jbrowse-plugin-graphgenomeviewer 4.1.1 → 4.2.0

package/README.md

@@ -22,7 +22,7 @@ above it.
 
 - **Copy number off a bar.** Walk rows tile each haplotype by the 5,548 bp
   kringle: GRCh38's six units are the six LPA exon pairs above, and HG00133
-  carries 27.
+  has 27.
 
 ![KIV-2 walk rows under LPA and the curated KIV-2 annotation](img/walk_rows_kiv2.png)
 
@@ -49,9 +49,9 @@ node in the view bands its bp in the linear view:
 - Genes from the session's annotation track, drawn on the graph
 - Hovering a callset or MAF row in the same view lifts that haplotype's walk
 - Bubbles from `gfatools bubble` or the graph itself, opened level by level
-- gbz-base haplotypes as walks: carriage as node thickness, walks lifted out as
-  metro-map lanes or side by side, a panel per walk or a row per sample, each
-  shading from its start to its end
+- gbz-base haplotypes as walks: the number of walks through a node as its
+  thickness, walks lifted out as metro-map lanes or side by side, a panel per
+  walk or a row per sample, each shading from its start to its end
 - GAF reads in the tube map, with their mismatches, from a gbz-base track
 - Figures as SVG, from the view's Export SVG or from a JSON spec with no browser
   ([docs/figures.md](docs/figures.md))

package/dist/chunks/{RgfaTabixAdapter-5MD2ZZ2F.js → RgfaTabixAdapter-QPKEJZXA.js}

@@ -1,3 +1,3 @@
-import{a as O,b as P,d as h,e as L}from"./chunk-KDIBFGZM.js";import"./chunk-KWAXLUPQ.js";import{a as B}from"./chunk-J4OLMLS5.js";import"./chunk-KULNKXPT.js";import{b as S}from"./chunk-FY3BTKY4.js";var C=S(O(),1),l=S(B(),1),M=S(P(),1);function x(t){let e=t.split("	");return{refName:e[0],start:+e[1],end:+e[2],id:e[3],rank:+e[4],tags:e[5]??""}}function $(t){let e=t.tags.split(" ").find(a=>a.startsWith("SM:Z:"));if(e===void 0)return;let n=e.slice(5).split(",").map(a=>a.trim()).filter(Boolean);return n.length>0?n:void 0}function w(t){return{id:t.slice(0,-1),strand:t.slice(-1)}}function A(t){let e=t.split("	"),n=w(e[3]),a=w(e[4]);return{source:n.id,sourceStrand:n.strand,target:a.id,targetStrand:a.strand,sourceSegment:{id:n.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:a.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function I(t){return`${t.source}${t.sourceStrand}${t.target}${t.targetStrand}`}var j=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function G(t){let{id:e,refName:n,start:a,end:r,rank:s,tags:m}=t,o=m.split(" ").filter(g=>j.test(g)),i=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${r-a}	SN:Z:${n}	SO:i:${a}	SR:i:${s}${i}`}function Z(t){let{source:e,sourceStrand:n,target:a,targetStrand:r}=t;return`L	${e}	${n}	${a}	${r}	0M`}function b(t,e){return t<e?-1:t>e?1:0}function T(t,e){let n=[...t.values()].sort((r,s)=>b(r.refName,s.refName)||r.start-s.start||b(r.id,s.id)),a=[...e.keys()].sort((r,s)=>b(r,s));return["H	VN:Z:1.0",...n.map(r=>G(r)),...a.map(r=>Z(e.get(r)))].join(`
-`)}function F(t){return t.filter(e=>e.rank>0)}var N=class extends C.BaseFeatureDataAdapter{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,n,a){super(e,n,a),this.fine=this.openIndex([])}openIndex(e){let n=h(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]);return{segments:n,links:h(this,[...e,"linksLocation"],[...e,"linksIndex"]),refNames:new L(n,this)}}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,n={}){let{signal:a,statusCallback:r}=n;return(0,M.ObservableCreate)(async s=>{let m=await this.fine.refNames.resolve(e,n);m!==void 0&&await(0,l.updateStatus)("Downloading segments",r,()=>this.fine.segments.getLines(m,e.start,e.end,{signal:a,lineCallback:o=>{let i=x(o),g=$(i);s.next(new l.SimpleFeature({uniqueId:i.id,refName:e.refName,start:i.start,end:i.end,name:i.id,type:"segment",rank:i.rank,stableName:i.refName,...g&&{samples:g,carriers:g.length}}))}})),s.complete()},a)}async getSubgraph(e,n={}){let{hops:a=0,signal:r,tier:s}=n,m=this.index(s),o=new Map,i=new Map,g=await m.refNames.resolve(e,{signal:r}),R=async(f,p,d)=>{let y=[];return await m.links.getLines(f,p,d,{signal:r,lineCallback:v=>{let c=A(v);i.set(I(c),c);for(let u of[c.sourceSegment,c.targetSegment])o.has(u.id)||(o.set(u.id,u),y.push(u))}}),y};if(g===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${e.assemblyName} mapped to its prefix in assemblyNameToPanSN`);await m.segments.getLines(g,e.start,e.end,{signal:r,lineCallback:f=>{let p=x(f);o.set(p.id,p)}});let k=F(await R(g,e.start,e.end));for(let f=0;f<a;f++){let p=await Promise.all(k.map(d=>R(d.refName,d.start,d.end)));k=F(p.flat())}return T(o,i)}};export{N as default};
-//# sourceMappingURL=RgfaTabixAdapter-5MD2ZZ2F.js.map
+import{a as O,b as P,d as h,e as L}from"./chunk-KDIBFGZM.js";import"./chunk-KWAXLUPQ.js";import{a as B}from"./chunk-J4OLMLS5.js";import"./chunk-KULNKXPT.js";import{b as S}from"./chunk-FY3BTKY4.js";var F=S(O(),1),l=S(B(),1),M=S(P(),1);function x(t){let e=t.split("	");return{refName:e[0],start:+e[1],end:+e[2],id:e[3],rank:+e[4],tags:e[5]??""}}function $(t){let e=t.tags.split(" ").find(a=>a.startsWith("SM:Z:"));if(e===void 0)return;let n=e.slice(5).split(",").map(a=>a.trim()).filter(Boolean);return n.length>0?n:void 0}function w(t){return{id:t.slice(0,-1),strand:t.slice(-1)}}function A(t){let e=t.split("	"),n=w(e[3]),a=w(e[4]);return{source:n.id,sourceStrand:n.strand,target:a.id,targetStrand:a.strand,sourceSegment:{id:n.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:a.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function I(t){return`${t.source}${t.sourceStrand}${t.target}${t.targetStrand}`}var j=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function G(t){let{id:e,refName:n,start:a,end:r,rank:s,tags:m}=t,o=m.split(" ").filter(g=>j.test(g)),i=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${r-a}	SN:Z:${n}	SO:i:${a}	SR:i:${s}${i}`}function Z(t){let{source:e,sourceStrand:n,target:a,targetStrand:r}=t;return`L	${e}	${n}	${a}	${r}	0M`}function b(t,e){return t<e?-1:t>e?1:0}function T(t,e){let n=[...t.values()].sort((r,s)=>b(r.refName,s.refName)||r.start-s.start||b(r.id,s.id)),a=[...e.keys()].sort((r,s)=>b(r,s));return["H	VN:Z:1.0",...n.map(r=>G(r)),...a.map(r=>Z(e.get(r)))].join(`
+`)}function C(t){return t.filter(e=>e.rank>0)}var N=class extends F.BaseFeatureDataAdapter{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,n,a){super(e,n,a),this.fine=this.openIndex([])}openIndex(e){let n=h(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]);return{segments:n,links:h(this,[...e,"linksLocation"],[...e,"linksIndex"]),refNames:new L(n,this)}}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,n={}){let{signal:a,statusCallback:r}=n;return(0,M.ObservableCreate)(async s=>{let m=await this.fine.refNames.resolve(e,n);m!==void 0&&await(0,l.updateStatus)("Downloading segments",r,()=>this.fine.segments.getLines(m,e.start,e.end,{signal:a,lineCallback:o=>{let i=x(o),g=$(i);s.next(new l.SimpleFeature({uniqueId:i.id,refName:e.refName,start:i.start,end:i.end,name:i.id,type:"segment",rank:i.rank,stableName:i.refName,...g&&{samples:g,sampleCount:g.length}}))}})),s.complete()},a)}async getSubgraph(e,n={}){let{hops:a=0,signal:r,tier:s}=n,m=this.index(s),o=new Map,i=new Map,g=await m.refNames.resolve(e,{signal:r}),R=async(f,p,d)=>{let y=[];return await m.links.getLines(f,p,d,{signal:r,lineCallback:v=>{let c=A(v);i.set(I(c),c);for(let u of[c.sourceSegment,c.targetSegment])o.has(u.id)||(o.set(u.id,u),y.push(u))}}),y};if(g===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${e.assemblyName} mapped to its prefix in assemblyNameToPanSN`);await m.segments.getLines(g,e.start,e.end,{signal:r,lineCallback:f=>{let p=x(f);o.set(p.id,p)}});let k=C(await R(g,e.start,e.end));for(let f=0;f<a;f++){let p=await Promise.all(k.map(d=>R(d.refName,d.start,d.end)));k=C(p.flat())}return T(o,i)}};export{N as default};
+//# sourceMappingURL=RgfaTabixAdapter-QPKEJZXA.js.map

package/dist/chunks/{RgfaTabixAdapter-5MD2ZZ2F.js.map → RgfaTabixAdapter-QPKEJZXA.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts", "../../src/RgfaTabixAdapter/rgfaBed.ts"],
-  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport {\n  formatSubgraph,\n  linkKey,\n  parseLinkLine,\n  parseSegmentLine,\n  segmentSamples,\n} from './rgfaBed.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { RgfaLink, RgfaSegment } from './rgfaBed.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\n// What a hop follows: alleles, never the backbone. A rank-0 segment reached\n// through a link is flanking backbone, usually outside the window, so querying\n// its links walks the reference away from the region, brings back more backbone,\n// and closes nothing. Every segment that closes a bubble is an allele interior,\n// and an allele interior is rank > 0 in both index formats (rGFA's SR tag, and\n// pggb's rank 0-or-1 against the anchor path). Reached backbone still becomes a\n// node and its edge still draws; it is only not walked through.\n//\n// This is gfabase's rule, arrived at from the other end. `gfabase sub` expands\n// from a seed either to the whole connected component (`--connected`, which its\n// own README calls overkill) or with `--cutpoints 1`, which takes the biconnected\n// component by *stopping at cutpoints*, the segments every end-to-end walk of\n// the chromosome must traverse. In a reference-anchored pangenome the cutpoints\n// are the backbone, and rank is what the index already states about it, so\n// `rank > 0` is that stopping rule without a connectivity index to build. The\n// third tool is the same shape again: `gfatools view -R` maps the region onto its\n// precomputed bubble decomposition and returns whole overlapping bubbles\n// (gfa_query_by_reg), which is complete for the same reason. Bandage's own\n// `--distance` is a node-step radius, but Bandage holds the entire graph in\n// memory, so its scope is a drawing filter rather than a fetch strategy.\n//\n// Measured with this rule: the E. coli paa window converges at one hop (17\n// segments at 1 and at 2), so the cut closes and stays closed. HPRC's amylase\n// window keeps growing (63 at 0, 78 at 1, 92 at 2) because its alleles have\n// alleles, and wall-clock is flat across all three, since a hop's queries go out\n// together and the remote index dominates.\n//\n// The exact version, when a graph ships a bubble index beside its segments:\n// gfatools' bubble rows carry the member segment ids of every bubble, so the\n// bubbles overlapping the region state which segments a complete cut must\n// contain. That turns the hop count into a termination condition rather than a\n// setting, and MinigraphBubbleAdapter already parses those rows.\nfunction offReference(segments: RgfaSegment[]) {\n  return segments.filter(segment => segment.rank > 0)\n}\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine\n  private coarse: GraphIndex | undefined\n\n  public constructor(\n    config: RgfaTabixAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.fine = this.openIndex([])\n  }\n\n  // refNames off the SEGMENT index: it is the one that names every stable\n  // sequence the graph is anchored to, where the link index only names those a\n  // link touches.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    return {\n      segments,\n      links: openTabixSlot(\n        this,\n        [...under, 'linksLocation'],\n        [...under, 'linksIndex'],\n      ),\n      refNames: new PanSNRefNames(segments, this),\n    }\n  }\n\n  private index(tier: SubgraphTier = 'fine') {\n    if (tier === 'fine') {\n      return this.fine\n    }\n    this.coarse ??= this.openIndex(['coarse'])\n    return this.coarse\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.fine.refNames.assemblyRefNames(opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading segments', statusCallback, () =>\n          this.fine.segments.getLines(tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: line => {\n              const segment = parseSegmentLine(line)\n              // `samples` is who, `carriers` is how many, and the second is not\n              // just a convenience: a lane colored by carriage is a jexl\n              // expression in a config, where counting a list means relying on\n              // jexl resolving `.length` through a member access on an array.\n              // The count is the axis the color reads, so the index states it.\n              const samples = segmentSamples(segment)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: segment.id,\n                  refName: query.refName,\n                  start: segment.start,\n                  end: segment.end,\n                  name: segment.id,\n                  type: 'segment',\n                  rank: segment.rank,\n                  stableName: segment.refName,\n                  ...(samples && { samples, carriers: samples.length }),\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n\n  // Extract the graph around a region as GFA text, for GraphGenomeView. The\n  // region's own segments come from segs.bed.gz; links.bed.gz supplies the edges\n  // incident to them *and* the coordinates of the segments on the other end,\n  // which typically sit on a different stable sequence (a rank>0 bubble) and so\n  // are not reachable by any coordinate query on this region.\n  //\n  // `hops` is extra rounds of link-following past the region's own segments\n  // and their immediate neighbours, each costing one tabix query per\n  // off-reference segment newly reached. One round is what closes a bubble, so\n  // it is the default the view asks for; see the frontier below. `signal` goes\n  // to every one of those queries, so a cut the view has replaced stops.\n  // `tier: 'coarse'` reads the `coarse` pair instead, the same way.\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { hops = 0, signal, tier } = opts\n    const index = this.index(tier)\n    const segments = new Map<string, RgfaSegment>()\n    const links = new Map<string, RgfaLink>()\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n\n    const addLinksOver = async (\n      refName: string,\n      start: number,\n      end: number,\n    ) => {\n      const reached: RgfaSegment[] = []\n      await index.links.getLines(refName, start, end, {\n        signal,\n        lineCallback: line => {\n          const link = parseLinkLine(line)\n          links.set(linkKey(link), link)\n          for (const segment of [link.sourceSegment, link.targetSegment]) {\n            if (!segments.has(segment.id)) {\n              segments.set(segment.id, segment)\n              reached.push(segment)\n            }\n          }\n        },\n      })\n      return reached\n    }\n\n    if (tabixRefName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${region.assemblyName} mapped to its prefix in assemblyNameToPanSN`,\n      )\n    }\n    await index.segments.getLines(tabixRefName, region.start, region.end, {\n      signal,\n      lineCallback: line => {\n        const segment = parseSegmentLine(line)\n        segments.set(segment.id, segment)\n      },\n    })\n    let frontier = offReference(\n      await addLinksOver(tabixRefName, region.start, region.end),\n    )\n    for (let hop = 0; hop < hops; hop++) {\n      // One hop's queries are independent of each other, so they go out\n      // together rather than one round-trip at a time. Their callbacks share\n      // the segment and link maps, which is safe because only one of them runs\n      // at a time, and the output is sorted at the end regardless of the order\n      // they arrive in.\n      const reached = await Promise.all(\n        frontier.map(segment =>\n          addLinksOver(segment.refName, segment.start, segment.end),\n        ),\n      )\n      frontier = offReference(reached.flat())\n    }\n\n    return formatSubgraph(segments, links)\n  }\n}\n", "// A segment as it appears in segs.bed.gz, and as it is repeated inside every\n// links.bed.gz row: `stableName start end segmentId rank [tags]`. The first\n// five are the SN/SO/SR tags rGFA already carries, projected to BED by\n// `gfatools gfa2bed -m`.\n//\n// `tags` is a space-separated list of GFA tags, written verbatim onto the\n// S-line formatSegment synthesizes, where the GFA parser reads them into\n// `GraphNode.tags` with no work here. It is the extension point for everything\n// the five columns cannot say: carriage on a path-derived graph (`SM:Z:`), the\n// collapse summary on a level-of-detail tier (`ct:Z:`, `cn:i:`, ...), a\n// precomputed layout position later. rGFA files have no sixth column at all,\n// so this is empty for them and nothing changes.\nexport interface RgfaSegment {\n  refName: string\n  start: number\n  end: number\n  id: string\n  rank: number\n  tags: string\n}\n\nexport interface RgfaLink {\n  source: string\n  sourceStrand: string\n  target: string\n  targetStrand: string\n  sourceSegment: RgfaSegment\n  targetSegment: RgfaSegment\n}\n\nexport function parseSegmentLine(line: string): RgfaSegment {\n  const cols = line.split('\\t')\n  return {\n    refName: cols[0]!,\n    start: +cols[1]!,\n    end: +cols[2]!,\n    id: cols[3]!,\n    rank: +cols[4]!,\n    tags: cols[5] ?? '',\n  }\n}\n\n// Carriage as an ordinary feature attribute, for the linear track rather than\n// the graph. The tag column reaches the graph view through the synthesized\n// S-line (formatSegment below, then gfaConverter reads SM into\n// `GraphNode.samples`), and that route ends at the graph: `getFeatures` builds\n// its own features and had no way to say who carries a segment, so a lane\n// colored by carriage was not expressible.\n//\n// `SM:Z:` is its own grammar check here. build_pggb_tabix.sh wrote a bare\n// comma-separated list in this column before the tag column existed, and those\n// files are still hosted; a bare list has no prefix to match, so it is dropped\n// rather than read as one sample named `K12,Sakai,CFT073`.\n//\n// Undefined rather than [] when the tag is absent, matching gfaConverter: an\n// rGFA has no sixth column at all, so a segment that says nothing about\n// carriage stays distinguishable from one carried by nobody.\nexport function segmentSamples(segment: RgfaSegment) {\n  const tag = segment.tags.split(' ').find(t => t.startsWith('SM:Z:'))\n  if (tag === undefined) {\n    return undefined\n  }\n  const samples = tag\n    .slice('SM:Z:'.length)\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\n// `s322+` \u2014 the L-line's segment id with its orientation appended, mirroring\n// the GFA record it came from.\nfunction parseEndpoint(field: string) {\n  return { id: field.slice(0, -1), strand: field.slice(-1) }\n}\n\nexport function parseLinkLine(line: string): RgfaLink {\n  const cols = line.split('\\t')\n  const source = parseEndpoint(cols[3]!)\n  const target = parseEndpoint(cols[4]!)\n  return {\n    source: source.id,\n    sourceStrand: source.strand,\n    target: target.id,\n    targetStrand: target.strand,\n    sourceSegment: {\n      id: source.id,\n      refName: cols[5]!,\n      start: +cols[6]!,\n      end: +cols[7]!,\n      rank: +cols[8]!,\n      tags: cols[13] ?? '',\n    },\n    targetSegment: {\n      id: target.id,\n      refName: cols[9]!,\n      start: +cols[10]!,\n      end: +cols[11]!,\n      rank: +cols[12]!,\n      tags: cols[14] ?? '',\n    },\n  }\n}\n\nexport function linkKey(link: RgfaLink) {\n  return `${link.source}${link.sourceStrand}${link.target}${link.targetStrand}`\n}\n\n// Both endpoints of a link are written into every row, so the same link is\n// indexed under each endpoint's stable sequence and arrives twice for a region\n// covering both. Callers dedupe on linkKey.\n\n// Segments carry no sequence here \u2014 the BED records only their span \u2014 so every\n// S-line is written with `*` and an LN tag, which is what the GFA spec asks for\n// and what packages/graph-core's parser reads back as the node length.\n// `NM:i:0`, `SM:Z:HG002.1,HG002.2` \u2014 the GFA tag grammar, checked rather than\n// trusted. Files built before the tag column existed put a bare comma-separated\n// sample list here, and passing that through would put a field that is not a\n// tag on an S-line, which is a malformed GFA rather than a missing annotation.\n// Dropping it degrades to the pre-tag behaviour instead.\nconst GFA_TAG = /^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/\n\nfunction formatSegment(segment: RgfaSegment) {\n  const { id, refName, start, end, rank, tags } = segment\n  const valid = tags.split(' ').filter(t => GFA_TAG.test(t))\n  const extra = valid.length === 0 ? '' : `\\t${valid.join('\\t')}`\n  return `S\\t${id}\\t*\\tLN:i:${end - start}\\tSN:Z:${refName}\\tSO:i:${start}\\tSR:i:${rank}${extra}`\n}\n\nfunction formatLink(link: RgfaLink) {\n  const { source, sourceStrand, target, targetStrand } = link\n  return `L\\t${source}\\t${sourceStrand}\\t${target}\\t${targetStrand}\\t0M`\n}\n\n// Codepoint order, not localeCompare: the byte-identical-output guarantee below\n// has to hold across locales.\nfunction compare(a: string, b: string) {\n  return a < b ? -1 : a > b ? 1 : 0\n}\n\n// Deterministic ordering: the same region always produces byte-identical GFA,\n// so a layout computed from it is reproducible.\nexport function formatSubgraph(\n  segments: Map<string, RgfaSegment>,\n  links: Map<string, RgfaLink>,\n) {\n  const sortedSegments = [...segments.values()].sort(\n    (a, b) =>\n      compare(a.refName, b.refName) || a.start - b.start || compare(a.id, b.id),\n  )\n  const sortedLinks = [...links.keys()].sort((a, b) => compare(a, b))\n  return [\n    'H\\tVN:Z:1.0',\n    ...sortedSegments.map(s => formatSegment(s)),\n    ...sortedLinks.map(k => formatLink(links.get(k)!)),\n  ].join('\\n')\n}\n"],
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+  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport {\n  formatSubgraph,\n  linkKey,\n  parseLinkLine,\n  parseSegmentLine,\n  segmentSamples,\n} from './rgfaBed.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { RgfaLink, RgfaSegment } from './rgfaBed.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\n// What a hop follows: alleles, never the backbone. A rank-0 segment reached\n// through a link is flanking backbone, usually outside the window, so querying\n// its links walks the reference away from the region, brings back more backbone,\n// and closes nothing. Every segment that closes a bubble is an allele interior,\n// and an allele interior is rank > 0 in both index formats (rGFA's SR tag, and\n// pggb's rank 0-or-1 against the anchor path). Reached backbone still becomes a\n// node and its edge still draws; it is only not walked through.\n//\n// This is gfabase's rule, arrived at from the other end. `gfabase sub` expands\n// from a seed either to the whole connected component (`--connected`, which its\n// own README calls overkill) or with `--cutpoints 1`, which takes the biconnected\n// component by *stopping at cutpoints*, the segments every end-to-end walk of\n// the chromosome must traverse. In a reference-anchored pangenome the cutpoints\n// are the backbone, and rank is what the index already states about it, so\n// `rank > 0` is that stopping rule without a connectivity index to build. The\n// third tool is the same shape again: `gfatools view -R` maps the region onto its\n// precomputed bubble decomposition and returns whole overlapping bubbles\n// (gfa_query_by_reg), which is complete for the same reason. Bandage's own\n// `--distance` is a node-step radius, but Bandage holds the entire graph in\n// memory, so its scope is a drawing filter rather than a fetch strategy.\n//\n// Measured with this rule: the E. coli paa window converges at one hop (17\n// segments at 1 and at 2), so the cut closes and stays closed. HPRC's amylase\n// window keeps growing (63 at 0, 78 at 1, 92 at 2) because its alleles have\n// alleles, and wall-clock is flat across all three, since a hop's queries go out\n// together and the remote index dominates.\n//\n// The exact version, when a graph ships a bubble index beside its segments:\n// gfatools' bubble rows carry the member segment ids of every bubble, so the\n// bubbles overlapping the region state which segments a complete cut must\n// contain. That turns the hop count into a termination condition rather than a\n// setting, and MinigraphBubbleAdapter already parses those rows.\nfunction offReference(segments: RgfaSegment[]) {\n  return segments.filter(segment => segment.rank > 0)\n}\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine\n  private coarse: GraphIndex | undefined\n\n  public constructor(\n    config: RgfaTabixAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.fine = this.openIndex([])\n  }\n\n  // refNames off the SEGMENT index: it is the one that names every stable\n  // sequence the graph is anchored to, where the link index only names those a\n  // link touches.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    return {\n      segments,\n      links: openTabixSlot(\n        this,\n        [...under, 'linksLocation'],\n        [...under, 'linksIndex'],\n      ),\n      refNames: new PanSNRefNames(segments, this),\n    }\n  }\n\n  private index(tier: SubgraphTier = 'fine') {\n    if (tier === 'fine') {\n      return this.fine\n    }\n    this.coarse ??= this.openIndex(['coarse'])\n    return this.coarse\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.fine.refNames.assemblyRefNames(opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading segments', statusCallback, () =>\n          this.fine.segments.getLines(tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: line => {\n              const segment = parseSegmentLine(line)\n              // `samples` lists the haplotypes whose paths visit the segment and\n              // `sampleCount` counts them. A lane's color reads the count, and\n              // a count in jexl would otherwise rely on `.length` resolving\n              // through a member access on an array.\n              const samples = segmentSamples(segment)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: segment.id,\n                  refName: query.refName,\n                  start: segment.start,\n                  end: segment.end,\n                  name: segment.id,\n                  type: 'segment',\n                  rank: segment.rank,\n                  stableName: segment.refName,\n                  ...(samples && { samples, sampleCount: samples.length }),\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n\n  // Extract the graph around a region as GFA text, for GraphGenomeView. The\n  // region's own segments come from segs.bed.gz; links.bed.gz supplies the edges\n  // incident to them *and* the coordinates of the segments on the other end,\n  // which typically sit on a different stable sequence (a rank>0 bubble) and so\n  // are not reachable by any coordinate query on this region.\n  //\n  // `hops` is extra rounds of link-following past the region's own segments\n  // and their immediate neighbours, each costing one tabix query per\n  // off-reference segment newly reached. One round is what closes a bubble, so\n  // it is the default the view asks for; see the frontier below. `signal` goes\n  // to every one of those queries, so a cut the view has replaced stops.\n  // `tier: 'coarse'` reads the `coarse` pair instead, the same way.\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { hops = 0, signal, tier } = opts\n    const index = this.index(tier)\n    const segments = new Map<string, RgfaSegment>()\n    const links = new Map<string, RgfaLink>()\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n\n    const addLinksOver = async (\n      refName: string,\n      start: number,\n      end: number,\n    ) => {\n      const reached: RgfaSegment[] = []\n      await index.links.getLines(refName, start, end, {\n        signal,\n        lineCallback: line => {\n          const link = parseLinkLine(line)\n          links.set(linkKey(link), link)\n          for (const segment of [link.sourceSegment, link.targetSegment]) {\n            if (!segments.has(segment.id)) {\n              segments.set(segment.id, segment)\n              reached.push(segment)\n            }\n          }\n        },\n      })\n      return reached\n    }\n\n    if (tabixRefName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${region.assemblyName} mapped to its prefix in assemblyNameToPanSN`,\n      )\n    }\n    await index.segments.getLines(tabixRefName, region.start, region.end, {\n      signal,\n      lineCallback: line => {\n        const segment = parseSegmentLine(line)\n        segments.set(segment.id, segment)\n      },\n    })\n    let frontier = offReference(\n      await addLinksOver(tabixRefName, region.start, region.end),\n    )\n    for (let hop = 0; hop < hops; hop++) {\n      // One hop's queries are independent of each other, so they go out\n      // together rather than one round-trip at a time. Their callbacks share\n      // the segment and link maps, which is safe because only one of them runs\n      // at a time, and the output is sorted at the end regardless of the order\n      // they arrive in.\n      const reached = await Promise.all(\n        frontier.map(segment =>\n          addLinksOver(segment.refName, segment.start, segment.end),\n        ),\n      )\n      frontier = offReference(reached.flat())\n    }\n\n    return formatSubgraph(segments, links)\n  }\n}\n", "// A segment as it appears in segs.bed.gz, and as it is repeated inside every\n// links.bed.gz row: `stableName start end segmentId rank [tags]`. The first\n// five are the SN/SO/SR tags rGFA already carries, projected to BED by\n// `gfatools gfa2bed -m`.\n//\n// `tags` is a space-separated list of GFA tags, written verbatim onto the\n// S-line formatSegment synthesizes, where the GFA parser reads them into\n// `GraphNode.tags` with no work here. It is the extension point for everything\n// the five columns cannot say: carriage on a path-derived graph (`SM:Z:`), the\n// collapse summary on a level-of-detail tier (`ct:Z:`, `cn:i:`, ...), a\n// precomputed layout position later. rGFA files have no sixth column at all,\n// so this is empty for them and nothing changes.\nexport interface RgfaSegment {\n  refName: string\n  start: number\n  end: number\n  id: string\n  rank: number\n  tags: string\n}\n\nexport interface RgfaLink {\n  source: string\n  sourceStrand: string\n  target: string\n  targetStrand: string\n  sourceSegment: RgfaSegment\n  targetSegment: RgfaSegment\n}\n\nexport function parseSegmentLine(line: string): RgfaSegment {\n  const cols = line.split('\\t')\n  return {\n    refName: cols[0]!,\n    start: +cols[1]!,\n    end: +cols[2]!,\n    id: cols[3]!,\n    rank: +cols[4]!,\n    tags: cols[5] ?? '',\n  }\n}\n\n// Carriage as an ordinary feature attribute, for the linear track rather than\n// the graph. The tag column reaches the graph view through the synthesized\n// S-line (formatSegment below, then gfaConverter reads SM into\n// `GraphNode.samples`), and that route ends at the graph: `getFeatures` builds\n// its own features and had no way to say who carries a segment, so a lane\n// colored by carriage was not expressible.\n//\n// `SM:Z:` is its own grammar check here. build_pggb_tabix.sh wrote a bare\n// comma-separated list in this column before the tag column existed, and those\n// files are still hosted; a bare list has no prefix to match, so it is dropped\n// rather than read as one sample named `K12,Sakai,CFT073`.\n//\n// Undefined rather than [] when the tag is absent, matching gfaConverter: an\n// rGFA has no sixth column at all, so a segment that says nothing about\n// carriage stays distinguishable from one carried by nobody.\nexport function segmentSamples(segment: RgfaSegment) {\n  const tag = segment.tags.split(' ').find(t => t.startsWith('SM:Z:'))\n  if (tag === undefined) {\n    return undefined\n  }\n  const samples = tag\n    .slice('SM:Z:'.length)\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\n// `s322+` \u2014 the L-line's segment id with its orientation appended, mirroring\n// the GFA record it came from.\nfunction parseEndpoint(field: string) {\n  return { id: field.slice(0, -1), strand: field.slice(-1) }\n}\n\nexport function parseLinkLine(line: string): RgfaLink {\n  const cols = line.split('\\t')\n  const source = parseEndpoint(cols[3]!)\n  const target = parseEndpoint(cols[4]!)\n  return {\n    source: source.id,\n    sourceStrand: source.strand,\n    target: target.id,\n    targetStrand: target.strand,\n    sourceSegment: {\n      id: source.id,\n      refName: cols[5]!,\n      start: +cols[6]!,\n      end: +cols[7]!,\n      rank: +cols[8]!,\n      tags: cols[13] ?? 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package/dist/jbrowse-plugin-graphgenomeviewer.esm.js

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drawsNodes(){return!e.layoutResult?.tubeMap&&!this.walkRowBars},get drawnRowLabels(){let t=this.walkRowBars;return t?[t.reference,...t.rows].map((n,r)=>({label:n.label,y:r*20})):e.rowLabels},get fitPadLeft(){return Math.max(D,...this.drawnRowLabels.map(t=>ar(t.label,0).x1+6))},get genePins(){fe(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?pt(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){fe(e.positionsVersion);let t=e.layoutResult?.nodePositions;if(!e.showBubbles||!this.drawsNodes||!e.graph||!t)return[];let n=new Map(e.walkChoices.map(r=>[r.name,r.label]));return Ao(e.graph,e.bubbles,t,r=>n.get(r)??r,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?ge(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return he(e.scale,e.pixelRows).scaleX},get scaleY(){return he(e.scale,e.pixelRows).scaleY},get axisScale(){return he(e.scale,e.pixelRows)},get layoutBounds(){let t=e.layoutResult,n=this.walkRowBars;return t?mt(t,{region:e.popStack.length===0?e.graphRegion:void 0,extent:n&&t.extent?Ye(n):void 0}):void 0}})).views(e=>({get geneTrack(){return on(e.geneTrackChoices,e.geneTrackId)},get deletionEdgeIndexes(){return new Map(e.deletions.map(t=>[t.edgeIndex,t.bypassed]))},get hiddenEdgeIndexes(){return new Set(e.showDeletionEdges?[]:e.deletions.map(t=>t.edgeIndex))},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,r=n?.tubeMap?n.nodePositions:void 0,o=!1,a=!1;if(t&&e.drawnGraph)for(let i of e.drawnGraph.nodes)r&&!r[i.id]||(t.midpoints.has(i.id)?i.stable&&i.stable.rank>0&&(o=!0):a=!0);return{offReference:o,unplaced:a}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?ga(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap?.pathColors,n=t&&this.tubeMapNodeColors?t.map((a,i)=>ir(i,t.length)):t,r=new Set(e.hoveredRowWalks),o=e.drawnGraph?.paths;return n&&o&&r.size>0?n.map((a,i)=>r.has(o[i]?.name??"")?a:xr):n},nodeSpan(t){let{nodeById:n,nodeNeighbors:r}=e;return n&&r?He({nodeId:t,nodeById:n,neighbors:r}):void 0}})).views(e=>({get pathLegend(){let t=e.graph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&Ft(t.length)?Re(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?e.nodeSpan(t):n?{start:n.start,end:n.end}:void 0}})).views(e=>({get hoverHighlight(){let t=e.graphRegion,n=e.hoveredSpan;return t&&n?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?Vn(t):[];return t?to(t,{maxGap:n.length>0?On(n):1/0}):[]}})).views(e=>({get 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0;if(!i||!s){r++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...Wt(a.axis,a.bp)}})}return{reads:n.slice(0,Ya),gaps:{untracked:r,unplaced:o,unread:Math.max(0,n.length-Ya)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowAt(t,n){let r=e.walkRowBars;if(!r)return;let o=Math.round((n-e.translateY)/(20*e.scaleY)),a=[r.reference,...r.rows][o],i=o*20*e.scaleY+e.translateY,s=(t-e.translateX)/e.scaleX-r.origin;return a&&Math.abs(n-i)<=Mr/2+2&&s>=0&&s<=a.bp?o:void 0},walkRowLaunchTarget(t){let n=e.walkRowBars,r=n?[n.reference,...n.rows][t]:void 0;if(!r?.axis)return;let o=r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`,a=t===0?e.graphRegion?.assemblyName:it(e.assemblyResolver,{sample:r.sample,haplotype:o});return{label:r.label,assembly:a,location:{sample:r.sample,haplotype:o,refName:r.axis.contig,...Wt(r.axis,r.bp)}}},get walkRowGenes(){let t=e.walkRowBars;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?Lr([t.reference,...t.rows],n):void 0}})).views(e=>({get launchableAssemblies(){return no(Fa(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&Ee({views:[...(0,N.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),r=n?at(n):void 0,o=r?it(e.assemblyResolver,r):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,d=a&&i&&s?He({nodeId:t,nodeById:i,neighbors:s}):void 0,c=a&&d?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...d}:void 0;return{own:r&&o?{location:gn(r),assembly:o}:void 0,reference:a&&c?{location:gn(c),assembly:a.assemblyName}:void 0,highlight:a&&c?{location:c,assembly:a.assemblyName}:void 0}}})).views(e=>({get host(){let t;try{t=(0,N.getContainingView)(e)}catch{return}return xa(t)?t:void 0}})).views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&Z(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(r=>r.refName===n.refName&&r.reversed)}})).views(e=>({get hostFrame(){let{host:t,graphRegion:n}=e;return e.hostPlacesX&&t&&n?yt(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?Ur(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?_r(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?Yr(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?jr(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?Jr(t,e.backboneGenes):[]},get 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zo(bn(e),Ld)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:r,selectedNode:o}=e,a=new Map;o!==null&&a.set(o,Rd),n!==null&&n!==o&&a.set(n,za),t.setNodeHighlights(a),t.setEdgeHighlight(r,za)},paint(t){let n=(0,Qa.getDpr)();t.updateTransform({scaleX:e.scaleX*n,scaleY:e.scaleY*n,translateX:e.translateX*n,translateY:e.translateY*n,dpr:n}),t.render(e.referenceStripShown?[0,0,0,0]:e.darkMode?ja:Ha)}})).views(e=>({buildDrawing(t,n){let{nodePositions:r,graph:o,nodeById:a}=e;if(!r||!o||!a)return;fe(e.viewportDirty,e.positionsVersion);let 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0,s=a?{gfa:a,region:o}:i&&t&&o?{gbz:{db:i,index:$e(n.haplotypeIndexLocation),region:o,haplotypes:e.cutHaplotypes?.map(u=>r?.[u]??u),referenceSample:n.referenceSample||r?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:n.subgraphSnarls}}:void 0;if(!s)return;let d=e.showGenes?e.geneTrack:void 0,c=d?(0,N.getSession)(e).tracks.find(u=>u.trackId===d.trackId):void 0,l=c?(0,ne.expandTabixShorthand)((0,ne.readConfObject)(c,"adapter"),"gffGzLocation"):void 0,g=l?.type==="Gff3TabixAdapter"?{file:$e(l.gffGzLocation),index:$e(l.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:g?.file&&g.index?g:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,quality:e.layoutQuality,bubbleSpread:e.bubbleSpread,walks:e.walkLayers.length?e.walkLayers.map(u=>u.color?u:u.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 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t?pa(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-D}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX?Hr(t):void 0},get connectorZoneBottom(){let t=e.tubeMapPicture,n=e.tubeMapFrame;return t&&n?n.y(t.bounds.minY)-2:0},get tubeMapConnectors(){let t=e.tubeMapReferenceNodes,n=e.tubeMapFrame,{host:r,graphRegion:o}=e,a=t&&n&&r?.initialized&&o?yt(r,o):void 0;return t&&n&&a?Xr(t,i=>i*a.scale+a.translateX,n.x,e.paneWidth):[]}})).views(e=>({get tubeMapKeys(){let t=e.layoutResult,n=t?.tubeMap?.layout.reads??[],r=e.tubeMapPicture,o=e.tubeMapFrame,a=r&&o&&Kr(o.yScale)?r.mismatches.filter(i=>qr(i,{x:o.x,width:e.paneWidth})):[];return{logWidths:t?.tubeMap!==void 0&&!t.referenceAxis,foldBp:e.tubeMapDeviations.length>0?e.tubeMapFold:void 0,forwardReads:n.some(i=>!i.is_reverse),reverseReads:n.some(i=>i.is_reverse),mismatches:new Set(a.map(i=>i.kind))}},tubeMapNodeAt(t,n){let r=e.layoutResult?.tubeMap,o=e.tubeMapFrame;return(r&&o?ma(r,o,t,n):null)??zr(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}})).actions(e=>({setError(t){e.error=t,e.isLoading=!1,e.statusMessage=""},finishLoading(){e.isLoading=!1,e.statusMessage=""},setStatusMessage(t){e.statusMessage=t},setFetchMs(t){e.lastFetchMs=t},setLayoutMs(t){e.lastLayoutMs=t},setGeometryMetrics(t,n,r){e.lastGeometryMs=t,e.lastGeometryStrokeCount=n,e.builtViewport={...r,viewportDirty:e.viewportDirty},e.geometryVersion++},markPainted(){e.paintedViewport=e.builtViewport},setLayoutQuality(t){e.layoutQuality=t},setLinearLayout(t){e.linearLayout=t},setLayoutMode(t){e.layoutMode=t},setReferencePath(t){e.referencePath=t;let n=e.graph;if(n?.anchoredBy==="paths"){let r=Bt(n,t);Ad(n,r),e.graph=r}},setDrawPaths(t){e.drawPaths=t},setShowPerf(t){e.showPerf=t},setColorScheme(t){e.colorScheme=t},setBubbleSpread(t){e.bubbleSpread=t},setNodeWidth(t){e.nodeWidth=t},setShowBubbles(t){e.showBubbles=t},setShowDeletionEdges(t){e.showDeletionEdges=t},setShowGenes(t){e.showGenes=t},setShowReferenceStrip(t){e.showReferenceStrip=t},setTubeMapFold(t){e.tubeMapFold=t},setGeneTrackId(t){e.geneTrackId=t},setRepeatTrackId(t){e.repeatTrackId=t},setRepeatKey(t){e.repeatKey=t},setWalkLayers(t){e.walkLayers=t},liftWalks(t){let n=new Map(e.walkLayers.map(r=>[r.walk,r]));e.walkLayers=t.map(r=>n.get(r)??{walk:r})},setFacet(t){t!==e.facet.field&&(e.facet.domain=[]),e.facet.field=t},setFacetColumns(t){e.facet.columns=t},toggleWalk(t){let n=e.walkLayers;e.walkLayers=n.some(r=>r.walk===t)?n.filter(r=>r.walk!==t):[...n,{walk:t}]},setWalkColor(t,n){e.walkLayers=e.walkLayers.map(r=>r.walk===t?{...r,color:{...r.color,...n}}:r)},setPaneHeight(t){e.paneHeight=t},setWalkRowSamples(t){e.walkRowSamples=t},pairWithLinearView(t){let n=e.connectedViewId;n!==void 0&&Be([...(0,N.getSession)(e).views]).some(o=>o.id===n)||(e.connectedViewId=t)},setHoveredNode(t){e.hoveredNode=t},setHoveredRowWalks(t){t.join(`
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Cd=(0,si.defineLaunchKeys)()({});function kn(e){e.addViewType(()=>new ii.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:wn(),launchKeys:Cd,ReactComponent:(0,ai.lazy)(()=>import("./chunks/GraphGenomeView-QOBHGMLE.js"))}))}var di=M(te(),1),ye=M(de(),1),Id=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Bd(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=o=>o&&Object.assign(Object.create(o),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Id.map(o=>r(n(o)))].filter(o=>o!==void 0)}function xn(e){e.addTrackType(()=>{let t=(0,di.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,ye.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new ye.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,ye.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Bd(e))n.addDisplayType(r);return n})}function Sn(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Li=M(Oe(),1),Gi=M(ui(),1);var li=M(te(),1),gi=M(mi(),1),Rn=M(ie(),1);function hi(){return(0,li.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Rn.types.enumeration("LayoutMode",Ue),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Rn.types.enumeration("ColorScheme",Ze),defaultValue:"auto"},...(0,gi.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var ki=M(Oe(),1);var De=M(te(),1),xi=M(de(),1),Si=M(qn(),1),Mn=M(xe(),1),Ri=M(bi(),1),E=M(ie(),1),At=M(wi(),1);var Ve=M(Kn(),1);var Ed=(0,ki.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-RTSJTM6A.js"));function Mi(e){return E.types.compose("LinearGraphDisplay",xi.BaseDisplay,(0,Ri.default)(),Gt(),E.types.model({type:E.types.literal("LinearGraphDisplay"),configuration:(0,De.ConfigurationReference)(e),pane:E.types.maybe(E.types.frozen()),cutRegion:E.types.maybe(E.types.frozen()),coarseCut:E.types.optional(E.types.boolean,!1),maxRegionBp:E.types.optional(E.types.number,Lt),subgraphContext:E.types.optional(E.types.number,1),subgraphHaplotypes:E.types.maybe(E.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:o,...a}=n;return{...a,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get defaultLayoutMode(){return(0,De.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,De.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??ti(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${be(n.end-n.start)}, max ${be(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,At.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,At.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=Nt(Tt(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let o=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:o?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:o?"coarse":void 0,...Z(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=sn(n,t.capFor(r),Z(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=Z(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Ra(t.cutRegion,n,r)?!1:(t.recutAt(n),!0)},switchLayout(n){let r=Z(t.chosenLayoutMode);t.setLayoutMode(n);let o=Z(n),a=t.host?wt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({forceLoad(){let n=t.settledWindow;n&&(t.setMaxRegionBp(Math.ceil(n.end-n.start)),t.settleOn(n))},afterAttach(){t.cutRegion&&!t.graph&&t.cut(),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?wt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?wt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,E.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Mn.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Si.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:ct,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),{label:"Settings",icon:oo,onClick:()=>{(0,Mn.getSession)(t).queueDialog(r=>[Ed,{model:t,open:!0,onClose:r}])}},...n]}}))}function Ln(e){e.addDisplayType(()=>{let t=hi();return Object.assign(new Gi.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Mi(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Li.lazy)(()=>import("./chunks/LinearGraphDisplay-TPXW6POY.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Ai=M(ut(),1);var Gn=M(te(),1),Ti=M(ie(),1);function Tn(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}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var Fd=(0,Gn.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Gn.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Ti.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Tn}),Ni=Fd;function Nn(e){e.addAdapterType(()=>new Ai.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Tn,configSchema:Ni,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CK7AE4QT.js").then(t=>t.default)}))}var Bi=M(ut(),1);var vt=M(te(),1),Ci=M(ie(),1);function Pi(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function vi(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Pi(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Pi(`${t}.links.bed.gz`,n,r)}:e}function An(e){let{coarse:t,baseUri:n}=e;return vi(typeof t=="object"&&t!==null?{...e,coarse:vi({baseUri:n,...t})}:e)}var Pt=(e,t)=>(0,vt.ConfigurationSchema)(e,{indexType:{model:Ci.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),$d=(0,vt.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Pt("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Pt("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Vd=(0,vt.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Pt("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Pt("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:$d},{explicitlyTyped:!0,preProcessSnapshot:An}),Ii=Vd;function Pn(e){e.addAdapterType(()=>new Bi.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:An,configSchema:Ii,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-5MD2ZZ2F.js").then(t=>t.default)}))}var Dd=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Wd(e){return zn(e).toLowerCase().endsWith(".gbz.db")}function Od(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 _d(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Wd(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Yn(e))return Un({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function vn(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Od),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>_d(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>Dd.has(n)?"GraphTrack":t(n,r))}var Vi=M(xe(),1),Di=M(Zi(),1),Cn=M(Ji(),1),Wi=M(es(),1);function Ei(e){let t;if(Q(e)){let{refName:n,start:r,end:o,assemblyName:a}=e;typeof n=="string"&&typeof r=="number"&&typeof o=="number"&&(t={refName:n,start:r,end:o,assemblyName:typeof a=="string"?a:void 0})}return t}function Hd(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Fi(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function jd(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Q(n)&&Array.isArray(n.displays)?n.displays.filter(r=>Q(r)&&r.type==="LinearGraphDisplay"):[])}function $i(e,t,n){let r=[],o=Be(e),a=new Set(o.map(i=>Q(i)?i.id:void 0));for(let i of o){if(Q(i)&&i.id===t)for(let s of jd(i)){let d=Ei(s.hoverHighlight);d&&Fi(d,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:d})}if(Q(i)&&i.type==="GraphGenomeView"&&Hd(i,t,a)){let s=Ei(i.hoverHighlight);s&&Fi(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var we=M(Se(),1),Xd=(0,Wi.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Di.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),zd=(0,Cn.observer)(function({model:t,region:n}){let{classes:r}=Xd(),o=t.getHighlightCoords(n);return o?(0,we.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Yd=(0,Cn.observer)(function({model:t}){let{views:n}=(0,Vi.getSession)(t);return(0,we.jsx)(we.Fragment,{children:$i([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,we.jsx)(zd,{model:t,region:o},`graph-hover-${r}`))})}),Oi=Yd;var _i=M(Se(),1),Ud="LinearGenomeView-TracksContainerComponent";function In(e){e.contributeToExtensionPoint(Ud,({model:t})=>(0,_i.jsx)(Oi,{model:t},"graphgenomeview-hover-highlight"))}var Hi="GraphGenomeView";var ji="4.1.1";var Bn=class extends Xi.default{constructor(){super(...arguments);this.name=Hi;this.version=ji}install(n){kn(n),Ln(n),xn(n),Sn(n),In(n),Pn(n),Nn(n),Xt(n),Yt(n),vn(n),n.addRpcMethod(()=>new Te(n)),n.addRpcMethod(()=>new Ge(n)),n.addRpcMethod(()=>new Le(n))}configure(n){try{(0,zi.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:ct,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{Bn as default};
+`)&&(e.hoveredRowWalks=t)},setHoveredBubble(t){e.hoveredBubble=t},setPointerInPane(t){e.pointerInPane=t},setLegendSize(t){e.legendSize=t},setHoveredEdge(t){e.hoveredEdge=t},setSelectedNode(t){e.selectedNode=t},setDraggingNode(t){e.draggingNode=t},setPanning(t){e.isPanning=t},stopDragging(){e.draggingNode=null,e.isPanning=!1},clearInteractionState(){e.hoveredNode=null,e.hoveredBubble=null,e.hoveredEdge=null,e.selectedNode=null,e.draggingNode=null,e.isPanning=!1},showNodeDetails(t){let n=e.nodeById?.get(t),r=e.nodeById,o=e.nodeNeighbors;if(n&&r&&o){let a=(0,N.getSession)(e),i=e.graphRegion,s=i?He({nodeId:t,nodeById:r,neighbors:o}):void 0;(0,N.isSessionModelWithWidgets)(a)&&a.showWidget(a.addWidget("BaseFeatureWidget","baseFeature",{featureData:{id:n.id,name:n.name,length:n.length,depth:n.depth,rank:n.stable?.rank,stableName:n.stable?.refName,contributingAssembly:at(n)?.sample,contributingHaplotype:at(n)?.haplotype,samples:n.samples?.join(", "),...i&&s?{refName:i.refName,assemblyName:i.assemblyName,start:s.start,end:s.end}:{}}}))}},setTransform(t,n,r){let{host:o}=e;e.viewportOwner==="host"&&o?o.horizontalScroll(e.translateX-n):(e.viewportOwner="user",e.scale=Pe(t),e.translateX=n),e.translateY=r},zoom(t,n,r){let{host:o}=e;if(e.viewportOwner==="host"&&o){o.zoomTo(o.bpPerPx/t,n);return}e.viewportOwner="user";let a=Uo(e,t,n,r,e.pixelRows);e.scale=a.scale,e.translateX=a.translateX,e.translateY=a.translateY},setViewportDirty(){e.viewportRebuildPending=!1,e.viewportDirty++},setPositionsDirty(){e.positionsVersion++},zoomToFit(){if(e.viewportOwner==="host"){let n=e.layoutBounds,r=e.facetGrid!==void 0,o=r?12:D,a=r?12:e.fitPadTop,i=e.viewBox.height-a-o;n&&i>0&&(e.translateY=Qt(n,i,e.scaleY,a));return}let t=e.fittedTransform;t&&(e.scale=t.scale,e.translateX=t.translateX,e.translateY=t.translateY)},clearPerfMetrics(){e.lastFetchMs=void 0,e.lastLayoutMs=void 0,e.lastGeometryMs=void 0,e.lastGeometryStrokeCount=void 0,e.builtViewport=void 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Cd=(0,si.defineLaunchKeys)()({});function kn(e){e.addViewType(()=>new ii.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:wn(),launchKeys:Cd,ReactComponent:(0,ai.lazy)(()=>import("./chunks/GraphGenomeView-QOBHGMLE.js"))}))}var di=M(te(),1),ye=M(de(),1),Id=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Bd(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=o=>o&&Object.assign(Object.create(o),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Id.map(o=>r(n(o)))].filter(o=>o!==void 0)}function xn(e){e.addTrackType(()=>{let t=(0,di.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,ye.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new ye.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,ye.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Bd(e))n.addDisplayType(r);return n})}function Sn(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Li=M(Oe(),1),Gi=M(ui(),1);var li=M(te(),1),gi=M(mi(),1),Rn=M(ie(),1);function hi(){return(0,li.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Rn.types.enumeration("LayoutMode",Ue),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Rn.types.enumeration("ColorScheme",Ze),defaultValue:"auto"},...(0,gi.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var ki=M(Oe(),1);var De=M(te(),1),xi=M(de(),1),Si=M(qn(),1),Mn=M(xe(),1),Ri=M(bi(),1),E=M(ie(),1),At=M(wi(),1);var Ve=M(Kn(),1);var Ed=(0,ki.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-RTSJTM6A.js"));function Mi(e){return E.types.compose("LinearGraphDisplay",xi.BaseDisplay,(0,Ri.default)(),Gt(),E.types.model({type:E.types.literal("LinearGraphDisplay"),configuration:(0,De.ConfigurationReference)(e),pane:E.types.maybe(E.types.frozen()),cutRegion:E.types.maybe(E.types.frozen()),coarseCut:E.types.optional(E.types.boolean,!1),maxRegionBp:E.types.optional(E.types.number,Lt),subgraphContext:E.types.optional(E.types.number,1),subgraphHaplotypes:E.types.maybe(E.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:o,...a}=n;return{...a,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get defaultLayoutMode(){return(0,De.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,De.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??ti(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${be(n.end-n.start)}, max ${be(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,At.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,At.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=Nt(Tt(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let o=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:o?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:o?"coarse":void 0,...Z(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=sn(n,t.capFor(r),Z(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=Z(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Ra(t.cutRegion,n,r)?!1:(t.recutAt(n),!0)},switchLayout(n){let r=Z(t.chosenLayoutMode);t.setLayoutMode(n);let o=Z(n),a=t.host?wt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({forceLoad(){let n=t.settledWindow;n&&(t.setMaxRegionBp(Math.ceil(n.end-n.start)),t.settleOn(n))},afterAttach(){t.cutRegion&&!t.graph&&t.cut(),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?wt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?wt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,E.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Mn.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Si.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:ct,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),{label:"Settings",icon:oo,onClick:()=>{(0,Mn.getSession)(t).queueDialog(r=>[Ed,{model:t,open:!0,onClose:r}])}},...n]}}))}function Ln(e){e.addDisplayType(()=>{let t=hi();return Object.assign(new Gi.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Mi(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Li.lazy)(()=>import("./chunks/LinearGraphDisplay-TPXW6POY.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Ai=M(ut(),1);var Gn=M(te(),1),Ti=M(ie(),1);function Tn(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}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var Fd=(0,Gn.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Gn.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Ti.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Tn}),Ni=Fd;function Nn(e){e.addAdapterType(()=>new Ai.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Tn,configSchema:Ni,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CK7AE4QT.js").then(t=>t.default)}))}var Bi=M(ut(),1);var vt=M(te(),1),Ci=M(ie(),1);function Pi(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function vi(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Pi(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Pi(`${t}.links.bed.gz`,n,r)}:e}function An(e){let{coarse:t,baseUri:n}=e;return vi(typeof t=="object"&&t!==null?{...e,coarse:vi({baseUri:n,...t})}:e)}var Pt=(e,t)=>(0,vt.ConfigurationSchema)(e,{indexType:{model:Ci.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),$d=(0,vt.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Pt("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Pt("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Vd=(0,vt.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Pt("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Pt("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:$d},{explicitlyTyped:!0,preProcessSnapshot:An}),Ii=Vd;function Pn(e){e.addAdapterType(()=>new Bi.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:An,configSchema:Ii,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-QPKEJZXA.js").then(t=>t.default)}))}var Dd=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Wd(e){return zn(e).toLowerCase().endsWith(".gbz.db")}function Od(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 _d(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Wd(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Yn(e))return Un({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function vn(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Od),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>_d(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>Dd.has(n)?"GraphTrack":t(n,r))}var Vi=M(xe(),1),Di=M(Zi(),1),Cn=M(Ji(),1),Wi=M(es(),1);function Ei(e){let t;if(Q(e)){let{refName:n,start:r,end:o,assemblyName:a}=e;typeof n=="string"&&typeof r=="number"&&typeof o=="number"&&(t={refName:n,start:r,end:o,assemblyName:typeof a=="string"?a:void 0})}return t}function Hd(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Fi(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function jd(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Q(n)&&Array.isArray(n.displays)?n.displays.filter(r=>Q(r)&&r.type==="LinearGraphDisplay"):[])}function $i(e,t,n){let r=[],o=Be(e),a=new Set(o.map(i=>Q(i)?i.id:void 0));for(let i of o){if(Q(i)&&i.id===t)for(let s of jd(i)){let d=Ei(s.hoverHighlight);d&&Fi(d,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:d})}if(Q(i)&&i.type==="GraphGenomeView"&&Hd(i,t,a)){let s=Ei(i.hoverHighlight);s&&Fi(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var we=M(Se(),1),Xd=(0,Wi.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Di.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),zd=(0,Cn.observer)(function({model:t,region:n}){let{classes:r}=Xd(),o=t.getHighlightCoords(n);return o?(0,we.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Yd=(0,Cn.observer)(function({model:t}){let{views:n}=(0,Vi.getSession)(t);return(0,we.jsx)(we.Fragment,{children:$i([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,we.jsx)(zd,{model:t,region:o},`graph-hover-${r}`))})}),Oi=Yd;var _i=M(Se(),1),Ud="LinearGenomeView-TracksContainerComponent";function In(e){e.contributeToExtensionPoint(Ud,({model:t})=>(0,_i.jsx)(Oi,{model:t},"graphgenomeview-hover-highlight"))}var Hi="GraphGenomeView";var ji="4.2.0";var Bn=class extends Xi.default{constructor(){super(...arguments);this.name=Hi;this.version=ji}install(n){kn(n),Ln(n),xn(n),Sn(n),In(n),Pn(n),Nn(n),Xt(n),Yt(n),vn(n),n.addRpcMethod(()=>new Te(n)),n.addRpcMethod(()=>new Ge(n)),n.addRpcMethod(()=>new Le(n))}configure(n){try{(0,zi.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:ct,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{Bn as default};
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