npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 6.27.0 → 7.0.0 - Mend

jbrowse-plugin-graphgenomeviewer 6.27.0 → 7.0.0

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package/dist/chunks/chunk-4O7LDKI5.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RAKOB6IV.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G45YY72K.js"],
+  "sourcesContent": ["import {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-BPLIXMH7.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/reference.ts\nvar WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([\n  [\"hg38\", \"GRCh38\"],\n  [\"hg19\", \"GRCh37\"],\n  [\"hs1\", \"CHM13\"],\n  [\"t2t-chm13\", \"CHM13\"],\n  [\"chm13v2\", \"CHM13\"]\n]);\nfunction wellKnownSample(assemblyName) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase());\n}\nfunction sampleOf(refName) {\n  const sample = refName.includes(\"#\") ? panSNSample(refName) : void 0;\n  return sample === void 0 || isGenericSample(sample) ? void 0 : sample;\n}\nfunction haplotypeOf(refName) {\n  return panSNHaplotype(refName) ?? panSNSample(refName);\n}\nfunction graphHaplotypes(graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map((p) => p.name));\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName);\n    }\n  }\n  const bySample = /* @__PURE__ */ new Map();\n  for (const refName of refNames) {\n    const sample = sampleOf(refName);\n    if (sample !== void 0) {\n      const haplotypes = bySample.get(sample) ?? bySample.set(sample, /* @__PURE__ */ new Set()).get(sample);\n      haplotypes.add(haplotypeOf(refName));\n    }\n  }\n  return bySample;\n}\nfunction backboneFrom(contigs, haplotypes) {\n  const samples = new Set(contigs.map((c) => sampleOf(c.refName)));\n  const [sample] = samples;\n  if (samples.size !== 1 || sample === void 0) {\n    return { contigs, prefixes: [], named: false };\n  }\n  const own = new Set(contigs.map((c) => haplotypeOf(c.refName)));\n  const unique = [...haplotypes.get(sample) ?? []].every((h) => own.has(h));\n  const shared = new Set(contigs.map((c) => panSNHaplotype(c.refName)));\n  const [haplotype] = shared;\n  return {\n    contigs,\n    prefixes: [\n      ...unique ? [sample] : [],\n      ...shared.size === 1 && haplotype ? [haplotype] : []\n    ],\n    named: true\n  };\n}\nfunction graphBackbone(graph) {\n  const spans = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable;\n      const end = start + node.length;\n      const span = spans.get(refName);\n      if (span) {\n        span.start = Math.min(span.start, start);\n        span.end = Math.max(span.end, end);\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end\n        });\n      }\n    }\n  }\n  const contigs = [...spans.values()];\n  return contigs.length ? backboneFrom(contigs, graphHaplotypes(graph)) : void 0;\n}\nfunction referenceLabel(graph, region) {\n  const backbone = graphBackbone(graph);\n  const contig = region ? panSNContig(region.refName) : backbone?.contigs.length === 1 ? backbone.contigs[0].contig : void 0;\n  const sample = backbone?.named ? panSNSample(backbone.contigs[0].refName) : void 0;\n  return contig && (sample ? `${sample} ${contig}` : contig);\n}\nfunction backboneAssembly(backbone, assemblies) {\n  const names = (a) => [a.name, ...a.aliases ?? []];\n  const naming = (prefix) => (a) => names(a).some((n) => n.toLowerCase() === prefix.toLowerCase());\n  const prefixes = [...backbone?.prefixes ?? []].reverse();\n  const sample = backbone?.prefixes.find((p) => !p.includes(\"#\"))?.toLowerCase();\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix));\n    if (assembly) {\n      return assembly;\n    }\n  }\n  return sample === void 0 ? void 0 : assemblies.find(\n    (a) => names(a).some((n) => wellKnownSample(n)?.toLowerCase() === sample)\n  );\n}\nfunction assemblyWalk(graph, assembly) {\n  const haplotypes = graphHaplotypes(graph);\n  return graph.anchorPaths?.find(\n    (walk) => backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length\n          }\n        ],\n        haplotypes\n      ),\n      [assembly]\n    )\n  );\n}\nfunction contigNames(contig) {\n  const bare = contig.replace(/^chr/i, \"\");\n  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? [\"M\", \"MT\"] : [bare];\n  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];\n}\nfunction refNameBinding(refNames, aliases = {}) {\n  const exact = new Set(refNames);\n  const byName = /* @__PURE__ */ new Map();\n  for (const refName of exact) {\n    const contig = panSNContig(refName);\n    const alias = aliases[contig];\n    for (const name of /* @__PURE__ */ new Set([\n      ...contigNames(contig),\n      ...alias ? [alias] : []\n    ])) {\n      byName.set(name, byName.has(name) ? void 0 : refName);\n    }\n  }\n  return (name) => exact.has(name) ? name : byName.get(name);\n}\nfunction featuresOnBackbone(features, backbone, aliases) {\n  const bind = refNameBinding(\n    backbone.contigs.map((c) => c.refName),\n    aliases\n  );\n  return features.flatMap((f) => {\n    const refName = bind(f.refName);\n    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];\n  });\n}\n\nexport {\n  WELL_KNOWN_SAMPLES,\n  wellKnownSample,\n  graphBackbone,\n  referenceLabel,\n  backboneAssembly,\n  assemblyWalk,\n  contigNames,\n  refNameBinding,\n  featuresOnBackbone\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;\nvar Steps = class {\n  constructor() {\n    this.nodes = new Int32Array(1 << 16);\n    this.reversed = new Uint8Array(1 << 16);\n    this.length = 0;\n  }\n  push(node, reversed) {\n    if (this.length === this.nodes.length) {\n      const nodes = new Int32Array(this.length * 2);\n      nodes.set(this.nodes);\n      this.nodes = nodes;\n      const rev = new Uint8Array(this.length * 2);\n      rev.set(this.reversed);\n      this.reversed = rev;\n    }\n    this.nodes[this.length] = node;\n    this.reversed[this.length++] = reversed;\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.push(node ?? segments.of(line.slice(start, end)), 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}\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 = new Steps();\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        readWalkBody(line, w.body, segments, steps);\n        if (steps.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.length);\n      }\n    }\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.slice(0, steps.length),\n      reversed: steps.reversed.slice(0, steps.length)\n    }\n  };\n}\n\nexport {\n  gfaTables\n};\n"],
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sn(e.geneTrackChoices,e.geneTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?fn(e.graph):void 0},get cutWalkRows(){let t=e.walkCut?.walkRowRuns;return t?yn(t):e.graph?Ce(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=Q(e),o=n.has(t)?n.get(t):void 0,s=e.sourceAdapter?.assemblyNameToPanSN??{},r=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...r,...r.flatMap(a=>s[a]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0},get geneLaneFilter(){let t;try{t=De(e)}catch{return}let n=ba(t,e.geneTrack?.trackId);return n.length?new la({filters:n,jexl:No(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?ya(n?t.filter(o=>n.passes(o)):t):void 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Wr(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=_r(t,n),s=(e.graph?.paths??[]).map(r=>W(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Cr(s.map(o)),unvalued:s.some(r=>o(r)==="")}},get tubeMapPanelSplit(){let{field:t,domain:n}=e.facetSetting,o=e.walkRowGroupBy,s=e.walkRowSampleTable;return t!==""?{by:t,domain:n}:o&&s&&this.walkRowGroupFields.includes(o.field)?{by:"column",...o,table:s}:void 0},get walkRowGroups(){let t=this.cohortWalkRows,n=e.walkRowSampleTable,o=e.walkRowGroupBy;return t&&n&&o&&this.walkRowGroupFields.includes(o.field)?Xr(Be(t.rows,e.walkRowSamples),n,o):void 0},get walkRowBars(){let t=this.cohortWalkRows;return t?{...t,rows:this.walkRowGroups?.rows??Be(t.rows,e.walkRowSamples)}:void 0},get drawsNodes(){return ne(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){pt(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?et(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){pt(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:co(e.graph,e.bubbles,t,n=>e.walkLabel(n),e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?Ae(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return ye(e.scale,e.pixelRows).scaleX},get scaleY(){return ye(e.scale,e.pixelRows).scaleY},get axisScale(){return ye(e.scale,e.pixelRows)}})).views(e=>({get deletionDrawing(){return e.graph?Ve(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,o=n?.tubeMap?n.nodePositions:void 0,s=!1,r=!1;if(t&&e.drawnGraph)for(let a of e.drawnGraph.nodes)o&&!o[a.id]||(t.midpoints.has(a.id)?a.stable&&a.stable.rank>0&&(s=!0):r=!0);return{offReference:s,unplaced:r}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?ut(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=t?.pathColors,o=e.drawnGraph?.paths,s=e.tubeMapColoring,r=n&&o&&s&&t.layout.reads.length===0?Wt(o,e.drawnGraph.referencePath,s.valueOf,s.palette):n&&o&&this.tubeMapNodeColors?Je(o,e.drawnGraph.referencePath,Dt):n&&o&&t.layout.reads.length===0&&(!Ne(o.length)||o.some(i=>i.members))?Je(o,e.drawnGraph.referencePath):n,a=new Set(e.hoveredRowWalks);return r&&o&&a.size>0?r.map((i,c)=>a.has(o[c]?.name??"")?i:Pe):r},nodeSpan(t){let{nodeById:n,nodeNeighbors:o}=e;return n&&o?vt({nodeId:t,nodeById:n,neighbors:o}):void 0},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap}})).views(e=>({get hoverGraph(){return e.hoverDrawing?.graph??e.drawnGraph}})).views(e=>({get hoverNodeById(){let t=e.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&new Map(t.nodes.map(n=>[n.id,n]))},get hoverNeighbors(){let t=e.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&de(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&Ne(t.length)&&!e.layoutResult?.tubeMapPanels&&!e.tubeMapNodeColors&&!t.some(s=>s.members)&&!e.tubeMapColoring?Ue(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble,o=e.hoverNodeById,s=e.hoverNeighbors;return t!==null?o&&s?vt({nodeId:t,nodeById:o,neighbors:s}):void 0:n&&!n.offReference?{start:n.start,end:n.end}:void 0}})).views(e=>({get hoverHighlight(){let 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s=La(e,o),r=La(e,n),a=t.filter(d=>r.includes(d.sample)),i=a.length>=2?a:t,c={init:{views:i.map(d=>({assembly:d.sample,loc:Xt(d),...o!==void 0&&s.includes(d.sample)?{tracks:[o]}:{}})),tracks:n?i.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};e.launchView?Na(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",c)):e.addView("LinearSyntenyView",c)}var Aa=Ra.views(e=>({get host(){let t;try{t=De(e)}catch{return}return js(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?ce(t):[];return t?Qr(t,{maxGap:n.length>0?mn(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=Q(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([r,a])=>[a,r])),s=r=>r!==void 0&&t.has(r)?t.get(r)?.name??r:void 0;return r=>s(o.get(r))??s(r)},get geneTracksByAssembly(){let t=new Map;for(let n of Q(e).tracks){let o=$(n,"adapter").type;if(!ht.has(o))continue;let 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$n({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:Be(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Qe(t,{width:e.paneWidth})},get cutsWholeWalks(){return Fn(ne(e.chosenLayoutMode),{walkStrip:e.walkStrip,host:!!e.host})},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?Dn(e.graph,[t.reference,...t.rows],o):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Ht(e.nodePositions?.[t],n=>({x:n.x*e.scaleX+e.translateX,y:n.y*e.scaleY+e.translateY}))}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],o=0,s=0;for(let r of t.rows){if(!r.axis){s++;continue}let a=Te(e.assemblyResolver,{sample:r.sample,haplotype:r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`}),i=a?e.geneTracksByAssembly.get(a):void 0;if(!a||!i){o++;continue}n.push({row:r.name,trackId:i.trackId,region:{assemblyName:a,refName:r.axis.contig,...Ln(r.axis,r.bp)}})}return{reads:n.slice(0,ao),gaps:{untracked:o,unplaced:s,unread:Math.max(0,n.length-ao)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let s=o.haplotype===void 0?void 0:`${o.sample}#${o.haplotype}`,r=t===0?e.graphRegion?.assemblyName:Te(e.assemblyResolver,{sample:o.sample,haplotype:s});return{label:o.label,assembly:r,location:{sample:o.sample,haplotype:s,refName:o.axis.contig,...Ln(o.axis,o.bp)}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return 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t=this.walkRowPlacement,n=it(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,s)=>({...o,y:t.rowY(s)})):n},get fitPadLeft(){return Math.max(C,...this.drawnRowLabels.map(t=>Xo(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?_e(n,this.walkRowPitch):void 0;return t?rt(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,s=o?t.reference:t.rows.find(r=>r.name===n);return s?{label:s.label,readout:zo(s,o?void 0:t.reference,t.unit,s.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,s=this.walkRowPitch,r=this.walkRowPlacement;if(!o||!s||!r)return;let a=r.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][a],c=r.rowY(a)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=s.barPx/2+2&&d>=0&&d<=i.bp?a:void 0},get fitPadTopBase(){let t=Er(e.tubeMapGenes);return C+Math.max(0,t-1)*Tr+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 s=this.fitPadTopBase,r=this.fitRoom,a=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(a(n+2*ue),i(s));return Math.min(a(C),i(s+o+ue))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ue:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(C,e.legendSize.width+2*ue):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(Zs/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?It(t.map(s=>s.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?Tt({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-_a)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ue+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-zc?t+2*ue:Yc},get canvasHeight(){let t=this.layoutBounds,n=e.paneWidth-C-this.fitPadRight,o=this.paneCeiling;if(!t)return o;let s=this.facetGrid;if(s)return Math.max(Qt,s.total+_a);let r=Math.max(Qt,e.legendSize.height+2*ue+e.referenceStripZonePx);return e.pixelRows?Math.min(o,Math.max(r,t.h+this.fitPadTop+C)):t.w>0&&n>0?Math.min(o,Math.max(r,t.h*Math.max(n/t.w,this.minFitScale)+this.fitPadTop+C)):o},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fittedTransform(){let t=this.layoutBounds,n=this.facetGrid;return t?n?Ie(t,n.width,n.height,e.pixelRows,{padLeft:se,padTop:se,padRight:se,padBottom:se}):Ie(t,e.paneWidth,this.canvasHeight,e.pixelRows,{minScale:this.minFitScale,padLeft:this.fitPadLeft,padTop:this.fitPadTop,padRight:this.fitPadRight}):void 0}})).views(e=>({viewportToBuild(){return Un(oa(e),ta)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,ea]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=Cn();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]:e.darkMode?tn:en)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:s,layoutResult:r,deletionDrawing:a}=e;if(!o||!s||!r||!a)return;pt(e.viewportDirty,e.positionsVersion);let i=xn(()=>e.viewportToBuild()),c=Rt({...tt(r,a,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:s,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:xn(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===r&&Ba(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return hr(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?wr(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,s=t&&`${t.refName}:${t.start}-${t.end}`,r=Oe(e.sourceGfaLocation),a=n?.type==="GbzBaseSyntenyAdapter"?Oe(n.gbzDbLocation):void 0,i=r?{gfa:r,region:s}:a&&t&&s?{gbz:{db:a,index:Oe(n.haplotypeIndexLocation),region:s,haplotypes:e.cutHaplotypes?.map(u=>o?.[u]??u),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?Q(e).tracks.find(u=>u.trackId===c.trackId):void 0,l=d?To($(d,"adapter"),"gffGzLocation"):void 0,p=l?.type==="Gff3TabixAdapter"?{file:Oe(l.gffGzLocation),index:Oe(l.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...i,genes:p?.file&&p.index?p:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...Zn({engine:e.layoutEngine,quality:e.layoutQuality,linearLayout:e.linearLayout,bubbleSpread:e.bubbleSpread,showDeletionEdges:e.showDeletionEdges,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,colorDomain:e.statedColorDomain}),walks:e.walkLayers.length?e.walkLayers.map(u=>u.color?u:u.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling}))},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${ne(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 track or a GFA url":`bandage-figure draws no ${ne(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?Jn(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,linearLayout:e.linearLayout,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.statedColorDomain,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,walkRowPitch:e.walkRowPitch,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps},spec:this.figureSpecUnavailable?void 0:this.figureSpec()}):void 0},get tubeMapFrame(){let t=e.layoutResult?.tubeMap;return t?Jt(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-C}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX&&!e.layoutResult?.tubeMapPanels?Gn(t):void 0},get tubeMapPanelRulerBoxes(){let{layoutResult:t}=e,n=t?.tubeMapPanels?.at(-1);return n&&t?.referenceAxis&&!e.hostPlacesX?Gn(Ot(n.result.tubeMap)):void 0},get connectorZoneBottom(){let t=e.tubeMapPicture,n=e.tubeMapFrame;return t&&n?n.y(t.bounds.minY)-2:0},get tubeMapConnectors(){let t=e.tubeMapConnectedBoxes,n=e.tubeMapFrame,o=t&&n?e.hostBpFrame:void 0;return t&&n&&o?yr(t,s=>s*o.scale+o.translateX,n.x,e.paneWidth):[]},get tubeMapPanelPictures(){let t=e.layoutResult?.tubeMapPanels;if(!t)return;let n=new Set(e.hoveredRowWalks),o=e.tubeMapColoring,s=a=>{let i=a.paths??[];return(o?Wt(i,a.referencePath,o.valueOf,o.palette):Je(i,a.referencePath)).map((d,l)=>{let p=i[l].name;return n.size>0&&!n.has(p)&&W(p).name!==a.referencePath?Pe:d})},{field:r}=e.facetSetting;return t.map(a=>{let i=a.result.tubeMap,{graph:c,coarse:d}=i;return{panel:a,label:a.label??(r==="walk"?e.walkLabel(a.paths[0]):a.key),picture:Ft(i),tubeColors:s(c),nodeColors:e.tubeMapNodeColors?ut(c,e.effectiveColorScheme,e.referenceRamp):void 0,deviations:d?$t(i,d.deviations):[]}})}})).views(e=>({get hoveredMember(){let t=e.hoveredNode,n=t===null?void 0:e.hoverDrawing?.members.get(t);if(!n)return t;let o=e.hoveredAt,s=e.hoveredPanel,r=s===null?void 0:this.tubeMapPanelViews?.[s],a;return r?.panel.result.tubeMap.layout.nodes.forEach(c=>{c.name===t&&(a=c)}),(o&&r&&a?Or(n,c=>e.nodeSpan(c),r.frame.x(a.x),r.frame.x(a.x+a.pixelWidth),o.x):void 0)??n[0]},get tubeMapPanelHover(){let t=e.hoveredNode,n=e.tubeMapPanelPictures;if(t===null||!n)return;let o=this.hoveredMember??t;return n.map(({panel:s})=>{let r=s.result.tubeMap,a=Gr(r,o);return a?{box:a,...$r(r.graph,a)}:void 0})},get tubeMapPanelViews(){let t=e.tubeMapPanelPictures,n=e.layoutResult;if(!t||!n)return;let o=t.length*On,s=t.reduce((c,d)=>c+d.panel.height,0),r=e.canvasHeight-e.fitPadTop-C-o,a=e.scaleY*(n.referenceAxis&&s>0?Math.max(Kc,Math.min(1,r/s)):1),i=e.translateY;return t.map(c=>{let{panel:d}=c,l=d.result.extent?.minY??0,p=i,u=p+On;return i=u+d.height*a,{...c,frame:Jt(d.result.tubeMap,{scaleX:e.scaleX,translateX:e.translateX,scaleY:a,translateY:u-l*a,usableHeight:1/0}),titleTop:p,top:u,bottom:i}})}})).views(e=>({tubeMapPanelAt(t){let n=e.tubeMapPanelViews?.findIndex(o=>o.titleTop<=t&&t<=o.bottom)??-1;return n<0?null:n}})).views(e=>({paintHover(t,n){let o=e.tubeMapPicture,s=e.tubeMapFrame,r=e.hoverLayerNode;if(o&&s){let{ctx:a,canvas:i}=t,c=Cn();a.setTransform(1,0,0,1,0,0),a.clearRect(0,0,i.width,i.height),a.setTransform(c,0,0,c,0,0);let d=e.tubeMapPanelViews;d?Fr(a,d,e.tubeMapPanelHover,{width:e.paneWidth,lit:r!==null}):vr(a,o,{...s,width:e.paneWidth,highlightNode:r}),kr(a,e.tubeMapConnectors,e.connectorZoneBottom,r),a.setTransform(1,0,0,1,0,0)}else t.uploadGeometry(n),t.setNodeHighlights(r===null?new Map:new Map([[r,so]])),t.setEdgeHighlight(e.hoveredEdge,so),t.updateTransform(e.paintTransform),t.renderHighlights()}})).views(e=>{let t=yt(()=>{let n=e.layoutResult,o=n?.tubeMapPanels!==void 0,s=o?[]:n?.tubeMap?.layout.reads??[],r=e.drawnGraph?.paths??[],a=e.tubeMapColoring;return{bundled:r.some(i=>i.members),values:a&&s.length===0?[...[...a.palette].map(([i,c])=>({value:i,color:c})),...a.unvalued?[{value:`${a.field}: none`,color:Br}]:[]]:void 0,roles:!(a&&s.length===0)&&(o||n?.tubeMap!==void 0&&(!!e.tubeMapNodeColors||s.length===0&&(!Ne(r.length)||r.some(i=>i.members)))),haplotypeTube:!o&&e.tubeMapNodeColors?Dt[0]:Ir,logWidths:n?.tubeMap!==void 0&&!n.referenceAxis,foldBp:e.tubeMapDeviations.length>0?e.tubeMapFold:void 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