npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 6.3.1 → 6.4.0 - Mend

jbrowse-plugin-graphgenomeviewer 6.3.1 → 6.4.0

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package/dist/chunks/chunk-GXQ7NYB3.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{A as B,G as ge,J as we,P as ye,b as fe,c as pe,d as de,g as be}from"./chunk-GB7CF6Z2.js";import{a as q}from"./chunk-WTOQRUK2.js";import{D as N,P as me,Q as he,a as y,c as ue}from"./chunk-B7GF3TC3.js";import{a as K,b as P,c as v,d as X,e as R,f as ne,g as A,j as z}from"./chunk-MYJYGSOH.js";import{a as V,c as le,d as j}from"./chunk-DILFGQIL.js";import{a as F}from"./chunk-64LZZURD.js";import{a as nt,b as H}from"./chunk-FY3BTKY4.js";var xe=nt((en,ve)=>{ve.exports=JBrowseExports["@mui/material/SvgIcon"]});var L=H(xe(),1);function ln(e){return P(e)?Me(e):void 0}function Me(e){return{sample:V(e.stable.refName),haplotype:le(e.stable.refName),refName:j(e.stable.refName),start:e.stable.start,end:e.stable.start+e.length}}function ot(e,o){let s=[...e].sort((t,i)=>t.start-i.start),r,n;for(let t of s)n=n&&t.start-n.end<=o?{start:n.start,end:Math.max(n.end,t.end)}:{start:t.start,end:t.end},(!r\|\|n.end-n.start>r.end-r.start)&&(r=n);return r}function 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+  "sourcesContent": ["module.exports = JBrowseExports[\"@mui/material/SvgIcon\"];", "'use client';\n\nexport { createSvgIcon as default } from '@mui/material/SvgIcon';", "import { isAnchored } from '@jbrowse/bandage-core/anchoredNodes'\nimport {\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from '@jbrowse/bandage-core/pansn'\n\nimport type { AnchoredNode } from '@jbrowse/bandage-core/anchoredNodes'\nimport type { Graph, GraphNode } from '@jbrowse/bandage-core/types'\n\nexport interface GraphLocation {\n  // PanSN sample name off the node's own stable sequence. The assembly that\n  // contributed the sequence, which is a *name*, not a resolved assembly \u2014 see\n  // resolveContributors.\n  sample: string\n  // `sample#hap` where the stable name states a haplotype (HPRC release 2.1\n  // names every node `NA20809#2#CM094351.1`), so a sample loaded as two\n  // assemblies opens the right one; undefined where it states none\n  haplotype: string | undefined\n  refName: string\n  start: number\n  end: number\n}\n\n// Where a node's own sequence lives, in the coordinates of the assembly that\n// contributed it. rGFA states this on every segment: SN names the stable\n// sequence and SO the offset on it, so this is exact at every rank.\n//\n// It is the other question from nodeReferenceSpan, which asks where a node sits\n// on the *reference* axis and can only approximate that off the backbone. A\n// rank>0 node has an exact coordinate of its own; what it has no coordinate for\n// is the reference.\nexport function nodeOwnLocation(node: GraphNode): GraphLocation | undefined {\n  return isAnchored(node) ? anchoredNodeLocation(node) : undefined\n}\n\nfunction anchoredNodeLocation(node: AnchoredNode): GraphLocation {\n  return {\n    sample: panSNSample(node.stable.refName),\n    haplotype: panSNHaplotype(node.stable.refName),\n    refName: panSNContig(node.stable.refName),\n    start: node.stable.start,\n    end: node.stable.start + node.length,\n  }\n}\n\nexport interface Contributor extends GraphLocation {\n  // lowest rank this assembly holds here: 0 means it is the reference backbone\n  rank: number\n  nodeCount: number\n}\n\ninterface Span {\n  start: number\n  end: number\n}\n\n// The widest run of spans with no gap larger than `maxGap`, which is the locus\n// this assembly contributes *here*. A bare union of every span would be wrong\n// on a graph where a sample also contributes sequence from a distant\n// duplication: the union then reads as a multi-megabase locus, and a linear view\n// launched at it shows neither end.\nfunction widestCluster(spans: Span[], maxGap: number) {\n  const sorted = [...spans].sort((a, b) => a.start - b.start)\n  let best: Span | undefined\n  let current: Span | undefined\n  for (const span of sorted) {\n    current =\n      current && span.start - current.end <= maxGap\n        ? { start: current.start, end: Math.max(current.end, span.end) }\n        : { start: span.start, end: span.end }\n    if (!best || current.end - current.start > best.end - best.start) {\n      best = current\n    }\n  }\n  return best\n}\n\ninterface Group {\n  sample: string\n  haplotype: string | undefined\n  refName: string\n  rank: number\n  spans: Span[]\n}\n\nfunction groupKey(loc: GraphLocation) {\n  return `${loc.haplotype ?? loc.sample}\\u0000${loc.refName}`\n}\n\n// Every assembly with a segment in this graph, and the locus each one covers on\n// its own coordinates.\n//\n// This is what makes a launch out of the graph possible at all: the graph names\n// its contributors in the data (rGFA's SN tag), so a node, a row and the graph\n// as a whole can each say which assembly they belong to without consulting an\n// alignment.\n//\n// Ordered reference-first, then by name, so the row order matches\n// sampleRowLayout's and neither reshuffles as the window moves.\nexport function contributingAssemblies(\n  graph: Graph,\n  { maxGap = Infinity }: { maxGap?: number } = {},\n): Contributor[] {\n  const groups = new Map<string, Group>()\n  for (const node of graph.nodes) {\n    if (isAnchored(node)) {\n      const loc = anchoredNodeLocation(node)\n      const key = groupKey(loc)\n      const group = groups.get(key)\n      if (group) {\n        group.spans.push({ start: loc.start, end: loc.end })\n        group.rank = Math.min(group.rank, node.stable.rank)\n      } else {\n        groups.set(key, {\n          sample: loc.sample,\n          haplotype: loc.haplotype,\n          refName: loc.refName,\n          rank: node.stable.rank,\n          spans: [{ start: loc.start, end: loc.end }],\n        })\n      }\n    }\n  }\n\n  // One entry per assembly (a haplotype where the names state one, else the\n  // sample): an assembly contributing on several contigs is launched at the\n  // contig it contributes most of, since a linear view opens on one region.\n  const bySample = new Map<string, Contributor>()\n  for (const group of groups.values()) {\n    const span = widestCluster(group.spans, maxGap)\n    if (span) {\n      const candidate = {\n        sample: group.sample,\n        haplotype: group.haplotype,\n        refName: group.refName,\n        start: span.start,\n        end: span.end,\n        rank: group.rank,\n        nodeCount: group.spans.length,\n      }\n      const key = group.haplotype ?? group.sample\n      const existing = bySample.get(key)\n      if (!existing || candidate.nodeCount > existing.nodeCount) {\n        bySample.set(key, candidate)\n      }\n    }\n  }\n\n  // Reference first, then by name: the same order sampleRowLayout gives its\n  // rows, so the menu lists the assemblies in the order they are stacked on\n  // screen. Sorting by rank instead would order them by minigraph's build\n  // order, which is not what the labels beside the drawing say.\n  return [...bySample.values()].sort(\n    (a, b) =>\n      Number(a.rank !== 0) - Number(b.rank !== 0) ||\n      a.sample.localeCompare(b.sample) ||\n      (a.haplotype ?? '').localeCompare(b.haplotype ?? ''),\n  )\n}\n\n// The assembly a location opens on: its haplotype's where the name states one\n// and the session holds it, else its sample's. A session holding both\n// haplotypes of a sample opens the right one; one holding a haplotype under\n// the bare sample name still opens it.\nexport function resolveLocationAssembly(\n  resolve: (sample: string) => string | undefined,\n  loc: Pick<GraphLocation, 'sample' | 'haplotype'>,\n) {\n  const byHaplotype =\n    loc.haplotype === undefined ? undefined : resolve(loc.haplotype)\n  return byHaplotype ?? resolve(loc.sample)\n}\n\n// Contributors that name an assembly this session has loaded, which are the\n// only ones a linear or synteny view can open on.\n//\n// The two cases this filters apart are both normal. An E. coli pangenome demo\n// loads every strain as its own assembly, so every contributor resolves and the\n// whole graph is navigable. An HPRC graph names hundreds of haplotypes that no\n// session would ever load as assemblies, so only the reference resolves \u2014\n// there the reference projection (nodeReferenceSpan) is the way back to a\n// coordinate, not this.\n//\n// `resolve` is a name lookup rather than a list of names, because a PanSN sample\n// is the *graph's* spelling and need not be the assembly's. HPRC's graph writes\n// `CHM13`, and the assembly holding that sequence is UCSC's `hs1`, with CHM13\n// among its aliases; matching on names alone leaves that donor unopenable unless\n// the reader renames their assembly after the graph. The resolved (canonical)\n// name replaces the sample, so a launch opens the assembly the session knows.\nexport function resolveContributors(\n  contributors: Contributor[],\n  resolve: (sample: string) => string | undefined,\n) {\n  return contributors.flatMap(c => {\n    const sample = resolveLocationAssembly(resolve, c)\n    return sample === undefined ? [] : [{ ...c, sample }]\n  })\n}\n\n// 1-based inclusive, which is what a locstring means. Unformatted digits: this\n// is parsed, not read. locLabel is the one people read.\nexport function locString(loc: GraphLocation) {\n  return `${loc.refName}:${loc.start + 1}-${loc.end}`\n}\n\nexport function locLabel(loc: { refName: string; start: number; end: number }) {\n  return `${loc.refName}:${(loc.start + 1).toLocaleString()}-${loc.end.toLocaleString()}`\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z\"\n}), 'CompareArrows');", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2\"\n}), 'HighlightAlt');", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z\"\n}), 'LineStyle');", "import CompareArrowsIcon from '@mui/icons-material/CompareArrows'\nimport HighlightAltIcon from '@mui/icons-material/HighlightAlt'\nimport LineStyleIcon from '@mui/icons-material/LineStyle'\n\nimport { locLabel } from './contributors'\n\nimport type { Contributor, GraphLocation } from './contributors'\nimport type { LaunchableSyntenyTrack } from './syntenyTracks'\nimport type { MenuItem } from '@jbrowse/core/ui'\n\nconst LINEAR_LABEL = 'Linear genome view'\nconst SYNTENY_LABEL = 'Linear synteny view'\nconst NO_SYNTENY_TRACK =\n  'No synteny track in this session aligns these assemblies'\n\nexport interface LinearTarget {\n  location: GraphLocation\n  assembly: string\n}\n\n// One flat item when there is one thing to open, a submenu when there is a\n// choice. Same shape as subgraphMenuItems uses in the other direction, so the\n// two ends of the graph <-> linear trip read the same way.\nfunction oneOrMany<T>({\n  label,\n  icon,\n  entries,\n  entryLabel,\n  onSelect,\n  disabledHelpText,\n  nameTheOnlyEntry = true,\n}: {\n  label: string\n  icon: React.ElementType\n  entries: T[]\n  entryLabel: (entry: T) => string\n  onSelect: (entry: T) => () => void\n  disabledHelpText?: string\n  // Whether a lone entry's name is worth appending to the item. It is when the\n  // entry is where you land (`GRCh38 chr6:31,980,000-32,050,000`) and not when\n  // it is the ingredient used to get there \u2014 a synteny track's name says\n  // nothing the item does not already say, and reading it costs the width of\n  // `pggb graph: all-vs-all synteny (wfmash)`.\n  nameTheOnlyEntry?: boolean\n}): MenuItem[] {\n  const [first] = entries\n  // Nothing to open: a *disabled* item with the reason in its tooltip, when\n  // there is a reason worth reading. An item that vanishes teaches nobody that\n  // the session is one synteny track short of a multi-genome view.\n  const empty: MenuItem[] = disabledHelpText\n    ? [{ label, icon, disabled: true, disabledHelpText, onClick: () => {} }]\n    : []\n  return entries.length === 0\n    ? empty\n    : entries.length === 1 && first\n      ? [\n          {\n            label: nameTheOnlyEntry ? `${label} \u2014 ${entryLabel(first)}` : label,\n            icon,\n            onClick: onSelect(first),\n          },\n        ]\n      : [\n          {\n            label,\n            icon,\n            type: 'subMenu',\n            subMenu: entries.map(entry => ({\n              label: entryLabel(entry),\n              onClick: onSelect(entry),\n            })),\n          },\n        ]\n}\n\n// The graph's way out: a linear view of any assembly the graph names here, and a\n// synteny view of all of them at once. Until this existed the triangle had two\n// edges \u2014 a linear view could open a graph or a synteny view of a locus, and the\n// graph could open nothing at all.\n//\n// `contributors` are already resolved against the session's assemblies. On an\n// E. coli pangenome every strain is its own assembly, so all of them appear and\n// the synteny item is the interesting one; on an HPRC graph the 400-odd\n// contributing haplotypes are not loaded assemblies and only the reference\n// appears, which is the honest answer rather than a missing feature.\nexport function graphLaunchMenuItems({\n  contributors,\n  syntenyTracks,\n  onShowLinear,\n  onShowSynteny,\n}: {\n  contributors: Contributor[]\n  syntenyTracks: LaunchableSyntenyTrack[]\n  onShowLinear: (target: LinearTarget) => void\n  onShowSynteny: (trackId: string) => void\n}): MenuItem[] {\n  // sorted widest first\n  const widest = syntenyTracks[0]?.coverage ?? contributors.length\n  return [\n    ...oneOrMany({\n      label: LINEAR_LABEL,\n      icon: LineStyleIcon,\n      entries: contributors,\n      entryLabel: c => `${c.sample} ${locLabel(c)}`,\n      onSelect: c => () => {\n        onShowLinear({ location: c, assembly: c.sample })\n      },\n    }),\n    ...(contributors.length >= 2\n      ? oneOrMany({\n          // the count the launch opens, which is what the widest track aligns\n          // and not always every contributor; see launchSyntenyView\n          label: `${SYNTENY_LABEL} (${widest} assemblies)`,\n          icon: CompareArrowsIcon,\n          entries: syntenyTracks,\n          entryLabel: track =>\n            track.coverage < widest\n              ? `${track.name} (${track.coverage} of ${widest})`\n              : track.name,\n          nameTheOnlyEntry: false,\n          disabledHelpText: NO_SYNTENY_TRACK,\n          onSelect: track => () => {\n            onShowSynteny(track.trackId)\n          },\n        })\n      : []),\n  ]\n}\n\n// A single node's way out, for the node context menu. Two different questions,\n// both worth offering:\n//\n//   - the node's own coordinates, on the assembly that contributed it. Exact,\n//     from the node's SN/SO, and available at every rank \u2014 but only openable\n//     when that assembly is loaded, which for an HPRC haplotype it is not.\n//   - where the node sits on the reference the graph was cut against. Always\n//     openable, and off the backbone it is the flanking projection rather than\n//     an exact span (see nodeReferenceSpan), so it is labelled as the region\n//     around the node rather than as the node.\n//\n// Labels are verbs. Review: \"the lineargenomeview menu item should say launch\n// if that is what it does\" \u2014 a bare `Linear genome view \u2014 hg38 chr6:\u2026` names a\n// place and leaves the reader to guess whether clicking scrolls the view beside\n// the graph or opens a new one. It does the first when there is one to scroll\n// (see showInLinearView), so \"Open in\" covers both without claiming a launch.\n//\n// Verb, assembly, and where \u2014 nothing else. Every word here is read inside a\n// menu opened on a node, so \"this node in the hg38 view\" and \"in linear view\"\n// restate the context they are already in; what a coordinate opens in is not in\n// question, and the assembly name is.\n//\n// Flat, not under a \"Launch view\" submenu: this menu is a handful of items and\n// every one is contextual to the node just clicked.\nexport function nodeLaunchMenuItems({\n  own,\n  reference,\n  highlight,\n  onShowLinear,\n  onHighlight,\n}: {\n  own: LinearTarget | undefined\n  reference: LinearTarget | undefined\n  // the node's exact reference span, where `reference` is padded to open on\n  highlight: LinearTarget | undefined\n  onShowLinear: (target: LinearTarget) => void\n  // absent when no linear view in the session is this graph's to mark\n  onHighlight?: (target: LinearTarget) => void\n}): MenuItem[] {\n  const entries = [\n    own\n      ? {\n          label: `Open in ${own.assembly} \u2014 ${locLabel(own.location)}`,\n          target: own,\n        }\n      : undefined,\n    // Only when it says something the item above doesn't. A backbone segment on\n    // a loaded reference answers both questions with the same assembly and\n    // nearly the same span, and offering that twice reads as two different\n    // places to go.\n    reference && reference.assembly !== own?.assembly\n      ? {\n          label: `Open in ${reference.assembly} \u2014 around this node`,\n          target: reference,\n        }\n      : undefined,\n  ].filter(entry => entry !== undefined)\n\n  // The reference projection, not the node's own coordinates: a highlight is\n  // drawn in the linear view already on screen, and that view is on the\n  // reference the subgraph was cut from.\n  return [\n    ...(onHighlight && highlight\n      ? [\n          {\n            label: `Highlight in ${highlight.assembly}`,\n            icon: HighlightAltIcon,\n            onClick: () => {\n              onHighlight(highlight)\n            },\n          },\n        ]\n      : []),\n    ...entries.map(({ label, target }) => ({\n      label,\n      icon: LineStyleIcon,\n      onClick: () => {\n        onShowLinear(target)\n      },\n    })),\n  ]\n}\n", "import {\n  buildNeighbors\n} from \"./chunk-ES2N6V56.js\";\nimport {\n  REFERENCE_RANK,\n  isAnchored\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/alleleProjection/projectAlleles.ts\nfunction parsePanSN(refName) {\n  const parts = refName.split(\"#\");\n  const haplotype = parts.length >= 2 ? Number(parts[1]) : Number.NaN;\n  return {\n    sample: parts[0] ?? refName,\n    haplotype: Number.isFinite(haplotype) ? haplotype : void 0\n  };\n}\nfunction collectRun(seed, byId, adj, claimed) {\n  const members = [];\n  const anchors = [];\n  const queue = [seed];\n  claimed.add(seed);\n  while (queue.length > 0) {\n    const id = queue.pop();\n    const node = byId.get(id);\n    if (node) {\n      members.push(node);\n      for (const neighborId of adj.get(id) ?? []) {\n        const neighbor = byId.get(neighborId);\n        if (neighbor) {\n          if (neighbor.stable.rank === REFERENCE_RANK) {\n            anchors.push(neighbor);\n          } else if (!claimed.has(neighborId)) {\n            claimed.add(neighborId);\n            queue.push(neighborId);\n          }\n        }\n      }\n    }\n  }\n  return { members, anchors };\n}\nfunction anchorSpan(anchors) {\n  const refNames = new Set(anchors.map((a) => a.stable.refName));\n  if (refNames.size !== 1 || anchors.length < 2) {\n    return void 0;\n  }\n  const sorted = [...anchors].sort((a, b) => a.stable.start - b.stable.start);\n  const first = sorted[0];\n  const last = sorted.at(-1);\n  const start = first.stable.start + first.length;\n  const end = last.stable.start;\n  return end >= start ? { start, end, entry: first } : void 0;\n}\nfunction runDistances(members, entry, adj) {\n  const byId = new Map(members.map((m) => [m.id, m]));\n  const dist = /* @__PURE__ */ new Map();\n  const queue = [];\n  for (const neighborId of adj.get(entry.id) ?? []) {\n    if (byId.has(neighborId)) {\n      dist.set(neighborId, 0);\n      queue.push(neighborId);\n    }\n  }\n  if (queue.length === 0) {\n    for (const member of members) {\n      dist.set(member.id, 0);\n      queue.push(member.id);\n    }\n  }\n  for (const id of queue) {\n    const reach = dist.get(id) + byId.get(id).length;\n    for (const neighborId of adj.get(id) ?? []) {\n      if (byId.has(neighborId)) {\n        const known = dist.get(neighborId);\n        if (known === void 0 || reach < known) {\n          dist.set(neighborId, reach);\n          queue.push(neighborId);\n        }\n      }\n    }\n  }\n  return dist;\n}\nfunction runOffsets(members, entry, adj) {\n  const dist = runDistances(members, entry, adj);\n  const ordered = [...members].sort((a, b) => dist.get(a.id) - dist.get(b.id));\n  const rank = new Map(ordered.map((m, i) => [m.id, i]));\n  const byId = new Map(members.map((m) => [m.id, m]));\n  const offsets = /* @__PURE__ */ new Map();\n  for (const [i, member] of ordered.entries()) {\n    let offset = 0;\n    for (const neighborId of adj.get(member.id) ?? []) {\n      const neighbor = byId.get(neighborId);\n      if (neighbor && rank.get(neighborId) < i) {\n        offset = Math.max(offset, offsets.get(neighborId) + neighbor.length);\n      }\n    }\n    offsets.set(member.id, offset);\n  }\n  return { offsets, ordered };\n}\nfunction projectAlleles(graph) {\n  const byId = new Map(\n    graph.nodes.filter(isAnchored).map((n) => [n.id, n])\n  );\n  const adj = buildNeighbors(graph);\n  const claimed = /* @__PURE__ */ new Set();\n  const alleles = [];\n  for (const node of byId.values()) {\n    if (node.stable.rank !== REFERENCE_RANK && !claimed.has(node.id)) {\n      const { members, anchors } = collectRun(node.id, byId, adj, claimed);\n      const span = anchorSpan(anchors);\n      if (span) {\n        const { offsets, ordered } = runOffsets(members, span.entry, adj);\n        alleles.push({\n          start: span.start,\n          refSpan: span.end - span.start,\n          nodeIds: ordered.map((m) => m.id),\n          nodeOffsets: ordered.map((m) => offsets.get(m.id)),\n          pathLength: ordered.reduce(\n            (max, m) => Math.max(max, offsets.get(m.id) + m.length),\n            0\n          )\n        });\n      }\n    }\n  }\n  return alleles.sort((a, b) => a.start - b.start);\n}\n\nexport {\n  parsePanSN,\n  projectAlleles\n};\n", "import {\n  projectAlleles\n} from \"./chunk-RVS2QCOX.js\";\nimport {\n  buildNeighbors\n} from \"./chunk-ES2N6V56.js\";\n\n// src/layout/placeOffReference.ts\nvar MIN_DELETION_BP = 1;\nvar MIN_ALLELE_SPAN_FRACTION = 0.015;\nfunction placeOffReference({\n  graph,\n  span,\n  rowY,\n  positions\n}) {\n  const minSpan = span * MIN_ALLELE_SPAN_FRACTION;\n  const alleles = projectAlleles(graph);\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const alleleDeletions = [];\n  for (const allele of alleles) {\n    const skipped = allele.refSpan - allele.pathLength;\n    if (skipped >= MIN_DELETION_BP) {\n      alleleDeletions.push({ nodeIds: allele.nodeIds, bp: skipped });\n    }\n    const drawn = Math.max(allele.refSpan, minSpan);\n    const scale = allele.pathLength > 0 ? drawn / allele.pathLength : 0;\n    allele.nodeIds.forEach((nodeId, i) => {\n      const node = byId.get(nodeId);\n      if (node) {\n        const offset = allele.nodeOffsets[i];\n        const even = drawn / allele.nodeIds.length;\n        const at = (bp) => allele.start + bp * scale;\n        const y = rowY(node);\n        positions[nodeId] = scale ? [\n          { x: at(offset), y },\n          { x: at(offset + node.length), y }\n        ] : [\n          { x: allele.start + i * even, y },\n          { x: allele.start + (i + 1) * even, y }\n        ];\n      }\n    });\n  }\n  const neighbors = buildNeighbors(graph);\n  const queue = Object.keys(positions);\n  for (const fromId of queue) {\n    const fromEnd = positions[fromId].at(-1).x;\n    for (const nextId of neighbors.get(fromId) ?? []) {\n      const next = byId.get(nextId);\n      if (next && !(nextId in positions)) {\n        const y = rowY(next);\n        positions[nextId] = [\n          { x: fromEnd, y },\n          { x: fromEnd + minSpan, y }\n        ];\n        queue.push(nextId);\n      }\n    }\n  }\n  return alleleDeletions;\n}\n\nexport {\n  placeOffReference\n};\n", "import {\n  placeOffReference\n} from \"./chunk-TZFWUT2C.js\";\nimport {\n  parsePanSN\n} from \"./chunk-RVS2QCOX.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  backboneNodes,\n  backbonePositions,\n  isOffReference,\n  referenceSpan\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/sampleRowLayout.ts\nfunction contributingSamples(graph, keep) {\n  const carried = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    if (isOffReference(node)) {\n      const { sample } = parsePanSN(node.stable.refName);\n      carried.set(sample, (carried.get(sample) ?? 0) + node.length);\n    }\n  }\n  const held = new Map(keep.map((sample, row) => [sample, row]));\n  return [...carried.keys()].sort(\n    (a, b) => (held.get(a) ?? Infinity) - (held.get(b) ?? Infinity) || carried.get(b) - carried.get(a) || a.localeCompare(b)\n  );\n}\nfunction sampleRowLayout(graph, region, keep = []) {\n  const backbone = backboneNodes(graph);\n  const samples = contributingSamples(graph, keep);\n  if (backbone.length === 0 || samples.length === 0) {\n    return void 0;\n  }\n  const span = referenceSpan(backbone, region);\n  const rowOf = new Map(samples.map((s, i) => [s, i + 1]));\n  const nodePositions = backbonePositions(backbone);\n  const spareRow = samples.length + 1;\n  const alleleDeletions = placeOffReference({\n    graph,\n    span,\n    rowY: (node) => {\n      const stable = node.stable;\n      const row = stable ? rowOf.get(parsePanSN(stable.refName).sample) : void 0;\n      return (row ?? spareRow) * ROW_HEIGHT_PX;\n    },\n    positions: nodePositions\n  });\n  const referenceSample = parsePanSN(backbone[0].stable.refName).sample;\n  const rowLabels = [\n    { label: referenceSample, y: 0 },\n    ...samples.map((sample) => ({\n      label: sample,\n      y: rowOf.get(sample) * ROW_HEIGHT_PX\n    }))\n  ];\n  return {\n    nodePositions,\n    rowLabels,\n    sampleRows: samples,\n    referenceAxis: true,\n    pixelRows: true,\n    alleleDeletions\n  };\n}\n\nexport {\n  sampleRowLayout\n};\n", "import {\n  canonicalStrand,\n  stepName,\n  tubeMapReads\n} from \"./chunk-TEDQJPMI.js\";\nimport {\n  pathCssColor,\n  pathGreyCssColor\n} from \"./chunk-7GBL7SJY.js\";\nimport {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/tubeMapLayout.ts\nimport { layoutTubeMap } from \"@jbrowse/tubemap-core\";\nfunction visitStrands(graph) {\n  const strands = /* @__PURE__ */ new Map();\n  for (const [segment, visits] of graph.pathVisits ?? []) {\n    for (const visit of visits) {\n      const key = `${visit.path}\t${segment}`;\n      const list = strands.get(key);\n      if (list) {\n        list.push(visit.strand);\n      } else {\n        strands.set(key, [visit.strand]);\n      }\n    }\n  }\n  return strands;\n}\nfunction tubeMapTracks(graph) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const strands = visitStrands(graph);\n  const paths = (graph.paths ?? []).map((path, index) => ({ path, index }));\n  const reference = paths.findIndex(\n    (p) => pathOrigin(p.path.name).name === graph.referencePath\n  );\n  if (reference > 0) {\n    paths.unshift(...paths.splice(reference, 1));\n  }\n  return paths.flatMap(({ path, index }) => {\n    const visitName = pathOrigin(path.name).name;\n    const seen = /* @__PURE__ */ new Map();\n    const sequence = path.nodeIds.flatMap((id) => {\n      const node = nodeById.get(id);\n      if (!node) {\n        return [];\n      }\n      const k = seen.get(node.name) ?? 0;\n      seen.set(node.name, k + 1);\n      const strand = strands.get(`${visitName}\t${node.name}`)?.[k] ?? canonicalStrand(node);\n      return [stepName(node, strand)];\n    });\n    return sequence.length > 0 ? [\n      {\n        id: index,\n        name: path.name,\n        sequence,\n        sourceTrackID: 0,\n        type: \"haplotype\"\n      }\n    ] : [];\n  });\n}\nfunction tubeMapNodes(graph) {\n  return graph.nodes.map((n) => ({\n    name: n.id,\n    seq: \"\",\n    sequenceLength: Math.max(1, n.length)\n  }));\n}\nfunction hasTubeMapPaths(graph) {\n  return (graph.paths?.length ?? 0) > 0;\n}\nvar STACK_PX = 600;\nvar MIN_TUBE_PX = 3;\nvar MAX_TUBE_PX = 15;\nfunction tubeWidth(trackCount) {\n  return Math.max(\n    MIN_TUBE_PX,\n    Math.min(MAX_TUBE_PX, Math.floor(STACK_PX / Math.max(1, trackCount)))\n  );\n}\nfunction runTubeMap(graph) {\n  const paths = graph.paths ?? [];\n  const tracks = tubeMapTracks(graph);\n  const reads = graph.reads ? tubeMapReads(graph, graph.reads, paths.length) : [];\n  const tubeColor = reads.length > 0 ? pathGreyCssColor : pathCssColor;\n  const pathColors = paths.map((_, i) => tubeColor(i, paths.length));\n  const layout = layoutTubeMap(tubeMapNodes(graph), tracks, reads, {\n    nodeWidthOption: \"compressed\",\n    trackWidth: tubeWidth(tracks.length)\n  });\n  return layout ? { layout, pathColors } : void 0;\n}\nfunction drawnNodes(layout) {\n  const nodes = [];\n  layout.nodes.forEach((node) => {\n    if (node.order >= 0) {\n      nodes.push(node);\n    }\n  });\n  return nodes;\n}\nfunction centreline(node, yOffset, x0, x1) {\n  const y = node.y + node.contentHeight / 2 - yOffset;\n  return [\n    { x: x0, y },\n    { x: x1, y }\n  ];\n}\nfunction extentOf(layout, yOffset) {\n  return {\n    minY: layout.bounds.minY - yOffset,\n    maxY: layout.bounds.maxY - yOffset\n  };\n}\nfunction tubeMapLayout(graph) {\n  const run = hasTubeMapPaths(graph) ? runTubeMap(graph) : void 0;\n  if (!run) {\n    return void 0;\n  }\n  const { layout, pathColors } = run;\n  const yOffset = layout.bounds.minY;\n  const nodePositions = {};\n  for (const node of drawnNodes(layout)) {\n    nodePositions[node.name] = centreline(\n      node,\n      yOffset,\n      node.x,\n      node.x + node.pixelWidth\n    );\n  }\n  const { minY, maxY } = extentOf(layout, yOffset);\n  return {\n    nodePositions,\n    tubeMap: { layout, yOffset, pathColors },\n    extent: {\n      minX: layout.bounds.minX,\n      maxX: layout.bounds.maxX,\n      minY,\n      maxY\n    }\n  };\n}\nfunction tubeMapColumns(graph, layout) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const byOrder = /* @__PURE__ */ new Map();\n  for (const node of drawnNodes(layout)) {\n    const list = byOrder.get(node.order);\n    if (list) {\n      list.push(node);\n    } else {\n      byOrder.set(node.order, [node]);\n    }\n  }\n  const columns = [];\n  let end = -Infinity;\n  for (const order of [...byOrder.keys()].sort((a, b) => a - b)) {\n    const nodes = byOrder.get(order);\n    let bp0 = Infinity;\n    let bp1 = -Infinity;\n    for (const node of nodes) {\n      const graphNode = nodeById.get(node.name);\n      if (graphNode && isBackbone(graphNode)) {\n        bp0 = Math.min(bp0, graphNode.stable.start);\n        bp1 = Math.max(bp1, graphNode.stable.start + node.sequenceLength);\n      }\n    }\n    if (bp0 === Infinity) {\n      bp0 = bp1 = end;\n    }\n    if (bp0 < end) {\n      bp0 = end;\n      bp1 = Math.max(end, bp1);\n    }\n    end = Math.max(end, bp1);\n    columns.push({\n      order,\n      x0: Math.min(...nodes.map((n) => n.x)),\n      x1: Math.max(...nodes.map((n) => n.x + n.pixelWidth)),\n      bp0,\n      bp1\n    });\n  }\n  const first = columns.find((c) => c.bp0 !== -Infinity);\n  for (const column of columns) {\n    if (column.bp0 === -Infinity) {\n      column.bp0 = column.bp1 = first?.bp0 ?? 0;\n    }\n  }\n  return columns;\n}\nfunction pathsReachBackbone(graph) {\n  return graph.nodes.some(isBackbone) && hasTubeMapPaths(graph);\n}\nfunction tubeMapReferenceLayout(graph) {\n  const run = pathsReachBackbone(graph) ? runTubeMap(graph) : void 0;\n  if (!run) {\n    return void 0;\n  }\n  const { layout, pathColors } = run;\n  const columns = tubeMapColumns(graph, layout);\n  const byOrder = new Map(columns.map((c) => [c.order, c]));\n  const yOffset = layout.bounds.minY;\n  const nodePositions = {};\n  for (const node of drawnNodes(layout)) {\n    const column = byOrder.get(node.order);\n    nodePositions[node.name] = centreline(node, yOffset, column.bp0, column.bp1);\n  }\n  return {\n    nodePositions,\n    tubeMap: { layout, yOffset, columns, pathColors },\n    referenceAxis: true,\n    pixelRows: true,\n    extent: extentOf(layout, yOffset)\n  };\n}\n\nexport {\n  visitStrands,\n  tubeMapTracks,\n  hasTubeMapPaths,\n  tubeWidth,\n  tubeMapLayout,\n  tubeMapReferenceLayout\n};\n", "import {\n  placeOffReference\n} from \"./chunk-TZFWUT2C.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  backboneNodes,\n  backbonePositions,\n  referenceSpan\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/anchoredLayout.ts\nfunction rankRows(graph) {\n  const present = /* @__PURE__ */ new Set();\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      present.add(node.stable.rank);\n    }\n  }\n  return new Map([...present].sort((a, b) => a - b).map((r, i) => [r, i]));\n}\nfunction anchoredLayout(graph, region) {\n  const backbone = backboneNodes(graph);\n  if (backbone.length === 0) {\n    return void 0;\n  }\n  const span = referenceSpan(backbone, region);\n  const rows = rankRows(graph);\n  const nodePositions = backbonePositions(backbone);\n  const alleleDeletions = placeOffReference({\n    graph,\n    span,\n    rowY: (node) => (node.stable ? rows.get(node.stable.rank) ?? rows.size : rows.size) * ROW_HEIGHT_PX,\n    positions: nodePositions\n  });\n  const rowLabels = [...rows].map(([rank, row]) => ({\n    label: rank === 0 ? \"Reference (rank 0)\" : `Rank ${rank}`,\n    y: row * ROW_HEIGHT_PX\n  }));\n  return {\n    nodePositions,\n    rowLabels,\n    referenceAxis: true,\n    pixelRows: true,\n    alleleDeletions\n  };\n}\n\nexport {\n  anchoredLayout\n};\n", "import {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/orderedLayout.ts\nvar GUTTER = 12;\nvar LANE_PX = ROW_HEIGHT_PX;\nfunction nodeWidth(node) {\n  return 10 + 8 * Math.log2(1 + node.length);\n}\nfunction compare(a, b) {\n  return a < b ? -1 : a > b ? 1 : 0;\n}\nfunction compareKeys(a, b) {\n  return compare(a.at, b.at) || compare(a.side, b.side) || compare(a.hops, b.hops);\n}\nvar UNREACHED = { at: Infinity, side: 0, hops: 0 };\nfunction referenceOrder(graph) {\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const key = orderKeys(graph);\n  return graph.nodes.map((n) => n.id).sort(\n    (a, b) => compareKeys(key.get(a) ?? UNREACHED, key.get(b) ?? UNREACHED) || compare(byId.get(a).name, byId.get(b).name) || compare(a, b)\n  );\n}\nfunction placeByWalks(graph, backbone) {\n  const isNode = new Set(graph.nodes.map((n) => n.id));\n  const startOf = new Map(backbone.map((n) => [n.id, n.stable.start]));\n  const next = /* @__PURE__ */ new Map();\n  const prev = /* @__PURE__ */ new Map();\n  backbone.forEach((n, i) => {\n    prev.set(n.id, backbone[i - 1]?.id);\n    next.set(n.id, backbone[i + 1]?.id);\n  });\n  let head = backbone[0]?.id;\n  const insertAfter = (at, id) => {\n    const after = next.get(at);\n    next.set(at, id);\n    prev.set(id, at);\n    next.set(id, after);\n    if (after !== void 0) {\n      prev.set(after, id);\n    }\n  };\n  const insertBefore = (at, id) => {\n    const before = prev.get(at);\n    if (before === void 0) {\n      head = id;\n      prev.set(id, void 0);\n      next.set(id, at);\n      prev.set(at, id);\n    } else {\n      insertAfter(before, id);\n    }\n  };\n  for (const path of graph.paths ?? []) {\n    let rising = 0;\n    let falling = 0;\n    let last;\n    for (const id of path.nodeIds) {\n      const start = startOf.get(id);\n      if (start !== void 0) {\n        if (last !== void 0 && start !== last) {\n          if (start > last) {\n            rising++;\n          } else {\n            falling++;\n          }\n        }\n        last = start;\n      }\n    }\n    const ids = falling > rising ? [...path.nodeIds].reverse() : path.nodeIds;\n    let from;\n    const leading = /* @__PURE__ */ new Set();\n    for (const id of ids) {\n      if (next.has(id)) {\n        if (from === void 0) {\n          for (const lead of leading) {\n            insertBefore(id, lead);\n          }\n        }\n        from = id;\n      } else if (isNode.has(id)) {\n        if (from === void 0) {\n          leading.add(id);\n        } else {\n          insertAfter(from, id);\n          from = id;\n        }\n      }\n    }\n  }\n  const placed = [];\n  for (let id = head; id !== void 0; id = next.get(id)) {\n    placed.push(id);\n  }\n  return placed;\n}\nfunction placeBySearch(adjacent, key) {\n  const queue = [...key.entries()].sort(([a, ka], [b, kb]) => compareKeys(ka, kb) || compare(a, b)).map(([id]) => id);\n  const placed = queue.length;\n  for (const id of queue) {\n    const from = key.get(id);\n    for (const nb of adjacent.get(id) ?? []) {\n      if (!key.has(nb)) {\n        key.set(nb, { at: from.at, side: 1, hops: from.hops + 1 });\n        queue.push(nb);\n      }\n    }\n  }\n  const searched = new Set(queue.slice(placed));\n  const sided = /* @__PURE__ */ new Set();\n  for (const seed of searched) {\n    if (sided.has(seed)) {\n      continue;\n    }\n    const { at } = key.get(seed);\n    const run = [seed];\n    sided.add(seed);\n    let farHalf = true;\n    for (const id of run) {\n      const { hops } = key.get(id);\n      let deadEnd = true;\n      let touchesLeft = false;\n      for (const nb of adjacent.get(id) ?? []) {\n        const other = key.get(nb);\n        if (other.at === at && searched.has(nb)) {\n          deadEnd &&= other.hops <= hops;\n          if (!sided.has(nb)) {\n            sided.add(nb);\n            run.push(nb);\n          }\n        } else if (other.at !== at) {\n          touchesLeft ||= other.at < at;\n          farHalf &&= other.at < at;\n        }\n      }\n      farHalf &&= !deadEnd || touchesLeft;\n    }\n    if (farHalf) {\n      for (const id of run) {\n        const k = key.get(id);\n        key.set(id, { ...k, side: -1, hops: -k.hops });\n      }\n    }\n  }\n}\nfunction orderKeys(graph) {\n  const ids = new Set(graph.nodes.map((n) => n.id));\n  const adjacent = /* @__PURE__ */ new Map();\n  for (const e of graph.edges) {\n    if (!ids.has(e.from) || !ids.has(e.to)) {\n      continue;\n    }\n    ;\n    (adjacent.get(e.from) ?? adjacent.set(e.from, []).get(e.from)).push(e.to);\n    (adjacent.get(e.to) ?? adjacent.set(e.to, []).get(e.to)).push(e.from);\n  }\n  const backbone = graph.nodes.filter(isBackbone).sort(\n    (a, b) => compare(a.stable.start, b.stable.start) || compare(a.name, b.name)\n  );\n  const key = /* @__PURE__ */ new Map();\n  placeByWalks(graph, backbone).forEach((id, rank) => {\n    key.set(id, { at: rank, side: 0, hops: 0 });\n  });\n  placeBySearch(adjacent, key);\n  return key;\n}\nfunction layerGraph(graph) {\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const order = referenceOrder(graph);\n  const key = new Map(order.map((id, i) => [id, i]));\n  const isRef = (id) => isBackbone(byId.get(id));\n  const preds = new Map(order.map((id) => [id, []]));\n  const succs = new Map(order.map((id) => [id, []]));\n  const link = (a, b) => {\n    preds.get(b).push(a);\n    succs.get(a).push(b);\n  };\n  for (const e of graph.edges) {\n    if (e.from === e.to || !key.has(e.from) || !key.has(e.to)) {\n      continue;\n    }\n    if (key.get(e.from) < key.get(e.to)) {\n      link(e.from, e.to);\n    } else {\n      link(e.to, e.from);\n    }\n  }\n  const backbone = order.filter(isRef);\n  for (let i = 1; i < backbone.length; i++) {\n    link(backbone[i - 1], backbone[i]);\n  }\n  const layerOf = /* @__PURE__ */ new Map();\n  for (const id of order) {\n    let l = 0;\n    for (const p of preds.get(id)) {\n      l = Math.max(l, layerOf.get(p) + 1);\n    }\n    layerOf.set(id, l);\n  }\n  for (let i = order.length - 1; i >= 0; i--) {\n    const id = order[i];\n    const s = succs.get(id);\n    if (isRef(id) || s.length === 0) {\n      continue;\n    }\n    let minSucc = Infinity;\n    for (const t of s) {\n      minSucc = Math.min(minSucc, layerOf.get(t));\n    }\n    const lo = layerOf.get(id);\n    const hi = Math.max(lo, minSucc - 1);\n    layerOf.set(id, Math.floor((lo + hi) / 2));\n  }\n  const layers = [];\n  for (const id of order) {\n    ;\n    (layers[layerOf.get(id)] ??= []).push(id);\n  }\n  return { layers, layerOf, preds };\n}\nfunction orderedLayout(graph) {\n  if (!graph.nodes.some(isBackbone)) {\n    return void 0;\n  }\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const isRef = (id) => isBackbone(byId.get(id));\n  const { layers, layerOf: layer, preds } = layerGraph(graph);\n  const layerWidth = layers.map((ids) => {\n    let w = 0;\n    for (const id of ids) {\n      w = Math.max(w, nodeWidth(byId.get(id)));\n    }\n    return w;\n  });\n  const layerX = [];\n  let x = 0;\n  for (let l = 0; l < layers.length; l++) {\n    layerX[l] = x;\n    x += layerWidth[l] + GUTTER;\n  }\n  const y = /* @__PURE__ */ new Map();\n  for (const ids of layers) {\n    const free = [];\n    for (const id of ids) {\n      if (isRef(id)) {\n        y.set(id, 0);\n        continue;\n      }\n      const placed = preds.get(id).filter((p) => y.has(p));\n      let ideal = 0;\n      for (const p of placed) {\n        ideal += y.get(p) / placed.length;\n      }\n      free.push({ id, ideal: ideal === 0 ? LANE_PX : ideal });\n    }\n    free.sort((a, b) => a.ideal - b.ideal);\n    const taken = /* @__PURE__ */ new Set([0]);\n    for (const { id, ideal } of free) {\n      let lane = Math.round(ideal / LANE_PX);\n      if (lane === 0) {\n        lane = ideal >= 0 ? 1 : -1;\n      }\n      for (let d = 1; taken.has(lane); d++) {\n        if (!taken.has(lane + d)) {\n          lane += d;\n        } else if (!taken.has(lane - d)) {\n          lane -= d;\n        }\n      }\n      taken.add(lane);\n      y.set(id, lane * LANE_PX);\n    }\n  }\n  const nodePositions = {};\n  for (const n of graph.nodes) {\n    const l = layer.get(n.id);\n    const w = nodeWidth(n);\n    const cx = layerX[l] + layerWidth[l] / 2;\n    const ny = y.get(n.id);\n    nodePositions[n.id] = [\n      { x: cx - w / 2, y: ny },\n      { x: cx + w / 2, y: ny }\n    ];\n  }\n  return { nodePositions, referenceAxis: false, pixelRows: true };\n}\n\nexport {\n  referenceOrder,\n  layerGraph,\n  orderedLayout\n};\n", "import {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\nimport {\n  panSNContig,\n  panSNSample\n} from \"./chunk-BPLIXMH7.js\";\n\n// src/layout/walkRows.ts\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nfunction stepsOf(pieces, lengthOf) {\n  const steps = [];\n  let end;\n  for (const piece of pieces) {\n    if (end !== void 0 && piece.start !== void 0 && piece.start > end) {\n      steps.push(piece.start - end);\n    }\n    steps.push(...piece.nodeIds);\n    const bp = piece.nodeIds.reduce(\n      (sum, id) => sum + (lengthOf.get(id) ?? 0),\n      0\n    );\n    end = piece.start === void 0 ? void 0 : piece.start + bp;\n  }\n  return steps;\n}\nfunction stepSpans(pieces, lengthOf) {\n  const spans = [];\n  let end;\n  for (const piece of pieces) {\n    if (piece.start === void 0 || end !== void 0 && piece.start < end) {\n      return void 0;\n    }\n    if (end !== void 0 && piece.start > end) {\n      spans.push({ start: end, end: piece.start });\n    }\n    let pos = piece.start;\n    for (const id of piece.nodeIds) {\n      const len = lengthOf.get(id) ?? 0;\n      spans.push({ start: pos, end: pos + len });\n      pos += len;\n    }\n    end = pos;\n  }\n  return spans;\n}\nfunction sliceBetween(steps, span, region, flanked = true) {\n  if (!region || !flanked) {\n    return { ids: steps, complete: true, from: -1, to: -1 };\n  }\n  let i0 = -1;\n  let i1 = -1;\n  let bestEnd = -Infinity;\n  let bestStart = Infinity;\n  steps.forEach((id, i) => {\n    const s = typeof id === \"string\" ? span.get(id) : void 0;\n    if (s) {\n      if (s.end <= region.start && s.end > bestEnd) {\n        bestEnd = s.end;\n        i0 = i;\n      }\n      if (s.start >= region.end && s.start < bestStart) {\n        bestStart = s.start;\n        i1 = i;\n      }\n    }\n  });\n  if (i0 < 0 || i1 < 0) {\n    return { ids: steps, complete: false, from: -1, to: -1 };\n  }\n  const ids = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));\n  return {\n    ids: i0 < i1 ? ids : ids.reverse(),\n    complete: true,\n    from: i0,\n    to: i1\n  };\n}\nfunction filterSamples(rows, samples) {\n  return samples ? rows.filter((r) => samples.includes(r.sample)).sort(\n    (a, b) => samples.indexOf(a.sample) - samples.indexOf(b.sample) || a.label.localeCompare(b.label)\n  ) : rows;\n}\nfunction walkRows(graph, region, unit) {\n  const paths = graph.paths ?? [];\n  const isReference = (p) => pathOrigin(p.name).name === graph.referencePath;\n  const referencePieces = paths.some(isReference) ? paths.filter(isReference).sort((a, b) => (a.start ?? 0) - (b.start ?? 0)) : paths.slice(0, 1);\n  const first = referencePieces[0];\n  const others = paths.filter((p) => !referencePieces.includes(p));\n  if (!first || others.length === 0) {\n    return void 0;\n  }\n  const walks = /* @__PURE__ */ new Map();\n  for (const path of others) {\n    walks.set(path.name, [...walks.get(path.name) ?? [], path]);\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const referenceStart = first.start ?? 0;\n  const cut = region && region.end > region.start ? region : void 0;\n  const span = /* @__PURE__ */ new Map();\n  for (const piece of referencePieces) {\n    let pos = piece.start ?? 0;\n    for (const id of piece.nodeIds) {\n      const len = lengthOf.get(id) ?? 0;\n      if (!span.has(id)) {\n        span.set(id, { start: pos, end: pos + len });\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || [...span.values()].some((s) => s.end <= cut.start) && [...span.values()].some((s) => s.start >= cut.end);\n  const rowOf = (pieces) => {\n    const path = pieces[0];\n    const ordered = [...pieces].sort((a, b) => (a.start ?? 0) - (b.start ?? 0));\n    const { ids, complete, from, to } = sliceBetween(\n      stepsOf(ordered, lengthOf),\n      span,\n      cut,\n      flanked\n    );\n    const spans = stepSpans(ordered, lengthOf);\n    const contig = path.contig ?? panSNContig(pathOrigin(path.name).name);\n    const axis = !spans?.length ? void 0 : from < 0 ? { contig, start: spans[0].start, reversed: false } : from < to ? { contig, start: spans[from].end, reversed: false } : { contig, start: spans[from].start, reversed: true };\n    const runs = [];\n    let bp = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    for (const id of ids) {\n      if (typeof id === \"number\") {\n        runs.push({ start: bp, bp: id, onReference: false, gap: true });\n        bp += id;\n        gapBp += id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf.get(id) ?? 0;\n      const s = span.get(id);\n      const last = runs.at(-1);\n      const at = last?.referenceStart;\n      const forward = s && at !== void 0 && step >= 0 && at + last.bp === s.start;\n      const backward = s && at !== void 0 && step <= 0 && s.end === at;\n      if (!s && last && !last.onReference && !last.gap) {\n        last.bp += len;\n      } else if (forward || backward) {\n        last.bp += len;\n        if (!forward) {\n          last.referenceStart = s.start;\n          last.reversed = true;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        runs.push({\n          start: bp,\n          bp: len,\n          onReference: s !== void 0,\n          referenceStart: s?.start\n        });\n        step = 0;\n      }\n      bp += len;\n      if (!s) {\n        offReferenceBp += len;\n      }\n    }\n    return {\n      name: path.name,\n      label: labelOf(path),\n      sample: sampleOf(path),\n      haplotype: path.haplotype,\n      bp,\n      offReferenceBp,\n      gapBp,\n      complete,\n      runs,\n      axis\n    };\n  };\n  const origin = cut ? cut.start : referenceStart;\n  return {\n    origin,\n    unit,\n    reference: rowOf(referencePieces),\n    rows: [...walks.values()].map(rowOf).sort(\n      (a, b) => Number(b.complete) - Number(a.complete) || b.bp - a.bp || a.label.localeCompare(b.label)\n    )\n  };\n}\n\nexport {\n  filterSamples,\n  walkRows\n};\n", "import {\n  walkRows\n} from \"./chunk-SZNZ2T6D.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  backboneNodes,\n  backbonePositions,\n  overlapsWindow\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/walkRowLayout.ts\nvar READOUT_ROOM = 1.3;\nfunction walkRowsExtent(walks, pitch = {\n  rowPx: ROW_HEIGHT_PX,\n  readouts: true\n}) {\n  let longest = walks.reference.bp;\n  for (const row of walks.rows) {\n    longest = Math.max(longest, row.bp);\n  }\n  return {\n    maxX: walks.origin + longest * (pitch.readouts ? READOUT_ROOM : 1),\n    maxY: walks.rows.length * pitch.rowPx\n  };\n}\nfunction walkRowLabels(rows, layout, pitch) {\n  if (!rows) {\n    return layout?.rowLabels ?? [];\n  }\n  if (pitch && !pitch.labelled) {\n    return [];\n  }\n  return [rows.reference, ...rows.rows].map((row, i) => ({\n    label: row.label,\n    y: i * (pitch?.rowPx ?? ROW_HEIGHT_PX)\n  }));\n}\nfunction walkRowLayout(graph, region) {\n  const backbone = backboneNodes(graph);\n  const walks = walkRows(graph, region);\n  if (backbone.length === 0 || !walks) {\n    return void 0;\n  }\n  const overWindow = region ? backbone.filter((n) => overlapsWindow(n, region)) : backbone;\n  const nodePositions = backbonePositions(\n    overWindow.length > 0 ? overWindow : backbone\n  );\n  const rowLabels = [\n    { label: walks.reference.label, y: 0 },\n    ...walks.rows.map((row, i) => ({\n      label: row.label,\n      y: (i + 1) * ROW_HEIGHT_PX\n    }))\n  ];\n  return {\n    nodePositions,\n    rowLabels,\n    referenceAxis: true,\n    pixelRows: true,\n    extent: walkRowsExtent(walks)\n  };\n}\n\nexport {\n  walkRowsExtent,\n  walkRowLabels,\n  walkRowLayout\n};\n", "import {\n  sampleRowLayout\n} from \"./chunk-LOEA5IHZ.js\";\nimport {\n  hasTubeMapPaths,\n  tubeMapLayout,\n  tubeMapReferenceLayout\n} from \"./chunk-W2I4DOL4.js\";\nimport {\n  anchoredLayout\n} from \"./chunk-L3O7AWLI.js\";\nimport {\n  orderedLayout\n} from \"./chunk-HNQPEMYE.js\";\nimport {\n  walkRowLayout\n} from \"./chunk-MP7LXLWV.js\";\nimport {\n  isBackbone,\n  isOffReference\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layoutModes.ts\nvar FORCE_LAYOUT_LABEL = \"Force-directed layout\";\nvar hasBackbone = (graph) => graph.nodes.some(isBackbone);\nvar hasWalks = (graph) => hasBackbone(graph) && (graph.paths?.length ?? 0) > 1;\nvar hasTubeMapBackbone = (graph) => hasBackbone(graph) && hasTubeMapPaths(graph);\nvar hasAlleles = (graph) => hasBackbone(graph) && graph.nodes.some(isOffReference);\nvar LAYOUT_MODES = [\n  {\n    value: \"auto\",\n    label: \"Anchored\",\n    description: \"x is reference bp, one row per stable rank. Needs rGFA tags or a reference path.\",\n    run: anchoredLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasBackbone,\n    drawsLocally: hasBackbone,\n    drawsNodes: true\n  },\n  {\n    value: \"samplerows\",\n    label: \"Sample rows\",\n    description: \"x is reference bp, one row per contributing assembly. Needs rGFA tags or a reference path.\",\n    run: sampleRowLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasAlleles,\n    drawsLocally: hasAlleles,\n    drawsNodes: true\n  },\n  {\n    value: \"walkrows\",\n    label: \"Walk rows\",\n    description: \"x is each walk's own bp: one bar per haplotype, blue on the reference's path and purple off it, so a repeat expansion reads as bar length, and each bar boxes its haplotype's own genes where the session has them. Needs W or P lines.\",\n    run: walkRowLayout,\n    cutMargins: false,\n    wholeWalks: true,\n    available: hasWalks,\n    drawsLocally: hasWalks,\n    drawsNodes: false\n  },\n  {\n    value: \"ordered\",\n    label: \"Ordered\",\n    description: \"x is reference order, not bp: every node gets room, bubbles read as lenses. Needs rGFA tags or a reference path.\",\n    run: orderedLayout,\n    cutMargins: false,\n    wholeWalks: false,\n    available: hasBackbone,\n    drawsLocally: hasBackbone,\n    drawsNodes: true\n  },\n  {\n    value: \"tubemap\",\n    label: \"Tube map\",\n    description: \"sequenceTubeMap: every path a coloured tube through boxed nodes, columns in node order and node widths log-scaled. Needs P or W lines.\",\n    run: tubeMapLayout,\n    cutMargins: false,\n    wholeWalks: false,\n    available: hasTubeMapPaths,\n    drawsLocally: hasTubeMapPaths,\n    drawsNodes: false\n  },\n  {\n    value: \"tubemapref\",\n    label: \"Tube map on reference\",\n    description: \"The tube map with each column at the reference bp it covers, so the tubes line up with the tracks around them. Needs P or W lines and a reference path.\",\n    run: tubeMapReferenceLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasTubeMapBackbone,\n    drawsLocally: hasTubeMapBackbone,\n    drawsNodes: false\n  },\n  {\n    value: \"force\",\n    label: FORCE_LAYOUT_LABEL,\n    description: \"OGDF FMMM, via the external Bandage engine.\",\n    run: () => void 0,\n    cutMargins: false,\n    wholeWalks: false,\n    available: () => true,\n    drawsLocally: () => false,\n    drawsNodes: true\n  }\n];\nvar LAYOUT_MODE_VALUES = LAYOUT_MODES.map((m) => m.value);\nfunction modeUsesLayoutEngine(value, graph) {\n  return !layoutModeByValue(value).drawsLocally(graph);\n}\nfunction layoutModeByValue(value) {\n  return LAYOUT_MODES.find((m) => m.value === value) ?? LAYOUT_MODES[0];\n}\n\nexport {\n  FORCE_LAYOUT_LABEL,\n  LAYOUT_MODES,\n  LAYOUT_MODE_VALUES,\n  modeUsesLayoutEngine,\n  layoutModeByValue\n};\n", "import {\n  alongRow,\n  boxesGenes,\n  rowPitch\n} from \"./chunk-V3MD3IZB.js\";\nimport {\n  LABEL_CHAR_PX\n} from \"./chunk-AB35TJST.js\";\nimport {\n  el\n} from \"./chunk-NNODIW4U.js\";\nimport {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\n\n// src/layout/walkStrip.ts\nfunction walkStripApplies(o) {\n  return o.walkStrip && o.mode.drawsNodes && !o.drawsPicture && !o.popped && !o.host && o.walks > 1;\n}\nfunction cutsWholeWalks(mode, o) {\n  return mode.wholeWalks || o.walkStrip && !o.host;\n}\nvar PAD_PX = 6;\nvar WALK_STRIP_CEILING_PX = 260;\nvar LABEL_FONT_PX = 11;\nvar MIN_ROW_PX = 3;\nvar READOUT_ROOM = 1.3;\nvar MARK_INK = \"#111\";\nvar TICK_PX = 3;\nfunction stripMarks(graph, rows, node) {\n  const visits = graph.pathVisits?.get(node.name) ?? [];\n  const marks = [];\n  for (const row of rows) {\n    const axis = row.axis;\n    if (!axis) {\n      continue;\n    }\n    const path = pathOrigin(row.name).name;\n    for (const v of visits) {\n      if (v.path !== path) {\n        continue;\n      }\n      const { start, end } = alongRow(axis, v.start, v.start + node.length);\n      if (end > 0 && start < row.bp) {\n        marks.push({ row: row.name, start, bp: end - start });\n      }\n    }\n  }\n  return marks;\n}\nvar spanCache = /* @__PURE__ */ new WeakMap();\nfunction spansOf(graph, name) {\n  let byName = spanCache.get(graph);\n  if (!byName) {\n    byName = /* @__PURE__ */ new Map();\n    spanCache.set(graph, byName);\n  }\n  if (byName.has(name)) {\n    return byName.get(name);\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const pieces = (graph.paths ?? []).filter((p) => p.name === name);\n  let spans;\n  if (pieces.every((p) => p.start !== void 0)) {\n    spans = { ids: [], starts: [], ends: [] };\n    for (const piece of [...pieces].sort((a, b) => a.start - b.start)) {\n      let pos = piece.start;\n      for (const id of piece.nodeIds) {\n        const len = lengthOf.get(id) ?? 0;\n        spans.ids.push(id);\n        spans.starts.push(pos);\n        spans.ends.push(pos + len);\n        pos += len;\n      }\n    }\n  }\n  byName.set(name, spans);\n  return spans;\n}\nfunction segmentAt(graph, row, offset, pxPerBp) {\n  const axis = row.axis;\n  const spans = axis && spansOf(graph, row.name);\n  if (!axis || !spans || offset < 0 || offset > row.bp) {\n    return void 0;\n  }\n  const at = axis.reversed ? axis.start - offset : axis.start + offset;\n  const tol = 0.5 / pxPerBp;\n  const bar = axis.reversed ? { start: axis.start - row.bp, end: axis.start } : { start: axis.start, end: axis.start + row.bp };\n  const from = Math.max(at - tol, bar.start);\n  const to = Math.min(at + tol, bar.end);\n  let lo = 0;\n  let hi = spans.starts.length;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (spans.ends[mid] <= from) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  let best;\n  let bestLen = -1;\n  let bestHolds = false;\n  for (let i = lo; i < spans.starts.length && spans.starts[i] < to; i++) {\n    const len = spans.ends[i] - spans.starts[i];\n    const holds = spans.starts[i] <= at && at < spans.ends[i];\n    if (len > bestLen || len === bestLen && holds && !bestHolds) {\n      bestLen = len;\n      best = spans.ids[i];\n      bestHolds = holds;\n    }\n  }\n  return best;\n}\nfunction walkStripFrame(bars, o) {\n  const maxHeight = o.maxHeight ?? WALK_STRIP_CEILING_PX;\n  const labelPx = o.labelPx ?? Math.max(...[bars.reference, ...bars.rows].map((r) => r.label.length)) * LABEL_CHAR_PX + 16;\n  const count = bars.rows.length + 1;\n  const { rowPx, barPx, labelled, readouts } = rowPitch(\n    count,\n    maxHeight - 2 * PAD_PX,\n    MIN_ROW_PX\n  );\n  const longest = Math.max(bars.reference.bp, ...bars.rows.map((r) => r.bp), 1);\n  const left = labelled ? labelPx : PAD_PX;\n  const usable = Math.max(1, o.width - left - PAD_PX);\n  const scaleX = usable / (longest * (readouts ? READOUT_ROOM : 1));\n  return {\n    scaleX,\n    scaleY: 1,\n    translateX: left - bars.origin * scaleX,\n    translateY: PAD_PX + rowPx / 2,\n    width: o.width,\n    height: count * rowPx + 2 * PAD_PX,\n    rowPx,\n    barPx,\n    readouts,\n    labelled,\n    boxesGenes: boxesGenes(rowPx, barPx)\n  };\n}\nfunction stripRowAt(bars, frame, x, y) {\n  const i = Math.round((y - frame.translateY) / frame.rowPx);\n  const row = [bars.reference, ...bars.rows][i];\n  const offset = (x - frame.translateX) / frame.scaleX - bars.origin;\n  return row && i >= 0 && offset >= 0 && offset <= row.bp ? { index: i, row, offset } : void 0;\n}\nfunction walkMarksTree(bars, frame, marks) {\n  const index = new Map(\n    [bars.reference, ...bars.rows].map((row, i) => [row.name, i])\n  );\n  const X = (offset) => (bars.origin + offset) * frame.scaleX + frame.translateX;\n  return el(\n    \"g\",\n    { \"data-testid\": \"graph-walk-marks\" },\n    ...marks.flatMap((m) => {\n      const i = index.get(m.row);\n      if (i === void 0) {\n        return [];\n      }\n      const y = i * frame.rowPx + frame.translateY;\n      const x = X(m.start);\n      const w = Math.max(2, m.bp * frame.scaleX);\n      const tick = (top) => el(\"rect\", { x, y: top, width: w, height: TICK_PX, fill: MARK_INK });\n      return [\n        tick(y - frame.barPx / 2 - TICK_PX - 1),\n        tick(y + frame.barPx / 2 + 1)\n      ];\n    })\n  );\n}\nfunction walkStripLabelsTree(bars, frame, bold = /* @__PURE__ */ new Set()) {\n  return el(\n    \"g\",\n    { \"font-family\": \"sans-serif\", \"font-size\": LABEL_FONT_PX, fill: \"#333\" },\n    ...(frame.labelled ? [bars.reference, ...bars.rows] : []).map(\n      (row, i) => el(\n        \"text\",\n        {\n          x: 6,\n          y: i * frame.rowPx + frame.translateY + 4,\n          \"font-weight\": bold.has(row.name) ? 600 : void 0\n        },\n        row.label\n      )\n    )\n  );\n}\nfunction stripGeneGaps(frame, rowGenes, gaps) {\n  if (!rowGenes?.size) {\n    return void 0;\n  }\n  return frame.boxesGenes ? gaps : { untracked: 0, unread: 0, ...gaps, crowded: true };\n}\n\nexport {\n  walkStripApplies,\n  cutsWholeWalks,\n  WALK_STRIP_CEILING_PX,\n  stripMarks,\n  segmentAt,\n  walkStripFrame,\n  stripRowAt,\n  walkMarksTree,\n  walkStripLabelsTree,\n  stripGeneGaps\n};\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6\"\n}), 'Settings');"],
+  "mappings": 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1	+ import{a as w,g as S,j as D}from"./chunk-GMSOU6VO.js";import{N as u,T as k}from"./chunk-B7GF3TC3.js";import{a as A,b as R}from"./chunk-NXZT63HN.js";import{a as y,b as N}from"./chunk-64LZZURD.js";import{b as c}from"./chunk-FY3BTKY4.js";var m=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];var L=c(A(),1),o=c(R(),1),b=c(N(),1),G=c(D(),1),e=c(y(),1),C=(0,G.makeStyles)()({section:{marginBottom:24},formControl:{minWidth:200}});function s({warn:l=!1,children:n}){return(0,e.jsx)(o.Typography,{variant:"caption",color:l?"warning.main":"text.secondary",children:n})}var T=(0,b.observer)(function({model:n}){return n.hasGraph&&!n.usesLayoutEngine?(0,e.jsx)(s,{warn:!0,children:"No effect on this layout: only the force-directed layout is drawn by the engine that reads this."}):null});function g({label:l,checked:n,onChange:t,children:p}){let{classes:i}=C();return(0,e.jsxs)("div",{className:i.section,children:[(0,e.jsx)(o.FormControlLabel,{control:(0,e.jsx)(o.Switch,{checked:n,onChange:d=>{t(d.target.checked)}}),label:l}),p]})}function h({label:l,value:n,options:t,testId:p,sx:i,onChange:d}){let{classes:r}=C();return(0,e.jsxs)(o.FormControl,{className:r.formControl,sx:i,children:[(0,e.jsx)(o.InputLabel,{children:l}),(0,e.jsx)(o.Select,{value:n,label:l,"data-testid":p,onChange:a=>{d(a.target.value)},children:t.map(({value:a,label:v,description:f})=>(0,e.jsx)(o.MenuItem,{value:a,children:f?(0,e.jsx)(o.Tooltip,{title:f,placement:"right",children:(0,e.jsx)("span",{children:v})}):v},a))})]})}var I=l=>l.map(({trackId:n,name:t})=>({value:n,label:t})),P=(0,b.observer)(function(n){let{model:t,open:p,onClose:i,children:d}=n,{classes:r}=C();return(0,e.jsxs)(L.Dialog,{open:p,onClose:i,title:"Graph settings",children:[(0,e.jsxs)(o.DialogContent,{children:[(0,e.jsx)("div",{className:r.section,children:(0,e.jsxs)(o.FormControl,{fullWidth:!0,children:[(0,e.jsx)(o.FormLabel,{component:"legend",children:"Layout quality"}),(0,e.jsx)(o.RadioGroup,{value:t.layoutQuality,onChange:a=>{t.setLayoutQuality(parseInt(a.target.value)),t.recomputeLayout()},children:m.map(a=>(0,e.jsx)(o.FormControlLabel,{value:a.value,control:(0,e.jsx)(o.Radio,{}),label:a.label},a.value))}),(0,e.jsx)(s,{children:"FMMM's iteration budget, the same scale Bandage exposes. 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package/dist/chunks/{chunk-A6GKF63C.js.map → chunk-X4DGSMS6.js.map} RENAMED Viewed

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../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 type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { COLOR_SCHEMES } from '@jbrowse/bandage-core/colorSchemes'\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  FormControl,\n  FormControlLabel,\n  FormLabel,\n  InputLabel,\n  MenuItem,\n  Radio,\n  RadioGroup,\n  Select,\n  Switch,\n  Tooltip,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\nimport type { SxProps } from '@mui/material'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\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      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\n// Layout quality and bubble spread are the engine's inputs, and an anchored\n// layout places a node from its coordinates without reaching it. Left enabled\n// so the force layout can be set up before switching to it.\nconst EngineOnly = observer(function EngineOnly({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  return model.hasGraph && !model.usesLayoutEngine ? (\n    <Caption warn>\n      No effect on this layout: only the force-directed layout is drawn by the\n      engine that reads this.\n    </Caption>\n  ) : null\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; an option's description is its tooltip\nfunction SettingSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  sx,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly { value: T; label: string; description?: string }[]\n  testId?: string\n  sx?: SxProps\n  onChange: (value: T) => void\n}) {\n  const { classes } = useStyles()\n  return (\n    <FormControl className={classes.formControl} sx={sx}>\n      <InputLabel>{label}</InputLabel>\n      <Select\n        value={value}\n        label={label}\n        data-testid={testId}\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(({ value, label, description }) => (\n          <MenuItem key={value} value={value}>\n            {description ? (\n              <Tooltip title={description} placement=\"right\">\n                <span>{label}</span>\n              </Tooltip>\n            ) : (\n              label\n            )}\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n\nconst trackOptions = (tracks: { trackId: string; name: string }[]) =>\n  tracks.map(({ trackId, name }) => ({ value: trackId, label: name }))\n\n// `children` is the host's own section, between node width and colour\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  open: boolean\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, open, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open={open} onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <div className={classes.section}>\n          <FormControl fullWidth>\n            <FormLabel component=\"legend\">Layout quality</FormLabel>\n            <RadioGroup\n              value={model.layoutQuality}\n              onChange={e => {\n                model.setLayoutQuality(parseInt(e.target.value))\n                void model.recomputeLayout()\n              }}\n            >\n              {LAYOUT_QUALITIES.map(q => (\n                <FormControlLabel\n                  key={q.value}\n                  value={q.value}\n                  control={<Radio />}\n                  label={q.label}\n                />\n              ))}\n            </RadioGroup>\n            <Caption>\n              FMMM&apos;s iteration budget, the same scale Bandage exposes.\n              Higher is slower: on a thousand-node cut the top setting is\n              seconds rather than tenths.\n            </Caption>\n            <EngineOnly model={model} />\n          </FormControl>\n        </div>\n\n        <SettingSwitch\n          label=\"Draw paths\"\n          checked={model.drawPaths}\n          onChange={draw => {\n            model.setDrawPaths(draw)\n          }}\n        >\n          <Caption>\n            Color each node and connector by the paths through it, one lane per\n            path in legend order, so a path that skips a node leaves its lane\n            empty\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        <SettingSwitch\n          label=\"Mark bubbles\"\n          checked={model.showBubbles}\n          onChange={show => {\n            model.setShowBubbles(show)\n          }}\n        >\n          <Caption>\n            A halo along the nodes of each bubble, labelled by what it is, with\n            the label opening the bubble on its own\n          </Caption>\n        </SettingSwitch>\n\n        <SettingSwitch\n          label=\"Genes on the backbone\"\n          checked={model.showGenes}\n          onChange={show => {\n            model.setShowGenes(show)\n          }}\n        >\n          <Caption>\n            Exons along the reference nodes that carry them and each gene's name\n            at its midpoint, from the assembly's annotation track\n          </Caption>\n          {model.geneTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Gene track\"\n              value={model.geneTrack?.trackId ?? ''}\n              options={trackOptions(model.geneTrackChoices)}\n              testId=\"graph-gene-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setGeneTrackId(trackId)\n                void model.reloadGenes()\n              }}\n            />\n          ) : null}\n          {model.repeatTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Repeat track\"\n              value={model.repeatTrack?.trackId ?? ''}\n              options={trackOptions(model.repeatTrackChoices)}\n              testId=\"graph-repeat-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setRepeatTrackId(trackId)\n                void model.reloadRepeats()\n              }}\n            />\n          ) : null}\n        </SettingSwitch>\n\n        {model.anchorPaths.length > 1 ? (\n          <div className={classes.section}>\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>\n              Which path the anchored layouts draw x against. A GFA with no rGFA\n              tags states its coordinates only in its paths, and marks none of\n              them as the reference.\n            </Caption>\n          </div>\n        ) : null}\n\n        <div className={classes.section}>\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              void model.recomputeLayout()\n            }}\n          />\n          <Caption>\n            How far the force layout opens a bubble. 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Rt(t,a){let n=t.walkRowBars;return n?N(n,{ramp:t.referenceRampDomain,genes:t.walkRowGeneKey}).map((r,o)=>{let{tree:i,width:s}=z([r],0,0,`${a}-rows-key-${o}`);return{key:`walk-rows-${o}`,width:s,height:b,draw:l=>(0,e.jsx)("g",{transform:`translate(${l-s} -12)`,children:(0,e.jsx)(Z,{el:i})},o)}}):[]}function kt({model:t,idPrefix:a}){let n=[],r=t.walkLift,o=r?void 0:t.referenceRampDomain;if(o){let f=Math.round(o.start),d=Math.round(o.end);n.push(g("ramp",w=>(0,e.jsx)(R,{id:`${a}-ramp`,x:w,stops:k({field:"reference",scheme:"rainbow"}),width:D}),D,"",`${f.toLocaleString()}-${d.toLocaleString()} (${L(d-f)})`)),t.referenceRampOffKeys.offReference&&n.push(x("off",$,"off the reference"))}if(n.push(...wt(t,a),...mt(t)),t.genePins.some(f=>f.exonsByNode.length>0)&&n.push(g("exon",f=>(0,e.jsx)("rect",{x:f+1,y:-10,width:h-2,height:10,rx:4,fill:"none",stroke:H,strokeWidth:2}),h,"","exon")),n.push(...yt(t),...bt(t,a),...Rt(t,a)),r&&!t.facetPanels&&(r.walks.forEach((f,d)=>{n.push(ht(t,f,`${a}-walk-${d}`))}),t.liftPaintsOffReference&&n.push(x("lift-off",$,"off the reference")),n.push(x("faded",M,`not on ${t.liftedWalksLabel}`))),n.length===0)return null;let i=G+t.referenceStripZonePx,s=t.paneWidth-G-6,l=Math.max(...n.map(f=>f.width))+12,p=s+6-l+6,u=n.reduce((f,d)=>f+d.height,0)+6,c=i+b;return(0,e.jsxs)("g",{"data-testid":"graph-svg-keys",children:[(0,e.jsx)("rect",{x:p-6,y:i,width:l,height:u,rx:3,fill:"#fff",fillOpacity:.82}),n.map(f=>{let d=c;return c+=f.height,(0,e.jsx)("g",{transform:`translate(0 ${d})`,children:f.draw(p+f.width)},f.key)})]})}function pt({x:t,y:a,text:n,fontSize:r,anchor:o,bold:i}){let 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null;let{columns:s,width:l,height:p}=o;return(0,e.jsx)(e.Fragment,{children:r.map((u,c)=>{let f=i.cells[c],d=f%s(l+P),w=Math.floor(f/s)(v+p+P),K=u.walks[0],A=ht(t,K,`${n}-facet-${c}`);return(0,e.jsxs)("g",{transform:`translate(${d} ${w})`,children:[(0,e.jsx)("g",{transform:`translate(0 ${b-2})`,children:A.draw(A.width+6)}),(0,e.jsx)("g",{transform:`translate(0 ${v})`,children:(0,e.jsx)(ft,{model:t,lift:u,drawPaths:!1,width:l,height:p,rasterize:a})})]},K.name)})})}function B({model:t,rasterize:a=!1,idPrefix:n}){let r=t.paneWidth,o=t.canvasHeight,i=!!t.layoutResult?.tubeMap,s={rasterizeLayers:a};return(0,e.jsxs)("g",{"data-testid":"graph-pane-svg",children:[t.facetPanels?(0,e.jsx)(Lt,{model:t,rasterize:a,idPrefix:n}):i?(0,e.jsx)(C.PaintLayer,{width:r,height:o,opts:s,paint:l=>{tt(it(l),t,{highlightNode:null})}}):(0,e.jsx)(ft,{model:t,lift:t.walkLift,drawPaths:t.effectiveDrawPaths,width:r,height:o,rasterize:a}),t.referenceStripShown?(0,e.jsx)(C.PaintLayer,{width:r,height:o,opts:s,paint:l=>{Q(it(l),t,{lit:void 0,dpr:1})}}):null,t.facetPanels?null:(0,e.jsxs)(e.Fragment,{children:[(0,e.jsx)(et,{model:t}),(0,e.jsx)(St,{model:t}),(0,e.jsx)(xt,{model:t}),(0,e.jsx)(V,{model:t}),(0,e.jsx)(J,{model:t}),(0,e.jsx)(q,{model:t}),(0,e.jsx)(kt,{model:t,idPrefix:n})]})]})}var dt=y(S(),1);function Pt({model:t,opts:a}){return(0,dt.jsx)(B,{model:t,rasterize:!!a?.rasterizeLayers,idPrefix:`graph-${t.id}`})}function qt(t,a){return(0,ct.renderDisplaySvg)(t,a,Pt)}export{qt as renderGraphTrackSvg};
2	+ //# sourceMappingURL=renderSvg-J7L374ND.js.map

package/dist/chunks/renderSvg-J7L374ND.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/display-kit/renderDisplaySvg", "global-externals:@jbrowse/core/util/paintLayer", "../../src/LinearGraphDisplay/renderSvg.tsx", "../../src/GraphGenomeView/components/PaneSvg.tsx"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/display-kit/renderDisplaySvg\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util/paintLayer\"];", "import { renderDisplaySvg } from '@jbrowse/display-kit/renderDisplaySvg'\n\nimport PaneSvg from '../GraphGenomeView/components/PaneSvg'\n\nimport type { LinearGraphDisplayModel } from './model'\nimport type { LgvSvgBodyProps } from '@jbrowse/display-kit/renderDisplaySvg'\nimport type { ExportSvgDisplayOptions } from '@jbrowse/display-kit/types'\n\nfunction GraphTrackSvgBody({\n  model,\n  opts,\n}: LgvSvgBodyProps<LinearGraphDisplayModel>) {\n  return (\n    <PaneSvg\n      model={model}\n      rasterize={!!opts?.rasterizeLayers}\n      idPrefix={`graph-${model.id}`}\n    />\n  )\n}\n\nexport function renderGraphTrackSvg(\n  model: LinearGraphDisplayModel,\n  opts?: ExportSvgDisplayOptions,\n) {\n  return renderDisplaySvg(model, opts, GraphTrackSvgBody)\n}\n", "import {\n  BUBBLE_KIND_COLORS,\n  BUBBLE_KIND_NAMES,\n} from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { FACET_GAP_PX, FACET_TITLE_PX } from '@jbrowse/bandage-core/facetGrid'\nimport { formatBp } from '@jbrowse/bandage-core/graphLabels'\nimport { LEGEND_INSET_PX } from '@jbrowse/bandage-core/labelLayout'\nimport {\n  walkRowsKey,\n  walkRowsKeyTree,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { Canvas2DRenderer } from '@jbrowse/bandage-core/renderer/Canvas2DRenderer'\nimport {\n  LIFT_BACKDROP_CSS,\n  REFERENCE_RAMP_ALT_CSS,\n} from '@jbrowse/bandage-core/renderer/GeometryBuilder'\nimport { svgCanvas } from '@jbrowse/bandage-core/renderer/svgCanvas'\nimport { rulerInk } from '@jbrowse/bandage-core/tubeMap/axis'\nimport { deviationInk } from '@jbrowse/bandage-core/tubeMap/deviations'\nimport {\n  FORWARD_READ_COLORS,\n  REVERSE_READ_COLORS,\n} from '@jbrowse/bandage-core/tubeMap/reads'\nimport { encodingStops } from '@jbrowse/bandage-core/walkEncoding'\nimport { walkKey } from '@jbrowse/bandage-core/walkKey'\nimport { PaintLayer } from '@jbrowse/core/util/paintLayer'\n\nimport BubbleHalos from './BubbleHalos'\nimport ElTree from './ElTree'\nimport GenePins, { EXON_COLOR } from './GenePins'\nimport LabelLayer from './LabelLayer'\nimport { paintReferenceStrip } from './ReferenceStripOverlay'\nimport { paintTubeMap } from './TubeMapOverlay'\nimport WalkRowsOverlay from './WalkRowsOverlay'\n\nimport type { GraphPaneModel } from '../model'\nimport type { LiftedWalk, WalkLift } from '@jbrowse/bandage-core/walkHighlight'\nimport type { Ctx2D } from '@jbrowse/core/util/paintLayer'\n\nconst FONT = { fontFamily: 'sans-serif', fontSize: 11 }\nconst CHAR_PX = 6.2\nconst ROW_PX = 16\nconst SWATCH_PX = 18\nconst BAR_PX = 48\nconst RASTER_SCALE = 2\nconst STRIP_SAMPLES = 6\n\nconst asCanvasCtx = (ctx: Ctx2D) => ctx as CanvasRenderingContext2D\n\n// The drawing's nodes and edges through the pane's own transform, so the\n// export lines up with the linear view's ruler wherever the screen does\nfunction Body({\n  model,\n  lift,\n  drawPaths,\n  width,\n  height,\n  rasterize,\n}: {\n  model: GraphPaneModel\n  lift: WalkLift | undefined\n  drawPaths: boolean\n  width: number\n  height: number\n  rasterize: boolean\n}) {\n  const built = model.buildDrawing(lift, drawPaths)\n  if (!built) {\n    return null\n  }\n  const transform = {\n    scaleX: model.scaleX,\n    scaleY: model.scaleY,\n    translateX: model.translateX,\n    translateY: model.translateY,\n  }\n  if (rasterize) {\n    const canvas = document.createElement('canvas')\n    canvas.width = Math.round(width * RASTER_SCALE)\n    canvas.height = Math.round(height * RASTER_SCALE)\n    const renderer = new Canvas2DRenderer(canvas)\n    renderer.uploadGeometry(built.batch)\n    renderer.updateTransform({\n      scaleX: transform.scaleX * RASTER_SCALE,\n      scaleY: transform.scaleY * RASTER_SCALE,\n      translateX: transform.translateX * RASTER_SCALE,\n      translateY: transform.translateY * RASTER_SCALE,\n      dpr: RASTER_SCALE,\n    })\n    renderer.render([0, 0, 0, 0])\n    return (\n      <image\n        width={width}\n        height={height}\n        href={canvas.toDataURL('image/png')}\n      />\n    )\n  }\n  const { canvas, markup } = svgCanvas(width, height)\n  const ctx = canvas.getContext('2d') as unknown as { clearRect?: () => void }\n  ctx.clearRect ??= () => {}\n  const renderer = new Canvas2DRenderer(canvas)\n  renderer.uploadGeometry(built.batch)\n  renderer.updateTransform({ ...transform, dpr: 1 })\n  renderer.render([0, 0, 0, 0])\n  return (\n    <svg width={width} height={height} overflow=\"hidden\">\n      <g dangerouslySetInnerHTML={{ __html: markup() }} />\n    </svg>\n  )\n}\n\nfunction Swatch({\n  id,\n  x,\n  y = -9,\n  stops,\n  width,\n  height = 8,\n}: {\n  id: string\n  x: number\n  y?: number\n  stops: { offset: number; color: string }[]\n  width: number\n  height?: number\n}) {\n  return stops.length > 1 ? (\n    <>\n      <defs>\n        <linearGradient id={id}>\n          {stops.map((s, i) => (\n            <stop key={i} offset={s.offset} stopColor={s.color} />\n          ))}\n        </linearGradient>\n      </defs>\n      <rect\n        x={x}\n        y={y}\n        width={width}\n        height={height}\n        rx={2}\n        fill={`url(#${id})`}\n      />\n    </>\n  ) : (\n    <rect\n      x={x}\n      y={y}\n      width={width}\n      height={height}\n      rx={2}\n      fill={stops[0]?.color}\n    />\n  )\n}\n\ninterface KeyRow {\n  key: string\n  width: number\n  height: number\n  draw: (right: number) => React.ReactNode\n}\n\n// A row of the key: a swatch, then its words, ending at `right`\nfunction swatchRow(\n  key: string,\n  swatch: (x: number) => React.ReactNode,\n  swatchWidth: number,\n  label: string,\n  after = '',\n  under?: string,\n): KeyRow {\n  const width = Math.max(\n    swatchWidth + 5 + (label.length + after.length) * CHAR_PX,\n    (under?.length ?? 0) * CHAR_PX,\n  )\n  return {\n    key,\n    width,\n    height: under ? ROW_PX * 2 : ROW_PX,\n    draw: right => {\n      const x = right - width\n      return (\n        <g key={key} {...FONT}>\n          {swatch(x)}\n          <text x={x + swatchWidth + 5} y={0}>\n            <tspan fontWeight=\"bold\">{label}</tspan>\n            {after}\n          </text>\n          {under ? (\n            <text x={x} y={ROW_PX}>\n              {under}\n            </text>\n          ) : null}\n        </g>\n      )\n    },\n  }\n}\n\nfunction walkRow(model: GraphPaneModel, walk: LiftedWalk, id: string) {\n  const key = walkKey(walk, model.walkReference)\n  const stops = encodingStops(walk.encoding)\n  const width = key.shades ? BAR_PX : SWATCH_PX\n  return swatchRow(\n    walk.name,\n    x => <Swatch id={id} x={x} stops={stops} width={width} />,\n    width,\n    model.walkLabel(walk.name),\n    key.delta + key.outside + key.reversed,\n    key.scale,\n  )\n}\n\nfunction flatRow(key: string, color: string, label: string) {\n  return swatchRow(\n    key,\n    x => (\n      <Swatch id={key} x={x} stops={[{ offset: 0, color }]} width={SWATCH_PX} />\n    ),\n    SWATCH_PX,\n    '',\n    label,\n  )\n}\n\n// The strip's own colours, a row per lifted walk, else the node scheme's\nfunction stripStops(model: GraphPaneModel) {\n  const lift = model.walkLift\n  if (lift) {\n    return lift.walks.map(w => encodingStops(w.encoding))\n  }\n  if (model.effectiveColorScheme === 'reference-position') {\n    return [encodingStops({ field: 'reference', scheme: 'rainbow' })]\n  }\n  const colors = model.referenceStripBlocks\n    .map(b => b.colors[0]!)\n    .filter((c, i, all) => c !== all[i - 1])\n  const n = Math.min(STRIP_SAMPLES, colors.length)\n  return [\n    Array.from({ length: n }, (_, i) => ({\n      offset: n > 1 ? i / (n - 1) : 0,\n      color:\n        colors[n > 1 ? Math.round((i * (colors.length - 1)) / (n - 1)) : 0]!,\n    })),\n  ]\n}\n\nfunction stripKeyRows(model: GraphPaneModel, idPrefix: string): KeyRow[] {\n  if (!model.referenceStripShown) {\n    return []\n  }\n  const rowPerWalk = (model.walkLift?.walks.length ?? 0) > 1\n  const bands = stripStops(model)\n  const rows = [\n    swatchRow(\n      'strip',\n      x => (\n        <>\n          {bands.map((stops, i) => (\n            <g key={i} transform={`translate(0 ${(i * 8) / bands.length})`}>\n              <Swatch\n                id={`${idPrefix}-strip-${i}`}\n                x={x}\n                y={-9}\n                stops={stops}\n                width={SWATCH_PX}\n                height={8 / bands.length}\n              />\n            </g>\n          ))}\n        </>\n      ),\n      SWATCH_PX,\n      '',\n      `top strip: reference segments at their bp${rowPerWalk ? ', a row per walk' : ''}`,\n    ),\n  ]\n  if (model.referenceStripFaded) {\n    rows.push(\n      flatRow(\n        'strip-faded',\n        LIFT_BACKDROP_CSS,\n        `reference not on ${rowPerWalk ? \"that row's walk\" : model.liftedWalksLabel}`,\n      ),\n    )\n  }\n  if (model.referenceStripOverhangs) {\n    rows.push(\n      swatchRow(\n        'overhang',\n        x => (\n          <path\n            transform={`translate(${x} -10)`}\n            d=\"M0,5 L8,0 L8,10 Z M18,5 L10,0 L10,10 Z\"\n            fill=\"#18181c\"\n          />\n        ),\n        SWATCH_PX,\n        '',\n        'the graph draws reference past this edge',\n      ),\n    )\n  }\n  return rows\n}\n\nfunction haloRows(model: GraphPaneModel): KeyRow[] {\n  const kindsByColor = new Map<string, Set<string>>()\n  for (const h of model.bubbleHalos) {\n    if (!h.whole) {\n      const color = BUBBLE_KIND_COLORS[h.kind]\n      const kinds = kindsByColor.get(color) ?? new Set<string>()\n      kinds.add(BUBBLE_KIND_NAMES[h.kind])\n      kindsByColor.set(color, kinds)\n    }\n  }\n  return [...kindsByColor].map(([color, kinds]) =>\n    swatchRow(\n      `halo-${color}`,\n      x => (\n        <line\n          x1={x + 5}\n          x2={x + 13}\n          y1={-5}\n          y2={-5}\n          stroke={color}\n          strokeOpacity={0.35}\n          strokeWidth={8}\n          strokeLinecap=\"round\"\n        />\n      ),\n      SWATCH_PX,\n      '',\n      `bubble: ${[...kinds].join(', ')}`,\n    ),\n  )\n}\n\nfunction pathRows(model: GraphPaneModel): KeyRow[] {\n  return model.pathLegend.map(({ name, label, color }) =>\n    swatchRow(\n      `path-${name}`,\n      x => (\n        <rect x={x} y={-6} width={SWATCH_PX} height={3} rx={2} fill={color} />\n      ),\n      SWATCH_PX,\n      '',\n      label,\n    ),\n  )\n}\n\nfunction readStops(colors: readonly string[]) {\n  return colors.flatMap((color, i) => [\n    { offset: i / colors.length, color },\n    { offset: (i + 1) / colors.length, color },\n  ])\n}\n\nfunction tubeMapRows(model: GraphPaneModel, idPrefix: string): KeyRow[] {\n  if (!model.layoutResult?.tubeMap) {\n    return []\n  }\n  const { logWidths, foldBp, forwardReads, reverseReads, mismatches } =\n    model.tubeMapKeys\n  const reads = model.readsShown\n  const rows: KeyRow[] = []\n  const glyph = (key: string, char: string, label: string) =>\n    swatchRow(\n      key,\n      x => (\n        <text\n          x={x + SWATCH_PX / 2}\n          y={0}\n          textAnchor=\"middle\"\n          fontFamily=\"monospace\"\n          fontSize={12}\n        >\n          {char}\n        </text>\n      ),\n      SWATCH_PX,\n      '',\n      label,\n    )\n  if (forwardReads) {\n    rows.push(\n      swatchRow(\n        'fwd',\n        x => (\n          <Swatch\n            id={`${idPrefix}-fwd`}\n            x={x}\n            stops={readStops(FORWARD_READ_COLORS)}\n            width={SWATCH_PX}\n          />\n        ),\n        SWATCH_PX,\n        '',\n        'read on the forward strand',\n      ),\n    )\n  }\n  if (reverseReads) {\n    rows.push(\n      swatchRow(\n        'rev',\n        x => (\n          <Swatch\n            id={`${idPrefix}-rev`}\n            x={x}\n            stops={readStops(REVERSE_READ_COLORS)}\n            width={SWATCH_PX}\n          />\n        ),\n        SWATCH_PX,\n        '',\n        'read on the reverse strand',\n      ),\n    )\n  }\n  if (reads && reads.shown < reads.total) {\n    rows.push(\n      swatchRow(\n        'sampled',\n        () => null,\n        SWATCH_PX,\n        '',\n        `${reads.shown.toLocaleString('en-US')} of ${reads.total.toLocaleString('en-US')} reads shown`,\n      ),\n    )\n  }\n  if (mismatches.has('substitution')) {\n    rows.push(glyph('sub', 'A', \"a read's base unlike the node's\"))\n  }\n  if (mismatches.has('insertion')) {\n    rows.push(glyph('ins', '*', 'bases a read inserts'))\n  }\n  if (mismatches.has('deletion')) {\n    rows.push(flatRow('del', 'grey', 'bases a read skips'))\n  }\n  if (foldBp !== undefined) {\n    rows.push(\n      swatchRow(\n        'fold',\n        x => (\n          <>\n            <rect x={x} y={-9} width={SWATCH_PX} height={7} fill=\"#b8b8c0\" />\n            <rect\n              x={x + SWATCH_PX / 2 - 1}\n              y={-9}\n              width={2}\n              height={7}\n              fill={deviationInk()}\n            />\n          </>\n        ),\n        SWATCH_PX,\n        '',\n        `a haplotype's variant under ${formatBp(foldBp)}`,\n      ),\n    )\n  }\n  if (logWidths) {\n    rows.push(\n      swatchRow(\n        'log',\n        x => (\n          <path\n            transform={`translate(${x} -9)`}\n            d={`M0.5,6 V1.5 H5.5 V6 M8.5,6 V1.5 H${SWATCH_PX - 0.5} V6`}\n            fill=\"none\"\n            stroke={rulerInk()}\n          />\n        ),\n        SWATCH_PX,\n        '',\n        'width grows with log of length',\n      ),\n    )\n  }\n  return rows\n}\n\nfunction walkRowsKeyRows(model: GraphPaneModel, idPrefix: string): KeyRow[] {\n  const bars = model.walkRowBars\n  if (!bars) {\n    return []\n  }\n  return walkRowsKey(bars, {\n    ramp: model.referenceRampDomain,\n    genes: model.walkRowGeneKey,\n  }).map((entry, i) => {\n    const { tree, width } = walkRowsKeyTree(\n      [entry],\n      0,\n      0,\n      `${idPrefix}-rows-key-${i}`,\n    )\n    return {\n      key: `walk-rows-${i}`,\n      width,\n      height: ROW_PX,\n      draw: (right: number) => (\n        <g key={i} transform={`translate(${right - width} -12)`}>\n          <ElTree el={tree} />\n        </g>\n      ),\n    }\n  })\n}\n\n// The keys the screen stacks in the top right corner, in its order\nfunction Keys({\n  model,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  idPrefix: string\n}) {\n  const rows: KeyRow[] = []\n  const lift = model.walkLift\n  const domain = lift ? undefined : model.referenceRampDomain\n  if (domain) {\n    const start = Math.round(domain.start)\n    const end = Math.round(domain.end)\n    rows.push(\n      swatchRow(\n        'ramp',\n        x => (\n          <Swatch\n            id={`${idPrefix}-ramp`}\n            x={x}\n            stops={encodingStops({ field: 'reference', scheme: 'rainbow' })}\n            width={BAR_PX}\n          />\n        ),\n        BAR_PX,\n        '',\n        `${start.toLocaleString()}-${end.toLocaleString()} (${formatBp(end - start)})`,\n      ),\n    )\n    if (model.referenceRampOffKeys.offReference) {\n      rows.push(flatRow('off', REFERENCE_RAMP_ALT_CSS, 'off the reference'))\n    }\n  }\n  rows.push(...stripKeyRows(model, idPrefix), ...haloRows(model))\n  if (model.genePins.some(pin => pin.exonsByNode.length > 0)) {\n    rows.push(\n      swatchRow(\n        'exon',\n        x => (\n          <rect\n            x={x + 1}\n            y={-10}\n            width={SWATCH_PX - 2}\n            height={10}\n            rx={4}\n            fill=\"none\"\n            stroke={EXON_COLOR}\n            strokeWidth={2}\n          />\n        ),\n        SWATCH_PX,\n        '',\n        'exon',\n      ),\n    )\n  }\n  rows.push(\n    ...pathRows(model),\n    ...tubeMapRows(model, idPrefix),\n    ...walkRowsKeyRows(model, idPrefix),\n  )\n  if (lift && !model.facetPanels) {\n    lift.walks.forEach((walk, i) => {\n      rows.push(walkRow(model, walk, `${idPrefix}-walk-${i}`))\n    })\n    if (model.liftPaintsOffReference) {\n      rows.push(\n        flatRow('lift-off', REFERENCE_RAMP_ALT_CSS, 'off the reference'),\n      )\n    }\n    rows.push(\n      flatRow('faded', LIFT_BACKDROP_CSS, `not on ${model.liftedWalksLabel}`),\n    )\n  }\n  if (rows.length === 0) {\n    return null\n  }\n  const top = LEGEND_INSET_PX + model.referenceStripZonePx\n  const right = model.paneWidth - LEGEND_INSET_PX - 6\n  const boxWidth = Math.max(...rows.map(r => r.width)) + 12\n  const left = right + 6 - boxWidth + 6\n  const boxHeight = rows.reduce((sum, r) => sum + r.height, 0) + 6\n  let y = top + ROW_PX\n  return (\n    <g data-testid=\"graph-svg-keys\">\n      <rect\n        x={left - 6}\n        y={top}\n        width={boxWidth}\n        height={boxHeight}\n        rx={3}\n        fill=\"#fff\"\n        fillOpacity={0.82}\n      />\n      {rows.map(row => {\n        const at = y\n        y += row.height\n        return (\n          <g key={row.key} transform={`translate(0 ${at})`}>\n            {row.draw(left + row.width)}\n          </g>\n        )\n      })}\n    </g>\n  )\n}\n\n// Words on a pale rounded backing, as the screen's labels sit\nfunction Chip({\n  x,\n  y,\n  text,\n  fontSize,\n  anchor,\n  bold,\n}: {\n  x: number\n  y: number\n  text: string\n  fontSize: number\n  anchor: 'start' | 'middle'\n  bold?: boolean\n}) {\n  const w = text.length * fontSize * 0.56 + 6\n  const left = anchor === 'middle' ? x - w / 2 : x - 3\n  return (\n    <>\n      <rect\n        x={left}\n        y={y - fontSize * 0.65}\n        width={w}\n        height={fontSize * 1.3}\n        rx={3}\n        fill=\"#fff\"\n        fillOpacity={0.8}\n      />\n      <text\n        x={x}\n        y={y + fontSize * 0.35}\n        textAnchor={anchor}\n        fontSize={fontSize}\n        fontWeight={bold ? 600 : undefined}\n        fill=\"#18181c\"\n      >\n        {text}\n      </text>\n    </>\n  )\n}\n\n// The node and deletion lengths written on the drawing, with their leaders\nfunction SizeLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.overlayLabels.sizes.map(({ key, text, x, y, kind, leader }) => (\n        <g key={key}>\n          {leader ? (\n            <line\n              x1={leader.arcX}\n              y1={leader.arcY}\n              x2={leader.labelX}\n              y2={leader.labelY}\n              stroke=\"#18181c\"\n            />\n          ) : null}\n          <Chip\n            x={x}\n            y={y}\n            text={text}\n            fontSize={10}\n            anchor=\"middle\"\n            bold={kind === 'deletion'}\n          />\n        </g>\n      ))}\n    </g>\n  )\n}\n\nfunction RowLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.drawnRowLabels.map(({ label, y }) => {\n        const screenY = y * model.scaleY + model.translateY\n        return screenY >= 0 && screenY <= model.canvasHeight ? (\n          <Chip\n            key={y}\n            x={10}\n            y={screenY}\n            text={label}\n            fontSize={11}\n            anchor=\"start\"\n          />\n        ) : null\n      })}\n    </g>\n  )\n}\n\n// Each lifted walk in a panel of its own, its key as the panel's title\nfunction Facets({\n  model,\n  rasterize,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize: boolean\n  idPrefix: string\n}) {\n  const panels = model.facetPanels\n  const grid = model.facetGrid\n  const place = model.facetPlacement\n  if (!panels || !grid || !place) {\n    return null\n  }\n  const { columns, width, height } = grid\n  return (\n    <>\n      {panels.map((lift, i) => {\n        const cell = place.cells[i]!\n        const x = (cell % columns) * (width + FACET_GAP_PX)\n        const y =\n          Math.floor(cell / columns) * (FACET_TITLE_PX + height + FACET_GAP_PX)\n        const walk = lift.walks[0]!\n        const title = walkRow(model, walk, `${idPrefix}-facet-${i}`)\n        return (\n          <g key={walk.name} transform={`translate(${x} ${y})`}>\n            <g transform={`translate(0 ${ROW_PX - 2})`}>\n              {title.draw(title.width + 6)}\n            </g>\n            <g transform={`translate(0 ${FACET_TITLE_PX})`}>\n              <Body\n                model={model}\n                lift={lift}\n                drawPaths={false}\n                width={width}\n                height={height}\n                rasterize={rasterize}\n              />\n            </g>\n          </g>\n        )\n      })}\n    </>\n  )\n}\n\n// The pane as the screen draws it, for the linear view's SVG export: the\n// canvas's ink, the tube map and reference strip painters, and the SVG\n// overlays the screen mounts over them. Hover and selection are left out.\nexport default function PaneSvg({\n  model,\n  rasterize = false,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize?: boolean\n  idPrefix: string\n}) {\n  const width = model.paneWidth\n  const height = model.canvasHeight\n  const tubeMap = !!model.layoutResult?.tubeMap\n  const opts = { rasterizeLayers: rasterize }\n  return (\n    <g data-testid=\"graph-pane-svg\">\n      {model.facetPanels ? (\n        <Facets model={model} rasterize={rasterize} idPrefix={idPrefix} />\n      ) : tubeMap ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintTubeMap(asCanvasCtx(ctx), model, { highlightNode: null })\n          }}\n        />\n      ) : (\n        <Body\n          model={model}\n          lift={model.walkLift}\n          drawPaths={model.effectiveDrawPaths}\n          width={width}\n          height={height}\n          rasterize={rasterize}\n        />\n      )}\n      {model.referenceStripShown ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintReferenceStrip(asCanvasCtx(ctx), model, {\n              lit: undefined,\n              dpr: 1,\n            })\n          }}\n        />\n      ) : null}\n      {model.facetPanels ? null : (\n        <>\n          <WalkRowsOverlay model={model} />\n          <RowLabels model={model} />\n          <SizeLabels model={model} />\n          <BubbleHalos model={model} />\n          <GenePins model={model} />\n          <LabelLayer model={model} />\n          <Keys model={model} idPrefix={idPrefix} />\n        </>\n      )}\n    </g>\n  )\n}\n"],
+  "mappings": 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+  "names": ["require_renderDisplaySvg", "__commonJSMin", "exports", "module", "require_paintLayer", "__commonJSMin", "exports", "module", "import_renderDisplaySvg", "import_paintLayer", "import_jsx_runtime", "FONT", "CHAR_PX", "ROW_PX", "SWATCH_PX", "BAR_PX", "RASTER_SCALE", "STRIP_SAMPLES", "asCanvasCtx", "ctx", "Body", "model", "lift", "drawPaths", "width", "height", "rasterize", "built", "transform", "canvas", "renderer", "Canvas2DRenderer", "markup", "svgCanvas", "Swatch", "id", "x", "y", "stops", "i", "swatchRow", "key", "swatch", "swatchWidth", "label", "after", "under", "right", "walkRow", "walk", "walkKey", "encodingStops", "flatRow", "color", "stripStops", "w", "colors", "b", "c", "all", "n", "_", "stripKeyRows", "idPrefix", "rowPerWalk", "bands", "rows", "LIFT_BACKDROP_CSS", "haloRows", "kindsByColor", "h", "BUBBLE_KIND_COLORS", "kinds", "BUBBLE_KIND_NAMES", "pathRows", "name", "readStops", "tubeMapRows", "logWidths", "foldBp", "forwardReads", "reverseReads", "mismatches", "reads", "glyph", "char", "FORWARD_READ_COLORS", "REVERSE_READ_COLORS", "deviationInk", "formatBp", "rulerInk", "walkRowsKeyRows", "bars", "walkRowsKey", "entry", "tree", "walkRowsKeyTree", "ElTree", "Keys", "domain", "start", "end", "REFERENCE_RAMP_ALT_CSS", "pin", "EXON_COLOR", "top", "LEGEND_INSET_PX", "boxWidth", "r", "left", "boxHeight", "sum", "row", "at", "Chip", "text", "fontSize", "anchor", "bold", "SizeLabels", "kind", "leader", "RowLabels", "screenY", "Facets", "panels", "grid", "place", "columns", "cell", "FACET_GAP_PX", "FACET_TITLE_PX", "title", "PaneSvg", "tubeMap", "opts", "paintTubeMap", "paintReferenceStrip", "WalkRowsOverlay_default", "BubbleHalos_default", "GenePins_default", "LabelLayer_default", "import_jsx_runtime", "GraphTrackSvgBody", "model", "opts", "PaneSvg", "renderGraphTrackSvg"]
+}