jbrowse-plugin-graphgenomeviewer 7.2.0 → 7.3.0

package/dist/chunks/{chunk-HLKZCTQ3.js.map → chunk-DBPEUVUC.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G6UIYQZR.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G6UIYQZR.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
   "sourcesContent": ["import { readConfObject } from '@jbrowse/core/configuration'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  const lanes = isStringArray(assemblyNames) ? assemblyNames.slice(1) : []\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  return isStringArray(assemblyNames) ? assemblyNames[0] : undefined\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (/^(#|track|browser)/.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !/^(#|track|browser)/.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. 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package/dist/chunks/{chunk-FME624X3.js → chunk-DUR437TH.js}

@@ -1,2 +1,2 @@
-import{h as B,k as M,n as F}from"./chunk-HLKZCTQ3.js";import{b as O,h as _}from"./chunk-CWNJR5XB.js";import{L as b,R as A}from"./chunk-PA4HKAUJ.js";import{e as R}from"./chunk-YU7T5WOQ.js";import{D as P,E,H as m,d as v,o as T,q as I,r as L,s as w,t as N,w as x,y as D,z as G}from"./chunk-UGCNPRKC.js";import{b as t,c as i,d as k}from"./chunk-JMBDTNUR.js";var S=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function f({label:o,value:n,options:e,testId:s,size:c,sx:d,disabled:a,title:h,shown:g,onChange:Q}){let C=R();return i(w,{size:c,sx:d,disabled:a,title:h,children:[t(x,{id:C,shrink:!0,children:o}),t(P,{labelId:C,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:l=>g??e.find(z=>z.value===l)?.label??l,onChange:l=>{Q(l.target.value)},children:e.map(l=>t(G,{value:l.value,disabled:l.disabled,title:l.disabled?void 0:l.description,children:t(D,{primary:l.label,secondary:l.disabled?l.description:void 0})},l.value))})]})}var u=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function r({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function y({title:o,children:n}){let{classes:e}=u();return i("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:c}=u();return i("div",{className:c.section,children:[t(N,{control:t(E,{checked:n,onChange:d=>{e(d.target.checked)}}),label:o}),s]})}function p({children:o,...n}){let{classes:e}=u();return i("div",{className:e.section,children:[t(f,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function H(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function W({label:o,choices:n,stored:e,auto:s,testId:c,onChange:d,children:a}){return n.length>0?t(p,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:c,onChange:d,children:a}):null}var $=k(function(n){let{model:e,onClose:s,children:c}=n,{classes:d}=u();return i(v,{open:!0,onClose:s,title:"Graph settings",children:[i(L,{children:[i(y,{title:"Subgraph",children:[c,t(p,{label:"Node limit",value:String(e.maxGraphNodes),options:H(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(r,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),i(y,{title:"Drawing",children:[e.anchorPaths.length>1?t(p,{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(r,{children:"The path the anchored layouts place x along"})}):null,t(p,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(r,{children:"Depth as width. 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-//# sourceMappingURL=chunk-FME624X3.js.map
+import{h as B,k as M,n as F}from"./chunk-DBPEUVUC.js";import{b as O,h as _}from"./chunk-44CJ2N3N.js";import{F as b,L as A}from"./chunk-PEDWEPNK.js";import{e as R}from"./chunk-YU7T5WOQ.js";import{D as P,E,H as m,d as v,o as T,q as I,r as L,s as w,t as N,w as x,y as D,z as G}from"./chunk-UGCNPRKC.js";import{b as t,c as i,d as k}from"./chunk-JMBDTNUR.js";var S=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function f({label:o,value:n,options:e,testId:s,size:c,sx:d,disabled:a,title:h,shown:g,onChange:Q}){let C=R();return i(w,{size:c,sx:d,disabled:a,title:h,children:[t(x,{id:C,shrink:!0,children:o}),t(P,{labelId:C,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:l=>g??e.find(z=>z.value===l)?.label??l,onChange:l=>{Q(l.target.value)},children:e.map(l=>t(G,{value:l.value,disabled:l.disabled,title:l.disabled?void 0:l.description,children:t(D,{primary:l.label,secondary:l.disabled?l.description:void 0})},l.value))})]})}var u=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function r({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function y({title:o,children:n}){let{classes:e}=u();return i("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:c}=u();return i("div",{className:c.section,children:[t(N,{control:t(E,{checked:n,onChange:d=>{e(d.target.checked)}}),label:o}),s]})}function p({children:o,...n}){let{classes:e}=u();return i("div",{className:e.section,children:[t(f,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function H(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function W({label:o,choices:n,stored:e,auto:s,testId:c,onChange:d,children:a}){return n.length>0?t(p,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:c,onChange:d,children:a}):null}var $=k(function(n){let{model:e,onClose:s,children:c}=n,{classes:d}=u();return i(v,{open:!0,onClose:s,title:"Graph settings",children:[i(L,{children:[i(y,{title:"Subgraph",children:[c,t(p,{label:"Node limit",value:String(e.maxGraphNodes),options:H(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(r,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),i(y,{title:"Drawing",children:[e.anchorPaths.length>1?t(p,{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(r,{children:"The path the anchored layouts place x along"})}):null,t(p,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(r,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),i(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(r,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(r,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(W,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:M(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(r,{children:"Where genes on the backbone come from"})}),t(W,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(r,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),i(y,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:d.section,children:t(r,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(p,{label:"Engine",value:e.layoutEngine,options:O,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(r,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(p,{label:"Layout quality",value:String(e.layoutQuality),options:S.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(r,{children:"The engine's iteration budget; higher is slower"})}),t(p,{label:"Bubble spread",value:e.bubbleSpread,options:_,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(r,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(r,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(I,{children:t(T,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),he=$;export{f as a,he as b};
+//# sourceMappingURL=chunk-DUR437TH.js.map

package/dist/chunks/{chunk-FME624X3.js.map → chunk-DUR437TH.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
   "sourcesContent": ["// src/layoutQualities.ts\nvar LAYOUT_QUALITIES = [\n  { value: 0, label: \"Fastest\" },\n  { value: 1, label: \"Fast\" },\n  { value: 2, label: \"Default\" },\n  { value: 3, label: \"Fine\" },\n  { value: 4, label: \"Best\" }\n];\n\nexport {\n  LAYOUT_QUALITIES\n};\n", "import { useId } from 'react'\n\nimport {\n  FormControl,\n  InputLabel,\n  ListItemText,\n  MenuItem,\n  Select,\n} from '@mui/material'\n\nimport type { SxProps } from '@mui/material'\n\ninterface SelectOption<T extends string> {\n  value: T\n  label: string\n  // an option's tooltip, and the reason under a disabled one, whose tooltip\n  // cannot open\n  description?: string\n  disabled?: boolean\n}\n\n// One dropdown with its label tied to it, so a screen reader names the combobox\nexport default function LabelledSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  size,\n  sx,\n  disabled,\n  title,\n  shown,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly SelectOption<T>[]\n  testId?: string\n  size?: 'small' | 'medium'\n  sx?: SxProps\n  disabled?: boolean\n  title?: string\n  // what the closed select reads, when not the picked option's label\n  shown?: string\n  onChange: (value: T) => void\n}) {\n  const labelId = useId()\n  return (\n    <FormControl size={size} sx={sx} disabled={disabled} title={title}>\n      <InputLabel id={labelId} shrink>\n        {label}\n      </InputLabel>\n      <Select\n        labelId={labelId}\n        value={value}\n        label={label}\n        notched\n        displayEmpty\n        data-testid={testId}\n        renderValue={picked =>\n          shown ?? options.find(o => o.value === picked)?.label ?? picked\n        }\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(o => (\n          <MenuItem\n            key={o.value}\n            value={o.value}\n            disabled={o.disabled}\n            title={o.disabled ? undefined : o.description}\n          >\n            <ListItemText\n              primary={o.label}\n              secondary={o.disabled ? o.description : undefined}\n            />\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { LAYOUT_ENGINES } from '@jbrowse/bandage-core/layoutEngines'\nimport { LAYOUT_QUALITIES } from '@jbrowse/bandage-core/layoutQualities'\nimport { NODE_WIDTHS } from '@jbrowse/bandage-core/nodeWidths'\nimport { MAX_PATH_COLORS } from '@jbrowse/bandage-core/pathColors'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControlLabel,\n  Switch,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from './LabelledSelect'\nimport { pickGeneTrack } from '../genes/geneFeatures'\nimport { pickRepeatTrack } from '../repeats/repeatFeatures'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  group: {\n    marginBottom: 16,\n  },\n  heading: {\n    marginBottom: 8,\n  },\n})\n\nfunction Caption({\n  warn = false,\n  children,\n}: {\n  warn?: boolean\n  children: ReactNode\n}) {\n  return (\n    <Typography\n      variant=\"caption\"\n      component=\"div\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\nfunction Group({ title, children }: { title: string; children: ReactNode }) {\n  const { classes } = useStyles()\n  return (\n    <section className={classes.group}>\n      <Typography variant=\"subtitle1\" className={classes.heading}>\n        {title}\n      </Typography>\n      {children}\n    </section>\n  )\n}\n\nfunction SettingSwitch({\n  label,\n  checked,\n  onChange,\n  children,\n}: {\n  label: string\n  checked: boolean\n  onChange: (checked: boolean) => void\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControlLabel\n        control={\n          <Switch\n            checked={checked}\n            onChange={e => {\n              onChange(e.target.checked)\n            }}\n          />\n        }\n        label={label}\n      />\n      {children}\n    </div>\n  )\n}\n\n// one dropdown setting, at the dialog's width, and its caption\nfunction SettingSelect<T extends string>({\n  children,\n  ...props\n}: Omit<Parameters<typeof LabelledSelect<T>>[0], 'size' | 'sx'> & {\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <LabelledSelect sx={{ minWidth: 200 }} {...props} />\n      {children}\n    </div>\n  )\n}\n\nconst NODE_LIMITS = [5000, 20_000, 50_000, 100_000]\n\n// the presets, with a limit a session states among them\nfunction nodeLimitOptions(current: number) {\n  return [...new Set([...NODE_LIMITS, current])]\n    .sort((a, b) => a - b)\n    .map(limit => ({ value: String(limit), label: limit.toLocaleString() }))\n}\n\ninterface NamedTrack {\n  trackId: string\n  name: string\n}\n\n// '' leaves the pick to the heuristic, so a session can go back to it\nfunction TrackPickSetting({\n  label,\n  choices,\n  stored,\n  auto,\n  testId,\n  onChange,\n  children,\n}: {\n  label: string\n  choices: NamedTrack[]\n  stored: string\n  auto: NamedTrack | undefined\n  testId: string\n  onChange: (trackId: string) => void\n  children: ReactNode\n}) {\n  return choices.length > 0 ? (\n    <SettingSelect\n      label={label}\n      value={choices.some(t => t.trackId === stored) ? stored : ''}\n      options={[\n        { value: '', label: `Automatic (${auto?.name ?? 'none'})` },\n        ...choices.map(({ trackId, name }) => ({\n          value: trackId,\n          label: name,\n        })),\n      ]}\n      testId={testId}\n      onChange={onChange}\n    >\n      {children}\n    </SettingSelect>\n  ) : null\n}\n\n// Toggles the menus already offer (halos, genes, color) stay out of here.\n// `children` is the host's own part of the subgraph group.\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <Group title=\"Subgraph\">\n          {children}\n          <SettingSelect\n            label=\"Node limit\"\n            value={String(model.maxGraphNodes)}\n            options={nodeLimitOptions(model.maxGraphNodes)}\n            testId=\"graph-node-limit-select\"\n            onChange={limit => {\n              model.setMaxGraphNodes(Number(limit))\n            }}\n          >\n            <Caption>\n              The most nodes a layout draws; past it the graph is declined. Walk\n              rows take no limit.\n            </Caption>\n          </SettingSelect>\n        </Group>\n\n        <Group title=\"Drawing\">\n          {model.anchorPaths.length > 1 ? (\n            <SettingSelect\n              label=\"Reference path\"\n              value={model.activeReferencePath ?? ''}\n              options={model.anchorPaths.map(({ name }) => ({\n                value: name,\n                label: name,\n              }))}\n              testId=\"graph-reference-path-select\"\n              onChange={name => {\n                model.setReferencePath(name)\n                void model.recomputeLayout()\n              }}\n            >\n              <Caption>The path the anchored layouts place x along</Caption>\n            </SettingSelect>\n          ) : null}\n\n          <SettingSelect\n            label=\"Node width\"\n            value={model.nodeWidth}\n            options={NODE_WIDTHS}\n            testId=\"graph-node-width-select\"\n            onChange={width => {\n              model.setNodeWidth(width)\n            }}\n          >\n            <Caption>\n              Depth as width. In a cut with walks, depth is how many haplotypes\n              carry the node.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSwitch\n            label=\"Draw paths\"\n            checked={model.drawPaths}\n            onChange={draw => {\n              model.setLayer('paths', draw)\n            }}\n          >\n            <Caption>\n              Color each node by the paths through it, one lane per path\n            </Caption>\n            {model.drawPaths && !model.effectiveDrawPaths ? (\n              <Caption warn>\n                {model.pathCount > MAX_PATH_COLORS\n                  ? `Off: ${model.pathCount.toLocaleString()} paths is past the ${MAX_PATH_COLORS} this can tell apart`\n                  : 'Off: this graph states no paths'}\n              </Caption>\n            ) : null}\n          </SettingSwitch>\n\n          <TrackPickSetting\n            label=\"Gene track\"\n            choices={model.geneTrackChoices}\n            stored={model.geneTrackId}\n            auto={pickGeneTrack(model.geneTrackChoices, '')}\n            testId=\"graph-gene-track-select\"\n            onChange={trackId => {\n              model.setGeneTrackId(trackId)\n            }}\n          >\n            <Caption>Where genes on the backbone come from</Caption>\n          </TrackPickSetting>\n\n          <TrackPickSetting\n            label=\"Repeat track\"\n            choices={model.repeatTrackChoices}\n            stored={model.repeatTrackId}\n            auto={pickRepeatTrack(model.repeatTrackChoices, '')}\n            testId=\"graph-repeat-track-select\"\n            onChange={trackId => {\n              model.setRepeatTrackId(trackId)\n            }}\n          >\n            <Caption>\n              The tandem repeat annotation walk rows measure and tile by\n            </Caption>\n          </TrackPickSetting>\n        </Group>\n\n        <Group title=\"Force-directed layout\">\n          {model.hasGraph && !model.usesLayoutEngine ? (\n            <div className={classes.section}>\n              <Caption warn>\n                No effect on the current layout until Layout is Force-directed\n              </Caption>\n            </div>\n          ) : null}\n\n          <SettingSelect\n            label=\"Engine\"\n            value={model.layoutEngine}\n            options={LAYOUT_ENGINES}\n            testId=\"graph-layout-engine-select\"\n            onChange={engine => {\n              model.setLayoutEngine(engine)\n            }}\n          >\n            <Caption>\n              Stress keeps the reference straight, so a zoom keeps the picture;\n              FMMM lets the whole graph settle.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Layout quality\"\n            value={String(model.layoutQuality)}\n            options={LAYOUT_QUALITIES.map(q => ({\n              value: String(q.value),\n              label: q.label,\n            }))}\n            testId=\"graph-layout-quality-select\"\n            onChange={quality => {\n              model.setLayoutQuality(Number(quality))\n            }}\n          >\n            <Caption>\n              The engine&apos;s iteration budget; higher is slower\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Bubble spread\"\n            value={model.bubbleSpread}\n            options={BUBBLE_SPREADS}\n            testId=\"graph-bubble-spread-select\"\n            onChange={spread => {\n              model.setBubbleSpread(spread)\n            }}\n          >\n            <Caption>How far the layout opens a bubble</Caption>\n          </SettingSelect>\n\n          {model.layoutEngine === 'stress' ? null : (\n            <SettingSwitch\n              label=\"Linear layout\"\n              checked={model.linearLayout}\n              onChange={linear => {\n                model.setLinearLayout(linear)\n              }}\n            >\n              <Caption>Keeps a chain of nodes on one line where it can</Caption>\n            </SettingSwitch>\n          )}\n        </Group>\n      </DialogContent>\n\n      <DialogActions>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GraphSettingsDialog\n"],
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package/dist/chunks/{chunk-6WA6WF6A.js → chunk-FIRQAKMX.js}

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package/dist/chunks/{chunk-6WA6WF6A.js.map → chunk-FIRQAKMX.js.map}

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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
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package/dist/chunks/chunk-JCAZTNYG.js

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

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+  "sources": ["../../src/RgfaTabixAdapter/walkCut.ts"],
+  "sourcesContent": ["import { walkRowRuns } from '@jbrowse/bandage-core/layout/walkRowRuns'\n\nimport type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'\nimport type { WalkRowRuns } from '@jbrowse/bandage-core/layout/walkRowRuns'\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"],
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+  "names": ["walkCutFor", "tables", "region", "walkRows", "walkRowRuns"]
+}

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e.drawnGraph?Z(e.drawnGraph):void 0},get nodeInk(){return ze(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?xe(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=t?n?Fa(n,t,t.unit):me(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[a,...r]=_o([o.reference,...o.rows],t?.calls);return{...o,reference:a,rows:r}},get walkRowSampleChoices(){let t=this.cohortWalkRows?.rows??[];return{samples:[...new Set(t.map(n=>n.sample))].sort(),disagreeing:[...new Set(t.filter(n=>n.call?.agrees===!1).map(n=>n.sample))]}},get walkRowSamplesTsv(){let t=e.sourceAdapter?.samplesTsvLocation;return t&&vn(t)?t:void 0},get walkRowGroupFields(){return io(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=fo(t,n),a=(e.graph?.paths??[]).map(r=>X(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:uo(a.map(o)),unvalued:a.some(r=>o(r)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,domain:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,domain:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows;return t&&Me(t.rows,e.walkRowSamples)},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?po(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get drawsNodes(){return F(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ge(e.positionsVersion);let t=e.layoutResult?.nodePositions;return 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t!==null?Tr(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return t&&n&&e.chosenHover!=="off"?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var Er=Gr.views(e=>({get host(){let t=e.containingView;return sr(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?J(t):[];return t?tr(t,{maxGap:n.length>0?kt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=Y(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([r,s])=>[s,r])),a=r=>r!==void 0&&t.has(r)?t.get(r)?.name??r:void 0;return r=>a(o.get(r))??a(r)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(it.has(n.adapterType))for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let a=ct(o,"");return 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n)a(e.nodeStrokes,e.nodeStrokeRuns.get(r));t.forEach(({from:r,to:s},i)=>{(n.has(r)||n.has(s))&&(a(e.edgeCurves,e.edgeCurveRuns.get(i)),a(e.arrows,e.arrowRuns.get(i)))})}function Ka(e){return e<.5?4*e*e*e:1-(-2*e+2)**3/2}function Bg(e,t,n,o){return!(e.referenceAxis||t.referenceAxis||e.pixelRows||t.pixelRows||t.tubeMap||o||n>Ha)}function Og(){return typeof requestAnimationFrame<"u"&&!("matchMedia"in window&&window.matchMedia("(prefers-reduced-motion: reduce)").matches)}function _g(e,t,n){let o={frame:0,finish:()=>{e(1)}},a=0,r=performance.now(),s=()=>{if(!t()){n();return}let i=performance.now();a+=Math.min(i-r,Xa),r=i;let c=Math.min(1,a/Da);e(Ka(c)),c<1?o.frame=requestAnimationFrame(s):n()};return o.frame=requestAnimationFrame(s),o}function $g(e,t,n,o){for(let[a,r]of Object.entries(e)){let s=t[a],i=n[a];!s||!i||r.forEach((c,d)=>{c.x=o===1?i[d].x:s[d].x+(i[d].x-s[d].x)*o,c.y=o===1?i[d].y:s[d].y+(i[d].y-s[d].y)*o})}}var Ja=8,qa=19,_r=Pe+qa,Za=48;function Qa(e,t,n){if(!(!e||!t))return Je(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var iw=Cr.views(e=>({get paneCeiling(){return Math.max(ot,e.paneHeight??zn)},get fitRoom(){return e.host?this.canvasHeight:this.paneCeiling},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=this.fitRoom,o=(e.walkRowGroups?.sections.length??0)*so;return qe(t.rows.length+1,n-this.fitPadTopBase-C-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?mo(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return Qa(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=he(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,a)=>({...o,y:t.rowY(a)})):n},get visibleRowLabels(){return this.drawnRowLabels.flatMap(({label:t,y:n})=>{let o=e.toScreen({x:0,y:n}).y;return o>=0&&o<=this.canvasHeight?[{label:t,y:n,top:o}]:[]})},get fitPadLeft(){return Math.max(C,...this.drawnRowLabels.map(t=>Tn(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?ue(n,this.walkRowPitch):void 0;return t?Te(t,{region:e.graphRegion,extent:o&&{...o,maxY:o.maxY+(this.walkRowPlacement?.headersPx??0)}}):void 0},get hoveredWalkRowText(){let t=e.walkRowBars,n=e.hoveredWalkRow;if(!t||n===null||this.walkRowPitch?.readouts!==!1)return;let o=t.reference.name===n,a=o?t.reference:t.rows.find(r=>r.name===n);return a?{label:a.label,readout:Wn(a,o?void 0:t.reference,t.unit,a.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,a=this.walkRowPitch,r=this.walkRowPlacement;if(!o||!a||!r)return;let s=r.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][s],c=r.rowY(s)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=a.barPx/2+2&&d>=0&&d<=i.bp?s:void 0},get fitPadTopBase(){let t=Po(e.tubeMapGenes);return C+Math.max(0,t-1)*No+e.referenceStripZonePx},get legendRoom(){let t=this.layoutBounds,{width:n,height:o}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let a=this.fitPadTopBase,r=this.fitRoom,s=l=>(e.paneWidth-this.fitPadLeft-l)/t.w,i=l=>e.pixelRows?t.h+l+C<=r?1/0:0:(r-l-C)/t.h,c=Math.min(s(n+2*ee),i(a));return Math.min(s(C),i(a+o+ee))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ee:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(C,e.legendSize.width+2*ee):C},get minFitScale(){let t=this.layoutBounds,n=e.layoutResult,o=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&o&&!n.referenceAxis?Math.min(Un/o,(this.paneCeiling-this.fitPadTop-C)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facetSetting;return t===""?void 0:n.length===0&&o===void 0?t:{field:t,domain:[...n],...o===void 0?{}:{columns:o}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:o}=e.facetSetting;return t?tt(t.map(a=>a.walks[0].name),e.hostPlacesX||n===""?"walk":n,o):void 0},facetGridIn(t){let n=this.facetPlacement,o=this.layoutBounds;return n&&o&&o.w>0?Qe({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facetSetting.columns}):void 0},get facetGrid(){return this.facetGridIn(this.fitRoom-_r)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ee+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-Za?t+2*ee:Ja},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(ot,o.total+_r);let a=Math.max(ot,e.legendSize.height+2*ee+e.referenceStripZonePx),r=this.fitPads,s=r.top+r.bottom;if(e.pixelRows)return Math.min(n,Math.max(a,t.h+s));let i=e.paneWidth-r.left-r.right;return t.w>0&&i>0?Math.min(n,Math.max(a,t.h*Math.max(i/t.w,this.minFitScale)+s)):n},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fitPads(){return this.facetGrid?{left:U,top:U,right:U,bottom:U}:{left:this.fitPadLeft,top:this.fitPadTop,right:this.fitPadRight,bottom:C}},get usableHeight(){let{top:t,bottom:n}=this.fitPads;return this.viewBox.height-t-n},get fittedTransform(){let t=this.layoutBounds,{width:n,height:o}=this.viewBox,a=this.fitPads;return t?Ae(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:a.left,padTop:a.top,padRight:a.right,padBottom:a.bottom}):void 0}})).views(e=>({viewportToBuild(){return Xn(Qn(e),qn)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,Jn]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=$o();return{scaleX:e.scaleX*t,scaleY:e.scaleY*t,translateX:e.translateX*t,translateY:e.translateY*t,dpr:t}}})).views(e=>({paint(t){t.updateTransform(e.paintTransform),t.render(e.referenceStripShown?[0,0,0,0]:Yn)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:a,layoutResult:r,deletionDrawing:s}=e;if(!o||!a||!r||!s)return;Ge(e.viewportDirty,e.positionsVersion);let i=Lt(()=>e.viewportToBuild()),c=Ue({..._e(r,s,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:a,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:Lt(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===r&&Or(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return xo(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Mo(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,a=t&&`${t.refName}:${t.start}-${t.end}`,r=le(e.sourceGfaLocation),s=n?.type==="GbzBaseSyntenyAdapter"?le(n.gbzDbLocation):void 0,i=r?{gfa:r,region:a}:s&&t&&a?{gbz:{db:s,index:le(n.haplotypeIndexLocation),region:a,haplotypes:e.cutHaplotypes?.map(p=>o?.[p]??p),referenceSample:n.referenceSample||o?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!i)return;let c=e.showGenes?e.geneTrack:void 0,d=c?e.sessionTrack(c.trackId):void 0,l=d?Rn(_(d,"adapter"),"gffGzLocation"):void 0,m=l?.type==="Gff3TabixAdapter"?{file:le(l.gffGzLocation),index:le(l.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...i,genes:m?.file&&m.index?m:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...Qt({engine:e.layoutEngine,quality:e.layoutQuality,linearLayout:e.linearLayout,bubbleSpread:e.bubbleSpread,showDeletionEdges:e.showDeletionEdges,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,colorDomain:e.statedColorDomain}),walks:e.walkLayers.length?e.walkLayers.map(p=>p.color?p:p.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling}))},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${F(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},get figureSpecUnavailable(){return e.drawsNodes?this.figureSpec()?void 0:"bandage-figure reads a graph cut from a gbz-base 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