jbrowse-plugin-graphgenomeviewer 4.0.19 → 4.0.21

package/dist/chunks/chunk-VIFXYTIS.js

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+import{a as c,b as u}from"./chunk-KULNKXPT.js";import{a as L}from"./chunk-FY3BTKY4.js";var j=L((Ne,N)=>{N.exports=JBrowseExports["tss-react/mui"]});var E=/:(\d+)-\d+$/;function l(e){let t=E.exec(e);return t?{name:e.slice(0,t.index),start:+t[1]}:{name:e,start:0}}function z(e,t){let n=[],r=new Map;for(let o of e){let s=c(o.name),a=o.start;for(let i of o.steps){let p={path:o.name,sample:s,start:a,strand:i.strand},h=r.get(i.id);h?h.push(p):r.set(i.id,[p]),a+=t(i.id)}n.push({name:o.name,sample:s,start:o.start,length:a-o.start})}return{anchorPaths:n,pathVisits:r}}function _(e,t){return e.find(r=>r.sample===t||r.name===t)??e[0]}var x=1;function G(e,t,n){let r=e;if(t&&t.length>0){let o=t.find(s=>s.path===n)??t[0];r={...e,stable:{refName:o.path,start:o.start,rank:o.path===n?0:x,strand:o.strand},samples:[...new Set(t.map(s=>s.sample))].sort()}}return r}function S(e,t){let{anchorPaths:n,pathVisits:r}=e,o=n&&r?_(n,t):void 0;return o&&r?{...e,nodes:e.nodes.map(s=>G(s,r.get(s.name),o.name)),anchoredBy:"paths",referencePath:o.name}:e}function K(e,t){return e.anchoredBy==="tags"?e:S(e,t)}function Z(e){let t=0;for(let n=0;n<e.length;n++)t=e.charCodeAt(n)+((t<<5)-t);return Math.abs(t%360)}function A(e,t){return e*360/t}var O=.7,M=.5,w=16;function ee(e){return e>0&&e<=w}function P(e,t){return`hsl(${A(e,t)}, ${O*100}%, ${M*100}%)`}function te(e,t){return`hsl(0, 0%, ${t>1?25+45*e/(t-1):45}%)`}function y(e){let t=l(e).name.split("#"),n=t.join("#");if(t.length>=3&&u(t[0])){let r=t.slice(2).join("#");return[r,r,n]}return[t[0],t.slice(0,2).join("#"),n]}function T(e){return String(e).replace(/\B(?=(\d{3})+$)/g,",")}function D(e,t){let{start:n}=l(e);return t.map(r=>`${r} @${T(n)}`)}function ne(e,t){let n=e.map(a=>y(a.name)),r=[0,1,2].flatMap(a=>[e.map((i,p)=>n[p][a]),e.map((i,p)=>D(i.name,n[p])[a])]),s=r.find(a=>new Set(a).size===e.length)??r.at(-1);return e.map((a,i)=>({name:a.name,label:s[i],color:t?.[i]??P(i,e.length)}))}function oe(e,t){return Math.max(e.nodeLengthPerMegabase*t/1e6,e.minimumNodeLength)}function R(e,t=5){let r=e.nodes.reduce((s,a)=>s+a.length,0)/1e6,o=Math.max(e.nodes.length*40,500);return{nodeLengthPerMegabase:r>0?o/r:1e4,minimumNodeLength:Math.max(5,t),edgeLength:5,nodeSegmentLength:20}}var d={power:1,effect:1};function H(e){return e.power===1&&e.effect===1}function I(e,t){let n=e.nodes.length,r=e.nodes.reduce((a,i)=>a+i.length,0),o=n>0?r/n:0,s=n>0?Math.max(n*40,500)/n:40;return a=>{if(o<=0)return s;let i=(a/o)**t.power;return Math.max(s*((i-1)*t.effect+1),5)}}var m=1e3,v={law:d,minNodeLength:0};function ae(e,t=v){let{law:n,minNodeLength:r}=t,o=R(e,r);if(H(n))return{nodes:e.nodes,opts:o};let s=I(e,n);return{nodes:e.nodes.map(a=>({...a,length:Math.round(s(a.length)*m)})),opts:{...o,nodeLengthPerMegabase:1e6/m,minimumNodeLength:5}}}var f=[{value:"auto",label:"Proportional",description:"Bandage's own scale: a node draws proportional to its length, so a 1 bp allele is a speck.",law:d,minNodeFactor:0},{value:"open",label:"Open bubbles",description:"Give every allele a drawn length, so a bubble reads as two arms rather than a knot.",law:d,minNodeFactor:2.5},{value:"wide",label:"Wide bubbles",description:"As open, spread further. Best on a window of a dozen bubbles.",law:d,minNodeFactor:10},{value:"compress",label:"Compress lengths",description:"Pull the longest and shortest nodes towards the graph\u2019s mean, so a cut spanning kb and bp fits one pane.",law:{power:.5,effect:.5},minNodeFactor:0}],pe=f.map(e=>e.value);function de(e){let t=f.find(n=>n.value===e);return{law:t?.law??d,minNodeLength:(t?.minNodeFactor??0)*40}}var C=[{value:"auto",label:"Auto"},{value:"uniform",label:"Uniform"},{value:"random",label:"Random"},{value:"rainbow",label:"Rainbow"},{value:"depth",label:"Depth"},{value:"node-length",label:"Node Length"},{value:"stable-rank",label:"Stable rank"},{value:"reference-position",label:"Reference position"},{value:"grey",label:"Grey"}],he=C.map(e=>e.value);function ce(e,t){return e!=="auto"?e:t?.anchoredBy?"reference-position":"uniform"}var F=[{value:"depth",label:"By depth",description:"Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform."},{value:"uniform",label:"Uniform",description:"Every node the same thickness."}],me=F.map(e=>e.value),U=.3,g=3;function W(e){let t=0,n=0;for(let r of e.nodes)t+=r.depth*r.length,n+=r.length;return n>0?t/n:0}function k(e,t){return!(t>0)||!(e.depth>0)?1:Math.min(g,Math.max(U,Math.sqrt(e.depth/t)))}function V(e,t,n,r){return t*(n==="depth"?k(e,r):1)}function $(e,t){return e*(t==="depth"?g:1)}function fe(e,t,n,r){let o=e?W(e):0;return{maxHalfWidthPx:$(n,r)/2,halfWidthPx:s=>{let a=t?.get(s);return a?V(a,n,r,o)/2:n/2}}}export{l as a,z as b,_ as c,S as d,K as e,Z as f,A as g,O as h,M as i,w as j,ee as k,P as l,te as m,ne as n,oe as o,ae as p,f as q,pe as r,de as s,C as t,he as u,ce as v,F as w,me as x,W as y,V as z,fe as A,j as B};
+//# sourceMappingURL=chunk-VIFXYTIS.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:tss-react/mui", "../../packages/core/src/pathAnchoring.ts", "../../packages/core/src/pathColors.ts", "../../packages/core/src/layout/drawnScale.ts", "../../packages/core/src/bubbleSpreads.ts", "../../packages/core/src/colorSchemes.ts", "../../packages/core/src/nodeWidths.ts"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"tss-react/mui\"];", "import { REFERENCE_RANK } from './anchoredNodes'\nimport { panSNSample } from './pansn'\n\nimport type { Graph, GraphNode, PathOrigin, PathVisit } from './types'\n\n// Reference coordinates for a GFA that tags none of its segments with one.\n//\n// rGFA writes the fact per segment (SN/SO/SR). A pggb / odgi / Minigraph-Cactus\n// graph writes the same fact once per path and leaves the arithmetic to the\n// reader: walking a path's steps in order, accumulating segment lengths,\n// assigns every segment that path visits an interval on the path's own\n// sequence. Same information, different encoding \u2014 so a general GFA is not a\n// degraded rGFA, and the anchored layouts work on it once the walk is done.\n//\n// It carries one thing rGFA cannot: a segment's *carriage*, the set of\n// assemblies that actually traverse it. rGFA's SR is build order, so there the\n// most a segment can say is which assembly first contributed it.\n\n// `odgi extract` names an extracted path for the interval it covers on its own\n// sequence: `K12#1#chr:1004500-1004961`. That suffix is the only place a cut\n// subgraph states where in the genome it sits, so it is split off here rather\n// than carried around as part of the name \u2014 no assembly has a sequence called\n// `K12#1#chr:1004500-1004961`, and PanSN parsing of it yields a contig no\n// linear view can open.\n//\n// Anchored on the digits rather than on a trailing colon, because a stable name\n// may legitimately contain one (the same hazard gfaParser's tag splitting has).\nconst RANGE_SUFFIX = /:(\\d+)-\\d+$/\n\nexport function pathOrigin(pathName: string) {\n  const match = RANGE_SUFFIX.exec(pathName)\n  return match\n    ? { name: pathName.slice(0, match.index), start: +match[1]! }\n    : { name: pathName, start: 0 }\n}\n\nexport interface PathSteps {\n  name: string\n  start: number\n  steps: { id: string; strand: '+' | '-' }[]\n}\n\n// The single walk. Every segment visit lands in `pathVisits` at the bp its own\n// path reaches it at; `anchorPaths` is what the walk learned about the paths\n// themselves, which is what a reference-path picker lists.\nexport function surveyPaths(\n  paths: PathSteps[],\n  lengthOf: (segmentId: string) => number,\n) {\n  const anchorPaths: PathOrigin[] = []\n  const pathVisits = new Map<string, PathVisit[]>()\n  for (const path of paths) {\n    const sample = panSNSample(path.name)\n    let pos = path.start\n    for (const step of path.steps) {\n      const visit = {\n        path: path.name,\n        sample,\n        start: pos,\n        strand: step.strand,\n      }\n      const existing = pathVisits.get(step.id)\n      if (existing) {\n        existing.push(visit)\n      } else {\n        pathVisits.set(step.id, [visit])\n      }\n      pos += lengthOf(step.id)\n    }\n    anchorPaths.push({\n      name: path.name,\n      sample,\n      start: path.start,\n      length: pos - path.start,\n    })\n  }\n  return { anchorPaths, pathVisits }\n}\n\n// Which path x is drawn on. This is a choice, not a fact: a general GFA's path\n// names are arbitrary and nothing in the file marks one of them as the\n// reference, so a preference is matched against a path's PanSN sample name (the\n// assembly a subgraph was cut against, which is how the launch path knows) and\n// then against its full name. With no preference the first path in the file\n// wins, which is where pggb and odgi leave the reference.\nexport function chooseReferencePath(\n  anchorPaths: PathOrigin[],\n  preferred: string | undefined,\n) {\n  const named = anchorPaths.find(\n    p => p.sample === preferred || p.name === preferred,\n  )\n  return named ?? anchorPaths[0]\n}\n\n// Rank on a path-derived graph is the one distinction the paths support: on the\n// reference path or off it. rGFA's higher ranks are minigraph's build order,\n// which a path GFA has no equivalent of, so drawing more rows than this would\n// be drawing structure the file does not state.\nconst OFF_REFERENCE_RANK = 1\n\n// A segment the reference path visits sits on the backbone at the offset that\n// visit reaches it. One it never visits is an alternate allele, placed on the\n// coordinates of the first path that does carry it \u2014 the same asymmetry rGFA\n// has, where a rank>0 segment's SO is an offset on the assembly that\n// contributed the sequence rather than on the reference.\n//\n// **First visit wins** when a path reaches the same segment more than once, and\n// collapsed repeats make that real rather than hypothetical: pggb folds the\n// E. coli rRNA operons into shared segments, so every strain's path walks them\n// twice (`odgi depth` reaches 10 over a five-strain graph at chr:4,167,000 and\n// chr:3,942,000). A node draws as one tube at one x, so the alternative to\n// picking a copy is one tube spanning both, claiming reference the segment does\n// not occupy. The repeat stays visible as depth: such a node's traversal count\n// is a multiple of the path count.\nfunction anchorNode(\n  node: GraphNode,\n  visits: PathVisit[] | undefined,\n  reference: string,\n): GraphNode {\n  let anchored = node\n  if (visits && visits.length > 0) {\n    const anchor = visits.find(v => v.path === reference) ?? visits[0]!\n    anchored = {\n      ...node,\n      stable: {\n        refName: anchor.path,\n        start: anchor.start,\n        rank: anchor.path === reference ? REFERENCE_RANK : OFF_REFERENCE_RANK,\n        strand: anchor.strand,\n      },\n      samples: [...new Set(visits.map(v => v.sample))].sort(),\n    }\n  }\n  return anchored\n}\n\n// Re-runnable against a different reference path at no parsing cost, which is\n// what the picker needs: the walk is already recorded in `pathVisits`, and only\n// which path counts as rank 0 changes.\nexport function anchorFromPaths(graph: Graph, preferred: string | undefined) {\n  const { anchorPaths, pathVisits } = graph\n  const reference =\n    anchorPaths && pathVisits\n      ? chooseReferencePath(anchorPaths, preferred)\n      : undefined\n  return reference && pathVisits\n    ? ({\n        ...graph,\n        nodes: graph.nodes.map(node =>\n          anchorNode(node, pathVisits.get(node.name), reference.name),\n        ),\n        anchoredBy: 'paths',\n        referencePath: reference.name,\n      } satisfies Graph)\n    : graph\n}\n\n// rGFA states coordinates on every segment, so only a graph that states none\n// has to derive them. A GFA with neither tags nor paths comes back untouched\n// and falls through to the force layout, which is the honest answer for it.\nexport function anchorGraph(graph: Graph, preferred: string | undefined) {\n  return graph.anchoredBy === 'tags' ? graph : anchorFromPaths(graph, preferred)\n}\n", "import { isGenericSample } from './pansn'\nimport { pathOrigin } from './pathAnchoring'\n\nimport type { GraphPath } from './types'\n\n// Deterministic colour from a string (djb2-style hash to an HSL hue). Fine for\n// the `random` node scheme, where a collision between two of thousands of nodes\n// means nothing. NOT what the path ribbons use: see pathHueAt.\nexport function nameHue(name: string) {\n  let hash = 0\n  for (let i = 0; i < name.length; i++) {\n    hash = name.charCodeAt(i) + ((hash << 5) - hash)\n  }\n  return Math.abs(hash % 360)\n}\n\n// Ribbon hues are spread evenly over the wheel by position in the path list,\n// not hashed from the path name. A hash draws from the wheel at random, and at\n// five paths two of them landing on the same hue is common rather than\n// unlucky: `Sakai#1#chr:1983339-1983535` and `NCTC86#1#chr:1709109-1710286`\n// hash 26 degrees apart, which is two purples and a legend that cannot be read\n// off the drawing. Evenly spaced, the worst case is the best available.\n//\n// The cost is that a path's colour depends on how many paths there are, so it\n// moves when the cut changes. That is what the legend is for, and it is the\n// same trade the Bandage demo this was ported from made.\nexport function pathHueAt(index: number, count: number) {\n  return (index * 360) / count\n}\n\nexport const PATH_SATURATION = 0.7\nexport const PATH_LIGHTNESS = 0.5\n\n// Past this many paths a graph cannot be drawn per path at all, and the WHOLE\n// of `drawPaths` goes off with it: the node stripes, the edge ribbons and the\n// key naming them.\n//\n// One number for all three because they are one statement, and they used to\n// disagree. Only the stripes were capped. So a Minigraph-Cactus cut, which\n// writes one W record per haplotype and walks every backbone link with all of\n// them, drew: no stripes at all, a key hundreds of rows tall, and one bezier\n// stroke per path per edge \u2014 measured at 99,800 strokes and 64 ms of geometry\n// for 200 paths over 499 links, against 2,495 strokes for the five-path pggb\n// cut the figures use. Every one of those is its own `beginPath`/`stroke` on\n// the Canvas2D backend, every frame.\n//\n// 16 is where the drawing stops SAYING anything, not where it stops being fast.\n// `pathHueAt` spreads the wheel evenly, so 16 hues are 22 degrees apart and\n// still tellable and 200 are one degree; the ribbon fan is PATH_RIBBON_SPACING\n// per path, so 16 of them is a legible fan and 200 is a band wider than the\n// nodes; and a key past about 16 rows is taller than the drawing beside it.\n// Above the cap the honest picture is the plain one \u2014 which is exactly what a\n// graph carrying no paths at all already draws.\nexport const MAX_PATH_COLORS = 16\n\n// Whether this graph's paths can be drawn as colours. Resolve it once and hand\n// the answer down: the geometry, the hit index and the key each used to decide\n// for themselves, which is how they came to disagree.\nexport function pathColorsLegible(pathCount: number) {\n  return pathCount > 0 && pathCount <= MAX_PATH_COLORS\n}\n\nexport function pathCssColor(index: number, count: number) {\n  return `hsl(${pathHueAt(index, count)}, ${PATH_SATURATION * 100}%, ${\n    PATH_LIGHTNESS * 100\n  }%)`\n}\n\n// Beside reads, which take the blues and the reds, a tube map's paths step\n// from dark grey to light, as sequenceTubeMap draws them under reads, so no\n// tube shares a read's colour\nexport function pathGreyCssColor(index: number, count: number) {\n  const lightness = count > 1 ? 25 + (45 * index) / (count - 1) : 45\n  return `hsl(0, 0%, ${lightness}%)`\n}\n\n// A path is named the way its file names it \u2014 `K12#1#chr:1004500-1004961` for a\n// P record `odgi extract` wrote, `HG00738#1` for a W record \u2014 and neither is a\n// legend entry. The label is the least of that name which still tells the paths\n// apart: the sample where samples are unique, the haplotype too where they are\n// not, the whole stable name where even that repeats. Widening it for every row\n// rather than only for the colliding ones, because a legend where one entry is\n// `HG00738#1` and its neighbour is `HG01071` reads as two kinds of thing.\n// A generic path, which vg files under a placeholder sample\n// (`_gbwt_ref#0#GI262359905`), is named by its contig alone.\nfunction labelTiers(name: string) {\n  const parts = pathOrigin(name).name.split('#')\n  const full = parts.join('#')\n  if (parts.length >= 3 && isGenericSample(parts[0]!)) {\n    const contig = parts.slice(2).join('#')\n    return [contig, contig, full]\n  }\n  return [parts[0]!, parts.slice(0, 2).join('#'), full]\n}\n\n// Locale-independent, unlike toLocaleString: a figure regenerated on a machine\n// with a different locale would otherwise differ from the committed one.\nfunction groupDigits(n: number) {\n  return String(n).replace(/\\B(?=(\\d{3})+$)/g, ',')\n}\n\n// A collapsed repeat puts one sequence through the same segments more than\n// once, and `odgi extract` emits one path per visit \u2014 nine visits over five\n// E. coli chromosomes at the rRNA operons, where every name tier above collides\n// because the sequence really is the same one. What separates those is the\n// offset each name carried, which is the one thing pathOrigin strips off.\nfunction offsetTiers(name: string, tiers: string[]) {\n  const { start } = pathOrigin(name)\n  return tiers.map(t => `${t} @${groupDigits(start)}`)\n}\n\nexport interface PathLegendEntry {\n  name: string\n  label: string\n  color: string\n}\n\n// `colors` is what each path was actually drawn in, where that is not\n// pathCssColor's hue\nexport function pathLegend(\n  paths: GraphPath[],\n  colors?: readonly string[],\n): PathLegendEntry[] {\n  const named = paths.map(p => labelTiers(p.name))\n  // narrowest first, and the offset is tried before the next name tier: two\n  // copies of one operon are told apart by where they are, not by widening a\n  // name that is genuinely identical\n  const candidates = [0, 1, 2].flatMap(t => [\n    paths.map((_, i) => named[i]![t]!),\n    paths.map((p, i) => offsetTiers(p.name, named[i]!)[t]!),\n  ])\n  const distinct = candidates.find(\n    labels => new Set(labels).size === paths.length,\n  )\n  // Nothing separates two paths with the same name and the same offset, so the\n  // widest labelling is as close as any can get.\n  const labels = distinct ?? candidates.at(-1)!\n  return paths.map((path, i) => ({\n    name: path.name,\n    label: labels[i]!,\n    color: colors?.[i] ?? pathCssColor(i, paths.length),\n  }))\n}\n", "import type { Graph, GraphNode } from '../types'\n\nexport interface BandageScaleOpts {\n  nodeLengthPerMegabase: number\n  minimumNodeLength: number\n  nodeSegmentLength: number\n  edgeLength: number\n}\n\n// Node drawn length, in FMMM units, as a function of bp. Used both by the layouts\n// that run here and by the options handed to the WASM engine, so a graph is drawn\n// at the same scale whichever one draws it. Bandage's own auto rule\n// (`AssemblyGraph::determineGraphInfo`):\n// pick units-per-megabase so the *mean* drawn node length lands on 40, with a\n// floor on total drawn length so a small graph doesn't collapse to a speck.\n//\n// This has to be derived per graph, not fixed. The scale that suits a bacterial\n// assembly's 10-100 kb contigs is wrong by orders of magnitude for a minigraph\n// pangenome window, whose nodes run 300 bp to a few kb: a fixed 1000 units/Mbp\n// makes every node shorter than the edges between them and the graph reads as\n// beads on a string, while 1 unit/bp makes each node a long sweeping curve and\n// the graph sprawls. For the 53-node E. coli window this lands near 35,000.\n//\n// It matters most at the small end. The WASM wrapper's own default of 1000\n// units/Mbp puts *every* node in a 400 bp pggb window below minimumNodeLength,\n// so all 31 clamp to the floor and a 1 bp SNP allele draws the same size as the\n// 164 bp backbone segment beside it \u2014 which is what made that figure read as a\n// chain of same-sized two-node bubbles. Bandage draws the same file with a 75:1\n// length ratio, the SNP alleles as specks.\n//\n// The remaining three are upstream Bandage's shipped defaults\n// (`program/settings.cpp`), which the WASM wrapper's own header does not match \u2014\n// it defaults all of them to 1.0, so they have to be passed explicitly.\nconst MEAN_NODE_LENGTH = 40\nconst MIN_TOTAL_GRAPH_LENGTH = 500\n\n// Bandage's own floor on a node's drawn length. Right for an assembly graph,\n// whose nodes are kb to Mb, and the reason a variation graph draws as a rope:\n// see BUBBLE_SPREADS, which is how a view asks for more.\nconst BANDAGE_MINIMUM_NODE_LENGTH = 5\n\n// The engine's own rule (`settings.h`, `getDrawnNodeLength`), so a seed computed\n// here spans exactly the chain the engine builds from the same numbers.\nexport function drawnNodeLength(opts: BandageScaleOpts, length: number) {\n  return Math.max(\n    (opts.nodeLengthPerMegabase * length) / 1_000_000,\n    opts.minimumNodeLength,\n  )\n}\n\nexport function bandageAutoScale(\n  graph: Graph,\n  // Floor on a node's drawn length, in the same FMMM units as the scale below.\n  // Anything at or under Bandage's own floor leaves the drawing exactly as it\n  // was, which is what keeps `'auto'` byte-identical to the shipped behaviour.\n  minNodeLength = BANDAGE_MINIMUM_NODE_LENGTH,\n): BandageScaleOpts {\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0)\n  const megabases = totalLength / 1_000_000\n  const target = Math.max(\n    graph.nodes.length * MEAN_NODE_LENGTH,\n    MIN_TOTAL_GRAPH_LENGTH,\n  )\n  return {\n    nodeLengthPerMegabase: megabases > 0 ? target / megabases : 10_000,\n    minimumNodeLength: Math.max(BANDAGE_MINIMUM_NODE_LENGTH, minNodeLength),\n    edgeLength: 5,\n    nodeSegmentLength: 20,\n  }\n}\n\n// How a node's bp becomes its drawn length, as a power law against the graph's\n// own mean. The idiom is Bandage's, moved onto the axis a pangenome needs it on:\n// upstream derives a node's *width* from its depth exactly this way\n// (`graph/graphicsitemnode.cpp`, `getNodeWidth`), at a `depthPower` of 0.5 and a\n// `depthEffectOnWidth` of 0.5, because depth in an assembly graph spans orders\n// of magnitude and drawing it linearly is unreadable.\n//\n//   drawn = meanDrawn * (((bp / meanBp) ^ power - 1) * effect + 1)\n//\n// Length in a *variation* graph spans those same orders of magnitude \u2014 a 1 bp\n// allele beside a 16 kb backbone segment \u2014 and upstream still maps it linearly,\n// because its own nodes are assembled contigs where that range does not arise.\n// That linear map is what draws a pggb window as one rope: past the small end\n// every allele falls under `minimumNodeLength` and clamps, so both arms of a\n// bubble land inside one node thickness of each other.\n//\n// power 1 with effect 1 is exactly proportional, so Bandage's shipped behaviour\n// is a point in this family rather than a mechanism sitting beside it. See\n// BUBBLE_SPREADS for the points a view can ask for.\nexport interface DrawnLengthLaw {\n  // exponent applied to a node's length relative to the graph's mean\n  power: number\n  // how much of that relative length survives. 0 draws every node at the mean,\n  // 1 applies the power law undamped.\n  effect: number\n}\n\nexport const PROPORTIONAL_LENGTH: DrawnLengthLaw = { power: 1, effect: 1 }\n\nexport function isProportional(law: DrawnLengthLaw) {\n  return law.power === 1 && law.effect === 1\n}\n\n// Drawn length in FMMM units for one node of `graph`, under `law`.\nexport function drawnLengthFor(graph: Graph, law: DrawnLengthLaw) {\n  const count = graph.nodes.length\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0)\n  const meanBp = count > 0 ? totalLength / count : 0\n  // The mean drawn length `bandageAutoScale` already targets, small-graph floor\n  // included, so a compressed drawing comes out the same overall size as the\n  // proportional one it replaces. That is the property a per-node floor does\n  // not have, and the reason raising one is unusable at scale: it lifts the\n  // hundreds of non-branching chain nodes along with the alleles, which on a\n  // 521-node cut inflates the drawing past what zoom-to-fit can frame.\n  const meanDrawn =\n    count > 0\n      ? Math.max(count * MEAN_NODE_LENGTH, MIN_TOTAL_GRAPH_LENGTH) / count\n      : MEAN_NODE_LENGTH\n  return (bp: number) => {\n    if (meanBp <= 0) {\n      return meanDrawn\n    }\n    const relative = (bp / meanBp) ** law.power\n    return Math.max(\n      meanDrawn * ((relative - 1) * law.effect + 1),\n      BANDAGE_MINIMUM_NODE_LENGTH,\n    )\n  }\n}\n\n// The engine's own length rule is linear with a floor and takes two numbers\n// (`settings.h`, `getDrawnNodeLength`), so a non-linear law cannot be expressed\n// through them. It can be expressed in the lengths themselves: node length\n// crosses the RPC boundary only to become a drawn length \u2014 `getLength()` has\n// exactly two call sites upstream, both inside that rule \u2014 so handing the engine\n// pre-transformed lengths and a 1:1 scale draws the law without touching the\n// WASM build. Scaled by this factor first because the binding reads a node's\n// length as an `unsigned`, and rounding drawn units straight to integers would\n// quantise the small end where the whole point is legibility.\nconst LAYOUT_LENGTH_PRECISION = 1000\n\n// How a view asks for its node lengths: a law, plus Bandage's own per-node\n// floor. Orthogonal on purpose \u2014 see BUBBLE_SPREADS for which does what.\nexport interface NodeLengthSpread {\n  law: DrawnLengthLaw\n  // in the same FMMM units as the drawn lengths. At or under Bandage's own\n  // floor this leaves the drawing exactly as it was.\n  minNodeLength: number\n}\n\nexport const PROPORTIONAL_SPREAD: NodeLengthSpread = {\n  law: PROPORTIONAL_LENGTH,\n  minNodeLength: 0,\n}\n\nexport interface LayoutScaling {\n  // the nodes to hand the engine. Under any law but the proportional one their\n  // `length` is a scaled drawn length rather than a bp count, which is why this\n  // is a separate array and never the graph's own nodes.\n  nodes: GraphNode[]\n  opts: BandageScaleOpts\n}\n\nexport function layoutScaling(\n  graph: Graph,\n  spread: NodeLengthSpread = PROPORTIONAL_SPREAD,\n): LayoutScaling {\n  const { law, minNodeLength } = spread\n  const opts = bandageAutoScale(graph, minNodeLength)\n  // The proportional law is what every committed force figure was drawn\n  // against, and it is already exactly what `bandageAutoScale` expresses, so it\n  // keeps the untransformed path rather than round-tripping through a rounding\n  // step FMMM would be free to amplify. Every floor-based spread comes through\n  // here too, unchanged.\n  if (isProportional(law)) {\n    return { nodes: graph.nodes, opts }\n  }\n  const drawn = drawnLengthFor(graph, law)\n  return {\n    nodes: graph.nodes.map(node => ({\n      ...node,\n      length: Math.round(drawn(node.length) * LAYOUT_LENGTH_PRECISION),\n    })),\n    opts: {\n      ...opts,\n      nodeLengthPerMegabase: 1_000_000 / LAYOUT_LENGTH_PRECISION,\n      // Bandage's own floor only. A law and a raised floor are alternatives\n      // rather than a stack: the law has already lifted the small end, and a\n      // floor on top of it would flatten exactly what it just spread.\n      minimumNodeLength: BANDAGE_MINIMUM_NODE_LENGTH,\n    },\n  }\n}\n\n// The mean drawn node length `bandageAutoScale` targets, exported so\n// BUBBLE_SPREADS can state its laws against it rather than against unanchored\n// constants.\nexport { MEAN_NODE_LENGTH }\n", "import { MEAN_NODE_LENGTH, PROPORTIONAL_LENGTH } from './layout/drawnScale'\n\nimport type { NodeLengthSpread } from './layout/drawnScale'\n\n// How far apart the force layout draws the two arms of a bubble, as the law\n// turning a node's bp into its drawn length. One table drives the persisted\n// enum, the dropdown and the value handed to the engine, the same way\n// LAYOUT_MODES and COLOR_SCHEMES do.\n//\n// Why this needs to be a control rather than a better default: the drawn-length\n// law is the one thing standing between a variation graph and a legible force\n// layout, and compressing it costs the property that node length is proportional\n// to bp. Bandage maps length linearly, which suits an assembly graph whose nodes\n// are kb to Mb. In a pangenome an allele is 1-50 bp against a backbone segment\n// of several kb, so on that map every alt clamps to the engine's 5-unit floor,\n// both arms of a bubble land inside one node thickness of each other, and FMMM\n// has nothing to spread \u2014 zoom-to-fit then delivers a single rope with the\n// variation invisible inside it. Compressing the law opens the bubbles and\n// flattens the length ratio, and which of those a reader wants depends on the\n// figure, so the view asks rather than assumes.\n//\n// The compression is Bandage's own, taken off the axis upstream uses it on: it\n// draws node *width* from depth as a power law against the mean, at power 0.5\n// and effect 0.5, for the same reason. 'open' is those two numbers. See\n// DrawnLengthLaw.\n//\n// Measured on an odgi extract of GRCh38#0#chrM:8,200-8,400 from HPRC release 2's\n// chrM pggb graph (61 nodes, 84 edges, 234 haplotype paths), fitted to a 900x560\n// pane: proportional is one squiggle with a single knot in it, and the bubbles\n// come apart into legible lenses once the law compresses.\n//\n// The floor and the law are different instruments and both are kept, because\n// neither does the other's job:\n//\n// - a FLOOR lifts the small end and leaves everything above it proportional. It\n//   is what a figure wants when one long node has to stay long \u2014 the ribbons in\n//   `pangenome/pggb_haplotype_paths` separate along a 1.2 kb deletion arc, and\n//   shortening that arc towards the mean piles them up. Its cost is that it is a\n//   per-node minimum, so it lifts a graph's non-branching chain nodes along with\n//   its alleles and the drawing inflates with node count: on the 521-node pggb\n//   cut in `pangenome/graph_resolution` it reached ~52,000 units and a 1.4% fit,\n//   which is why that figure could once afford a spread on its 7-node half only.\n// - the LAW compresses both ends towards the mean, so the drawing stays the size\n//   it already was whatever the node count, and a cut spanning 6 bp to 16 kb\n//   fits one pane. Its cost is the top end: a node that has to read as long no\n//   longer does.\n//\n// So a figure about bubble shape at scale takes 'compress', and a figure about\n// what is drawn along one long edge takes 'open'.\n//\n// 'auto' is the proportional map, unchanged, so every existing figure and the\n// `bandageAutoScale` length-proportionality test are untouched by this existing.\nexport const BUBBLE_SPREADS = [\n  {\n    value: 'auto',\n    label: 'Proportional',\n    description:\n      \"Bandage's own scale: a node draws proportional to its length, so a 1 bp allele is a speck.\",\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 0,\n  },\n  {\n    value: 'open',\n    label: 'Open bubbles',\n    description:\n      'Give every allele a drawn length, so a bubble reads as two arms rather than a knot.',\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 2.5,\n  },\n  {\n    value: 'wide',\n    label: 'Wide bubbles',\n    description:\n      'As open, spread further. Best on a window of a dozen bubbles.',\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 10,\n  },\n  {\n    value: 'compress',\n    label: 'Compress lengths',\n    description:\n      'Pull the longest and shortest nodes towards the graph\\u2019s mean, so a cut spanning kb and bp fits one pane.',\n    law: { power: 0.5, effect: 0.5 },\n    minNodeFactor: 0,\n  },\n] as const\n\nexport type BubbleSpread = (typeof BUBBLE_SPREADS)[number]['value']\n\nexport const BUBBLE_SPREAD_VALUES = BUBBLE_SPREADS.map(s => s.value)\n\n// The law and floor behind a spread, resolved so the model has one place that\n// knows how a spread becomes numbers. An unknown value draws proportionally\n// rather than throwing, which is what a session persisted by a newer build\n// degrades to.\nexport function spreadFor(spread: string): NodeLengthSpread {\n  const entry = BUBBLE_SPREADS.find(s => s.value === spread)\n  return {\n    law: entry?.law ?? PROPORTIONAL_LENGTH,\n    minNodeLength: (entry?.minNodeFactor ?? 0) * MEAN_NODE_LENGTH,\n  }\n}\n", "import type { Graph } from './types'\n\n// One table drives the persisted enum and both colour dropdowns, the same way\n// LAYOUT_MODES drives the layout enum and its menu. The values and their labels\n// used to live in two lists in two directories, so adding a scheme meant editing\n// both and a mismatch showed up as a dropdown entry that selected nothing.\n//\n// Kept out of the components directory because the model needs it too.\nexport const COLOR_SCHEMES = [\n  // Mirrors `layoutModes`' 'auto': a value the model resolves rather than a\n  // colour of its own. It exists because 'uniform' was the default, so a\n  // launched graph opened flat grey and both tutorials spent a step saying \"now\n  // pick a colour\" \u2014 one figure literally drives that click. A graph with\n  // reference coordinates resolves to 'reference-position', which is the one\n  // ramp a linear track beside it can be painted with too; a graph with none\n  // keeps 'uniform', because there the ramp would be a hue nothing earned.\n  //\n  // Resolve through `effectiveColorScheme`; the dropdown reads the raw prop, so\n  // \"Auto\" stays selectable and visible as what it is.\n  { value: 'auto', label: 'Auto' },\n  { value: 'uniform', label: 'Uniform' },\n  { value: 'random', label: 'Random' },\n  { value: 'rainbow', label: 'Rainbow' },\n  { value: 'depth', label: 'Depth' },\n  { value: 'node-length', label: 'Node Length' },\n  { value: 'stable-rank', label: 'Stable rank' },\n  { value: 'reference-position', label: 'Reference position' },\n  { value: 'grey', label: 'Grey' },\n] as const\n\nexport type ColorScheme = (typeof COLOR_SCHEMES)[number]['value']\n\n// What the renderer can actually paint with: every scheme except the one that\n// stands for \"work it out\". Stated as its own type so `getNodeColor`'s switch\n// has no 'auto' arm to forget.\nexport type ResolvedColorScheme = Exclude<ColorScheme, 'auto'>\n\nexport const COLOR_SCHEME_VALUES = COLOR_SCHEMES.map(s => s.value)\n\n// 'auto' asks the GRAPH, not the layout: a hue along the reference means\n// something whenever the segments have reference coordinates, force-directed\n// drawings included.\nexport function resolveColorScheme(\n  scheme: ColorScheme,\n  graph: Graph | undefined,\n): ResolvedColorScheme {\n  return scheme !== 'auto'\n    ? scheme\n    : graph?.anchoredBy\n      ? 'reference-position'\n      : 'uniform'\n}\n", "import type { Graph, GraphNode } from './types'\nimport type { NodeInk } from './util/hitDetection'\n\n// How thick a node draws. Bandage widens a node by its depth, the square root\n// of its depth against the graph's mean, so a contig every read covers is fat\n// and a spurious one is a hair. In a pangenome cut depth is carriage, how many\n// walks go through the node, and the same rule makes the reference thick and a\n// private allele thin. One table drives the persisted enum and the dropdown,\n// the way BUBBLE_SPREADS does.\nexport const NODE_WIDTHS = [\n  {\n    value: 'depth',\n    label: 'By depth',\n    description:\n      'Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform.',\n  },\n  {\n    value: 'uniform',\n    label: 'Uniform',\n    description: 'Every node the same thickness.',\n  },\n] as const\n\nexport type NodeWidth = (typeof NODE_WIDTHS)[number]['value']\n\nexport const NODE_WIDTH_VALUES = NODE_WIDTHS.map(w => w.value)\n\nconst MIN_FACTOR = 0.3\nconst MAX_FACTOR = 3\n\n// Length-weighted, as Bandage's mean depth is, so a cut's long reference nodes\n// set the norm and the alleles read against it.\nexport function meanDepth(graph: Graph) {\n  let weighted = 0\n  let length = 0\n  for (const node of graph.nodes) {\n    weighted += node.depth * node.length\n    length += node.length\n  }\n  return length > 0 ? weighted / length : 0\n}\n\nexport function depthWidthFactor(node: GraphNode, mean: number) {\n  if (!(mean > 0) || !(node.depth > 0)) {\n    return 1\n  }\n  return Math.min(\n    MAX_FACTOR,\n    Math.max(MIN_FACTOR, Math.sqrt(node.depth / mean)),\n  )\n}\n\n// How wide a node is drawn, in screen px. One function for the geometry and\n// for the hit test, so the pointer finds a node exactly where its ink is.\nexport function nodeWidthPx(\n  node: GraphNode,\n  contigThickness: number,\n  nodeWidth: NodeWidth,\n  mean: number,\n) {\n  return (\n    contigThickness * (nodeWidth === 'depth' ? depthWidthFactor(node, mean) : 1)\n  )\n}\n\nexport function maxNodeWidthPx(contigThickness: number, nodeWidth: NodeWidth) {\n  return contigThickness * (nodeWidth === 'depth' ? MAX_FACTOR : 1)\n}\n\n// How far each node's ink reaches from its centreline, for the hit test: the\n// widths the geometry draws with, from the same function.\nexport function nodeInk(\n  graph: Graph | undefined,\n  nodeById: ReadonlyMap<string, GraphNode> | undefined,\n  contigThickness: number,\n  nodeWidth: NodeWidth,\n): NodeInk {\n  const mean = graph ? meanDepth(graph) : 0\n  return {\n    maxHalfWidthPx: maxNodeWidthPx(contigThickness, nodeWidth) / 2,\n    halfWidthPx: id => {\n      const node = nodeById?.get(id)\n      return node\n        ? nodeWidthPx(node, contigThickness, nodeWidth, mean) / 2\n        : contigThickness / 2\n    },\n  }\n}\n"],
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+}

package/dist/jbrowse-plugin-graphgenomeviewer.esm.js

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Wi(e){let t=e.getElementTypesInGroup("display"),n=a=>t.find(o=>o.name===a),r=a=>a&&Object.assign(Object.create(a),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...$i.map(a=>r(n(a)))].filter(a=>a!==void 0)}function Bt(e){e.addTrackType(()=>{let t=(0,_o.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,re.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new re.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,re.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Wi(e))n.addDisplayType(r);return n})}function Ct(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var oa=x(ke(),1),aa=x($o(),1);var Xo=x(_(),1),Yo=x(zo(),1),Et=x(z(),1);function 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Je=(e,t)=>(0,Qe.ConfigurationSchema)(e,{indexType:{model:pa.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Yi=(0,Qe.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Je("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Je("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Ui=(0,Qe.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Je("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Je("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Yi},{explicitlyTyped:!0,preProcessSnapshot:_t}),ma=Ui;function 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a?(0,ae.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:a.left,width:a.width}}):null}),os=(0,Wt.observer)(function({model:t}){let{views:n}=(0,fa.getSession)(t);return(0,ae.jsx)(ae.Fragment,{children:ba([...n],t.id,t.assemblyNames).map(({key:r,region:a})=>(0,ae.jsx)(rs,{model:t,region:a},`graph-hover-${r}`))})}),xa=os;var Sa=x(de(),1),as="LinearGenomeView-TracksContainerComponent";function zt(e){e.contributeToExtensionPoint(as,({model:t})=>(0,Sa.jsx)(xa,{model:t},"graphgenomeview-hover-highlight"))}var ka="GraphGenomeView";var Ma="4.0.19";var Xt=class extends Ra.default{constructor(){super(...arguments);this.name=ka;this.version=Ma}install(n){vt(n),Vt(n),Bt(n),Ct(n),zt(n),jt(n),Ot(n),ct(n),pt(n),$t(n),n.addRpcMethod(()=>new me(n)),n.addRpcMethod(()=>new pe(n)),n.addRpcMethod(()=>new ue(n))}configure(n){try{(0,La.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Ce,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{Xt as default};
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t=ta();return Object.assign(new ma.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ua(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,pa.lazy)(()=>import("./chunks/LinearGraphDisplay-4CMVCEM5.js"))}),{adapterCapabilities:["getSubgraph"]})})}var ha=S(Ee(),1);var Ot=S(j(),1),la=S(X(),1);function Wt(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:r?"CSI":"TBI",location:{uri:`${t}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var ts=(0,Ot.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Ot.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:la.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Wt}),ga=ts;function _t(e){e.addAdapterType(()=>new ha.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Wt,configSchema:ga,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-NRDD66AK.js").then(t=>t.default)}))}var ka=S(Ee(),1);var Qe=S(j(),1),ya=S(X(),1);function ba(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function fa(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:ba(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:ba(`${t}.links.bed.gz`,n,r)}:e}function jt(e){let{coarse:t,baseUri:n}=e;return fa(typeof t=="object"&&t!==null?{...e,coarse:fa({baseUri:n,...t})}:e)}var Je=(e,t)=>(0,Qe.ConfigurationSchema)(e,{indexType:{model:ya.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),ns=(0,Qe.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Je("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Je("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),rs=(0,Qe.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Je("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Je("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:ns},{explicitlyTyped:!0,preProcessSnapshot:jt}),wa=rs;function $t(e){e.addAdapterType(()=>new ka.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:jt,configSchema:wa,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-NQEERXXI.js").then(t=>t.default)}))}var os=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function as(e){return"uri"in e?rn(e.uri).name:"localPath"in e?e.localPath:e.name}function is(e){return as(e).toLowerCase().endsWith(".gbz.db")}function ss(e){let t=e.adapter;return t?.type==="GbzBaseSyntenyAdapter"&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function ds(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&is(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&on(e))return an({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function zt(e){e.addToExtensionPoint("Core-preProcessTrackConfig",ss),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,a)=>ds(n,r,a)??t(n,r,a)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>os.has(n)?"GraphTrack":t(n,r))}var Ra=S(se(),1),La=S(Fa(),1),Xt=S(Ea(),1),Ga=S(Da(),1);function oe(e){return typeof e=="object"&&e!==null}function xa(e){let t;if(oe(e)){let{refName:n,start:r,end:a,assemblyName:o}=e;typeof n=="string"&&typeof r=="number"&&typeof a=="number"&&(t={refName:n,start:r,end:a,assemblyName:typeof o=="string"?o:void 0})}return t}function cs(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Sa(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function us(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>oe(n)&&Array.isArray(n.displays)?n.displays.filter(r=>oe(r)&&r.type==="LinearGraphDisplay"):[])}function Ma(e,t,n){let r=[],a=new Set(fe(e).map(o=>oe(o)?o.id:void 0));for(let o of e){if(oe(o)&&o.id===t)for(let i of us(o)){let s=xa(i.hoverHighlight);s&&Sa(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph-track",region:s})}if(oe(o)&&o.type==="GraphGenomeView"&&cs(o,t,a)){let i=xa(o.hoverHighlight);i&&Sa(i,n)&&r.push({key:typeof o.id=="string"?o.id:"graph",region:i})}}return r}var ae=S(de(),1),ps=(0,Ga.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,La.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),ms=(0,Xt.observer)(function({model:t,region:n}){let{classes:r}=ps(),a=t.getHighlightCoords(n);return a?(0,ae.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:a.left,width:a.width}}):null}),ls=(0,Xt.observer)(function({model:t}){let{views:n}=(0,Ra.getSession)(t);return(0,ae.jsx)(ae.Fragment,{children:Ma([...n],t.id,t.assemblyNames).map(({key:r,region:a})=>(0,ae.jsx)(ms,{model:t,region:a},`graph-hover-${r}`))})}),Ta=ls;var Aa=S(de(),1),gs="LinearGenomeView-TracksContainerComponent";function Yt(e){e.contributeToExtensionPoint(gs,({model:t})=>(0,Aa.jsx)(Ta,{model:t},"graphgenomeview-hover-highlight"))}var Na="GraphGenomeView";var Pa="4.0.21";var Ut=class extends Ia.default{constructor(){super(...arguments);this.name=Na;this.version=Pa}install(n){Bt(n),Ht(n),Et(n),Ft(n),Yt(n),$t(n),_t(n),pt(n),lt(n),zt(n),n.addRpcMethod(()=>new me(n)),n.addRpcMethod(()=>new pe(n)),n.addRpcMethod(()=>new ue(n))}configure(n){try{(0,va.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Be,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{Ut as default};
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