npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 7.2.1 → 7.3.0 - Mend

jbrowse-plugin-graphgenomeviewer 7.2.1 → 7.3.0

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package/dist/chunks/WalkTabixSyntenyAdapter-7VDCNSFD.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{a as K}from"./chunk-YKSUKPYY.js";import{b as q,d as U,e as X,f as O,g as z,h as G}from"./chunk-2O3YVA2I.js";import"./chunk-JCAZTNYG.js";import{a as H}from"./chunk-KOB7YIMR.js";import{p as M,q as _,r as T}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-6KUHGRHU.js";import"./chunk-6MUBJVBG.js";import{e as $,p as j,r as D}from"./chunk-B2EP6FOQ.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{a as A,c as I,d as W,g as F,h as w,i as x}from"./chunk-7HWHWPRW.js";import"./chunk-T4R3ZVEM.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as R}from"./chunk-TENPGIPX.js";var se=50;function re(r){let i=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=se&&(t==="I"&&s==="D"\|\|t==="D"&&s==="I")?(i.push(["X",a]),e++):i.push([t,a])}return i}function v(r){return Array.from(r.ids,(i,e)=>2*i+r.rev[e])}function P(r,i){let e=r.get(i);return e===void 0?0:e.end-e.start}function V(r){let i=new Map,e=s=>{let n=P(r,s),o=i.get(n);return o===void 0&&(o="N".repeat(n),i.set(n,o)),o},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=v(s),t.set(s,n)),n};return(s,n)=>_({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var B=100;function E(r,i,e){let t=r.at(-1);e>0&&(t?.[0]===i?t[1]+=e:r.push([i,e]))}function Z(r){let i=t=>P(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+i(s)}),a};return(t,a)=>{let s=v(a),n=v(t),[o,l]=M(n,s,i),[u,f]=M(n.map(g=>g^1).reverse(),s,i),c=f>l,p=c?u:o,N=Math.max(l,f);if(N<B)return[];let d=e(s),h=e(n),y=g=>c?n.length-1-p[g][0]:p[g][0],m=[];p.forEach(([,g],k)=>{if(k>0){let[ee,te]=[y(k-1),y(k)].sort((ae,ne)=>ae-ne);E(m,"I",h[te]-h[ee+1]),E(m,"D",d[g]-d[p[k-1][1]+1])}E(m,"=",i(s[g]))});let[b,S]=[y(0),y(p.length-1)].sort((g,k)=>g-k);return[{queryStart:h[b],queryEnd:h[S+1],targetStart:d[p[0][1]],targetEnd:d[p.at(-1)[1]+1],strand:c?"-":"+",edits:m,sharedBases:N}]}}function oe(r){let i=new Map,e=new Set;r.ids.forEach((t,a)=>{i.has(t)?e.add(t):i.set(t,r.rev[a])});for(let t of e)i.delete(t);return i}function J(r){let i=new Map,e=t=>{let a=i.get(t);return a===void 0&&(a=oe(t),i.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,o=0;for(let[l,u]of e(t)){let f=s.get(l);f===u?n+=P(r,l):f!==void 0&&(o+=P(r,l))}return{same:n,opposite:o}}}function Q(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let{same:n,opposite:o}=t(a,s);return n>=B&&o>=B?e(a,s):i(a,s)}}var ie=1e4;function Y(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let n=i(a,s),o=n[0]?.strand,{same:l,opposite:u}=t(a,s);return o===void 0\|\|Math.min(l,u)<ie?n:[...n,...e(a,s).filter(f=>f.strand!==o)]}}function C({chain:r,target:i,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=re(r.edits);return G({target:{name:i.name,assemblyName:t,refName:a,start:i.hapStart+r.targetStart,end:i.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:W(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:T(n),matches:n.reduce((o,[l,u])=>o+(l==="="?u:0),0),columns:n.reduce((o,[,l])=>o+l,0)})}var me=r=>I(r.name)??r.name,L=class extends q{constructor(){super(...arguments);this.walks=new K(j(this,["walksLocation"],["walksIndex"]),this);this.refNames=new D(this.walks.file,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&A(o)!==s).map(o=>({name:O(n,o),label:o,group:A(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0\|\|t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolve(e,{signal:t.signal});if(a===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:$(a,e),links:!1}).catch(o=>{throw z(o,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0\|\|s.some(m=>F(n,m)\|\|F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks ${t.refName}:${l.toLocaleString()}-${u.toLocaleString()}`),p=Y(f.nodes),N=x(this),d=c.filter(m=>m.name===e),h=m=>o===void 0?0:o.findIndex(b=>F(m.name,b));return c.filter(m=>m.name!==e&&h(m)>=0).sort((m,b)=>h(m)-h(b)).flatMap(m=>d.flatMap(b=>p(m,b).map(S=>C({chain:S,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(N,me(m))}))))}async pairFeatures(e,t,a,s){let n=a.map(c=>({pair:c,featurePrefix:w(this,c.queryAssemblyName),matePrefix:w(this,c.targetAssemblyName)})),{graph:o,fragments:l}=await this.laneWalks(e,t,n.flatMap(c=>[c.featurePrefix,c.matePrefix]),s,X(a)),u=Q(o.nodes),f=c=>l.filter(p=>F(p.name,c));return n.flatMap(({pair:c,featurePrefix:p,matePrefix:N})=>f(p).flatMap(d=>f(N).flatMap(h=>u(h,d).map(y=>C({chain:y,target:d,query:h,assemblyName:c.queryAssemblyName,refName:W(d.name),mateAssemblyName:c.targetAssemblyName})))))}getFeatures(e,t={}){return H(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=U(t),o=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let l of o)a.next(l)}a.complete()},t.signal)}};export{L as default};
2	+ //# sourceMappingURL=WalkTabixSyntenyAdapter-7VDCNSFD.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-7VDCNSFD.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
+  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type { WalkFragment, WalkNode } from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  return (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return { same, opposite }\n  }\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport { anchorAligner, chainFeature, lanePairAligner } from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { WalkFragment } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n    this,\n  )\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.file,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolve(region, { signal: opts.signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep: walksKept(prefixes, refName),\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneAssemblyName(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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+  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "handlesOf", "fragment", "id", "nodeLength", "nodes", "node", "walkAligner", "standIn", "sequenceOf", "length", "sequence", "handles", "cachedHandles", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "x", "y", "singleVisits", "rev", "twice", "directionShares", "visits", "visitsOf", "found", "theirs", "opposite", "other", "lanePairAligner", "subsequence", "chained", "shares", "TURNED_MIN_BP", "anchorAligner", "records", "taken", "chain", "chainFeature", "assemblyName", "refName", "mateAssemblyName", "matchFeature", "panSNContig", "pairCigar", "sum", "n", "haplotypeOf", "fragment", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "WalkIndex", "openTabixSlot", "PanSNRefNames", "anchor", "opts", "haplotypes", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "region", "refName", "prefixes", "status", "updateStatus", "walksKept", "error", "laneZoomNotice", "wanted", "lane", "target", "panSNMatchesPrefix", "start", "end", "graph", "fragments", "align", "anchorAligner", "references", "f", "rank", "a", "query", "reference", "chain", "chainFeature", "pairs", "sides", "pair", "side", "lanePairsStatus", "lanePairAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
+}

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

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at=Qn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ae(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Xo(o),n=R(e);return r===void 0?void 0:Ko(Pe(n,r),Pe(n,t.assemblyName))},cutChangedFrom(t){let o=$o(F(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{}}}}));function zt(){return M.compose("GraphGenomeView",Sn,at,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:kt(ze),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:kt(Te)})).views(e=>({get 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O("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",ze),defaultValue:"auto"},color:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",Te),defaultValue:"nodes"},...ta({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var fe=JBrowseExports["@jbrowse/core/svg/svgReady"],ci=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ra=ci("computeSvgReady");var pm=fe&&fe.__esModule?fe.default:fe;var st=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var na=st&&st.__esModule?st.default:st;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],ui=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),aa=ui("editPlotMenuItems");var dm=we&&we.__esModule?we.default:we;var Me=JBrowseExports["@jbrowse/render-core/displayPhase"],ia=e=>Me!=null&&e in Object(Me)?Me[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),sa=ia("computeActivityPhase");var pa=ia("computeDisplayStatusPhase"),lm=Me&&Me.__esModule?Me.default:Me;function Xt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var di=new Set(["scale","translateX","translateY"]);function mi(e){return Object.fromEntries(Object.keys(br.properties).filter(t=>!di.has(t)).map(t=>[t,e[t]]))}var Kt=10;function li(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/Kt:void 0}var hi=ee(()=>import("./chunks/GraphTrackSettingsDialog-ZW7ALMDV.js"));function ca(e){return M.compose("LinearGraphDisplay",mn,na(),at,M.model({type:M.literal("LinearGraphDisplay"),configuration:xo(e),layoutEngine:zo(jo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:Z(t,"layoutMode"),color:Z(t,"color"),size:Z(t,"size"),layers:Z(t,"layers"),facet:Z(t,"facet"),rows:Z(t,"rows"),hover:Z(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ae(o))??(r&&St(r))},get coarseAboveBpPerPx(){return li(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=Kt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${ce(o.end-o.start)}, max ${ce(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ra({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return pa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>sa({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=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ro(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(Kt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Ur(o,t.capFor(r),F(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=F(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Xt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&Xr(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{H(t)&&t.recuts===a&&wt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Xe(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||F(o).cutMargins!==F(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await R(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});H(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&Yo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),L(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),L(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;L(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),L(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-qe)?.total??0)+qe;(t.facetGrid?.total??0)+qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),L(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Xe(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Xe(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Xt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...mi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&R(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Uo(o))return[];let n=Ae(o),a=St(r),i=t.haplotypeNames,p=t.subgraphHaplotypes,s=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:p?p.length===0:!n&&!a,onClick:()=>{s([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:p===void 0,onClick:()=>{s(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(p?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){R(t).queueDialog(o=>[hi,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-WD6YDV2I.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();nt(o,{label:"Graph genome view",icon:Qe,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:sn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:pn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...aa(t)]}}))}function qt(e){e.addDisplayType(()=>{let t=oa();return Object.assign(new ea({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ca(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:ee(()=>import("./chunks/LinearGraphDisplay-SPOPTJEN.js"))}),{adapterCapabilities:["getSubgraph"]})})}function gi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Le(t,o,r)}:e}var yi=O("MinigraphBubbleAdapter",{bubblesLocation:E("/path/to/graph.bb.bed.gz"),index:z("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:gi}),ua=yi;function Zt(e){e.addAdapterType(()=>new te({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:ua,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-QCOMFPLL.js").then(t=>t.default)}))}function da(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Le(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Le(`${t}.links.bed.gz`,o,r)}:e}function bi(e){let{coarse:t,baseUri:o,csi:r}=e;return Oe(da(typeof t=="object"&&t!==null?{...e,coarse:da({baseUri:o,csi:r,...t})}:e))}var fi=O("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:E("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:z("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.tier.links.bed.gz"),linksIndex:z("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),wi=O("RgfaTabixAdapter",{segmentsLocation:E("/path/to/graph.segs.bed.gz"),segmentsIndex:z("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.links.bed.gz"),linksIndex:z("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:E(""),walksIndex:z("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:fi},{explicitlyTyped:!0,preProcessSnapshot:bi}),ma=wi;function Qt(e){e.addAdapterType(()=>new te({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ma,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-O3NMNRZ2.js").then(t=>t.default)}))}var Mi=O("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:E("/path/to/graph.walks.bed.gz"),walksIndex:z("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:E(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Oe}),la=Mi;function eo(e){e.addAdapterType(()=>new te({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:la,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-I3PY6HJ2.js").then(t=>t.default)}))}var ki=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Si(e){return ht(e).toLowerCase().endsWith(".gbz.db")}function xi(e){let t=e.adapter;return t?.type!==void 0&&Kr.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Ri(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Lo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Ti(e,t,o){let r=n=>Fo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Si(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Ho(e))return r("RgfaTabixAdapter");if(ht(e).endsWith(Go)&&(t!==void 0||Po(e)))return r("RgfaTabixWalks")}}function to(e){e.addToExtensionPoint("Core-preProcessTrackConfig",xi),e.addToExtensionPoint("Core-preProcessTrackConfig",Ri),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Ti(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>ki.has(o)?"GraphTrack":t(o,r))}function ha(e){let t;if($(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Gi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function ga(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Li(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>$(o)&&Array.isArray(o.displays)?o.displays.filter(r=>$(r)&&r.type==="LinearGraphDisplay"):[])}function ya(e,t,o){let r=[],n=$e(e),a=new Set(n.map(i=>$(i)?i.id:void 0));for(let i of n){if($(i)&&i.id===t)for(let p of Li(i)){let s=ha(p.hoverHighlight);s&&ga(s,o)&&r.push({key:typeof p.id=="string"?p.id:"graph-track",region:s})}if($(i)&&i.type==="GraphGenomeView"&&Gi(i,t,a)){let p=ha(i.hoverHighlight);p&&ga(p,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:p})}}return r}var vi=an()(e=>({highlight:{height:"100%",position:"absolute",background:We(e.palette.primary.main,.08),borderLeft:`1px solid ${We(e.palette.primary.main,.4)}`,borderRight:`1px solid ${We(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Ai=ft(function({model:t,region:o}){let{classes:r}=vi(),n=t.getHighlightCoords(o);return n?A("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Pi=ft(function({model:t}){let{views:o}=R(t);return A(fo,{children:ya([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>A(Ai,{model:t,region:n},`graph-hover-${r}`))})}),ba=Pi;var Ci="LinearGenomeView-TracksContainerComponent";function oo(e){e.contributeToExtensionPoint(Ci,({model:t})=>A(ba,{model:t},"graphgenomeview-hover-highlight"))}function Bi(e){return e.views(t=>({get adapterConfig(){return qr(t,t.parentTrack.configuration)}}))}function ro(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof ln&&Jt.includes(t.name)&&t.extendStateModel(Bi),t))}var fa="GraphGenomeView";var wa="7.2.1";var no=class extends cn{constructor(){super(...arguments);this.name=fa;this.version=wa}install(o){$t(o),qt(o),Yt(o),Ut(o),oo(o),Qt(o),Zt(o),Et(o),eo(o),Vt(o),to(o),ro(o),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ne(o)),o.addRpcMethod(()=>new Ee(o)),o.addRpcMethod(()=>new Ie(o))}configure(o){try{go(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Qe,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{no as default};
+`).then(()=>{o.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(r=>{o.notify(`Could not copy the figure spec: ${String(r)}`)})}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>dr;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{R(e).queueDialog(a=>[cr,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{R(e).queueDialog(a=>[ur,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...q(tr.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=Tt.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=F(e.chosenLayoutMode),r=Zn.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${_t(o)}${o.value==="force"?` (${r})`:""}`,icon:Rn,subMenu:[..._o.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?Zn.map(([i,p])=>({...a,label:`${_t(n)} (${p})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:_t(n),checked:e.chosenLayoutMode===n.value,onClick:()=>{e.switchLayout(n.value)}}]}),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${e.colorSchemeLock?.value??this.colorSchemeLabel(e.chosenColorScheme)}`,icon:Tn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:q(Tt.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show...",icon:or,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of nn({contributors:o,linearContributors:e.host?o.filter(a=>a.sample!==r):o,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:a=>{e.showInLinearView(a)},onShowSynteny:a=>{e.showSyntenyView(a)}}))nt(t,n);return t}}));var at=Qn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ae(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Xo(o),n=R(e);return r===void 0?void 0:Ko(Pe(n,r),Pe(n,t.assemblyName))},cutChangedFrom(t){let o=$o(F(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{}}}}));function zt(){return M.compose("GraphGenomeView",Sn,at,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:kt(ze),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:kt(Te)})).views(e=>({get grammar(){return{layoutMode:e.layoutMode,color:e.color,size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar(t){Object.assign(e,t)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(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;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(ue(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${ce(a)}) \u2014 zoom in to view graph (max ${ce(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===ue(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=R(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(Rt(n,r)):void 0):o(r&&Rt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),H(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(ue(t)))},afterAttach(){e.graph||e.load(),L(e,C(()=>e.walkStrip,()=>{e.loadedTrackId&&!F(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var ii=kn()({});function $t(e){e.addViewType(()=>new Mn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:zt(),launchKeys:ii,ReactComponent:ee(()=>import("./chunks/GraphGenomeView-WJ3FIDY2.js"))}))}var Jt=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function si(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Jt.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Yt(e){e.addTrackType(()=>{let t=O("GraphTrack",{},{baseConfiguration:yn(e),explicitIdentifier:"trackId"}),o=new gn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:bn(e,"GraphTrack",t)});for(let r of si(e))o.addDisplayType(r);return o})}function Ut(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var it=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var ea=it&&it.__esModule?it.default:it;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],pi=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),ta=pi("trackHeightConfigSchemaFields"),em=be&&be.__esModule?be.default:be;function oa(){return O("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",ze),defaultValue:"auto"},color:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",Te),defaultValue:"nodes"},...ta({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var fe=JBrowseExports["@jbrowse/core/svg/svgReady"],ci=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ra=ci("computeSvgReady");var pm=fe&&fe.__esModule?fe.default:fe;var st=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var na=st&&st.__esModule?st.default:st;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],ui=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),aa=ui("editPlotMenuItems");var dm=we&&we.__esModule?we.default:we;var Me=JBrowseExports["@jbrowse/render-core/displayPhase"],ia=e=>Me!=null&&e in Object(Me)?Me[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),sa=ia("computeActivityPhase");var pa=ia("computeDisplayStatusPhase"),lm=Me&&Me.__esModule?Me.default:Me;function Xt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var di=new Set(["scale","translateX","translateY"]);function mi(e){return Object.fromEntries(Object.keys(br.properties).filter(t=>!di.has(t)).map(t=>[t,e[t]]))}var Kt=10;function li(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/Kt:void 0}var hi=ee(()=>import("./chunks/GraphTrackSettingsDialog-ZW7ALMDV.js"));function ca(e){return M.compose("LinearGraphDisplay",mn,na(),at,M.model({type:M.literal("LinearGraphDisplay"),configuration:xo(e),layoutEngine:zo(jo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:Z(t,"layoutMode"),color:Z(t,"color"),size:Z(t,"size"),layers:Z(t,"layers"),facet:Z(t,"facet"),rows:Z(t,"rows"),hover:Z(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ae(o))??(r&&St(r))},get coarseAboveBpPerPx(){return li(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=Kt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${ce(o.end-o.start)}, max ${ce(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ra({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return pa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>sa({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=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ro(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(Kt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Ur(o,t.capFor(r),F(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=F(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Xt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&Xr(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{H(t)&&t.recuts===a&&wt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Xe(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||F(o).cutMargins!==F(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await R(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});H(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&Yo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),L(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),L(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;L(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),L(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-qe)?.total??0)+qe;(t.facetGrid?.total??0)+qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),L(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Xe(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Xe(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Xt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...mi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&R(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Uo(o))return[];let n=Ae(o),a=St(r),i=t.haplotypeNames,p=t.subgraphHaplotypes,s=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:p?p.length===0:!n&&!a,onClick:()=>{s([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:p===void 0,onClick:()=>{s(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(p?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){R(t).queueDialog(o=>[hi,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-WD6YDV2I.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();nt(o,{label:"Graph genome view",icon:Qe,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:sn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:pn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...aa(t)]}}))}function qt(e){e.addDisplayType(()=>{let t=oa();return Object.assign(new ea({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ca(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:ee(()=>import("./chunks/LinearGraphDisplay-SPOPTJEN.js"))}),{adapterCapabilities:["getSubgraph"]})})}function gi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Le(t,o,r)}:e}var yi=O("MinigraphBubbleAdapter",{bubblesLocation:E("/path/to/graph.bb.bed.gz"),index:z("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:gi}),ua=yi;function Zt(e){e.addAdapterType(()=>new te({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:ua,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-QCOMFPLL.js").then(t=>t.default)}))}function da(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Le(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Le(`${t}.links.bed.gz`,o,r)}:e}function bi(e){let{coarse:t,baseUri:o,csi:r}=e;return Oe(da(typeof t=="object"&&t!==null?{...e,coarse:da({baseUri:o,csi:r,...t})}:e))}var fi=O("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:E("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:z("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.tier.links.bed.gz"),linksIndex:z("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),wi=O("RgfaTabixAdapter",{segmentsLocation:E("/path/to/graph.segs.bed.gz"),segmentsIndex:z("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.links.bed.gz"),linksIndex:z("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:E(""),walksIndex:z("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:fi},{explicitlyTyped:!0,preProcessSnapshot:bi}),ma=wi;function Qt(e){e.addAdapterType(()=>new te({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ma,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-O3NMNRZ2.js").then(t=>t.default)}))}var Mi=O("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:E("/path/to/graph.walks.bed.gz"),walksIndex:z("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:E(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Oe}),la=Mi;function eo(e){e.addAdapterType(()=>new te({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:la,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-7VDCNSFD.js").then(t=>t.default)}))}var ki=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Si(e){return ht(e).toLowerCase().endsWith(".gbz.db")}function xi(e){let t=e.adapter;return t?.type!==void 0&&Kr.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Ri(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Lo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Ti(e,t,o){let r=n=>Fo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Si(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Ho(e))return r("RgfaTabixAdapter");if(ht(e).endsWith(Go)&&(t!==void 0||Po(e)))return r("RgfaTabixWalks")}}function to(e){e.addToExtensionPoint("Core-preProcessTrackConfig",xi),e.addToExtensionPoint("Core-preProcessTrackConfig",Ri),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Ti(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>ki.has(o)?"GraphTrack":t(o,r))}function ha(e){let t;if($(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Gi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function ga(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Li(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>$(o)&&Array.isArray(o.displays)?o.displays.filter(r=>$(r)&&r.type==="LinearGraphDisplay"):[])}function ya(e,t,o){let r=[],n=$e(e),a=new Set(n.map(i=>$(i)?i.id:void 0));for(let i of n){if($(i)&&i.id===t)for(let p of Li(i)){let s=ha(p.hoverHighlight);s&&ga(s,o)&&r.push({key:typeof p.id=="string"?p.id:"graph-track",region:s})}if($(i)&&i.type==="GraphGenomeView"&&Gi(i,t,a)){let p=ha(i.hoverHighlight);p&&ga(p,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:p})}}return r}var vi=an()(e=>({highlight:{height:"100%",position:"absolute",background:We(e.palette.primary.main,.08),borderLeft:`1px solid ${We(e.palette.primary.main,.4)}`,borderRight:`1px solid ${We(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Ai=ft(function({model:t,region:o}){let{classes:r}=vi(),n=t.getHighlightCoords(o);return n?A("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Pi=ft(function({model:t}){let{views:o}=R(t);return A(fo,{children:ya([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>A(Ai,{model:t,region:n},`graph-hover-${r}`))})}),ba=Pi;var Ci="LinearGenomeView-TracksContainerComponent";function oo(e){e.contributeToExtensionPoint(Ci,({model:t})=>A(ba,{model:t},"graphgenomeview-hover-highlight"))}function Bi(e){return e.views(t=>({get adapterConfig(){return qr(t,t.parentTrack.configuration)}}))}function ro(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof ln&&Jt.includes(t.name)&&t.extendStateModel(Bi),t))}var fa="GraphGenomeView";var wa="7.3.0";var no=class extends cn{constructor(){super(...arguments);this.name=fa;this.version=wa}install(o){$t(o),qt(o),Yt(o),Ut(o),oo(o),Qt(o),Zt(o),Et(o),eo(o),Vt(o),to(o),ro(o),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ne(o)),o.addRpcMethod(()=>new Ee(o)),o.addRpcMethod(()=>new Ie(o))}configure(o){try{go(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Qe,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{no as default};
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