jbrowse-plugin-graphgenomeviewer 6.5.0 → 6.6.0

package/dist/chunks/RgfaTabixAdapter-GNFUR2FW.js

@@ -0,0 +1,3 @@
+import{a as D,b as _,d as L,e as M}from"./chunk-2SIR336R.js";import"./chunk-KWAXLUPQ.js";import"./chunk-YBLNN5FU.js";import"./chunk-DILFGQIL.js";import{a as Z}from"./chunk-J4OLMLS5.js";import{b as x}from"./chunk-FY3BTKY4.js";var O=x(D(),1),R=x(Z(),1),j=x(_(),1);function y(r){let e=r.split("	"),a=e.length>=8,i=a?5:0;return{anchored:a,segment:{refName:e[i],start:+e[i+1],end:+e[i+2],id:e[3],rank:+e[4],tags:e[a?8:5]??""}}}function T(r){let e=r.tags.split(" ").find(i=>i.startsWith("SM:Z:"));if(e===void 0)return;let a=e.slice(5).split(",").map(i=>i.trim()).filter(Boolean);return a.length>0?a:void 0}function A(r){return{id:r.slice(0,-1),strand:r.slice(-1)}}function b(r){let e=r.split("	"),a=A(e[3]),i=A(e[4]);return{source:a.id,sourceStrand:a.strand,target:i.id,targetStrand:i.strand,sourceSegment:{id:a.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:i.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function l(r){return`${r.source}${r.sourceStrand}${r.target}${r.targetStrand}`}function F(r,e,a){let i=n=>n.rank!==0||n.refName!==a.refName?0:n.end<=a.start?-1:n.start>=a.end?1:0,t=new Map(r),s=new Map;for(let n of e)if(r.has(n.source)||r.has(n.target)||i(n.sourceSegment)*i(n.targetSegment)===-1){s.set(l(n),n);for(let o of[n.sourceSegment,n.targetSegment])t.has(o.id)||t.set(o.id,o)}for(let n of e)t.has(n.source)&&t.has(n.target)&&s.set(l(n),n);return{segments:t,links:s}}function v(r,e,a){let i=t=>t.refName!==a.refName||t.end<=a.start||t.start>=a.end;return[...I(r.filter(t=>t.rank>0),e,a.end-a.start),...I(r.filter(t=>t.rank===0&&i(t)),new Set(r.map(t=>t.id)),0)]}function I(r,e,a){let i=[...r].sort((s,n)=>N(s.refName,n.refName)||s.start-n.start),t=[];for(let s of i){let n=t.at(-1);n?.refName===s.refName&&s.start-n.end<=a?(n.needed||=s.start>n.end||e.has(s.id),n.end=Math.max(n.end,s.end)):t.push({refName:s.refName,start:s.start,end:s.end,needed:e.has(s.id)})}return t.filter(s=>s.needed).map(({refName:s,start:n,end:o})=>({refName:s,start:n,end:o}))}function P(r,e,a){let i=t=>e.has(t.id)||a.some(s=>s.refName===t.refName&&t.start>=s.start&&t.end<=s.end);return r.filter(t=>i(t.sourceSegment)&&i(t.targetSegment))}var z=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function E(r){let{id:e,refName:a,start:i,end:t,rank:s,tags:n}=r,o=n.split(" ").filter(d=>z.test(d)),g=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${t-i}	SN:Z:${a}	SO:i:${i}	SR:i:${s}${g}`}function H(r){let{source:e,sourceStrand:a,target:i,targetStrand:t}=r;return`L	${e}	${a}	${i}	${t}	0M`}function N(r,e){return r<e?-1:r>e?1:0}function w(r,e){let a=[...r.values()].sort((t,s)=>N(t.refName,s.refName)||t.start-s.start||N(t.id,s.id)),i=[...e.keys()].sort((t,s)=>N(t,s));return["H	VN:Z:1.0",...a.map(t=>E(t)),...i.map(t=>H(e.get(t)))].join(`
+`)}function B(r){return r.filter(e=>e.rank>0)}var $=class extends O.BaseFeatureDataAdapter{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,a,i){super(e,a,i),this.fine=this.openIndex([])}openIndex(e){let a=L(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]);return{segments:a,links:L(this,[...e,"linksLocation"],[...e,"linksIndex"]),refNames:new M(a,this)}}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,a={}){let{signal:i,statusCallback:t}=a;return(0,j.ObservableCreate)(async s=>{let n=await this.fine.refNames.resolve(e,a);n!==void 0&&await(0,R.updateStatus)("Downloading segments",t,()=>this.fine.segments.getLines(n,e.start,e.end,{signal:i,lineCallback:o=>{let{segment:g,anchored:d}=y(o);if(d&&g.refName!==n)return;let u=T(g);s.next(new R.SimpleFeature({uniqueId:g.id,refName:e.refName,start:g.start,end:g.end,name:g.id,type:"segment",rank:g.rank,stableName:g.refName,...u&&{samples:u,sampleCount:u.length}}))}})),s.complete()},i)}async getSubgraph(e,a={}){let{hops:i=0,signal:t,tier:s}=a,n=this.index(s),o=new Map,g=new Map,d=await n.refNames.resolve(e,{signal:t}),u=async(c,m,f)=>{let p=[];return await n.links.getLines(c,m,f,{signal:t,lineCallback:G=>{let S=b(G);g.set(l(S),S);for(let h of[S.sourceSegment,S.targetSegment])o.has(h.id)||(o.set(h.id,h),p.push(h))}}),p};if(d===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${e.assemblyName} mapped to its prefix in assemblyNameToPanSN`);let C={anchored:!1};if(await n.segments.getLines(d,e.start,e.end,{signal:t,lineCallback:c=>{let m=y(c);C.anchored||=m.anchored,o.set(m.segment.id,m.segment)}}),C.anchored){let c=[];await n.links.getLines(d,e.start,e.end,{signal:t,lineCallback:f=>{c.push(b(f))}});let m=F(o,c,{refName:d,start:e.start,end:e.end});return w(m.segments,m.links)}let k=B(await u(d,e.start,e.end));for(let c=0;c<i;c++){let m=await Promise.all(k.map(f=>u(f.refName,f.start,f.end)));k=B(m.flat())}if(i>0){let c=v([...o.values()],new Set(k.map(f=>f.id)),{refName:d,start:e.start,end:e.end}),m=[];await Promise.all(c.map(f=>n.links.getLines(f.refName,f.start,f.end,{signal:t,lineCallback:p=>{m.push(b(p))}})));for(let f of P(m,o,c)){g.set(l(f),f);for(let p of[f.sourceSegment,f.targetSegment])o.has(p.id)||o.set(p.id,p)}}return w(o,g)}};export{$ as default};
+//# sourceMappingURL=RgfaTabixAdapter-GNFUR2FW.js.map

package/dist/chunks/RgfaTabixAdapter-GNFUR2FW.js.map

@@ -0,0 +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  anchoredCut,\n  closingLinks,\n  closingSpans,\n  formatSubgraph,\n  linkKey,\n  parseLinkLine,\n  parseSegmentRow,\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, anchored } = parseSegmentRow(line)\n              // An anchored index also returns the alleles under the region,\n              // which lie on other stable sequences and have no place on this\n              // one.\n              if (anchored && segment.refName !== tabixRefName) {\n                return\n              }\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. After the last round, one more read\n  // per stretch of stable sequence the cut holds closes it (closingSpans), so\n  // an allele reached from both ends draws whole. The view asks for one hop; a\n  // hopless cut stays as cheap as it was. `signal` goes to every one of those\n  // 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    const layout = { anchored: false }\n    await index.segments.getLines(tabixRefName, region.start, region.end, {\n      signal,\n      lineCallback: line => {\n        const row = parseSegmentRow(line)\n        layout.anchored ||= row.anchored\n        segments.set(row.segment.id, row.segment)\n      },\n    })\n    // An anchored index files every allele and every link under the reference\n    // interval its bubble hangs from, so one read of each file holds the whole\n    // graph under the region and there is nothing to hop to or close.\n    if (layout.anchored) {\n      const found: RgfaLink[] = []\n      await index.links.getLines(tabixRefName, region.start, region.end, {\n        signal,\n        lineCallback: line => {\n          found.push(parseLinkLine(line))\n        },\n      })\n      const cut = anchoredCut(segments, found, {\n        refName: tabixRefName,\n        start: region.start,\n        end: region.end,\n      })\n      return formatSubgraph(cut.segments, cut.links)\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    if (hops > 0) {\n      const spans = closingSpans(\n        [...segments.values()],\n        new Set(frontier.map(segment => segment.id)),\n        { refName: tabixRefName, start: region.start, end: region.end },\n      )\n      const found: RgfaLink[] = []\n      await Promise.all(\n        spans.map(span =>\n          index.links.getLines(span.refName, span.start, span.end, {\n            signal,\n            lineCallback: line => {\n              found.push(parseLinkLine(line))\n            },\n          }),\n        ),\n      )\n      for (const link of closingLinks(found, segments, spans)) {\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          }\n        }\n      }\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  return parseSegmentRow(line).segment\n}\n\n// gfa-to-tabix's anchored layout files a segment under the reference interval\n// its bubble hangs from and states the segment's own coordinate after the rank:\n// `anchorName anchorStart anchorEnd segmentId rank stableName start end [tags]`.\n// One query over a region then returns every segment of every bubble under it,\n// and `anchored` tells a cut it has nothing left to follow.\nexport function parseSegmentRow(line: string) {\n  const cols = line.split('\\t')\n  const anchored = cols.length >= 8\n  const own = anchored ? 5 : 0\n  return {\n    anchored,\n    segment: {\n      refName: cols[own]!,\n      start: +cols[own + 1]!,\n      end: +cols[own + 2]!,\n      id: cols[3]!,\n      rank: +cols[4]!,\n      tags: cols[anchored ? 8 : 5] ?? '',\n    } satisfies RgfaSegment,\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// The cut an anchored index gives: `under` is what the segment file returned\n// for the window, every segment of every bubble under it, and `found` is what\n// the link file returned. gfa-to-tabix files a link widely enough that `found`\n// holds every link touching a segment in `under` and every link between the\n// segments those lead to, plus links of neither kind, which are dropped here.\n// A backbone link that jumps the whole window, as a deletion or inversion\n// spanning it does, touches nothing in `under` and is kept by its own rule.\nexport function anchoredCut(\n  under: Map<string, RgfaSegment>,\n  found: RgfaLink[],\n  window: StableSpan,\n) {\n  const side = (segment: RgfaSegment) =>\n    segment.rank !== 0 || segment.refName !== window.refName\n      ? 0\n      : segment.end <= window.start\n        ? -1\n        : segment.start >= window.end\n          ? 1\n          : 0\n  const segments = new Map(under)\n  const links = new Map<string, RgfaLink>()\n  for (const link of found) {\n    if (\n      under.has(link.source) ||\n      under.has(link.target) ||\n      side(link.sourceSegment) * side(link.targetSegment) === -1\n    ) {\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        }\n      }\n    }\n  }\n  for (const link of found) {\n    if (segments.has(link.source) && segments.has(link.target)) {\n      links.set(linkKey(link), link)\n    }\n  }\n  return { segments, links }\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\nexport interface StableSpan {\n  refName: string\n  start: number\n  end: number\n}\n\n// Where a cut reads links once more to close itself. A hop reads the links of\n// the segments the round before it reached, so a link between two segments of\n// the last round is never read and an allele reached from both ends draws as\n// two stubs. rGFA lays an allele out as one stretch of the stable sequence that\n// introduced it, so pieces of one sequence within the window's length of each\n// other merge into a span, and reading it brings the pieces between too.\n// Backbone reached past the window is unread for the same reason; its spans\n// join only abutting pieces, since the reference past the window is not the\n// cut's to fill. 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Following anything else is what another hop is for.\nexport function closingLinks(\n  found: RgfaLink[],\n  held: Map<string, RgfaSegment>,\n  spans: StableSpan[],\n) {\n  const inside = (segment: RgfaSegment) =>\n    held.has(segment.id) ||\n    spans.some(\n      span =>\n        span.refName === segment.refName &&\n        segment.start >= span.start &&\n        segment.end <= span.end,\n    )\n  return found.filter(\n    link => inside(link.sourceSegment) && inside(link.targetSegment),\n  )\n}\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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+  "names": ["import_BaseAdapter", "import_util", "import_rxjs", "parseSegmentRow", "line", "cols", "anchored", "own", "segmentSamples", "segment", "tag", "t", "samples", "s", "parseEndpoint", "field", "parseLinkLine", "source", "target", "linkKey", "link", "anchoredCut", "under", "found", "window", "side", "segments", "links", "closingSpans", "held", "unread", "outside", "mergedSpans", "maxGap", "sorted", "a", "b", "compare", "spans", "span", "refName", "start", "end", "closingLinks", "inside", "GFA_TAG", "formatSegment", "id", "rank", "tags", "valid", "extra", "formatLink", "sourceStrand", "targetStrand", "formatSubgraph", "sortedSegments", "sortedLinks", "k", "offReference", "segments", "segment", "RgfaTabixAdapter", "config", "getSubAdapter", "pluginManager", "under", "openTabixSlot", "PanSNRefNames", "tier", "opts", "query", "signal", "statusCallback", "observer", "tabixRefName", "line", "anchored", "parseSegmentRow", "samples", "segmentSamples", "region", "hops", "index", "links", "addLinksOver", "refName", "start", "end", "reached", "link", "parseLinkLine", "linkKey", "layout", "row", "found", "cut", "anchoredCut", "formatSubgraph", "frontier", "hop", "spans", "closingSpans", "span", "closingLinks"]
+}

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

@@ -5,5 +5,5 @@ import{a as ea}from"./chunks/chunk-PLV6SE4Y.js";import{B as Aa,D as Na,a as te,b
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Blob([e],{type:n})),r=document.createElement("a");r.href=o,r.download=t,r.click(),setTimeout(()=>{URL.revokeObjectURL(o)},0)}var _s=Es.actions(e=>({showInLinearView(t){let n=(0,he.getSession)(e),o=t.assembly===e.graphRegion?.assemblyName,r=hs({session:n,location:t.location,assembly:t.assembly,connectedViewId:e.connectedViewId,tracks:Bs({session:n,assemblyName:t.assembly,first:o?e.sourceTrackId:void 0})});o&&e.pairWithLinearView(r)},highlightInLinearView(t){fs({session:(0,he.getSession)(e),location:t.location,assembly:t.assembly,connectedViewId:e.connectedViewId})},showSyntenyView(t){bs({session:(0,he.getSession)(e),contributors:e.launchableAssemblies,trackId:t,graphTrackId:e.sourceTrackId})}})).views(e=>({get syntenyLaunchTracks(){let t=e.launchableAssemblies.map(n=>n.sample);return t.length>=2?Ds((0,he.getSession)(e),t):[]}})).views(e=>({walkRowSampleMenuItems(){let{disagreeing:t}=e.walkRowSampleChoices,n=e.walkRowSamples,o=r=>r.join(`
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 `);return[{type:"radio",label:"Every sample",checked:n===void 0,onClick:()=>{e.setWalkRowSamples(void 0)}},...t.length>0?[{type:"radio",label:"Where walk and call disagree",checked:o(t),onClick:()=>{e.setWalkRowSamples(t)}}]:[],{type:"radio",label:"Choose samples...",checked:n!==void 0&&!o(t),onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Ti,{model:e,onClose:r}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return[{type:"radio",label:"None",checked:t===void 0,onClick:()=>{e.setWalkRowGroupBy(void 0)}},...e.walkRowGroupFields.map(n=>({type:"radio",label:n,checked:t===n,onClick:()=>{e.setWalkRowGroupBy({field:n})}}))]},layoutOptionMenuItems(){return[...Ce.has(e.chosenLayoutMode)?[{label:"Fold variants",subMenu:Ni.map(({bp:t,label:n})=>({type:"radio",label:n,checked:e.tubeMapFold===t,disabled:t>0&&e.graph?.reads!==void 0,onClick:()=>{e.setTubeMapFold(t),e.recomputeLayout()}}))}]:[],...e.chosenLayoutMode==="walkrows"&&e.repeatChoices.length>0?[{label:"Repeat",subMenu:[{type:"radio",label:"Whole window",checked:e.repeatKey==="",onClick:()=>{e.setRepeatKey("")}},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({type:"radio",label:`${n} \xB7 ${o.toLocaleString()} bp unit`,checked:e.repeatKey===t,onClick:()=>{e.setRepeatKey(t)}}))]}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars?[{label:"Samples",subMenu:this.walkRowSampleMenuItems()}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){return[{type:"checkbox",label:"Show bubble halos",checked:e.showBubbles,onClick:()=>{e.setShowBubbles(!e.showBubbles)}},{type:"checkbox",label:"Show deletion edges",checked:e.showDeletionEdges,onClick:()=>{e.toggleDeletionEdges()}},{type:"checkbox",label:"Show hover highlight",checked:e.chosenHighlightOnHover,onClick:()=>{e.setHighlightOnHover(!e.chosenHighlightOnHover)}},{type:"checkbox",label:"Show genes on the backbone",checked:e.showGenes,onClick:()=>{e.setShowGenes(!e.showGenes)}},...e.referenceStripApplies?[{type:"checkbox",label:"Show reference strip",checked:e.showReferenceStrip,onClick:()=>{e.setShowReferenceStrip(!e.showReferenceStrip)}}]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:si,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&Vs(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}},{label:"Copy figure spec",icon:ni,disabled:e.figureSpecUnavailable!==void 0,disabledHelpText:e.figureSpecUnavailable,onClick:()=>{let t=e.figureSpec(),n=(0,he.getSession)(e);navigator.clipboard.writeText(`${JSON.stringify(t,null,2)}
-`).then(()=>{n.notify("Figure spec copied. Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg","info")}).catch(o=>{n.notify(`Could not copy the figure spec: ${String(o)}`)})}}]},highlightMenuItems(){let t=e.walkChoices;if(t.length===0||!e.liftsWalks)return[];let n=r=>e.walkLayers.some(a=>a.walk===r),o=t.length>Ai;return[{type:"subHeader",label:"Highlight"},...o?[{label:"Choose haplotypes...",onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Gi,{model:e,onClose:r}])}}]:[],...(o?t.filter(r=>n(r.name)):t).map(r=>({type:"checkbox",label:r.label,checked:n(r.name),onClick:()=>{e.toggleWalk(r.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Pi,{model:e,onClose:r}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...xr.map(({value:r,label:a})=>({type:"radio",label:r==="walk"?"A panel per haplotype":a,checked:e.facet.field===r,onClick:()=>{e.setFacet(r)}}))]:[]]},colorSchemeLabel(t){let n=Pn.find(o=>o.value===t)?.label??t;return t==="auto"?`${n} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:n},graphMenuItems(){let t=this.layoutOptionMenuItems();return[{label:`Layout: ${_(e.chosenLayoutMode).label.replace(/ layout$/,"")}`,icon:ri,subMenu:[...Sr.map(n=>({type:"radio",label:n.label,checked:e.chosenLayoutMode===n.value,disabled:e.graph?!n.available(e.graph):!1,onClick:()=>{e.switchLayout(n.value)}})),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.zoomToFit()}}]]},{label:`Color: ${this.colorSchemeLabel(e.chosenColorScheme)}`,icon:ii,subMenu:Pn.map(n=>({type:"radio",label:this.colorSchemeLabel(n.value),checked:e.chosenColorScheme===n.value,onClick:()=>{e.setColorScheme(n.value)}}))},{label:"Show...",icon:di,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[];for(let n of Aa({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:o=>{e.showInLinearView(o)},onShowSynteny:o=>{e.showSyntenyView(o)}}))(0,Os.pushLaunchViewMenuItem)(t,n);return t}}));function pn(){return _s}var Ao=f(K(),1);function $s(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function No(e){let t=(0,Ao.readConfObject)(e,"assemblyNames"),n=$s(t)?t.slice(1):[];return n.length>0?n:void 0}function un(e){let t=(0,Ao.readConfObject)(e,"assemblyNames");return $s(t)?t[0]:void 0}function mn(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function up(e){return("uri"in e?e.uri.split(/[?#]/)[0]:"localPath"in e?e.localPath:"name"in e?e.name:"").split(/[\\/]/).at(-1)??""}function Io(){return z.types.compose("GraphGenomeView",Hs.BaseViewModel,pn(),z.types.model({type:z.types.literal("GraphGenomeView"),gfaLocation:z.types.maybe(z.types.frozen()),loadedRegion:z.types.maybe(z.types.frozen()),loadedTrackId:z.types.optional(z.types.string,""),subgraphContext:z.types.optional(z.types.number,1),subgraphHaplotypes:z.types.maybe(z.types.frozen()),maxRegionBp:z.types.optional(z.types.number,ot)})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(n){t(n),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get cutHaplotypes(){return e.subgraphHaplotypes},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,Ws.getSession)(e).tracks.find(t=>t.trackId===e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;return{clearGraph(){t(),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let n=e.loadedRegion;if(e.gfaLocation)return e.displayName||e.setDisplayName(up(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let o=e.sourceTrack,r=n.end-n.start,a=o?mn(un(o),n.assemblyName):void 0;if(!o)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(r>e.maxRegionBp)e.setError(new Error(`Region too large (${xe(r)}) \u2014 zoom in to view graph (max ${xe(e.maxRegionBp)})`));else return e.cutSubgraph(be(e,o),n,{hops:e.subgraphContext,haplotypes:e.subgraphHaplotypes,...e.cutsWholeWalks?{snarls:"overlapping"}:{}})}}}).actions(e=>({retryLoad(){e.load()},switchLayout(t){let n=e.cutsWholeWalks;return e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,z.addDisposer)(e,(0,js.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!_(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var mp=(0,Ys.defineLaunchKeys)()({});function Co(e){e.addViewType(()=>new zs.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Io(),launchKeys:mp,ReactComponent:(0,Xs.lazy)(()=>import("./chunks/GraphGenomeView-ZB4ED45M.js"))}))}var Us=f(K(),1),Be=f(fe(),1),Eo=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function lp(e){let t=e.getElementTypesInGroup("display"),n=r=>t.find(a=>a.name===r),o=r=>r&&Object.assign(Object.create(r),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Eo.map(r=>o(n(r)))].filter(r=>r!==void 0)}function Bo(e){e.addTrackType(()=>{let t=(0,Us.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Be.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Be.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Be.createBaseTrackModel)(e,"GraphTrack",t)});for(let o of lp(e))n.addDisplayType(o);return n})}function Fo(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...o}=t;return n.addView("GraphGenomeView",o),t})}var wc=f(Oe(),1),yc=f(qs(),1);var Qs=f(K(),1),ec=f(Zs(),1),Do=f(ne(),1);function tc(){return(0,Qs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Do.types.enumeration("LayoutMode",vt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Do.types.enumeration("ColorScheme",Tt),defaultValue:"auto"},highlightOnHover:{type:"boolean",defaultValue:!0},...(0,ec.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var mc=f(Oe(),1);var Fe=f(K(),1),lc=f(fe(),1),gc=f(oc(),1),hc=f(ir(),1),Vo=f(ae(),1),fc=f(ac(),1),I=f(ne(),1),ln=f(sc(),1);var cc=f(ce(),1),dc=(0,te.createSvgIcon)((0,cc.jsx)("path",{d:"M19 15.18V7c0-2.21-1.79-4-4-4s-4 1.79-4 4v10c0 1.1-.9 2-2 2s-2-.9-2-2V8.82C8.16 8.4 9 7.3 9 6c0-1.66-1.34-3-3-3S3 4.34 3 6c0 1.3.84 2.4 2 2.82V17c0 2.21 1.79 4 4 4s4-1.79 4-4V7c0-1.1.9-2 2-2s2 .9 2 2v8.18c-1.16.41-2 1.51-2 2.82 0 1.66 1.34 3 3 3s3-1.34 3-3c0-1.3-.84-2.4-2-2.82"}),"Route");var wt=f(St(),1);function pc(e){return e instanceof Error&&(e.name==="NodeLimitError"||e.regionTooLarge===!0||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function uc(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let n=e.end-e.start;return t.end-t.start>=n&&t.end>e.start-n&&t.start<e.end+n}var gp=(0,mc.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-UPAINCUZ.js"));function bc(e){return I.types.compose("LinearGraphDisplay",lc.BaseDisplay,(0,fc.default)(),pn(),I.types.model({type:I.types.literal("LinearGraphDisplay"),configuration:(0,Fe.ConfigurationReference)(e),pane:I.types.maybe(I.types.frozen()),overviewRowsChoice:I.types.maybe(I.types.frozen()),overviewRowOrder:I.types.maybe(I.types.frozen()),cutRegion:I.types.maybe(I.types.frozen()),coarseCut:I.types.optional(I.types.boolean,!1),maxRegionBp:I.types.optional(I.types.number,ot),subgraphContext:I.types.optional(I.types.number,1),subgraphHaplotypes:I.types.maybe(I.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,overviewRowsChoice:o,overviewRowOrder:r,...a}=t;if(!n)return a;let{type:i,...s}=n;return{...s,...a}}).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0})).views(t=>({get adapterConfig(){return be(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,Fe.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,Fe.getConf)(t,"colorScheme")},get defaultHighlightOnHover(){return(0,Fe.getConf)(t,"highlightOnHover")},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??No(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let o=t.adapterConfig.coarse?.aboveBpPerPx;return typeof o=="number"?o:void 0}})).views(t=>({tierAt(n){let o=t.coarseAboveBpPerPx;return o!==void 0&&n>o?"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 (${xe(n.end-n.start)}, max ${xe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return(0,gc.computeSvgReady)({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return(0,ln.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,ln.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,t.dense=void 0},setDense(n){t.dense=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let o=mn(un(t.parentTrack.configuration),n.assemblyName);if(o){t.clearGraph(),t.setError(new Error(o));return}let r=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:r?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:r?"coarse":void 0,..._(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let o=t.tierAt(n.bpPerPx);return t.coarseCut=o==="coarse",t.cutRegion=go(n,t.capFor(o),_(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let o=_(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||uc(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Qi(t.cutRegion,n,o)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,I.isAlive)(t)&&pc(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let o=_(t.chosenLayoutMode);t.setLayoutMode(n);let r=_(n),a=t.host?Qt(t.host):void 0;return a&&!t.regionTooLarge&&(r.cutMargins!==o.cutMargins||r.wholeWalks!==o.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,I.addDisposer)(t,(0,wt.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,I.addDisposer)(t,(0,wt.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,o)=>n?.scale===o?.scale&&n?.translateX===o?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,I.addDisposer)(t,(0,wt.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,I.addDisposer)(t,(0,wt.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:o}=t,r=n&&o?Qt(o):void 0;r&&t.settleOn(r)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Qt(t.host):void 0,o=t.sourceTrackId;if(!n||!o||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let r=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:o,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:r,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-r),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,I.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Vo.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({cutMenuItems(){if(t.adapterConfig.type!=="GbzBaseSyntenyAdapter")return[];let n=No(t.parentTrack.configuration),o=t.subgraphHaplotypes,r=a=>{t.setSubgraphHaplotypes(a),t.cut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:"Every haplotype in the graph",checked:o?o.length===0:!n,onClick:()=>{r([])}},...n?[{type:"radio",label:`The track's ${n.length} assemblies`,checked:o===void 0,onClick:()=>{r(void 0)}}]:[],{type:"radio",label:"Chosen in Settings...",checked:(o?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){(0,Vo.getSession)(t).queueDialog(n=>[gp,{model:t,open:!0,onClose:n}])},async renderSvg(n){let{renderGraphTrackSvg:o}=await import("./chunks/renderSvg-J7L374ND.js");return o(t,n)},trackMenuItems(){let n=t.launchMenuItems();(0,hc.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Ht,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let o=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...o.length>0?[{label:"Haplotypes",icon:dc,subMenu:o}]:[],...t.graphMenuItems(),{label:"Settings",icon:Na,onClick:()=>{this.openSettings()}},...n]}}))}function Oo(e){e.addDisplayType(()=>{let t=tc();return Object.assign(new yc.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:bc(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,wc.lazy)(()=>import("./chunks/LinearGraphDisplay-TQX7ZJZF.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Rc=f(Wt(),1);var _o=f(K(),1),kc=f(ne(),1);function $o(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:o?"CSI":"TBI",location:{uri:`${t}.${o?"csi":"tbi"}`,baseUri:n}}}:e}var hp=(0,_o.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,_o.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:kc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:$o}),Sc=hp;function Ho(e){e.addAdapterType(()=>new Rc.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:$o,configSchema:Sc,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CAXB5FGR.js").then(t=>t.default)}))}var Tc=f(Wt(),1);var hn=f(K(),1),Lc=f(ne(),1);function xc(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Mc(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:xc(`${t}.segs.bed.gz`,n,o),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:xc(`${t}.links.bed.gz`,n,o)}:e}function Wo(e){let{coarse:t,baseUri:n}=e;return Mc(typeof t=="object"&&t!==null?{...e,coarse:Mc({baseUri:n,...t})}:e)}var gn=(e,t)=>(0,hn.ConfigurationSchema)(e,{indexType:{model:Lc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),fp=(0,hn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:gn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:gn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),bp=(0,hn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:gn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:gn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:fp},{explicitlyTyped:!0,preProcessSnapshot:Wo}),vc=bp;function jo(e){e.addAdapterType(()=>new Tc.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:Wo,configSchema:vc,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-GYRNCGT2.js").then(t=>t.default)}))}var wp=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function yp(e){return or(e).toLowerCase().endsWith(".gbz.db")}function kp(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 Sp(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&yp(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&rr(e))return ar({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Xo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",kp),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,o,r)=>Sp(n,o,r)??t(n,o,r)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,o)=>wp.has(n)?"GraphTrack":t(n,o))}var Nc=f(ae(),1),fn=f(zc(),1),zo=f(Xc(),1),Ic=f(Yc(),1);function Gc(e){let t;if(Q(e)){let{refName:n,start:o,end:r,assemblyName:a}=e;typeof n=="string"&&typeof o=="number"&&typeof r=="number"&&(t={refName:n,start:o,end:r,assemblyName:typeof a=="string"?a:void 0})}return t}function Rp(e,t,n){let o=e.connectedViewId;return o===void 0||o===t||!n.has(o)}function Pc(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function xp(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Q(n)&&Array.isArray(n.displays)?n.displays.filter(o=>Q(o)&&o.type==="LinearGraphDisplay"):[])}function Ac(e,t,n){let o=[],r=gt(e),a=new Set(r.map(i=>Q(i)?i.id:void 0));for(let i of r){if(Q(i)&&i.id===t)for(let s of xp(i)){let c=Gc(s.hoverHighlight);c&&Pc(c,n)&&o.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(Q(i)&&i.type==="GraphGenomeView"&&Rp(i,t,a)){let s=Gc(i.hoverHighlight);s&&Pc(s,n)&&o.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return o}var De=f(ce(),1),Mp=(0,Ic.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,fn.alpha)(e.palette.primary.main,.08),borderLeft:`1px solid ${(0,fn.alpha)(e.palette.primary.main,.4)}`,borderRight:`1px solid ${(0,fn.alpha)(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Lp=(0,zo.observer)(function({model:t,region:n}){let{classes:o}=Mp(),r=t.getHighlightCoords(n);return r?(0,De.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),vp=(0,zo.observer)(function({model:t}){let{views:n}=(0,Nc.getSession)(t);return(0,De.jsx)(De.Fragment,{children:Ac([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,De.jsx)(Lp,{model:t,region:r},`graph-hover-${o}`))})}),Cc=vp;var Ec=f(ce(),1),Tp="LinearGenomeView-TracksContainerComponent";function Yo(e){e.contributeToExtensionPoint(Tp,({model:t})=>(0,Ec.jsx)(Cc,{model:t},"graphgenomeview-hover-highlight"))}var Bc=f(fe(),1);function Gp(e){return e.views(t=>({get adapterConfig(){return be(t,t.parentTrack.configuration)}}))}function Uo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Bc.DisplayType&&Eo.includes(t.name)&&t.extendStateModel(Gp),t))}var Fc="GraphGenomeView";var Dc="6.5.0";var Ko=class extends Vc.default{constructor(){super(...arguments);this.name=Fc;this.version=Dc}install(n){Co(n),Oo(n),Bo(n),Fo(n),Yo(n),jo(n),Ho(n),$n(n),Wn(n),Xo(n),Uo(n),n.addRpcMethod(()=>new Qe(n)),n.addRpcMethod(()=>new Ze(n)),n.addRpcMethod(()=>new Je(n))}configure(n){try{(0,Oc.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Ht,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{Ko as default};
+`).then(()=>{n.notify("Figure spec copied. Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg","info")}).catch(o=>{n.notify(`Could not copy the figure spec: ${String(o)}`)})}}]},highlightMenuItems(){let t=e.walkChoices;if(t.length===0||!e.liftsWalks)return[];let n=r=>e.walkLayers.some(a=>a.walk===r),o=t.length>Ai;return[{type:"subHeader",label:"Highlight"},...o?[{label:"Choose haplotypes...",onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Gi,{model:e,onClose:r}])}}]:[],...(o?t.filter(r=>n(r.name)):t).map(r=>({type:"checkbox",label:r.label,checked:n(r.name),onClick:()=>{e.toggleWalk(r.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Pi,{model:e,onClose:r}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...xr.map(({value:r,label:a})=>({type:"radio",label:r==="walk"?"A panel per haplotype":a,checked:e.facet.field===r,onClick:()=>{e.setFacet(r)}}))]:[]]},colorSchemeLabel(t){let n=Pn.find(o=>o.value===t)?.label??t;return t==="auto"?`${n} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:n},graphMenuItems(){let t=this.layoutOptionMenuItems();return[{label:`Layout: ${_(e.chosenLayoutMode).label.replace(/ layout$/,"")}`,icon:ri,subMenu:[...Sr.map(n=>({type:"radio",label:n.label,checked:e.chosenLayoutMode===n.value,disabled:e.graph?!n.available(e.graph):!1,onClick:()=>{e.switchLayout(n.value)}})),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.zoomToFit()}}]]},{label:`Color: ${this.colorSchemeLabel(e.chosenColorScheme)}`,icon:ii,subMenu:Pn.map(n=>({type:"radio",label:this.colorSchemeLabel(n.value),checked:e.chosenColorScheme===n.value,onClick:()=>{e.setColorScheme(n.value)}}))},{label:"Show...",icon:di,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[];for(let n of Aa({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:o=>{e.showInLinearView(o)},onShowSynteny:o=>{e.showSyntenyView(o)}}))(0,Os.pushLaunchViewMenuItem)(t,n);return t}}));function pn(){return _s}var Ao=f(K(),1);function $s(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function No(e){let t=(0,Ao.readConfObject)(e,"assemblyNames"),n=$s(t)?t.slice(1):[];return n.length>0?n:void 0}function un(e){let t=(0,Ao.readConfObject)(e,"assemblyNames");return $s(t)?t[0]:void 0}function mn(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function up(e){return("uri"in e?e.uri.split(/[?#]/)[0]:"localPath"in e?e.localPath:"name"in e?e.name:"").split(/[\\/]/).at(-1)??""}function Io(){return z.types.compose("GraphGenomeView",Hs.BaseViewModel,pn(),z.types.model({type:z.types.literal("GraphGenomeView"),gfaLocation:z.types.maybe(z.types.frozen()),loadedRegion:z.types.maybe(z.types.frozen()),loadedTrackId:z.types.optional(z.types.string,""),subgraphContext:z.types.optional(z.types.number,1),subgraphHaplotypes:z.types.maybe(z.types.frozen()),maxRegionBp:z.types.optional(z.types.number,ot)})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(n){t(n),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get cutHaplotypes(){return e.subgraphHaplotypes},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,Ws.getSession)(e).tracks.find(t=>t.trackId===e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;return{clearGraph(){t(),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let n=e.loadedRegion;if(e.gfaLocation)return e.displayName||e.setDisplayName(up(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let o=e.sourceTrack,r=n.end-n.start,a=o?mn(un(o),n.assemblyName):void 0;if(!o)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(r>e.maxRegionBp)e.setError(new Error(`Region too large (${xe(r)}) \u2014 zoom in to view graph (max ${xe(e.maxRegionBp)})`));else return e.cutSubgraph(be(e,o),n,{hops:e.subgraphContext,haplotypes:e.subgraphHaplotypes,...e.cutsWholeWalks?{snarls:"overlapping"}:{}})}}}).actions(e=>({retryLoad(){e.load()},switchLayout(t){let n=e.cutsWholeWalks;return e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,z.addDisposer)(e,(0,js.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!_(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var mp=(0,Ys.defineLaunchKeys)()({});function Co(e){e.addViewType(()=>new zs.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Io(),launchKeys:mp,ReactComponent:(0,Xs.lazy)(()=>import("./chunks/GraphGenomeView-ZB4ED45M.js"))}))}var Us=f(K(),1),Be=f(fe(),1),Eo=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function lp(e){let t=e.getElementTypesInGroup("display"),n=r=>t.find(a=>a.name===r),o=r=>r&&Object.assign(Object.create(r),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Eo.map(r=>o(n(r)))].filter(r=>r!==void 0)}function Bo(e){e.addTrackType(()=>{let t=(0,Us.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Be.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Be.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Be.createBaseTrackModel)(e,"GraphTrack",t)});for(let o of lp(e))n.addDisplayType(o);return n})}function Fo(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...o}=t;return n.addView("GraphGenomeView",o),t})}var wc=f(Oe(),1),yc=f(qs(),1);var Qs=f(K(),1),ec=f(Zs(),1),Do=f(ne(),1);function tc(){return(0,Qs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Do.types.enumeration("LayoutMode",vt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Do.types.enumeration("ColorScheme",Tt),defaultValue:"auto"},highlightOnHover:{type:"boolean",defaultValue:!0},...(0,ec.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var mc=f(Oe(),1);var Fe=f(K(),1),lc=f(fe(),1),gc=f(oc(),1),hc=f(ir(),1),Vo=f(ae(),1),fc=f(ac(),1),I=f(ne(),1),ln=f(sc(),1);var cc=f(ce(),1),dc=(0,te.createSvgIcon)((0,cc.jsx)("path",{d:"M19 15.18V7c0-2.21-1.79-4-4-4s-4 1.79-4 4v10c0 1.1-.9 2-2 2s-2-.9-2-2V8.82C8.16 8.4 9 7.3 9 6c0-1.66-1.34-3-3-3S3 4.34 3 6c0 1.3.84 2.4 2 2.82V17c0 2.21 1.79 4 4 4s4-1.79 4-4V7c0-1.1.9-2 2-2s2 .9 2 2v8.18c-1.16.41-2 1.51-2 2.82 0 1.66 1.34 3 3 3s3-1.34 3-3c0-1.3-.84-2.4-2-2.82"}),"Route");var wt=f(St(),1);function pc(e){return e instanceof Error&&(e.name==="NodeLimitError"||e.regionTooLarge===!0||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function uc(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let n=e.end-e.start;return t.end-t.start>=n&&t.end>e.start-n&&t.start<e.end+n}var gp=(0,mc.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-UPAINCUZ.js"));function bc(e){return I.types.compose("LinearGraphDisplay",lc.BaseDisplay,(0,fc.default)(),pn(),I.types.model({type:I.types.literal("LinearGraphDisplay"),configuration:(0,Fe.ConfigurationReference)(e),pane:I.types.maybe(I.types.frozen()),overviewRowsChoice:I.types.maybe(I.types.frozen()),overviewRowOrder:I.types.maybe(I.types.frozen()),cutRegion:I.types.maybe(I.types.frozen()),coarseCut:I.types.optional(I.types.boolean,!1),maxRegionBp:I.types.optional(I.types.number,ot),subgraphContext:I.types.optional(I.types.number,1),subgraphHaplotypes:I.types.maybe(I.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,overviewRowsChoice:o,overviewRowOrder:r,...a}=t;if(!n)return a;let{type:i,...s}=n;return{...s,...a}}).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0})).views(t=>({get adapterConfig(){return be(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,Fe.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,Fe.getConf)(t,"colorScheme")},get defaultHighlightOnHover(){return(0,Fe.getConf)(t,"highlightOnHover")},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??No(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let o=t.adapterConfig.coarse?.aboveBpPerPx;return typeof o=="number"?o:void 0}})).views(t=>({tierAt(n){let o=t.coarseAboveBpPerPx;return o!==void 0&&n>o?"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 (${xe(n.end-n.start)}, max ${xe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return(0,gc.computeSvgReady)({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return(0,ln.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,ln.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,t.dense=void 0},setDense(n){t.dense=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let o=mn(un(t.parentTrack.configuration),n.assemblyName);if(o){t.clearGraph(),t.setError(new Error(o));return}let r=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:r?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:r?"coarse":void 0,..._(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let o=t.tierAt(n.bpPerPx);return t.coarseCut=o==="coarse",t.cutRegion=go(n,t.capFor(o),_(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let o=_(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||uc(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Qi(t.cutRegion,n,o)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,I.isAlive)(t)&&pc(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let o=_(t.chosenLayoutMode);t.setLayoutMode(n);let r=_(n),a=t.host?Qt(t.host):void 0;return a&&!t.regionTooLarge&&(r.cutMargins!==o.cutMargins||r.wholeWalks!==o.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,I.addDisposer)(t,(0,wt.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,I.addDisposer)(t,(0,wt.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,o)=>n?.scale===o?.scale&&n?.translateX===o?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,I.addDisposer)(t,(0,wt.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,I.addDisposer)(t,(0,wt.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:o}=t,r=n&&o?Qt(o):void 0;r&&t.settleOn(r)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Qt(t.host):void 0,o=t.sourceTrackId;if(!n||!o||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let r=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:o,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:r,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-r),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,I.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Vo.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({cutMenuItems(){if(t.adapterConfig.type!=="GbzBaseSyntenyAdapter")return[];let n=No(t.parentTrack.configuration),o=t.subgraphHaplotypes,r=a=>{t.setSubgraphHaplotypes(a),t.cut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:"Every haplotype in the graph",checked:o?o.length===0:!n,onClick:()=>{r([])}},...n?[{type:"radio",label:`The track's ${n.length} assemblies`,checked:o===void 0,onClick:()=>{r(void 0)}}]:[],{type:"radio",label:"Chosen in Settings...",checked:(o?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){(0,Vo.getSession)(t).queueDialog(n=>[gp,{model:t,open:!0,onClose:n}])},async renderSvg(n){let{renderGraphTrackSvg:o}=await import("./chunks/renderSvg-J7L374ND.js");return o(t,n)},trackMenuItems(){let n=t.launchMenuItems();(0,hc.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Ht,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let o=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...o.length>0?[{label:"Haplotypes",icon:dc,subMenu:o}]:[],...t.graphMenuItems(),{label:"Settings",icon:Na,onClick:()=>{this.openSettings()}},...n]}}))}function Oo(e){e.addDisplayType(()=>{let t=tc();return Object.assign(new yc.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:bc(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,wc.lazy)(()=>import("./chunks/LinearGraphDisplay-TQX7ZJZF.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Rc=f(Wt(),1);var _o=f(K(),1),kc=f(ne(),1);function $o(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:o?"CSI":"TBI",location:{uri:`${t}.${o?"csi":"tbi"}`,baseUri:n}}}:e}var hp=(0,_o.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,_o.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:kc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:$o}),Sc=hp;function Ho(e){e.addAdapterType(()=>new Rc.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:$o,configSchema:Sc,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CAXB5FGR.js").then(t=>t.default)}))}var Tc=f(Wt(),1);var hn=f(K(),1),Lc=f(ne(),1);function xc(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Mc(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:xc(`${t}.segs.bed.gz`,n,o),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:xc(`${t}.links.bed.gz`,n,o)}:e}function Wo(e){let{coarse:t,baseUri:n}=e;return Mc(typeof t=="object"&&t!==null?{...e,coarse:Mc({baseUri:n,...t})}:e)}var gn=(e,t)=>(0,hn.ConfigurationSchema)(e,{indexType:{model:Lc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),fp=(0,hn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:gn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:gn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),bp=(0,hn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:gn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:gn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:fp},{explicitlyTyped:!0,preProcessSnapshot:Wo}),vc=bp;function jo(e){e.addAdapterType(()=>new Tc.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:Wo,configSchema:vc,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-GNFUR2FW.js").then(t=>t.default)}))}var wp=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function yp(e){return or(e).toLowerCase().endsWith(".gbz.db")}function kp(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 Sp(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&yp(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&rr(e))return ar({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Xo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",kp),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,o,r)=>Sp(n,o,r)??t(n,o,r)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,o)=>wp.has(n)?"GraphTrack":t(n,o))}var Nc=f(ae(),1),fn=f(zc(),1),zo=f(Xc(),1),Ic=f(Yc(),1);function Gc(e){let t;if(Q(e)){let{refName:n,start:o,end:r,assemblyName:a}=e;typeof n=="string"&&typeof o=="number"&&typeof r=="number"&&(t={refName:n,start:o,end:r,assemblyName:typeof a=="string"?a:void 0})}return t}function Rp(e,t,n){let o=e.connectedViewId;return o===void 0||o===t||!n.has(o)}function Pc(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function xp(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Q(n)&&Array.isArray(n.displays)?n.displays.filter(o=>Q(o)&&o.type==="LinearGraphDisplay"):[])}function Ac(e,t,n){let o=[],r=gt(e),a=new Set(r.map(i=>Q(i)?i.id:void 0));for(let i of r){if(Q(i)&&i.id===t)for(let s of xp(i)){let c=Gc(s.hoverHighlight);c&&Pc(c,n)&&o.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(Q(i)&&i.type==="GraphGenomeView"&&Rp(i,t,a)){let s=Gc(i.hoverHighlight);s&&Pc(s,n)&&o.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return o}var De=f(ce(),1),Mp=(0,Ic.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,fn.alpha)(e.palette.primary.main,.08),borderLeft:`1px solid ${(0,fn.alpha)(e.palette.primary.main,.4)}`,borderRight:`1px solid ${(0,fn.alpha)(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Lp=(0,zo.observer)(function({model:t,region:n}){let{classes:o}=Mp(),r=t.getHighlightCoords(n);return r?(0,De.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),vp=(0,zo.observer)(function({model:t}){let{views:n}=(0,Nc.getSession)(t);return(0,De.jsx)(De.Fragment,{children:Ac([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,De.jsx)(Lp,{model:t,region:r},`graph-hover-${o}`))})}),Cc=vp;var Ec=f(ce(),1),Tp="LinearGenomeView-TracksContainerComponent";function Yo(e){e.contributeToExtensionPoint(Tp,({model:t})=>(0,Ec.jsx)(Cc,{model:t},"graphgenomeview-hover-highlight"))}var Bc=f(fe(),1);function Gp(e){return e.views(t=>({get adapterConfig(){return be(t,t.parentTrack.configuration)}}))}function Uo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Bc.DisplayType&&Eo.includes(t.name)&&t.extendStateModel(Gp),t))}var Fc="GraphGenomeView";var Dc="6.6.0";var Ko=class extends Vc.default{constructor(){super(...arguments);this.name=Fc;this.version=Dc}install(n){Co(n),Oo(n),Bo(n),Fo(n),Yo(n),jo(n),Ho(n),$n(n),Wn(n),Xo(n),Uo(n),n.addRpcMethod(()=>new Qe(n)),n.addRpcMethod(()=>new Ze(n)),n.addRpcMethod(()=>new Je(n))}configure(n){try{(0,Oc.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Ht,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{Ko as default};
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