControlLabel", "Switch", "e", "SettingSelect", "props", "LabelledSelect", "NODE_LIMITS", "nodeLimitOptions", "current", "a", "b", "limit", "TrackPickSetting", "choices", "stored", "auto", "testId", "t", "trackId", "name", "GraphSettingsDialog", "observer", "model", "onClose", "Dialog", "DialogContent", "NODE_WIDTHS", "width", "draw", "MAX_PATH_COLORS", "pickGeneTrack", "pickRepeatTrack", "LAYOUT_ENGINES", "engine", "LAYOUT_QUALITIES", "q", "quality", "BUBBLE_SPREADS", "spread", "linear", "DialogActions", "Button", "GraphSettingsDialog_default"]
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.14.0/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 { EDGE_WIDTHS } from '@jbrowse/bandage-core/edgeWidths'\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          <SettingSelect\n            label=\"Link width\"\n            value={model.linkWidth}\n            options={EDGE_WIDTHS}\n            testId=\"graph-link-width-select\"\n            onChange={links => {\n              model.setLinkWidth(links)\n            }}\n          >\n            <Caption>\n              Walks as width, so a common route reads heavy and a private one\n              thin.\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 ? 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 }

package/dist/chunks/{chunk-6WUWQX2P.js → chunk-CNEUOM7X.js}

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package/dist/chunks/{chunk-6WUWQX2P.js.map → chunk-CNEUOM7X.js.map}

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package/dist/chunks/{chunk-P3FBI5ML.js → chunk-DOC7QIE2.js}

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package/dist/chunks/{chunk-P3FBI5ML.js.map → chunk-DOC7QIE2.js.map}

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